fix: script modify_VE_spread_orientations so Zarr arrays are cast to numpy

Author: aplowman

matflow/data/scripts/damask/modify_VE_spread_orientations.py

@@ -2,7 +2,24 @@
 
 
 def modify_VE_spread_orientations(volume_element, phases, stddev_degrees):
-    VE = spread_orientations(volume_element, phases, sigmas=stddev_degrees)
+    # need to convert Zarr arrays to numpy arrays first:
+    VE = volume_element
+    ori_copy = VE["orientations"]
+    ori_copy["quaternions"] = ori_copy["quaternions"][:]
+    VE_copy = {
+        "size": VE["size"],
+        "grid_size": VE["grid_size"][:],
+        "orientations": ori_copy,
+        "element_material_idx": VE["element_material_idx"][:],
+        "constituent_material_idx": VE["constituent_material_idx"][:],
+        "constituent_material_fraction": VE["constituent_material_fraction"][:],
+        "constituent_phase_label": VE["constituent_phase_label"][:],
+        "constituent_orientation_idx": VE["constituent_orientation_idx"][:],
+        "material_homog": VE["material_homog"][:],
+    }
+    VE = spread_orientations(
+        volume_element=VE_copy, phase_names=phases, sigmas=stddev_degrees
+    )
     VE["grid_size"] = tuple(int(i) for i in VE["grid_size"])
     VE["size"] = tuple(float(i) for i in VE["size"])
     return {"volume_element": VE}

matflow/data/workflows/spread_orientations.yaml

@@ -1,19 +1,30 @@
-doc: 
+doc:
   - >
     Demonstration of modifying a volume element by applying a perturbation to its orientations.
 
 tasks:
-  - schema: generate_microstructure_seeds_from_random
-    inputs:
-      VE_size: [1, 1, 1]
-      num_grains: 4
-      phase_label: Al
-
   - schema: generate_volume_element_from_voronoi
     inputs:
       homog_label: SX
       VE_grid_size: [8, 8, 8]
-  
+      microstructure_seeds::from_random:
+        num_seeds: 4
+        box_size: [1, 1, 1]
+        phase_label: Al
+      orientations:
+        data:
+          - [1, 0, 0, 0]
+          - [1, 0, 0, 0]
+          - [1, 0, 0, 0]
+          - [1, 0, 0, 0]
+        unit_cell_alignment:
+          x: a
+          y: b
+          z: c
+        representation:
+          type: quaternion
+          quat_order: scalar_vector
+
   - schema: modify_VE_spread_orientations # underscore to separate the levels of the task schema objective/method
     inputs:
       phases: [Al]