Implement modify VE spread orientations

README.md

@@ -49,7 +49,7 @@ This is a list tracking which workflows/tasks we have reimplemented/tested in th
 | ⇒ method: [add_buffer_zones/damask](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L760)                         | ✅      | [modify_VE/add_buffer_zones](https://docs.matflow.io/stable/reference/template_components/task_schemas.html#modify-ve-add-buffer-zones)                                                                                                                                  |
 | ⇒ method: [new_orientations/damask](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L770)                         | ❌      | Unimplemented                                                                                                                                                                                                                                                            |
 | ⇒ method: [geometry](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L775)                                        | ❌      | Unimplemented                                                                                                                                                                                                                                                            |
-| ⇒ method: [spread_orientations/damask](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L780)                      | ❌      | Unimplemented                                                                                                                                                                                                                                                            |
+| ⇒ method: [spread_orientations/damask](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L780)                      | ✅      | [modify_VE/spread_orientations](https://docs.matflow.io/stable/reference/template_components/task_schemas.html#modify-ve-spread-orientations)                                                                                                                            |
 | ⇒ method: [grid_size/damask](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L786)                                | ✅      | [modify_VE/grid_size](https://docs.matflow.io/stable/reference/template_components/task_schemas.html#modify-ve-grid-size)                                                                                                                                                |
 | **generate_load_case**                                                                                                                                                              |        |                                                                                                                                                                                                                                                                          |
 | ⇒ method: [mixed/formable](https://github.com/LightForm-group/UoM-CSF-matflow/blob/569fa7bdc7006d04bd6ed2d4e4b6a114df23492e/task_schemas.yml#L912)                                  | ✅      | [define_load_case](https://docs.matflow.io/stable/reference/template_components/task_schemas.html#define-load-case) / [LoadCase](https://docs.matflow.io/stable/reference/template_components/parameters.html#load-case)                                                 |

matflow/data/scripts/damask/modify_VE_spread_orientations.py

@@ -0,0 +1,25 @@
+from damask_parse.utils import spread_orientations
+
+
+def modify_VE_spread_orientations(volume_element, phases, 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/template_components/task_schemas.yaml

@@ -1067,3 +1067,21 @@
       script_data_in: direct
       script_data_out: direct
       script_exe: python_script
+
+- objective: modify_VE
+  method: spread_orientations
+  inputs:
+    - parameter: volume_element
+    - parameter: phases
+    - parameter: stddev_degrees
+  outputs:
+    - parameter: volume_element
+  actions:
+    - environments:
+        - scope:
+            type: any
+          environment: damask_parse_env
+      script: <<script:damask/modify_VE_spread_orientations.py>>
+      script_data_in: direct
+      script_data_out: direct
+      script_exe: python_script

matflow/data/workflows/spread_orientations.yaml

@@ -0,0 +1,31 @@
+doc:
+  - >
+    Demonstration of modifying a volume element by applying a perturbation to its orientations.
+
+tasks:
+  - 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]
+      stddev_degrees: [0.01]