searchindex.js

Search.setIndex({"alltitles":{"About":[[0,null]],"Acknowledgements":[[0,"acknowledgements"],[78,"acknowledgements"],[79,"acknowledgements"],[82,"acknowledgements"]],"Adding new format classes":[[4,"adding-new-format-classes"]],"Advanced use - Choosing reflections to use for minimisation":[[1,"advanced-use-choosing-reflections-to-use-for-minimisation"]],"Advanced use - Controlling the scaling models":[[1,"advanced-use-controlling-the-scaling-models"]],"Algorithms":[[19,null]],"Applying the corrected metrology":[[82,"applying-the-corrected-metrology"]],"Array Family":[[20,null]],"Attendees":[[99,"attendees"]],"Basic parameters":[[34,"basic-parameters"],[36,"basic-parameters"],[37,"basic-parameters"],[38,"basic-parameters"],[39,"basic-parameters"],[40,"basic-parameters"],[41,"basic-parameters"],[42,"basic-parameters"],[43,"basic-parameters"],[44,"basic-parameters"],[45,"basic-parameters"],[46,"basic-parameters"],[47,"basic-parameters"],[49,"basic-parameters"],[50,"basic-parameters"],[51,"basic-parameters"],[52,"basic-parameters"],[53,"basic-parameters"],[54,"basic-parameters"],[55,"basic-parameters"],[56,"basic-parameters"],[58,"basic-parameters"],[59,"basic-parameters"],[60,"basic-parameters"],[61,"basic-parameters"],[62,"basic-parameters"],[63,"basic-parameters"],[64,"basic-parameters"],[65,"basic-parameters"],[66,"basic-parameters"],[67,"basic-parameters"],[68,"basic-parameters"],[69,"basic-parameters"],[70,"basic-parameters"],[71,"basic-parameters"],[73,"basic-parameters"]],"Basis vector search strategies":[[4,"basis-vector-search-strategies"]],"Board":[[94,"board"]],"Bookkeeping":[[77,"bookkeeping"]],"Bravais Lattice Refinement":[[83,"bravais-lattice-refinement"],[85,"bravais-lattice-refinement"],[86,"bravais-lattice-refinement"]],"Bravais lattice determination":[[87,"bravais-lattice-determination"]],"Build instructions":[[48,"build-instructions"]],"Built-in help":[[7,"built-in-help"]],"Centred or pseudocentred?":[[78,"centred-or-pseudocentred"]],"Check indexing symmetry":[[79,"check-indexing-symmetry"]],"Checking the symmetry":[[86,"checking-the-symmetry"]],"Citing DIALS":[[89,"citing-dials"]],"Class Methods":[[4,"class-methods"]],"Cluster Comparisons":[[77,"cluster-comparisons"]],"Community support activities":[[94,"community-support-activities"]],"Conclusions":[[78,"conclusions"],[79,"conclusions"]],"Contact":[[89,"contact"]],"Contents":[[4,"contents"]],"Conventions":[[2,null]],"Converting to a centred lattice":[[78,"converting-to-a-centred-lattice"]],"Coordinate frames":[[2,"coordinate-frames"]],"DIALS 1: 12th-13th June 2012 (Diamond Light Source, UK)":[[98,null]],"DIALS Application to XFEL Crystallography":[[96,"dials-application-to-xfel-crystallography"]],"DIALS How-To guides":[[88,null]],"DIALS Journal Articles":[[96,"dials-journal-articles"]],"DIALS License":[[91,null]],"DIALS Newsletter Articles":[[96,"dials-newsletter-articles"]],"DIALS Reports":[[96,"dials-reports"]],"DIALS Synchrotron Applications":[[96,"dials-synchrotron-applications"]],"DIALS UK":[[0,"dials-uk"]],"DIALS US":[[0,"dials-us"]],"DIALS for 3DED/MicroED":[[96,"dials-for-3ded-microed"]],"DIALS for neutron diffraction":[[95,"dials-for-neutron-diffraction"]],"DIALS-3: 22nd May 2013 (Cambridge, UK)":[[99,null]],"DIALS: Diffraction Integration for Advanced Light Sources":[[89,null]],"DPF3 Part 1: Correcting poor initial geometry":[[79,null]],"DPF3 Part 2: A question of centring":[[78,null]],"Data":[[75,"data"],[76,"data"],[77,"data"],[87,"data"]],"Data collection videos":[[74,"data-collection-videos"]],"Data files":[[3,null]],"Dataset 1":[[76,"dataset-1"],[76,"id1"],[76,"id11"]],"Dataset 2":[[76,"dataset-2"],[76,"id2"],[76,"id12"]],"Dataset 3":[[76,"dataset-3"],[76,"id3"],[76,"id13"]],"Dataset 4":[[76,"dataset-4"],[76,"id4"],[76,"id14"]],"Dataset 5":[[76,"dataset-5"],[76,"id5"],[76,"id15"]],"Dataset 6":[[76,"dataset-6"],[76,"id6"],[76,"id8"],[76,"id10"],[76,"id16"]],"Dataset 7":[[76,"dataset-7"],[76,"id7"],[76,"id17"]],"Datasets 1-5 & 7":[[76,"datasets-1-5-7"],[76,"id9"]],"Defining a scaling model":[[4,"defining-a-scaling-model"]],"Delta CC-half":[[77,"delta-cc-half"]],"Details":[[35,"details"]],"Detector distance":[[75,"detector-distance"]],"Determining lattice symmetry":[[75,"determining-lattice-symmetry"]],"Developer Examples":[[5,null]],"Development Builds":[[90,"development-builds"]],"Development Teams":[[0,"development-teams"]],"Dials parameters":[[48,"dials-parameters"]],"Discover a better experimental model":[[79,"discover-a-better-experimental-model"]],"Distl parameters":[[48,"distl-parameters"]],"Documentation":[[8,null]],"Downloading the DIALS regression test data":[[9,"downloading-the-dials-regression-test-data"]],"Entry points":[[4,"entry-points"]],"Example":[[40,"example"]],"Example use cases":[[43,"example-use-cases"]],"Examples use cases":[[73,"examples-use-cases"]],"Excluding bad frames":[[74,"excluding-bad-frames"]],"Experiment list files":[[3,"experiment-list-files"]],"Explorations of Reciprocal Space":[[77,"explorations-of-reciprocal-space"]],"Exploratory analysis":[[75,"exploratory-analysis"]],"Export":[[93,"export"]],"Export the data":[[74,"export-the-data"]],"Exporting":[[87,"exporting"]],"Exporting as MTZ":[[86,"exporting-as-mtz"]],"Exporting to unmerged MTZ":[[83,"exporting-to-unmerged-mtz"],[85,"exporting-to-unmerged-mtz"]],"Extending DIALS":[[4,null]],"Extending dials.index":[[4,"extending-dials-index"]],"Extending dials.scale":[[4,"extending-dials-scale"]],"Extending profile models":[[4,"extending-profile-models"]],"Extensions":[[31,null]],"Feedback":[[80,"feedback"]],"Find Spots":[[79,"find-spots"],[83,"find-spots"],[85,"find-spots"],[86,"find-spots"]],"Find spots":[[74,"find-spots"]],"Find the Bravais lattice (optional)":[[74,"find-the-bravais-lattice-optional"]],"Find the beam centre":[[74,"find-the-beam-centre"]],"Full parameter definitions":[[34,"full-parameter-definitions"],[35,"full-parameter-definitions"],[36,"full-parameter-definitions"],[37,"full-parameter-definitions"],[38,"full-parameter-definitions"],[39,"full-parameter-definitions"],[40,"full-parameter-definitions"],[41,"full-parameter-definitions"],[42,"full-parameter-definitions"],[43,"full-parameter-definitions"],[44,"full-parameter-definitions"],[45,"full-parameter-definitions"],[46,"full-parameter-definitions"],[47,"full-parameter-definitions"],[49,"full-parameter-definitions"],[50,"full-parameter-definitions"],[51,"full-parameter-definitions"],[52,"full-parameter-definitions"],[53,"full-parameter-definitions"],[54,"full-parameter-definitions"],[55,"full-parameter-definitions"],[56,"full-parameter-definitions"],[57,"full-parameter-definitions"],[58,"full-parameter-definitions"],[59,"full-parameter-definitions"],[60,"full-parameter-definitions"],[61,"full-parameter-definitions"],[62,"full-parameter-definitions"],[63,"full-parameter-definitions"],[64,"full-parameter-definitions"],[65,"full-parameter-definitions"],[66,"full-parameter-definitions"],[67,"full-parameter-definitions"],[68,"full-parameter-definitions"],[69,"full-parameter-definitions"],[70,"full-parameter-definitions"],[71,"full-parameter-definitions"],[73,"full-parameter-definitions"]],"Funding":[[89,"funding"]],"Further processing":[[75,"further-processing"]],"Further refinement":[[75,"further-refinement"]],"General":[[80,"general"]],"General Notes":[[74,"general-notes"]],"Generate a mask for the beam center (optional)":[[74,"generate-a-mask-for-the-beam-center-optional"]],"Getting started":[[7,null]],"Goals":[[94,"goals"]],"Guide to common scaling options":[[1,"guide-to-common-scaling-options"]],"HTML report":[[83,"html-report"],[85,"html-report"]],"Import":[[76,"import"],[79,"import"],[83,"import"],[85,"import"],[86,"import"],[87,"import"]],"Import and Spotfinding":[[84,"import-and-spotfinding"]],"Import images":[[74,"import-images"]],"Importing":[[93,"importing"]],"Importing and spotfinding":[[97,"importing-and-spotfinding"]],"Indexing":[[74,"indexing"],[75,"indexing"],[76,"indexing"],[79,"indexing"],[83,"indexing"],[84,"indexing"],[85,"indexing"],[86,"indexing"],[87,"indexing"]],"Indexing SSX data with dials.ssx_index":[[97,"indexing-ssx-data-with-dials-ssx-index"]],"Indexing with the corrected beam centre":[[79,"indexing-with-the-corrected-beam-centre"]],"Inspecting the results":[[86,"inspecting-the-results"]],"Installation":[[7,"installation"],[90,null],[90,"id1"]],"Installation for Developers":[[9,null]],"Integrating SSX data with dials.ssx_integrate":[[97,"integrating-ssx-data-with-dials-ssx-integrate"]],"Integration":[[74,"integration"],[75,"integration"],[76,"integration"],[83,"integration"],[85,"integration"],[86,"integration"],[87,"integration"]],"Intensity Clustering":[[77,"intensity-clustering"]],"Introduction":[[34,"introduction"],[35,"introduction"],[36,"introduction"],[37,"introduction"],[38,"introduction"],[39,"introduction"],[40,"introduction"],[41,"introduction"],[42,"introduction"],[43,"introduction"],[44,"introduction"],[45,"introduction"],[46,"introduction"],[47,"introduction"],[48,"introduction"],[49,"introduction"],[50,"introduction"],[51,"introduction"],[52,"introduction"],[53,"introduction"],[54,"introduction"],[55,"introduction"],[56,"introduction"],[57,"introduction"],[58,"introduction"],[59,"introduction"],[60,"introduction"],[61,"introduction"],[62,"introduction"],[63,"introduction"],[64,"introduction"],[65,"introduction"],[66,"introduction"],[67,"introduction"],[68,"introduction"],[69,"introduction"],[70,"introduction"],[71,"introduction"],[73,"introduction"],[75,"introduction"],[76,"introduction"],[77,"introduction"],[78,"introduction"],[79,"introduction"],[82,"introduction"],[83,"introduction"],[84,"introduction"],[85,"introduction"],[86,"introduction"],[87,"introduction"]],"Keeping a Development Environment current":[[9,"keeping-a-development-environment-current"]],"Lattice search strategies":[[4,"lattice-search-strategies"]],"Library Reference":[[32,null]],"Lysozyme nanocrystals":[[76,null]],"Mac and Linux binary installers":[[90,"mac-and-linux-binary-installers"]],"Mac graphical binary installers":[[90,"mac-graphical-binary-installers"]],"Metrics":[[92,null]],"ModuleNotFoundError: No module named \u2018gltbx_gl_ext\u2019":[[9,"modulenotfounderror-no-module-named-gltbx-gl-ext"]],"Multi-crystal analysis with DIALS and xia2.multiplex":[[77,null]],"Multi-dataset symmetry determination":[[74,"multi-dataset-symmetry-determination"]],"Multi-lattice Tutorial":[[84,null]],"Multi-tile refinement":[[82,"multi-tile-refinement"]],"MyD88TIR small wedges":[[75,null]],"Next steps":[[7,"next-steps"]],"Note about pedestal and offset":[[74,"note-about-pedestal-and-offset"]],"Organising committee":[[98,"organising-committee"]],"Orientation matrix":[[2,"orientation-matrix"]],"Orthogonalisation convention":[[2,"orthogonalisation-convention"]],"Other datasets":[[74,"other-datasets"]],"Output for SADABS (alternate path)":[[87,"output-for-sadabs-alternate-path"]],"Parameters":[[7,"parameters"]],"Post Experiment Processing":[[77,"post-experiment-processing"]],"Practicalities for large datasets":[[1,"practicalities-for-large-datasets"]],"Preferential Orientation":[[77,"preferential-orientation"]],"Preparing for multi-tile refinement":[[82,"preparing-for-multi-tile-refinement"]],"Process":[[77,"process"]],"Processing Sequences with Missing Images":[[93,null]],"Processing Small Molecule MicroED/3DED: Biotin":[[74,null]],"Processing in Detail":[[85,null]],"Processing in Detail with DUI":[[86,null]],"Program and presentations":[[98,"program-and-presentations"],[99,"program-and-presentations"]],"Program documentation":[[72,null]],"Projects":[[95,null]],"Publications":[[96,null]],"Questioning the lattice symmetry":[[78,"questioning-the-lattice-symmetry"]],"Re-import with the correct beam center":[[74,"re-import-with-the-correct-beam-center"]],"Reading experiment and data":[[6,null]],"Refine the geometry":[[74,"refine-the-geometry"]],"Refinement":[[83,"refinement"],[85,"refinement"],[86,"refinement"],[87,"refinement"],[93,"refinement"]],"Refinement and Integration":[[84,"refinement-and-integration"]],"Refining multi-tile detector metrology with DIALS":[[82,null]],"Refining the detector distance":[[75,"refining-the-detector-distance"]],"Reflection files":[[3,"reflection-files"]],"Resource administration":[[94,"resource-administration"]],"SARS-CoV-2 main protease (Mpro)":[[83,null]],"SSX processing guide":[[97,null]],"Scale the data together":[[74,"scale-the-data-together"]],"Scaling":[[74,"scaling"],[75,"scaling"],[86,"scaling"],[87,"scaling"]],"Scaling against a reference dataset":[[1,"scaling-against-a-reference-dataset"]],"Scaling and Merging":[[83,"scaling-and-merging"],[85,"scaling-and-merging"]],"Scaling and merging":[[76,"scaling-and-merging"]],"Scaling and merging data":[[97,"scaling-and-merging-data"]],"Scan-varying refinement":[[76,"scan-varying-refinement"]],"Scripted processing":[[75,"scripted-processing"]],"Sets 0-9":[[77,"sets-0-9"]],"Sets 10-19":[[77,"sets-10-19"]],"Sets 20-29":[[77,"sets-20-29"]],"Setting up a Development Environment on Linux or Mac":[[9,"setting-up-a-development-environment-on-linux-or-mac"]],"Small-molecule data reduction tutorial":[[87,null]],"Software activities":[[94,"software-activities"]],"Solve the structure":[[74,"solve-the-structure"]],"Sourcing the DIALS environment":[[7,"sourcing-the-dials-environment"]],"Spot finding":[[87,"spot-finding"]],"Spot-finding":[[75,"spot-finding"],[76,"spot-finding"]],"Stable Release: DIALS 3.28.0":[[90,"stable-release-dials-3-28-0"]],"Staff":[[94,"staff"]],"Static model refinement":[[76,"static-model-refinement"]],"Summary of coordinate frames":[[2,"summary-of-coordinate-frames"]],"Symmetry Determination":[[87,"symmetry-determination"]],"Symmetry analysis":[[83,"symmetry-analysis"],[85,"symmetry-analysis"]],"Symmetry, Scaling and Merging":[[84,"symmetry-scaling-and-merging"]],"Table of Contents":[[20,"table-of-contents"],[31,"table-of-contents"]],"Testing the server":[[48,"testing-the-server"]],"The DXTBX goniometer model":[[2,"the-dxtbx-goniometer-model"]],"The diffractometer equation":[[2,"the-diffractometer-equation"]],"The laboratory frame":[[2,"the-laboratory-frame"]],"Tilt axis orientation":[[75,"tilt-axis-orientation"]],"Tutorial data":[[83,"tutorial-data"],[85,"tutorial-data"],[86,"tutorial-data"]],"Tutorials":[[81,null]],"US DIALS National Resource":[[94,null]],"Unit Cell Comparisons":[[77,"unit-cell-comparisons"]],"Unit cell refinement":[[87,"unit-cell-refinement"]],"User guide for scaling data with DIALS":[[1,null]],"Using DIALS at Diamond Light Source":[[80,null]],"Using DIALS with xia2":[[80,"using-dials-with-xia2"]],"Util":[[33,null]],"What to do next":[[82,"what-to-do-next"]],"Workshops":[[100,null]],"Writing a new format class":[[4,"writing-a-new-format-class"]],"dials.algorithms.background":[[10,null]],"dials.algorithms.indexing":[[11,null]],"dials.algorithms.indexing.basis_vector_search":[[11,"module-dials.algorithms.indexing.basis_vector_search"]],"dials.algorithms.indexing.indexer":[[11,"module-dials.algorithms.indexing.indexer"]],"dials.algorithms.indexing.lattice_search":[[11,"module-dials.algorithms.indexing.lattice_search"]],"dials.algorithms.indexing.max_cell":[[11,"module-dials.algorithms.indexing.max_cell"]],"dials.algorithms.indexing.model_evaluation":[[11,"module-dials.algorithms.indexing.model_evaluation"]],"dials.algorithms.indexing.stills_indexer":[[11,"module-dials.algorithms.indexing.stills_indexer"]],"dials.algorithms.integration":[[12,null]],"dials.algorithms.profile_model":[[13,null]],"dials.algorithms.refinement":[[14,null]],"dials.algorithms.scaling":[[15,null]],"dials.algorithms.spot_finding":[[16,null]],"dials.algorithms.spot_prediction":[[17,null]],"dials.algorithms.symmetry":[[18,null]],"dials.algorithms.symmetry.cosym":[[18,"module-dials.algorithms.symmetry.cosym"]],"dials.align_crystal":[[34,null]],"dials.anvil_correction":[[35,null]],"dials.apply_mask":[[36,null]],"dials.check_indexing_symmetry":[[37,null]],"dials.combine_experiments":[[38,null]],"dials.compare_orientation_matrices":[[39,null]],"dials.cosym":[[40,null]],"dials.create_profile_model":[[41,null]],"dials.estimate_gain":[[42,null]],"dials.estimate_resolution":[[43,null]],"dials.export":[[44,null]],"dials.export_bitmaps":[[45,null]],"dials.filter_reflections":[[46,null]],"dials.find_spots":[[47,null]],"dials.find_spots_server/client":[[49,null]],"dials.generate_mask":[[50,null]],"dials.image_viewer":[[51,null]],"dials.import":[[52,null]],"dials.import_xds":[[53,null]],"dials.index":[[54,null]],"dials.integrate":[[55,null]],"dials.merge_cbf":[[56,null]],"dials.missing_reflections":[[57,null]],"dials.plot_scan_varying_model":[[58,null]],"dials.predict":[[59,null]],"dials.refine":[[60,null]],"dials.refine_bravais_settings":[[61,null]],"dials.reindex":[[62,null]],"dials.report":[[63,null]],"dials.scale":[[64,null]],"dials.search_beam_position":[[65,null]],"dials.show":[[66,null]],"dials.slice_sequence":[[67,null]],"dials.spot_counts_per_image":[[68,null]],"dials.stereographic_projection":[[69,null]],"dials.symmetry":[[70,null]],"dials.two_theta_refine":[[71,null]],"distl/dials apache server":[[48,null]],"dxtbx":[[27,null]],"dxtbx.imageset":[[26,null]],"dxtbx.model.beam":[[21,null]],"dxtbx.model.crystal":[[22,null]],"dxtbx.model.detector":[[23,null]],"dxtbx.model.experiment_list":[[24,null]],"dxtbx.model.goniometer":[[25,null]],"dxtbx.model.profile":[[28,null]],"dxtbx.model.scan":[[29,null]],"dxtbx.serialize":[[30,null]],"model.model":[[15,"module-dials.algorithms.scaling.model.model"]],"outlier_rejection":[[15,"module-dials.algorithms.scaling.outlier_rejection"]],"understand Static Method":[[4,"understand-static-method"]],"xia2.multiplex":[[73,null]]},"docnames":["about","dials_scale_user_guide","documentation/conventions","documentation/data_files","documentation/developer_examples/extending_dials","documentation/developer_examples/index","documentation/developer_examples/read_experiment_and_data","documentation/getting_started","documentation/index","documentation/installation_developer","documentation/library_reference/algorithms/dials.algorithms.background","documentation/library_reference/algorithms/dials.algorithms.indexing","documentation/library_reference/algorithms/dials.algorithms.integration","documentation/library_reference/algorithms/dials.algorithms.profile_model","documentation/library_reference/algorithms/dials.algorithms.refinement","documentation/library_reference/algorithms/dials.algorithms.scaling","documentation/library_reference/algorithms/dials.algorithms.spot_finding","documentation/library_reference/algorithms/dials.algorithms.spot_prediction","documentation/library_reference/algorithms/dials.algorithms.symmetry","documentation/library_reference/algorithms/index","documentation/library_reference/array_family/index","documentation/library_reference/dxtbx/beam","documentation/library_reference/dxtbx/crystal","documentation/library_reference/dxtbx/detector","documentation/library_reference/dxtbx/experiment_list","documentation/library_reference/dxtbx/goniometer","documentation/library_reference/dxtbx/imageset","documentation/library_reference/dxtbx/index","documentation/library_reference/dxtbx/profile","documentation/library_reference/dxtbx/scan","documentation/library_reference/dxtbx/serialize","documentation/library_reference/extensions/index","documentation/library_reference/index","documentation/library_reference/util/index","documentation/programs/dials_align_crystal","documentation/programs/dials_anvil_correction","documentation/programs/dials_apply_mask","documentation/programs/dials_check_indexing_symmetry","documentation/programs/dials_combine_experiments","documentation/programs/dials_compare_orientation_matrices","documentation/programs/dials_cosym","documentation/programs/dials_create_profile_model","documentation/programs/dials_estimate_gain","documentation/programs/dials_estimate_resolution","documentation/programs/dials_export","documentation/programs/dials_export_bitmaps","documentation/programs/dials_filter_reflections","documentation/programs/dials_find_spots","documentation/programs/dials_find_spots_apache_server","documentation/programs/dials_find_spots_server","documentation/programs/dials_generate_mask","documentation/programs/dials_image_viewer","documentation/programs/dials_import","documentation/programs/dials_import_xds","documentation/programs/dials_index","documentation/programs/dials_integrate","documentation/programs/dials_merge_cbf","documentation/programs/dials_missing_reflections","documentation/programs/dials_plot_scan_varying_model","documentation/programs/dials_predict","documentation/programs/dials_refine","documentation/programs/dials_refine_bravais_settings","documentation/programs/dials_reindex","documentation/programs/dials_report","documentation/programs/dials_scale","documentation/programs/dials_search_beam_position","documentation/programs/dials_show","documentation/programs/dials_slice_sequence","documentation/programs/dials_spot_counts_per_image","documentation/programs/dials_stereographic_projection","documentation/programs/dials_symmetry","documentation/programs/dials_two_theta_refine","documentation/programs/index","documentation/programs/xia2_multiplex","documentation/tutorials/3DED/Biotin","documentation/tutorials/3DED/MyD88","documentation/tutorials/3DED/lysozyme_nanocrystals","documentation/tutorials/br_lyso_multi","documentation/tutorials/centring_vs_pseudocentring","documentation/tutorials/correcting_poor_initial_geometry_tutorial","documentation/tutorials/diamond","documentation/tutorials/index","documentation/tutorials/metrology_corrections","documentation/tutorials/mpro_x0692","documentation/tutorials/multi_lattice_tutorial","documentation/tutorials/processing_in_detail_betalactamase","documentation/tutorials/processing_in_detail_betalactamase_dui","documentation/tutorials/small_molecule_tutorial","howto","index","installation","license","metrics","missing-images","national_resource","projects","publications","ssx_processing_guide","workshops/DIALS-1","workshops/dials3d","workshops/index"],"envversion":{"sphinx":66,"sphinx.domains.c":3,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":9,"sphinx.domains.index":1,"sphinx.domains.javascript":3,"sphinx.domains.math":2,"sphinx.domains.python":4,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1},"filenames":["about.rst","dials_scale_user_guide.rst","documentation/conventions.rst","documentation/data_files.rst","documentation/developer_examples/extending_dials.rst","documentation/developer_examples/index.rst","documentation/developer_examples/read_experiment_and_data.rst","documentation/getting_started.rst","documentation/index.rst","documentation/installation_developer.rst","documentation/library_reference/algorithms/dials.algorithms.background.rst","documentation/library_reference/algorithms/dials.algorithms.indexing.rst","documentation/library_reference/algorithms/dials.algorithms.integration.rst","documentation/library_reference/algorithms/dials.algorithms.profile_model.rst","documentation/library_reference/algorithms/dials.algorithms.refinement.rst","documentation/library_reference/algorithms/dials.algorithms.scaling.rst","documentation/library_reference/algorithms/dials.algorithms.spot_finding.rst","documentation/library_reference/algorithms/dials.algorithms.spot_prediction.rst","documentation/library_reference/algorithms/dials.algorithms.symmetry.rst","documentation/library_reference/algorithms/index.rst","documentation/library_reference/array_family/index.rst","documentation/library_reference/dxtbx/beam.rst","documentation/library_reference/dxtbx/crystal.rst","documentation/library_reference/dxtbx/detector.rst","documentation/library_reference/dxtbx/experiment_list.rst","documentation/library_reference/dxtbx/goniometer.rst","documentation/library_reference/dxtbx/imageset.rst","documentation/library_reference/dxtbx/index.rst","documentation/library_reference/dxtbx/profile.rst","documentation/library_reference/dxtbx/scan.rst","documentation/library_reference/dxtbx/serialize.rst","documentation/library_reference/extensions/index.rst","documentation/library_reference/index.rst","documentation/library_reference/util/index.rst","documentation/programs/dials_align_crystal.rst","documentation/programs/dials_anvil_correction.rst","documentation/programs/dials_apply_mask.rst","documentation/programs/dials_check_indexing_symmetry.rst","documentation/programs/dials_combine_experiments.rst","documentation/programs/dials_compare_orientation_matrices.rst","documentation/programs/dials_cosym.rst","documentation/programs/dials_create_profile_model.rst","documentation/programs/dials_estimate_gain.rst","documentation/programs/dials_estimate_resolution.rst","documentation/programs/dials_export.rst","documentation/programs/dials_export_bitmaps.rst","documentation/programs/dials_filter_reflections.rst","documentation/programs/dials_find_spots.rst","documentation/programs/dials_find_spots_apache_server.rst","documentation/programs/dials_find_spots_server.rst","documentation/programs/dials_generate_mask.rst","documentation/programs/dials_image_viewer.rst","documentation/programs/dials_import.rst","documentation/programs/dials_import_xds.rst","documentation/programs/dials_index.rst","documentation/programs/dials_integrate.rst","documentation/programs/dials_merge_cbf.rst","documentation/programs/dials_missing_reflections.rst","documentation/programs/dials_plot_scan_varying_model.rst","documentation/programs/dials_predict.rst","documentation/programs/dials_refine.rst","documentation/programs/dials_refine_bravais_settings.rst","documentation/programs/dials_reindex.rst","documentation/programs/dials_report.rst","documentation/programs/dials_scale.rst","documentation/programs/dials_search_beam_position.rst","documentation/programs/dials_show.rst","documentation/programs/dials_slice_sequence.rst","documentation/programs/dials_spot_counts_per_image.rst","documentation/programs/dials_stereographic_projection.rst","documentation/programs/dials_symmetry.rst","documentation/programs/dials_two_theta_refine.rst","documentation/programs/index.rst","documentation/programs/xia2_multiplex.rst","documentation/tutorials/3DED/Biotin.rst","documentation/tutorials/3DED/MyD88.rst","documentation/tutorials/3DED/lysozyme_nanocrystals.rst","documentation/tutorials/br_lyso_multi.rst","documentation/tutorials/centring_vs_pseudocentring.rst","documentation/tutorials/correcting_poor_initial_geometry_tutorial.rst","documentation/tutorials/diamond.rst","documentation/tutorials/index.rst","documentation/tutorials/metrology_corrections.rst","documentation/tutorials/mpro_x0692.rst","documentation/tutorials/multi_lattice_tutorial.rst","documentation/tutorials/processing_in_detail_betalactamase.rst","documentation/tutorials/processing_in_detail_betalactamase_dui.rst","documentation/tutorials/small_molecule_tutorial.rst","howto.rst","index.rst","installation.rst","license.rst","metrics.rst","missing-images.rst","national_resource.rst","projects.rst","publications.rst","ssx_processing_guide.rst","workshops/DIALS-1.rst","workshops/dials3d.rst","workshops/index.rst"],"indexentries":{"__init__() (dials.algorithms.background.radialaverage method)":[[10,"dials.algorithms.background.RadialAverage.__init__",false]],"__init__() (dials.algorithms.indexing.assign_indices.assignindicesglobal method)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesGlobal.__init__",false]],"__init__() (dials.algorithms.indexing.assign_indices.assignindiceslocal method)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesLocal.__init__",false]],"__init__() (dials.algorithms.indexing.assign_indices.assignindicesstrategy method)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesStrategy.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.fft1d method)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT1D.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.fft3d method)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT3D.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectorminimiser method)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectortarget method)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.__init__",false]],"__init__() (dials.algorithms.indexing.basis_vector_search.strategy method)":[[11,"dials.algorithms.indexing.basis_vector_search.Strategy.__init__",false]],"__init__() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.__init__",false]],"__init__() (dials.algorithms.indexing.lattice_search.ffbindexer method)":[[11,"dials.algorithms.indexing.lattice_search.FfbIndexer.__init__",false]],"__init__() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)":[[11,"dials.algorithms.indexing.lattice_search.LowResSpotMatch.__init__",false]],"__init__() (dials.algorithms.indexing.lattice_search.pinkindexer method)":[[11,"dials.algorithms.indexing.lattice_search.PinkIndexer.__init__",false]],"__init__() (dials.algorithms.indexing.lattice_search.strategy method)":[[11,"dials.algorithms.indexing.lattice_search.Strategy.__init__",false]],"__init__() (dials.algorithms.indexing.model_evaluation.modelevaluation method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelEvaluation.__init__",false]],"__init__() (dials.algorithms.indexing.model_evaluation.modelrank method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRank.__init__",false]],"__init__() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.__init__",false]],"__init__() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.__init__",false]],"__init__() (dials.algorithms.indexing.nearest_neighbor.neighboranalysis method)":[[11,"dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis.__init__",false]],"__init__() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.__init__",false]],"__init__() (dials.algorithms.indexing.symmetry.symmetryhandler method)":[[11,"dials.algorithms.indexing.symmetry.SymmetryHandler.__init__",false]],"__init__() (dials.algorithms.integration.integrator.executor method)":[[12,"dials.algorithms.integration.integrator.Executor.__init__",false]],"__init__() (dials.algorithms.integration.integrator.integrator method)":[[12,"dials.algorithms.integration.integrator.Integrator.__init__",false]],"__init__() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.__init__",false]],"__init__() (dials.algorithms.integration.integrator.integratorexecutor method)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor.__init__",false]],"__init__() (dials.algorithms.integration.integrator.joblist method)":[[12,"dials.algorithms.integration.integrator.JobList.__init__",false]],"__init__() (dials.algorithms.integration.integrator.parameters method)":[[12,"dials.algorithms.integration.integrator.Parameters.__init__",false]],"__init__() (dials.algorithms.integration.integrator.parameters.filter method)":[[12,"dials.algorithms.integration.integrator.Parameters.Filter.__init__",false]],"__init__() (dials.algorithms.integration.integrator.parameters.profile method)":[[12,"dials.algorithms.integration.integrator.Parameters.Profile.__init__",false]],"__init__() (dials.algorithms.integration.integrator.parameters.profile.validation method)":[[12,"dials.algorithms.integration.integrator.Parameters.Profile.Validation.__init__",false]],"__init__() (dials.algorithms.integration.integrator.processor2d method)":[[12,"dials.algorithms.integration.integrator.Processor2D.__init__",false]],"__init__() (dials.algorithms.integration.integrator.processor3d method)":[[12,"dials.algorithms.integration.integrator.Processor3D.__init__",false]],"__init__() (dials.algorithms.integration.integrator.processorflat3d method)":[[12,"dials.algorithms.integration.integrator.ProcessorFlat3D.__init__",false]],"__init__() (dials.algorithms.integration.integrator.processorsingle2d method)":[[12,"dials.algorithms.integration.integrator.ProcessorSingle2D.__init__",false]],"__init__() (dials.algorithms.integration.integrator.processorstills method)":[[12,"dials.algorithms.integration.integrator.ProcessorStills.__init__",false]],"__init__() (dials.algorithms.integration.integrator.profilemodellerexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor.__init__",false]],"__init__() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor.__init__",false]],"__init__() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.__init__",false]],"__init__() (dials.algorithms.refinement.engine.adaptlbfgs method)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs.__init__",false]],"__init__() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.__init__",false]],"__init__() (dials.algorithms.refinement.engine.gaussnewtoniterations method)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.__init__",false]],"__init__() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.__init__",false]],"__init__() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.__init__",false]],"__init__() (dials.algorithms.refinement.reflection_manager.blockcalculator method)":[[14,"dials.algorithms.refinement.reflection_manager.BlockCalculator.__init__",false]],"__init__() (dials.algorithms.refinement.reflection_manager.lauereflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.LaueReflectionManager.__init__",false]],"__init__() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.__init__",false]],"__init__() (dials.algorithms.refinement.reflection_manager.tofreflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.TOFReflectionManager.__init__",false]],"__init__() (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.__init__",false]],"__init__() (dials.algorithms.refinement.target.leastsquarespositionalresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff.__init__",false]],"__init__() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.__init__",false]],"__init__() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.__init__",false]],"__init__() (dials.algorithms.refinement.weighting_strategies.constantweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy.__init__",false]],"__init__() (dials.algorithms.refinement.weighting_strategies.lauemixedweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy.__init__",false]],"__init__() (dials.algorithms.refinement.weighting_strategies.lauestatisticalweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy.__init__",false]],"__init__() (dials.algorithms.refinement.weighting_strategies.stillsweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy.__init__",false]],"__init__() (dials.algorithms.scaling.model.model.arrayscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.__init__",false]],"__init__() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.__init__",false]],"__init__() (dials.algorithms.scaling.model.model.kbscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.__init__",false]],"__init__() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.__init__",false]],"__init__() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.__init__",false]],"__init__() (dials.algorithms.scaling.outlier_rejection.normdevoutlierrejection method)":[[15,"dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection.__init__",false]],"__init__() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)":[[15,"dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.__init__",false]],"__init__() (dials.algorithms.scaling.outlier_rejection.simplenormdevoutlierrejection method)":[[15,"dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection.__init__",false]],"__init__() (dials.algorithms.scaling.outlier_rejection.targetedoutlierrejection method)":[[15,"dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection.__init__",false]],"__init__() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)":[[16,"dials.algorithms.spot_finding.factory.BackgroundGradientFilter.__init__",false]],"__init__() (dials.algorithms.spot_finding.factory.filterrunner method)":[[16,"dials.algorithms.spot_finding.factory.FilterRunner.__init__",false]],"__init__() (dials.algorithms.spot_finding.factory.peakcentroiddistancefilter method)":[[16,"dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter.__init__",false]],"__init__() (dials.algorithms.spot_finding.factory.spotdensityfilter method)":[[16,"dials.algorithms.spot_finding.factory.SpotDensityFilter.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.extractpixelsfromimage method)":[[16,"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.extractpixelsfromimage2dnoshoeboxes method)":[[16,"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.extractspots method)":[[16,"dials.algorithms.spot_finding.finder.ExtractSpots.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.extractspotsparalleltask method)":[[16,"dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.lauespotfinder method)":[[16,"dials.algorithms.spot_finding.finder.LaueSpotFinder.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.spotfinder method)":[[16,"dials.algorithms.spot_finding.finder.SpotFinder.__init__",false]],"__init__() (dials.algorithms.spot_finding.finder.tofspotfinder method)":[[16,"dials.algorithms.spot_finding.finder.TOFSpotFinder.__init__",false]],"__init__() (dials.algorithms.spot_prediction.reflection_predictor.reflectionpredictor method)":[[17,"dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.cosymanalysis method)":[[18,"dials.algorithms.symmetry.cosym.CosymAnalysis.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.scoresubgroup method)":[[18,"dials.algorithms.symmetry.cosym.ScoreSubGroup.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.scoresymmetryelement method)":[[18,"dials.algorithms.symmetry.cosym.ScoreSymmetryElement.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.symmetryanalysis method)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.target.lightarray method)":[[18,"dials.algorithms.symmetry.cosym.target.LightArray.__init__",false]],"__init__() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.__init__",false]],"__init__() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.__init__",false]],"__init__() (dials.algorithms.symmetry.laue_group.lauegroupanalysis method)":[[18,"dials.algorithms.symmetry.laue_group.LaueGroupAnalysis.__init__",false]],"__init__() (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient method)":[[18,"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.__init__",false]],"__init__() (dials.algorithms.symmetry.laue_group.scoresubgroup method)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSubGroup.__init__",false]],"__init__() (dials.algorithms.symmetry.laue_group.scoresymmetryelement method)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSymmetryElement.__init__",false]],"__init__() (dials.algorithms.symmetry.symmetry_base method)":[[18,"dials.algorithms.symmetry.symmetry_base.__init__",false]],"__init__() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.__init__",false]],"__init__() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext method)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.__init__",false]],"__init__() (dials.extensions.null_background_ext.nullbackgroundext method)":[[31,"dials.extensions.null_background_ext.NullBackgroundExt.__init__",false]],"__init__() (dials.extensions.simple_background_ext.simplebackgroundext method)":[[31,"dials.extensions.simple_background_ext.SimpleBackgroundExt.__init__",false]],"__init__() (dials.extensions.simple_centroid_ext.simplecentroidext method)":[[31,"dials.extensions.simple_centroid_ext.SimpleCentroidExt.__init__",false]],"__init__() (dials.util.command_line.progressbar method)":[[33,"dials.util.command_line.ProgressBar.__init__",false]],"__init__() (dials.util.command_line.progressbartimer method)":[[33,"dials.util.command_line.ProgressBarTimer.__init__",false]],"__init__() (dials.util.export_mtz.mtzwriterbase method)":[[33,"dials.util.export_mtz.MTZWriterBase.__init__",false]],"__init__() (dials.util.export_mtz.wavelengthgroup method)":[[33,"dials.util.export_mtz.WavelengthGroup.__init__",false]],"__init__() (dials.util.options.argumentparser method)":[[33,"dials.util.options.ArgumentParser.__init__",false]],"__init__() (dials.util.options.argumentparserbase method)":[[33,"dials.util.options.ArgumentParserBase.__init__",false]],"__init__() (dials.util.options.importer method)":[[33,"dials.util.options.Importer.__init__",false]],"__init__() (dials.util.options.optionparser method)":[[33,"dials.util.options.OptionParser.__init__",false]],"__init__() (dials.util.options.philcommandparser method)":[[33,"dials.util.options.PhilCommandParser.__init__",false]],"__init__() (dxtbx.imageset.externallookup method)":[[26,"dxtbx.imageset.ExternalLookup.__init__",false]],"__init__() (dxtbx.imageset.externallookupitembool method)":[[26,"dxtbx.imageset.ExternalLookupItemBool.__init__",false]],"__init__() (dxtbx.imageset.externallookupitemdouble method)":[[26,"dxtbx.imageset.ExternalLookupItemDouble.__init__",false]],"__init__() (dxtbx.imageset.imagegrid method)":[[26,"dxtbx.imageset.ImageGrid.__init__",false]],"__init__() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.__init__",false]],"__init__() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.__init__",false]],"__init__() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.__init__",false]],"__init__() (dxtbx.imageset.memreader method)":[[26,"dxtbx.imageset.MemReader.__init__",false]],"__init__() (dxtbx.model.crystal method)":[[22,"dxtbx.model.Crystal.__init__",false]],"__init__() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.__init__",false]],"__init__() (dxtbx.model.experiment_list.beamcomparison method)":[[24,"dxtbx.model.experiment_list.BeamComparison.__init__",false]],"__init__() (dxtbx.model.experiment_list.detectorcomparison method)":[[24,"dxtbx.model.experiment_list.DetectorComparison.__init__",false]],"__init__() (dxtbx.model.experiment_list.goniometercomparison method)":[[24,"dxtbx.model.experiment_list.GoniometerComparison.__init__",false]],"__init__() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.__init__",false]],"__init__() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.__init__",false]],"__init__() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.__init__",false]],"__init__() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.__init__",false]],"__init__() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.__init__",false]],"__init__() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.__init__",false]],"__init__() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.__init__",false]],"accumulate() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.accumulate",false]],"accumulate() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.accumulate",false]],"achieved() (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.achieved",false]],"achieved() (dials.algorithms.refinement.target.leastsquarespositionalresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff.achieved",false]],"achieved() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.achieved",false]],"achieved() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.achieved",false]],"adaptlbfgs (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs",false]],"adaptlstbx (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx",false]],"add() (dials.algorithms.background.radialaverage method)":[[10,"dials.algorithms.background.RadialAverage.add",false]],"add() (dials.algorithms.integration.integrator.joblist method)":[[12,"dials.algorithms.integration.integrator.JobList.add",false]],"add() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.add",false]],"add_batch_list() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.add_batch_list",false]],"add_column() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.add_column",false]],"add_constant_to_diagonal() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.add_constant_to_diagonal",false]],"add_crystal() (dials.util.export_mtz.mtzwriterbase method)":[[33,"dials.util.export_mtz.MTZWriterBase.add_crystal",false]],"add_dataset() (dials.util.export_mtz.madmergedmtzwriter method)":[[33,"dials.util.export_mtz.MADMergedMTZWriter.add_dataset",false]],"add_dataset() (dials.util.export_mtz.mergedmtzwriter method)":[[33,"dials.util.export_mtz.MergedMTZWriter.add_dataset",false]],"add_empty_dataset() (dials.util.export_mtz.mtzwriterbase method)":[[33,"dials.util.export_mtz.MTZWriterBase.add_empty_dataset",false]],"add_experiment() (dials.util.export_mtz.wavelengthgroup method)":[[33,"dials.util.export_mtz.WavelengthGroup.add_experiment",false]],"add_group() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.add_group",false]],"add_panel() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.add_panel",false]],"add_row() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.add_row",false]],"algorithm() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext static method)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.algorithm",false]],"all_laue() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_laue",false]],"all_rotations() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_rotations",false]],"all_same_type() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_same_type",false]],"all_sequences() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_sequences",false]],"all_stills() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_stills",false]],"all_tof() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.all_tof",false]],"append() (dials.algorithms.indexing.model_evaluation.modelrank method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRank.append",false]],"append() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.append",false]],"append() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.append",false]],"append() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.append",false]],"apply_change_of_basis_ops() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.apply_change_of_basis_ops",false]],"apply_hkl_offset() (in module dials.algorithms.indexing.indexer)":[[11,"dials.algorithms.indexing.indexer.apply_hkl_offset",false]],"apply_symmetry() (dials.algorithms.indexing.symmetry.symmetryhandler method)":[[11,"dials.algorithms.indexing.symmetry.SymmetryHandler.apply_symmetry",false]],"are_experiment_identifiers_consistent() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.are_experiment_identifiers_consistent",false]],"argumenthandlingerrorinfo (class in dials.util.options)":[[33,"dials.util.options.ArgumentHandlingErrorInfo",false]],"argumentparser (class in dials.util.options)":[[33,"dials.util.options.ArgumentParser",false]],"argumentparserbase (class in dials.util.options)":[[33,"dials.util.options.ArgumentParserBase",false]],"arrayscalingmodel (class in dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel",false]],"as_dict() (dials.algorithms.symmetry.cosym.cosymanalysis method)":[[18,"dials.algorithms.symmetry.cosym.CosymAnalysis.as_dict",false]],"as_dict() (dials.algorithms.symmetry.cosym.scoresubgroup method)":[[18,"dials.algorithms.symmetry.cosym.ScoreSubGroup.as_dict",false]],"as_dict() (dials.algorithms.symmetry.cosym.scoresymmetryelement method)":[[18,"dials.algorithms.symmetry.cosym.ScoreSymmetryElement.as_dict",false]],"as_dict() (dials.algorithms.symmetry.cosym.symmetryanalysis method)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis.as_dict",false]],"as_dict() (dials.algorithms.symmetry.laue_group.lauegroupanalysis method)":[[18,"dials.algorithms.symmetry.laue_group.LaueGroupAnalysis.as_dict",false]],"as_dict() (dials.algorithms.symmetry.laue_group.scoresubgroup method)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSubGroup.as_dict",false]],"as_dict() (dials.algorithms.symmetry.laue_group.scoresymmetryelement method)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSymmetryElement.as_dict",false]],"as_file() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_file",false]],"as_file() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.as_file",false]],"as_hdf5() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_hdf5",false]],"as_imageset() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.as_imageset",false]],"as_integer_ratio() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.as_integer_ratio",false]],"as_json() (dials.algorithms.symmetry.cosym.cosymanalysis method)":[[18,"dials.algorithms.symmetry.cosym.CosymAnalysis.as_json",false]],"as_json() (dials.algorithms.symmetry.laue_group.lauegroupanalysis method)":[[18,"dials.algorithms.symmetry.laue_group.LaueGroupAnalysis.as_json",false]],"as_json() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.as_json",false]],"as_miller_array() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_miller_array",false]],"as_msgpack() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_msgpack",false]],"as_msgpack_file() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_msgpack_file",false]],"as_msgpack_to_file() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_msgpack_to_file",false]],"as_pickle() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.as_pickle",false]],"as_str() (dxtbx.model.crystal method)":[[22,"dxtbx.model.Crystal.as_str",false]],"as_str() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.as_str",false]],"as_str() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.as_str",false]],"assert_experiment_identifiers_are_consistent() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.assert_experiment_identifiers_are_consistent",false]],"assignindicesglobal (class in dials.algorithms.indexing.assign_indices)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesGlobal",false]],"assignindiceslocal (class in dials.algorithms.indexing.assign_indices)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesLocal",false]],"assignindicesstrategy (class in dials.algorithms.indexing.assign_indices)":[[11,"dials.algorithms.indexing.assign_indices.AssignIndicesStrategy",false]],"background_algorithm (dials.array_family.flex.reflection_table attribute)":[[20,"dials.array_family.flex.reflection_table.background_algorithm",false]],"background_includes_bad_pixels (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.background_includes_bad_pixels",false]],"backgroundgradientfilter (class in dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.BackgroundGradientFilter",false]],"bad_for_refinement (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.bad_for_refinement",false]],"bad_for_scaling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.bad_for_scaling",false]],"bad_reference (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.bad_reference",false]],"bad_shoebox (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.bad_shoebox",false]],"bad_spot (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.bad_spot",false]],"base_package_options (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.base_package_options",false]],"basic_imageset_from_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.basic_imageset_from_dict",false]],"basic_imageset_to_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.basic_imageset_to_dict",false]],"basisvectorminimiser (class in dials.algorithms.indexing.basis_vector_search.optimise)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser",false]],"basisvectortarget (class in dials.algorithms.indexing.basis_vector_search.optimise)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget",false]],"beamcomparison (class in dxtbx.model.experiment_list)":[[24,"dxtbx.model.experiment_list.BeamComparison",false]],"beamfactory (class in dxtbx.model.beam)":[[21,"dxtbx.model.beam.BeamFactory",false]],"beams() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.beams",false]],"best_model() (dials.algorithms.indexing.model_evaluation.modelrank method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRank.best_model",false]],"best_model() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.best_model",false]],"best_model() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.best_model",false]],"bit_count() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.bit_count",false]],"bit_length() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.bit_length",false]],"blockcalculator (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.BlockCalculator",false]],"build_up() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.build_up",false]],"calc_2d_rmsd_and_displacements() (in module dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.calc_2D_rmsd_and_displacements",false]],"calc_acentric_subgroups() (in module dials.algorithms.indexing.symmetry)":[[11,"dials.algorithms.indexing.symmetry.calc_acentric_subgroups",false]],"calc_exp_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.calc_exp_rmsd_table",false]],"calc_n_param_from_bins() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.calc_n_param_from_bins",false]],"calculate_entering_flags() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.calculate_entering_flags",false]],"calculate_esds() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.calculate_esds",false]],"calculate_gradients() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.calculate_gradients",false]],"calculate_new_offset() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.calculate_new_offset",false]],"calculate_weighted_mean() (dials.util.export_mtz.wavelengthgroup method)":[[33,"dials.util.export_mtz.WavelengthGroup.calculate_weighted_mean",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.constantweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy.calculate_weights",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.externaldelpsiweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy.calculate_weights",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.lauemixedweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy.calculate_weights",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.lauestatisticalweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy.calculate_weights",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.statisticalweightingstrategy static method)":[[14,"dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy.calculate_weights",false]],"calculate_weights() (dials.algorithms.refinement.weighting_strategies.stillsweightingstrategy method)":[[14,"dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy.calculate_weights",false]],"callback_after_step() (dials.algorithms.refinement.engine.adaptlbfgs method)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs.callback_after_step",false]],"callback_after_step() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.callback_after_step",false]],"candidate_orientation_matrices() (in module dials.algorithms.indexing.basis_vector_search.combinations)":[[11,"dials.algorithms.indexing.basis_vector_search.combinations.candidate_orientation_matrices",false]],"centroid_algorithm (dials.array_family.flex.reflection_table attribute)":[[20,"dials.array_family.flex.reflection_table.centroid_algorithm",false]],"centroid_outlier (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.centroid_outlier",false]],"centroid_px_to_mm() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.centroid_px_to_mm",false]],"change_basis() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.change_basis",false]],"change_of_basis_op_to_best_cell() (in module dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.change_of_basis_op_to_best_cell",false]],"change_of_basis_ops_to_minimum_cell() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.change_of_basis_ops_to_minimum_cell",false]],"check_flags() (dials.algorithms.spot_finding.factory.filterrunner method)":[[16,"dials.algorithms.spot_finding.factory.FilterRunner.check_flags",false]],"choose_best_orientation_matrix() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.choose_best_orientation_matrix",false]],"clean_experiment_identifiers_map() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.clean_experiment_identifiers_map",false]],"clear() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.clear",false]],"clear() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.clear",false]],"clear_cache() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.clear_cache",false]],"coefficient() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.coefficient",false]],"coloured() (in module dials.util.command_line)":[[33,"dials.util.command_line.coloured",false]],"cols() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.cols",false]],"combined_scores() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.combined_scores",false]],"command (class in dials.util.command_line)":[[33,"dials.util.command_line.Command",false]],"complete_set() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.complete_set",false]],"complete_set() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.complete_set",false]],"complex() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.complex",false]],"complex() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.complex",false]],"components (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.components",false]],"compute_background() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_background",false]],"compute_background() (dials.extensions.null_background_ext.nullbackgroundext method)":[[31,"dials.extensions.null_background_ext.NullBackgroundExt.compute_background",false]],"compute_background() (dials.extensions.simple_background_ext.simplebackgroundext method)":[[31,"dials.extensions.simple_background_ext.SimpleBackgroundExt.compute_background",false]],"compute_bbox() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_bbox",false]],"compute_centroid() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_centroid",false]],"compute_centroid() (dials.extensions.simple_centroid_ext.simplecentroidext method)":[[31,"dials.extensions.simple_centroid_ext.SimpleCentroidExt.compute_centroid",false]],"compute_corrections() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_corrections",false]],"compute_d() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_d",false]],"compute_d_single() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_d_single",false]],"compute_fitted_intensity() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_fitted_intensity",false]],"compute_functional() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectortarget method)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget.compute_functional",false]],"compute_functional() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch static method)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.compute_functional",false]],"compute_functional() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.compute_functional",false]],"compute_functional_and_gradients() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectorminimiser method)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser.compute_functional_and_gradients",false]],"compute_functional_and_gradients() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectortarget method)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget.compute_functional_and_gradients",false]],"compute_functional_and_gradients() (dials.algorithms.refinement.engine.adaptlbfgs method)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_and_gradients",false]],"compute_functional_and_gradients() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_and_gradients",false]],"compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.engine.adaptlbfgs method)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_gradients_and_curvatures",false]],"compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.compute_functional_gradients_and_curvatures",false]],"compute_functional_gradients_and_curvatures() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_and_curvatures",false]],"compute_functional_gradients_diag() (dials.algorithms.refinement.engine.lbfgscurvs method)":[[14,"dials.algorithms.refinement.engine.LBFGScurvs.compute_functional_gradients_diag",false]],"compute_functional_gradients_diag() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_diag",false]],"compute_functional_score_for_dimension_assessment() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.compute_functional_score_for_dimension_assessment",false]],"compute_gradients() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.compute_gradients",false]],"compute_gradients_fd() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.compute_gradients_fd",false]],"compute_mask() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_mask",false]],"compute_miller_indices_in_asu() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_miller_indices_in_asu",false]],"compute_partiality() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_partiality",false]],"compute_phi_range() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_phi_range",false]],"compute_ray_intersections() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_ray_intersections",false]],"compute_residuals() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.compute_residuals",false]],"compute_residuals_and_gradients() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.compute_residuals_and_gradients",false]],"compute_restraints_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.compute_restraints_functional_gradients_and_curvatures",false]],"compute_restraints_residuals_and_gradients() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.compute_restraints_residuals_and_gradients",false]],"compute_summed_intensity() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_summed_intensity",false]],"compute_threshold() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext method)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.compute_threshold",false]],"compute_zeta() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_zeta",false]],"compute_zeta_multi() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.compute_zeta_multi",false]],"concat() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.concat",false]],"config_refinery() (dials.algorithms.refinement.refiner.refinerfactory static method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.config_refinery",false]],"config_restraints() (dials.algorithms.refinement.refiner.refinerfactory static method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.config_restraints",false]],"config_sparse() (dials.algorithms.refinement.refiner.refinerfactory static method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.config_sparse",false]],"config_target() (dials.algorithms.refinement.refiner.refinerfactory static method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.config_target",false]],"configdict (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.configdict",false]],"configure_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.configure_components",false]],"configure_components() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.configure_components",false]],"configure_components() (dials.algorithms.scaling.model.model.kbscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.configure_components",false]],"configure_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.configure_components",false]],"configure_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.configure_components",false]],"configure_filter() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)":[[16,"dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_filter",false]],"configure_modules (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.configure_modules",false]],"configure_threshold() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)":[[16,"dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_threshold",false]],"conjugate() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.conjugate",false]],"consecutive_refinement_order (dials.algorithms.scaling.model.model.arrayscalingmodel property)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.consecutive_refinement_order",false]],"consecutive_refinement_order (dials.algorithms.scaling.model.model.dosedecay property)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.consecutive_refinement_order",false]],"consecutive_refinement_order (dials.algorithms.scaling.model.model.kbscalingmodel property)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.consecutive_refinement_order",false]],"consecutive_refinement_order (dials.algorithms.scaling.model.model.physicalscalingmodel property)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.consecutive_refinement_order",false]],"consecutive_refinement_order() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.consecutive_refinement_order",false]],"consolidate_histories() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.consolidate_histories",false]],"constantweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy",false]],"contains_invalid_pixels() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.contains_invalid_pixels",false]],"convergence_as_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.convergence_as_shift_over_esd",false]],"convert_to_cambridge() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.convert_to_cambridge",false]],"copy() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.copy",false]],"copy() (dxtbx.imageset.memreader method)":[[26,"dxtbx.imageset.MemReader.copy",false]],"correlationcoefficientaccumulator (class in dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator",false]],"cosymanalysis (class in dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.CosymAnalysis",false]],"crystal (class in dxtbx.model)":[[22,"dxtbx.model.Crystal",false]],"crystal (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.crystal",false]],"crystal() (in module dxtbx.serialize.load)":[[30,"dxtbx.serialize.load.crystal",false]],"crystalfactory (class in dxtbx.model.crystal)":[[22,"dxtbx.model.crystal.CrystalFactory",false]],"crystals() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.crystals",false]],"curvatures() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.curvatures",false]],"curvatures_fd() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.curvatures_fd",false]],"damping_value (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.damping_value",false]],"data (dxtbx.imageset.externallookupitembool property)":[[26,"dxtbx.imageset.ExternalLookupItemBool.data",false]],"data (dxtbx.imageset.externallookupitemdouble property)":[[26,"dxtbx.imageset.ExternalLookupItemDouble.data",false]],"data() (dials.algorithms.integration.integrator.integratorexecutor method)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor.data",false]],"data() (dials.algorithms.integration.integrator.profilemodellerexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor.data",false]],"data() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor.data",false]],"data() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.data",false]],"data() (dials.algorithms.symmetry.cosym.target.lightarray method)":[[18,"dials.algorithms.symmetry.cosym.target.LightArray.data",false]],"data() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.data",false]],"default (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.default",false]],"default (dials.extensions.simple_centroid_ext.simplecentroidext attribute)":[[31,"dials.extensions.simple_centroid_ext.SimpleCentroidExt.default",false]],"del_last_row() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.del_last_row",false]],"del_selected() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.del_selected",false]],"denominator (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.denominator",false]],"denominator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.denominator",false]],"dest_dir_prefix (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.dest_dir_prefix",false]],"detector (class in dxtbx.model)":[[23,"dxtbx.model.Detector",false]],"detectorcomparison (class in dxtbx.model.experiment_list)":[[24,"dxtbx.model.experiment_list.DetectorComparison",false]],"detectorfactory (class in dxtbx.model.detector)":[[23,"dxtbx.model.detector.DetectorFactory",false]],"detectors() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.detectors",false]],"determine_auto_absorption_params() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.determine_auto_absorption_params",false]],"determine_esq_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.determine_Esq_outlier_index_arrays",false]],"determine_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.determine_outlier_index_arrays",false]],"determine_reindex_operator_against_reference() (in module dials.algorithms.symmetry.reindex_to_reference)":[[18,"dials.algorithms.symmetry.reindex_to_reference.determine_reindex_operator_against_reference",false]],"dials.algorithms.background":[[10,"module-dials.algorithms.background",false]],"dials.algorithms.indexing":[[11,"module-dials.algorithms.indexing",false]],"dials.algorithms.indexing.assign_indices":[[11,"module-dials.algorithms.indexing.assign_indices",false]],"dials.algorithms.indexing.basis_vector_search":[[11,"module-dials.algorithms.indexing.basis_vector_search",false]],"dials.algorithms.indexing.basis_vector_search.combinations":[[11,"module-dials.algorithms.indexing.basis_vector_search.combinations",false]],"dials.algorithms.indexing.basis_vector_search.optimise":[[11,"module-dials.algorithms.indexing.basis_vector_search.optimise",false]],"dials.algorithms.indexing.compare_orientation_matrices":[[11,"module-dials.algorithms.indexing.compare_orientation_matrices",false]],"dials.algorithms.indexing.indexer":[[11,"module-dials.algorithms.indexing.indexer",false]],"dials.algorithms.indexing.lattice_search":[[11,"module-dials.algorithms.indexing.lattice_search",false]],"dials.algorithms.indexing.max_cell":[[11,"module-dials.algorithms.indexing.max_cell",false]],"dials.algorithms.indexing.model_evaluation":[[11,"module-dials.algorithms.indexing.model_evaluation",false]],"dials.algorithms.indexing.nearest_neighbor":[[11,"module-dials.algorithms.indexing.nearest_neighbor",false]],"dials.algorithms.indexing.refinement":[[11,"module-dials.algorithms.indexing.refinement",false]],"dials.algorithms.indexing.stills_indexer":[[11,"module-dials.algorithms.indexing.stills_indexer",false]],"dials.algorithms.indexing.symmetry":[[11,"module-dials.algorithms.indexing.symmetry",false]],"dials.algorithms.integration.integrator":[[12,"module-dials.algorithms.integration.integrator",false]],"dials.algorithms.profile_model":[[13,"module-dials.algorithms.profile_model",false]],"dials.algorithms.refinement.engine":[[14,"module-dials.algorithms.refinement.engine",false]],"dials.algorithms.refinement.refiner":[[14,"module-dials.algorithms.refinement.refiner",false]],"dials.algorithms.refinement.reflection_manager":[[14,"module-dials.algorithms.refinement.reflection_manager",false]],"dials.algorithms.refinement.target":[[14,"module-dials.algorithms.refinement.target",false]],"dials.algorithms.refinement.target_stills":[[14,"module-dials.algorithms.refinement.target_stills",false]],"dials.algorithms.refinement.weighting_strategies":[[14,"module-dials.algorithms.refinement.weighting_strategies",false]],"dials.algorithms.scaling":[[15,"module-dials.algorithms.scaling",false]],"dials.algorithms.scaling.model.model":[[15,"module-dials.algorithms.scaling.model.model",false]],"dials.algorithms.scaling.outlier_rejection":[[15,"module-dials.algorithms.scaling.outlier_rejection",false]],"dials.algorithms.spot_finding.factory":[[16,"module-dials.algorithms.spot_finding.factory",false]],"dials.algorithms.spot_finding.finder":[[16,"module-dials.algorithms.spot_finding.finder",false]],"dials.algorithms.spot_prediction.reflection_predictor":[[17,"module-dials.algorithms.spot_prediction.reflection_predictor",false]],"dials.algorithms.symmetry":[[18,"module-dials.algorithms.symmetry",false]],"dials.algorithms.symmetry.cosym":[[18,"module-dials.algorithms.symmetry.cosym",false]],"dials.algorithms.symmetry.cosym.engine":[[18,"module-dials.algorithms.symmetry.cosym.engine",false]],"dials.algorithms.symmetry.cosym.target":[[18,"module-dials.algorithms.symmetry.cosym.target",false]],"dials.algorithms.symmetry.laue_group":[[18,"module-dials.algorithms.symmetry.laue_group",false]],"dials.algorithms.symmetry.reindex_to_reference":[[18,"module-dials.algorithms.symmetry.reindex_to_reference",false]],"dials.extensions.dispersion_spotfinder_threshold_ext":[[31,"module-dials.extensions.dispersion_spotfinder_threshold_ext",false]],"dials.extensions.gaussian_rs_profile_model_ext":[[31,"module-dials.extensions.gaussian_rs_profile_model_ext",false]],"dials.extensions.null_background_ext":[[31,"module-dials.extensions.null_background_ext",false]],"dials.extensions.simple_background_ext":[[31,"module-dials.extensions.simple_background_ext",false]],"dials.extensions.simple_centroid_ext":[[31,"module-dials.extensions.simple_centroid_ext",false]],"dials.util.command_line":[[33,"module-dials.util.command_line",false]],"dials.util.export_mtz":[[33,"module-dials.util.export_mtz",false]],"dials.util.export_text":[[33,"module-dials.util.export_text",false]],"dials.util.image":[[33,"module-dials.util.image",false]],"dials.util.installer":[[33,"module-dials.util.installer",false]],"dials.util.ioutil":[[33,"module-dials.util.ioutil",false]],"dials.util.nexus":[[33,"module-dials.util.nexus",false]],"dials.util.options":[[33,"module-dials.util.options",false]],"dialsindexerror":[[11,"dials.algorithms.indexing.DialsIndexError",false]],"dialsindexrefineerror":[[11,"dials.algorithms.indexing.DialsIndexRefineError",false]],"diff_phil (dials.util.options.argumentparser property)":[[33,"dials.util.options.ArgumentParser.diff_phil",false]],"diff_phil (dials.util.options.philcommandparser property)":[[33,"dials.util.options.PhilCommandParser.diff_phil",false]],"difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices)":[[11,"dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle",false]],"dim (dials.algorithms.refinement.target.target property)":[[14,"dials.algorithms.refinement.target.Target.dim",false]],"dim (dials.algorithms.symmetry.cosym.target.target attribute)":[[18,"dials.algorithms.symmetry.cosym.target.Target.dim",false]],"disablempmixin (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.DisableMPmixin",false]],"dispersionspotfinderthresholdext (class in dials.extensions.dispersion_spotfinder_threshold_ext)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt",false]],"dont_integrate (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.dont_integrate",false]],"dosedecay (class in dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.DoseDecay",false]],"dump() (in module dials.util.nexus)":[[33,"dials.util.nexus.dump",false]],"dx (dxtbx.imageset.externallookup property)":[[26,"dxtbx.imageset.ExternalLookup.dx",false]],"dxtbx.imageset":[[26,"module-dxtbx.imageset",false]],"dxtbx.model.beam":[[21,"module-dxtbx.model.beam",false]],"dxtbx.model.crystal":[[22,"module-dxtbx.model.crystal",false]],"dxtbx.model.detector":[[23,"module-dxtbx.model.detector",false]],"dxtbx.model.experiment_list":[[24,"module-dxtbx.model.experiment_list",false]],"dxtbx.model.goniometer":[[25,"module-dxtbx.model.goniometer",false]],"dxtbx.model.profile":[[28,"module-dxtbx.model.profile",false]],"dxtbx.model.scan":[[29,"module-dxtbx.model.scan",false]],"dxtbx.serialize.imageset":[[30,"module-dxtbx.serialize.imageset",false]],"dxtbx.serialize.load":[[30,"module-dxtbx.serialize.load",false]],"dxtbx.serialize.xds":[[30,"module-dxtbx.serialize.xds",false]],"dy (dxtbx.imageset.externallookup property)":[[26,"dxtbx.imageset.ExternalLookup.dy",false]],"e_refine() (in module dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.e_refine",false]],"eliminate_sys_absent() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.eliminate_sys_absent",false]],"empty() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.empty",false]],"empty() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.empty",false]],"empty_standard() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.empty_standard",false]],"end() (dials.util.command_line.command class method)":[[33,"dials.util.command_line.Command.end",false]],"error_model (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.error_model",false]],"estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.estimate_global_threshold",false]],"evaluate() (dials.algorithms.indexing.model_evaluation.modelevaluation method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelEvaluation.evaluate",false]],"evaluate() (dials.algorithms.indexing.model_evaluation.strategy method)":[[11,"dials.algorithms.indexing.model_evaluation.Strategy.evaluate",false]],"exception (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.exception",false]],"excluded_for_refinement (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.excluded_for_refinement",false]],"excluded_for_scaling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.excluded_for_scaling",false]],"executor (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Executor",false]],"exp_nos (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.exp_nos",false]],"experiment_identifiers() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.experiment_identifiers",false]],"experiment_list() (in module dxtbx.serialize.load)":[[30,"dxtbx.serialize.load.experiment_list",false]],"experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.experiment_list_for_crystal",false]],"experiment_type (dials.algorithms.refinement.reflection_manager.lauereflectionmanager attribute)":[[14,"dials.algorithms.refinement.reflection_manager.LaueReflectionManager.experiment_type",false]],"experiment_type (dials.algorithms.refinement.reflection_manager.reflectionmanager attribute)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.experiment_type",false]],"experiment_type (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager attribute)":[[14,"dials.algorithms.refinement.reflection_manager.StillsReflectionManager.experiment_type",false]],"experimentlist (class in dxtbx.model)":[[24,"dxtbx.model.ExperimentList",false]],"experimentlistfactory (class in dxtbx.model.experiment_list)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory",false]],"export_as_json() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.export_as_json",false]],"export_mtz() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.export_mtz",false]],"export_reflections() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.export_reflections",false]],"export_text() (in module dials.util.export_text)":[[33,"dials.util.export_text.export_text",false]],"extend() (dials.algorithms.indexing.model_evaluation.modelrank method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRank.extend",false]],"extend() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.extend",false]],"extend() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.extend",false]],"extend() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.extend",false]],"external_lookup (dxtbx.imageset.imageset property)":[[26,"dxtbx.imageset.ImageSet.external_lookup",false]],"external_lookup (dxtbx.imageset.imagesetdata property)":[[26,"dxtbx.imageset.ImageSetData.external_lookup",false]],"externaldelpsiweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy",false]],"externallookup (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ExternalLookup",false]],"externallookupitembool (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ExternalLookupItemBool",false]],"externallookupitemdouble (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ExternalLookupItemDouble",false]],"extract_reference_intensities() (in module dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.extract_reference_intensities",false]],"extract_shoeboxes() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.extract_shoeboxes",false]],"extractpixelsfromimage (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage",false]],"extractpixelsfromimage2dnoshoeboxes (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes",false]],"extractspots (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.ExtractSpots",false]],"extractspotsparalleltask (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask",false]],"failed_during_background_modelling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.failed_during_background_modelling",false]],"failed_during_profile_fitting (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.failed_during_profile_fitting",false]],"failed_during_summation (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.failed_during_summation",false]],"ffbindexer (class in dials.algorithms.indexing.lattice_search)":[[11,"dials.algorithms.indexing.lattice_search.FfbIndexer",false]],"fft1d (class in dials.algorithms.indexing.basis_vector_search)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT1D",false]],"fft3d (class in dials.algorithms.indexing.basis_vector_search)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT3D",false]],"filename (dxtbx.imageset.externallookupitembool property)":[[26,"dxtbx.imageset.ExternalLookupItemBool.filename",false]],"filename (dxtbx.imageset.externallookupitemdouble property)":[[26,"dxtbx.imageset.ExternalLookupItemDouble.filename",false]],"filename_or_none() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.filename_or_none",false]],"filename_to_absolute() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.filename_to_absolute",false]],"filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_likelihood",false]],"filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_n_indexed",false]],"filter_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_volume",false]],"filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.filter_doubled_cell",false]],"filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations)":[[11,"dials.algorithms.indexing.basis_vector_search.combinations.filter_known_symmetry",false]],"filter_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.filter_obs",false]],"filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations)":[[11,"dials.algorithms.indexing.basis_vector_search.combinations.filter_similar_orientations",false]],"filterrunner (class in dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.FilterRunner",false]],"final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase attribute)":[[15,"dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.final_outlier_arrays",false]],"finalise() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.finalise",false]],"finalise() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.finalise",false]],"finalize() (dials.algorithms.integration.integrator.integratorexecutor method)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor.finalize",false]],"finalize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor.finalize",false]],"finalize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor.finalize",false]],"finalize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)":[[12,"dials.algorithms.integration.integrator.Integrator2D.finalize_reflections",false]],"finalize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)":[[12,"dials.algorithms.integration.integrator.Integrator3D.finalize_reflections",false]],"finalize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)":[[12,"dials.algorithms.integration.integrator.IntegratorFlat3D.finalize_reflections",false]],"finalize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)":[[12,"dials.algorithms.integration.integrator.IntegratorSingle2D.finalize_reflections",false]],"finalize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)":[[12,"dials.algorithms.integration.integrator.IntegratorStills.finalize_reflections",false]],"find() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.find",false]],"find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft1d method)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT1D.find_basis_vectors",false]],"find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft3d method)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT3D.find_basis_vectors",false]],"find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.find_basis_vectors",false]],"find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.strategy method)":[[11,"dials.algorithms.indexing.basis_vector_search.Strategy.find_basis_vectors",false]],"find_crystal_models() (dials.algorithms.indexing.lattice_search.ffbindexer method)":[[11,"dials.algorithms.indexing.lattice_search.FfbIndexer.find_crystal_models",false]],"find_crystal_models() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)":[[11,"dials.algorithms.indexing.lattice_search.LowResSpotMatch.find_crystal_models",false]],"find_crystal_models() (dials.algorithms.indexing.lattice_search.pinkindexer method)":[[11,"dials.algorithms.indexing.lattice_search.PinkIndexer.find_crystal_models",false]],"find_crystal_models() (dials.algorithms.indexing.lattice_search.strategy method)":[[11,"dials.algorithms.indexing.lattice_search.Strategy.find_crystal_models",false]],"find_lattices() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.find_lattices",false]],"find_matching_symmetry() (in module dials.algorithms.indexing.symmetry)":[[11,"dials.algorithms.indexing.symmetry.find_matching_symmetry",false]],"find_max_cell() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.find_max_cell",false]],"find_max_cell() (in module dials.algorithms.indexing.max_cell)":[[11,"dials.algorithms.indexing.max_cell.find_max_cell",false]],"find_overlaps() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.find_overlaps",false]],"find_spots() (dials.algorithms.spot_finding.finder.spotfinder method)":[[16,"dials.algorithms.spot_finding.finder.SpotFinder.find_spots",false]],"finished() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.finished",false]],"finished() (dials.util.command_line.progressbar method)":[[33,"dials.util.command_line.ProgressBar.finished",false]],"fit_profiles() (dials.algorithms.integration.integrator.integrator method)":[[12,"dials.algorithms.integration.integrator.Integrator.fit_profiles",false]],"fix_initial_parameter() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.fix_initial_parameter",false]],"fix_initial_parameter() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.fix_initial_parameter",false]],"fix_initial_parameter() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.fix_initial_parameter",false]],"fixed_components (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.fixed_components",false]],"flatten_experiments() (in module dials.util.options)":[[33,"dials.util.options.flatten_experiments",false]],"flatten_reflections() (in module dials.util.options)":[[33,"dials.util.options.flatten_reflections",false]],"foreground_includes_bad_pixels (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.foreground_includes_bad_pixels",false]],"format_epilog() (dials.util.options.argumentparserbase method)":[[33,"dials.util.options.ArgumentParserBase.format_epilog",false]],"format_help() (dials.util.options.argumentparser method)":[[33,"dials.util.options.ArgumentParser.format_help",false]],"fraction_indexed (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.fraction_indexed",false]],"frame_hist() (in module dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.frame_hist",false]],"from_args() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_args",false]],"from_bytes() (dials.array_family.flex.reflection_table.flags class method)":[[20,"dials.array_family.flex.reflection_table.flags.from_bytes",false]],"from_data() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.from_data",false]],"from_data() (dials.algorithms.scaling.model.model.dosedecay class method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.from_data",false]],"from_data() (dials.algorithms.scaling.model.model.kbscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.from_data",false]],"from_data() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.from_data",false]],"from_data() (dials.algorithms.scaling.model.model.scalingmodelbase class method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.from_data",false]],"from_dict() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.from_dict",false]],"from_dict() (dials.algorithms.scaling.model.model.dosedecay class method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.from_dict",false]],"from_dict() (dials.algorithms.scaling.model.model.kbscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.from_dict",false]],"from_dict() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.from_dict",false]],"from_dict() (dials.algorithms.scaling.model.model.scalingmodelbase class method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.from_dict",false]],"from_dict() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext class method)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.from_dict",false]],"from_dict() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.from_dict",false]],"from_dict() (dxtbx.model.crystal static method)":[[22,"dxtbx.model.Crystal.from_dict",false]],"from_dict() (dxtbx.model.crystal.crystalfactory static method)":[[22,"dxtbx.model.crystal.CrystalFactory.from_dict",false]],"from_dict() (dxtbx.model.detector static method)":[[23,"dxtbx.model.Detector.from_dict",false]],"from_dict() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.from_dict",false]],"from_dict() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_dict",false]],"from_dict() (dxtbx.model.goniometer.goniometer static method)":[[25,"dxtbx.model.goniometer.Goniometer.from_dict",false]],"from_dict() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.from_dict",false]],"from_dict() (dxtbx.model.goniometer.multiaxisgoniometer static method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.from_dict",false]],"from_dict() (dxtbx.model.mosaiccrystalkabsch2010 class method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.from_dict",false]],"from_dict() (dxtbx.model.mosaiccrystalsauter2014 class method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.from_dict",false]],"from_dict() (dxtbx.model.profile.profilemodelfactory static method)":[[28,"dxtbx.model.profile.ProfileModelFactory.from_dict",false]],"from_dict() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.from_dict",false]],"from_file() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_file",false]],"from_file() (dxtbx.model.experimentlist static method)":[[24,"dxtbx.model.ExperimentList.from_file",false]],"from_filenames() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_filenames",false]],"from_hdf5() (dials.array_family.flex.reflection_table class method)":[[20,"dials.array_family.flex.reflection_table.from_hdf5",false]],"from_imageset() (dxtbx.imageset.imagegrid static method)":[[26,"dxtbx.imageset.ImageGrid.from_imageset",false]],"from_imageset_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_imageset_and_crystal",false]],"from_json() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_json",false]],"from_json_file() (dials.algorithms.refinement.engine.journal class method)":[[14,"dials.algorithms.refinement.engine.Journal.from_json_file",false]],"from_json_file() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_json_file",false]],"from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)":[[22,"dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix",false]],"from_msgpack() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_msgpack",false]],"from_msgpack_file() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_msgpack_file",false]],"from_observations() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_observations",false]],"from_parameters() (dials.algorithms.indexing.indexer.indexer static method)":[[11,"dials.algorithms.indexing.indexer.Indexer.from_parameters",false]],"from_parameters() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)":[[16,"dials.algorithms.spot_finding.factory.SpotFinderFactory.from_parameters",false]],"from_parameters_and_experiments() (dials.algorithms.refinement.target.targetfactory static method)":[[14,"dials.algorithms.refinement.target.TargetFactory.from_parameters_and_experiments",false]],"from_parameters_data_experiments() (dials.algorithms.refinement.refiner.refinerfactory class method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.from_parameters_data_experiments",false]],"from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.from_parameters_reflections_experiments",false]],"from_phil() (dials.algorithms.integration.integrator.parameters static method)":[[12,"dials.algorithms.integration.integrator.Parameters.from_phil",false]],"from_phil() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.from_phil",false]],"from_phil() (dxtbx.model.crystal.crystalfactory static method)":[[22,"dxtbx.model.crystal.CrystalFactory.from_phil",false]],"from_phil() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.from_phil",false]],"from_phil() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.from_phil",false]],"from_phil() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.from_phil",false]],"from_pickle() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_pickle",false]],"from_pickle_file() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_pickle_file",false]],"from_predictions() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_predictions",false]],"from_predictions_multi() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.from_predictions_multi",false]],"from_sequence_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_sequence_and_crystal",false]],"from_serialized_format() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_serialized_format",false]],"from_stills_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_stills_and_crystal",false]],"from_template() (dxtbx.imageset.imagesetfactory static method)":[[26,"dxtbx.imageset.ImageSetFactory.from_template",false]],"from_templates() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_templates",false]],"from_templates() (dxtbx.model.experimentlist static method)":[[24,"dxtbx.model.ExperimentList.from_templates",false]],"from_xds() (dxtbx.model.experiment_list.experimentlistfactory static method)":[[24,"dxtbx.model.experiment_list.ExperimentListFactory.from_xds",false]],"gain (dxtbx.imageset.externallookup property)":[[26,"dxtbx.imageset.ExternalLookup.gain",false]],"gaussianrsprofilemodelext (class in dials.extensions.gaussian_rs_profile_model_ext)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt",false]],"gaussnewtoniterations (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations",false]],"generate_from_phil() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.generate_from_phil",false]],"generate_phil_scope() (in module dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.generate_phil_scope",false]],"generate_phil_scope() (in module dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.generate_phil_scope",false]],"get() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.get",false]],"get_a_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.get_A_as_sqr",false]],"get_a_inverse_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.get_A_inverse_as_sqr",false]],"get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_accepted_refs_size",false]],"get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle",false]],"get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.get_angles",false]],"get_array_range() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_array_range",false]],"get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.get_axes",false]],"get_beam() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_beam",false]],"get_beam() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_beam",false]],"get_beam() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_beam",false]],"get_beam() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_beam",false]],"get_beam() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.get_beam",false]],"get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_centroid_analyser",false]],"get_col_names() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.get_col_names",false]],"get_corrected_data() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_corrected_data",false]],"get_corrected_data() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_corrected_data",false]],"get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.get_correlation_matrix_for_step",false]],"get_crystal_symmetry() (dxtbx.model.crystal method)":[[22,"dxtbx.model.Crystal.get_crystal_symmetry",false]],"get_data() (dials.util.image.reader method)":[[33,"dials.util.image.reader.get_data",false]],"get_data() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_data",false]],"get_detector() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_detector",false]],"get_detector() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_detector",false]],"get_detector() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_detector",false]],"get_detector() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_detector",false]],"get_detector() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.get_detector",false]],"get_detectorbase() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_detectorbase",false]],"get_direction() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_direction",false]],"get_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.get_domain_size_ang",false]],"get_elapsed_time() (dials.util.command_line.progressbartimer method)":[[33,"dials.util.command_line.ProgressBarTimer.get_elapsed_time",false]],"get_entry() (in module dials.util.nexus)":[[33,"dials.util.nexus.get_entry",false]],"get_experiments() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.get_experiments",false]],"get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_fixed_rotation",false]],"get_flags() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.get_flags",false]],"get_format_class() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_format_class",false]],"get_format_class() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_format_class",false]],"get_free_reflections() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.get_free_reflections",false]],"get_free_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_free_reflections",false]],"get_gain() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_gain",false]],"get_gain() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_gain",false]],"get_goniometer() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_goniometer",false]],"get_goniometer() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_goniometer",false]],"get_goniometer() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_goniometer",false]],"get_goniometer() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_goniometer",false]],"get_goniometer() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.get_goniometer",false]],"get_grid_size() (dxtbx.imageset.imagegrid method)":[[26,"dxtbx.imageset.ImageGrid.get_grid_size",false]],"get_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.get_half_mosaicity_deg",false]],"get_image_identifier() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_image_identifier",false]],"get_image_identifier() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_image_identifier",false]],"get_indexed() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_indexed",false]],"get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil)":[[33,"dials.util.ioutil.get_inverse_ub_matrix_from_xparm",false]],"get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle",false]],"get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis",false]],"get_mask() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_mask",false]],"get_mask() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_mask",false]],"get_master_path() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_master_path",false]],"get_matches() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.get_matches",false]],"get_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_matches",false]],"get_max_inscribed_resolution() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.get_max_inscribed_resolution",false]],"get_max_resolution() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.get_max_resolution",false]],"get_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.get_mosaicity",false]],"get_names() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.get_names",false]],"get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.get_names",false]],"get_nrows() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.get_nrows",false]],"get_num_matches() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.get_num_matches",false]],"get_num_matches_for_experiment() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.get_num_matches_for_experiment",false]],"get_num_matches_for_panel() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.get_num_matches_for_panel",false]],"get_num_scan_points() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_num_scan_points",false]],"get_num_steps() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.get_num_steps",false]],"get_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_obs",false]],"get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_omega_angle",false]],"get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_omega_axis",false]],"get_panel_intersection() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.get_panel_intersection",false]],"get_param_reporter() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.get_param_reporter",false]],"get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.get_parameter_correlation_matrix",false]],"get_params() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_params",false]],"get_path() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_path",false]],"get_path() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_path",false]],"get_pedestal() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_pedestal",false]],"get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_phi_angle",false]],"get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_phi_axis",false]],"get_raw_data() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_raw_data",false]],"get_ray_intersection() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.get_ray_intersection",false]],"get_rotation_axis() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_rotation_axis",false]],"get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum",false]],"get_sample_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.get_sample_size",false]],"get_scan() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_scan",false]],"get_scan() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_scan",false]],"get_scan() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_scan",false]],"get_scan() (dxtbx.imageset.imagesetlazy method)":[[26,"dxtbx.imageset.ImageSetLazy.get_scan",false]],"get_scan() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.get_scan",false]],"get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)":[[25,"dxtbx.model.goniometer.KappaGoniometer.get_scan_axis",false]],"get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis",false]],"get_setting_rotation() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_setting_rotation",false]],"get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point",false]],"get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points",false]],"get_shared_components() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.get_shared_components",false]],"get_shared_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.get_shared_components",false]],"get_shared_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.get_shared_components",false]],"get_space_group_type_from_xparm() (in module dials.util.ioutil)":[[33,"dials.util.ioutil.get_space_group_type_from_xparm",false]],"get_spectrum() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_spectrum",false]],"get_subset_for_symmetry() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.get_subset_for_symmetry",false]],"get_template() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.get_template",false]],"get_template() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_template",false]],"get_template() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.get_template",false]],"get_vendor() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.get_vendor",false]],"get_vendortype() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.get_vendortype",false]],"get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.get_weighting_strategy_override",false]],"goniometer (class in dxtbx.model.goniometer)":[[25,"dxtbx.model.goniometer.Goniometer",false]],"goniometercomparison (class in dxtbx.model.experiment_list)":[[24,"dxtbx.model.experiment_list.GoniometerComparison",false]],"goniometerfactory (class in dxtbx.model.goniometer)":[[25,"dxtbx.model.goniometer.GoniometerFactory",false]],"goniometers() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.goniometers",false]],"gradient_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.gradient_threshold",false]],"groups_cache() (in module dials.algorithms.indexing.symmetry)":[[11,"dials.algorithms.indexing.symmetry.groups_cache",false]],"has_dynamic_mask() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.has_dynamic_mask",false]],"has_key() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.has_key",false]],"has_projection_2d() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.has_projection_2d",false]],"has_single_file_reader() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.has_single_file_reader",false]],"heading() (in module dials.util.command_line)":[[33,"dials.util.command_line.heading",false]],"help_keys() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.help_keys",false]],"hierarchy() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.hierarchy",false]],"hist() (in module dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.hist",false]],"histories() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.histories",false]],"history (dials.algorithms.refinement.refiner.refiner property)":[[14,"dials.algorithms.refinement.refiner.Refiner.history",false]],"hkl_offset (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.hkl_offset",false]],"id_ (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.id_",false]],"id_ (dials.algorithms.scaling.model.model.dosedecay attribute)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.id_",false]],"id_ (dials.algorithms.scaling.model.model.kbscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.id_",false]],"id_ (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.id_",false]],"id_ (dials.algorithms.scaling.model.model.scalingmodelbase attribute)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.id_",false]],"identifiers (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.identifiers",false]],"identifiers() (dxtbx.imageset.memreader method)":[[26,"dxtbx.imageset.MemReader.identifiers",false]],"identifiers() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.identifiers",false]],"identify_outliers() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.identify_outliers",false]],"imag (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.imag",false]],"imagegrid (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageGrid",false]],"imagesequence (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageSequence",false]],"imagesequence_from_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.imagesequence_from_dict",false]],"imagesequence_to_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.imagesequence_to_dict",false]],"imageset (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageSet",false]],"imageset() (in module dxtbx.serialize.load)":[[30,"dxtbx.serialize.load.imageset",false]],"imageset_from_anyset() (dxtbx.imageset.imagesetfactory static method)":[[26,"dxtbx.imageset.ImageSetFactory.imageset_from_anyset",false]],"imageset_from_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.imageset_from_dict",false]],"imageset_to_dict() (in module dxtbx.serialize.imageset)":[[30,"dxtbx.serialize.imageset.imageset_to_dict",false]],"imagesetdata (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageSetData",false]],"imagesetfactory (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageSetFactory",false]],"imagesetlazy (class in dxtbx.imageset)":[[26,"dxtbx.imageset.ImageSetLazy",false]],"imagesets() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.imagesets",false]],"imgcif() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.imgCIF",false]],"imgcif() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.imgCIF",false]],"imgcif() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.imgCIF",false]],"imgcif() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.imgCIF",false]],"imgcif_h() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.imgCIF_H",false]],"imgcif_h() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.imgCIF_H",false]],"imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.imgCIF_H",false]],"imgcif_h() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.imgCIF_H",false]],"importer (class in dials.util.options)":[[33,"dials.util.options.Importer",false]],"in_powder_ring (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.in_powder_ring",false]],"include_gui_packages (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.include_gui_packages",false]],"includes_bad_pixels (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.includes_bad_pixels",false]],"indent (dials.util.command_line.command attribute)":[[33,"dials.util.command_line.Command.indent",false]],"index() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.index",false]],"index() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.index",false]],"index_reflections() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.index_reflections",false]],"indexed (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.indexed",false]],"indexer (class in dials.algorithms.indexing.indexer)":[[11,"dials.algorithms.indexing.indexer.Indexer",false]],"indices() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.indices",false]],"indices() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.indices",false]],"initialise() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.initialise",false]],"initialise_smooth_input() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.initialise_smooth_input",false]],"initialize() (dials.algorithms.integration.integrator.integratorexecutor method)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor.initialize",false]],"initialize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor.initialize",false]],"initialize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor.initialize",false]],"initialize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)":[[12,"dials.algorithms.integration.integrator.Integrator2D.initialize_reflections",false]],"initialize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)":[[12,"dials.algorithms.integration.integrator.Integrator3D.initialize_reflections",false]],"initialize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)":[[12,"dials.algorithms.integration.integrator.IntegratorFlat3D.initialize_reflections",false]],"initialize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)":[[12,"dials.algorithms.integration.integrator.IntegratorSingle2D.initialize_reflections",false]],"initialize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)":[[12,"dials.algorithms.integration.integrator.IntegratorStills.initialize_reflections",false]],"insert() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.insert",false]],"installer (class in dials.util.installer)":[[33,"dials.util.installer.installer",false]],"installer_dir (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.installer_dir",false]],"integrate() (dials.algorithms.integration.integrator.integrator method)":[[12,"dials.algorithms.integration.integrator.Integrator.integrate",false]],"integrate() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.integrate",false]],"integrated (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.integrated",false]],"integrated_prf (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.integrated_prf",false]],"integrated_sum (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.integrated_sum",false]],"integrator (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Integrator",false]],"integrator2d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Integrator2D",false]],"integrator3d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Integrator3D",false]],"integrator3dthreaded (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded",false]],"integratorexecutor (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor",false]],"integratorflat3d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.IntegratorFlat3D",false]],"integratorsingle2d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.IntegratorSingle2D",false]],"integratorstills (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.IntegratorStills",false]],"inv_d2() (dials.algorithms.background.radialaverage method)":[[10,"dials.algorithms.background.RadialAverage.inv_d2",false]],"invalidphilerror":[[33,"dials.util.options.InvalidPhilError",false]],"is_consistent() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.is_consistent",false]],"is_consistent() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.is_consistent",false]],"is_integer() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.is_integer",false]],"is_marked_for_rejection() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.is_marked_for_rejection",false]],"is_marked_for_rejection() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.is_marked_for_rejection",false]],"is_overloaded() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.is_overloaded",false]],"is_scaled (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.is_scaled",false]],"is_similar_to() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.is_similar_to",false]],"is_similar_to() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.is_similar_to",false]],"is_similar_to() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.is_similar_to",false]],"is_similar_to() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.is_similar_to",false]],"is_single_file_reader() (dxtbx.imageset.memreader static method)":[[26,"dxtbx.imageset.MemReader.is_single_file_reader",false]],"items() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.items",false]],"iter_levelorder() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.iter_levelorder",false]],"iter_panels() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.iter_panels",false]],"iter_preorder() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.iter_preorder",false]],"iterate_experiments_and_indices() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.iterate_experiments_and_indices",false]],"jacobian_condition_number() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.jacobian_condition_number",false]],"job() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.job",false]],"joblist (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.JobList",false]],"journal (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.Journal",false]],"kappa() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.kappa",false]],"kappagoniometer (class in dxtbx.model.goniometer)":[[25,"dxtbx.model.goniometer.KappaGoniometer",false]],"kbscalingmodel (class in dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel",false]],"kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method)":[[18,"dials.algorithms.symmetry.symmetry_base.kernel_normalisation",false]],"keys() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.keys",false]],"known_axis() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.known_axis",false]],"laue_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.laue_manager",false]],"lauegroupanalysis (class in dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.LaueGroupAnalysis",false]],"laueleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff",false]],"lauemixedweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy",false]],"lauereflectionmanager (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.LaueReflectionManager",false]],"lauespotfinder (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.LaueSpotFinder",false]],"lauestatisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy",false]],"lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine)":[[18,"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs",false]],"lbfgscurvs (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.LBFGScurvs",false]],"leastsquarespositionalresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff",false]],"leastsquarespositionalresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoffSparse",false]],"leastsquaresstillsresidualwithrmsdcutoff (class in dials.algorithms.refinement.target_stills)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff",false]],"leastsquaresstillsresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target_stills)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoffSparse",false]],"levenbergmarquardtiterations (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations",false]],"lightarray (class in dials.algorithms.symmetry.cosym.target)":[[18,"dials.algorithms.symmetry.cosym.target.LightArray",false]],"limit_image_range() (dials.algorithms.scaling.model.model.arrayscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.limit_image_range",false]],"limit_image_range() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.limit_image_range",false]],"limit_image_range() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.limit_image_range",false]],"limit_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.limit_image_range",false]],"load() (in module dials.util.nexus)":[[33,"dials.util.nexus.load",false]],"load_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.load_error_model",false]],"load_image() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)":[[16,"dials.algorithms.spot_finding.factory.SpotFinderFactory.load_image",false]],"log_summary() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.log_summary",false]],"lowresspotmatch (class in dials.algorithms.indexing.lattice_search)":[[11,"dials.algorithms.indexing.lattice_search.LowResSpotMatch",false]],"madmergedmtzwriter (class in dials.util.export_mtz)":[[33,"dials.util.export_mtz.MADMergedMTZWriter",false]],"make_apps (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.make_apps",false]],"make_beam() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.make_beam",false]],"make_combined_plots() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.make_combined_plots",false]],"make_detector() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.make_detector",false]],"make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.make_goniometer",false]],"make_imageset() (dxtbx.imageset.imagesetfactory static method)":[[26,"dxtbx.imageset.ImageSetFactory.make_imageset",false]],"make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer",false]],"make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer",false]],"make_polarized_beam() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.make_polarized_beam",false]],"make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.make_polychromatic_beam",false]],"make_scan() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.make_scan",false]],"make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.make_scan_from_properties",false]],"make_sequence() (dxtbx.imageset.imagesetfactory static method)":[[26,"dxtbx.imageset.ImageSetFactory.make_sequence",false]],"map_centroids_to_reciprocal_space() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.map_centroids_to_reciprocal_space",false]],"mark_for_rejection() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.mark_for_rejection",false]],"mark_for_rejection() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.mark_for_rejection",false]],"mask (dxtbx.imageset.externallookup property)":[[26,"dxtbx.imageset.ExternalLookup.mask",false]],"masker() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.masker",false]],"masker() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.masker",false]],"master_path() (dxtbx.imageset.memreader static method)":[[26,"dxtbx.imageset.MemReader.master_path",false]],"match() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.match",false]],"match_by_hkle() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.match_by_hkle",false]],"match_wavelengths() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.match_wavelengths",false]],"match_with_reference() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.match_with_reference",false]],"max_length (dials.util.command_line.command attribute)":[[33,"dials.util.command_line.Command.max_length",false]],"max_possible_wl (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.max_possible_wl",false]],"max_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.max_shift_over_esd",false]],"mean() (dials.algorithms.background.radialaverage method)":[[10,"dials.algorithms.background.RadialAverage.mean",false]],"median_unit_cell() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.median_unit_cell",false]],"memreader (class in dxtbx.imageset)":[[26,"dxtbx.imageset.MemReader",false]],"merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)":[[23,"dxtbx.model.detector.merge_panel_scope_extracts_by_id",false]],"mergedmtzwriter (class in dials.util.export_mtz)":[[33,"dials.util.export_mtz.MergedMTZWriter",false]],"message (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.message",false]],"metric_supergroup() (in module dials.algorithms.indexing.symmetry)":[[11,"dials.algorithms.indexing.symmetry.metric_supergroup",false]],"min_wl (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.min_wl",false]],"minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine)":[[18,"dials.algorithms.symmetry.cosym.engine.minimize_scipy",false]],"minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine)":[[18,"dials.algorithms.symmetry.cosym.engine.minimize_scitbx_lbfgs",false]],"ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)":[[18,"dials.algorithms.symmetry.symmetry_base.ml_aniso_normalisation",false]],"ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)":[[18,"dials.algorithms.symmetry.symmetry_base.ml_iso_normalisation",false]],"model_likelihood (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.model_likelihood",false]],"modelevaluation (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.ModelEvaluation",false]],"modelrank (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRank",false]],"modelrankfilter (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter",false]],"modelrankweighted (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted",false]],"module":[[10,"module-dials.algorithms.background",false],[11,"module-dials.algorithms.indexing",false],[11,"module-dials.algorithms.indexing.assign_indices",false],[11,"module-dials.algorithms.indexing.basis_vector_search",false],[11,"module-dials.algorithms.indexing.basis_vector_search.combinations",false],[11,"module-dials.algorithms.indexing.basis_vector_search.optimise",false],[11,"module-dials.algorithms.indexing.compare_orientation_matrices",false],[11,"module-dials.algorithms.indexing.indexer",false],[11,"module-dials.algorithms.indexing.lattice_search",false],[11,"module-dials.algorithms.indexing.max_cell",false],[11,"module-dials.algorithms.indexing.model_evaluation",false],[11,"module-dials.algorithms.indexing.nearest_neighbor",false],[11,"module-dials.algorithms.indexing.refinement",false],[11,"module-dials.algorithms.indexing.stills_indexer",false],[11,"module-dials.algorithms.indexing.symmetry",false],[12,"module-dials.algorithms.integration.integrator",false],[13,"module-dials.algorithms.profile_model",false],[14,"module-dials.algorithms.refinement.engine",false],[14,"module-dials.algorithms.refinement.refiner",false],[14,"module-dials.algorithms.refinement.reflection_manager",false],[14,"module-dials.algorithms.refinement.target",false],[14,"module-dials.algorithms.refinement.target_stills",false],[14,"module-dials.algorithms.refinement.weighting_strategies",false],[15,"module-dials.algorithms.scaling",false],[15,"module-dials.algorithms.scaling.model.model",false],[15,"module-dials.algorithms.scaling.outlier_rejection",false],[16,"module-dials.algorithms.spot_finding.factory",false],[16,"module-dials.algorithms.spot_finding.finder",false],[17,"module-dials.algorithms.spot_prediction.reflection_predictor",false],[18,"module-dials.algorithms.symmetry",false],[18,"module-dials.algorithms.symmetry.cosym",false],[18,"module-dials.algorithms.symmetry.cosym.engine",false],[18,"module-dials.algorithms.symmetry.cosym.target",false],[18,"module-dials.algorithms.symmetry.laue_group",false],[18,"module-dials.algorithms.symmetry.reindex_to_reference",false],[21,"module-dxtbx.model.beam",false],[22,"module-dxtbx.model.crystal",false],[23,"module-dxtbx.model.detector",false],[24,"module-dxtbx.model.experiment_list",false],[25,"module-dxtbx.model.goniometer",false],[26,"module-dxtbx.imageset",false],[28,"module-dxtbx.model.profile",false],[29,"module-dxtbx.model.scan",false],[30,"module-dxtbx.serialize.imageset",false],[30,"module-dxtbx.serialize.load",false],[30,"module-dxtbx.serialize.xds",false],[31,"module-dials.extensions.dispersion_spotfinder_threshold_ext",false],[31,"module-dials.extensions.gaussian_rs_profile_model_ext",false],[31,"module-dials.extensions.null_background_ext",false],[31,"module-dials.extensions.simple_background_ext",false],[31,"module-dials.extensions.simple_centroid_ext",false],[33,"module-dials.util.command_line",false],[33,"module-dials.util.export_mtz",false],[33,"module-dials.util.export_text",false],[33,"module-dials.util.image",false],[33,"module-dials.util.installer",false],[33,"module-dials.util.ioutil",false],[33,"module-dials.util.nexus",false],[33,"module-dials.util.options",false]],"mosaiccrystalkabsch2010 (class in dxtbx.model)":[[22,"dxtbx.model.MosaicCrystalKabsch2010",false]],"mosaiccrystalsauter2014 (class in dxtbx.model)":[[22,"dxtbx.model.MosaicCrystalSauter2014",false]],"mtzwriterbase (class in dials.util.export_mtz)":[[33,"dials.util.export_mtz.MTZWriterBase",false]],"mu (dials.algorithms.refinement.engine.levenbergmarquardtiterations property)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.mu",false]],"multi_axis() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.multi_axis",false]],"multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.multi_axis_goniometer_from_phil",false]],"multiaxisgoniometer (class in dxtbx.model.goniometer)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer",false]],"n() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.n",false]],"n_indexed (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.n_indexed",false]],"n_params (dials.algorithms.scaling.model.model.scalingmodelbase property)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.n_params",false]],"name (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.name",false]],"name (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext attribute)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.name",false]],"name (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.name",false]],"name (dials.extensions.null_background_ext.nullbackgroundext attribute)":[[31,"dials.extensions.null_background_ext.NullBackgroundExt.name",false]],"name (dials.extensions.simple_background_ext.simplebackgroundext attribute)":[[31,"dials.extensions.simple_background_ext.SimpleBackgroundExt.name",false]],"name (dials.extensions.simple_centroid_ext.simplecentroidext attribute)":[[31,"dials.extensions.simple_centroid_ext.SimpleCentroidExt.name",false]],"name (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.name",false]],"names (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.names",false]],"ncols() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.ncols",false]],"neighboranalysis (class in dials.algorithms.indexing.nearest_neighbor)":[[11,"dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis",false]],"new() (dxtbx.imageset.imagesetfactory static method)":[[26,"dxtbx.imageset.ImageSetFactory.new",false]],"nframes_hist() (in module dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.nframes_hist",false]],"normdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection",false]],"not_suitable_for_refinement (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.not_suitable_for_refinement",false]],"nrows() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.nrows",false]],"nullbackgroundext (class in dials.extensions.null_background_ext)":[[31,"dials.extensions.null_background_ext.NullBackgroundExt",false]],"nullify_all_single_file_reader_format_instances() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.nullify_all_single_file_reader_format_instances",false]],"num_reflections() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.num_reflections",false]],"num_scan_points (dxtbx.model.goniometer.goniometer property)":[[25,"dxtbx.model.goniometer.Goniometer.num_scan_points",false]],"numerator (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.numerator",false]],"numerator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)":[[18,"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.numerator",false]],"observed (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.observed",false]],"optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise)":[[11,"dials.algorithms.indexing.basis_vector_search.optimise.optimise_basis_vectors",false]],"optionparser (class in dials.util.options)":[[33,"dials.util.options.OptionParser",false]],"outlier_in_scaling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.outlier_in_scaling",false]],"outlierrejectionbase (class in dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase",false]],"overlapped_bg (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.overlapped_bg",false]],"overlapped_fg (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.overlapped_fg",false]],"overloaded (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.overloaded",false]],"overwrite_from_phil() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.overwrite_from_phil",false]],"p_cc_given_not_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)":[[18,"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_not_s",false]],"p_cc_given_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)":[[18,"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_s",false]],"p_s_given_cc (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)":[[18,"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_s_given_cc",false]],"parameter_vector_norm() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.parameter_vector_norm",false]],"parameters (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Parameters",false]],"parameters.filter (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Parameters.Filter",false]],"parameters.profile (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Parameters.Profile",false]],"parameters.profile.validation (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Parameters.Profile.Validation",false]],"params() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.params",false]],"parse_args() (dials.util.options.argumentparser method)":[[33,"dials.util.options.ArgumentParser.parse_args",false]],"parse_args() (dials.util.options.philcommandparser method)":[[33,"dials.util.options.PhilCommandParser.parse_args",false]],"parse_known_args() (dials.util.options.argumentparserbase method)":[[33,"dials.util.options.ArgumentParserBase.parse_known_args",false]],"partial_data() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.partial_data",false]],"partial_set() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.partial_set",false]],"partial_set() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.partial_set",false]],"paths() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.paths",false]],"paths() (dxtbx.imageset.memreader method)":[[26,"dxtbx.imageset.MemReader.paths",false]],"peakcentroiddistancefilter (class in dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter",false]],"pedestal (dxtbx.imageset.externallookup property)":[[26,"dxtbx.imageset.ExternalLookup.pedestal",false]],"per_image() (dials.algorithms.refinement.reflection_manager.blockcalculator method)":[[14,"dials.algorithms.refinement.reflection_manager.BlockCalculator.per_image",false]],"per_width() (dials.algorithms.refinement.reflection_manager.blockcalculator method)":[[14,"dials.algorithms.refinement.reflection_manager.BlockCalculator.per_width",false]],"phil (dials.util.options.argumentparser property)":[[33,"dials.util.options.ArgumentParser.phil",false]],"phil (dials.util.options.philcommandparser property)":[[33,"dials.util.options.PhilCommandParser.phil",false]],"phil() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext static method)":[[31,"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.phil",false]],"phil() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext static method)":[[31,"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.phil",false]],"phil() (dials.extensions.simple_background_ext.simplebackgroundext static method)":[[31,"dials.extensions.simple_background_ext.SimpleBackgroundExt.phil",false]],"phil_help (dials.algorithms.indexing.basis_vector_search.fft1d attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT1D.phil_help",false]],"phil_help (dials.algorithms.indexing.basis_vector_search.fft3d attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT3D.phil_help",false]],"phil_help (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_help",false]],"phil_help (dials.algorithms.indexing.basis_vector_search.strategy attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.Strategy.phil_help",false]],"phil_help (dials.algorithms.indexing.lattice_search.ffbindexer attribute)":[[11,"dials.algorithms.indexing.lattice_search.FfbIndexer.phil_help",false]],"phil_help (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)":[[11,"dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_help",false]],"phil_help (dials.algorithms.indexing.lattice_search.pinkindexer attribute)":[[11,"dials.algorithms.indexing.lattice_search.PinkIndexer.phil_help",false]],"phil_help (dials.algorithms.indexing.lattice_search.strategy attribute)":[[11,"dials.algorithms.indexing.lattice_search.Strategy.phil_help",false]],"phil_scope (dials.algorithms.indexing.basis_vector_search.fft1d attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT1D.phil_scope",false]],"phil_scope (dials.algorithms.indexing.basis_vector_search.fft3d attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.FFT3D.phil_scope",false]],"phil_scope (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_scope",false]],"phil_scope (dials.algorithms.indexing.basis_vector_search.strategy attribute)":[[11,"dials.algorithms.indexing.basis_vector_search.Strategy.phil_scope",false]],"phil_scope (dials.algorithms.indexing.lattice_search.ffbindexer attribute)":[[11,"dials.algorithms.indexing.lattice_search.FfbIndexer.phil_scope",false]],"phil_scope (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)":[[11,"dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_scope",false]],"phil_scope (dials.algorithms.indexing.lattice_search.pinkindexer attribute)":[[11,"dials.algorithms.indexing.lattice_search.PinkIndexer.phil_scope",false]],"phil_scope (dials.algorithms.indexing.lattice_search.strategy attribute)":[[11,"dials.algorithms.indexing.lattice_search.Strategy.phil_scope",false]],"phil_scope (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.phil_scope",false]],"phil_scope (dials.algorithms.scaling.model.model.dosedecay attribute)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.phil_scope",false]],"phil_scope (dials.algorithms.scaling.model.model.kbscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.phil_scope",false]],"phil_scope (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.phil_scope",false]],"philcommandparser (class in dials.util.options)":[[33,"dials.util.options.PhilCommandParser",false]],"physicalscalingmodel (class in dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel",false]],"pinkindexer (class in dials.algorithms.indexing.lattice_search)":[[11,"dials.algorithms.indexing.lattice_search.PinkIndexer",false]],"pixel_list_to_reflection_table() (in module dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.pixel_list_to_reflection_table",false]],"pixel_list_to_shoeboxes() (in module dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.pixel_list_to_shoeboxes",false]],"plot() (dials.array_family.flex.reflection_table static method)":[[20,"dials.array_family.flex.reflection_table.plot",false]],"plot_displacements() (in module dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.plot_displacements",false]],"plot_histogram() (dials.algorithms.indexing.nearest_neighbor.neighboranalysis method)":[[11,"dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis.plot_histogram",false]],"plot_model_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.plot_model_components",false]],"plot_model_components() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.plot_model_components",false]],"plot_model_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.plot_model_components",false]],"plot_model_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.plot_model_components",false]],"plot_scaling_models() (in module dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.plot_scaling_models",false]],"predict() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.predict",false]],"predict_for_free_reflections() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.predict_for_free_reflections",false]],"predict_for_indexed() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.predict_for_indexed",false]],"predict_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.predict_for_reflection_table",false]],"predict_for_reflection_table() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.predict_for_reflection_table",false]],"predict_for_reflection_table() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.predict_for_reflection_table",false]],"predicted (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.predicted",false]],"predictor() (dials.algorithms.spot_prediction.reflection_predictor.reflectionpredictor method)":[[17,"dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor.predictor",false]],"prepare_datasets_for_symmetry_analysis() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.prepare_datasets_for_symmetry_analysis",false]],"prepare_for_step() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.prepare_for_step",false]],"print_exp_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.print_exp_rmsd_table",false]],"print_out_of_sample_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.print_out_of_sample_rmsd_table",false]],"print_panel_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.print_panel_rmsd_table",false]],"print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.lauereflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.LaueReflectionManager.print_stats_on_matches",false]],"print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.print_stats_on_matches",false]],"print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.StillsReflectionManager.print_stats_on_matches",false]],"print_step_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.print_step_table",false]],"print_time (dials.util.command_line.command attribute)":[[33,"dials.util.command_line.Command.print_time",false]],"process() (dials.algorithms.integration.integrator.executor method)":[[12,"dials.algorithms.integration.integrator.Executor.process",false]],"process() (dials.algorithms.integration.integrator.integratorexecutor method)":[[12,"dials.algorithms.integration.integrator.IntegratorExecutor.process",false]],"process() (dials.algorithms.integration.integrator.profilemodellerexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor.process",false]],"process() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor.process",false]],"processor2d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Processor2D",false]],"processor3d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.Processor3D",false]],"processorclass (dials.algorithms.integration.integrator.integrator2d attribute)":[[12,"dials.algorithms.integration.integrator.Integrator2D.ProcessorClass",false]],"processorclass (dials.algorithms.integration.integrator.integrator3d attribute)":[[12,"dials.algorithms.integration.integrator.Integrator3D.ProcessorClass",false]],"processorclass (dials.algorithms.integration.integrator.integratorflat3d attribute)":[[12,"dials.algorithms.integration.integrator.IntegratorFlat3D.ProcessorClass",false]],"processorclass (dials.algorithms.integration.integrator.integratorsingle2d attribute)":[[12,"dials.algorithms.integration.integrator.IntegratorSingle2D.ProcessorClass",false]],"processorclass (dials.algorithms.integration.integrator.integratorstills attribute)":[[12,"dials.algorithms.integration.integrator.IntegratorStills.ProcessorClass",false]],"processorflat3d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ProcessorFlat3D",false]],"processorsingle2d (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ProcessorSingle2D",false]],"processorstills (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ProcessorStills",false]],"product_name (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.product_name",false]],"product_specific_finalize_install() (dials.util.installer.installer method)":[[33,"dials.util.installer.installer.product_specific_finalize_install",false]],"profilemodelfactory (class in dxtbx.model.profile)":[[28,"dxtbx.model.profile.ProfileModelFactory",false]],"profilemodellerexecutor (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ProfileModellerExecutor",false]],"profiles() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.profiles",false]],"profilevalidatorexecutor (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ProfileValidatorExecutor",false]],"progressbar (class in dials.util.command_line)":[[33,"dials.util.command_line.ProgressBar",false]],"progressbartimer (class in dials.util.command_line)":[[33,"dials.util.command_line.ProgressBarTimer",false]],"radialaverage (class in dials.algorithms.background)":[[10,"dials.algorithms.background.RadialAverage",false]],"random_split() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.random_split",false]],"read() (dxtbx.imageset.memreader method)":[[26,"dxtbx.imageset.MemReader.read",false]],"read_file() (dials.util.image.reader method)":[[33,"dials.util.image.reader.read_file",false]],"reader (class in dials.util.image)":[[33,"dials.util.image.reader",false]],"reader() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.reader",false]],"reader() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.reader",false]],"real (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.real",false]],"realspacegridsearch (class in dials.algorithms.indexing.basis_vector_search)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch",false]],"reason_for_termination (dials.algorithms.refinement.engine.journal attribute)":[[14,"dials.algorithms.refinement.engine.Journal.reason_for_termination",false]],"record_intensity_combination_imid() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.record_intensity_combination_Imid",false]],"reference_spot (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.reference_spot",false]],"refine() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.refine",false]],"refine() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.refine",false]],"refine() (in module dials.algorithms.indexing.refinement)":[[11,"dials.algorithms.indexing.refinement.refine",false]],"refiner (class in dials.algorithms.refinement.refiner)":[[14,"dials.algorithms.refinement.refiner.Refiner",false]],"refinerfactory (class in dials.algorithms.refinement.refiner)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory",false]],"refinery (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.Refinery",false]],"reflection_table (class in dials.array_family.flex)":[[20,"dials.array_family.flex.reflection_table",false]],"reflection_table.flags (class in dials.array_family.flex)":[[20,"dials.array_family.flex.reflection_table.flags",false]],"reflectionmanager (class in dials.algorithms.integration.integrator)":[[12,"dials.algorithms.integration.integrator.ReflectionManager",false]],"reflectionmanager (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager",false]],"reflectionmanagerfactory (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory",false]],"reflectionpredictor (class in dials.algorithms.spot_prediction.reflection_predictor)":[[17,"dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor",false]],"reflections_after_outlier_rejection() (dials.algorithms.refinement.refiner.refinerfactory class method)":[[14,"dials.algorithms.refinement.refiner.RefinerFactory.reflections_after_outlier_rejection",false]],"reflections_and_experiments_from_files() (in module dials.util.options)":[[33,"dials.util.options.reflections_and_experiments_from_files",false]],"reject_outliers() (in module dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.reject_outliers",false]],"remove_on_experiment_identifiers() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.remove_on_experiment_identifiers",false]],"remove_on_experiment_identifiers() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.remove_on_experiment_identifiers",false]],"remove_sources_default (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.remove_sources_default",false]],"reorder() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.reorder",false]],"replace() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.replace",false]],"report() (dials.algorithms.integration.integrator.integrator method)":[[12,"dials.algorithms.integration.integrator.Integrator.report",false]],"report() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.report",false]],"report_progress() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.report_progress",false]],"reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.reset_accepted_reflections",false]],"reset_ids() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.reset_ids",false]],"reset_scan_points() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.reset_scan_points",false]],"resize() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.resize",false]],"resolution_filter_from_array() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.resolution_filter_from_array",false]],"resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.resolution_filter_from_reflections_experiments",false]],"restart() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.restart",false]],"result (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.Result",false]],"rmsd_names (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_names",false]],"rmsd_names (dials.algorithms.refinement.target.target attribute)":[[14,"dials.algorithms.refinement.target.Target.rmsd_names",false]],"rmsd_names (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_names",false]],"rmsd_names (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_names",false]],"rmsd_units (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_units",false]],"rmsd_units (dials.algorithms.refinement.target.target attribute)":[[14,"dials.algorithms.refinement.target.Target.rmsd_units",false]],"rmsd_units (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_units",false]],"rmsd_units (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)":[[14,"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_units",false]],"rmsds (dials.algorithms.indexing.model_evaluation.result attribute)":[[11,"dials.algorithms.indexing.model_evaluation.Result.rmsds",false]],"rmsds() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.rmsds",false]],"rmsds() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.rmsds",false]],"rmsds_for_experiment() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.rmsds_for_experiment",false]],"rmsds_for_panel() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.rmsds_for_panel",false]],"rmsds_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.rmsds_for_reflection_table",false]],"rmsds_for_reflection_table() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.rmsds_for_reflection_table",false]],"rotate_around_origin() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.rotate_around_origin",false]],"rotate_around_origin() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.rotate_around_origin",false]],"rotate_crystal() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.rotate_crystal",false]],"rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices)":[[11,"dials.algorithms.indexing.compare_orientation_matrices.rotation_matrix_differences",false]],"rotation_scan_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.rotation_scan_manager",false]],"rows() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.rows",false]],"run() (dials.algorithms.refinement.engine.gaussnewtoniterations method)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.run",false]],"run() (dials.algorithms.refinement.engine.lbfgscurvs method)":[[14,"dials.algorithms.refinement.engine.LBFGScurvs.run",false]],"run() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.run",false]],"run() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.run",false]],"run() (dials.algorithms.refinement.engine.simplelbfgs method)":[[14,"dials.algorithms.refinement.engine.SimpleLBFGS.run",false]],"run() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.run",false]],"run() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)":[[15,"dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.run",false]],"run() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)":[[16,"dials.algorithms.spot_finding.factory.BackgroundGradientFilter.run",false]],"run() (dials.algorithms.spot_finding.factory.peakcentroiddistancefilter method)":[[16,"dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter.run",false]],"run() (dials.algorithms.spot_finding.factory.spotdensityfilter method)":[[16,"dials.algorithms.spot_finding.factory.SpotDensityFilter.run",false]],"run() (dials.algorithms.symmetry.cosym.cosymanalysis method)":[[18,"dials.algorithms.symmetry.cosym.CosymAnalysis.run",false]],"run_lbfgs() (dials.algorithms.refinement.engine.adaptlbfgs method)":[[14,"dials.algorithms.refinement.engine.AdaptLbfgs.run_lbfgs",false]],"scaled (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.scaled",false]],"scaling_models() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.scaling_models",false]],"scalingmodelbase (class in dials.algorithms.scaling.model.model)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase",false]],"scanfactory (class in dxtbx.model.scan)":[[29,"dxtbx.model.scan.ScanFactory",false]],"scans() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.scans",false]],"scanvaryingrefiner (class in dials.algorithms.refinement.refiner)":[[14,"dials.algorithms.refinement.refiner.ScanVaryingRefiner",false]],"score_by_fraction_indexed() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_fraction_indexed",false]],"score_by_rmsd_xy() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_rmsd_xy",false]],"score_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_volume",false]],"score_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.score_vectors",false]],"scorecorrelationcoefficient (class in dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient",false]],"scoresubgroup (class in dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.ScoreSubGroup",false]],"scoresubgroup (class in dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSubGroup",false]],"scoresymmetryelement (class in dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.ScoreSymmetryElement",false]],"scoresymmetryelement (class in dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.ScoreSymmetryElement",false]],"search() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.search",false]],"search_directions (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_directions",false]],"search_vectors (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)":[[11,"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_vectors",false]],"select() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.select",false]],"select_on_experiment_identifiers() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.select_on_experiment_identifiers",false]],"select_on_experiment_identifiers() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.select_on_experiment_identifiers",false]],"selection_used_for_refinement() (dials.algorithms.refinement.refiner.refiner method)":[[14,"dials.algorithms.refinement.refiner.Refiner.selection_used_for_refinement",false]],"sensor() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.sensor",false]],"set_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.set_angles",false]],"set_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.set_axes",false]],"set_beam() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.set_beam",false]],"set_beam() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.set_beam",false]],"set_beam() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_beam",false]],"set_cholesky_factor() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.set_cholesky_factor",false]],"set_detector() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.set_detector",false]],"set_detector() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.set_detector",false]],"set_detector() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_detector",false]],"set_dimensions() (dials.algorithms.symmetry.cosym.target.target method)":[[18,"dials.algorithms.symmetry.cosym.target.Target.set_dimensions",false]],"set_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.set_domain_size_ang",false]],"set_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.set_error_model",false]],"set_fixed_rotation() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.set_fixed_rotation",false]],"set_flags() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.set_flags",false]],"set_format_class() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_format_class",false]],"set_goniometer() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.set_goniometer",false]],"set_goniometer() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.set_goniometer",false]],"set_goniometer() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_goniometer",false]],"set_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.set_half_mosaicity_deg",false]],"set_last_cell() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.set_last_cell",false]],"set_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.set_mosaicity",false]],"set_nproc() (dials.algorithms.refinement.engine.disablempmixin method)":[[14,"dials.algorithms.refinement.engine.DisableMPmixin.set_nproc",false]],"set_nproc() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.set_nproc",false]],"set_params() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_params",false]],"set_rotation_axis() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.set_rotation_axis",false]],"set_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.set_rotation_axis_datum",false]],"set_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_scaled",false]],"set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_unscaled",false]],"set_scan() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.set_scan",false]],"set_scan() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.set_scan",false]],"set_scan() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_scan",false]],"set_selected() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.set_selected",false]],"set_setting_rotation() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.set_setting_rotation",false]],"set_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.set_setting_rotation_at_scan_points",false]],"set_shoebox_background_value() (in module dials.algorithms.background)":[[10,"dials.algorithms.background.set_shoebox_background_value",false]],"set_template() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_template",false]],"set_valid_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.set_valid_image_range",false]],"set_vendor() (dxtbx.imageset.imagesetdata method)":[[26,"dxtbx.imageset.ImageSetData.set_vendor",false]],"setup_indexing() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.setup_indexing",false]],"setup_mu() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.setup_mu",false]],"shoebox_memory() (dials.algorithms.integration.integrator.joblist method)":[[12,"dials.algorithms.integration.integrator.JobList.shoebox_memory",false]],"shoeboxes_to_reflection_table() (in module dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.shoeboxes_to_reflection_table",false]],"show() (dxtbx.model.crystal method)":[[22,"dxtbx.model.Crystal.show",false]],"show_experiments() (dials.algorithms.indexing.indexer.indexer method)":[[11,"dials.algorithms.indexing.indexer.Indexer.show_experiments",false]],"sigmas() (dials.algorithms.symmetry.cosym.target.lightarray method)":[[18,"dials.algorithms.symmetry.cosym.target.LightArray.sigmas",false]],"simple() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.simple",false]],"simple() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.simple",false]],"simple_directional() (dxtbx.model.beam.beamfactory static method)":[[21,"dxtbx.model.beam.BeamFactory.simple_directional",false]],"simplebackgroundext (class in dials.extensions.simple_background_ext)":[[31,"dials.extensions.simple_background_ext.SimpleBackgroundExt",false]],"simplecentroidext (class in dials.extensions.simple_centroid_ext)":[[31,"dials.extensions.simple_centroid_ext.SimpleCentroidExt",false]],"simplelbfgs (class in dials.algorithms.refinement.engine)":[[14,"dials.algorithms.refinement.engine.SimpleLBFGS",false]],"simplenormdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection",false]],"single_axis() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.single_axis",false]],"single_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.single_axis_goniometer_from_phil",false]],"single_axis_reverse() (dxtbx.model.goniometer.goniometerfactory static method)":[[25,"dxtbx.model.goniometer.GoniometerFactory.single_axis_reverse",false]],"single_file() (dxtbx.model.scan.scanfactory static method)":[[29,"dxtbx.model.scan.ScanFactory.single_file",false]],"size() (dials.algorithms.symmetry.cosym.target.lightarray method)":[[18,"dials.algorithms.symmetry.cosym.target.LightArray.size",false]],"size() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.size",false]],"size() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.size",false]],"sort() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.sort",false]],"source_packages (dials.util.installer.installer attribute)":[[33,"dials.util.installer.installer.source_packages",false]],"sparsegradientsmixin (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.SparseGradientsMixin",false]],"split() (dials.algorithms.integration.integrator.joblist method)":[[12,"dials.algorithms.integration.integrator.JobList.split",false]],"split() (dials.algorithms.integration.integrator.reflectionmanager method)":[[12,"dials.algorithms.integration.integrator.ReflectionManager.split",false]],"split_by_experiment_id() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.split_by_experiment_id",false]],"split_indices_by_experiment_id() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.split_indices_by_experiment_id",false]],"split_jacobian_into_blocks() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.split_jacobian_into_blocks",false]],"split_matches_into_blocks() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.split_matches_into_blocks",false]],"split_partial_indices() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.split_partial_indices",false]],"split_partials() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.split_partials",false]],"split_partials_with_shoebox() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.split_partials_with_shoebox",false]],"spotdensityfilter (class in dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.SpotDensityFilter",false]],"spotfinder (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.SpotFinder",false]],"spotfinderfactory (class in dials.algorithms.spot_finding.factory)":[[16,"dials.algorithms.spot_finding.factory.SpotFinderFactory",false]],"stars (dials.algorithms.symmetry.cosym.scoresubgroup property)":[[18,"dials.algorithms.symmetry.cosym.ScoreSubGroup.stars",false]],"stars (dials.algorithms.symmetry.cosym.scoresymmetryelement property)":[[18,"dials.algorithms.symmetry.cosym.ScoreSymmetryElement.stars",false]],"start() (dials.util.command_line.command class method)":[[33,"dials.util.command_line.Command.start",false]],"statisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy",false]],"step_backward() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.step_backward",false]],"step_forward() (dials.algorithms.refinement.engine.adaptlstbx method)":[[14,"dials.algorithms.refinement.engine.AdaptLstbx.step_forward",false]],"step_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)":[[14,"dials.algorithms.refinement.engine.GaussNewtonIterations.step_threshold",false]],"stills_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.stills_manager",false]],"stillsindexer (class in dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer",false]],"stillsindexerbasisvectorsearch (class in dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexerBasisVectorSearch",false]],"stillsindexerknownorientation (class in dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexerKnownOrientation",false]],"stillsindexerlatticesearch (class in dials.algorithms.indexing.stills_indexer)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexerLatticeSearch",false]],"stillsreflectionmanager (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.StillsReflectionManager",false]],"stillsweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)":[[14,"dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy",false]],"strategy (class in dials.algorithms.indexing.basis_vector_search)":[[11,"dials.algorithms.indexing.basis_vector_search.Strategy",false]],"strategy (class in dials.algorithms.indexing.lattice_search)":[[11,"dials.algorithms.indexing.lattice_search.Strategy",false]],"strategy (class in dials.algorithms.indexing.model_evaluation)":[[11,"dials.algorithms.indexing.model_evaluation.Strategy",false]],"strong (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.strong",false]],"subgroups_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis.subgroups_table",false]],"subsort() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.subsort",false]],"summary() (dials.algorithms.integration.integrator.integrator method)":[[12,"dials.algorithms.integration.integrator.Integrator.summary",false]],"summary() (dials.algorithms.integration.integrator.integrator3dthreaded method)":[[12,"dials.algorithms.integration.integrator.Integrator3DThreaded.summary",false]],"summary_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis.summary_table",false]],"sym_ops_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis.sym_ops_table",false]],"symmetry_base (class in dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.symmetry_base",false]],"symmetryanalysis (class in dials.algorithms.symmetry.cosym)":[[18,"dials.algorithms.symmetry.cosym.SymmetryAnalysis",false]],"symmetryhandler (class in dials.algorithms.indexing.symmetry)":[[11,"dials.algorithms.indexing.symmetry.SymmetryHandler",false]],"system_phil (dials.util.options.argumentparser property)":[[33,"dials.util.options.ArgumentParser.system_phil",false]],"system_phil (dials.util.options.philcommandparser property)":[[33,"dials.util.options.PhilCommandParser.system_phil",false]],"target (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.Target",false]],"target (class in dials.algorithms.symmetry.cosym.target)":[[18,"dials.algorithms.symmetry.cosym.target.Target",false]],"targetedoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)":[[15,"dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection",false]],"targetfactory (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.TargetFactory",false]],"tau (dials.algorithms.refinement.engine.levenbergmarquardtiterations attribute)":[[14,"dials.algorithms.refinement.engine.LevenbergMarquardtIterations.tau",false]],"test_for_termination() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.test_for_termination",false]],"test_objective_increasing_but_not_nref() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.test_objective_increasing_but_not_nref",false]],"test_rmsd_convergence() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.test_rmsd_convergence",false]],"to_bytes() (dials.array_family.flex.reflection_table.flags method)":[[20,"dials.array_family.flex.reflection_table.flags.to_bytes",false]],"to_crystal() (in module dxtbx.serialize.xds)":[[30,"dxtbx.serialize.xds.to_crystal",false]],"to_dict() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.to_dict",false]],"to_dict() (dxtbx.model.crystal method)":[[22,"dxtbx.model.Crystal.to_dict",false]],"to_dict() (dxtbx.model.detector method)":[[23,"dxtbx.model.Detector.to_dict",false]],"to_dict() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.to_dict",false]],"to_dict() (dxtbx.model.goniometer.goniometer method)":[[25,"dxtbx.model.goniometer.Goniometer.to_dict",false]],"to_dict() (dxtbx.model.goniometer.multiaxisgoniometer method)":[[25,"dxtbx.model.goniometer.MultiAxisGoniometer.to_dict",false]],"to_dict() (dxtbx.model.mosaiccrystalkabsch2010 method)":[[22,"dxtbx.model.MosaicCrystalKabsch2010.to_dict",false]],"to_dict() (dxtbx.model.mosaiccrystalsauter2014 method)":[[22,"dxtbx.model.MosaicCrystalSauter2014.to_dict",false]],"to_imageset() (in module dxtbx.serialize.xds)":[[30,"dxtbx.serialize.xds.to_imageset",false]],"to_json_file() (dials.algorithms.refinement.engine.journal method)":[[14,"dials.algorithms.refinement.engine.Journal.to_json_file",false]],"to_xds (class in dxtbx.serialize.xds)":[[30,"dxtbx.serialize.xds.to_xds",false]],"tofleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)":[[14,"dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff",false]],"tofreflectionmanager (class in dials.algorithms.refinement.reflection_manager)":[[14,"dials.algorithms.refinement.reflection_manager.TOFReflectionManager",false]],"tofspotfinder (class in dials.algorithms.spot_finding.finder)":[[16,"dials.algorithms.spot_finding.finder.TOFSpotFinder",false]],"traceback (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.traceback",false]],"trunccauchy_pdf() (in module dials.algorithms.symmetry.laue_group)":[[18,"dials.algorithms.symmetry.laue_group.trunccauchy_pdf",false]],"try_read_experiments() (dials.util.options.importer method)":[[33,"dials.util.options.Importer.try_read_experiments",false]],"try_read_experiments_from_images() (dials.util.options.importer method)":[[33,"dials.util.options.Importer.try_read_experiments_from_images",false]],"try_read_reflections() (dials.util.options.importer method)":[[33,"dials.util.options.Importer.try_read_reflections",false]],"two_theta() (dxtbx.model.detector.detectorfactory static method)":[[23,"dxtbx.model.detector.DetectorFactory.two_theta",false]],"type (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.type",false]],"types() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.types",false]],"unit_cells_are_similar_to() (in module dials.algorithms.symmetry)":[[18,"dials.algorithms.symmetry.unit_cells_are_similar_to",false]],"unset_flags() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.unset_flags",false]],"update() (dials.algorithms.scaling.model.model.arrayscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.ArrayScalingModel.update",false]],"update() (dials.algorithms.scaling.model.model.dosedecay method)":[[15,"dials.algorithms.scaling.model.model.DoseDecay.update",false]],"update() (dials.algorithms.scaling.model.model.kbscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.KBScalingModel.update",false]],"update() (dials.algorithms.scaling.model.model.physicalscalingmodel method)":[[15,"dials.algorithms.scaling.model.model.PhysicalScalingModel.update",false]],"update() (dials.algorithms.scaling.model.model.scalingmodelbase method)":[[15,"dials.algorithms.scaling.model.model.ScalingModelBase.update",false]],"update() (dials.array_family.flex.reflection_table method)":[[20,"dials.array_family.flex.reflection_table.update",false]],"update() (dials.util.command_line.progressbar method)":[[33,"dials.util.command_line.ProgressBar.update",false]],"update() (dials.util.command_line.progressbartimer method)":[[33,"dials.util.command_line.ProgressBarTimer.update",false]],"update_analysis() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)":[[11,"dials.algorithms.indexing.model_evaluation.ModelRankFilter.update_analysis",false]],"update_detector_px_mm_data() (dxtbx.imageset.imagesequence method)":[[26,"dxtbx.imageset.ImageSequence.update_detector_px_mm_data",false]],"update_detector_px_mm_data() (dxtbx.imageset.imageset method)":[[26,"dxtbx.imageset.ImageSet.update_detector_px_mm_data",false]],"update_journal() (dials.algorithms.refinement.engine.refinery method)":[[14,"dials.algorithms.refinement.engine.Refinery.update_journal",false]],"update_matches() (dials.algorithms.refinement.target.target method)":[[14,"dials.algorithms.refinement.target.Target.update_matches",false]],"update_residuals() (dials.algorithms.refinement.reflection_manager.lauereflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.LaueReflectionManager.update_residuals",false]],"update_residuals() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.ReflectionManager.update_residuals",false]],"update_residuals() (dials.algorithms.refinement.reflection_manager.tofreflectionmanager method)":[[14,"dials.algorithms.refinement.reflection_manager.TOFReflectionManager.update_residuals",false]],"used_in_modelling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.used_in_modelling",false]],"used_in_refinement (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.used_in_refinement",false]],"user_excluded_in_scaling (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.user_excluded_in_scaling",false]],"validation (dials.util.options.argumenthandlingerrorinfo attribute)":[[33,"dials.util.options.ArgumentHandlingErrorInfo.validation",false]],"values (dials.array_family.flex.reflection_table.flags attribute)":[[20,"dials.array_family.flex.reflection_table.flags.values",false]],"warn_if_setting_unused_refinement_protocol_params() (dials.algorithms.indexing.stills_indexer.stillsindexer method)":[[11,"dials.algorithms.indexing.stills_indexer.StillsIndexer.warn_if_setting_unused_refinement_protocol_params",false]],"wavelengthgroup (class in dials.util.export_mtz)":[[33,"dials.util.export_mtz.WavelengthGroup",false]],"wavelengths (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.wavelengths",false]],"weight() (dials.algorithms.background.radialaverage method)":[[10,"dials.algorithms.background.RadialAverage.weight",false]],"weighted_mean (dials.util.export_mtz.wavelengthgroup attribute)":[[33,"dials.util.export_mtz.WavelengthGroup.weighted_mean",false]],"where() (dxtbx.model.experimentlist method)":[[24,"dxtbx.model.ExperimentList.where",false]],"write_columns() (in module dials.util.export_mtz)":[[33,"dials.util.export_mtz.write_columns",false]],"xds_detector_name() (in module dxtbx.serialize.xds)":[[30,"dxtbx.serialize.xds.xds_detector_name",false]],"xds_inp() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.XDS_INP",false]],"xparm_xds() (dxtbx.serialize.xds.to_xds method)":[[30,"dxtbx.serialize.xds.to_xds.xparm_xds",false]]},"objects":{"dials.algorithms":[[10,0,0,"-","background"],[11,0,0,"-","indexing"],[13,0,0,"-","profile_model"],[15,0,0,"-","scaling"],[18,0,0,"-","symmetry"]],"dials.algorithms.background":[[10,1,1,"","RadialAverage"],[10,3,1,"","set_shoebox_background_value"]],"dials.algorithms.background.RadialAverage":[[10,2,1,"","__init__"],[10,2,1,"","add"],[10,2,1,"","inv_d2"],[10,2,1,"","mean"],[10,2,1,"","weight"]],"dials.algorithms.indexing":[[11,4,1,"","DialsIndexError"],[11,4,1,"","DialsIndexRefineError"],[11,0,0,"-","assign_indices"],[11,0,0,"-","basis_vector_search"],[11,0,0,"-","compare_orientation_matrices"],[11,0,0,"-","indexer"],[11,0,0,"-","lattice_search"],[11,0,0,"-","max_cell"],[11,0,0,"-","model_evaluation"],[11,0,0,"-","nearest_neighbor"],[11,0,0,"-","refinement"],[11,0,0,"-","stills_indexer"],[11,0,0,"-","symmetry"]],"dials.algorithms.indexing.assign_indices":[[11,1,1,"","AssignIndicesGlobal"],[11,1,1,"","AssignIndicesLocal"],[11,1,1,"","AssignIndicesStrategy"]],"dials.algorithms.indexing.assign_indices.AssignIndicesGlobal":[[11,2,1,"","__init__"]],"dials.algorithms.indexing.assign_indices.AssignIndicesLocal":[[11,2,1,"","__init__"]],"dials.algorithms.indexing.assign_indices.AssignIndicesStrategy":[[11,2,1,"","__init__"]],"dials.algorithms.indexing.basis_vector_search":[[11,1,1,"","FFT1D"],[11,1,1,"","FFT3D"],[11,1,1,"","RealSpaceGridSearch"],[11,1,1,"","Strategy"],[11,0,0,"-","combinations"],[11,0,0,"-","optimise"]],"dials.algorithms.indexing.basis_vector_search.FFT1D":[[11,2,1,"","__init__"],[11,2,1,"","find_basis_vectors"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.basis_vector_search.FFT3D":[[11,2,1,"","__init__"],[11,2,1,"","find_basis_vectors"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch":[[11,2,1,"","__init__"],[11,2,1,"","compute_functional"],[11,2,1,"","find_basis_vectors"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"],[11,2,1,"","score_vectors"],[11,6,1,"","search_directions"],[11,6,1,"","search_vectors"]],"dials.algorithms.indexing.basis_vector_search.Strategy":[[11,2,1,"","__init__"],[11,2,1,"","find_basis_vectors"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.basis_vector_search.combinations":[[11,3,1,"","candidate_orientation_matrices"],[11,3,1,"","filter_known_symmetry"],[11,3,1,"","filter_similar_orientations"]],"dials.algorithms.indexing.basis_vector_search.optimise":[[11,1,1,"","BasisVectorMinimiser"],[11,1,1,"","BasisVectorTarget"],[11,3,1,"","optimise_basis_vectors"]],"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser":[[11,2,1,"","__init__"],[11,2,1,"","compute_functional_and_gradients"]],"dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget":[[11,2,1,"","__init__"],[11,2,1,"","compute_functional"],[11,2,1,"","compute_functional_and_gradients"]],"dials.algorithms.indexing.compare_orientation_matrices":[[11,3,1,"","difference_rotation_matrix_axis_angle"],[11,3,1,"","rotation_matrix_differences"]],"dials.algorithms.indexing.indexer":[[11,1,1,"","Indexer"],[11,3,1,"","apply_hkl_offset"]],"dials.algorithms.indexing.indexer.Indexer":[[11,2,1,"","__init__"],[11,2,1,"","export_as_json"],[11,2,1,"","export_reflections"],[11,2,1,"","find_lattices"],[11,2,1,"","find_max_cell"],[11,2,1,"","from_parameters"],[11,2,1,"","index"],[11,2,1,"","index_reflections"],[11,2,1,"","refine"],[11,2,1,"","setup_indexing"],[11,2,1,"","show_experiments"]],"dials.algorithms.indexing.lattice_search":[[11,1,1,"","FfbIndexer"],[11,1,1,"","LowResSpotMatch"],[11,1,1,"","PinkIndexer"],[11,1,1,"","Strategy"]],"dials.algorithms.indexing.lattice_search.FfbIndexer":[[11,2,1,"","__init__"],[11,2,1,"","find_crystal_models"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.lattice_search.LowResSpotMatch":[[11,2,1,"","__init__"],[11,2,1,"","find_crystal_models"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.lattice_search.PinkIndexer":[[11,2,1,"","__init__"],[11,2,1,"","find_crystal_models"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.lattice_search.Strategy":[[11,2,1,"","__init__"],[11,2,1,"","find_crystal_models"],[11,5,1,"","phil_help"],[11,5,1,"","phil_scope"]],"dials.algorithms.indexing.max_cell":[[11,3,1,"","find_max_cell"]],"dials.algorithms.indexing.model_evaluation":[[11,1,1,"","ModelEvaluation"],[11,1,1,"","ModelRank"],[11,1,1,"","ModelRankFilter"],[11,1,1,"","ModelRankWeighted"],[11,1,1,"","Result"],[11,1,1,"","Strategy"],[11,3,1,"","filter_doubled_cell"]],"dials.algorithms.indexing.model_evaluation.ModelEvaluation":[[11,2,1,"","__init__"],[11,2,1,"","evaluate"]],"dials.algorithms.indexing.model_evaluation.ModelRank":[[11,2,1,"","__init__"],[11,2,1,"","append"],[11,2,1,"","best_model"],[11,2,1,"","extend"]],"dials.algorithms.indexing.model_evaluation.ModelRankFilter":[[11,2,1,"","__init__"],[11,2,1,"","append"],[11,2,1,"","best_model"],[11,2,1,"","extend"],[11,2,1,"","filter_by_likelihood"],[11,2,1,"","filter_by_n_indexed"],[11,2,1,"","filter_by_volume"],[11,2,1,"","update_analysis"]],"dials.algorithms.indexing.model_evaluation.ModelRankWeighted":[[11,2,1,"","__init__"],[11,2,1,"","best_model"],[11,2,1,"","combined_scores"],[11,2,1,"","score_by_fraction_indexed"],[11,2,1,"","score_by_rmsd_xy"],[11,2,1,"","score_by_volume"]],"dials.algorithms.indexing.model_evaluation.Result":[[11,5,1,"","crystal"],[11,5,1,"","fraction_indexed"],[11,5,1,"","hkl_offset"],[11,5,1,"","model_likelihood"],[11,5,1,"","n_indexed"],[11,5,1,"","rmsds"]],"dials.algorithms.indexing.model_evaluation.Strategy":[[11,2,1,"","evaluate"]],"dials.algorithms.indexing.nearest_neighbor":[[11,1,1,"","NeighborAnalysis"]],"dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis":[[11,2,1,"","__init__"],[11,2,1,"","plot_histogram"]],"dials.algorithms.indexing.refinement":[[11,3,1,"","refine"]],"dials.algorithms.indexing.stills_indexer":[[11,1,1,"","StillsIndexer"],[11,1,1,"","StillsIndexerBasisVectorSearch"],[11,1,1,"","StillsIndexerKnownOrientation"],[11,1,1,"","StillsIndexerLatticeSearch"],[11,3,1,"","calc_2D_rmsd_and_displacements"],[11,3,1,"","e_refine"],[11,3,1,"","plot_displacements"]],"dials.algorithms.indexing.stills_indexer.StillsIndexer":[[11,2,1,"","__init__"],[11,2,1,"","choose_best_orientation_matrix"],[11,2,1,"","experiment_list_for_crystal"],[11,2,1,"","identify_outliers"],[11,2,1,"","index"],[11,2,1,"","refine"],[11,2,1,"","warn_if_setting_unused_refinement_protocol_params"]],"dials.algorithms.indexing.symmetry":[[11,1,1,"","SymmetryHandler"],[11,3,1,"","calc_acentric_subgroups"],[11,3,1,"","find_matching_symmetry"],[11,3,1,"","groups_cache"],[11,3,1,"","metric_supergroup"]],"dials.algorithms.indexing.symmetry.SymmetryHandler":[[11,2,1,"","__init__"],[11,2,1,"","apply_symmetry"]],"dials.algorithms.integration":[[12,0,0,"-","integrator"]],"dials.algorithms.integration.integrator":[[12,1,1,"","Executor"],[12,1,1,"","Integrator"],[12,1,1,"","Integrator2D"],[12,1,1,"","Integrator3D"],[12,1,1,"","Integrator3DThreaded"],[12,1,1,"","IntegratorExecutor"],[12,1,1,"","IntegratorFlat3D"],[12,1,1,"","IntegratorSingle2D"],[12,1,1,"","IntegratorStills"],[12,1,1,"","JobList"],[12,1,1,"","Parameters"],[12,1,1,"","Processor2D"],[12,1,1,"","Processor3D"],[12,1,1,"","ProcessorFlat3D"],[12,1,1,"","ProcessorSingle2D"],[12,1,1,"","ProcessorStills"],[12,1,1,"","ProfileModellerExecutor"],[12,1,1,"","ProfileValidatorExecutor"],[12,1,1,"","ReflectionManager"],[12,3,1,"","frame_hist"],[12,3,1,"","generate_phil_scope"],[12,3,1,"","hist"],[12,3,1,"","nframes_hist"]],"dials.algorithms.integration.integrator.Executor":[[12,2,1,"","__init__"],[12,2,1,"","process"]],"dials.algorithms.integration.integrator.Integrator":[[12,2,1,"","__init__"],[12,2,1,"","fit_profiles"],[12,2,1,"","integrate"],[12,2,1,"","report"],[12,2,1,"","summary"]],"dials.algorithms.integration.integrator.Integrator2D":[[12,5,1,"","ProcessorClass"],[12,2,1,"","finalize_reflections"],[12,2,1,"","initialize_reflections"]],"dials.algorithms.integration.integrator.Integrator3D":[[12,5,1,"","ProcessorClass"],[12,2,1,"","finalize_reflections"],[12,2,1,"","initialize_reflections"]],"dials.algorithms.integration.integrator.Integrator3DThreaded":[[12,2,1,"","__init__"],[12,2,1,"","finalise"],[12,2,1,"","initialise"],[12,2,1,"","integrate"],[12,2,1,"","report"],[12,2,1,"","summary"]],"dials.algorithms.integration.integrator.IntegratorExecutor":[[12,2,1,"","__init__"],[12,2,1,"","data"],[12,2,1,"","finalize"],[12,2,1,"","initialize"],[12,2,1,"","process"]],"dials.algorithms.integration.integrator.IntegratorFlat3D":[[12,5,1,"","ProcessorClass"],[12,2,1,"","finalize_reflections"],[12,2,1,"","initialize_reflections"]],"dials.algorithms.integration.integrator.IntegratorSingle2D":[[12,5,1,"","ProcessorClass"],[12,2,1,"","finalize_reflections"],[12,2,1,"","initialize_reflections"]],"dials.algorithms.integration.integrator.IntegratorStills":[[12,5,1,"","ProcessorClass"],[12,2,1,"","finalize_reflections"],[12,2,1,"","initialize_reflections"]],"dials.algorithms.integration.integrator.JobList":[[12,2,1,"","__init__"],[12,2,1,"","add"],[12,2,1,"","shoebox_memory"],[12,2,1,"","split"]],"dials.algorithms.integration.integrator.Parameters":[[12,1,1,"","Filter"],[12,1,1,"","Profile"],[12,2,1,"","__init__"],[12,2,1,"","from_phil"]],"dials.algorithms.integration.integrator.Parameters.Filter":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.Parameters.Profile":[[12,1,1,"","Validation"],[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.Parameters.Profile.Validation":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.Processor2D":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.Processor3D":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.ProcessorFlat3D":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.ProcessorSingle2D":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.ProcessorStills":[[12,2,1,"","__init__"]],"dials.algorithms.integration.integrator.ProfileModellerExecutor":[[12,2,1,"","__init__"],[12,2,1,"","data"],[12,2,1,"","finalize"],[12,2,1,"","initialize"],[12,2,1,"","process"]],"dials.algorithms.integration.integrator.ProfileValidatorExecutor":[[12,2,1,"","__init__"],[12,2,1,"","data"],[12,2,1,"","finalize"],[12,2,1,"","initialize"],[12,2,1,"","process"]],"dials.algorithms.integration.integrator.ReflectionManager":[[12,2,1,"","__init__"],[12,2,1,"","accumulate"],[12,2,1,"","data"],[12,2,1,"","finished"],[12,2,1,"","job"],[12,2,1,"","num_reflections"],[12,2,1,"","split"]],"dials.algorithms.refinement":[[14,0,0,"-","engine"],[14,0,0,"-","refiner"],[14,0,0,"-","reflection_manager"],[14,0,0,"-","target"],[14,0,0,"-","target_stills"],[14,0,0,"-","weighting_strategies"]],"dials.algorithms.refinement.engine":[[14,1,1,"","AdaptLbfgs"],[14,1,1,"","AdaptLstbx"],[14,1,1,"","DisableMPmixin"],[14,1,1,"","GaussNewtonIterations"],[14,1,1,"","Journal"],[14,1,1,"","LBFGScurvs"],[14,1,1,"","LevenbergMarquardtIterations"],[14,1,1,"","Refinery"],[14,1,1,"","SimpleLBFGS"]],"dials.algorithms.refinement.engine.AdaptLbfgs":[[14,2,1,"","__init__"],[14,2,1,"","callback_after_step"],[14,2,1,"","compute_functional_and_gradients"],[14,2,1,"","compute_functional_gradients_and_curvatures"],[14,2,1,"","run_lbfgs"]],"dials.algorithms.refinement.engine.AdaptLstbx":[[14,2,1,"","__init__"],[14,2,1,"","build_up"],[14,2,1,"","calculate_esds"],[14,2,1,"","parameter_vector_norm"],[14,2,1,"","restart"],[14,2,1,"","set_cholesky_factor"],[14,2,1,"","step_backward"],[14,2,1,"","step_forward"]],"dials.algorithms.refinement.engine.DisableMPmixin":[[14,2,1,"","set_nproc"]],"dials.algorithms.refinement.engine.GaussNewtonIterations":[[14,2,1,"","__init__"],[14,5,1,"","convergence_as_shift_over_esd"],[14,5,1,"","damping_value"],[14,5,1,"","gradient_threshold"],[14,5,1,"","max_shift_over_esd"],[14,2,1,"","run"],[14,5,1,"","step_threshold"]],"dials.algorithms.refinement.engine.Journal":[[14,2,1,"","add_column"],[14,2,1,"","add_row"],[14,2,1,"","del_last_row"],[14,2,1,"","from_json_file"],[14,2,1,"","get_nrows"],[14,5,1,"","reason_for_termination"],[14,2,1,"","set_last_cell"],[14,2,1,"","to_json_file"]],"dials.algorithms.refinement.engine.LBFGScurvs":[[14,2,1,"","compute_functional_gradients_diag"],[14,2,1,"","run"]],"dials.algorithms.refinement.engine.LevenbergMarquardtIterations":[[14,2,1,"","add_constant_to_diagonal"],[14,6,1,"","mu"],[14,2,1,"","report_progress"],[14,2,1,"","run"],[14,2,1,"","setup_mu"],[14,5,1,"","tau"]],"dials.algorithms.refinement.engine.Refinery":[[14,2,1,"","__init__"],[14,2,1,"","get_correlation_matrix_for_step"],[14,2,1,"","get_num_steps"],[14,2,1,"","jacobian_condition_number"],[14,2,1,"","prepare_for_step"],[14,2,1,"","run"],[14,2,1,"","set_nproc"],[14,2,1,"","split_jacobian_into_blocks"],[14,2,1,"","test_for_termination"],[14,2,1,"","test_objective_increasing_but_not_nref"],[14,2,1,"","test_rmsd_convergence"],[14,2,1,"","update_journal"]],"dials.algorithms.refinement.engine.SimpleLBFGS":[[14,2,1,"","run"]],"dials.algorithms.refinement.refiner":[[14,1,1,"","Refiner"],[14,1,1,"","RefinerFactory"],[14,1,1,"","ScanVaryingRefiner"]],"dials.algorithms.refinement.refiner.Refiner":[[14,2,1,"","__init__"],[14,2,1,"","calc_exp_rmsd_table"],[14,2,1,"","get_experiments"],[14,2,1,"","get_free_reflections"],[14,2,1,"","get_matches"],[14,2,1,"","get_param_reporter"],[14,2,1,"","get_parameter_correlation_matrix"],[14,6,1,"","history"],[14,2,1,"","predict_for_indexed"],[14,2,1,"","predict_for_reflection_table"],[14,2,1,"","print_exp_rmsd_table"],[14,2,1,"","print_out_of_sample_rmsd_table"],[14,2,1,"","print_panel_rmsd_table"],[14,2,1,"","print_step_table"],[14,2,1,"","rmsds"],[14,2,1,"","rmsds_for_reflection_table"],[14,2,1,"","run"],[14,2,1,"","selection_used_for_refinement"]],"dials.algorithms.refinement.refiner.RefinerFactory":[[14,2,1,"","config_refinery"],[14,2,1,"","config_restraints"],[14,2,1,"","config_sparse"],[14,2,1,"","config_target"],[14,2,1,"","from_parameters_data_experiments"],[14,2,1,"","reflections_after_outlier_rejection"]],"dials.algorithms.refinement.reflection_manager":[[14,1,1,"","BlockCalculator"],[14,1,1,"","LaueReflectionManager"],[14,1,1,"","ReflectionManager"],[14,1,1,"","ReflectionManagerFactory"],[14,1,1,"","StillsReflectionManager"],[14,1,1,"","TOFReflectionManager"]],"dials.algorithms.refinement.reflection_manager.BlockCalculator":[[14,2,1,"","__init__"],[14,2,1,"","per_image"],[14,2,1,"","per_width"]],"dials.algorithms.refinement.reflection_manager.LaueReflectionManager":[[14,2,1,"","__init__"],[14,5,1,"","experiment_type"],[14,2,1,"","print_stats_on_matches"],[14,2,1,"","update_residuals"]],"dials.algorithms.refinement.reflection_manager.ReflectionManager":[[14,2,1,"","__init__"],[14,5,1,"","experiment_type"],[14,2,1,"","filter_obs"],[14,2,1,"","finalise"],[14,2,1,"","get_accepted_refs_size"],[14,2,1,"","get_centroid_analyser"],[14,2,1,"","get_free_reflections"],[14,2,1,"","get_indexed"],[14,2,1,"","get_matches"],[14,2,1,"","get_obs"],[14,2,1,"","get_sample_size"],[14,2,1,"","print_stats_on_matches"],[14,2,1,"","reset_accepted_reflections"],[14,2,1,"","update_residuals"]],"dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory":[[14,2,1,"","from_parameters_reflections_experiments"],[14,2,1,"","get_col_names"],[14,2,1,"","get_weighting_strategy_override"],[14,2,1,"","laue_manager"],[14,2,1,"","rotation_scan_manager"],[14,2,1,"","stills_manager"]],"dials.algorithms.refinement.reflection_manager.StillsReflectionManager":[[14,5,1,"","experiment_type"],[14,2,1,"","print_stats_on_matches"]],"dials.algorithms.refinement.reflection_manager.TOFReflectionManager":[[14,2,1,"","__init__"],[14,2,1,"","update_residuals"]],"dials.algorithms.refinement.target":[[14,1,1,"","LaueLeastSquaresResidualWithRmsdCutoff"],[14,1,1,"","LeastSquaresPositionalResidualWithRmsdCutoff"],[14,1,1,"","LeastSquaresPositionalResidualWithRmsdCutoffSparse"],[14,1,1,"","SparseGradientsMixin"],[14,1,1,"","TOFLeastSquaresResidualWithRmsdCutoff"],[14,1,1,"","Target"],[14,1,1,"","TargetFactory"]],"dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff":[[14,2,1,"","__init__"],[14,2,1,"","achieved"],[14,5,1,"","rmsd_names"],[14,5,1,"","rmsd_units"]],"dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff":[[14,2,1,"","__init__"],[14,2,1,"","achieved"]],"dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff":[[14,5,1,"","rmsd_names"],[14,5,1,"","rmsd_units"]],"dials.algorithms.refinement.target.Target":[[14,2,1,"","__init__"],[14,2,1,"","achieved"],[14,2,1,"","calculate_gradients"],[14,2,1,"","compute_functional_gradients_and_curvatures"],[14,2,1,"","compute_residuals"],[14,2,1,"","compute_residuals_and_gradients"],[14,2,1,"","compute_restraints_functional_gradients_and_curvatures"],[14,2,1,"","compute_restraints_residuals_and_gradients"],[14,6,1,"","dim"],[14,2,1,"","get_num_matches"],[14,2,1,"","get_num_matches_for_experiment"],[14,2,1,"","get_num_matches_for_panel"],[14,2,1,"","predict"],[14,2,1,"","predict_for_free_reflections"],[14,2,1,"","predict_for_reflection_table"],[14,5,1,"","rmsd_names"],[14,5,1,"","rmsd_units"],[14,2,1,"","rmsds"],[14,2,1,"","rmsds_for_experiment"],[14,2,1,"","rmsds_for_panel"],[14,2,1,"","rmsds_for_reflection_table"],[14,2,1,"","split_matches_into_blocks"],[14,2,1,"","update_matches"]],"dials.algorithms.refinement.target.TargetFactory":[[14,2,1,"","from_parameters_and_experiments"]],"dials.algorithms.refinement.target_stills":[[14,1,1,"","LeastSquaresStillsResidualWithRmsdCutoff"],[14,1,1,"","LeastSquaresStillsResidualWithRmsdCutoffSparse"]],"dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff":[[14,2,1,"","__init__"],[14,2,1,"","achieved"],[14,2,1,"","predict_for_reflection_table"],[14,5,1,"","rmsd_names"],[14,5,1,"","rmsd_units"]],"dials.algorithms.refinement.weighting_strategies":[[14,1,1,"","ConstantWeightingStrategy"],[14,1,1,"","ExternalDelPsiWeightingStrategy"],[14,1,1,"","LaueMixedWeightingStrategy"],[14,1,1,"","LaueStatisticalWeightingStrategy"],[14,1,1,"","StatisticalWeightingStrategy"],[14,1,1,"","StillsWeightingStrategy"]],"dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy":[[14,2,1,"","__init__"],[14,2,1,"","calculate_weights"]],"dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy":[[14,2,1,"","calculate_weights"]],"dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy":[[14,2,1,"","__init__"],[14,2,1,"","calculate_weights"]],"dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy":[[14,2,1,"","__init__"],[14,2,1,"","calculate_weights"]],"dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy":[[14,2,1,"","calculate_weights"]],"dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy":[[14,2,1,"","__init__"],[14,2,1,"","calculate_weights"]],"dials.algorithms.scaling":[[15,0,0,"-","outlier_rejection"]],"dials.algorithms.scaling.model":[[15,0,0,"-","model"]],"dials.algorithms.scaling.model.model":[[15,1,1,"","ArrayScalingModel"],[15,1,1,"","DoseDecay"],[15,1,1,"","KBScalingModel"],[15,1,1,"","PhysicalScalingModel"],[15,1,1,"","ScalingModelBase"],[15,3,1,"","calc_n_param_from_bins"],[15,3,1,"","calculate_new_offset"],[15,3,1,"","determine_auto_absorption_params"],[15,3,1,"","initialise_smooth_input"],[15,3,1,"","make_combined_plots"],[15,3,1,"","plot_scaling_models"]],"dials.algorithms.scaling.model.model.ArrayScalingModel":[[15,2,1,"","__init__"],[15,2,1,"","configure_components"],[15,6,1,"","consecutive_refinement_order"],[15,2,1,"","from_data"],[15,2,1,"","from_dict"],[15,5,1,"","id_"],[15,2,1,"","limit_image_range"],[15,5,1,"","phil_scope"],[15,2,1,"","plot_model_components"],[15,2,1,"","update"]],"dials.algorithms.scaling.model.model.DoseDecay":[[15,2,1,"","__init__"],[15,2,1,"","configure_components"],[15,6,1,"","consecutive_refinement_order"],[15,2,1,"","fix_initial_parameter"],[15,2,1,"","from_data"],[15,2,1,"","from_dict"],[15,2,1,"","get_shared_components"],[15,5,1,"","id_"],[15,2,1,"","limit_image_range"],[15,5,1,"","phil_scope"],[15,2,1,"","plot_model_components"],[15,2,1,"","update"]],"dials.algorithms.scaling.model.model.KBScalingModel":[[15,2,1,"","__init__"],[15,2,1,"","configure_components"],[15,6,1,"","consecutive_refinement_order"],[15,2,1,"","from_data"],[15,2,1,"","from_dict"],[15,5,1,"","id_"],[15,5,1,"","phil_scope"],[15,2,1,"","update"]],"dials.algorithms.scaling.model.model.PhysicalScalingModel":[[15,2,1,"","__init__"],[15,2,1,"","configure_components"],[15,6,1,"","consecutive_refinement_order"],[15,2,1,"","fix_initial_parameter"],[15,2,1,"","from_data"],[15,2,1,"","from_dict"],[15,2,1,"","get_shared_components"],[15,5,1,"","id_"],[15,2,1,"","limit_image_range"],[15,5,1,"","phil_scope"],[15,2,1,"","plot_model_components"],[15,2,1,"","update"]],"dials.algorithms.scaling.model.model.ScalingModelBase":[[15,2,1,"","__init__"],[15,6,1,"","components"],[15,6,1,"","configdict"],[15,2,1,"","configure_components"],[15,2,1,"","consecutive_refinement_order"],[15,6,1,"","error_model"],[15,2,1,"","fix_initial_parameter"],[15,6,1,"","fixed_components"],[15,2,1,"","from_data"],[15,2,1,"","from_dict"],[15,2,1,"","get_shared_components"],[15,5,1,"","id_"],[15,6,1,"","is_scaled"],[15,2,1,"","limit_image_range"],[15,2,1,"","load_error_model"],[15,6,1,"","n_params"],[15,2,1,"","plot_model_components"],[15,2,1,"","record_intensity_combination_Imid"],[15,2,1,"","set_error_model"],[15,2,1,"","set_scaling_model_as_scaled"],[15,2,1,"","set_scaling_model_as_unscaled"],[15,2,1,"","set_valid_image_range"],[15,2,1,"","to_dict"],[15,2,1,"","update"]],"dials.algorithms.scaling.outlier_rejection":[[15,1,1,"","NormDevOutlierRejection"],[15,1,1,"","OutlierRejectionBase"],[15,1,1,"","SimpleNormDevOutlierRejection"],[15,1,1,"","TargetedOutlierRejection"],[15,3,1,"","determine_Esq_outlier_index_arrays"],[15,3,1,"","determine_outlier_index_arrays"],[15,3,1,"","reject_outliers"]],"dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection":[[15,2,1,"","__init__"]],"dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase":[[15,2,1,"","__init__"],[15,5,1,"","final_outlier_arrays"],[15,2,1,"","run"]],"dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection":[[15,2,1,"","__init__"]],"dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection":[[15,2,1,"","__init__"]],"dials.algorithms.spot_finding":[[16,0,0,"-","factory"],[16,0,0,"-","finder"]],"dials.algorithms.spot_finding.factory":[[16,1,1,"","BackgroundGradientFilter"],[16,1,1,"","FilterRunner"],[16,1,1,"","PeakCentroidDistanceFilter"],[16,1,1,"","SpotDensityFilter"],[16,1,1,"","SpotFinderFactory"],[16,3,1,"","generate_phil_scope"]],"dials.algorithms.spot_finding.factory.BackgroundGradientFilter":[[16,2,1,"","__init__"],[16,2,1,"","run"]],"dials.algorithms.spot_finding.factory.FilterRunner":[[16,2,1,"","__init__"],[16,2,1,"","check_flags"]],"dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter":[[16,2,1,"","__init__"],[16,2,1,"","run"]],"dials.algorithms.spot_finding.factory.SpotDensityFilter":[[16,2,1,"","__init__"],[16,2,1,"","run"]],"dials.algorithms.spot_finding.factory.SpotFinderFactory":[[16,2,1,"","configure_filter"],[16,2,1,"","configure_threshold"],[16,2,1,"","from_parameters"],[16,2,1,"","load_image"]],"dials.algorithms.spot_finding.finder":[[16,1,1,"","ExtractPixelsFromImage"],[16,1,1,"","ExtractPixelsFromImage2DNoShoeboxes"],[16,1,1,"","ExtractSpots"],[16,1,1,"","ExtractSpotsParallelTask"],[16,1,1,"","LaueSpotFinder"],[16,1,1,"","SpotFinder"],[16,1,1,"","TOFSpotFinder"],[16,3,1,"","pixel_list_to_reflection_table"],[16,3,1,"","pixel_list_to_shoeboxes"],[16,3,1,"","shoeboxes_to_reflection_table"]],"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage":[[16,2,1,"","__init__"]],"dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes":[[16,2,1,"","__init__"]],"dials.algorithms.spot_finding.finder.ExtractSpots":[[16,2,1,"","__init__"]],"dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask":[[16,2,1,"","__init__"]],"dials.algorithms.spot_finding.finder.LaueSpotFinder":[[16,2,1,"","__init__"]],"dials.algorithms.spot_finding.finder.SpotFinder":[[16,2,1,"","__init__"],[16,2,1,"","find_spots"]],"dials.algorithms.spot_finding.finder.TOFSpotFinder":[[16,2,1,"","__init__"]],"dials.algorithms.spot_prediction":[[17,0,0,"-","reflection_predictor"]],"dials.algorithms.spot_prediction.reflection_predictor":[[17,1,1,"","ReflectionPredictor"]],"dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor":[[17,2,1,"","__init__"],[17,2,1,"","predictor"]],"dials.algorithms.symmetry":[[18,3,1,"","apply_change_of_basis_ops"],[18,3,1,"","change_of_basis_ops_to_minimum_cell"],[18,0,0,"-","cosym"],[18,3,1,"","eliminate_sys_absent"],[18,3,1,"","get_subset_for_symmetry"],[18,0,0,"-","laue_group"],[18,3,1,"","median_unit_cell"],[18,3,1,"","prepare_datasets_for_symmetry_analysis"],[18,0,0,"-","reindex_to_reference"],[18,3,1,"","resolution_filter_from_array"],[18,3,1,"","resolution_filter_from_reflections_experiments"],[18,1,1,"","symmetry_base"],[18,3,1,"","unit_cells_are_similar_to"]],"dials.algorithms.symmetry.cosym":[[18,1,1,"","CosymAnalysis"],[18,1,1,"","ScoreSubGroup"],[18,1,1,"","ScoreSymmetryElement"],[18,1,1,"","SymmetryAnalysis"],[18,3,1,"","change_of_basis_op_to_best_cell"],[18,0,0,"-","engine"],[18,3,1,"","extract_reference_intensities"],[18,0,0,"-","target"]],"dials.algorithms.symmetry.cosym.CosymAnalysis":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"],[18,2,1,"","as_json"],[18,2,1,"","run"]],"dials.algorithms.symmetry.cosym.ScoreSubGroup":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"],[18,6,1,"","stars"]],"dials.algorithms.symmetry.cosym.ScoreSymmetryElement":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"],[18,6,1,"","stars"]],"dials.algorithms.symmetry.cosym.SymmetryAnalysis":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"],[18,2,1,"","subgroups_table"],[18,2,1,"","summary_table"],[18,2,1,"","sym_ops_table"]],"dials.algorithms.symmetry.cosym.engine":[[18,1,1,"","lbfgs_with_curvs"],[18,3,1,"","minimize_scipy"],[18,3,1,"","minimize_scitbx_lbfgs"]],"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs":[[18,2,1,"","__init__"],[18,2,1,"","callback_after_step"],[18,2,1,"","compute_functional_and_gradients"],[18,2,1,"","compute_functional_gradients_and_curvatures"],[18,2,1,"","compute_functional_gradients_diag"]],"dials.algorithms.symmetry.cosym.target":[[18,1,1,"","LightArray"],[18,1,1,"","Target"]],"dials.algorithms.symmetry.cosym.target.LightArray":[[18,2,1,"","__init__"],[18,2,1,"","data"],[18,2,1,"","sigmas"],[18,2,1,"","size"]],"dials.algorithms.symmetry.cosym.target.Target":[[18,2,1,"","__init__"],[18,2,1,"","compute_functional"],[18,2,1,"","compute_functional_score_for_dimension_assessment"],[18,2,1,"","compute_gradients"],[18,2,1,"","compute_gradients_fd"],[18,2,1,"","curvatures"],[18,2,1,"","curvatures_fd"],[18,5,1,"","dim"],[18,2,1,"","set_dimensions"]],"dials.algorithms.symmetry.laue_group":[[18,1,1,"","CorrelationCoefficientAccumulator"],[18,1,1,"","LaueGroupAnalysis"],[18,1,1,"","ScoreCorrelationCoefficient"],[18,1,1,"","ScoreSubGroup"],[18,1,1,"","ScoreSymmetryElement"],[18,3,1,"","trunccauchy_pdf"]],"dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator":[[18,2,1,"","__init__"],[18,2,1,"","accumulate"],[18,2,1,"","coefficient"],[18,2,1,"","denominator"],[18,2,1,"","n"],[18,2,1,"","numerator"]],"dials.algorithms.symmetry.laue_group.LaueGroupAnalysis":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"],[18,2,1,"","as_json"]],"dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient":[[18,2,1,"","__init__"],[18,6,1,"","p_cc_given_not_s"],[18,6,1,"","p_cc_given_s"],[18,6,1,"","p_s_given_cc"]],"dials.algorithms.symmetry.laue_group.ScoreSubGroup":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"]],"dials.algorithms.symmetry.laue_group.ScoreSymmetryElement":[[18,2,1,"","__init__"],[18,2,1,"","as_dict"]],"dials.algorithms.symmetry.reindex_to_reference":[[18,3,1,"","determine_reindex_operator_against_reference"]],"dials.algorithms.symmetry.symmetry_base":[[18,2,1,"","__init__"],[18,2,1,"","kernel_normalisation"],[18,2,1,"","ml_aniso_normalisation"],[18,2,1,"","ml_iso_normalisation"]],"dials.array_family.flex":[[20,1,1,"","reflection_table"]],"dials.array_family.flex.reflection_table":[[20,2,1,"","__init__"],[20,2,1,"","append"],[20,2,1,"","are_experiment_identifiers_consistent"],[20,2,1,"","as_file"],[20,2,1,"","as_hdf5"],[20,2,1,"","as_miller_array"],[20,2,1,"","as_msgpack"],[20,2,1,"","as_msgpack_file"],[20,2,1,"","as_msgpack_to_file"],[20,2,1,"","as_pickle"],[20,2,1,"","assert_experiment_identifiers_are_consistent"],[20,5,1,"","background_algorithm"],[20,2,1,"","calculate_entering_flags"],[20,5,1,"","centroid_algorithm"],[20,2,1,"","centroid_px_to_mm"],[20,2,1,"","clean_experiment_identifiers_map"],[20,2,1,"","clear"],[20,2,1,"","cols"],[20,2,1,"","compute_background"],[20,2,1,"","compute_bbox"],[20,2,1,"","compute_centroid"],[20,2,1,"","compute_corrections"],[20,2,1,"","compute_d"],[20,2,1,"","compute_d_single"],[20,2,1,"","compute_fitted_intensity"],[20,2,1,"","compute_mask"],[20,2,1,"","compute_miller_indices_in_asu"],[20,2,1,"","compute_partiality"],[20,2,1,"","compute_phi_range"],[20,2,1,"","compute_ray_intersections"],[20,2,1,"","compute_summed_intensity"],[20,2,1,"","compute_zeta"],[20,2,1,"","compute_zeta_multi"],[20,2,1,"","concat"],[20,2,1,"","contains_invalid_pixels"],[20,2,1,"","copy"],[20,2,1,"","del_selected"],[20,2,1,"","empty"],[20,2,1,"","empty_standard"],[20,2,1,"","experiment_identifiers"],[20,2,1,"","extend"],[20,2,1,"","extract_shoeboxes"],[20,2,1,"","find_overlaps"],[20,1,1,"","flags"],[20,2,1,"","from_file"],[20,2,1,"","from_hdf5"],[20,2,1,"","from_msgpack"],[20,2,1,"","from_msgpack_file"],[20,2,1,"","from_observations"],[20,2,1,"","from_pickle"],[20,2,1,"","from_predictions"],[20,2,1,"","from_predictions_multi"],[20,2,1,"","get"],[20,2,1,"","get_flags"],[20,2,1,"","has_key"],[20,2,1,"","help_keys"],[20,2,1,"","insert"],[20,2,1,"","is_consistent"],[20,2,1,"","is_overloaded"],[20,2,1,"","items"],[20,2,1,"","iterate_experiments_and_indices"],[20,2,1,"","keys"],[20,2,1,"","map_centroids_to_reciprocal_space"],[20,2,1,"","match"],[20,2,1,"","match_by_hkle"],[20,2,1,"","match_with_reference"],[20,2,1,"","ncols"],[20,2,1,"","nrows"],[20,2,1,"","plot"],[20,2,1,"","random_split"],[20,2,1,"","remove_on_experiment_identifiers"],[20,2,1,"","reorder"],[20,2,1,"","reset_ids"],[20,2,1,"","resize"],[20,2,1,"","rows"],[20,2,1,"","select"],[20,2,1,"","select_on_experiment_identifiers"],[20,2,1,"","set_flags"],[20,2,1,"","set_selected"],[20,2,1,"","size"],[20,2,1,"","sort"],[20,2,1,"","split_by_experiment_id"],[20,2,1,"","split_indices_by_experiment_id"],[20,2,1,"","split_partial_indices"],[20,2,1,"","split_partials"],[20,2,1,"","split_partials_with_shoebox"],[20,2,1,"","subsort"],[20,2,1,"","types"],[20,2,1,"","unset_flags"],[20,2,1,"","update"]],"dials.array_family.flex.reflection_table.flags":[[20,2,1,"","as_integer_ratio"],[20,5,1,"","background_includes_bad_pixels"],[20,5,1,"","bad_for_refinement"],[20,5,1,"","bad_for_scaling"],[20,5,1,"","bad_reference"],[20,5,1,"","bad_shoebox"],[20,5,1,"","bad_spot"],[20,2,1,"","bit_count"],[20,2,1,"","bit_length"],[20,5,1,"","centroid_outlier"],[20,2,1,"","conjugate"],[20,5,1,"","denominator"],[20,5,1,"","dont_integrate"],[20,5,1,"","excluded_for_refinement"],[20,5,1,"","excluded_for_scaling"],[20,5,1,"","failed_during_background_modelling"],[20,5,1,"","failed_during_profile_fitting"],[20,5,1,"","failed_during_summation"],[20,5,1,"","foreground_includes_bad_pixels"],[20,2,1,"","from_bytes"],[20,5,1,"","imag"],[20,5,1,"","in_powder_ring"],[20,5,1,"","includes_bad_pixels"],[20,5,1,"","indexed"],[20,5,1,"","integrated"],[20,5,1,"","integrated_prf"],[20,5,1,"","integrated_sum"],[20,2,1,"","is_integer"],[20,5,1,"","name"],[20,5,1,"","names"],[20,5,1,"","not_suitable_for_refinement"],[20,5,1,"","numerator"],[20,5,1,"","observed"],[20,5,1,"","outlier_in_scaling"],[20,5,1,"","overlapped_bg"],[20,5,1,"","overlapped_fg"],[20,5,1,"","overloaded"],[20,5,1,"","predicted"],[20,5,1,"","real"],[20,5,1,"","reference_spot"],[20,5,1,"","scaled"],[20,5,1,"","strong"],[20,2,1,"","to_bytes"],[20,5,1,"","used_in_modelling"],[20,5,1,"","used_in_refinement"],[20,5,1,"","user_excluded_in_scaling"],[20,5,1,"","values"]],"dials.extensions":[[31,0,0,"-","dispersion_spotfinder_threshold_ext"],[31,0,0,"-","gaussian_rs_profile_model_ext"],[31,0,0,"-","null_background_ext"],[31,0,0,"-","simple_background_ext"],[31,0,0,"-","simple_centroid_ext"]],"dials.extensions.dispersion_spotfinder_threshold_ext":[[31,1,1,"","DispersionSpotFinderThresholdExt"],[31,3,1,"","estimate_global_threshold"]],"dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt":[[31,2,1,"","__init__"],[31,2,1,"","compute_threshold"],[31,5,1,"","name"],[31,2,1,"","phil"]],"dials.extensions.gaussian_rs_profile_model_ext":[[31,1,1,"","GaussianRSProfileModelExt"]],"dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt":[[31,2,1,"","algorithm"],[31,5,1,"","default"],[31,2,1,"","from_dict"],[31,5,1,"","name"],[31,2,1,"","phil"]],"dials.extensions.null_background_ext":[[31,1,1,"","NullBackgroundExt"]],"dials.extensions.null_background_ext.NullBackgroundExt":[[31,2,1,"","__init__"],[31,2,1,"","compute_background"],[31,5,1,"","name"]],"dials.extensions.simple_background_ext":[[31,1,1,"","SimpleBackgroundExt"]],"dials.extensions.simple_background_ext.SimpleBackgroundExt":[[31,2,1,"","__init__"],[31,2,1,"","compute_background"],[31,5,1,"","name"],[31,2,1,"","phil"]],"dials.extensions.simple_centroid_ext":[[31,1,1,"","SimpleCentroidExt"]],"dials.extensions.simple_centroid_ext.SimpleCentroidExt":[[31,2,1,"","__init__"],[31,2,1,"","compute_centroid"],[31,5,1,"","default"],[31,5,1,"","name"]],"dials.util":[[33,0,0,"-","command_line"],[33,0,0,"-","export_mtz"],[33,0,0,"-","export_text"],[33,0,0,"-","image"],[33,0,0,"-","installer"],[33,0,0,"-","ioutil"],[33,0,0,"-","nexus"],[33,0,0,"-","options"]],"dials.util.command_line":[[33,1,1,"","Command"],[33,1,1,"","ProgressBar"],[33,1,1,"","ProgressBarTimer"],[33,3,1,"","coloured"],[33,3,1,"","heading"]],"dials.util.command_line.Command":[[33,2,1,"","end"],[33,5,1,"","indent"],[33,5,1,"","max_length"],[33,5,1,"","print_time"],[33,2,1,"","start"]],"dials.util.command_line.ProgressBar":[[33,2,1,"","__init__"],[33,2,1,"","finished"],[33,2,1,"","update"]],"dials.util.command_line.ProgressBarTimer":[[33,2,1,"","__init__"],[33,2,1,"","get_elapsed_time"],[33,2,1,"","update"]],"dials.util.export_mtz":[[33,1,1,"","MADMergedMTZWriter"],[33,1,1,"","MTZWriterBase"],[33,1,1,"","MergedMTZWriter"],[33,1,1,"","WavelengthGroup"],[33,3,1,"","add_batch_list"],[33,3,1,"","convert_to_cambridge"],[33,3,1,"","export_mtz"],[33,3,1,"","log_summary"],[33,3,1,"","match_wavelengths"],[33,3,1,"","rotate_crystal"],[33,3,1,"","write_columns"]],"dials.util.export_mtz.MADMergedMTZWriter":[[33,2,1,"","add_dataset"]],"dials.util.export_mtz.MTZWriterBase":[[33,2,1,"","__init__"],[33,2,1,"","add_crystal"],[33,2,1,"","add_empty_dataset"]],"dials.util.export_mtz.MergedMTZWriter":[[33,2,1,"","add_dataset"]],"dials.util.export_mtz.WavelengthGroup":[[33,2,1,"","__init__"],[33,2,1,"","add_experiment"],[33,2,1,"","calculate_weighted_mean"],[33,5,1,"","exp_nos"],[33,5,1,"","identifiers"],[33,5,1,"","max_possible_wl"],[33,5,1,"","min_wl"],[33,5,1,"","wavelengths"],[33,5,1,"","weighted_mean"]],"dials.util.export_text":[[33,3,1,"","export_text"]],"dials.util.image":[[33,1,1,"","reader"]],"dials.util.image.reader":[[33,2,1,"","get_data"],[33,2,1,"","read_file"]],"dials.util.installer":[[33,1,1,"","installer"]],"dials.util.installer.installer":[[33,5,1,"","base_package_options"],[33,5,1,"","configure_modules"],[33,5,1,"","dest_dir_prefix"],[33,5,1,"","include_gui_packages"],[33,5,1,"","installer_dir"],[33,5,1,"","make_apps"],[33,5,1,"","product_name"],[33,2,1,"","product_specific_finalize_install"],[33,5,1,"","remove_sources_default"],[33,5,1,"","source_packages"]],"dials.util.ioutil":[[33,3,1,"","get_inverse_ub_matrix_from_xparm"],[33,3,1,"","get_space_group_type_from_xparm"]],"dials.util.nexus":[[33,3,1,"","dump"],[33,3,1,"","get_entry"],[33,3,1,"","load"]],"dials.util.options":[[33,1,1,"","ArgumentHandlingErrorInfo"],[33,1,1,"","ArgumentParser"],[33,1,1,"","ArgumentParserBase"],[33,1,1,"","Importer"],[33,4,1,"","InvalidPhilError"],[33,1,1,"","OptionParser"],[33,1,1,"","PhilCommandParser"],[33,3,1,"","flatten_experiments"],[33,3,1,"","flatten_reflections"],[33,3,1,"","reflections_and_experiments_from_files"]],"dials.util.options.ArgumentHandlingErrorInfo":[[33,5,1,"","exception"],[33,5,1,"","message"],[33,5,1,"","name"],[33,5,1,"","traceback"],[33,5,1,"","type"],[33,5,1,"","validation"]],"dials.util.options.ArgumentParser":[[33,2,1,"","__init__"],[33,6,1,"","diff_phil"],[33,2,1,"","format_help"],[33,2,1,"","parse_args"],[33,6,1,"","phil"],[33,6,1,"","system_phil"]],"dials.util.options.ArgumentParserBase":[[33,2,1,"","__init__"],[33,2,1,"","format_epilog"],[33,2,1,"","parse_known_args"]],"dials.util.options.Importer":[[33,2,1,"","__init__"],[33,2,1,"","try_read_experiments"],[33,2,1,"","try_read_experiments_from_images"],[33,2,1,"","try_read_reflections"]],"dials.util.options.OptionParser":[[33,2,1,"","__init__"]],"dials.util.options.PhilCommandParser":[[33,2,1,"","__init__"],[33,6,1,"","diff_phil"],[33,2,1,"","parse_args"],[33,6,1,"","phil"],[33,6,1,"","system_phil"]],"dxtbx":[[26,0,0,"-","imageset"]],"dxtbx.imageset":[[26,1,1,"","ExternalLookup"],[26,1,1,"","ExternalLookupItemBool"],[26,1,1,"","ExternalLookupItemDouble"],[26,1,1,"","ImageGrid"],[26,1,1,"","ImageSequence"],[26,1,1,"","ImageSet"],[26,1,1,"","ImageSetData"],[26,1,1,"","ImageSetFactory"],[26,1,1,"","ImageSetLazy"],[26,1,1,"","MemReader"]],"dxtbx.imageset.ExternalLookup":[[26,2,1,"","__init__"],[26,6,1,"","dx"],[26,6,1,"","dy"],[26,6,1,"","gain"],[26,6,1,"","mask"],[26,6,1,"","pedestal"]],"dxtbx.imageset.ExternalLookupItemBool":[[26,2,1,"","__init__"],[26,6,1,"","data"],[26,6,1,"","filename"]],"dxtbx.imageset.ExternalLookupItemDouble":[[26,2,1,"","__init__"],[26,6,1,"","data"],[26,6,1,"","filename"]],"dxtbx.imageset.ImageGrid":[[26,2,1,"","__init__"],[26,2,1,"","from_imageset"],[26,2,1,"","get_grid_size"]],"dxtbx.imageset.ImageSequence":[[26,2,1,"","__init__"],[26,2,1,"","complete_set"],[26,2,1,"","get_array_range"],[26,2,1,"","get_beam"],[26,2,1,"","get_detector"],[26,2,1,"","get_goniometer"],[26,2,1,"","get_scan"],[26,2,1,"","get_template"],[26,2,1,"","partial_set"],[26,2,1,"","set_beam"],[26,2,1,"","set_detector"],[26,2,1,"","set_goniometer"],[26,2,1,"","set_scan"],[26,2,1,"","update_detector_px_mm_data"]],"dxtbx.imageset.ImageSet":[[26,2,1,"","__init__"],[26,2,1,"","as_imageset"],[26,2,1,"","clear_cache"],[26,2,1,"","complete_set"],[26,2,1,"","data"],[26,6,1,"","external_lookup"],[26,2,1,"","get_beam"],[26,2,1,"","get_corrected_data"],[26,2,1,"","get_detector"],[26,2,1,"","get_detectorbase"],[26,2,1,"","get_format_class"],[26,2,1,"","get_gain"],[26,2,1,"","get_goniometer"],[26,2,1,"","get_image_identifier"],[26,2,1,"","get_mask"],[26,2,1,"","get_path"],[26,2,1,"","get_pedestal"],[26,2,1,"","get_raw_data"],[26,2,1,"","get_scan"],[26,2,1,"","get_spectrum"],[26,2,1,"","get_vendortype"],[26,2,1,"","has_dynamic_mask"],[26,2,1,"","indices"],[26,2,1,"","is_marked_for_rejection"],[26,2,1,"","mark_for_rejection"],[26,2,1,"","masker"],[26,2,1,"","params"],[26,2,1,"","partial_set"],[26,2,1,"","paths"],[26,2,1,"","reader"],[26,2,1,"","set_beam"],[26,2,1,"","set_detector"],[26,2,1,"","set_goniometer"],[26,2,1,"","set_scan"],[26,2,1,"","size"],[26,2,1,"","update_detector_px_mm_data"]],"dxtbx.imageset.ImageSetData":[[26,2,1,"","__init__"],[26,6,1,"","external_lookup"],[26,2,1,"","get_beam"],[26,2,1,"","get_data"],[26,2,1,"","get_detector"],[26,2,1,"","get_format_class"],[26,2,1,"","get_goniometer"],[26,2,1,"","get_image_identifier"],[26,2,1,"","get_master_path"],[26,2,1,"","get_params"],[26,2,1,"","get_path"],[26,2,1,"","get_scan"],[26,2,1,"","get_template"],[26,2,1,"","get_vendor"],[26,2,1,"","has_single_file_reader"],[26,2,1,"","is_marked_for_rejection"],[26,2,1,"","mark_for_rejection"],[26,2,1,"","masker"],[26,2,1,"","partial_data"],[26,2,1,"","reader"],[26,2,1,"","set_beam"],[26,2,1,"","set_detector"],[26,2,1,"","set_format_class"],[26,2,1,"","set_goniometer"],[26,2,1,"","set_params"],[26,2,1,"","set_scan"],[26,2,1,"","set_template"],[26,2,1,"","set_vendor"]],"dxtbx.imageset.ImageSetFactory":[[26,2,1,"","from_template"],[26,2,1,"","imageset_from_anyset"],[26,2,1,"","make_imageset"],[26,2,1,"","make_sequence"],[26,2,1,"","new"]],"dxtbx.imageset.ImageSetLazy":[[26,2,1,"","get_beam"],[26,2,1,"","get_corrected_data"],[26,2,1,"","get_detector"],[26,2,1,"","get_gain"],[26,2,1,"","get_goniometer"],[26,2,1,"","get_mask"],[26,2,1,"","get_scan"]],"dxtbx.imageset.MemReader":[[26,2,1,"","__init__"],[26,2,1,"","copy"],[26,2,1,"","identifiers"],[26,2,1,"","is_single_file_reader"],[26,2,1,"","master_path"],[26,2,1,"","paths"],[26,2,1,"","read"]],"dxtbx.model":[[22,1,1,"","Crystal"],[23,1,1,"","Detector"],[24,1,1,"","ExperimentList"],[22,1,1,"","MosaicCrystalKabsch2010"],[22,1,1,"","MosaicCrystalSauter2014"],[21,0,0,"-","beam"],[22,0,0,"-","crystal"],[23,0,0,"-","detector"],[24,0,0,"-","experiment_list"],[25,0,0,"-","goniometer"],[28,0,0,"-","profile"],[29,0,0,"-","scan"]],"dxtbx.model.Crystal":[[22,2,1,"","__init__"],[22,2,1,"","as_str"],[22,2,1,"","from_dict"],[22,2,1,"","get_crystal_symmetry"],[22,2,1,"","show"],[22,2,1,"","to_dict"]],"dxtbx.model.Detector":[[23,2,1,"","__init__"],[23,2,1,"","add_group"],[23,2,1,"","add_panel"],[23,2,1,"","from_dict"],[23,2,1,"","get_max_inscribed_resolution"],[23,2,1,"","get_max_resolution"],[23,2,1,"","get_names"],[23,2,1,"","get_panel_intersection"],[23,2,1,"","get_ray_intersection"],[23,2,1,"","has_projection_2d"],[23,2,1,"","hierarchy"],[23,2,1,"","is_similar_to"],[23,2,1,"","iter_levelorder"],[23,2,1,"","iter_panels"],[23,2,1,"","iter_preorder"],[23,2,1,"","rotate_around_origin"],[23,2,1,"","to_dict"]],"dxtbx.model.ExperimentList":[[24,2,1,"","__init__"],[24,2,1,"","all_laue"],[24,2,1,"","all_rotations"],[24,2,1,"","all_same_type"],[24,2,1,"","all_sequences"],[24,2,1,"","all_stills"],[24,2,1,"","all_tof"],[24,2,1,"","append"],[24,2,1,"","as_file"],[24,2,1,"","as_json"],[24,2,1,"","beams"],[24,2,1,"","change_basis"],[24,2,1,"","clear"],[24,2,1,"","consolidate_histories"],[24,2,1,"","crystals"],[24,2,1,"","detectors"],[24,2,1,"","empty"],[24,2,1,"","extend"],[24,2,1,"","find"],[24,2,1,"","from_file"],[24,2,1,"","from_templates"],[24,2,1,"","goniometers"],[24,2,1,"","histories"],[24,2,1,"","identifiers"],[24,2,1,"","imagesets"],[24,2,1,"","indices"],[24,2,1,"","is_consistent"],[24,2,1,"","nullify_all_single_file_reader_format_instances"],[24,2,1,"","profiles"],[24,2,1,"","remove_on_experiment_identifiers"],[24,2,1,"","replace"],[24,2,1,"","scaling_models"],[24,2,1,"","scans"],[24,2,1,"","select_on_experiment_identifiers"],[24,2,1,"","to_dict"],[24,2,1,"","where"]],"dxtbx.model.MosaicCrystalKabsch2010":[[22,2,1,"","__init__"],[22,2,1,"","as_str"],[22,2,1,"","from_dict"],[22,2,1,"","get_mosaicity"],[22,2,1,"","is_similar_to"],[22,2,1,"","set_mosaicity"],[22,2,1,"","to_dict"]],"dxtbx.model.MosaicCrystalSauter2014":[[22,2,1,"","__init__"],[22,2,1,"","as_str"],[22,2,1,"","from_dict"],[22,2,1,"","get_A_as_sqr"],[22,2,1,"","get_A_inverse_as_sqr"],[22,2,1,"","get_domain_size_ang"],[22,2,1,"","get_half_mosaicity_deg"],[22,2,1,"","is_similar_to"],[22,2,1,"","set_domain_size_ang"],[22,2,1,"","set_half_mosaicity_deg"],[22,2,1,"","to_dict"]],"dxtbx.model.beam":[[21,1,1,"","BeamFactory"]],"dxtbx.model.beam.BeamFactory":[[21,2,1,"","complex"],[21,2,1,"","from_dict"],[21,2,1,"","from_phil"],[21,2,1,"","imgCIF"],[21,2,1,"","imgCIF_H"],[21,2,1,"","make_beam"],[21,2,1,"","make_polarized_beam"],[21,2,1,"","make_polychromatic_beam"],[21,2,1,"","simple"],[21,2,1,"","simple_directional"]],"dxtbx.model.crystal":[[22,1,1,"","CrystalFactory"]],"dxtbx.model.crystal.CrystalFactory":[[22,2,1,"","from_dict"],[22,2,1,"","from_mosflm_matrix"],[22,2,1,"","from_phil"]],"dxtbx.model.detector":[[23,1,1,"","DetectorFactory"],[23,3,1,"","merge_panel_scope_extracts_by_id"]],"dxtbx.model.detector.DetectorFactory":[[23,2,1,"","complex"],[23,2,1,"","from_dict"],[23,2,1,"","from_phil"],[23,2,1,"","generate_from_phil"],[23,2,1,"","imgCIF"],[23,2,1,"","imgCIF_H"],[23,2,1,"","make_detector"],[23,2,1,"","overwrite_from_phil"],[23,2,1,"","sensor"],[23,2,1,"","simple"],[23,2,1,"","two_theta"]],"dxtbx.model.experiment_list":[[24,1,1,"","BeamComparison"],[24,1,1,"","DetectorComparison"],[24,1,1,"","ExperimentListFactory"],[24,1,1,"","GoniometerComparison"]],"dxtbx.model.experiment_list.BeamComparison":[[24,2,1,"","__init__"]],"dxtbx.model.experiment_list.DetectorComparison":[[24,2,1,"","__init__"]],"dxtbx.model.experiment_list.ExperimentListFactory":[[24,2,1,"","from_args"],[24,2,1,"","from_dict"],[24,2,1,"","from_filenames"],[24,2,1,"","from_imageset_and_crystal"],[24,2,1,"","from_json"],[24,2,1,"","from_json_file"],[24,2,1,"","from_pickle_file"],[24,2,1,"","from_sequence_and_crystal"],[24,2,1,"","from_serialized_format"],[24,2,1,"","from_stills_and_crystal"],[24,2,1,"","from_templates"],[24,2,1,"","from_xds"]],"dxtbx.model.experiment_list.GoniometerComparison":[[24,2,1,"","__init__"]],"dxtbx.model.goniometer":[[25,1,1,"","Goniometer"],[25,1,1,"","GoniometerFactory"],[25,1,1,"","KappaGoniometer"],[25,1,1,"","MultiAxisGoniometer"]],"dxtbx.model.goniometer.Goniometer":[[25,2,1,"","__init__"],[25,2,1,"","from_dict"],[25,2,1,"","get_fixed_rotation"],[25,2,1,"","get_num_scan_points"],[25,2,1,"","get_rotation_axis"],[25,2,1,"","get_rotation_axis_datum"],[25,2,1,"","get_setting_rotation"],[25,2,1,"","get_setting_rotation_at_scan_point"],[25,2,1,"","get_setting_rotation_at_scan_points"],[25,2,1,"","is_similar_to"],[25,6,1,"","num_scan_points"],[25,2,1,"","reset_scan_points"],[25,2,1,"","rotate_around_origin"],[25,2,1,"","set_fixed_rotation"],[25,2,1,"","set_rotation_axis"],[25,2,1,"","set_rotation_axis_datum"],[25,2,1,"","set_setting_rotation"],[25,2,1,"","set_setting_rotation_at_scan_points"],[25,2,1,"","to_dict"]],"dxtbx.model.goniometer.GoniometerFactory":[[25,2,1,"","from_dict"],[25,2,1,"","from_phil"],[25,2,1,"","imgCIF"],[25,2,1,"","imgCIF_H"],[25,2,1,"","kappa"],[25,2,1,"","known_axis"],[25,2,1,"","make_goniometer"],[25,2,1,"","make_kappa_goniometer"],[25,2,1,"","make_multi_axis_goniometer"],[25,2,1,"","multi_axis"],[25,2,1,"","multi_axis_goniometer_from_phil"],[25,2,1,"","single_axis"],[25,2,1,"","single_axis_goniometer_from_phil"],[25,2,1,"","single_axis_reverse"]],"dxtbx.model.goniometer.KappaGoniometer":[[25,2,1,"","__init__"],[25,2,1,"","get_alpha_angle"],[25,2,1,"","get_direction"],[25,2,1,"","get_kappa_angle"],[25,2,1,"","get_kappa_axis"],[25,2,1,"","get_omega_angle"],[25,2,1,"","get_omega_axis"],[25,2,1,"","get_phi_angle"],[25,2,1,"","get_phi_axis"],[25,2,1,"","get_scan_axis"]],"dxtbx.model.goniometer.MultiAxisGoniometer":[[25,2,1,"","__init__"],[25,2,1,"","from_dict"],[25,2,1,"","get_angles"],[25,2,1,"","get_axes"],[25,2,1,"","get_names"],[25,2,1,"","get_scan_axis"],[25,2,1,"","set_angles"],[25,2,1,"","set_axes"],[25,2,1,"","to_dict"]],"dxtbx.model.profile":[[28,1,1,"","ProfileModelFactory"]],"dxtbx.model.profile.ProfileModelFactory":[[28,2,1,"","from_dict"]],"dxtbx.model.scan":[[29,1,1,"","ScanFactory"]],"dxtbx.model.scan.ScanFactory":[[29,2,1,"","add"],[29,2,1,"","from_dict"],[29,2,1,"","from_phil"],[29,2,1,"","imgCIF"],[29,2,1,"","imgCIF_H"],[29,2,1,"","make_scan"],[29,2,1,"","make_scan_from_properties"],[29,2,1,"","search"],[29,2,1,"","single_file"]],"dxtbx.serialize":[[30,0,0,"-","imageset"],[30,0,0,"-","load"],[30,0,0,"-","xds"]],"dxtbx.serialize.imageset":[[30,3,1,"","basic_imageset_from_dict"],[30,3,1,"","basic_imageset_to_dict"],[30,3,1,"","filename_or_none"],[30,3,1,"","filename_to_absolute"],[30,3,1,"","imagesequence_from_dict"],[30,3,1,"","imagesequence_to_dict"],[30,3,1,"","imageset_from_dict"],[30,3,1,"","imageset_to_dict"]],"dxtbx.serialize.load":[[30,3,1,"","crystal"],[30,3,1,"","experiment_list"],[30,3,1,"","imageset"]],"dxtbx.serialize.xds":[[30,3,1,"","to_crystal"],[30,3,1,"","to_imageset"],[30,1,1,"","to_xds"],[30,3,1,"","xds_detector_name"]],"dxtbx.serialize.xds.to_xds":[[30,2,1,"","XDS_INP"],[30,2,1,"","__init__"],[30,2,1,"","get_beam"],[30,2,1,"","get_detector"],[30,2,1,"","get_goniometer"],[30,2,1,"","get_scan"],[30,2,1,"","get_template"],[30,2,1,"","xparm_xds"]]},"objnames":{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","function","Python function"],"4":["py","exception","Python exception"],"5":["py","attribute","Python attribute"],"6":["py","property","Python property"]},"objtypes":{"0":"py:module","1":"py:class","2":"py:method","3":"py:function","4":"py:exception","5":"py:attribute","6":"py:property"},"terms":{"00h":80,"0190s":[],"02d":77,"0537s":[],"05ch11231":[0,89],"0631s":[],"06m":80,"07ghz":82,"0b100101":20,"0b1101":20,"0s":53,"100um":64,"1016s":[],"1072s":[],"1121s":83,"1123s":85,"1141s":[],"12th":100,"13_integr":80,"13th":100,"14122e":83,"1484s":[],"1498s":[],"1650s":[],"167e":82,"1902s":[],"1_integr":64,"1a":64,"1d":[11,54,83,85,86],"1e":[14,18,23,24,25,38,41,44,51,54,55,59,64],"1e4":[54,60,61],"1e6":64,"1s":53,"2015_11_10":48,"2037s":[],"2069s":[],"20k":1,"20s":80,"20th":[40,47,55,64,67,70,73],"21a":84,"21b":84,"21c":84,"22424e":85,"22nd":100,"2664s":[],"2721s":[],"27_dial":77,"27_refined_cel":77,"28_dial":77,"28_scale":77,"28_scaled_unmerg":77,"2973s":[],"29_dial":77,"2_1":[76,78],"2_integr":64,"2d":[1,2,12,14,47,55,64,99],"2f":44,"2ul":[10,12,26],"2\u03b8":[47,51,71,73],"3079s":[],"3145s":[],"3327s":[],"354e":85,"3964s":[],"3d":[1,11,12,47,52,54,64,75,83,85,86,96,97,99],"3ded":[75,81],"3deg":40,"3e":87,"3rd":98,"4274s":[],"45141e":83,"46307e":85,"4639s":[],"4843s":[],"4936s":[],"4a":100,"4b":100,"4e":40,"5252s":[],"5483s":[],"562e":82,"58327e":83,"5919306617286774e":3,"5958s":[],"5e":[38,87],"5e5":64,"5i3l":78,"5rel":83,"5th":78,"6349s":[],"654e":85,"6947s":[],"6983s":[],"7185s":[],"7262s":[],"772524827250213e":3,"7759s":[],"793e":85,"7beq":75,"7e":87,"801406_1":74,"801574_1":74,"802003_1":74,"810542_1":74,"8352s":[],"8385s":[],"8498s":[],"8758s":[],"9013s":[],"904199434387693e":3,"9273s":[],"9m":77,"A":[0,1,2,3,4,6,11,12,14,15,16,17,18,20,21,22,23,24,25,26,28,29,30,31,33,35,40,43,44,47,49,52,54,55,60,61,62,64,65,71,73,74,75,76,79,81,82,83,84,85,87,91,93,95,96,97,98],"AFTER":62,"AM":96,"AND":[33,91],"ARE":91,"AS":[89,91,96],"AT":96,"After":[1,35,48,74,75,76,79,82,83,84,85,86,87,93,97],"Again":[79,84],"All":[1,7,25,44,80,83,85,91],"An":[2,3,4,11,14,15,18,20,31,33,41,44,47,50,51,55,59,76,86,87,96,98],"As":[1,2,4,7,35,40,44,47,75,79,80,82,83,84,85,86,97,98],"At":[0,2,7,24,54,60,61,75,78,79,82,83,85,86,87,98],"BE":91,"BUT":91,"BY":91,"Be":53,"Both":[2,54,60,61],"But":75,"By":[1,2,7,34,52,54,56,60,61,62,64,67,69,71,75,77,82,83,84,85,86,87],"Cannot":47,"Could":79,"Do":[12,14,16,20,41,47,51,54,55,59,65,73],"Each":[40,54,67,87],"FOR":91,"For":[1,2,7,9,11,14,15,20,38,41,42,44,47,48,51,52,53,54,55,56,59,60,61,73,74,75,76,77,79,80,82,83,84,85,87,89,90,94,97],"From":[0,74,75,82,83,84,85,86,87,93,96],"Further":48,"Having":[83,85],"Here":[74,75,77,78,79,80,82,83,85,86,87,95],"How":96,"I":[1,3,11,18,38,40,43,44,55,64,70,73,74,75,77,80,82,83,84,85,86,87,96],"IF":91,"IN":91,"IS":[91,96],"If":[1,4,7,9,11,14,15,16,18,20,22,24,33,34,35,38,40,43,44,46,47,48,50,52,54,55,60,61,64,65,67,69,70,71,73,74,75,77,78,79,80,82,83,84,85,86,87,97],"In":[0,1,2,4,7,11,14,15,21,23,40,47,52,54,55,60,61,62,74,75,77,78,79,82,83,84,85,86,87,93,94,98],"It":[2,3,11,14,35,37,40,41,50,53,54,55,60,61,64,72,73,74,75,77,78,79,82,83,84,85,86,87,97],"Its":[2,36],"ME":96,"More":[4,7,64,65,72,78,83,85,86],"Most":[15,80],"Mostly":[83,85,86],"My":4,"NO":91,"NOT":[18,91],"No":[38,40,83,84,85,97],"Not":[20,38,45,51,52,54,60,61],"OF":91,"ON":91,"OR":91,"OUT":91,"Of":2,"On":[2,49,75,76,78,86,100],"Or":[72,90],"Other":[4,60,65,86],"Over":[74,96],"SUCH":91,"Should":38,"So":[4,74,75,77,79,82,86,87],"Some":[74,75,79,82,83,85,86],"Such":2,"THE":91,"THIS":91,"TO":91,"That":[2,14,75],"The":[0,1,3,4,6,7,9,11,12,14,15,16,17,18,20,22,23,24,25,26,29,30,31,33,35,36,38,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,65,67,70,71,73,74,75,76,77,78,79,80,82,83,84,85,86,87,89,90,93,94,95,96,97,98,99],"Then":[9,14,54,60,61,76,77,83,85,86,90,97],"There":[1,2,7,75,76,77,78,79,82,83,85,86,89,98],"These":[1,2,3,4,14,15,33,38,48,54,61,64,73,75,76,77,79,81,83,85,86,97],"They":[47,74],"This":[1,2,3,4,7,11,14,15,18,21,23,24,25,29,33,34,35,36,37,38,40,41,42,44,46,47,48,50,51,52,53,54,55,56,57,59,60,61,62,64,67,70,71,73,74,75,76,77,78,79,80,82,83,84,85,86,87,93,94,95,97],"Those":75,"To":[0,1,2,4,7,11,14,20,47,49,53,73,75,76,78,79,83,84,85,86,89,90,93,97,98],"WE":96,"We":[0,2,4,7,14,16,25,74,75,76,78,79,80,82,83,85,86,89,90],"What":[83,85,86],"When":[2,25,35,47,52,54,60,61,71,74,76,79,86],"Where":[18,54,60,61],"Which":[77,87],"While":[1,9,87],"With":[14,35,74,75,76,77,82],"You":[7,40,48,74,77,78,79,80,82,83,85,86,97],"Your":[4,48,80],"_":[2,22,35],"_0":35,"_1":[2,35],"_2":2,"_3":2,"__cxx11":[22,23,24,25,26],"__future__":[4,6],"__id__":3,"__init__":[4,6,10,11,12,14,15,16,17,18,20,22,23,24,25,26,30,31,33],"__main__":6,"__name__":6,"__path__":4,"_compon":4,"_detector":26,"_do_outlier_reject":15,"_goniomet":4,"_goniometer_factori":4,"_i":[2,35],"_n":2,"_object":[10,12,14,22,23,24,25,26],"_outlier_indic":15,"_processor":12,"_processorrot":12,"_reindex":40,"_rmsds_core":14,"_src_path_root":4,"_\u03ba":2,"_\u03c6":2,"_\u03c9":2,"a1":[18,83,85],"a2":[7,18,97],"a222":78,"a_matrix":54,"aaron":[0,94],"ab":[2,83,85],"abandon":80,"abbey":75,"abc":2,"abil":42,"abl":[40,83,85,86,87,97],"abov":[1,4,9,37,38,40,41,44,47,51,55,59,64,65,70,71,74,75,77,83,85,86,87,91],"abraham":[76,96],"absenc":[18,35,70,73,80,83,85,87],"absent":[18,40,69,73,83,84,85],"absolut":[1,18,20,30,44,54,60,61,73],"absolute_angle_toler":[11,18,40,54,70,73],"absolute_cutoff":[14,54,60,61],"absolute_import":4,"absolute_num_interv":[54,60,61,74,76],"absolute_toler":33,"absorb":64,"absorpt":[1,15,35,55,64,73,83,85,86,87],"absorption_correct":[1,55,64],"absorption_level":[1,64,73,87],"abstract":[0,2,14,15],"ac":[2,90,96],"ac02":[0,89],"aca":100,"acad":96,"acceler":[11,54,94],"accept":[2,7,14,47,50,51,54,73,74,83,85,86],"access":[1,14,21,48,82,86,89],"accessor":14,"accord":[11,14,18,42,46,47,77,78],"account":[1,2,35,47,50,51,54,83,85,86,87],"accumul":[0,12,18],"accur":[14,47,50,51,74,79,87,96,98],"accuraci":[54,60,61],"achiev":[7,14,35,54,57,60,61,82,87],"acknowledg":89,"acronym":44,"across":[0,1,43,54,60,61,64,73,75,76,83,87,97],"act":[47,51,67],"acta":[0,2,11,18,40,70,73,76,80,89,96],"action":[54,60,61],"actual":[2,14,15,74,77,82,85],"ad":96,"ada":95,"adam":[0,2,11,96],"adapt":[14,76,95],"adaptlbfg":[14,19],"adaptlstbx":[14,19],"add":[9,10,12,14,15,20,29,33,44,47,53,54,60,71,74,75,77,82,83,85,86,90,95,97],"add_batch_list":[32,33],"add_column":14,"add_constant_to_diagon":14,"add_cryst":33,"add_dataset":33,"add_empty_dataset":33,"add_experi":33,"add_group":23,"add_panel":23,"add_row":14,"add_standard_column":53,"addit":[0,1,7,14,15,20,26,33,41,43,44,46,47,49,54,55,60,61,64,76,82,83,85,86,87,94,95,97],"additional_stat":64,"address":[0,79,94,98],"addsym":74,"adher":[83,85,86],"adjust":[1,65,74,75,76,83,85,86,87],"adob":72,"adopt":2,"advanc":[0,16,20,81,83,85,86,88,98],"advantag":[83,85,86],"adventur":98,"advic":[0,78],"advis":[1,91,97],"advisori":94,"adxv":[82,85],"ae":96,"af":[10,12,14,23,24,25,26],"affect":[1,42,54,60,61,73,75,76,79,83,85,86,94],"afonin":96,"ag":84,"aggreg":11,"agre":[1,2,77],"agreement":[54,83,85,86,87],"aguila":96,"ah":96,"ahead":[26,75,78,79],"aim":[1,77,87],"aimless":[1,44,76,83,85,86],"aj":96,"ak":75,"al":[11,65,73,80,100],"albula":82,"algorithm":[0,1,2,4,20,31,32,38,40,41,42,47,50,51,54,55,59,60,61,64,72,73,75,79,82,83,84,85,86,89,95,96,97,99],"algoritm":94,"alia":[11,12,15,33,64],"align":[2,11,21,23,25,34,76,77,78,79,87],"align_cryst":72,"all_lau":24,"all_rot":24,"all_same_typ":24,"all_sequ":24,"all_stil":24,"all_tof":24,"aller":96,"alloc":[22,23,24,25,26,55],"allow":[1,3,11,14,16,18,23,24,34,38,44,46,48,52,54,60,61,62,64,74,75,76,77,78,82,83,85,86,87,89,93,94,95,97],"allow_multiple_sequ":[52,93],"allow_non":[35,37,38,40,41,42,43,44,45,46,47,49,50,51,52,54,55,56,57,59,60,61,63,64,65,66,67,68,69,70,71,73],"almost":[54,75,77,78,83,85],"along":[2,11,23,33,34,40,52,54,65,75,76,78,82],"alongisd":64,"alongsid":[1,74,93],"alonso":96,"alpha":[2,25,40,54,60,61,73,87],"alpha_i":35,"alreadi":[1,4,14,16,21,23,25,26,29,54,60,61,64,73,75,77,79,83,85,86,87],"also":[1,2,3,4,7,11,14,15,18,20,21,22,23,25,26,33,37,44,48,50,54,60,61,62,64,67,69,71,73,74,75,76,77,78,79,82,83,84,85,86,87,90,97],"alter":[45,75,77,86],"altern":[1,4,7,11,52,53,54,60,61,62,64,67,78,80,83,97],"although":[1,38,61,74,76,78,79,82,83,85,86,93],"altogeth":18,"altruism":0,"alun":[0,98],"alway":[1,9,47,53,55,78,79,86],"ambigu":[18,40,62,73,77,78,96],"ami":0,"ammaar":0,"amongst":42,"amount":[35,41,51,55,59,64,74],"amplifi":14,"amplitud":[33,64,78,84],"amyloid":96,"analog":2,"analys":[18,37,40,52,54,60,61,73,75,83,85,86,89,94],"analyse_output":82,"analysi":[14,18,37,40,49,54,57,60,61,64,70,73,78,79,81,82,84,86,87,89,94,96,97,98],"analysis_lev0":82,"analysis_lev1":82,"analytical_correct":64,"analyz":[48,94],"anastassi":98,"ancestor":4,"andi":96,"andrew":[0,40,98,99],"andrey":78,"ang":54,"angl":[2,6,11,18,21,23,25,33,39,40,52,54,55,60,61,64,69,70,71,73,74,75,77,83,85,86,87],"angle_toler":22,"angstrom":[1,11,41,47,50,51,54,55,59,73,78,79,82,83,85,86],"angular":[2,11,18,54,60,61,82,83,85],"ani":[3,4,7,11,14,15,18,20,24,33,38,40,44,47,49,52,54,60,61,62,64,67,73,75,77,78,80,82,83,84,85,86,87,89,91,93],"anisotrop":18,"annlib":33,"annlib_adaptbx":33,"annot":6,"annual":94,"anom_amplitud":33,"anom_array":33,"anom_multipl":33,"anomal":[1,18,33,43,64,73,75,77,80,83,85,86,87],"anoth":[1,20,54,62,75,76,79,83,85,97],"ansitowin32":33,"anticip":[35,83,85],"anvil":35,"anvil_correct":72,"anyon":0,"anyway":[83,85,86],"ao":96,"ap":[74,75,78,79,80,83,84,85,100],"apach":72,"apache_install_di":48,"apart":[7,82,83,85,86],"api":[22,24,25,26],"app":80,"appar":[77,82,85,86],"apparatus":[2,4],"appear":[2,18,29,36,45,72,74,75,77,80,83,85,86],"append":[4,11,14,20,24,44],"appendix":18,"appl":[2,11,40,65,80,96],"appli":[0,1,3,4,11,14,15,18,20,21,24,44,46,52,54,55,60,61,62,64,73,74,76,77,79,83,85,86,87],"applic":[0,18,44,55,73,74,83,85,86,90],"apply_change_of_basis_op":[18,19],"apply_hkl_offset":11,"apply_mask":72,"apply_sigma_correct":18,"apply_symmetri":11,"appreci":11,"approach":[1,11,77,96],"appropri":[2,7,11,12,14,15,23,40,43,54,60,61,64,67,75,76,77,80,82,86,87],"approxim":[14,35,37,43,64,73,75,78,82],"apr":[48,96],"aquila":[75,96],"ar":96,"arb":96,"arbitrari":31,"arbitrarili":2,"arc":[51,75],"architectur":96,"archiv":[7,76,79],"are_experiment_identifiers_consist":20,"area":[1,47,75,85,86,98],"aren":40,"arg":[4,11,14,24,33],"arg1":[10,12,14,20,22,23,24,25,26],"arg2":[10,12,20,22,23,24,25,26],"arg3":[10,12,20,23,24,25,26],"arg4":[10,12,20,25,26],"arg5":[10,12,20,25],"arg6":[10,25],"arg7":25,"argpars":33,"argu":2,"argument":[7,14,15,20,26,31,33,50,52,54,65,67,94],"argumenthandlingerrorinfo":[32,33],"argumentpars":[6,32,33],"argumentparserbas":[32,33],"arima":96,"aris":91,"arm":25,"around":[1,18,20,34,47,50,51,54,60,61,75,77,79,86,98],"arrang":[2,82,94],"array":[1,4,11,14,15,18,32,33,42,55,56,64,73,89,96,98],"array_famili":[3,4,11,20],"arrayscalingmodel":15,"art":[75,86],"artefact":82,"articl":75,"as_dict":18,"as_fil":[20,24],"as_hdf5":20,"as_imageset":26,"as_integer_ratio":20,"as_json":[18,24],"as_miller_array":20,"as_msgpack":20,"as_msgpack_fil":20,"as_msgpack_to_fil":20,"as_pickl":20,"as_str":22,"ascii":[3,75,86],"ascrib":11,"ashton":[0,96,98],"asid":79,"ask":[48,77,89],"asmit":0,"aspect":[2,76,94],"assembl":[75,94],"assert":[6,52],"assert_experiment_identifiers_are_consist":20,"assert_is_compatible_unit_cel":22,"assess":[11,48,74,75,77,83,85,86,94,96,97],"assign":[11,22,47,54,73,78,83,85,86,87],"assign_indic":11,"assignindicesglob":11,"assignindicesloc":11,"assignindicesstrategi":11,"assist":[0,73,89],"associ":[4,11,14,15,54,60,61,69,93],"assum":[1,2,7,14,20,21,22,23,25,29,35,37,46,48,65,75,76,80,82,87],"assumpt":[1,23,35,77,79],"assur":54,"asu":[20,37,74],"asymmetr":[44,57,73,78,95],"asymptot":[83,85],"atom":[0,2,64,77],"attach":25,"attempt":[4,24,34,35,53,54,64,77,87,97],"attende":100,"attent":[75,77,86],"attenu":35,"attribut":[14,15,33],"attributes_level":7,"aug":96,"augment":36,"august":100,"aurelius":96,"author":74,"auto":[1,11,18,40,44,45,47,49,51,52,54,55,60,61,63,64,65,70,73,83,85,86],"auto_reduct":[54,60,61],"autoindex":[54,80,83,85,86],"autom":[0,98],"automat":[1,9,11,18,33,40,48,54,60,61,67,73,75,76,80,83,84,85,86,87,96],"automatic_default_fre":80,"automatic_default_scaled_unmerg":80,"autotyp":18,"auxiliari":14,"avail":[0,1,4,9,14,21,26,35,47,55,64,75,76,78,79,80,82,83,84,85,86,87,90,94,95,97],"averag":[1,38,42,47,56,64,65,83,85,86],"average_detector":38,"average_hierarchy_level":38,"avoid":[0,14,33,54,60,61,73,75,82,83,85],"aw":96,"away":[73,76,82],"awkward":75,"ax":14,"axe":[2,25,34,35,52,58,63,75,76,77,79],"axford":[11,96],"axi":[2,4,6,21,22,23,25,33,34,38,52,54,60,61,65,73,74,76,77,78,79,83,84,85,86],"axial":[70,87],"axis_and_angle_as_r3_rotation_matrix":6,"ay":96,"aydin":96,"a\u00b2":[83,85],"b":[1,2,14,15,18,21,22,40,54,60,61,62,64,73,74,75,77,78,79,80,82,83,84,85,86,87,96],"b_cart":[83,85],"b_factor":11,"b_iso":[11,54],"ba":96,"bacaj":96,"back":[1,55,64,74,75,77,82,86],"background":[3,19,20,31,32,41,47,51,55,75,79,83,84,85,86,96],"background_algorithm":20,"background_cutoff":65,"background_gradi":47,"background_includes_bad_pixel":20,"background_s":[16,47],"backgroundgradientfilt":[16,19],"backstop":[50,82],"bacteri":96,"bad":[14,55,75,79,80,82,83,85,86,93],"bad_for_refin":20,"bad_for_sc":20,"bad_pixel_threshold":65,"bad_refer":[20,55],"bad_shoebox":20,"bad_spot":20,"balanc":48,"band":[54,75],"bandwidth":54,"bank":75,"bar":[33,65],"barad":96,"barn":96,"base":[0,1,4,9,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,28,29,30,31,33,38,43,46,47,54,60,61,64,65,71,73,80,83,85,86,87,96,98],"base_package_opt":33,"bash":[7,75,76,77],"basi":[2,11,18,24,39,54,61,62,74,75,77,78,83,84,85,87],"basic":[1,2,7,14,77,83,85,86],"basic_imageset_from_dict":[27,30],"basic_imageset_to_dict":[27,30],"basic_str":[22,23,24,25,26],"basis_vector":11,"basis_vector_combin":54,"basis_vector_search":[4,19],"basis_vector_search_strategi":4,"basisvectorminimis":11,"basisvectorsearch":11,"basisvectortarget":11,"batch":[1,33,44,52,64,73,74,77,80,87,97],"batch_offset":[29,33,52],"batch_rang":43,"batch_siz":97,"batenburg":98,"batteri":0,"batyuk":96,"baxter":96,"bbox":[3,12],"bc":2,"beal":96,"beam":[0,1,2,3,4,6,11,20,22,23,24,26,27,32,33,34,35,37,38,41,47,51,52,54,55,58,59,60,61,65,69,75,76,77,78,82,83,85,86,93,95,96,98],"beam_centr":23,"beam_posit":65,"beam_position_method":65,"beam_prob":52,"beam_restraint":54,"beam_typ":52,"beambas":[10,24,26],"beamcomparison":[24,27],"beamfactori":[21,27],"beamlin":[2,4,35,44,48,79,82,83,84,85,86,89,94,96,98],"beamstop":74,"bean":96,"beaten":98,"becaus":[2,11,42,74,75,79,82,83,85,86],"becker":96,"becom":[1,2,14,64,77,79],"bedem":96,"befor":[2,7,20,23,35,37,38,41,54,55,60,61,64,69,74,75,76,77,78,82,83,84,85,86,87,90],"beforehand":75,"begin":[1,2,20,54,74,83,85,86],"behav":[42,83,85],"behavior":[],"behaviour":[54,60,61,75],"behen":51,"beilsten":[0,96],"belong":[37,52,78],"benefici":[74,86],"benefit":[0,89,98],"benjamin":0,"benschoten":96,"bergmann":96,"berkeley":[0,89,91,94,100],"bernstein":[2,40,94,96],"best":[1,2,4,11,18,40,44,45,54,60,61,64,71,73,74,75,77,82,83,84,85,86,96],"best_model":11,"best_monoclinic_beta":[11,18,40,61,70,73,75,83],"best_subgroup":18,"best_unit_cel":[33,44,64],"beta":[2,18,40,61,70,73,83,85,86,87],"betalactamase_sum":85,"better":[0,48,65,74,75,77,83,85,86,93],"bewar":82,"beyond":[74,83,85,86,95],"bfgs":[14,18],"bh":96,"bhowmick":[0,96],"bi":[83,85],"bias":[54,60,61,73],"bib":80,"bibliograph":2,"bibtex":80,"bideshi":96,"big":[20,75,83,85,86],"billi":0,"bin":[1,15,20,37,38,43,45,47,48,51,54,55,61,64,65,73,74,75,80,82,83,84,85,86],"bin_size_fract":[54,60,61,82],"bin_step":65,"bin_width":65,"binab":96,"binari":[20,91],"bind":96,"binning_method":[43,73],"biol":[76,89,96],"biolog":[0,89,96,98,99],"biomed":89,"biosci":[74,96],"biostruct":[96,98],"biotin":81,"biotin16":74,"biotin_p212121":74,"biotin_p222":74,"biran":96,"bit":[3,20,24,75,77],"bit_count":20,"bit_length":20,"bitmap":45,"bk":96,"bl":96,"bl32xu_group2_data":77,"blah_":93,"blame":77,"blank":76,"blaschk":96,"blind":77,"block":[14,24,40,54,55,60,61,64,67,77,82,83,85,86,93],"block_centr":14,"block_siz":[12,67,83,85],"block_size_unit":12,"block_width":[54,60,61,74,76],"blockcalcul":[14,19],"blockwis":1,"blue":[45,75,83,85,86],"blur":[47,51],"bm":96,"bn":[74,96],"bodi":[54,60,61,94],"bogacz":96,"bogan":96,"bold":73,"bolotovski":[0,11,96],"bool":[4,10,11,12,14,15,16,18,20,21,22,23,24,25,26,37,38,40,41,43,44,45,46,47,50,51,52,53,54,55,56,58,59,60,61,63,64,65,66,68,69,70,71,73],"boolean":[15,20,31,46],"boost":[0,22,23,24,25,26,35,74],"boost_python":12,"bootstrap":9,"bootstrap_cryst":54,"border":[20,47,50,51,54],"boston":100,"botha":96,"bottom":[74,75,79,86,97],"bouldin":[],"bound":[3,11,12,18,20,47,50,51,54,55,67],"boundari":[73,83,85],"bourenkov":0,"bourn":7,"boutet":96,"box":[3,12,20,47,54,74,75,86],"bq":[74,96],"bracket":40,"bragg":79,"branch":86,"bravai":[40,61,75,79,84],"bravais_setting_":61,"bravais_setting_1":[61,83,85],"bravais_setting_2":[75,83,85],"bravais_setting_3":85,"bravais_setting_4":85,"bravais_setting_5":[76,78,84,85],"bravais_setting_n":[83,85],"bravais_summari":[83,85],"bravais_t":11,"breadth":23,"break":[75,93],"brehmer":96,"brewster":[0,89,94,96],"bricogn":[0,11,98],"bright":[45,51,74,83,85],"brilliant":98,"bring":[74,77,94],"brookhaven":2,"brookner":96,"brotat":73,"brought":98,"browser":[72,74,77,83,85],"bruhn":[74,96],"brunger":96,"br\u00e4uer":96,"buffer":[20,59,73],"buffer_s":59,"bug":89,"buijss":96,"build":[0,9,14,80,94],"build_dial":33,"build_up":14,"built":[4,20,94],"bullet":98,"buse":2,"busi":91,"butryn":96,"button":[79,83,85,86],"bypass":56,"byte":20,"bytearray":20,"byteord":20,"bz2":[44,79,84],"c":[0,1,2,7,10,12,14,22,23,24,25,26,35,40,54,61,62,65,67,74,75,77,78,79,83,84,85,86,87,91,94,96],"c2":[18,40,61,70,73,75,83,85],"c222":85,"c2221":85,"c2sum_1":[85,86],"c2sum_1_":85,"c3h7no2":44,"c_grid":10,"ca":[96,100],"calc_2d_rmsd_and_displac":11,"calc_acentric_subgroup":11,"calc_exp_rmsd_t":14,"calc_n_param_from_bin":15,"calcul":[0,1,2,6,11,12,14,15,18,20,34,35,37,39,40,41,43,47,51,54,55,59,60,61,62,64,65,69,73,75,77,79,83,84,85,86,87,96],"calculate_entering_flag":20,"calculate_esd":14,"calculate_gradi":14,"calculate_new_offset":15,"calculate_weight":14,"calculate_weighted_mean":33,"calero":96,"calibr":[51,67,74,75,76,82],"calibrate_pdb":51,"calibrate_silv":51,"calibrate_unit_cel":51,"call":[2,14,16,20,35,40,47,48,54,55,73,75,77,83,85,86,97],"callback":14,"callback_after_step":[14,18,83,85],"cambridg":[33,100],"came":75,"camera":74,"camp":0,"campaign":83,"campbel":11,"can":[1,2,3,4,7,9,11,14,16,21,23,24,33,35,37,38,40,42,44,45,47,48,50,51,52,53,54,55,56,60,61,62,64,65,69,70,73,74,75,76,77,78,79,80,82,83,84,85,86,87,90,93,94,97,98],"candid":[4,11,54,83,85,86],"candidate_basis_vector":4,"candidate_crystal_model":4,"candidate_orientation_matric":11,"candidate_outlier_reject":54,"candidate_spot":54,"canon":25,"capabl":[48,75,89],"caption":35,"captur":[83,85,86],"carbajo":96,"carbon":[0,35],"care":[20,53,74,75,77,82,83,85,86],"careless":79,"carragh":[74,96],"carri":[40,83,85,86],"cartesian":[2,11],"cascio":96,"case":[1,2,4,7,11,14,15,20,21,23,25,35,40,44,47,52,53,54,55,60,61,62,64,74,75,76,77,78,79,82,83,84,85,86,87,93,94,97,98],"cat":76,"catalyst":96,"cauchi":18,"caus":[14,15,75,78,79,83,85,86,91,93,97],"caution":14,"cautionari":79,"cb_op":[11,18,61,74,75,78,79,83,84,85],"cb_op_inp_min":18,"cbf":[3,4,21,23,25,33,45,47,48,49,51,52,56,66,76,80,82,83,84,85,87,93,94,97],"cbf_handl":[21,23,25,29],"cbf_handle_struct":21,"cbflib":33,"cc":[18,40,43,73,74,75,78,79,80,82,83,84,85,86,87],"cc1":[1,18,74,83,84,85],"cc_against":18,"cc_ano":[74,83,84,85],"cc_for":18,"cc_half":[43,73,80],"cc_half_fit":[43,73],"cc_half_method":[43,73],"cc_half_significance_level":[43,73],"cc_n_bin":61,"cc_pearson":[75,83,84,85],"cc_ref":[43,73],"cc_sig_fac":18,"cc_spearman":[75,83,84,85],"cc_true":18,"cc_weight":[18,40,73],"ccd":[23,42,79],"ccdc":74,"ccds":[83,85,86],"cchalf":[64,73],"cci":48,"ccp4":[0,73,74,76,77,78,80,85,86,89,96,98,99,100],"ccp4_scr":80,"ccp4i2":86,"ccref":[43,73],"ccs":79,"cctbx":[0,1,2,4,9,11,14,18,20,22,24,48,80,94,96],"cctbx_bundl":33,"cctbx_project":48,"cctbx_sgtbx_ext":22,"cc\u00bd":[18,40,43,73,74,77,83,85],"cd":[7,33,48,74,75,77,80,82,90,96],"cdot":[2,35],"ce2":[1,97],"ceas":77,"cell":[2,11,14,18,22,33,35,40,41,44,45,46,47,50,51,54,55,58,59,60,61,64,65,70,71,73,74,75,76,78,79,80,82,83,84,85,86,96,97],"cent":96,"center":[18,40,61,65,70,73,78,83,85],"cento":48,"centr":[14,18,20,23,37,41,47,51,52,54,55,58,59,60,61,65,73,75,76,77,81,83,85,86,95,98],"central":[78,80,82],"centre_xi":76,"centroid":[3,4,11,20,31,41,44,47,50,51,53,54,55,59,60,61,67,71,79,82,83,84,85,86],"centroid_":3,"centroid_algorithm":20,"centroid_definit":[41,51,55,59],"centroid_diff_i":[63,82],"centroid_diff_max":63,"centroid_diff_x":[63,82],"centroid_outli":20,"centroid_px_to_mm":20,"centroidanalysi":14,"certain":[11,35,38,54,55,60,61,64,73,74,87],"ceta":74,"cgi":48,"ch":[44,75],"chain":[4,78],"challeng":[74,75,78,79,86,96,98],"chanc":[77,83,85,86,97],"chang":[1,2,9,18,24,33,39,41,51,54,55,59,61,62,64,67,73,74,75,76,77,78,82,83,84,85,86,94,96,97,98],"change_basi":24,"change_of_basis_op":[11,18,24,62,70,75,78,83,85],"change_of_basis_op_to_best_cel":[18,19],"change_of_basis_ops_to_minimum_cel":[18,19],"channel":96,"chapui":2,"char":[22,23,24,25,26],"char_trait":[22,23,24,25,26],"charact":[12,51,52],"characteris":82,"characterist":96,"characteristic_grid":[11,54],"charg":94,"chatterje":96,"cheah":96,"cheat":75,"check":[1,4,7,9,16,18,20,24,26,33,37,38,54,64,70,75,77,80,82,83,85,93],"check_consistent_index":64,"check_doubled_cel":[11,54],"check_flag":16,"check_format":[6,24,26,30,33],"check_head":26,"check_indexing_symmetri":[72,79],"check_misindex":54,"check_reference_geometri":52,"checkbox":[75,86],"checkpoint":[54,60,61],"chem":96,"chemic":[44,73,96],"chen":96,"cheng":[74,96],"chernev":96,"chess":100,"chi":[54,60,61],"chiang":[74,96],"chiral":[74,75,83,85,87,96],"chmod":75,"chnos":[74,87],"choi":96,"choic":[1,2,15,18,20,34,38,39,40,41,43,44,45,47,51,52,54,55,58,59,60,61,63,64,69,70,73,74,77,78,83,85,86,87],"choleski":14,"chollet":96,"choos":[2,18,38,44,54,60,61,64,73,74,75,78,82,83,85,86,88],"choose_best_orientation_matrix":11,"chose":[76,82,86],"chosen":[1,2,4,11,14,15,18,20,35,38,43,54,58,60,61,63,64,75,77,78,83,84,85,86],"christian":0,"chunksiz":[47,83,85],"cif":[2,40,44,62,64,71,73,77],"cif_fil":[21,23,25,29],"cif_pet":44,"circ":2,"circl":[2,47,50,51,74,77,83,85],"circular_grid":[41,51,55,59],"circumst":[29,54,60,61,93],"circumv":79,"citat":80,"cite":[73,100],"cj":96,"clabber":[75,76,96],"claim":[4,75],"clarif":7,"clark":[0,89,96],"clash":33,"class":[2,6,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,28,29,30,31,33,41,45,47,50,51,52,55,56,59,74,75,76,83,84,85],"classifi":[15,47],"classmethod":[4,14,15,20,22,31,33],"clean":[54,75,82],"clean_experiment_identifiers_map":20,"cleanup":33,"clear":[2,20,24,40,75,78,79,82,83,85,86,87,93,98],"clear_cach":26,"clemen":0,"clibd":80,"click":[72,74,75,78,79,80,81,82,84,85,86,87,90],"client":72,"client_serv":48,"clock":96,"close":[1,14,24,47,54,60,61,67,74,75,76,78,82,83,85,86],"close_to_spindle_cutoff":[14,54,60,61,82],"closer":[48,75,82],"closest":[48,53,83],"cloud":86,"cls":4,"clumsi":29,"cluster":[16,18,38,40,47,48,55,73,83,85,94,96,97],"cluster_1":[40,97],"cluster_2":97,"cluster_20":77,"cluster_analysi":54,"cluster_html":73,"cluster_id":[40,97],"cm":96,"co":96,"coars":[54,65],"code":[0,2,4,6,9,51,75,91,94,96,97],"codebas":94,"coeffici":[18,35,37,40,61,73,79,82,83,85,86],"cohen":96,"coincid":[2,25],"col":[6,20],"col_select":[14,60,71],"colin":85,"collabor":[0,89,98,99],"collabra":18,"collat":35,"collect":[0,11,15,49,67,75,77,78,79,82,83,84,85,86,87,89,94,96,97,98],"colleti":96,"collinear":11,"color_cutoff":65,"color_schem":51,"colorama":33,"colorbar":65,"colour":[32,33,45,63,69,83,85,86],"colour_map":69,"colour_schem":45,"colspot":30,"column":[1,3,6,14,20,33,53,54,55,60,61,64,71,78,79,84],"com":[9,41,48,51,55,59,74,76,80],"comb":38,"combin":[1,2,11,15,18,20,24,38,40,44,46,47,50,51,54,55,60,61,64,71,73,74,75,76,77,79,82,83,84,85,87,93],"combine0":77,"combine_crystal_model":[71,73],"combine_experi":[72,82,93],"combine_parti":[33,44],"combine_scan":54,"combined_scor":11,"come":[20,77],"comfort":86,"comma":65,"command":[1,4,7,9,32,33,48,52,64,72,74,75,76,77,80,81,82,83,84,85,86,87,90,94,97],"command_lin":[18,33],"committe":100,"common":[2,14,18,29,40,64,70,73,74,75,77,78,79,83,85,86,88],"commun":[75,96],"communic":2,"comp":[74,83,84,85],"compact":[2,11,18,24,44,52,82],"companion":[83,85,86],"compar":[15,37,38,44,64,73,74,75,76,77,78,79,82,83,85,86,97],"compare_beam":[24,33],"compare_detector":[24,33],"compare_goniomet":[24,33],"compare_model":38,"compare_orientation_matric":[11,72],"comparison":[2,11,20,24,37,38,39,53,54,64,82],"compat":[20,38,75,79],"compens":[76,85],"compil":[9,48,90],"complement":20,"complet":[0,7,14,21,43,48,54,57,60,61,64,73,74,75,77,78,79,80,82,83,84,85,86,87,93,94,98],"complete_set":26,"complex":[4,7,20,21,23,38,83,86],"compli":44,"compliant":76,"compon":[0,1,2,4,15,25,40,47,57,64,77,83,85,86],"compos":[4,14,15,25,54,60,61,87],"compose_model_p":[54,60,61],"composit":[2,38,44,73,87],"compound":0,"comprehens":98,"compress":[7,44,45,79],"compress_level":45,"compromis":1,"comput":[1,2,11,18,20,31,39,41,44,47,51,55,59,65,68,73,77,80,83,86,94,95,96,97,98],"compute_background":[20,31],"compute_bbox":20,"compute_centroid":[20,31],"compute_correct":20,"compute_d":20,"compute_d_singl":20,"compute_delta_cchalf":77,"compute_fitted_intens":20,"compute_funct":[11,18],"compute_functional_and_gradi":[11,14,18],"compute_functional_gradients_and_curvatur":[14,18],"compute_functional_gradients_diag":[14,18],"compute_functional_score_for_dimension_assess":18,"compute_gradi":18,"compute_gradients_fd":18,"compute_mask":20,"compute_mean_background":[16,47],"compute_miller_indices_in_asu":20,"compute_parti":20,"compute_phi_rang":20,"compute_ray_intersect":20,"compute_residu":14,"compute_residuals_and_gradi":14,"compute_restraints_functional_gradients_and_curvatur":14,"compute_restraints_residuals_and_gradi":14,"compute_summed_intens":20,"compute_threshold":31,"compute_zeta":20,"compute_zeta_multi":20,"concat":20,"concaten":[14,20],"concentr":[54,60,61],"concern":[2,79],"conclud":[40,78,82,83,84,85,86],"concomit":98,"concret":14,"concurr":[14,64],"cond":14,"conda3":90,"conda_bas":9,"condit":[14,54,60,61,70,75,91],"conduct":[94,96],"conf":48,"confid":[18,37,40,74,75,77,83,84,85,86],"config":47,"config_opt":33,"config_refineri":14,"config_restraint":14,"config_spars":14,"config_target":14,"configdict":[4,15],"configur":[4,9,14,15,20,21,23,33,48,54,60,61,64,71,80,82,83,85,87],"configuration_paramet":4,"configure_compon":[4,15],"configure_filt":16,"configure_modul":33,"configure_threshold":16,"conform":96,"confus":2,"conjug":20,"conjunct":[47,55],"connect":[47,57,63],"connected":[1,64,73],"consecut":[4,15,52,56,64],"consecutive_refinement_ord":[4,15],"consequenti":91,"conserv":11,"consid":[37,41,47,50,51,54,55,59,65,73,75,77,78,83,85,87],"consider":[47,78,83,85,86],"consist":[1,2,11,14,18,20,40,54,61,62,64,73,75,77,78,79,83,84,85,86,87,98],"consolid":24,"consolidate_histori":24,"const_ref":[10,12,23,25,26],"constant":[2,14,20,54,55,60,61,76,87],"constant2d":55,"constant3d":55,"constantweightingstrategi":[14,19],"constrain":[1,11,54,60,61,64,83,85,86],"constraint":[1,11,14,54,60,61,71,75,83,84,85,86,87],"constraints_manag":14,"construct":[4,11,14,16,20,21,23,25,29,30,54,75,76],"constructor":[21,33],"consult":54,"consum":74,"contact":80,"contain":[1,3,4,9,11,14,15,16,18,20,24,34,38,40,44,46,47,52,53,54,55,60,61,62,63,64,71,73,74,75,76,77,79,82,83,84,85,86,97,99],"contains_invalid_pixel":20,"content":[30,33,44,74,75,83,84,85,86],"context":[2,95],"contigu":[47,93],"continu":[0,54,60,61,74,75,78,79,83,84,85,86,93,94],"contract":[0,89,91],"contradict":35,"contrari":78,"contrast":[75,86],"contribut":[0,18,54,60,61,77],"contributor":[0,91],"control":[0,14,38,40,43,44,54,55,60,61,70,71,75,86,88,96,98],"conveni":[1,2,40,47,55,64,70,73],"convent":[8,22,52,54,62,65,67,78,83,87],"converg":[14,41,51,55,59,64,82],"convergence_as_shift_over_esd":14,"convers":96,"convert":[2,12,14,16,18,20,21,22,23,24,25,26,28,29,30,52,54,71,74,87],"convert_reflections_z_to_deg":11,"convert_sequences_to_stil":52,"convert_stills_to_sequ":[52,97],"convert_to_cambridg":[32,33],"convinc":79,"convolut":[47,51,65],"convolution_width":65,"cooper":11,"coord":18,"coordin":[18,20,22,23,25,47,50,51,52,54,60,61,73],"cope":[6,98],"copi":[0,4,14,20,24,26,50,75,76,78,82,93],"copyright":91,"coquell":96,"core":[0,82,87,96,97],"core_paramet":11,"corner":[47,50,51,82,83,85,86],"correct":[1,2,3,4,7,15,18,20,23,30,35,37,40,44,47,50,51,52,55,64,66,73,75,76,77,78,81,83,85,86,87,97],"corrected_integr":82,"corrected_refin":82,"corrected_sv_refin":82,"correl":[3,14,18,37,40,54,60,61,62,71,73,75,77,79,80,82,83,85,86,87],"correlation_plot":[60,71],"correlationcoefficientaccumul":[18,19],"correspond":[4,6,11,14,33,36,54,55,74,75,78,79,83,85,86],"corrplot":71,"cos":[2,35,73,77],"cos_angl":73,"cosin":44,"cost":85,"cosym":[19,32,64,72,73,74,77,97],"cosymanalysi":[18,19],"count":[18,20,40,67,73,75,77,79,83,84,85,86,98],"counting_sort":[43,73],"coupl":1,"cours":[2,83,86,87],"cov":81,"covari":[54,60,61,86],"cover":[1,20,47,55,77,83,85,86],"coverag":[1,82],"cpu":[82,98],"cpv17":96,"crawshaw":96,"creat":[1,4,7,9,14,15,16,20,22,23,24,26,28,38,48,50,53,54,55,60,61,64,71,75,76,77,83,85,86,87,97],"create_profile_model":[55,72],"cred":[40,47,55,64,67,70,73],"criteria":[14,43,46,77,83,85],"criterion":[14,54,60,61,64,83,85,86],"critic":[77,82,94,96,98],"croll":75,"cross":[20,64,75,76,83,85],"cross_valid":64,"cross_validation_mod":64,"crossov":[1,82],"crucial":36,"cryo":96,"cryst":[0,11,18,40,65,70,73,78,80],"crystal":[0,1,2,3,4,6,11,15,18,24,27,30,32,33,34,38,40,44,47,48,52,53,54,55,58,60,61,63,64,66,67,69,70,71,73,74,75,76,78,79,80,81,82,83,84,85,86,87,93,94,96,97],"crystal_a":11,"crystal_b":11,"crystal_fram":20,"crystal_id":[61,84],"crystal_model":[11,22],"crystal_nam":[33,44,64],"crystalbas":[22,24],"crystalfactori":[22,27],"crystallin":96,"crystallogr":[2,76,89,96],"crystallograph":[0,1,2,71,73,77,78,83,94,96],"crystallographi":[0,1,2,11,74,75,89,95,97,98,100],"crystfel":98,"cs":[74,82,96],"cs03r":80,"csh":[7,48],"ctruncat":[78,85],"cubic":35,"cuda":[11,54],"culprit":79,"cumbersom":77,"curl":[9,48,76,90],"current":[2,4,7,14,18,24,33,44,54,56,60,61,64,70,76,78,79,82,83,85,86,90,93,94,95,97,98],"current_image_0":15,"cursor":86,"curtail":11,"curv":[18,43,54,75,79,82],"curvatur":[14,18,40,73],"curvatures_fd":18,"cusp":34,"custom":[4,64,73],"cut":[1,44,54,60,61,64,75,98],"cut_data":64,"cutoff":[1,11,18,38,40,43,44,54,55,60,61,64,73,74,77,83,85,86],"cutoff_criterion":54,"cyan":86,"cycl":[15,41,51,54,55,59,60,64,65,73,79,82,83,85,86],"cyst_0":87,"d":[0,1,2,4,11,18,22,23,25,29,30,31,40,44,46,47,50,51,54,59,64,74,75,76,79,80,82,83,85,89,96,98],"d62":[18,70],"d66":0,"d67":[18,70,80],"d70":11,"d74":[18,40,80],"d78":73,"d_":82,"d_ep":73,"d_max":[37,41,46,47,50,51,55,57,64,73,74,75,76,83,84,85,86],"d_min":[1,11,18,33,37,38,40,41,44,46,47,48,49,50,51,54,55,57,59,64,65,70,73,74,75,76,77,83,84,85,86,87],"d_min_fin":54,"d_min_method_1":49,"d_min_method_2":49,"d_min_start":54,"d_min_step":[54,83,85],"d_rang":[1,64,73],"d_space":[45,46,47,50,51],"d_star_toler":54,"da":96,"dallakyan":[74,96],"dalton":[0,96],"damag":[1,73,74,75,79,82,83,85,86,91],"damerel":96,"damping_valu":14,"daniel":[0,94],"dano":33,"daresburi":0,"darmanin":75,"dasgupta":96,"data":[0,4,5,7,8,11,12,14,15,16,18,20,24,26,33,35,40,41,43,44,47,48,49,52,53,54,55,56,60,61,62,63,64,67,70,71,73,78,79,80,81,82,84,88,89,91,93,94,95,96,98,99,100],"data_par":76,"datablock":[24,76],"datafil":[1,80,83,84,85],"datafram":20,"dataset":[15,18,20,33,40,44,47,54,55,60,61,62,64,70,73,75,77,78,79,82,83,84,85,86,88,94,98],"dataset_id":33,"dataset_select":64,"datastructur":[15,97],"datatyp":14,"date":[14,82],"datum":[2,35],"dave":[82,98],"davi":[],"david":[0,94,98,99],"day":99,"dbscan":54,"dc":96,"de":[0,89,96],"dead":[46,82],"dead_pixel_range_i":65,"dead_pixel_range_x":65,"dead_tim":46,"deal":[2,76,82,86],"dealt":79,"debug":[14,44,54,55,58,60,82,83,85,86],"debug_centroid_analysi":[54,60,61],"dec":96,"decad":0,"decay":[1,15,64,74,83,85,87],"decay_correct":[1,64,86],"decay_interv":[1,64],"decay_restraint":[1,64],"decay_term":1,"decid":[4,77],"decim":[44,54,60,61],"decis":2,"declar":76,"decod":24,"decompos":[2,58,63],"decomposit":[58,63],"decompress":14,"deconvolut":[41,51,55,59],"decreas":[73,74,75,82,83,84,85,86],"dectri":[48,82],"deem":44,"deep":82,"def":[4,6],"default":[1,7,11,14,15,18,20,24,31,33,34,35,43,44,45,48,52,53,54,56,60,61,62,64,65,67,69,71,73,75,76,79,80,82,83,84,85,86,87,94,97],"defin":[2,14,15,18,43,46,47,50,51,54,55,64,73,74,75,76,87],"define_entry_point":4,"definit":[2,14,15,21,33,75,76,79],"defpix":30,"deg":[6,14,21,22,23,25,29,40,82,83,84,85,86,97],"degeneraci":75,"degrado":96,"degre":[1,2,11,15,18,20,23,25,35,40,41,51,54,55,59,60,61,64,67,69,73,75,78,82,83,84,85,86,87],"del_last_row":14,"del_select":20,"deleg":[4,14],"delet":[14,38,55],"delete_integration_shoebox":64,"delete_shoebox":[38,55],"deliv":89,"deliver":[94,96],"delpsi":14,"delpsi_const":[14,54,60,61],"delpsic":14,"delpsidstar":[54,60,61],"delta":[11,14,18,40,41,51,54,55,59,60,61,64,73,74,79,83,84,85,86,97],"delta_cc_half":77,"deltacchalf":[64,73,75],"deltapsi":[14,54,60,61],"deltatt_transvers":[54,60,61],"demand":86,"demonstr":[6,77,78,86,98],"den":96,"dendrogram":[38,40,73],"denomin":[18,20],"dens":14,"densiti":[11,18,35,54,73,78],"depart":[0,89,95],"depend":[1,2,14,18,35,40,44,48,60,63,64,73,77,82,83,85,86,87,94,96,97],"depont":96,"deposit":74,"deprec":[54,64],"depth":[1,4,23],"derefer":26,"derek":0,"deriv":[2,4,6,14,22,86,87,91],"describ":[2,3,7,18,48,54,60,61,75,76,78,83,84,85,86,87,96,97],"descript":[2,3,4,7,21,23,47,54,64,75,83,85,86,97],"descriptor":[],"design":[0,2,11,23,25,54,95,96,98],"desir":[2,9,41,64,73,83,84,85,87],"desktop":82,"despit":[75,79,82,85,86],"dest_dir_prefix":33,"detail":[0,1,3,4,7,14,48,64,65,72,73,75,77,78,79,81,82,83,84,87],"detect":[14,54,60,61,74,79,83,85,87,98],"detector":[0,1,2,3,4,6,10,11,14,20,21,24,26,27,30,32,38,41,42,45,46,47,48,50,51,52,54,55,56,59,60,61,64,74,76,77,79,81,83,85,86,87,89,93,96,98],"detector1":[54,60,61],"detector_gain":55,"detector_spac":[41,51,55,59],"detectorbas":26,"detectorcomparison":[24,27],"detectorfactori":[23,27],"detectornod":23,"determin":[1,2,3,4,11,14,15,18,20,22,38,40,44,47,51,52,54,55,58,60,61,62,63,64,70,73,76,77,79,83,85,86,96],"determine_auto_absorption_param":15,"determine_esq_outlier_index_array":15,"determine_outlier_index_array":15,"determine_reindex_operator_against_refer":[18,19],"detract":77,"dev":[40,54,60,61,76,80,83,84,85,90],"dev20150903":90,"dev20191028":80,"dev20251129":[],"dev20251206":[],"dev20251219":[],"dev20251221":[],"dev20260116":[],"dev20260120":[],"develop":[2,4,7,8,47,89,94,95,96,98,99],"devenish":[0,96],"deviat":[15,35,40,47,54,55,61,64,71,73,75,78,80,82,83,84,85,93],"df":[75,77,83,85,86,87],"dg":[74,76,89,96],"dh":79,"di":[75,77,83,85,86,87,96],"diagnost":[78,79],"diagon":[14,18,78],"dial":[2,3,5,6,8,19,20,31,32,33,72,73,74,75,76,78,79,81,83,84,85,86,87,93,100],"dials_array_family_flex_ext":[10,12,20],"dials_data":83,"dials_dyn":44,"dials_env":[7,90],"dials_scale_user_guid":[83,85],"dials_scratch":[54,60,61],"dials_tutori":80,"dials_util_ext":20,"dialsindexerror":[11,19],"dialsindexrefineerror":[11,19],"diamet":74,"diamond":[0,35,81,82,83,84,85,86,89,90,91,99,100],"diamond_build":90,"diao":96,"dict":[14,15,18,20,21,23,24,25,26,33],"dictat":14,"dictionari":[4,15,18,21,22,23,24,25,28,29,30,44],"didn":[83,85,86],"diederich":[40,98],"diff":33,"diff_phil":33,"differ":[1,2,4,6,14,18,33,38,39,40,42,50,54,55,64,70,73,75,76,77,78,82,83,85,86,87,94,96,97,98],"difference_rotation_matrix_axis_angl":11,"differenti":[75,83,85,86],"difficult":[11,54,75,79,82,86],"difficulti":[74,78,79],"diffract":[0,2,3,11,21,35,37,40,42,44,45,47,51,54,55,60,64,65,67,70,73,74,75,76,78,79,82,83,85,86,94,96,97,98,99,100],"diffus":[95,96],"difior":96,"digit":52,"dim":[14,18],"dimens":[11,14,18,23,40,54,60,61,64,73,75,77,83,85,86],"dimension":[18,54,83,85,96],"dimensionless":11,"dimer":78,"dimitrio":0,"direct":[0,2,3,4,11,20,21,23,25,34,38,44,48,52,53,54,60,61,65,70,74,75,77,78,79,80,82,83,85,86,89,91,94,97],"direction_toler":24,"director":94,"directori":[4,7,9,24,29,30,44,45,52,53,58,61,74,75,76,77,80,83,87,90,93],"disabl":[1,14,38,47,50,51,54],"disable_parallax_correct":[47,50,51],"disable_unit_cell_volume_sanity_check":54,"disablempmixin":[14,19],"discard":[54,64,65],"disclaim":91,"disconnect":2,"discov":[4,82],"discret":[54,60,61,64],"discuss":[0,77,83,84,85,86,94,98],"diseas":0,"disk":48,"disord":78,"dispatch":9,"dispers":[31,45,47,51,76],"dispersion_extend":47,"dispersion_spotfinder_threshold_ext":31,"dispersionspotfinderthresholdext":[31,32],"displac":[2,11],"display":[7,38,40,45,48,51,73,76,78,83,85,86],"dispos":[77,79],"disproportion":[83,85,86],"disregard":1,"dist":[48,76],"dist1":54,"dist3":54,"dist_path":4,"distanc":[2,11,16,20,23,40,47,51,52,54,55,60,61,65,73,74,76,82,83,84,85],"distinct":[2,73,77],"distinct_clust":73,"distl":[49,72],"distort":[76,79,83,85,86],"distribut":[4,18,54,60,61,66,76,77,83,85,86,91,97],"dive":75,"diverg":[3,21,41,51,52,55,59,75,83,84,85,86],"divid":[20,54,60,61,64],"divis":4,"divisori":3,"dj":96,"djb":75,"dk":[79,96],"dl":79,"dls":[33,80,83,85],"dls_sw":80,"dmax":[17,20,75,83,84,85],"dmin":[17,20,75,83,84,85],"do_spars":14,"do_stil":14,"doak":96,"dobbek":96,"docker":96,"docstr":64,"document":[1,55,64,80,91],"doe":[2,7,14,17,36,44,51,52,54,56,63,74,75,82,83,85,86],"doesn":26,"doi":[11,18,47,54,60,61,76,83],"dolomanov":0,"domain":[54,75],"domain_size_ang":22,"domain_size_toler":22,"domin":[83,85,86],"don":[1,33,35,38,72,82],"done":[3,14,15,44,46,47,54,55,58,60,61,63,69,74,75,76,77,78,79,82,83,85,86,87,93],"dont_integr":20,"dose":[64,73,82],"dose_decay":[15,64,73],"dosedecay":15,"dosedecayscalingmodel":15,"dot":[77,83,85],"doubl":[4,10,14,20,22,23,25,26,82,90],"doubt":74,"douthit":96,"download":[7,48,72,74,75,76,79,83,84,85,86,90],"downstream":[44,64,73,75,76,77,83,84,85,86,87],"doyl":96,"dozen":77,"dp":96,"dpf3":81,"dpf3_247398":79,"dps":[79,86],"dr":[0,54,60,61,96],"draw":74,"drevon":0,"driessen":[54,60,61],"drift":[75,76],"driven":86,"drmaa":[47,55],"drop":86,"drug":0,"ds":96,"duck":20,"due":[1,14,15,64,73,74,83,85,86,87],"dui":81,"dummi":76,"dumoux":96,"dump":[24,32,33],"dure":[1,2,4,14,15,40,41,48,49,50,51,54,55,59,60,61,64,73,74,75,76,77,78,83,84,85,86,96,97],"dw":96,"dx":[26,52,54,60,61,76],"dxtbx":[3,4,10,11,14,20,32,50,74,76,82,83,84,85,96],"dxtbx_ed_format":[74,76],"dxtbx_format_image_ext":[23,26],"dxtbx_imageset_ext":26,"dxtbx_masking_ext":26,"dxtbx_model_ext":[10,20,21,25,26],"dxtbx_name":30,"dy":[26,52,54,60,61,76],"dyn":[48,96],"dynam":[44,45,51,52,55,59,96],"dynamic_shadow":[45,51,52],"dzikowski":96,"e":[1,2,3,4,6,7,11,14,15,18,20,25,35,40,43,47,49,52,54,55,60,61,62,64,65,67,70,73,74,75,77,78,83,84,85,86,87,90,93,96,97],"e1":[58,63,96],"e2":[7,58,63],"e2_rang":[1,64,73],"e3":[58,63],"e_refin":11,"ea":96,"earli":79,"earlier":[75,76],"eas":14,"easi":[78,83,85,86],"easier":[23,25,75,83,85],"easiest":53,"easili":[2,4,75],"echo":93,"echol":[0,96],"ed":96,"edg":[47,50,51,54,55,60,61,74,76,77,87,98],"edit":[3,36,74,82,86],"editor":[74,75],"edmand":[0,96],"eec":11,"effect":[2,14,35,47,54,60,61,64,75,77,82,83,85,86],"effici":[1,3,14],"effort":[0,82,94],"eg":96,"ehrensberg":96,"eiger":[48,77],"eiger16mnov2015":48,"eighteen":75,"eisenberg":96,"either":[0,1,2,4,20,24,40,44,47,48,51,52,53,54,59,60,61,64,69,71,74,75,80,83,85,86,97],"el":96,"elbaum":96,"electron":[0,11,21,47,52,54,74,75,76,89,94,96,98],"element":[2,14,15,18,20,25,40,77,79,83,85,86],"elif":96,"elimin":[11,18,69,77],"eliminate_sys_abs":[18,19,69],"ellips":[51,76],"ellipse_param":51,"ellipsoid":[41,51,55,59,97],"ellipt":76,"els":[1,6,23,53,86],"email":94,"eman":[54,60,61],"emax":[15,43,64,73],"emb":63,"emphasi":98,"employ":[14,79],"employe":89,"empti":[20,24,33,48,53],"empty_standard":20,"en":[18,65],"enabl":[0,4,38,45,51,52,53,55,73,95,96,97,98],"encapsul":[21,23,25],"encod":3,"encount":[79,80],"encourag":1,"end":[2,14,15,20,33,40,46,47,52,55,60,64,65,70,73,74,75,78,79,82,83,85,86,87,89,97,99],"endeavour":89,"endors":91,"energi":[0,35,89],"enforc":[54,75,78,83,85],"eng":[74,96],"engin":[14,18,40,44,54,60,61,64,73],"enhanc":[1,96],"enough":[54,60,61,74,79,82,93],"ensur":[2,14,23,26,38,40,64,75,82,83,85,86,87,94],"enter":[3,7,14,20,64,75,86],"enthusiast":77,"entir":[4,47,65,74,78,87],"entri":[2,20,78,97],"enum":20,"env":4,"environ":[0,4,48,76,80,82,90],"enzym":96,"enzymol":96,"eof":[52,76,85],"ep":[18,54],"epilog":[6,33],"epoch":[3,29,52,83,85],"epsilon":[11,18,54],"eqnarray":2,"equal":[16,18,20,35,43,47,54,55,57,60,61,64,67,73,78],"equat":[14,40],"equip":2,"equival":[2,14,15,49,52,61,64,69,79,83,85,86],"era":98,"eriksson":96,"erko":96,"error":[1,9,14,15,18,35,40,44,52,54,60,61,64,70,71,73,75,76,83,85,86,93,96],"error_model":[1,15,64],"error_model_group":[1,64],"error_param":15,"ersatz":44,"esd":[14,87],"especi":[11,54,74,85,86],"essenc":4,"essenti":[2,14,74,77,83,85,86],"est_standard_dev":4,"estim":[1,11,14,18,40,42,43,48,49,54,55,60,61,64,68,71,73,77,80,83,85,86,87],"estimate_gain":72,"estimate_global_threshold":[31,32],"estimate_resolut":[72,73,77],"estimate_tim":33,"et":[11,65,73,74,80,96],"etc":[2,18,33,60,71,77,80,87,97],"euclidean":54,"euler":39,"ev":96,"eval":98,"evalccd":44,"evalu":[11,14,15,46,54,77,89,96],"evan":[0,11,18,70,89,96,98,99],"even":[1,2,11,14,44,75,78,79,83,86,91],"event":91,"eventu":[73,83,85,86],"ever":[54,79,98],"everi":[14,38,40,47,51,54,55,56,60,61,64,67,70,73,77,82,83,85,86],"everyth":[7,20,21,23,25,53,75,77],"everywher":[23,79],"evid":[74,75,77,78,96],"evolv":[0,94],"ewald":[14,20,54,60,61,75],"ewald_proximal_volume_max":54,"ewald_proximity_resolution_cutoff":54,"ex":20,"exact":[6,23,53,75,79,82],"examin":[11,38,55,74,96],"exampl":[1,2,3,4,6,7,8,20,21,23,34,35,36,37,38,39,41,42,44,45,46,47,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,75,76,77,78,79,82,83,84,85,86,87,93,94,95,97],"exceed":[14,52],"excel":79,"except":[11,33,47,54,60,61,75,76],"excis":[54,60,61],"excit":44,"excitation_error_cutoff":44,"exclud":[1,14,15,33,40,44,47,49,54,55,60,61,64,65,67,70,73,75,77,78,83,85],"exclude_dataset":[1,64,77],"exclude_imag":[1,18,40,47,55,64,70,73,74],"exclude_images_multipl":[40,47,55,64,67,70,73],"exclude_inconsistent_unit_cel":[40,70],"exclude_intensity_perc":65,"exclude_pixel_range_i":65,"exclude_pixel_range_x":65,"exclude_single_crystal_clust":38,"excluded_for_refin":20,"excluded_for_sc":20,"excluded_prefix":[40,70],"exclus":[1,40,47,51,55,64,67,70,73,77],"execut":[16,75],"executor":[12,19],"executorwrapp":12,"exemplari":91,"exercis":[78,79],"exist":[0,1,4,9,15,18,20,23,50,52,53,73,83,85,86,98],"exit":[3,20],"exocytosi":96,"exp":[35,40,47,55,64,70,73,74,75,79,82,83,84,85],"exp_no":33,"expand":[2,69,76],"expand_to_p1":69,"expect":[2,7,14,18,35,44,64,74,75,76,78,79,82,83,85,86,98],"expected_cc":18,"expens":[14,86],"experi":[0,1,2,4,5,11,12,14,15,16,17,18,20,23,24,30,31,33,35,36,37,38,40,41,44,46,47,50,52,53,54,55,56,59,60,61,62,64,65,66,67,70,71,73,74,75,76,79,82,83,84,85,86,87,89,93,96,97,98],"experienc":79,"experiment":[2,3,4,7,11,20,26,38,52,54,60,61,62,64,65,67,71,75,76,77,78,83,85,86,87,88,97,98],"experiment_data":6,"experiment_file_object_list":33,"experiment_id_map":20,"experiment_identifi":[20,33],"experiment_list":[3,4,11,27,30,32,33],"experiment_list_for_cryst":11,"experiment_typ":14,"experimentlist":[3,4,11,14,16,18,20,24,27,33],"experimentlistfactori":[24,27],"experiments_":[87,93],"experiments_0":[38,40,87],"experiments_1":[38,40,82,87],"experiments_2":[40,87],"experiments_3":[40,87],"experiments_filenam":[38,67],"expert":[0,86],"expert_level":[7,38,40,41,43,45,46,47,50,51,52,54,55,56,58,59,60,61,62,63,64,67,70,71,73,83,85],"explain":[40,75,77],"explan":9,"explicit":[1,2,53,54,55,60,61,75,83,85,86],"explor":[2,75,79,83,86,96],"exponenti":[15,73],"export":[1,18,30,33,45,64,72,73,75,76,82,88],"export_as_json":11,"export_bitmap":72,"export_mtz":[32,33],"export_reflect":11,"export_text":[32,33],"expos":[0,14],"exposur":[46,52,83,85,86],"exposure_tim":[3,29],"express":[2,46,87,91],"expt":[1,3,6,34,35,36,37,38,39,40,41,42,43,44,45,46,47,50,51,52,53,54,55,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,74,75,77,78,79,82,83,84,85,87,93,97],"extend":[5,11,20,24,33,41,51,55,59,73,79,82,83,85,86,95],"extens":[1,4,20,32,41,45,47,51,55,59,60,71,75,76,89,95],"extent":[1,73,83,85],"extern":[4,14,16,63,75,86,94],"external_deltapsi":[54,60,61],"external_depend":63,"external_lookup":26,"externaldelpsiweightingstrategi":[14,19],"externallookup":[26,27],"externallookupitem":26,"externallookupitembool":[26,27],"externallookupitemdoubl":[26,27],"extra":[14,20,30,48,53,54,60,61,82,86],"extra_filenam":30,"extract":[11,16,18,20,33,53,79,83,84,85,86],"extract_reference_intens":[18,19],"extract_shoebox":20,"extractpixelsfromimag":[16,19],"extractpixelsfromimage2dnoshoebox":[16,19],"extractspot":[16,19],"extractspotsparalleltask":[16,19],"extrapol":52,"extrapolate_scan":52,"extrem":[54,60,61,63,79,82,96,98],"eye":[79,83,85,86],"f":[2,6,18,75,76,77,83,84,85,86,87,96],"fabl":96,"face":[78,82,89],"facil":[0,44,89,94,98],"facilit":[0,98],"fact":[40,75,76,78,79,82],"factor":[1,3,14,15,18,35,40,54,64,65,67,73,74,78,80,82,83,84,85,86,87],"factori":[4,14,16,21,23,25,26,28,29,33,82],"fail":[14,54,60,61,74,75,83,84,85,87,93],"fail_on_bad_index":[41,51,55,59],"failed_during_background_model":20,"failed_during_profile_fit":[20,46],"failed_during_summ":[20,46],"failur":[54,60,61,73,79],"fair":[74,75,76,79,82,83,85,86],"fall":[38,47,50,51,55,73,75,82,83,85],"falloff":[38,43,55],"fals":[1,4,6,11,14,15,16,17,20,22,23,24,26,31,33,37,38,40,41,43,44,45,46,47,48,50,51,52,53,54,55,56,58,59,60,61,64,65,66,68,69,70,71,73,74,75,76,83],"famili":32,"familiar":86,"familiaris":1,"far":[77,82,87],"fast":[11,23,33,38,47,50,51,52,54,60,61,74,75,76,85,96],"fast_axi":[3,23,38,52,76,83,85],"fast_axis_toler":[23,24],"fast_direct":23,"fast_slow_beam_centr":[52,74],"faster":[47,50,51,54,60,61],"favour":[75,78,83,85,86],"fd":96,"fe":96,"featur":[74,75,76,78,89,96],"feb":96,"februari":100,"feburari":100,"fed":74,"federici":96,"feedback":49,"feel":[75,83,85],"fel":98,"femtosecond":[75,96],"feng":96,"fetch":51,"fewer":[38,54,75,97],"ffbidx":54,"ffbindex":11,"fft":[11,54,75,83,85,86],"fft1d":[4,11,54,83,85,97],"fft3d":[4,11,54,86],"ffts":[11,54],"fi":76,"fib":94,"field":[0,11,33,86,98],"fifth":86,"fifti":[74,96],"figsiz":11,"figur":[65,74,75,79,82],"file":[0,1,4,7,8,20,21,23,24,25,29,30,33,35,36,37,38,40,41,42,43,44,45,46,47,48,50,51,52,53,54,55,56,59,60,61,62,63,64,70,71,73,74,75,76,77,78,79,80,82,83,84,85,86,87,90,93,97],"file_nam":[11,48],"filenam":[11,14,16,18,20,24,26,29,30,33,36,38,41,44,46,47,50,52,53,54,55,59,60,61,62,64,67,69,70,71,75,77,86,97],"filename_object_list":33,"filename_or_data":16,"filename_or_non":[27,30],"filename_prefix":44,"filename_to_absolut":[27,30],"filepath":64,"fill":45,"filnam":53,"filter":[11,12,14,15,16,18,38,40,41,44,45,46,47,48,50,51,54,55,59,64,71,73,75,76,83,84,85,86],"filter_by_likelihood":11,"filter_by_n_index":11,"filter_by_volum":11,"filter_doubled_cel":11,"filter_ic":[11,54],"filter_ice_r":[33,44],"filter_integrated_centroid":71,"filter_known_symmetri":11,"filter_ob":14,"filter_overlap":[11,54],"filter_reflect":72,"filter_similar_orient":11,"filter_spot":16,"filterrunn":[16,19],"final":[1,12,14,54,60,64,71,73,74,75,77,82,83,85,86,87,89],"final_outlier_array":15,"finalis":[12,14],"finalize_reflect":12,"find":[0,1,4,9,11,16,24,38,42,45,47,50,51,52,54,55,65,73,77,78,82,84,90,93],"find_basis_vector":[4,11],"find_crystal_model":[4,11],"find_lattic":11,"find_matching_symmetri":11,"find_max_cel":11,"find_overlap":20,"find_rotation_axi":75,"find_spot":[3,16,20,48,49,54,68,72,74,75,76,77,79,82,83,84,85,86,87,97],"find_spots_cli":49,"find_spots_serv":72,"finder":[16,83,85],"fine":[20,54,60,61,75,82,83,85,86,93,98],"finish":[12,33,64,83,85,86],"finit":18,"firefox":77,"first":[1,4,12,15,18,23,25,26,34,38,40,45,46,47,52,54,55,57,60,61,65,69,71,74,75,76,77,78,79,82,83,84,85,86,87,93,96,97,98],"fischetti":96,"fit":[3,12,35,41,43,51,55,59,61,64,71,73,74,75,77,78,79,82,83,84,85,86,91],"fit_method":[41,51,55,59],"fit_profil":12,"fitter":20,"fix":[2,14,15,25,35,38,41,51,52,54,55,59,60,61,64,74,75,76,78,79,80,82,83,85],"fix_initi":64,"fix_initial_paramet":15,"fix_list":[54,60,61,76],"fixed_compon":15,"fixed_rot":[3,25,38,52],"fixed_rotation_matrix":25,"fixed_rotation_toler":[24,25],"flag":[3,6,14,15,16,20,44,46,54,55,60,61,66,71,73,83,85],"flag_express":46,"flag_filt":44,"flaig":96,"flat":[12,35,47,75,83,85,86],"flatten":[12,18,33],"flatten_experi":[6,32,33],"flatten_reflect":[6,32,33],"flex":[3,4,11,14,15,20],"flex_ext":[],"flight":[16,24,95],"float":[4,10,11,14,15,18,20,21,22,23,25,33,35,37,38,40,41,43,44,45,46,47,50,51,52,54,55,57,58,59,60,61,63,64,65,67,69,70,71,73],"flood_fil":54,"floor":2,"flueckig":75,"flux":[21,52,83,85],"fn":11,"focus":[74,77,84,89,95,96],"focuss":77,"fold":[64,94],"folder":[4,48,53,77,85,86],"follow":[0,1,2,3,6,7,9,14,18,40,43,46,48,52,54,55,65,67,74,75,76,77,78,79,82,83,84,85,86,90,91,93,94,97,98],"font_siz":69,"fontsiz":45,"footprint":74,"for_a_sampl":18,"forc":[14,16,17,20,38,41,44,47,51,54,55,59,60,61,74,79,83],"force_2d":47,"force_stat":[17,20,41,51,54,55,59,60,61,74,76],"force_static_model":[33,44],"foreground":[31,55,75,83,84,85],"foreground_background":55,"foreground_foreground":55,"foreground_includes_bad_pixel":20,"foreseen":79,"forgiv":82,"fork":[24,95],"form":[2,7,14,30,43,47,54,55,60,61,73,75,77,78,79,83,85,86,91],"formal":98,"format":[1,2,3,18,20,23,24,26,30,33,40,44,45,47,51,52,55,56,58,64,70,73,74,75,76,80,82,83,84,85,86,87,96,97,99],"format_class":26,"format_epilog":33,"format_help":33,"format_kwarg":[24,26,33],"formatbaseclass1":4,"formatbaseclass2":4,"formatbruk":4,"formatbrukerfixedchi":4,"formatbrukerphotonii":4,"formatcbfminipilatus":[4,83],"formatcbfminipilatusdls6msn100":[84,85],"formatcbfminipilatusmybeamlin":4,"formatcbfminitimepix":76,"formatmyclass":4,"formatsmvcetad_tui":74,"formatsmvtimepix_su_516x516":75,"formatt":33,"formatter_class":33,"formula":[14,18,40,73,83,85],"fortran":96,"forum":[89,98],"forward":[40,55,77],"found":[2,4,6,11,16,20,40,47,48,49,52,54,64,65,74,75,76,79,80,82,83,84,85,86,97],"four":[1,74,77,87],"fourier":[54,70],"fpercent":33,"frac":[2,35,82,83,85,86],"frac_binsize_cutoff":14,"fraction":[2,3,11,16,21,38,41,46,47,51,52,54,55,59,60,61,73,83,85],"fraction_index":11,"fraction_of_bin_s":[54,60,61],"fractionalis":2,"fragment":83,"frame":[3,11,12,14,20,21,22,23,25,33,34,35,40,44,47,48,55,64,69,70,73,76,77,83,85,86,98],"frame0":12,"frame1":12,"frame_hist":[12,19],"frame_numb":48,"frame_value_":76,"frame_value_018":76,"frames_per_block":52,"framework":[0,2,4,6,89,96],"frank":98,"fransson":96,"fraser":96,"free":[0,64,73,74,75,78,80,83,85,89,96,98],"free_set_offset":64,"free_set_percentag":64,"freedom":[2,40,54,60,61,73,82],"freerflag":74,"frequenc":[11,54],"frequent":7,"fresh":86,"fri":96,"friedel":[74,79,83,85],"frisina":96,"from_arg":24,"from_byt":20,"from_data":[4,15],"from_dict":[4,15,21,22,23,24,25,28,29,31],"from_fil":[3,20,24],"from_filenam":24,"from_hdf5":20,"from_imageset":26,"from_imageset_and_cryst":24,"from_json":24,"from_json_fil":[14,24],"from_mosflm_matrix":22,"from_msgpack":20,"from_msgpack_fil":20,"from_observ":20,"from_paramet":[11,16],"from_parameters_and_experi":14,"from_parameters_data_experi":14,"from_parameters_reflections_experi":14,"from_phil":[12,21,22,23,25,29],"from_pickl":20,"from_pickle_fil":24,"from_predict":20,"from_predictions_multi":20,"from_sequence_and_cryst":24,"from_serialized_format":24,"from_stills_and_cryst":24,"from_sunbird":48,"from_templ":[24,26],"from_xd":24,"front":[74,96],"fs":[83,84,85],"fuent":[0,89,96,99],"full":[1,3,4,14,21,23,75,77,82,83,85,86,97],"full_matrix":[1,64],"full_matrix_engin":64,"full_matrix_max_iter":[1,64],"fuller":96,"fuller_kapton":55,"fulli":[0,2,44,46,55,75,82,83,84,85],"function":[1,2,7,11,12,14,15,16,18,20,26,36,40,43,54,55,60,61,64,65,75,82,83,85,86,94,95],"functool":[],"fund":[0,95],"fundament":[2,14],"futur":[95,98,99],"futurewarn":[],"g":[0,1,2,3,6,7,11,14,15,18,20,30,40,47,49,52,54,55,60,61,62,64,65,67,70,73,74,77,78,80,83,84,85,87,89,90,96,97],"g06727c3":76,"g07bf91aea":[],"g1a2d56924":[],"g2db66ff8a":[],"g5d3eb2eaa":[],"g66408cc4e":[],"g6c0f426d3":[],"g6ee8e44a5":[],"g73f70f18":80,"g952fa688d":[],"gain":[0,23,26,33,42,45,47,51,52,74,75,76,79,83,85],"gain_map":[42,47],"gaithersburg":35,"gallo":96,"gambin":75,"gamma":[2,18,40,73,87],"ganesh":[74,96],"garib":[0,99],"gasparotto":11,"gauss":14,"gaussian":[15,31,41,47,51,55,59,83,85,86],"gaussian_r":[4,31,41,51,55,59],"gaussian_rs_profile_model_ext":[4,31],"gaussianrsprofilemodelext":[31,32],"gaussnewton":[54,60,61,64],"gaussnewtoniter":[14,19],"gb":[80,82],"gb25dc57d4":[],"gc183a3529":[],"gcddd4e3e7":[],"gd1df3f6b2":[],"gd99e5841f":[40,83,85],"gee":96,"gemmi":33,"general":[0,3,4,20,35,55,75,82,83,85,86,87,89,94],"generalis":0,"generat":[0,1,11,12,18,24,25,29,33,45,46,47,50,51,52,54,57,58,61,63,64,67,68,69,73,76,77,83,84,85,87,95,97,98],"generate_distortion_map":76,"generate_from_phil":23,"generate_mask":[72,74,76],"generate_phil_scop":[12,16,19],"generic":75,"genuin":40,"geometri":[2,3,4,11,33,44,52,53,54,60,61,67,75,76,78,81,82,83,85,86,87,96,97,99],"gerard":[0,98],"gerstel":[0,89,96],"get":[1,4,8,14,16,17,20,23,24,25,26,29,30,33,55,75,77,82,83,85,86],"get_a_as_sqr":22,"get_a_inverse_as_sqr":22,"get_accepted_refs_s":14,"get_alpha_angl":25,"get_angl":25,"get_angle_from_array_index":6,"get_array_rang":[6,26],"get_ax":25,"get_beam":[26,30],"get_cbf_head":4,"get_centroid_analys":14,"get_col_nam":14,"get_corrected_data":26,"get_correlation_matrix_for_step":14,"get_crystal_symmetri":22,"get_data":[26,33],"get_detector":[26,30],"get_detectorbas":26,"get_direct":25,"get_domain_size_ang":22,"get_elapsed_tim":33,"get_entri":[32,33],"get_experi":14,"get_fixed_rot":[6,25],"get_flag":[6,20],"get_format_class":26,"get_free_reflect":14,"get_gain":26,"get_goniomet":[26,30],"get_grid_s":26,"get_half_mosaicity_deg":22,"get_image_identifi":26,"get_index":14,"get_inverse_ub_matrix_from_xparm":[32,33],"get_kappa_angl":25,"get_kappa_axi":25,"get_mask":26,"get_master_path":26,"get_match":14,"get_max_inscribed_resolut":23,"get_max_resolut":23,"get_mosa":22,"get_nam":[23,25],"get_nrow":14,"get_num_match":14,"get_num_matches_for_experi":14,"get_num_matches_for_panel":14,"get_num_scan_point":25,"get_num_step":14,"get_ob":14,"get_omega_angl":25,"get_omega_axi":25,"get_panel_intersect":23,"get_param":26,"get_param_report":14,"get_parameter_correlation_matrix":14,"get_path":26,"get_pedest":26,"get_phi_angl":25,"get_phi_axi":25,"get_raw_data":26,"get_raw_data_from_imageset":56,"get_ray_intersect":23,"get_rotation_axi":25,"get_rotation_axis_datum":[6,25],"get_s0":6,"get_sample_s":14,"get_scan":[26,30],"get_scan_axi":25,"get_setting_rot":[6,25],"get_setting_rotation_at_scan_point":25,"get_shared_compon":15,"get_space_group_type_from_xparm":[32,33],"get_spectrum":26,"get_subset_for_symmetri":[18,19],"get_templ":[26,30],"get_vendor":26,"get_vendortyp":26,"get_wavelength":6,"get_weighting_strategy_overrid":14,"gevorkov":11,"gf37b0db7a":80,"gf88516da7":84,"giacovazzo":2,"gilchrist":96,"gildea":[0,11,18,40,73,89,96],"gingeri":96,"ginn":96,"github":[9,76,80,83,85,90,97],"githubusercont":[9,48,74,76],"give":[1,2,7,14,18,20,40,45,46,54,60,61,62,67,70,73,75,77,78,79,82,83,84,85,86,97],"given":[0,1,2,4,11,14,15,16,17,18,20,22,23,25,28,30,35,39,40,41,44,46,47,49,51,52,54,55,56,59,63,64,65,68,69,70,73,75,79,83,85,86,97],"gj":96,"glacio":74,"glatzel":96,"gleb":0,"glen":96,"glide":87,"glm":[20,55],"global":[47,54,55,60,61,65,75],"global_threshold":[45,47,51,76],"globular":[83,85,86],"glownia":96,"gltbx":33,"glu":9,"gl\u00f6ckner":96,"gmail":80,"gmodel":55,"gmt":84,"gn":[64,96],"go":[40,47,55,64,70,73,74,75,77,78,79,80,81,82,83,84,85,86,87],"goal":[2,89],"goe":74,"goldschmidt":96,"gon_kappa":85,"gon_omega":85,"gon_phi":85,"gone":[83,85,86],"gonen":96,"gonimomet":2,"goniomet":[3,4,6,24,26,27,32,34,35,38,52,54,60,61,75,76,79,83,85,93,96],"goniometerbas":25,"goniometercomparison":[24,27],"goniometerfactori":[25,27],"goniometershadowmask":26,"goniostat":2,"gonzalez":96,"gonz\u00e1lez":96,"good":[11,38,64,73,74,75,77,78,79,80,82,83,85,86,87,91],"gov":[35,48],"gpu":98,"gpus":94,"grad":18,"gradient":[14,18,54,60,61],"gradient_calculation_blocks":[14,54,60,61],"gradient_cutoff":[16,47],"gradient_threshold":14,"graem":[0,98,99],"grain":[54,60,61],"grant":[0,89,94],"graph":[54,57,60,61,74,86],"graph_verbos":11,"graphic":[0,77,83,85,86],"grate":0,"grayscal":51,"great":[0,74,78,86,89,98],"greater":[18,41,44,47,51,54,55,59,64,65,79,97],"greatest":[11,82],"green":[83,85,86],"greisman":96,"greyscal":45,"grid":[1,11,37,41,49,51,54,55,59,64,65,79,82,83,85,86,97],"grid_h":37,"grid_k":37,"grid_l":37,"grid_method":[41,51,55,59],"grid_search_scop":54,"grid_siz":[26,41,51,55,59,63,82],"gridsiz":69,"grime":96,"gross":[0,2,11,96],"grossli":79,"ground":0,"group":[1,2,4,11,15,18,22,23,33,37,40,43,45,46,47,50,51,52,54,60,61,62,64,70,73,74,75,76,77,78,79,80,82,83,84,85,86,87,89,96,97],"group_info":11,"group_siz":[64,73,75],"groups_cach":11,"grow":[74,77,78],"gruen":[76,96],"guarante":[18,55,86,87],"guenther":96,"guess":[65,73],"guess_posit":65,"gui":[51,94],"guid":[9,64],"guidanc":0,"gul":96,"gwyndaf":[0,98,99],"gxparm":53,"gz":[44,48,85,87,90],"gzip":76,"g\u00e4tcke":96,"h":[0,2,20,35,37,54,62,74,75,76,78,79,83,84,85,96],"h5":48,"haa":96,"habit":96,"half":[40,43,54,73,75,78,80,83,85,86,87],"half_dataset":[33,43,73],"half_mosaicity_deg":22,"half_mosaicity_toler":22,"hall":[82,96],"hammersley":2,"han":[0,96],"hand":[36,100],"handi":9,"handl":[2,16,20,23,24,25,29,33,75,76,77,84,97,99],"happen":[74,79,83,84,85,86],"happi":[83,84,85,86],"hard":75,"hardwar":0,"harmon":[1,64,73,87],"harri":[0,99],"has_dynamic_mask":26,"has_key":20,"has_projection_2d":23,"has_single_file_read":26,"hat":35,"hattn":[0,96],"haupt":96,"hay":96,"hcluster":54,"hdf5":[20,24,38,94],"hdrmx":100,"head":[32,33],"header":[4,9,23,26,29,52,74,75,78,79,84],"health":[0,89,94],"hear":80,"heart":0,"heat":86,"heatmap":[45,51,63],"heavi":[0,64,77],"hecksel":96,"hedman":96,"heed":79,"height":[47,54,55,60,61,73],"hekstra":96,"held":[0,2],"hellmich":96,"help":[1,4,6,18,21,24,29,33,35,36,37,38,40,41,42,43,44,45,46,47,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,69,70,71,73,74,75,77,79,82,83,85,86,87,89,94,97,98],"help_key":20,"help_messag":6,"helper":[20,33],"hemisper":20,"hemispher":11,"hemozoin":96,"henc":[29,35,83],"hennessi":[74,96],"herbert":94,"heurist":86,"hewitt":96,"hice":96,"hidden":[14,82],"hide":[40,83,85],"hieararchy_level":82,"hierarch":[38,40,54,60,61,73,82],"hierarchi":[4,23,52,54,60,61,76,82],"hierarchy_level":[54,60,61,82],"high":[0,1,11,18,35,37,38,40,46,47,48,50,51,54,55,64,73,74,75,76,77,79,80,82,83,84,85,86,87,89,97,98,100],"higher":[1,4,11,54,64,74,75,79,83,85,86],"highest":[1,11,38,40,55,62,79,82,83,84,85,86],"highlight":[77,86],"hilgart":96,"hint":[74,77,79,86],"hist":[12,19],"histogram":[12,54,75,77,83,84,85],"histogram_bin":[11,54],"histor":98,"histori":[14,24,54,60,61,84,86],"history_as_integr":24,"history_as_sc":24,"histrogram":47,"hj":96,"hk":96,"hkl":[2,17,30,39,44,53,69,79,87],"hkl_limit":69,"hkl_offset":[11,62,79],"hkl_toler":54,"hklf":[44,74],"hklin":[76,85],"hklout":[33,44,74,76,82,85,87,93],"hm":96,"hodgson":96,"hohman":96,"hold":[2,20],"holder":91,"hollenbeck":96,"holm":75,"holton":96,"home":[0,7,76],"hope":4,"hopkin":96,"horizont":[2,65],"horrel":96,"host":[20,48,49,80],"hostnam":49,"hot":47,"hot_mask":[16,47],"hot_mask_prefix":[16,47],"houben":96,"hough":96,"hour":48,"howev":[0,1,2,14,41,42,44,53,55,62,69,75,76,77,78,79,80,82,83,84,85,86,87,91,93,97],"hp":[79,96],"ht":96,"html":[1,40,43,48,63,64,65,70,74,75,77,84,97],"http":[35,48],"httpd":48,"https":[9,11,18,47,48,54,60,61,65,74,76,80,83,87,90,97],"hubbel":35,"human":3,"hundr":77,"hunter":[75,96],"hussein":96,"huw":0,"hw":96,"hybrid":0,"hypothesi":86,"h\u00f6gbom":96,"i04":[83,84,85,86],"i04_thaumatin":80,"i19":35,"i2":[18,40,61,70,73,75,83],"i23":40,"i3_1_0001":48,"i7":82,"i_mean_over_sigma_mean":[43,73],"i_over_sigma":55,"ian":0,"ibarra":96,"ibg":[75,82,83,84,85],"ibrahim":96,"ice":[44,45,46,47,49,50,51,54,55,82,83,85,86,96],"ice_r":[45,46,47,50,51,55],"id":[1,3,16,20,33,44,46,52,54,60,61,64,67,68,73,74,75,79,83,84,85,89,96],"id_":[4,15],"idea":[0,77],"ideal":[4,33,75,78,87,93],"ident":[6,40,61,77,83,85,87,93],"identif":[54,60,61],"identifi":[4,11,20,23,24,26,33,40,42,47,52,54,55,57,60,61,64,66,70,73,77,79,83,85,86,87],"identifier_typ":52,"identify_outli":11,"idiomat":29,"idxref":30,"iexp":14,"ifs":54,"ifss":54,"ifssr":54,"ignor":[11,26,33,52,54,59,60,61,78],"ignore_shadow":59,"ignore_trusted_rang":23,"ignore_unhandl":[33,52],"ignore_unknown":26,"ih":[15,64,83,85],"ih_tabl":15,"ihtabl":15,"ii":96,"iii":11,"ij":18,"il":100,"illumin":[83,85,86],"illustr":[35,77,98],"im":[83,85],"imag":[0,1,2,3,4,6,11,12,14,15,16,18,20,23,24,26,29,30,31,33,38,40,41,42,45,46,47,48,49,50,51,52,54,55,56,59,60,61,64,65,66,67,68,69,70,73,75,76,77,78,79,80,82,83,84,85,86,87,88,94,96,97,98],"image1":47,"image_":[52,56,66],"image_0001":49,"image_1":52,"image_1_":52,"image_2":52,"image_2_":52,"image_fil":4,"image_group":[64,73,75],"image_pedest":74,"image_pl":23,"image_prefix":56,"image_rang":[3,15,26,29,33,52,54,65,67,74,77],"image_s":[3,23,52,83,85],"image_statist":66,"image_view":[72,74,75,76,78,79,82,83,85,86,87],"image_volum":[20,31],"imagebool":26,"imagebuff":26,"imagecif":96,"imagedoubl":[23,26],"imagegrid":[26,27],"imager_00":47,"imagesequ":[3,26,27],"imagesequence_from_dict":[27,30],"imagesequence_to_dict":[27,30],"imageset":[3,6,16,20,24,27,30,32,36,45,47,50,54,55,56,74,75,83,84,85,86,93],"imageset_from_anyset":26,"imageset_from_dict":[27,30],"imageset_index":45,"imageset_to_dict":[27,30],"imagesetdata":[26,27],"imagesetfactori":[26,27],"imagesetlazi":[26,27],"imagin":79,"imaginari":20,"imean":[33,84,85],"img":[74,75,79],"imgcif":[2,20,21,23,25,29],"imgcif_h":[21,23,25,29],"imid":[1,15,64,83,85],"immedi":[55,76,82,85,86],"impact":[2,14,74,87],"imping":55,"implement":[4,11,14,15,16,18,20,23,26,31,40,41,51,55,59,70,79,89,96],"impli":[29,54,60,61,64,79,83,85,86,91],"implic":20,"implicit":[2,44,55],"import":[1,2,3,4,6,7,15,24,32,33,42,47,50,53,54,65,68,72,75,77,78,82,88],"import_xd":72,"important_numb":4,"impos":[76,84],"improp":75,"improv":[1,64,74,77,78,79,82,83,84,85,86,87,94,96,97],"in_beam_plan":[54,60,61],"in_plac":24,"in_powder_r":20,"in_spindle_plan":[54,60,61,74,76],"inaccur":79,"inadequaci":2,"incid":[35,54,60,61],"incident":91,"includ":[0,1,4,11,14,18,24,33,43,44,47,48,49,50,54,55,58,60,61,62,64,65,71,73,74,75,76,77,78,79,82,83,85,86,87,89,91,94],"include_bad_refer":55,"include_gui_packag":33,"include_unused_reflect":60,"includes_bad_pixel":20,"inclus":[14,40,46,47,54,55,60,61,64,70,73,75],"incom":[1,83,85,86],"incompat":2,"incomplet":[74,75,76,87],"inconsist":54,"incorpor":[82,99],"incorrect":[37,54,75,78,79,83,85,87],"increas":[7,14,54,64,73,74,79,82,83,85,86,94,97,98],"increment":[18,64,75,77],"inde":[75,79,80],"indent":[4,18,33],"independ":[41,54,60,61,77,82,83,85,86,87,97],"index":[2,3,6,14,15,17,18,19,20,26,32,37,40,41,44,45,46,47,51,52,53,55,59,60,61,62,63,64,65,69,71,72,73,77,78,80,82,88,93,94,96],"index_assign":[7,54],"index_error":54,"index_magnitud":54,"index_qu":54,"index_reflect":11,"indexed_1":69,"indexed_2":69,"indexed_experi":11,"indexerknownorient":11,"indic":[2,3,4,11,14,15,20,24,26,39,45,48,49,51,53,54,55,57,60,61,64,69,73,74,75,76,77,78,79,82,83,84,85,86],"indirect":91,"individu":[1,9,40,44,64,66,69,73,74,75,76,77,82,83,84,85,87,93,94],"individualist":98,"industri":[0,74,96],"ine":38,"inelast":[47,75],"infil":30,"infinit":[2,14],"inflat":63,"influenza":96,"info":[11,33,83,85],"inform":[1,2,7,9,14,15,18,23,26,41,44,47,48,52,53,54,60,61,65,71,73,74,77,78,83,84,85,86,89],"infrastructur":0,"inherit":[4,14],"init":[30,33],"initi":[1,11,12,14,15,21,23,25,29,47,54,55,60,61,64,65,73,75,76,78,81,83,85,86,98],"initial_wavelength":[16,47],"initialis":[12,14,15,16,17,18,31,33,83,85],"initialise_smooth_input":15,"initialize_reflect":12,"inject":[26,96],"injector":20,"innov":91,"inp":[30,44,53],"input":[3,6,7,11,14,15,16,18,20,29,30,31,33,36,37,38,40,41,44,46,47,51,52,53,54,55,56,58,60,61,62,64,65,67,70,71,73,74,77,82,83,84,85,86,87,97],"input_filenam":30,"ins":[44,74,87],"insensit":47,"insert":[4,20],"insid":[20,47,77],"insidi":79,"insight":[75,77,96],"inspect":[1,4,60,71,77,79,82,83,84,85,97],"inspir":[0,78,79],"instal":[4,8,32,33,48,72,74,76,78,79,80,81,82,84,85,86,87],"install_format":[4,74],"installer_dir":33,"instanc":[10,12,14,16,20,23,24,25,26,29,33,77,79],"instanti":[4,24],"instead":[4,40,43,64,70,75,78,79,86],"institut":[0,35,89,94],"instruciton":44,"instruct":[9,44,75,79,86,90,93],"instrument":[0,44,82,89,94,95],"instrument_nam":44,"instrument_short_nam":44,"insu6_1_mast":48,"int":[2,11,12,14,15,16,18,20,23,24,25,26,33,37,38,39,40,41,42,43,44,45,46,47,49,50,51,52,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,73],"integ":[2,20,54,67,84],"integr":[0,1,3,15,19,20,30,32,35,40,41,44,46,47,50,51,53,57,61,62,63,64,67,70,71,72,73,77,78,79,80,82,88,93,94,95,96,98,99],"integrate_all_reflect":55,"integrate_hkl":53,"integrated_":[76,93],"integrated_0":97,"integrated_1":[73,76,87,97],"integrated_2":[64,73,76,87],"integrated_3":[76,87],"integrated_4":[76,87],"integrated_5":76,"integrated_6":76,"integrated_7":76,"integrated_data":33,"integrated_experi":76,"integrated_prf":[20,44],"integrated_sum":[20,44],"integrator2d":[12,19],"integrator3d":[12,19],"integrator3dthread":[12,19],"integratorexecutor":[12,19],"integratorflat3d":[12,19],"integratorsingle2d":[12,19],"integratorstil":[12,19],"intellectu":0,"intellig":33,"intend":[7,35,44,49,54,60],"intens":[0,1,3,11,15,18,20,33,35,37,40,43,44,46,47,49,54,55,62,64,65,73,74,75,78,79,83,84,85,86,87,95,96,97,98],"intensity_choic":[1,33,64],"intensity_rang":[1,64,73],"intent":53,"interact":[0,64,75,76,86,87],"interest":[2,16,47,73,74,82],"interfac":[0,14,16,18,41,51,55,59,75,81,86,94],"intermedi":[45,54,55,96],"intern":[2,26,60,64,73,77,94],"internet":[51,63],"interpret":[6,47,53,64,74,75,76,77,79,97],"interrupt":[40,47,55,64,67,70,73,91],"intersect":[46,65],"intersection_min_width":65,"intersection_rang":65,"intersection_union_ratio_cutoff":54,"interv":[1,15,40,47,54,55,60,61,64,67,70,73,83,85],"interval_width_degre":[54,60,61],"intgrat":30,"intris":14,"introduc":[2,76,77],"introductori":81,"inv":14,"inv_d2":10,"invalid":[15,20,50,75,83,84,85],"invalidphilerror":[32,33],"invers":[2,3,14,40,41,51,55,59,65,73,79,83,85],"inverse_greyscal":45,"inverse_scale_factor":[3,15],"inverse_scale_factor_vari":3,"inverse_ub_matrix":33,"inversion_window_width":65,"invert":[51,52,79,83,85],"invert_rotation_axi":52,"investig":[15,75,76,78,83,85,94,96],"invis":96,"invit":0,"invok":1,"involv":[15,18,35,77],"invvar":64,"io":[4,65,83,85,97],"ion":96,"iotbx":[18,22],"ioutil":33,"ipanel":14,"iqr":[47,51,54,55,60,61],"iqr_multipli":[54,60,61],"iri":0,"irradi":55,"irrespect":83,"is_consist":[20,24],"is_integ":20,"is_marked_for_reject":26,"is_overload":20,"is_scal":[4,15],"is_similar_to":[22,23,25],"is_single_file_read":26,"is_stil":[16,20],"isbn":0,"isi":95,"isigi_cutoff":[38,55],"isigma":[43,64,73],"isigma_cutoff":[1,64],"isigma_rang":[1,64,73],"isn":82,"isoform":54,"isol":78,"isomorph":[73,77,96],"isotrop":[11,18,40,78],"issu":[14,55,75,77,78,79,80,83,85,86,89,93,97],"item":[11,16,20,33,54,55,60,61,75,83,84,85],"iter":[1,11,14,16,20,23,40,41,51,54,55,59,60,61,64,65,73,79],"iter_levelord":23,"iter_panel":23,"iter_preord":23,"iterate_experiments_and_indic":20,"ithaca":100,"iucr":2,"iucrj":96,"ivanova":96,"iwata":96,"j":[2,11,18,20,35,40,47,54,65,67,73,75,77,80,84,96],"j0":[47,54,65,67],"j1":[47,54,65,67],"ja":96,"jacobian":[14,54,60,61],"jacobian_condition_numb":14,"jaho":96,"jame":[0,99],"jan":[74,96],"jana2020":44,"jb":96,"jbluic":96,"jd":75,"je":96,"jenkin":0,"jessica":74,"jf":[74,96],"jh":96,"ji":96,"jiang":96,"jiggeri":6,"jim":[0,98],"jiscmail":89,"jl":96,"jm":[76,89,96],"jn":96,"job":[12,16,47,54,55,60,61,64,75,82,83,85,86],"job_card":30,"joblist":[12,19],"johan":0,"john":96,"johnson":96,"join":[73,94],"joinpath":4,"joint":[1,3,54,60,61,64,82],"joint_analysi":64,"joint_index":54,"joint_json":68,"jon":0,"joti":96,"journal":[0,14,19,54,60,61],"jp":[76,96],"jpeg":45,"js":96,"json":[3,11,18,24,30,34,36,38,40,43,44,52,55,60,63,64,65,68,69,70,71,76,77,83,85,97],"jul":96,"juli":100,"jump":[79,85],"jun":[76,96],"june":100,"junk":[83,85],"just":[4,11,14,18,23,24,25,54,64,74,75,79,82,83,84,85,86,94,97,98],"jw":96,"k":[0,2,11,18,20,37,40,54,62,76,79,83,84,85,96],"k1":[54,60,61],"k2":[54,60,61],"k3":[54,60,61],"kabsch":[0,98],"kaila":96,"kaiser":96,"kaminski":96,"kappa":[25,52],"kappadirect":25,"kappagoniomet":[25,27],"kappascanaxi":25,"kapton":55,"kapton_2019":55,"kapton_half_width_mm":55,"kapton_thickness_mm":55,"karan":0,"katrin":0,"kay":98,"kb":[1,4,15,64,73],"kbscalingmodel":15,"kd":96,"ke":96,"keabl":96,"keedi":96,"keen":79,"keep":[1,14,38,43,44,54,60,61,67,71,73,74,77,82,86,98],"kelli":96,"kenner":96,"kept":[6,54,60,61,76,77,82],"kern":96,"kernel":[18,40,47,51,65,70,73],"kernel_normalis":18,"kernel_s":[42,45,47,51],"kevin":0,"key":[4,6,14,18,20,48,77,83,85,86],"key0":20,"key1":20,"keyerror":20,"keyword":31,"kg":35,"khr":9,"kilohertz":11,"kim":96,"kind":[77,79],"kingdom":91,"kj":75,"klar":96,"klureza":96,"km":96,"knew":75,"know":[0,20,21,23,25,55,73,74,75,78,83,85,86],"knowledg":[0,2,35],"known":[11,20,25,47,54,65,75,78,79,82,83,85,86,97],"known_axi":25,"known_crystal_model":11,"known_orient":11,"known_symmetri":54,"ko":96,"kobayashi":96,"kobe":75,"kobilka":96,"koglin":96,"koiwai":96,"kok":96,"koroidov":96,"kovaleva":96,"kroll":96,"kroon":98,"kruse":96,"kubin":96,"kumar":96,"kunstlev":[0,2,11,96],"kuykendal":96,"kw":[74,96],"kwarg":[11,14,16,24,31,33],"kwds":14,"l":[2,14,18,20,37,54,62,75,76,78,79,83,84,85,87,89,96],"l1":76,"l2":76,"l_0":35,"l_1":35,"l_i":35,"l_min":[11,54],"lab":[0,2,45,51,100],"label":[2,14,43,45,47,60,69,71,73,84],"label_indic":69,"labelit":[48,79],"laboratori":[0,11,21,35,69,75,76,89,91,94,99],"lack":[83,85,86],"lactamas":[85,86],"lai":96,"laksmono":96,"lambda":35,"lamella":96,"lamp":96,"landscap":96,"lane":96,"laptop":94,"larg":[0,14,44,51,54,60,61,64,71,73,75,76,77,82,83,85,86,87,88,97,98],"larger":[11,54,55,57,60,61,79,94],"largest":[11,14,38,40],"larvicid":96,"laser":[0,96,98],"lassall":96,"last":[12,14,54,60,61,65,75],"latch":79,"late":78,"later":[60,71,74,86,87],"latest":[7,14,65,80],"latim":96,"latt":74,"latter":[75,83,85],"lattic":[2,3,11,18,20,40,44,54,73,76,77,79,81,96,97,99],"lattice_group":[18,40,70,73],"lattice_id":18,"lattice_search":19,"lattice_search_strategi":4,"lattice_symmetri":18,"lattice_symmetry_max_delta":[18,40,70,73],"latticesearch":11,"laue":[11,14,16,18,24,40,47,54,60,61,70,73,74,77,83,84,85,95,96],"laue_group":[18,70,73],"laue_manag":14,"lauegroupanalysi":[18,19],"laueleastsquaresresidualwithrmsdcutoff":[14,19],"lauemixedweightingstrategi":[14,19],"lauereflectionmanag":[14,19],"lauespotfind":[16,19],"lauestatisticalweightingstrategi":[14,19],"launch":[75,86],"law":[83,85],"lawrenc":[0,89,91,94],"layout":86,"lazi":26,"lb":96,"lbfgs":[11,14,18,64,83,85],"lbfgs_core_param":11,"lbfgs_termination_param":11,"lbfgs_with_curv":[18,19],"lbfgscurv":[14,19,54,60,61],"lbl":48,"lbnl":[0,89],"lcls":[82,100],"lcys":87,"le":[11,18,54,79],"lead":[1,54,60,61,78,79,83,85,86,94,97],"learn":[74,75,82,89,96],"learnt":98,"least":[1,14,54,60,61,64,75,83,85,86],"leastsquarespositionalresidualwithrmsdcutoff":[14,19],"leastsquarespositionalresidualwithrmsdcutoffspars":[14,19],"leastsquaresstillsresidualwithrmsdcutoff":[14,19],"leastsquaresstillsresidualwithrmsdcutoffspars":[14,19],"leav":[75,86],"lebedev":78,"lebrett":96,"led":0,"lee":0,"left":[2,35,79,86],"leginon":[74,96],"leginon_offset":74,"leinweb":0,"leiserowitz":96,"lemk":96,"lemmin":96,"lemont":100,"len":[4,6,76],"length":[11,14,18,20,33,35,54,73,74,78,82,85],"lepag":40,"lepage_max_delta":61,"lesli":[0,55,98,99],"less":[7,18,40,44,47,50,51,54,55,61,64,70,73,74,75,78,79,82,83,85,86,87],"lesson":[74,96],"let":[4,74,75,77,79,82,83,85,86],"level":[0,1,4,12,18,38,43,45,47,54,60,61,64,73,75,82,86,87,97],"levenberg":[14,83,85],"levenbergmarquardtiter":[14,19],"levi":2,"levmar":[54,60,61,64],"liabil":91,"liabl":91,"liang":[75,96],"lib":80,"libgl":9,"librari":[8,30,74,94],"libtbx":[4,6,11,15,18],"libtbx_refresh":4,"lichtenberg":96,"lie":[0,2,54,60,61,78],"liebschner":96,"life":79,"light":[0,35,81,82,83,84,85,86,91,100],"lightarray":[18,19],"like":[0,1,2,3,4,7,11,14,26,38,53,55,74,75,77,79,80,82,83,85,86,87],"likelihood":[18,40,41,51,55,59,70,74,77,83,84,85,86],"likelihood_cutoff":[11,54],"limit":[11,14,37,40,41,43,46,47,49,50,51,54,55,56,59,64,66,68,73,74,75,76,77,80,82,83,84,85,86,87,91,96,98],"limit_image_rang":15,"limit_resolution_bi":54,"lin":96,"line":[1,7,9,12,24,33,52,64,72,74,75,78,80,81,82,83,85,86,87,94,97],"linear":[11,14,35,54,55,64,73,83,85,86],"linear2d":55,"linear3d":55,"linearis":14,"link":[14,66,87],"linkag":54,"linux":[7,24,75,80,82],"lisova":96,"list":[4,7,11,12,14,15,16,18,20,24,25,26,29,30,31,33,35,38,44,47,50,52,53,54,55,57,60,61,64,65,74,75,76,77,78,79,83,85,91,93,95,97],"list_of_identifi":20,"liter":47,"littl":[20,23,25,74,75,76,77,82,83,85,87],"lj":96,"ll":[75,82,85,86],"ll_toler":[41,51,55,59],"lm":[64,96],"lmax":[1,64,73],"load":[6,16,20,24,26,30,32,33,48,51,64,77,80,83,85,86,94],"load_error_model":15,"load_imag":16,"load_model":[24,33,51],"loc":18,"loc_in_list":33,"local":[4,7,45,47,54,63,75,86,90,94],"localhost":48,"locat":[3,18,33,50,54,60,61,85,86],"loe":98,"log":[1,11,14,18,33,35,37,38,40,41,43,44,47,50,51,52,53,54,55,59,60,61,62,64,65,70,71,73,74,75,76,77,79,80,82,83,84,85,86,97],"log2":54,"log_summari":[32,33],"logarithm":54,"logic":47,"login":9,"loglinear2d":55,"loglinear3d":55,"lombard":100,"lond":96,"long":[10,12,14,23,24,25,26,64,75,78,83,85,86,87,96],"longer":[76,82,83,84,85],"longest":4,"look":[3,4,47,52,54,60,61,74,75,76,77,78,79,82,83,85,86,87,98],"lookup":[47,52,54,55,76],"lookup_symbol":54,"loop":[14,77],"lorentz":[83,85,86],"loss":[73,91],"lot":[74,77,82,84,86],"love":80,"lovelac":95,"low":[1,11,37,47,50,51,54,64,73,74,75,76,77,79,80,82,83,84,85,86,87],"low_memory_mean":[54,60,61],"low_res_spot_match":[4,54],"lower":[11,18,54,55,60,61,64,74,82,83,85,86],"lower_bound":18,"lowest":[20,43,64,75,79,83,85,86],"lowresspotmatch":11,"lp":[3,20,53,83,85,86],"lr":96,"ls":[75,77,93],"lsf":[47,55],"lstbx":14,"lucier":[74,96],"luck":74,"lui":[0,99],"lukacik":96,"lundin":96,"lure":11,"lvalu":[10,12,22,23,24,25,26],"lys_ed_dataset_":76,"lys_ed_dataset_1":76,"lys_ed_dataset_2":76,"lys_ed_dataset_3":76,"lys_ed_dataset_4":76,"lys_ed_dataset_5":76,"lys_ed_dataset_6":76,"lys_ed_dataset_7":76,"lysozym":77,"lyubimov":96,"m":[2,11,35,40,74,75,77,80,83,84,85,86,89,96,97],"m1000":74,"m2":96,"ma":[96,100],"mac":7,"machin":[48,49,97,98],"machineri":96,"macosx":90,"macro":[54,60,65,79,82,83,85,86],"macrocycl":[54,60,61,75,79,82,83,85,86],"macrocyl":[79,83,85,86],"macromolecul":[83,85],"macromolecular":[0,1,71,95,96,100],"made":[1,2,15,23,33,35,38,40,54,60,61,75,83,85,86,87],"madmergedmtzwrit":[32,33],"magic":4,"magic_paramet":4,"magnif":74,"magnitud":[2,35,63,64,79],"mahalanobi":[54,60,61],"main":[0,3,9,14,23,34,53,54,55,64,72,78,80,81,85,97],"maintain":[14,48,94],"mainten":94,"major":[7,55,75,79,86],"make":[0,2,4,9,15,20,23,25,45,54,55,56,60,61,64,71,74,75,76,77,78,79,82,83,85,86,89,93],"make_app":33,"make_beam":21,"make_combined_plot":15,"make_detector":23,"make_goniomet":25,"make_imageset":26,"make_kappa_goniomet":25,"make_multi_axis_goniomet":25,"make_polarized_beam":21,"make_polychromatic_beam":21,"make_scan":29,"make_scan_from_properti":29,"make_sequ":26,"makita":96,"malaria":96,"mald":75,"mamedov":96,"manag":[1,12,14,54,60,61,64,83,85,99],"mandatori":14,"manglik":96,"mani":[0,2,4,16,38,40,48,74,75,77,78,79,80,83,85,86,94],"manifest":79,"manner":[77,83,85,86,97],"manual":[52,74,75,87],"map":[11,18,20,40,42,45,47,50,51,53,63,66,70,77,78,79,83,85,86,96],"map_centroids_to_reciprocal_spac":20,"mar":[11,96],"marcin":0,"margin":[17,20,41,51,55,78],"mark":[47,75,83,85,86],"mark_for_reject":26,"marker":[83,85],"marker_s":69,"marko":0,"markus":0,"marom":96,"marquadt":14,"marquardt":[14,83,85],"mashor":[74,96],"mask":[3,16,20,23,26,31,36,46,47,50,51,52,55,67,76,83,85],"mask_gener":16,"mask_param":51,"masker":26,"mass":[35,41,51,55,59,83,85],"master":[48,74,76,77],"master_path":26,"masuda":96,"mat":44,"mat3":[22,25],"mat3_doubl":25,"match":[11,14,18,20,29,33,38,48,54,60,61,67,75,82,83,85,86,87],"match_by_hkl":20,"match_wavelength":[32,33],"match_with_refer":20,"materi":[0,23,35,52,83,85,91],"math":11,"mathbf":[2,35],"mathew":96,"mathsf":2,"matplotlib":[20,60,71],"matric":[2,39,84],"matrix":[1,6,14,18,20,22,39,40,44,52,54,58,60,61,63,64,71,73,75,82,83,84,85,87],"matter":[51,87],"matthew":0,"matur":82,"max":[40,41,46,51,52,54,55,59,64,65,73,74,75,78,79,80,82,83,84,85,86,97],"max_angular_differ":18,"max_batch_s":38,"max_cal":[18,40,73],"max_cel":[19,54,65,83,85,86],"max_cell_estim":54,"max_cell_multipli":11,"max_cell_volume_change_fract":[41,51,55,59],"max_clust":38,"max_cluster_height":73,"max_cluster_height_cc":73,"max_cluster_height_co":73,"max_combin":[11,54],"max_cycl":[64,73],"max_delta":[11,18,54],"max_dist":[54,73],"max_ep":73,"max_fre":73,"max_height_fract":[11,54],"max_imag":42,"max_it":[41,51,55,59],"max_iter":[14,18,40,54,60,61,64,73],"max_lattic":[11,54,84,97],"max_length":33,"max_memory_usag":55,"max_n_group":[54,60,61],"max_output_cel":54,"max_output_clust":73,"max_pair":54,"max_percent_remov":[64,73],"max_possible_wl":33,"max_quad":54,"max_refin":54,"max_refl":54,"max_reflect":[65,66],"max_reflections_per_experi":38,"max_sample_s":14,"max_scor":[],"max_separ":[20,41,47,51,55,59,74],"max_shift_over_esd":14,"max_spot":[54,74],"max_spot_s":[16,47,76],"max_strong_pixel_fract":[16,47],"max_triplet":54,"max_vector":54,"maxd":16,"maxim":[54,60,61,65],"maximis":44,"maximum":[11,15,16,17,18,20,38,40,41,43,44,46,47,51,52,54,55,60,61,64,65,73,77,83,85,86,87],"maximum_sample_s":[54,55,60,61],"maximum_trusted_valu":47,"may":[0,1,2,3,4,7,9,11,12,14,15,18,34,35,40,41,42,46,47,48,49,51,52,54,55,60,61,63,64,67,71,73,75,76,77,78,79,80,82,83,85,86,87,90,91,94,96,97,100],"mayb":77,"mayer":[74,96],"mb":[83,85],"mc":[75,78,79,80,83,84,85,96],"mcauley":96,"mcd":[54,60,61,83,85,86],"mcdonagh":96,"mcfarlan":96,"mcgilvray":[74,96],"mcphillip":96,"mcqueen":96,"md":[35,96],"mea":84,"mean":[2,4,10,15,36,42,45,47,51,54,60,61,64,73,75,77,78,82,83,84,85,86],"meaning":2,"meant":76,"measur":[1,2,3,11,14,54,61,64,73,75,77,83,84,85,86,96],"mechan":[0,82],"med":[82,83,85,96],"med_a":[40,97],"med_alpha":[40,97],"med_b":[40,97],"med_beta":[40,97],"med_c":[40,97],"med_gamma":[40,97],"median":[18,40,44,54,60,61,64,73],"median_unit_cel":[18,19],"medic":[0,89,94],"medium":[1,64,73,87],"meet":[0,89,94,98,99,100],"member":[26,94],"memori":[1,11,14,26,38,54,55,64,82,83,85,94],"memread":[26,27],"mendez":[0,96],"menlo":100,"mental":74,"mention":87,"mercado":[74,96],"merchant":91,"mere":93,"merg":[1,20,33,40,43,44,50,54,56,60,61,64,73,74,75,77,86,87,88],"merge_cbf":72,"merge_imageset_mask":50,"merge_n_imag":56,"merge_panel_scope_extracts_by_id":[23,27],"merged_array":33,"merged_mtz":[1,64],"mergedhalfdataset":33,"mergedmtzwrit":[32,33],"mess":[24,55],"messag":[7,33],"messagepack":3,"messerschmidt":96,"messi":79,"messier":79,"messing":96,"met":91,"metadata":[24,33,44,52,53,64,74,75,76,83,85,86,97],"metal":87,"metalloenzym":96,"method":[0,1,2,7,11,14,15,16,18,20,25,26,29,40,41,43,47,49,51,54,55,59,60,61,64,65,67,70,73,74,75,79,83,85,86,94,96,97,100],"method_i":65,"method_x":65,"methodolog":98,"metr":35,"metric":[40,43,54,61,73,74,75,78,79,83,84,85,86,94],"metric_subgroup":18,"metric_supergroup":11,"metrolog":[51,81],"meyer":2,"mh":[75,96],"mi":[75,96],"miahnahri":96,"michel":[0,89,96],"micro":[0,75,81,94],"microcryst":[74,75,96],"microfocus":98,"micron":89,"microscop":[74,76],"microsecond":96,"micrscop":94,"mid":82,"middl":74,"midpoint":[64,65],"might":[2,4,14,35,75,78,79,82,83,85,86],"mikolajek":96,"milathianaki":96,"mileston":94,"mill":[94,96],"miller":[2,3,18,20,33,39,51,53,54,57,69,77,78,84,86],"miller_index":3,"miller_indic":11,"millimet":[83,85],"millimetr":[3,75],"million":1,"mimick":78,"min":[41,46,51,52,55,59,73,74,75,78,79,82,83,84,85],"min_cc_half":[18,40,70,73],"min_cel":[11,54],"min_cell_volum":54,"min_chunks":[16,47],"min_cluster_s":[54,73],"min_complet":[64,73,77],"min_component_s":57,"min_group":64,"min_group_s":[54,60,61],"min_i_mean_over_sigma_mean":[18,40,70,73],"min_ih":[64,75],"min_isigi":[33,44,64,83,85],"min_isigma":64,"min_lattic":54,"min_loc":[45,47,51],"min_multipl":[64,73],"min_n_reflect":[41,51,55,59],"min_nref_per_paramet":[54,60,61],"min_pair":[18,40,73],"min_parti":[64,73,83,85],"min_partition_s":55,"min_per_area":1,"min_per_dataset":1,"min_pixel":55,"min_point":73,"min_points_buff":73,"min_reflect":[40,64,73],"min_reflections_per_experi":38,"min_sampl":54,"min_sample_s":14,"min_scal":44,"min_spot":[41,51,54,55,59,97],"min_spot_s":[16,47,49,74,76,82,83,84,85],"min_wl":33,"min_zeta":[41,51,55,59],"mind":74,"mini":4,"minicbf":76,"minim":[14,18,40,44,73,77,83,85,94,96,97],"minimis":[14,18,39,54,60,61,64,73,83,85,86,88],"minimize_scipi":[18,19],"minimize_scitbx_lbfg":[18,19],"minimum":[11,14,17,18,20,40,41,43,44,46,47,51,54,55,59,60,61,64,70,73,77,83,84,85],"minimum_angular_separ":[11,54],"minimum_number_of_reflect":[54,60,61],"minimum_sample_s":[54,55,60,61],"miniut":98,"minor":[7,78],"minut":[82,94,98],"mirror":[48,75,83,85,87],"mis":[79,82],"misigma":[43,73],"misindex":[37,54,79],"misorient":82,"miss":[57,74,75,82,88],"misset":[2,83,85,86],"missing_reflect":72,"mitig":11,"mittan":94,"mitzner":96,"mix":[54,60,61],"mixin":14,"mj":96,"mkdir":[48,74,75,76,77,82],"ml":[40,74,83,85,96],"ml_aniso":[18,40,70,73],"ml_aniso_normalis":18,"ml_iso":[18,40,70,73],"ml_iso_normalis":18,"mm":[3,14,20,23,35,47,50,51,52,54,60,61,75,79,82,83,84,85,86,96],"mm_search_scop":[54,65],"mmcif":[44,71,77],"mmm":77,"mmtbx":33,"mn\u2084ca":96,"mod_python":48,"mode":[4,15,18,33,34,40,52,54,60,61,62,64,73,75,76,77,83,85,86],"model":[0,3,6,10,11,12,14,18,19,20,26,27,30,31,32,33,34,35,36,38,39,40,41,42,44,45,47,50,51,52,53,54,55,58,59,60,61,62,63,64,65,66,67,69,70,71,73,74,75,77,78,82,83,84,85,86,87,88,93,96,97,98],"model_evalu":19,"model_likelihood":11,"model_param":15,"modelevalu":11,"modelnam":4,"modelrank":11,"modelrankfilt":11,"modelrankweight":11,"models_1":39,"models_2":39,"models_with_profil":41,"modern":[2,94],"modif":[56,91],"modifi":[15,40,41,47,48,50,54,65,67,74,82,83,84,85],"modpython":48,"modul":[2,4,14,15,18,33,64,78,80,85,86],"modular":82,"modulation_correct":[1,64],"mol":[74,96],"molecul":[0,81,96],"molecular":[74,75,76,78,96,99],"moment":[24,54,60,61,82],"monitor":94,"mono":[11,54],"monochromat":[52,95],"monoclin":[18,40,61,70,73,75,83,85,86],"montero":[0,89,96,99],"month":96,"moor":14,"moral":79,"moreau":94,"mori":96,"moriarti":[0,2,96],"mosaic":[3,22,41,51,54,55,59,75,80,83,85,97],"mosaiccrystalkabsch2010":[22,27],"mosaiccrystalsauter2014":[22,27],"mosaicity_max_limit":[41,51,55,59],"mosaicity_toler":22,"mosflm":[0,2,22,44,52,55,98],"mosflm_a_matrix":22,"mosflm_beam_centr":52,"mosquito":96,"motion":96,"motiv":[64,83,85],"motor":2,"motorlog":48,"mount":[2,35],"mous":[74,75,86],"move":[23,33,54,60,61,74,78,82,85,86,94],"movement":0,"movi":74,"mp":[47,54,55,60,61,74,78,79,80,83,84,85],"mp_chunksiz":16,"mp_method":16,"mp_njob":16,"mp_nproc":16,"mplex":77,"mpm":48,"mpm_prefork_modul":48,"mpro":81,"mpro_x0692":83,"mr":96,"mrc":99,"ms":[46,75,96],"msgpack":20,"mt":75,"mtb":[75,76,96],"mtz":[1,33,40,43,44,62,64,73,74,75,76,77,80,82,84,93],"mtz_unmerg":80,"mtzs":76,"mtzwriterbas":[32,33],"mu":[14,23,35,83,85],"much":[0,9,74,75,79,82,83,85,86,87],"mullick":96,"mult":[74,83,84,85],"multi":[1,2,15,16,18,20,33,38,40,42,44,45,48,51,52,54,55,60,61,64,73,81,83,85,86,96],"multi_axi":25,"multi_axis_goniometer_from_phil":25,"multi_crystal_analysi":73,"multi_dataset":[1,64],"multi_panel":[45,51,52],"multiaxisgoniomet":[25,27],"multipanelimagevolum":20,"multipl":[1,3,4,11,16,33,34,36,38,39,40,43,45,47,50,51,52,54,55,60,61,64,65,67,69,70,71,73,74,75,77,79,80,82,83,84,85,86,87,93,97,98,99],"multiple_lattice_search":54,"multiplex":[72,81,96],"multipli":[20,35,41,47,51,54,55,59,60,61],"multiplicities_h_0":77,"multiplicities_k_0":77,"multiplicities_l_0":77,"multiprocess":[14,24,54,55,60,61,83,85],"multitemperatur":96,"multivari":[41,51,55,59,86],"muon":95,"murshudov":[0,96,99],"must":[1,2,4,7,14,15,20,33,36,52,53,54,55,60,61,64,65,67,75,76,77,83,85,86,91],"mutual":[2,51],"muuss":75,"mv":82,"mx":[80,83,85,98],"mx27124":83,"my_format_modul":4,"mybeamlin":4,"mycalingmodel":4,"myd88":[75,81],"myeloid":75,"myformat":4,"mylatticesearch":4,"mymodel_phil_str":4,"myparam":7,"mypath":4,"myproject":4,"myscalingmodel":4,"mystrategi":4,"mystrategy_phil_str":4,"n":[0,2,3,4,6,11,18,20,21,22,33,35,40,55,59,65,73,74,83,84,85,86,96],"n_absorption_bin":[1,64],"n_bin":[15,38,47,51,55,64,73],"n_convolut":65,"n_cycl":[41,51,55,59],"n_digit":44,"n_equat":14,"n_index":11,"n_indexed_cutoff":[11,54],"n_indexed_threshold":54,"n_indexed_weight":[11,54],"n_iqr":[47,51],"n_macro_cycl":[41,51,54,55,59,65,79],"n_merg":44,"n_modulation_bin":[1,64],"n_new_param":15,"n_old_param":15,"n_param":15,"n_paramet":[14,83,85],"n_point":[11,54],"n_ref":18,"n_refl":[38,83,85],"n_refl_panel_list":38,"n_resolution_bin":[1,64],"n_shell":73,"n_sigma":[41,51,55,59],"n_spot":54,"n_static_macrocycl":60,"n_subset":38,"n_subset_method":38,"n_subset_split":55,"n_trial":[54,60,61],"n_xtal":[40,97],"na":75,"naismith":96,"nakan":[0,96],"name":[2,3,4,6,7,14,15,20,23,24,25,26,30,31,33,35,36,42,44,45,48,50,51,52,54,60,61,63,64,67,71,79,80,82,83,84,85,86,87,91],"namespac":4,"nangca":96,"nango":96,"nannenga":96,"nano":98,"nanoimag":74,"nanson":75,"narrow":[11,47,51,54,86],"nass":96,"nat":[75,96],"nathaniel":0,"nation":[0,35,89,91],"nativ":[18,20,80,82,84],"nativig":85,"natl":[2,96],"natur":[54,60,61,85,86,96],"nave":54,"navig":[83,86],"nb":20,"nbin":[16,43,64,73],"ncol":20,"ncs":78,"ndarray":18,"near":[11,14,75,79,82],"nearest":[54,55,57,67,86],"nearest_neighbor":11,"nearest_neighbor_percentil":[11,54],"nearest_neighbour":[11,54],"neat":[79,82],"necessari":[1,2,11,15,20,40,55,74,76,77,82,83,85,87,93],"necessit":26,"need":[1,2,4,9,14,16,21,24,25,40,41,47,51,53,55,59,61,64,74,75,76,77,78,79,82,83,85,86,87,90,94,98],"needl":64,"neff":[18,40,73],"negat":[20,44,74,76,77,80],"neglig":[75,83,85,91],"negro":[74,96],"neighbor":[55,65],"neighboranalysi":11,"neighbour":[54,57,83,85,86],"neither":91,"nelson":96,"ness":54,"nest":[4,15,46],"net":[18,48,83,86,89],"network":96,"netzcc":[40,74,77,83,84,85,86],"neuron":96,"neutron":[0,2,52],"never":82,"nevertheless":[2,78,82],"new":[0,1,2,7,9,14,15,16,23,26,48,54,60,61,64,72,74,75,76,78,79,82,83,85,86,89,90,94,95,96,98],"new_image_0":15,"new_image_rang":15,"new_norm_fac":15,"newli":[83,85],"newton":14,"next":[6,40,75,77,83,84,85,86],"nexus":[33,42,44,94],"nfold":64,"nframe":55,"nframes_hist":[12,19],"ng":96,"nice":[33,74,75],"nicer":82,"nichola":0,"nick":98,"nieusma":[74,96],"nigel":0,"nigg":40,"night":[80,90],"nigm":89,"nih":89,"nilsson":96,"nis":74,"nist":35,"nj":[74,96],"njob":[47,55],"nk":[89,96],"nn":54,"nn_hist":11,"nn_per_bin":[11,54],"no_shoeboxes_2d":16,"noauto":73,"node":[23,86],"nois":[42,47,51,73,76,83,85],"noise_penalti":73,"noise_ratio":[],"noise_toler":[],"non":[11,14,53,54,60,61,73,83,85,86],"non_linear_l":14,"non_linear_ls_mixin":14,"none":[1,4,6,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,29,30,31,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,50,51,52,53,54,55,57,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,79,97],"nonisomorph":1,"nonumb":2,"norm":14,"norm_fac":15,"normal":[14,20,21,35,38,41,51,52,54,55,59,60,61,79,80,83,85,86],"normal_matrix":14,"normalis":[1,15,18,35,37,40,43,64,70,73,83,85],"normalise_bin":37,"normdevoutlierreject":15,"not_suitable_for_refin":20,"notabl":82,"note":[14,35,53,75,77,78,79,82,83,84,85,86,87,90,97],"noth":[25,52,75],"notic":[78,82,83,85,86,91],"notwithstand":[2,79,82],"nov":96,"novemb":100,"novo":96,"now":[4,6,33,74,75,76,77,78,79,82,83,84,85,86,93],"np":18,"nproc":[1,14,16,18,40,47,49,54,55,60,61,64,65,73,74,83,85],"nref":[74,75,79,82,83,84,85,86],"nref_per_degre":14,"nrow":20,"nsigma":55,"nsigma_":[45,51],"nsigma_b":[45,51],"nthread":20,"ntri":74,"null":[31,54,55,60,61,82],"null_background_ext":31,"nullbackgroundext":[31,32],"nullify_all_single_file_reader_format_inst":24,"num":[83,84,85,97],"num_candidate_vector":54,"num_halfsphere_point":54,"num_reflect":12,"num_scan_point":25,"number":[1,2,4,7,11,12,14,15,16,17,18,20,33,37,38,40,41,43,44,45,47,48,49,51,52,54,55,56,59,60,61,64,65,66,67,68,70,71,73,74,75,77,79,82,83,84,85,86,87,89,96,97],"number_of_dataset":73,"number_of_dimens":73,"number_of_partit":55,"numer":[0,1,14,18,20],"nune":96,"nureki":96,"nw":96,"nx":47,"nxmx":44,"nxs":44,"ny":[47,100],"o":[0,2,22,74,76,80,96],"o2":96,"oa":96,"ob":[74,83,84,85,96],"obj":[4,15,24,28],"object":[2,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,28,29,30,31,33,52,54,60,61,67,82,98,99],"objective_on":14,"obliqu":[18,40,61,70,73],"observ":[11,14,16,18,20,35,40,41,44,54,60,61,63,66,67,70,75,77,79,80,82,83,84,85,86,87],"obtain":[1,2,4,14,15,40,54,60,61,76,78,79,83,96,97],"obvious":[6,76,83,85],"oc":[78,79,80,84,85],"occas":[41,77],"occur":[75,76,83,85,86],"oct":96,"octob":100,"odd":78,"offer":[79,98],"offset":[11,15,23,52,54,64,65,75,79,82,83,85],"offsetparallaxcorrectedpxmmstrategi":52,"often":[1,2,4,11,35,54,75],"ogata":96,"ok":[80,86,87],"okay":[74,75],"old":79,"old_test_flag_valu":73,"older":[42,86],"oleg":0,"oliv":0,"omega":[2,25,52],"omit":[83,85],"onc":[7,40,47,52,54,74,75,77,82,83,84,85,86,87],"one":[0,1,2,6,11,14,15,16,20,24,36,38,40,44,47,50,53,54,55,60,61,62,64,70,71,73,74,75,76,77,78,79,82,83,84,85,86,87,93,97],"one_osc_width":15,"ongo":98,"onli":[1,2,4,6,7,11,14,18,26,33,36,38,44,45,46,47,54,55,56,57,60,61,64,65,70,71,73,74,75,77,78,79,82,83,84,85,86,87,93,97],"onlin":[35,75,76],"only_save_target":64,"only_target":[1,64],"ons":33,"onto":[11,54,78,79,94],"onward":78,"ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo":80,"oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo":80,"op":[18,74,78,79,80,83,84,85,87],"open":[0,3,51,72,74,75,77,83,85,86,90,96],"oper":[2,4,14,18,24,37,39,40,46,47,48,61,62,74,75,77,78,79,82,83,84,85,86,87],"oppos":64,"opposite_of_grad_object":14,"optic":[73,98],"optim":[1,18,75,83,85,86,94,96],"optimis":[11,64,65,73,74,75,79,83,85,86,97],"optimise_basis_vector":11,"optimise_initial_basis_vector":54,"optimise_input":73,"option":[3,4,6,7,11,15,18,33,34,38,39,40,44,45,46,47,50,51,52,54,55,56,58,60,61,62,63,64,65,67,68,69,70,71,73,75,77,78,82,83,84,85,86,87,88,93,97],"optionpars":[32,33],"orang":74,"order":[1,4,9,11,14,15,20,23,33,36,38,52,54,55,56,60,61,64,65,75,79,82,83,85,86,87],"org":[11,18,47,48,54,60,61,76,83,87],"organic":[74,87],"organis":[77,100],"orient":[11,35,39,41,51,54,55,58,59,60,61,63,73,74,76,82,83,85,86,87,96,97,98],"orientation_decomposit":[58,63],"origin":[2,3,4,20,23,38,46,52,54,65,67,73,75,76,77,79,80,83,85,86,95],"origin_toler":[23,24],"orthogon":[2,35,54,60,61],"orthonorm":2,"orthorhomb":[74,76,78,79],"orvill":96,"os":[4,90],"osc_rang":15,"osc_start":29,"osc_width":29,"oscil":[1,3,12,15,29,38,52,54,60,61,64,76,78,83,85],"other_crystal_model":11,"other_index":20,"others":[74,79,98],"otherwis":[14,21,46,47,50,51,54,60,61,65,75,76,82,83,85,86,91],"out_beam_plan":[54,60,61],"out_spindle_plan":[54,60,61,74,76],"outer":[43,48,73,82,87],"outgo":1,"outlier":[1,14,15,18,40,54,55,60,61,64,73,74,77,82,83,84,85,86],"outlier_detector":14,"outlier_in_sc":[15,20],"outlier_index_array":15,"outlier_prob":[41,51,55,59],"outlier_reject":[18,19,64,73],"outlier_rejection_after_filt":18,"outlier_zmax":[64,86],"outlierrejectionbas":15,"outlin":[76,79,83,85],"outofsequencefil":76,"output":[1,3,6,7,14,20,33,34,35,36,37,38,40,41,42,43,44,45,46,47,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,70,71,73,74,75,76,77,79,82,83,84,85,86,97],"output_clust":73,"output_unintegrated_reflect":55,"outreach":94,"outright":79,"outset":77,"outsid":[2,14,20,38,67],"outward":[77,79],"overal":[18,40,41,44,51,54,55,59,60,61,73,75,76,77,79,80,82,83,84,85,86,87,97],"overbias":64,"overcom":97,"overflowerror":20,"overinfl":1,"overlaid":51,"overlap":[20,46,54,75,83,85,86,87],"overlapped_bg":20,"overlapped_fg":20,"overlaps_bord":[11,54],"overlaps_filt":55,"overlay":75,"overload":[14,20,75,80,82,83,84,85],"overparameteris":1,"overrid":[4,14,18,41,43,45,47,51,52,54,55,59,60,61,67,73,76,82],"overridden":[14,52],"overview":1,"overwrit":[23,25,38,52,82],"overwrite_existing_model":64,"overwrite_from_phil":23,"overwritten":75,"owada":96,"owen":96,"owner":91,"oxford":2,"oxid":96,"p":[0,2,3,11,18,40,48,70,71,74,75,76,77,78,79,80,82,83,84,85,86,87,96,97],"p1":[18,22,54,74,75,77,83,85,97],"p2":[74,83,85],"p21":[74,85],"p21212":74,"p212121":74,"p22121":84,"p222":[74,84,87],"p2221":74,"p4":[77,82,97],"p43212":[54,77],"p4p":[71,77,87],"p6m":82,"p6m_60_panel":82,"p_cc_given_":18,"p_cc_given_not_":18,"p_s_given_cc":18,"paciorek":2,"packag":[0,2,4,9,89,90,94,96,98],"packed_u_accessor":14,"pad":[17,20,23,41,45,51,55,82],"page":[11,18,48,54,65,74,75,79,80],"pair":[1,2,14,18,20,23,34,40,43,48,54,56,64,65,67,73,74,76,77,79,83,85],"pairwis":[11,39,40,73,77],"palatinus":96,"paley":[0,94,96],"panda":20,"panel":[3,14,23,38,45,46,47,50,51,52,54,55,56,60,61,74,75,76,77,82,83,85,86],"panel_param":23,"paper":[75,76],"parallax":[47,50,51,52],"parallax_correct":52,"parallaxcorrectedpxmmstrategi":[3,83,85],"parallel":[1,2,16,24,35,38,48,82,83,85,86,96,98],"parallelepip":[54,60,61],"param":[4,6,11,12,14,15,16,18,20,21,22,23,25,26,29,30,31,33,55],"param_report":14,"paramet":[1,2,4,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,29,30,31,33,74,75,76,82,83,84,85,86,87,94,97],"parameter_correlation_plot":14,"parameter_esd":4,"parameter_t":60,"parameter_valu":64,"parameter_vector_norm":14,"parameteris":[1,2,14,15,54,60,61,74,75,76,82,83,85,97],"parameterreport":14,"parameters_dict":[4,15],"parametr":99,"paramt":94,"pareja":96,"parent":[76,86],"parenthes":46,"pari":11,"park":[96,100],"parkhurst":[0,11,76,89,96,99],"pars":[4,6,33],"parse_arg":[6,33],"parse_known_arg":33,"parser":[6,33],"part":[1,2,14,20,47,54,60,61,74,75,81,82,83,85,86,94,97],"parti":[0,9],"partial":[1,3,18,20,40,44,46,54,60,61,64,70,71,73,75,78,82,83,84,85,96],"partial_data":26,"partial_set":26,"partiality_cutoff":[44,64,73,83,85],"partiality_threshold":[1,33,40,44,70,71],"particular":[2,4,26,47,54,60,61,75,76,77,79,86,87,91,97],"pascal":96,"pass":[6,7,14,18,23,45,46,49,51,52,64,75,77,78,82,83,84,85,87],"passag":35,"past":[38,55],"paste":[75,82],"pastor":96,"patch":7,"paterson":96,"path":[1,4,7,26,34,35,36,37,38,40,43,44,45,47,48,49,50,51,52,53,54,55,56,60,61,62,63,64,65,68,69,70,73,75,82,90],"pathlib":4,"patholog":73,"pattern":[37,74,76,78,79,82,83,85,96,98],"patterson":[18,40,74,77,83,84,85,86,96],"patterson_group":18,"paus":79,"pay":[75,77,86],"pb":96,"pbs":[47,55],"pcm":83,"pd":96,"pdb":[2,40,44,51,62,64,73,75,78,83],"pdb_version":44,"pdf":[18,54,58,60,61,72],"peachi":25,"peak":[11,47,51,54,75,83,84,85,86,95],"peak_search":54,"peak_volume_cutoff":[11,54],"peakcentroiddistancefilt":[16,19],"peakfind":47,"pearson":18,"pearson_correlation_coeffici":18,"peculiar":76,"pedest":[23,26,52,83,85],"penalti":73,"penros":14,"peptid":96,"per":[1,14,15,24,35,36,38,40,41,43,47,51,54,55,59,60,61,64,68,73,74,75,77,80,83,84,85,86,93,97],"per_degre":[41,51,55,59],"per_imag":[14,65,68],"per_image_statist":47,"per_width":14,"percent":[33,54,78],"percent_bandwidth":54,"percentag":[33,64,65,73],"percentil":[11,54],"perfect":35,"perform":[0,2,6,9,11,14,15,18,20,37,40,41,43,44,54,55,57,60,61,64,69,73,74,75,79,82,83,84,85,86,87,89,94,97],"perhap":[1,44,79],"period":[4,11,83,85,86],"permiss":[7,55,91],"permit":91,"pernici":79,"perpendicular":[34,69,77],"perraki":98,"perspect":[87,98],"pet":44,"peter":96,"petrov":0,"pflugrath":[0,98],"pfuetzner":96,"ph":96,"pham":96,"pharmaceut":[74,96],"phase":[11,74,78,96],"phaser":74,"phenix":73,"phi":[2,14,22,25,52,54,60,61,64,69,76,79,82,83,85,86],"phi_angl":69,"phic":[82,83,85],"phil":[0,3,4,6,7,11,12,14,15,18,21,22,23,25,29,31,33,51,55,64,75,76,99],"phil_help":11,"phil_scop":[4,6,11,15,18],"philcommandpars":[32,33],"philo":96,"philosophi":0,"phio":[82,83,85],"photon":[0,75,96,98],"photosynthet":96,"photosystem":96,"physic":[1,2,4,15,35,64,73,83,85,86,87,96,98],"physicalscalingmodel":15,"pick":[75,76,78,86],"pickl":[11,16,20,24,38,47,51,76],"pictur":74,"pigment":96,"pilatus":[4,48,79,82,83,85,86],"pim":[77,84],"pink":[11,83,85],"pink_index":54,"pinkindex":11,"pipelin":[0,78,80,83,85,96,97],"pixel":[2,3,16,20,23,31,36,41,42,45,47,50,51,52,54,55,60,61,63,65,74,75,79,80,82,83,84,85,86,89,96,97,98],"pixel_label":16,"pixel_list_to_reflection_t":[16,19],"pixel_list_to_shoebox":[16,19],"pixel_s":[3,23,52,75,83,85],"pixellistlabel":16,"pixels1":36,"pixels2":36,"pixels_per_bin":63,"pj":96,"pkg":90,"pkg_util":4,"place":[14,20,24,34,44,52,74,76,78,82,83,85],"placement":0,"plan":95,"plane":[2,20,21,34,54,55,60,61,69,75,76,87],"plane_norm":69,"plate":[35,77,83,85,86],"platform":90,"platon":74,"plausibl":[83,85],"play":[75,83,85],"pleas":[4,9,64,73,78,79,80,81,82,84,85,86,87,89,94],"plenti":82,"plop":74,"plot":[1,12,15,20,31,58,60,63,64,65,68,69,71,74,75,77,82,83,84,85,86,97],"plot_centroid_analysi":[54,60,61],"plot_displac":11,"plot_histogram":11,"plot_model_compon":15,"plot_scaling_model":15,"plot_scan_varying_model":[72,75],"plot_search_scop":65,"plug":[74,76],"plugin":4,"plus":[3,14,15,30,83,85,86],"pmatrix":2,"pmc":[74,75,76,96],"pmc10161776":96,"pmc10191843":96,"pmc11363319":96,"pmc11462730":96,"pmc11700371":96,"pmc12128884":96,"pmc3382516":96,"pmc3448510":96,"pmc3689530":96,"pmc3732582":96,"pmc4008696":96,"pmc4052861":96,"pmc4052878":96,"pmc4070675":96,"pmc4119952":96,"pmc4151126":96,"pmc4156696":96,"pmc4188007":96,"pmc4248568":96,"pmc4257623":96,"pmc4260607":96,"pmc4273327":96,"pmc4321488":96,"pmc4321489":96,"pmc4344359":96,"pmc4397907":96,"pmc4403592":96,"pmc4461207":96,"pmc4607316":96,"pmc4721965":96,"pmc4791177":96,"pmc4822564":96,"pmc5139990":96,"pmc5161637":96,"pmc5201176":96,"pmc5619854":96,"pmc5754760":96,"pmc5930348":96,"pmc5947772":96,"pmc6096487":[76,96],"pmc6130462":96,"pmc6450062":96,"pmc6485242":96,"pmc6834081":96,"pmc7137103":96,"pmc7417479":96,"pmc7615503":96,"pmc7737759":[74,96],"pmc8110528":75,"pmc8313502":[74,96],"pmc8740827":96,"pmc8770144":96,"pmc9159281":96,"pmid":[74,75,76,96],"png":[6,11,45,58,68,69,71,77,82],"point":[2,3,7,11,14,18,20,38,40,44,54,55,66,73,74,75,76,77,78,79,82,83,84,85,86,87,93],"pointer":26,"pointgroup":54,"pointless":[18,40,44,70,76,78,85],"pointless_combin":76,"pointless_reindex_":76,"poisson":[42,79,83,85,86],"poitevin":96,"pokeri":6,"polar":[21,38,52,83,85,96],"polarization_fract":[3,21,38,52],"polarization_fraction_toler":24,"polarization_norm":[3,21,38,52],"polarization_normal_toler":24,"polarization_plane_norm":21,"polici":14,"polish":86,"polychromat":[11,52,54,96],"polychromaticbeam":21,"polygon":[47,50,51],"polyhedrin":96,"polynomi":[43,73],"poon":[0,54,60,61],"poor":[1,47,54,60,61,74,75,76,77,78,81,82,83,85,86],"poorer":1,"pop":86,"poppl":96,"popul":[15,20,26,33,97],"port":49,"posit":[0,1,2,3,11,14,15,20,33,40,47,54,55,60,61,64,65,67,70,73,74,75,76,77,79,80,82,83,84,85,86,87],"positional_coordin":[54,60,61],"posix":76,"possibl":[0,1,2,4,11,14,18,33,34,37,40,54,57,60,61,70,74,75,76,77,78,79,80,83,84,85,86,87,91,94],"post":[12,83,85,86,89,96],"potenti":[14,54,60,61,62,73,74,77,83,85],"pothineni":96,"potter":[74,96],"powder":[45,46,47,50,51,75,76,82,83,84,85],"powder_arc":51,"powel":[0,99],"poweleit":[74,96],"power":[11,54,77,83,85],"pp":0,"pr":75,"practic":[2,14,74,75,78,83,85,86,88],"pre":[1,12,83,85,86],"preced":14,"precis":[44,83,85],"pred_param":14,"predict":[3,11,14,16,17,20,40,41,44,51,54,55,60,61,72,75,76,82,83,84,85,86],"predict_for_free_reflect":14,"predict_for_index":14,"predict_for_reflection_t":14,"predict_reflect":51,"prediction_parameteris":14,"predictionparamet":14,"predictionparameteris":14,"predictor":[14,17],"prefer":[9,18,40,47,61,70,73,75,77,82,83,85,86],"prefilt":15,"prefix":[7,12,44,45,47,54,60,61,90],"preliminari":73,"prepar":[7,14,18,64,74,77,80,87],"prepare_datasets_for_symmetry_analysi":[18,19],"prepare_for_step":14,"preprocess":[47,51,83,85],"prerequisit":9,"preselect":[83,85],"presenc":[18,40,78,87,96],"present":[0,14,15,18,33,40,44,46,53,54,60,61,62,67,72,73,77,78,79,82,83,84,85,86,87,89,100],"preserv":[],"press":[2,79,86],"pressur":35,"presum":[23,75],"pretend":4,"pretti":[18,79,86],"preview":[83,85,86],"previous":[15,64,76,77,82,83,85,86],"prf":[3,20,40,55,75,82,83,84,85],"primari":[25,33,34,75],"primarili":[11,20,44,54,83,85,86],"prime":[0,2],"primit":[11,54,61,74,78,79,83,85,86,87],"princip":[14,40,77,94],"principl":[11,21,34],"print":[6,7,12,14,18,33,46,47,58,61,65,66,75,79,83,85,86],"print_exp_rmsd_t":14,"print_funct":4,"print_help":6,"print_out_of_sample_rmsd_t":14,"print_panel_rmsd_t":14,"print_stats_on_match":14,"print_step_t":14,"print_tim":33,"printabl":72,"printf":77,"prior":[2,11,55,75,83,85,86,87,91],"prioriti":52,"privat":14,"probabl":[1,11,18,40,41,51,54,55,59,60,61,74,77,83,84,85],"probe":[21,52,83,85],"problem":[0,14,75,78,79,80,83,85,86,93],"problemat":14,"proc":[75,76,96],"procedur":[11,40,73,75,83,85,86],"proceed":[0,11,54,60,61,75,77,78,79,83,84,85,86,87,93],"process":[0,1,3,7,12,14,16,20,31,38,40,41,44,47,48,51,52,53,54,55,59,60,61,64,72,73,76,78,79,80,81,82,83,84,87,88,89,94,96,98,100],"process_includ":6,"processor":[12,14,16,48,55,73,83,85,86],"processor2d":[12,19],"processor3d":[12,19],"processorclass":12,"processorflat3d":[12,19],"processorsingle2d":[12,19],"processorstil":[12,19],"procur":91,"produc":[7,20,38,44,54,55,60,61,67,75,76,78,79,82,83,85,86,97],"product":[2,11,91,94],"product_nam":33,"product_specific_finalize_instal":33,"profil":[1,3,12,20,24,27,31,32,35,40,41,44,47,51,55,59,64,65,73,75,78,79,82,83,84,85,86,94,95],"profile_fitt":12,"profile_model":[3,4,19,20,32],"profile_model_report":12,"profile_validation_report":12,"profilemodelfactori":[27,28],"profilemodellerexecutor":[12,19],"profilevalidatorexecutor":[12,19],"profit":91,"program":[1,3,7,8,34,35,36,37,40,41,42,44,46,47,50,51,52,53,54,55,56,59,61,62,63,64,70,73,74,75,78,79,80,83,84,85,86,87,94,97,100],"progress":[0,18,33,65,84,94,95],"progressbar":[32,33],"progressbartim":[32,33],"prohibit":1,"project":[0,2,11,44,45,51,64,65,69,77,80,84,89,94,96,98,99],"project_nam":[33,44,64],"project_root":48,"project_src":48,"promot":91,"prompt":75,"proper":[7,17,20,33,74,75,76,78,79],"properti":[1,2,11,14,15,18,25,26,29,33,35,47,96],"proport":75,"propos":[83,85,86],"prospect":98,"proteas":81,"protein":[64,74,75,76,83,96],"protocol":[20,76],"proton":96,"prototyp":0,"provid":[0,1,4,7,11,14,15,18,20,23,24,33,36,38,40,43,47,50,51,52,53,54,55,62,64,67,70,71,73,74,75,76,77,78,79,82,83,85,86,90,91,94,97,98],"proxim":[47,54],"prudent":[75,86],"ps":96,"pseudo":78,"pseudocentr":79,"pseudoinvers":14,"psi":[2,14,54,60,61],"psi_i":2,"psi_x":2,"psi_z":2,"pt":[74,96],"public":[0,14,75,76,89],"publish":[0,75,83],"pull":[4,86],"pure":[2,14],"purpos":[60,75,78,82,83,85,86,91],"push":75,"put":7,"putat":[54,75,79],"pv":96,"pwd":76,"px":[3,20,47,50,51,52,74,75,79,82,83,84,85],"px_mm":23,"px_mm_strategi":3,"px_sz":[54,60,61],"py":[4,9,74,76],"python":[0,3,4,7,9,22,23,24,25,26,65,80,94,96],"python2":80,"pytorch":11,"q":[84,96],"q1":[82,83,85],"q3":[82,83,85],"qe":3,"quad":[54,76],"quadrat":64,"qualiti":[0,1,45,48,49,73,74,75,79,82,83,84,85,86,96,98],"quantil":[54,60,61],"quantiti":6,"quantum":3,"quarter":[82,86],"quasi":[18,40,70,73,95],"quasi_random":[1,64,73],"queri":14,"question":[77,79,81],"quick":[1,49,64,75,82],"quick_pars":33,"quicker":82,"quit":[11,21,44,54,74,75,76,79],"r":[0,1,2,6,11,15,18,35,40,43,47,50,51,64,70,73,74,77,78,84,93,96],"r2":96,"r24":94,"r24gm154040":[0,89,94],"r_":[2,18,77],"r_0":2,"r_anom":[74,83,85],"r_free_array":33,"r_free_flag":73,"r_mea":[74,83,84,85],"r_mrg":[74,83,84,85],"r_pim":[74,83,84,85],"ra":96,"rachel":0,"rad":[3,14,54,60,61],"radial":[11,47,54,60,61],"radial_profil":47,"radial_transvers":[54,60,61],"radialaverag":[10,19],"radian":[11,20,54,55],"radiat":[1,73,74,75,79,82,83,85,86,96],"radic":96,"radius":[54,65],"rahaman":75,"rainbow":[45,51],"rais":[15,20,40,52,54,60,61,70],"ram":82,"ran":77,"random":[14,20,38,54,55,60,61,64,65,73,82,83,85,98],"random_se":[54,55,60,61],"random_split":20,"rang":[1,15,16,18,26,40,47,50,51,52,54,55,60,61,64,65,67,70,73,75,80,83,84,85,86],"rank":40,"rapid":[0,77,97,98],"rapidata":100,"raster":[48,77],"rate":[82,86,98,100],"rather":[1,2,7,64,75,76,77,79,82,83,85,86,87,98],"ratio":[14,20,40,77],"ration":20,"raw":[3,9,44,45,47,48,54,56,66,74,76,83,85,86],"rawdata":48,"rawdescriptionhelpformatt":33,"ray":[0,2,11,22,33,35,52,74,75,79,83,85,89,95,96,98,100],"rb":96,"re":[16,34,61,62,73,76,77,84,96],"reach":[14,54,60,61,98],"read":[1,2,3,4,5,20,23,24,25,26,29,33,40,56,74,75,79,83,84,85,86,96],"read_experi":[6,33],"read_experiments_from_imag":33,"read_fil":33,"read_reflect":[6,33],"read_varying_cryst":53,"readabl":3,"reader":[26,32,33,72,75,79],"readi":[7,44,76,86],"readthedoc":65,"real":[2,4,11,20,77,78,79,82,83,85,86,96,97],"real_space_a":[3,22,30],"real_space_b":[3,22,30],"real_space_c":[3,22,30],"real_space_grid_search":[4,11,54,86,97],"realist":77,"realli":[74,77,82],"realspacegridsearch":11,"reason":[1,2,54,60,61,74,75,76,77,78,79,83,84,85,87],"reason_for_termin":14,"rebuild":78,"recent":[33,80,89,98],"receptor":75,"reciproc":[1,2,3,4,11,14,18,20,22,31,34,40,41,44,47,51,54,55,59,73,75,78,79,83,85,86,87],"reciprocal_lattice_point":11,"reciprocal_lattice_vector":[4,11],"reciprocal_lattice_view":[75,77,78,79,82,83,85,86,87],"reciprocal_spac":[41,51,55,59],"reciprocal_space_grid":54,"recognis":[24,75,79],"recombin":93,"recommend":[1,3,7,54,60,61,64,74,75,76,83,84,85],"reconcil":2,"reconstruct":11,"record":[2,4,14,15,44,54,60,61,74,75,77,78,79,80,82,83,84,85,87],"record_intensity_combination_imid":15,"recov":35,"recreat":76,"rectangl":[47,50,51,76],"rectangular":14,"recycle_unindexed_reflections_cutoff":54,"red":[45,74,75,83,85,86],"redefin":2,"redistribut":91,"reduc":[1,2,14,15,35,40,45,47,51,54,60,61,67,73,74,77,83,85,86,87],"reduct":[14,53,54,78,81,83,85,86,97,98],"reductas":96,"redund":84,"redundant_comput":54,"ree":0,"ref":[10,43,73],"refactor":94,"refelct":64,"refer":[2,8,14,18,20,21,22,23,25,29,37,38,40,41,43,51,52,55,58,59,62,63,64,67,72,73,76,82,83,85,86,88,97],"reference_from_experi":[38,82,93],"reference_geometri":[52,76],"reference_miller_set":18,"reference_model":[40,62,64],"reference_profil":55,"reference_spot":[20,46],"refin":[1,3,4,11,15,18,19,20,32,38,41,44,46,51,54,55,58,59,61,63,64,71,72,73,77,78,79,80,81,88,96,97,99],"refine_all_candid":54,"refine_bravais_set":[72,74,75,76,78,79,83,84,85,86,87],"refine_candidates_with_known_symmetri":54,"refine_shel":54,"refined_cel":[71,87],"refined_experi":76,"refined_lev0":82,"refined_lev1":82,"refinement_ord":64,"refinement_param":[],"refinement_protocol":54,"refinerfactori":[14,19],"refineri":[14,19,54,60,61,64],"refl":[1,3,6,35,37,38,40,41,43,44,46,47,51,53,54,55,57,59,60,61,62,63,64,65,66,67,68,70,71,73,74,75,77,78,79,80,82,83,84,85,87,93,97],"reflect":[2,4,6,10,11,12,14,15,16,17,18,20,31,33,35,37,38,40,41,43,44,46,47,51,53,54,55,57,59,60,61,62,64,65,66,67,69,70,71,73,74,75,76,78,79,80,82,83,84,85,86,87,88,97,99],"reflection_file_object_list":33,"reflection_manag":14,"reflection_predictor":17,"reflection_select":[1,64,73],"reflection_t":[3,4,11,12,14,15,16,18,20,32,33],"reflection_table_selector":55,"reflectionmanag":[12,14,19],"reflectionmanagerfactori":[14,19],"reflectionpredictor":[17,19],"reflections_":[87,93],"reflections_0":[38,40,87],"reflections_1":[38,40,87],"reflections_2":[40,87],"reflections_3":[40,87],"reflections_after_outlier_reject":14,"reflections_and_experiments_from_fil":[32,33],"reflections_filenam":[38,67],"reflections_per_bin":[43,73],"reflections_per_degre":[41,51,54,55,59,60,61],"refman":14,"refresh":4,"regard":[75,86],"regardless":1,"regev":96,"region":[2,11,16,46,47,57,65,75,76,78,82,86],"region_of_interest":[16,47],"regist":4,"registri":4,"regress":94,"regular":[1,40,47,55,64,67,70,73,77,79,82,84,97],"regular_grid":[41,51,55,59],"rehanek":96,"reindex":[18,20,24,40,54,61,72,73,74,75,76,77,78,79,83,84,85,86,87],"reindex_to_refer":18,"reintegr":55,"reinvent":0,"reject":[1,14,15,18,43,46,47,50,51,54,55,60,61,64,73,74,82,83,84,85,86],"reject_fract":46,"reject_outli":15,"rejectiob":15,"rejector":[54,55,60,61],"relat":[1,2,11,14,15,18,20,37,39,47,54,58,60,61,63,64,73,74,77,78,79,82,83,85,86,87],"relationship":[2,3,52],"relative_b_correct":64,"relative_length_toler":[11,18,40,54,70,73],"relative_to_complete_set":73,"relative_to_static_orient":[58,63],"releas":[7,40,83,85],"relev":[14,43,44,53,83,85,86,87],"reli":93,"reliabl":[64,74,83,85,87],"relocat":63,"relp":[54,60,61],"remain":[0,2,11,14,38,54,55,60,61,75,76,79,83,84,85,86],"remap":[16,20],"rememb":[74,79,82],"remind":[1,82],"remot":[63,80],"remov":[1,4,20,35,40,50,53,54,55,60,61,64,67,71,73,74,75,77,83,84,85,86,93],"remove_invalid":53,"remove_on_experiment_identifi":[20,24],"remove_profile_fitting_failur":73,"remove_sources_default":33,"renumb":33,"reopen":24,"reorder":20,"repeat":[38,47,64,74,75,76,77,82,86,97],"repetit":64,"replac":[24,38,52,74,75,76,78],"replot":[60,71],"report":[1,12,14,40,42,48,55,64,68,70,71,72,75,77,79,84,86,89,97],"report_progress":14,"repositori":[4,9,54,60,61,76],"repredict_on":54,"repres":[2,12,20,40,44,52,82,83,85,86,94],"represent":[2,15,18,20,52],"reprint":[74,75,76,96],"reprocess":[74,85,86],"reproduc":[75,76,78,83,85,86,91],"request":[4,14,20,26,43,48,54,60,61,79,82,89],"requir":[4,7,11,14,15,18,20,40,44,52,53,54,55,60,61,63,65,73,74,75,76,78,79,80,81,82,83,84,85,86,87,89,93,94,96,98],"rerun":[84,87],"res":[48,76],"rescal":[73,83,85],"rescale_after_resolution_cutoff":73,"research":[0,89,91,94],"reserv":91,"reset":[14,20,64,74],"reset_accepted_reflect":14,"reset_error_model":64,"reset_id":20,"reset_scan_point":25,"residu":[14,54,60,61,77,82,83,85,86],"resiz":[20,86],"resolut":[1,11,17,18,20,37,38,40,41,43,44,45,46,47,48,49,50,51,54,55,60,61,64,68,73,74,75,76,77,78,79,80,82,83,84,85,86,87,96],"resolution_analysi":68,"resolution_depend":64,"resolution_filter_from_array":[18,19],"resolution_filter_from_reflections_experi":[18,19],"resolution_r":45,"resolution_rang":[47,50,51],"resolv":[73,75,77,83,85,86],"resolve_indexing_ambigu":73,"resourc":[1,89],"respect":[18,35,39,64,77,80],"respons":[47,49,75],"rest":[1,11,40,75],"restart":14,"restrain":[1,54,60,61,64,76],"restraint":[14,54,60,61,64,75,76,87],"restraints_param":14,"restraints_parameteris":14,"restrict":[44,54,60,61],"result":[1,2,11,14,15,18,35,37,38,39,40,42,43,44,51,53,54,58,60,61,64,65,67,68,75,76,78,79,82,83,84,85,87,93,97],"retain":[38,44,55,77,91],"retrospect":98,"return":[1,4,6,11,12,14,15,16,17,18,20,21,22,23,24,25,26,29,30,31,33,49,54,60,61,75,86],"return_unhandl":33,"reus":[0,95],"reusabl":2,"reveal":[75,78,96],"revers":[4,11,20,25,44,79],"revis":[86,96],"revisit":77,"reweight":64,"rewrit":82,"rey":96,"rf":96,"rg":96,"rh":96,"rho":35,"ribonucleotid":96,"rice":[74,96],"richard":0,"rigaku":23,"right":[2,4,35,74,75,79,82,91],"rigid":[54,60,61,82],"rigor":75,"rij":[18,40,73],"ring":[44,45,46,47,49,50,51,54,55,75,76,82,83,84,85,96],"riordan":[0,96],"risk":77,"rivera":96,"rj":[89,96],"rl":96,"rlp":[3,20,44,54],"rlp_mosaic":[41,51,55,59],"rmat":33,"rmea":[64,75,77,80,83,85,86,87],"rmerg":[43,73,75,77,80,83,85,86,87],"rmsd":[11,14,54,60,61,64,74,75,78,79,80,82,83,84,85,97],"rmsd_cutoff":[11,54,60,61],"rmsd_deltapsi":14,"rmsd_i":[14,74,75,79,82,83,84,85,86],"rmsd_min_px":54,"rmsd_name":14,"rmsd_phi":[14,82,83,84,85,86],"rmsd_target_mm":54,"rmsd_toler":64,"rmsd_unit":14,"rmsd_wavelength":14,"rmsd_weight":[11,54],"rmsd_x":[14,74,75,79,82,83,84,85,86],"rmsd_xi":[83,85],"rmsd_z":[74,75,79,82,83,84,85],"rmsds":[11,14,54,60,61,74,75,79,82,83,84,85,86],"rmsds_for_experi":14,"rmsds_for_panel":14,"rmsds_for_reflection_t":14,"robert":0,"robinson":96,"robust":[20,54,55,60,61,77,96],"rock":75,"rodriguez":96,"roi":47,"roo":96,"room":96,"root":[4,54,60,61,75],"rooyen":96,"rosenberg":96,"rossmann":11,"rotat":[0,1,2,4,6,11,14,20,22,25,33,34,35,38,39,47,52,54,55,58,60,61,63,64,69,73,74,75,76,77,79,82,83,84,85,86,93,96,97,98],"rotate_around_origin":[23,25],"rotate_cryst":[32,33],"rotation_angle_deg":55,"rotation_axi":[3,25,38],"rotation_axis_toler":[24,25],"rotation_matrix_differ":11,"rotation_scan_manag":14,"rotational_coordin":[54,60,61],"rotogram":54,"rotogram_grid_point":54,"rough":[11,43,79],"rougher":86,"round":[1,54,64,73,74,75,79,80,83,85],"rousseeuw":[54,60,61],"routin":[1,64,87],"row":[14,20,40],"rp":96,"rpim":[1,75,77,80,83,85,86,87],"rs":89,"rs_proximity_threshold_multipli":[16,47],"rsmds":14,"rt_mx":18,"rub":2,"rudzki":96,"rule":[54,60,61,65],"run":[1,4,6,7,9,14,15,16,18,38,40,43,44,48,53,54,56,60,61,64,74,75,76,77,79,80,82,83,84,85,86,87,94,97],"run_lbfg":14,"runtim":[4,76],"runtimeerror":11,"rupp":2,"rw":96,"s":[2,4,6,14,18,20,35,43,49,51,54,55,60,61,64,71,73,74,75,77,79,82,83,85,86,87,96],"s0":[6,21,23,43],"s0021889810010782":[54,60,61],"s1":[3,23,41,51,55,59],"s1600576714007626":47,"s1600576724003182":11,"s2053273319015559":11,"s2059798317010348":76,"sad":[44,87,96],"sadab":44,"saeed":0,"sampl":[2,11,14,18,23,35,52,54,55,60,61,74,75,77,82,83,85,86,87,96],"sample_to_sourc":21,"sample_to_source_dist":[21,52],"sanchez":96,"sandi":96,"sandwich":35,"sangwan":96,"sanishvili":96,"saniti":54,"sar":81,"saracini":96,"satisfi":[82,86],"satur":45,"saturn":23,"sauter":[0,2,11,48,54,60,61,65,89,96,98],"sauter_poon":[54,60,61],"save":[3,20,38,40,41,47,50,52,55,59,64,75,76,82,83,84,85,86,87,97],"save_coordin":69,"saw":74,"sawaya":96,"say":[7,54,60,61,79,86],"sb":96,"sbgrid":75,"sc":80,"sca":73,"scalar":11,"scale":[2,3,18,19,20,22,24,32,35,40,43,44,45,48,57,72,73,77,79,80,88,95,96],"scale_and_filter_result":64,"scale_compon":4,"scale_correct":1,"scale_interv":[1,64,86],"scale_rang":44,"scalecomponentbas":4,"scaled_unmerg":[43,44,77],"scaler":15,"scaling_model":24,"scaling_model_ext":4,"scaling_opt":64,"scaling_refineri":64,"scalingmodelbas":[4,15],"scan":[2,3,4,6,14,16,17,20,24,25,26,27,32,38,40,41,44,47,48,49,51,52,53,54,55,58,59,60,61,64,66,67,69,70,73,74,75,77,82,83,84,85,86,87,93,98],"scan_axi":[25,52],"scan_margin":[14,54,60,61],"scan_rang":[16,47,55],"scan_step":[41,51,55,59],"scan_toler":[24,33],"scan_vari":[41,51,54,55,59,60,61,74,75,76,82,83,93],"scanaxi":25,"scanfactori":[27,29],"scanvaryingrefin":[14,19],"scapin":[74,96],"scatter":[1,2,47,54,60,61,64,75,83,85,86,96],"scene":98,"sceptic":79,"schafer":96,"schemat":35,"scheme":[14,64,83,85,86],"schlicht":96,"school":[77,100],"schriber":96,"schuck":96,"schuermann":0,"sci":[74,96],"scienc":[0,33,80,83,89,94,96],"scientif":[0,95],"scientist":94,"scipi":[18,40,73],"scisoft":[33,80,83],"scitbx":[4,6,10,11,12,14,18,22,23,24,25,26,40,73],"scitbx_array_family_flex_ext":[10,12,14,20,23,24,25,26],"scitbx_array_family_shared_ext":12,"scope":[11,12,15,33,37,54],"scope_extract":[14,18,21,22],"score":[1,11,18,40,54,64,70,74,77,78,80,83,84,85,86,87],"score_by_fraction_index":11,"score_by_rmsd_xi":11,"score_by_volum":11,"score_vector":11,"scorecorrelationcoeffici":[18,19],"scoresubgroup":[18,19],"scoresymmetryel":[18,19],"scratch":[9,80,85],"screen":[83,85],"screw":84,"script":[4,6,7,9,33,38,77],"scroll":[74,86],"sd":[18,83,85,87],"sds":18,"se":96,"seamless":0,"search":[11,29,37,38,54,60,61,65,75,78,79,84,97],"search_beam_posit":[72,79],"search_depth":54,"search_direct":11,"search_vector":11,"second":[1,18,34,74,78,79,83,85,86],"secondari":73,"sect":2,"section":[1,3,75,77,78,83,85,86],"see":[1,2,4,7,9,11,18,47,48,54,55,60,61,64,65,73,74,75,77,78,79,82,83,85,86,87,90,97],"seed":[18,40,54,55,60,61,65,70,73],"seed_dataset":18,"seem":[1,44,75,82],"seen":[76,82,83,85,86],"seibert":96,"sel":14,"select":[1,6,11,14,15,18,20,38,40,41,43,46,51,54,55,59,60,61,64,73,75,77,79,83,85,86,87],"select_good_intens":46,"select_on_experiment_identifi":[20,24],"selection_used_for_refin":14,"self":[4,6,12,20],"self_index":20,"sellberg":96,"seltzer":35,"semi":84,"semin":0,"semisynthetic_multilattice_data":84,"semisynthetic_multilattice_data_2":84,"senior":94,"sens":45,"sensibl":[1,77,83,85,86,87,97],"sensit":[0,11,40],"sensor":[2,23],"sensor_pad":[83,85],"sensor_unknown":3,"sep":96,"separ":[1,14,15,38,40,43,47,54,55,60,61,64,65,71,73,74,75,76,82,83,84,85,93],"separate_block":[54,60,61],"separate_experi":[54,60,61],"separate_fil":55,"separate_imag":[54,60,61],"separate_independent_set":60,"separate_panel":[54,60,61],"septemb":100,"sequenc":[2,3,15,16,24,26,30,36,47,52,54,55,60,61,64,67,79,80,82,83,84,85,87,97],"sequenti":[39,75],"sequestr":0,"seri":[0,11,54,98],"serial":[0,4,11,15,24,27,32,54,60,61,75,89,96,97,98,100],"serial_crystallographi":97,"serialis":24,"serv":80,"server":[49,72],"servic":[74,91],"session":[9,98],"set":[1,2,3,4,6,7,11,12,14,15,16,18,20,24,26,29,30,33,34,37,38,40,42,43,44,45,46,47,50,51,52,53,54,55,56,57,59,60,61,62,64,65,66,69,70,73,74,75,76,78,79,82,83,84,85,86,87,89,90,93,96,97,98],"set_angl":25,"set_ax":25,"set_beam":26,"set_cholesky_factor":14,"set_detector":26,"set_dimens":18,"set_domain_size_ang":22,"set_domain_size_ang_valu":54,"set_error_model":15,"set_fixed_rot":25,"set_flag":20,"set_format_class":26,"set_goniomet":26,"set_half_mosaicity_deg":22,"set_last_cel":14,"set_mosa":22,"set_mosaic_half_deg_valu":54,"set_nproc":14,"set_param":26,"set_rotation_axi":25,"set_rotation_axis_datum":25,"set_scaling_model_as_sc":15,"set_scaling_model_as_unsc":15,"set_scan":26,"set_scan_varying_error":[54,60,61],"set_select":20,"set_setting_rot":25,"set_setting_rotation_at_scan_point":25,"set_shoebox_background_valu":[10,19],"set_templ":26,"set_valid_image_rang":15,"set_vendor":26,"setting_rot":[38,52],"setting_rotation_matrix":25,"setting_rotation_toler":[24,25],"setup":[4,14,33,90],"setup_index":11,"setup_mu":14,"setuptool":4,"seuffert":96,"seven":76,"sever":[1,9,49,77,78,83,85,86],"sfac":74,"sfx":75,"sge":[47,55],"sgtbx":[11,18,22,24,54],"sh":[7,75,90],"shadow":[11,45,47,50,51,52,59,82],"shall":[76,79,84,91],"shape":[50,64,83,85,86,87],"share":[3,10,12,14,23,24,25,26,38,60,64,73,93],"shared_ptr":[10,24,26],"shell":[1,7,43,47,73,74,75,76,77,87],"shelx":[44,71,73,74,87],"shelxd":74,"shelxt":[74,87],"shevela":96,"shi":96,"shift":[14,54,60,61,63,79,82,83,85,86],"shoebox":[3,10,16,20,38,41,47,51,55,59,64,75,83,85,86,87],"shoebox_memori":12,"shoeboxes_to_reflection_t":[16,19],"shoeman":96,"short":[3,44,49,78,82,83,85],"short_capt":[40,43,47,52,54,55,60,61,64,70,73],"shorter":[11,21,75],"shortest":11,"shorthand":[40,47,55,64,70,73],"shot":[54,96,97],"show":[4,22,31,33,40,45,47,51,57,72,74,75,76,77,79,82,83,85,86,87,97],"show_all_pix":51,"show_all_reflection_data":66,"show_beam_cent":51,"show_centroid":66,"show_correct":66,"show_ctr_mass":51,"show_diff_phil":[6,33],"show_experi":11,"show_flag":66,"show_hkl":51,"show_ice_r":51,"show_identifi":66,"show_index":51,"show_integr":51,"show_intens":66,"show_mail_handle_error":6,"show_mask":[45,51],"show_max_pix":51,"show_miller_indic":51,"show_predict":51,"show_profile_fit":66,"show_raw":66,"show_registri":4,"show_resolution_r":51,"show_rotation_axi":51,"show_scan_vari":[22,66],"show_shared_model":66,"show_shoebox":51,"show_threshold_pix":51,"shown":[3,4,7,52,64,74,83,85,86],"shutterless":98,"si":[74,83,84,85],"side":[14,59,75,82],"siebert":96,"sierecki":75,"sierra":96,"sig":[38,40,44,83,84,85],"sig_":14,"sig_min":14,"sigf":84,"sigi":[38,43,55,64,73,75,80,82,83,84,85],"sigimean":[84,85],"sigma":[1,18,20,40,41,51,52,54,55,59,60,61,64,70,73,75,76,77,80,83,84,85,86,87],"sigma_":[45,51],"sigma_b":[41,45,51,55,59],"sigma_b_multipli":20,"sigma_background":47,"sigma_cc":18,"sigma_d":[83,85,86],"sigma_diverg":[3,21,52],"sigma_i":[82,83,85,86],"sigma_m":[41,51,55,59,83,85,86],"sigma_m_algorithm":[41,51,55,59],"sigma_phi_deg":54,"sigma_strong":[47,76],"sigma_tau":[43,73],"sign":[14,20,74,83,85,86],"signal":[1,75,96],"signal_strength":48,"signatur":[10,12,14,22,23,24,25,26],"signific":[20,35,38,43,47,55,64,70,73,74,76,82,83,85,86,97],"significance_filt":[38,55],"significance_level":70,"significant_clust":73,"sikorski":96,"silver":[51,98],"similar":[1,4,15,18,40,47,52,54,75,77,78,83,84,85,86,97],"simon":96,"simpl":[1,4,14,15,20,21,23,24,31,33,47,50,51,54,55,64,73,82,86],"simple1":[41,51,55,59],"simple1angular1":[41,51,55,59],"simple1angular3":[41,51,55,59],"simple6":[41,51,55,59],"simple6angular1":[41,51,55,59],"simple_background_ext":31,"simple_centroid_ext":31,"simple_data_filenam":54,"simple_direct":21,"simplebackgroundext":[31,32],"simplecentroidext":[31,32],"simplelbfg":[14,19,54,60,61,64],"simplenormdevoutlierreject":15,"simpli":[1,2,7,14,35,40,83,85,86,93,94],"simplic":97,"simplifi":[2,21],"simul":96,"simultan":[75,86,96],"sin":2,"sinc":[2,11,35,54,55,83,85,86,87],"singl":[1,2,4,11,12,14,15,16,18,20,24,25,29,38,40,41,45,47,48,51,52,54,55,56,59,60,61,64,65,67,70,71,73,75,77,78,82,83,84,85,86,87,93,94,96],"single_axi":25,"single_axis_goniometer_from_phil":25,"single_axis_revers":[4,25],"single_fil":29,"single_file_indic":26,"singleton":40,"singular":14,"sirohiw":96,"sit":79,"site":[7,76,94],"situ":77,"situat":[14,75,82,83,85],"six":[76,87],"size":[1,4,11,18,20,23,26,35,38,39,41,42,43,44,45,47,50,51,52,54,55,56,58,59,60,61,62,63,64,65,67,69,73,74,75,82,83,84,85,86,97],"size_max":52,"size_min":52,"size_t":[12,15,16,20,23,24,26],"sj":75,"sj\u00f6berg":96,"skinner":96,"skip":[75,97],"skip_deriv":14,"slice":[20,54,67,75,98],"slice_sequ":72,"slide":0,"slider":[74,83,85],"slight":[29,75,82,83,85,86],"slippag":2,"slope":[75,77,80,83,85,86,87],"slow":[1,23,38,44,47,50,51,52,64,73,74,75,76,97],"slow_axi":[3,23,38,52,76,83,85],"slow_axis_toler":[23,24],"slow_direct":23,"slow_fast_beam_centr":52,"sm":96,"small":[1,2,11,54,60,61,77,78,79,81,82,83,85,86,96],"small_molecul":73,"smaller":[18,40,54,56,60,61,67,70,73,74,75],"smallest":[14,54,60,61],"smart_sigma":55,"smeet":0,"smith":96,"smooth":[1,65,75,83,85,86,87,93],"smoother":[15,54,60,61,74,76,86],"smtbx":33,"smv":[74,75],"snapshot":[11,75,96,98],"snare":96,"snippet":82,"snow":77,"soc":96,"soft":76,"softwar":[0,2,7,11,76,83,84,85,89,91,95,96,98],"sohnck":87,"sokara":96,"soli":96,"solid":11,"solti":96,"solut":[11,14,40,54,64,74,75,76,77,78,79,80,83,84,85,86],"solution_scor":54,"solv":[78,79,83,85,86,87,94],"solvent":74,"somehow":77,"someth":[77,79,83,85],"sometim":[11,52,74,83,85],"somewhat":7,"somewher":77,"song":96,"sophist":[75,83,86],"sorri":93,"sort":[6,20,24,33,38,55,79,85],"sort_by_imageset_path_and_image_index":38,"sort_opt":33,"sorted_":76,"sorted_1":76,"sorted_2":76,"sorted_3":76,"sorted_4":76,"sorted_5":76,"sorted_6":76,"sorted_7":76,"sourc":[0,4,9,11,12,14,15,16,17,18,21,22,23,24,25,26,28,29,30,31,33,35,44,52,79,81,82,83,84,85,86,90,91,95,96,100],"source_nam":44,"source_packag":33,"source_short_nam":44,"space":[1,2,4,7,11,14,15,18,20,22,31,33,37,40,41,43,44,45,46,47,50,51,54,55,59,60,61,62,64,73,74,75,76,78,79,80,82,83,84,85,86,87,97],"space_group":[11,18,22,30,33,34,39,40,43,45,46,47,50,51,54,62,70,73,74,75,78,82,83,84,85,87,97],"space_group_hall_symbol":3,"space_group_info":11,"space_group_numb":30,"space_group_symbol":22,"spacegroup":[51,76,80],"spallat":95,"spars":[14,18,40,54,60,61,82,96,97],"sparsegradientsmixin":[14,19],"sparselevmar":[54,60,61],"spatial":11,"speaker":0,"special":[2,4,11,51,54,60,61,64,74,75,76,77,86,91],"special_correct":4,"specialcompon":4,"specif":[0,2,4,7,54,55,60,71,75,76,77,83,85,86,91,94],"specifi":[1,2,11,14,15,20,33,34,36,38,40,43,46,47,50,51,52,53,54,55,60,61,62,64,65,67,69,70,71,73,75,82,90,97],"spectral":11,"spectroscopi":96,"spectrum":26,"speed":[0,45,54,55,60,61,74,82,83,85,86,97,98],"spell":77,"spend":78,"sphere":[14,20,54,60,61,75],"spheric":[1,54,60,61,64,73,87],"spherical_grid":[41,51,55,59],"spherical_relp_model":[54,60,61],"spindl":[14,20,54,60,61,82,83,85,86],"spinner":33,"spiral":79,"spirit":0,"split":[4,12,14,20,24,38,47,51,52,54,55,60,61,64,67,78,79,82,83,84,85,87,93,97],"split_0":84,"split_1":84,"split_by_experiment_id":20,"split_experi":[55,82,84,87,93],"split_indices_by_experiment_id":20,"split_jacobian_into_block":14,"split_json":68,"split_matches_into_block":14,"split_parti":20,"split_partial_indic":20,"split_partials_with_shoebox":20,"spot":[4,11,16,20,35,41,42,44,45,47,49,50,51,53,54,55,59,60,61,65,68,78,80,82,84,93,97],"spot_count":49,"spot_count_no_ic":49,"spot_counts_per_imag":72,"spot_dens":47,"spot_find":[19,32],"spot_predict":[19,32],"spot_xd":53,"spotdensityfilt":[16,19],"spotfind":[16,19,47,48,76,80,83,85,88,94,96],"spotfinderfactori":[16,19],"spread":[22,64,77,79,80],"spring":77,"sqr":6,"sqrt":[2,14,18,40,73,83,85],"squar":[14,54,60,61,75,83,85,86],"src":[4,33],"sriniva":96,"ssrl":100,"ssrl_p6":48,"ssx":88,"ssx_index":88,"ssx_integr":88,"ssx_reduc":97,"stabil":94,"stabilis":76,"stabl":[7,87],"stacey":75,"stack":12,"stack_imag":51,"stack_mod":51,"stadler":0,"staff":[4,89],"stage":[2,35,74,75,76,78,83,85,86,87],"stan":96,"standard":[1,2,15,20,21,23,25,35,40,47,53,55,64,71,73,75,76,77,80,82,84,87,94,96,97],"standard_error":[18,40,73],"standardis":2,"star":[18,78],"start":[1,2,8,15,18,23,25,33,40,47,48,52,54,55,60,61,64,65,69,70,73,74,75,76,77,78,79,80,82,83,85,86,87,90,99],"stat":[48,64],"state":[2,14,54,60,61,83,85],"static":[11,12,14,16,17,18,20,21,22,23,24,25,26,28,29,31,41,44,51,54,55,58,59,60,61,63,74,75,82,83,86,87],"static_on":23,"staticmethod":4,"station":89,"statist":[1,14,42,43,44,47,48,54,60,61,64,66,68,73,74,75,77,78,79,82,83,84,85,86,87,94,97],"statisticalweightingstrategi":[14,19],"status":[3,80],"stay":[14,77],"std":[10,22,23,24,25,26,40,64,73,80],"std_string":[20,23,24,25],"stdcutoff":[64,73],"stddev":77,"stdin":52,"steadi":86,"steep":[43,73,85],"stef":0,"steller":[11,54],"step":[9,14,18,40,44,45,54,55,60,61,64,65,71,74,75,76,77,78,79,82,83,84,85,86,87,98],"step_backward":14,"step_forward":14,"step_siz":[11,54],"step_threshold":14,"stepanov":96,"stepwis":97,"stereograph":[69,77],"stereographic_project":72,"stevenson":96,"stfc":[89,95],"still":[1,3,11,12,14,16,20,24,52,54,55,60,61,64,74,75,76,77,79,82,83,84,85,86,96,97],"stills_index":19,"stills_manag":14,"stills_process":[16,20,97],"stillsindex":11,"stillsindexerbasisvectorsearch":11,"stillsindexerknownorient":11,"stillsindexerlatticesearch":11,"stillsreflectionmanag":[14,19],"stillsweightingstrategi":[14,19],"stop":[11,15,40,41,47,49,51,55,59,64,70,73,75,76,83,85],"storag":14,"store":[0,3,4,14,18,48,58,75,76],"str":[4,6,11,15,18,20,21,22,24,25,26,33,34,36,37,38,40,41,42,44,45,46,47,50,51,52,53,54,55,58,59,60,61,62,64,65,67,69,70,71,73],"straight":[79,82,83,85,86],"straightforward":[74,77,78,87],"strain":96,"strategi":[11,14,16,47,54,60,61,83,85,96],"streambuf":20,"streamwrapp":33,"strength":[1,75,77,87,96],"strict":[83,84,85,91],"string":[7,12,14,20,33,40,43,47,49,54,55,60,61,64,69,70,71,73],"strong":[1,3,16,20,44,47,49,51,54,55,63,64,65,68,71,74,75,76,77,78,79,82,83,84,85,86,87,97],"struct":[3,76,89,96],"structur":[0,7,14,24,54,60,61,64,75,76,77,78,79,83,84,85,86,87,89,94,96,97,98],"struggl":74,"stuart":[11,96,98],"studi":[0,96],"stuff":[12,33],"style":[4,54,73],"stype":23,"sub":[4,40,46,54,60,61,74,77,78,83,84,85,86,89],"subclass":[4,14,15],"subdirectori":[75,77,85,86],"subgroup":18,"subgroups_t":18,"subject":18,"submiss":94,"submit":[4,96],"suboptim":74,"subprocess":4,"subsampl":55,"subsect":76,"subsequ":[9,15,76,78,82,83,85,86,87],"subset":[1,14,38,46,54,55,60,61,64,65,73,77,79,82,83,85,86],"subsort":20,"substanti":87,"substitut":[7,91],"substrat":96,"substructur":77,"subt":35,"subtl":[78,96],"subtract":[31,41,55,74,79,86],"subtract_background":41,"succeed":79,"success":[16,18,74,75,76,77,83,85,86,97],"sudo":90,"suffic":[54,60,61],"suffici":[1,7,40,79,84,86],"suffix":[33,40],"sugahara":96,"suggest":[74,75,77,80,82,83,84,85,87],"suit":[7,44,48],"suitabl":[1,15,18,44,54,60,61,64,73,75,76,83,84,85,86,87,97],"sum":[1,3,6,18,20,29,40,44,51,55,56,64,75,82,83,84,85,86],"sum_":56,"summari":[0,12,33,66,77,82,83,84,85,86,87,97],"summaris":[3,75,97],"summary_t":18,"summat":[1,20,35,40,55,64,75,82,83,84,85],"super":[4,94],"supercel":82,"supercomput":94,"superpos":78,"suppli":[14,52,54,55,60,61,64,65,76],"support":[0,4,7,11,20,43,44,45,51,52,54,56,60,61,71,72,80,89],"sure":[9,73,74,75,78,79,86],"surfac":[1,15,35,82,83,85,86,87],"surface_weight":[1,64],"survey":98,"suspect":[78,79],"sutherlin":96,"sutton":[11,96],"suzuki":96,"sv_refin":82,"sweep":[1,15,64,73,77,80,83,84,85,87,88,97],"sweep00":77,"sweep1":80,"sweep30":77,"switch":[7,18,77,82,84],"sxd":95,"sym":18,"sym_op":18,"sym_op_scor":18,"sym_ops_t":18,"symbol":[2,12,54,84],"symm":[37,74],"symmetr":[1,40,70,74,77,83,84,85,87],"symmetri":[1,11,15,19,32,37,40,44,54,60,61,64,69,71,72,73,76,77,82,96],"symmetris":18,"symmetry_bas":[18,19],"symmetryanalysi":[18,19],"symmetryhandl":11,"symop":79,"symop_threshold":37,"synaptotagmin":96,"synchroton":94,"synchrotron":[0,75,79,89,94,95,97,98],"syntax":[1,75],"synthet":[35,84],"synuclein":96,"sys":[4,20],"sys_absent_threshold":54,"system":[0,2,7,20,33,55,75,76,77,80,83,85,96],"system_phil":33,"systemat":[1,18,40,69,70,73,78,79,80,82,83,85,86],"systematic_abs":70,"s\u00fcdhof":96,"t":[1,2,4,15,22,23,25,26,29,33,35,38,40,72,74,75,76,77,82,83,85,86,89,96],"t0":[83,85],"t1":79,"ta":96,"tab":[72,77,86],"tabl":[1,2,3,4,14,15,16,18,33,35,38,46,47,53,55,58,60,61,64,66,75,76,78,79,82,83,84,85,86],"tabul":35,"tailor":16,"takanori":0,"take":[4,15,17,18,20,38,40,46,48,52,53,54,55,59,60,61,64,70,75,77,78,79,82,83,85,86,87,93,96],"taken":[1,35,53,54,58,60,61,63,76,77,83,85,86,87],"tale":79,"talk":0,"tam":96,"tanaka":96,"tandem":98,"tang":0,"tanh":[43,73],"tantalis":98,"tape":55,"tar":[7,48,76,77,79,84,85,86,87,90],"tara":0,"target":[1,11,14,15,18,19,54,60,61,64,71,74,75,82,83,85,86],"target_angl":11,"target_bravais_str":11,"target_cycl":64,"target_lattic":54,"target_model":64,"target_mtz":64,"target_space_group":11,"target_stil":14,"target_symmetri":11,"target_symmetry_primit":11,"target_unit_cel":11,"targetedoutlierreject":15,"targetfactori":[14,19],"tarik":0,"task":[16,55,77,83,85,86],"tasso":98,"tau":14,"tau2":76,"tau3":76,"tau_2":76,"tau_3":76,"tbc":98,"tc":96,"tchon":0,"team":94,"technic":98,"techniqu":98,"technolog":[0,35,98],"tell":[75,78,82,86,93],"tem":74,"tempel":[78,79],"temperatur":96,"templat":[3,21,22,23,24,25,26,29,33,52,76,80,83,85,86,93],"ten":[77,94],"tend":[75,76],"tendenc":76,"term":[1,2,14,20,54,60,61,64,74,83,85,86,87],"termin":[14,18,54,60,61,64,80,82,90],"termination_param":18,"termination_paramet":18,"terwillig":96,"test":[1,11,14,15,18,33,37,40,54,62,64,70,73,76,77,79,84,86,87,94],"test_for_termin":14,"test_miller_set":18,"test_objective_increasing_but_not_nref":14,"test_rmsd_converg":14,"tetragon":[77,82],"text":[2,24,33,35,74,75,83,85,86],"textrm":[77,82],"tgz":48,"th_8_2":82,"th_8_2_":80,"thank":[78,79],"thaum_m10s15_3_":82,"thaumatin":[80,82],"themselv":[1,23],"theori":[78,91],"therapi":0,"therefor":[1,4,14,54,60,61,74,83,85,87],"thereof":55,"thermofish":74,"theta":[23,54,60,61,87],"thick":[23,35,52,54,55,60,61,83,85],"thin":[1,18,73,96],"thing":[4,6,42,53,74,82,98],"think":[2,79,98],"third":[0,1,9,52,74],"thomaston":96,"thompson":[0,96],"thomson":[74,96],"thorn":96,"thorough":78,"though":[7,74,75,77,82,83,85,87],"thought":[78,79],"thousand":94,"thread":20,"three":[1,2,3,11,53,54,58,60,61,63,74,75,77,83,85,86,89,96,98],"threshold":[1,15,16,31,37,38,40,41,44,45,47,51,54,55,59,70,71,73,74,75,76,79,83,85,86],"threshold_funct":16,"threshold_prob":[54,60,61],"throughout":[0,2,82],"throughput":48,"throw":[38,47],"thrown":82,"thus":[75,83,85,86],"thygesen":75,"ti":75,"tick":[75,86],"tie":[54,60,61,75],"tie_to_group":[54,60,61],"tie_to_target":[54,60,61,75,76],"tiff":45,"tight":[86,96],"tile":[81,83,85,86],"tilt":74,"time":[0,2,4,16,20,24,26,33,46,64,73,74,76,77,78,82,83,84,85,86,95,96,98],"timepix":[75,76],"timer":33,"timestamp":[24,52,97],"tini":[12,26],"tiny_int_2":12,"tir":[75,81],"titl":[33,74,84],"tj":96,"tl":96,"tmp":80,"tmp4xxusn":80,"to_byt":20,"to_cryst":[27,30],"to_dict":[15,22,23,24,25],"to_imageset":[27,30],"to_json_fil":14,"to_shelx":74,"to_xd":[27,30],"today":98,"tof":[47,95],"tofleastsquaresresidualwithrmsdcutoff":[14,19],"tofreflectionmanag":[14,19],"tofspotfind":[16,19],"togeth":[1,2,64,73,75,76,77,82,98],"toggl":[4,77,83,85],"token":23,"toler":[11,18,20,38,41,44,51,54,55,59,64,73,76,87],"toll":75,"tom":98,"tomographi":96,"tono":96,"took":[80,82],"tool":[53,77,78,79,83,85,86,88,89,94],"toolbox":[2,96],"toolkit":[7,38,79,95,96],"top":[4,12,65,74,75,79],"topic":79,"toro":11,"tort":91,"total":[11,14,47,49,75,77,80,82,83,85,86,87],"total_intens":49,"total_reflect":[41,51,55,59],"touch":[77,94],"toward":[1,74,75,82,94,98],"toxic":96,"tp":[80,84],"traceback":33,"track":[14,54,60,61,77,79,83,85,86,94],"track_condition_numb":[54,60,61],"track_gradi":[54,60,61],"track_jacobian_structur":[54,60,61],"track_normal_matrix":[54,60,61],"track_out_of_sample_rmsd":[54,60,61],"track_parameter_correl":[54,60,61],"track_step":[54,60,61],"trade":[54,60,61],"train":[85,86,94],"tran":96,"transduct":75,"transfer":0,"transform":[2,11,39,54,61,84,86,87],"transit":78,"translat":[30,54,60,61,78,83,85],"transmiss":[21,52,83,85],"transvers":[54,60,61],"treat":[54,60,61,77,82,93],"treat_single_image_as_stil":[54,60,61],"tree":86,"trek":98,"tri":[1,7,24,33,47,64,74,75,77,78,79,80,82,83,85,97],"trial":54,"tricki":77,"triclin":[61,71,75,76,83,85,86,87],"trigger":[54,60,61,64,73],"trim":[54,60,61,74],"trim_scan_to_observ":[54,60,61],"trimh":54,"triml":54,"triplet":54,"trivial":[4,79],"trivial_accessor":[10,12,23,25,26],"troubleshoot":79,"trough":[85,86],"trp_ag_":84,"true":[1,2,4,6,11,14,15,16,18,20,21,22,23,24,25,26,29,30,31,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,73,74,76,78,82,83,85,86,93,97],"truncat":[18,54,55,60,61,83,84,85],"trunccauchy_pdf":[18,19],"trust":[0,47,50,52,75,79],"trusted_rang":[3,23,52,83,85],"trustworthi":[46,83,85,86],"try_read_experi":33,"try_read_experiments_from_imag":33,"try_read_reflect":33,"trypsin":84,"ts":[74,96],"tsai":96,"tukey":[54,55,60,61,82,83,84,85,86],"tune":[55,83,85,86],"tuning_const":55,"tupl":[4,11,14,15,16,18,20,21,22,23,25,26,33,54,60,61],"turn":[1,2,11,25,54,55,60,61,64,73,74,77,79,82,83,85,86,94],"tutori":[1,7,8,75,76,77,78,79,80,82,93,100],"tutorial_data":[82,85],"tw":75,"tweak":84,"twice":[54,60,61,83,85,86],"twin":[18,62,77,80],"twist":75,"two":[1,2,3,4,15,18,20,23,35,39,52,54,60,61,65,67,74,75,77,78,79,83,85,86,87,94],"two_theta":[23,73],"two_theta_angl":23,"two_theta_direct":23,"two_theta_refin":[72,73,77,87],"two_theta_refine_2theta":77,"tyoe":33,"type":[1,3,4,6,7,11,14,15,17,18,20,22,23,24,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,80,83,84,85,86,90],"typic":[1,2,7,11,18,35,40,47,48,54,55,60,61,64,67,70,73,75,79,82,83,85,86,87],"u":[2,4,20,74,75,82,83,84,85,87,96],"u_0":2,"ub":[2,54,75,82,83,84,85,87,96],"ub_matrix":3,"uc_abs_angle_toler":22,"uc_rel_length_toler":22,"uctbx":[2,11,22],"uervirojnangkoorn":96,"uhlig":96,"uk":[90,94,100],"ultim":78,"un":35,"unabl":[83,85],"uncertainti":[1,40,54,73,76,83,85,86,87],"unclear":2,"unconstrain":87,"unconvent":78,"uncorrect":[64,82,83,85,86],"undergon":78,"underlying":97,"understand":[0,79,83,84,85,86,98],"understood":86,"undertaken":73,"underway":[82,95],"unequ":[83,85,86],"unfeas":44,"unfortun":[2,79,82],"unhandl":[24,33,52],"unicod":[2,76],"uniform":[83,85,86],"unindex":[54,55,74,75,79,83,84,85,86],"unindexed_reflect":11,"unintegr":[55,83,85],"uniq":[74,83,84,85],"uniqu":[20,24,52,54,64,73,75,77,80,83,84,85,86,87],"unit":[2,11,18,20,22,33,40,41,44,45,46,47,50,51,54,55,57,58,59,60,61,64,70,71,73,74,75,76,78,79,80,82,83,84,85,86,91,97],"unit_cel":[2,11,18,22,33,41,44,45,46,47,50,51,54,55,59,60,61,64,73,74,75,76,78,79,82,83,84,85,97],"unit_cell_clust":[40,73],"unit_cells_are_similar_to":[18,19],"unit_s0":21,"uniti":[64,79],"universal":[2,11],"universiti":[2,94],"unknown":[2,26,44],"unless":[1,7,20,21,33,54,60,61,64,73,75],"unlik":87,"unmerg":[1,43,44,73,74,75,80,86,99],"unmerged_mtz":[1,64],"unpack":[7,76],"unphys":[41,51,55,59,83,85],"unpolar":21,"unrealist":54,"unreason":75,"unrecognis":79,"unrel":[83,85],"unscal":[15,44,76,79,83,85,86],"unset_flag":20,"unsign":[10,12,14,23,24,25,26],"unstabl":[1,64],"unsuit":53,"untick":86,"untrust":[47,50,51,74,76],"unus":60,"unusu":76,"unwant":50,"unwarp":79,"unweight":14,"updat":[9,14,15,20,33,44,54,60,64,82,83,84,85,86,99],"update_analysi":11,"update_detector_px_mm_data":26,"update_journ":14,"update_match":14,"update_residu":14,"upgrad":94,"upon":[15,77,97],"upper":[18,55,64,73,86],"upper_bound":18,"uptick":74,"us":[35,75,77,78,79,82,86,89],"usa":[0,2,35],"usag":[6,7,64,73,83,85,87],"use":[0,2,3,4,7,9,11,12,14,15,16,18,20,21,22,23,24,25,26,29,33,34,35,37,38,40,41,42,44,45,46,47,48,50,51,52,53,54,55,56,59,60,61,62,63,64,65,67,70,71,72,74,75,76,77,78,79,81,82,83,84,85,86,87,88,89,90,91,93,94,95,96,97,98],"use_al":[1,64,73],"use_all_reflect":82,"use_beam_refer":52,"use_curvatur":[18,40,73],"use_dataman_shel":73,"use_dataset":64,"use_detector_refer":52,"use_dynamic_mask":55,"use_free_set":64,"use_gonio_refer":52,"use_internal_vari":64,"use_lattice_symmetri":73,"use_p1_indices_as_se":54,"use_starting_angl":69,"used_in_index":4,"used_in_model":20,"used_in_refin":[14,20,46],"useless":79,"user":[0,2,4,7,11,14,36,46,47,48,55,64,79,80,81,83,85,86,89,90,94,100],"user_excluded_in_sc":20,"usr":[7,90],"usual":[2,14,41,42,47,73,74,75,79,80,82,83,85,86,87,93],"util":[6,12,14,18,32,35,38,48,72],"utilis":98,"uuid":52,"v":[2,7,83,85,96,97],"v5":44,"v5_next":44,"vaccin":0,"vajjhala":75,"valid":[12,14,15,26,33,48,49,54,55,60,61,64,84],"valid_foreground_threshold":[12,55],"valu":[1,3,7,10,11,14,15,18,20,33,35,40,41,42,43,44,46,47,48,51,52,54,55,56,58,59,60,61,64,65,66,73,74,75,76,77,78,79,82,83,85,86,87,97],"valuabl":74,"value_max":[15,40,43,44,45,46,47,52,54,55,60,61,64,70,73],"value_min":[15,38,40,41,42,43,44,45,46,47,49,50,51,52,54,55,56,57,59,60,61,63,64,65,68,69,70,71,73],"valueerror":[15,33],"van":[54,60,61,96],"var":14,"vari":[1,14,17,20,41,44,51,53,54,55,58,59,60,61,74,75,82,83,84,85,86,87,93],"variabl":[2,52,64,75,76,82,86],"varianc":[1,3,14,15,40,45,47,51,53,55,64,73,77,83,85,86],"variat":[74,83,85,86,87,96],"varieti":94,"various":[1,2,11,14,43,44,52,54,61,63,64,73,75,76,83,85,86,90,95],"ve":[20,22,75,77],"vec":2,"vec2":23,"vec2_doubl":[20,23],"vec3":[22,23,25],"vec3_doubl":[4,11,20,23,25],"vector":[1,2,3,6,11,14,18,20,21,23,34,35,40,52,54,60,61,78,83,85,86],"vectori":2,"vendor":26,"venugopalan":96,"verbos":[33,48,54,60,61,83,85,97],"veri":[1,11,20,35,54,74,75,77,79,82,83,85,86,87],"verifi":[6,24],"versa":14,"version":[7,14,35,44,48,49,76,80,82,86],"versus":[78,83,85,86],"vertic":[2,55,65,79],"via":[0,2,4,9,18,20,45,56,77,86,87,89,97],"view":[4,40,47,51,75,76,78,79,83,85,86,87,96,98],"viewer":[2,74,75,76,78,79,82,83,85,86,87],"viewhkl":74,"vinetski":96,"virtual":44,"virtual_fram":44,"visibl":[65,77,83,85,86],"visit":[48,94],"visual":94,"vital":0,"viz":[54,60,61],"vk":96,"vlacho":0,"vo":96,"void":[10,12,14,22,23,24,25,26],"vollmar":[89,96],"volum":[11,41,43,51,54,55,59,60,61,73,74,75,77,78,79,83,84,85,86,87,94,98],"volume_cutoff":[11,54],"volume_weight":[11,54],"vondelft":98,"vonrhein":0,"voxel":54,"voxel_grid_point":54,"vri":96,"vs":[1,43,54,60,61,73,74,83,85,86,98],"vv":97,"vypritskaia":96,"w":[0,2,11,14,15,96],"w_":18,"wagner":96,"wait":74,"wakatsuki":96,"wall":96,"walsh":96,"wander":75,"wang":[74,96],"want":[1,48,74,75,78,79,82,83,85,86,87],"ward":54,"warkentin":96,"warn":[78,79],"warn_if_setting_unused_refinement_protocol_param":11,"warranti":91,"wast":98,"water":96,"waterman":[0,11,74,76,89,96,98,99],"wave":11,"wavelength":[3,6,14,18,21,22,33,38,44,47,52,54,60,61,64,73,74,75,76,80,83,84,85,87],"wavelength_rang":[21,47,52],"wavelength_spread":[41,51,55,59],"wavelength_toler":[24,33,44,73],"wavelength_weight":[14,54,60,61],"wavelengthgroup":[32,33],"way":[2,33,74,75,78,79,80,82,83,91,93,94,95,97],"weak":[1,64,76,78,79,80,82,97],"weaker":[74,78],"weatherbi":96,"web":[48,72,74],"webber":0,"webpag":48,"webserv":48,"wedg":[1,11,54,81,86],"week":94,"weekend":0,"wei":96,"weight":[10,11,14,15,18,40,54,60,61,64,73,82,83,85],"weighted_mean":33,"weighting_schem":64,"weighting_strategi":[14,54,60,61],"weighting_strategy_overrid":14,"welcom":0,"well":[11,29,44,58,63,73,74,75,76,77,79,82,83,85,86],"wellcom":[0,89],"wen":96,"weng":96,"wening":96,"wernet":96,"wersig":96,"west":100,"westbrook":2,"wf":96,"wget":[9,48,90],"whatev":[79,83,85,86],"wheel":0,"whenev":4,"wherea":[47,64,75,82,83,85,86,97],"whether":[1,4,14,15,18,20,33,38,47,51,54,55,58,60,61,63,64,66,70,73,83,85,86,91],"whi":[83,85,98],"whilst":[2,3,54,60,61],"white":[95,96,98],"whitelegg":96,"whole":[1,4,47,50,51,54,60,61,64,73,77,79,82,83,85,86],"whose":[2,20,47,50,51,54,55,60,61],"wi":96,"wide":[1,7,20,47,51,54,65,75,77],"wide_search_bin":[54,65],"wider":[54,60,61],"width":[12,14,15,18,38,46,47,50,51,54,60,61,65,67,76,82,83,85,86],"wiki":[7,9,18],"wikipedia":18,"wildcard":86,"will":[1,2,3,4,6,7,9,11,12,14,15,18,20,21,22,23,24,25,33,34,38,40,41,43,44,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,64,65,69,70,71,73,74,75,76,77,78,79,82,83,85,86,87,90,93,94,95,97,98],"william":[0,96],"wilson":[40,74,80,83,85,96],"window":[7,65,74,76,79,86,90],"winn":80,"winter":[0,11,18,40,80,89,96,98,99],"wish":[0,87],"within":[0,1,2,4,7,14,20,37,47,50,51,52,54,59,60,61,64,65,67,73,75,80,82,83,85,86,87,89,98],"within_spot_sigma":55,"without":[3,7,33,77,79,82,86,87,91,93],"wj":[74,96],"wl":33,"wojdyr":0,"woldey":96,"wolfgang":98,"wolfram":[78,79],"won":[75,77,82],"word":79,"work":[0,2,4,7,9,11,14,21,25,33,54,55,60,61,64,65,74,75,77,78,79,80,82,85,86,87,89,93,95,98],"workaround":82,"workflow":96,"workshop":[0,11,85,86,94],"world":0,"worldwid":94,"worri":[79,82,86],"wors":[78,82,83,85,86],"worsen":85,"worst":45,"worth":[73,77,79,83,84,85,86],"wouldn":4,"wp6":98,"wrap":[29,97,98],"wrapper":18,"write":[3,7,20,33,40,44,46,47,54,60,61,71,75,78,79,82,83,84,85,86,97],"write_column":[32,33],"write_hot_mask":[16,47],"write_hot_pixel_mask":16,"writer":33,"written":[0,2,7,44,45,52,75,83,84,85,91],"wrong":[14,75,79,82,83,85],"wrt":2,"www":48,"wx":14,"wxtbx":33,"wy":14,"wz":14,"x":[0,1,2,11,14,18,20,21,22,23,25,33,35,40,43,47,50,51,52,54,60,61,62,64,65,74,75,76,77,78,79,82,83,85,86,89,90,95,96,98,100],"x0":[47,50,51],"x0692":83,"x0692_1_":83,"x0692_1_0":83,"x1":[47,50,51],"x212b":[2,76],"x247398":79,"x86_64":[7,90],"xaamdi":35,"xc":[47,50,51,82,83,85],"xchem":83,"xd":22,"xdg":75,"xds":[0,24,30,44,53,54,79,82,83,85,86,98],"xds_ascii":[30,44,53],"xds_detector_nam":[27,30],"xds_experi":53,"xds_file":53,"xds_inp":[24,30],"xds_model":53,"xds_other":24,"xfel":[89,94],"xi":73,"xia":77,"xia2":[30,72,74,81,83,85,87,96,97],"xjf":[7,90],"xml":[49,55],"xo":[82,83,85],"xparm":[30,33,44,53],"xparm_xd":30,"xprep":[71,74,87],"xray":21,"xs":22,"xscale":[1,44],"xtal":[44,64,84],"xtal_height_above_kapton_mm":55,"xu":75,"xvf":79,"xy":[54,60,61,83,85],"xy_rmsd_threshold":54,"xycorr":30,"xyz":18,"xyzcal":3,"xyzob":[3,14,20],"xz":[7,44,77,90],"xzf":90,"y":[1,2,11,14,18,20,21,22,23,25,40,43,47,50,51,52,54,60,61,62,64,65,74,75,76,77,78,79,82,83,85,86,96],"y0":[47,50,51],"y1":[47,50,51],"yachandra":96,"yamashita":96,"yang":96,"yano":96,"yao":96,"yash":0,"yc":[47,50,51,82,83,85],"yd":22,"year":[89,98],"yellow":74,"yet":[82,83,85,86],"yeung":96,"yield":87,"yo":[82,83,85],"yoon":75,"young":[0,89,96],"ys":22,"yumoto":96,"z":[14,18,20,21,22,23,25,33,40,43,62,64,74,77,78,79,83,85,86,89],"z_cc":18,"z_cc_against":18,"z_cc_for":18,"z_cc_net":18,"zadvornyy":96,"zatsepin":75,"zcc":[18,40,74,77,83,84,85,86],"zeldin":[0,96],"zenodo":[83,87],"zero":[1,2,11,35,47,54,55,60,61,64,65,67,70,71,74,82],"zerr":74,"zeta":[20,41,51,55,59,83,85,86],"zhang":96,"zhao":[75,96],"zhou":96,"zhu":96,"zinger":74,"zlib":45,"zmax":15,"zone":[11,59,75],"zoo":77,"zoom":[74,75,77,78,83,85],"zou":[75,96],"zouni":96,"zwart":96,"\u00b5m":75,"\u00e5":[6,21,74,75,77,83,85,86,96],"\u00e5ngstr\u00f6ms":75,"\u0161rajer":96,"\u03b1":[75,96],"\u03b2":[40,73,75],"\u03b3":75,"\u03b4":[40,73,86],"\u03b4cc\u00bd":[64,73,75,77],"\u03ba":2,"\u03c3":[40,73,83,85],"\u03c3\u00b2":[83,85],"\u03c6":[2,83,85,86],"\u03c9":2},"titles":["About","User guide for scaling data with DIALS","Conventions","Data files","Extending DIALS","Developer Examples","Reading experiment and data","Getting started","Documentation","Installation for Developers","dials.algorithms.background","dials.algorithms.indexing","dials.algorithms.integration","dials.algorithms.profile_model","dials.algorithms.refinement","dials.algorithms.scaling","dials.algorithms.spot_finding","dials.algorithms.spot_prediction","dials.algorithms.symmetry","Algorithms","Array Family","dxtbx.model.beam","dxtbx.model.crystal","dxtbx.model.detector","dxtbx.model.experiment_list","dxtbx.model.goniometer","dxtbx.imageset","dxtbx","dxtbx.model.profile","dxtbx.model.scan","dxtbx.serialize","Extensions","Library Reference","Util","dials.align_crystal","dials.anvil_correction","dials.apply_mask","dials.check_indexing_symmetry","dials.combine_experiments","dials.compare_orientation_matrices","dials.cosym","dials.create_profile_model","dials.estimate_gain","dials.estimate_resolution","dials.export","dials.export_bitmaps","dials.filter_reflections","dials.find_spots","distl/dials apache server","dials.find_spots_server/client","dials.generate_mask","dials.image_viewer","dials.import","dials.import_xds","dials.index","dials.integrate","dials.merge_cbf","dials.missing_reflections","dials.plot_scan_varying_model","dials.predict","dials.refine","dials.refine_bravais_settings","dials.reindex","dials.report","dials.scale","dials.search_beam_position","dials.show","dials.slice_sequence","dials.spot_counts_per_image","dials.stereographic_projection","dials.symmetry","dials.two_theta_refine","Program documentation","xia2.multiplex","Processing Small Molecule MicroED/3DED: Biotin","MyD88TIR small wedges","Lysozyme nanocrystals","Multi-crystal analysis with DIALS and xia2.multiplex","DPF3 Part 2: A question of centring","DPF3 Part 1: Correcting poor initial geometry","Using DIALS at Diamond Light Source","Tutorials","Refining multi-tile detector metrology with DIALS","SARS-CoV-2 main protease (Mpro)","Multi-lattice Tutorial","Processing in Detail","Processing in Detail with DUI","Small-molecule data reduction tutorial","DIALS How-To guides","DIALS: Diffraction Integration for Advanced Light Sources","Installation","DIALS License","Metrics","Processing Sequences with Missing Images","US DIALS National Resource","Projects","Publications","SSX processing guide","DIALS 1: 12th-13th June 2012 (Diamond Light Source, UK)","DIALS-3: 22nd May 2013 (Cambridge, UK)","Workshops"],"titleterms":{"12th":98,"13th":98,"22nd":99,"3ded":[74,96],"A":78,"About":0,"Further":75,"How":88,"No":9,"Other":74,"The":2,"To":88,"What":82,"acknowledg":[0,78,79,82],"activ":94,"add":4,"administr":94,"advanc":[1,89],"algorithm":[10,11,12,13,14,15,16,17,18,19],"align_cryst":34,"altern":87,"analysi":[75,77,83,85],"anvil_correct":35,"apach":48,"appli":82,"applic":96,"apply_mask":36,"array":20,"articl":96,"attende":99,"axi":75,"background":10,"bad":74,"basi":4,"basic":[34,36,37,38,39,40,41,42,43,44,45,46,47,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73],"basis_vector_search":11,"beam":[21,74,79],"better":79,"binari":90,"biotin":74,"board":94,"bookkeep":77,"bravai":[74,83,85,86,87],"build":[48,90],"built":7,"cambridg":99,"case":[43,73],"cc":77,"cell":[77,87],"center":74,"centr":[74,78,79],"check":[79,86],"check_indexing_symmetri":37,"choos":1,"cite":89,"class":4,"client":49,"cluster":77,"collect":74,"combine_experi":38,"committe":98,"common":1,"communiti":94,"compare_orientation_matric":39,"comparison":77,"conclus":[78,79],"contact":89,"content":[4,20,31],"control":1,"convent":2,"convert":78,"coordin":2,"correct":[74,79,82],"cosym":[18,40],"cov":83,"create_profile_model":41,"crystal":[22,77],"crystallographi":96,"current":9,"data":[1,3,6,9,74,75,76,77,83,85,86,87,97],"dataset":[1,74,76],"defin":4,"definit":[34,35,36,37,38,39,40,41,42,43,44,45,46,47,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73],"delta":77,"detail":[35,85,86],"detector":[23,75,82],"determin":[74,75,87],"develop":[0,5,9,90],"dial":[0,1,4,7,9,10,11,12,13,14,15,16,17,18,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,77,80,82,88,89,90,91,94,95,96,97,98,99],"diamond":[80,98],"diffract":[89,95],"diffractomet":2,"discov":79,"distanc":75,"distl":48,"document":[8,72],"download":9,"dpf3":[78,79],"dui":86,"dxtbx":[2,21,22,23,24,25,26,27,28,29,30],"entri":4,"environ":[7,9],"equat":2,"estimate_gain":42,"estimate_resolut":43,"exampl":[5,40,43,73],"exclud":74,"experi":[3,6,77],"experiment":79,"experiment_list":24,"explor":77,"exploratori":75,"export":[44,74,83,85,86,87,93],"export_bitmap":45,"extend":4,"extens":31,"famili":20,"feedback":80,"file":3,"filter_reflect":46,"find":[74,75,76,79,83,85,86,87],"find_spot":47,"find_spots_serv":49,"format":4,"frame":[2,74],"full":[34,35,36,37,38,39,40,41,42,43,44,45,46,47,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73],"fund":89,"general":[74,80],"generat":74,"generate_mask":50,"geometri":[74,79],"get":7,"gltbx_gl_ext":9,"goal":94,"goniomet":[2,25],"graphic":90,"guid":[1,88,97],"half":77,"help":7,"html":[83,85],"imag":[74,93],"image_view":51,"imageset":26,"import":[52,74,76,79,83,84,85,86,87,93,97],"import_xd":53,"index":[4,11,54,74,75,76,79,83,84,85,86,87,97],"initi":79,"inspect":86,"instal":[7,9,90],"instruct":48,"integr":[12,55,74,75,76,83,84,85,86,87,89,97],"intens":77,"introduct":[34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,76,77,78,79,82,83,84,85,86,87],"journal":96,"june":98,"keep":9,"laboratori":2,"larg":1,"lattic":[4,74,75,78,83,84,85,86,87],"lattice_search":11,"librari":32,"licens":91,"light":[80,89,98],"linux":[9,90],"list":3,"lysozym":76,"mac":[9,90],"main":83,"mask":74,"matrix":2,"max_cel":11,"may":99,"merg":[76,83,84,85,97],"merge_cbf":56,"method":4,"metric":92,"metrolog":82,"micro":[74,96],"minimis":1,"miss":93,"missing_reflect":57,"model":[1,2,4,15,21,22,23,24,25,28,29,76,79],"model_evalu":11,"modul":9,"modulenotfounderror":9,"molecul":[74,87],"mpro":83,"mtz":[83,85,86],"multi":[74,77,82,84],"multiplex":[73,77],"myd88tir":75,"name":9,"nanocryst":76,"nation":94,"neutron":95,"new":4,"newslett":96,"next":[7,82],"note":74,"offset":74,"option":[1,74],"organis":98,"orient":[2,75,77],"orthogonalis":2,"outlier_reject":15,"output":87,"paramet":[7,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73],"part":[78,79],"path":87,"pedest":74,"plot_scan_varying_model":58,"point":4,"poor":79,"post":77,"practic":1,"predict":59,"preferenti":77,"prepar":82,"present":[98,99],"process":[74,75,77,85,86,93,97],"profil":[4,28],"profile_model":13,"program":[72,98,99],"project":95,"proteas":83,"pseudocentr":78,"public":96,"question":78,"re":74,"read":6,"reciproc":77,"reduct":87,"refer":[1,32],"refin":[14,60,74,75,76,82,83,84,85,86,87,93],"refine_bravais_set":61,"reflect":[1,3],"regress":9,"reindex":62,"releas":90,"report":[63,83,85,96],"resourc":94,"result":86,"sadab":87,"sar":83,"scale":[1,4,15,64,74,75,76,83,84,85,86,87,97],"scan":[29,76],"script":75,"search":4,"search_beam_posit":65,"sequenc":93,"serial":30,"server":48,"set":[9,77],"show":66,"slice_sequ":67,"small":[74,75,87],"softwar":94,"solv":74,"sourc":[7,80,89,98],"space":77,"spot":[74,75,76,79,83,85,86,87],"spot_counts_per_imag":68,"spot_find":16,"spot_predict":17,"spotfind":[84,97],"ssx":97,"ssx_index":97,"ssx_integr":97,"stabl":90,"staff":94,"start":7,"static":[4,76],"step":7,"stereographic_project":69,"stills_index":11,"strategi":4,"structur":74,"summari":2,"support":94,"symmetri":[18,70,74,75,78,79,83,84,85,86,87],"synchrotron":96,"tabl":[20,31],"team":0,"test":[9,48],"tile":82,"tilt":75,"togeth":74,"tutori":[81,83,84,85,86,87],"two_theta_refin":71,"uk":[0,98,99],"understand":4,"unit":[77,87],"unmerg":[83,85],"us":[0,94],"use":[1,43,73,80],"user":1,"util":33,"vari":76,"vector":4,"video":74,"wedg":75,"workshop":100,"write":4,"xfel":96,"xia2":[73,77,80]}})