debugging now

Author: jonwright

ImageD11/nbGui/S3DXRD/pbp_1_indexing.ipynb

@@ -134,7 +134,10 @@
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
     "\n",
-    "from ImageD11.nbGui.S3DXRD.run_pbp_recon_chunk import merge_chunk_outputs\n",
+    "try:\n",
+    "    from ImageD11.nbGui.S3DXRD.run_pbp_recon_chunk import merge_chunk_outputs\n",
+    "except:\n",
+    "    merge_chunk_outputs = None # Old version\n",
     "import ImageD11.sinograms.point_by_point\n",
     "import ImageD11.sinograms.dataset\n",
     "import ImageD11.columnfile\n",
@@ -402,7 +405,7 @@
    },
    "outputs": [],
    "source": [
-    "if use_cluster:\n",
+    "if merge_chunk_outputs is not None and use_cluster:\n",
     "    grains_prefix = ds.pbpfile.replace(ds.analysispath, os.path.join(ds.analysispath, 'slurm_pbp')).replace('.txt', f'_{phase_str}_')\n",
     "    bash_script_path, grains_files = pbp_object.submit_slurm_chunks(grains_prefix,\n",
     "                                                                    PYTHONPATH,\n",

ImageD11/nbGui/S3DXRD/pbp_2_visualise.ipynb

@@ -80,6 +80,7 @@
    },
    "outputs": [],
    "source": [
+    "import os\n",
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
     "import matplotlib.cm as cm\n",

ImageD11/nbGui/S3DXRD/tomo_2_map_minor_phase.ipynb

@@ -115,11 +115,9 @@
    },
    "outputs": [],
    "source": [
-    "if IMAGED11_PATH is not None:\n",
-    "    exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
-    "    PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)\n",
-    "else:\n",
-    "    PYTHONPATH = None # use the system python"
+    "# We have to run this at ESRF because the astra slurm script is using it\n",
+    "exec(open('/data/id11/nanoscope/install_ImageD11_from_git.py').read())\n",
+    "PYTHONPATH = setup_ImageD11_from_git(CHECKOUT_PATH, IMAGED11_PATH)"
    ]
   },
   {

ImageD11/nbGui/install_ImageD11_from_git.py

@@ -69,9 +69,8 @@ def setup_ImageD11_from_git(path=None, checkout="ImageD11"):
     if checkout is None and path is None:
         # we assume you want the system python
         import ImageD11
-
-        folder = os.path.split(ImageD11.__file__)[-1]
-        pythonpath = os.path.split(folder)[-1]
+        folder = os.path.split(ImageD11.__file__)[0]
+        pythonpath = os.path.split(folder)[0]
         # probably cvmfs ..., but if it holds /data/
         if pythonpath.find("/data/") > 0:
             pythonpath = pythonpath[pythonpath.find("/data/") :]

test/papermill_test_notebooks.py

@@ -64,7 +64,12 @@ def clean_esrf_path(
         import ImageD11
         checkout_name = None
         checkout_folder = None
-        print("We should be using the system python")
+        folder = os.path.split(ImageD11.__file__)[0]
+        pythonpath = os.path.split(folder)[0]
+        # probably cvmfs ..., but if it holds /data/
+        if pythonpath.find("/data/") > 0:
+            pythonpath = pythonpath[pythonpath.find("/data/") :]
+        print("We should be using the system python", pythonpath)
     else:
         # If we are working from git, this is where to find the code
         items = os.path.abspath(__file__).split( os.path.sep ) # this files location (test)