BUG: ExtractVertexGeometry - Fix crashes/bugs in the filter.

Signed-off-by: Michael Jackson <[email protected]>

src/Plugins/ComplexCore/docs/ExtractVertexGeometryFilter.md

@@ -2,13 +2,16 @@
 
 ## Group (Subgroup)
 
-Core Filters (Conversion)
+Core Filters (Geometry)
 
 ## Description
 
 This filter will extract all the voxel centers of an Image Geometry or a RectilinearGrid geometry
-into a new VertexGeometry. The user is given the option to copy or move cell arrays over to the
-newly created VertexGeometry.
+into a new Vertex Geometry. The user is given the option to copy or move cell arrays over to the
+newly created VertexGeometry. The user can also supply a mask array which has the effect of only
+creating a vertex if the mask value = TRUE.
+
+![Example showing the use of a Mask array to only generate specific points.](Images/ExtractVertexGeometry_1.png)
 
 % Auto generated parameter table will be inserted here
 

src/Plugins/ComplexCore/pipelines/ExtractVertexGeometry.d3dpipeline

@@ -0,0 +1,188 @@
+{
+  "isDisabled": false,
+  "name": "Untitled Pipeline",
+  "pipeline": [
+    {
+      "args": {
+        "cell_attribute_matrix_name": "Cell Data",
+        "cell_ensemble_attribute_matrix_name": "CellEnsembleData",
+        "data_container_name": "DataContainer",
+        "input_file": "Data/Small_IN100/Slice_1.ang"
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::ReadAngDataFilter",
+        "uuid": "5b062816-79ac-47ce-93cb-e7966896bcbd"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "euler_angles_array_path": "DataContainer/Cell Data/EulerAngles",
+        "rotation_axis": [
+          0.0,
+          0.0,
+          1.0,
+          90.0
+        ]
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::RotateEulerRefFrameFilter",
+        "uuid": "0458edcd-3655-4465-adc8-b036d76138b5"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "created_image_geometry": "DataContainer",
+        "remove_original_geometry": true,
+        "rotate_slice_by_slice": false,
+        "rotation_axis": [
+          0.0,
+          1.0,
+          0.0,
+          180.0
+        ],
+        "rotation_matrix": [
+          [
+            0.0,
+            0.0,
+            0.0
+          ],
+          [
+            0.0,
+            0.0,
+            0.0
+          ],
+          [
+            0.0,
+            0.0,
+            0.0
+          ]
+        ],
+        "rotation_representation": 0,
+        "selected_image_geometry": "DataContainer"
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::RotateSampleRefFrameFilter",
+        "uuid": "d2451dc1-a5a1-4ac2-a64d-7991669dcffc"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "array_thresholds": {
+          "inverted": false,
+          "thresholds": [
+            {
+              "array_path": "DataContainer/Cell Data/Confidence Index",
+              "comparison": 0,
+              "inverted": false,
+              "type": "array",
+              "union": 0,
+              "value": 0.9
+            }
+          ],
+          "type": "collection",
+          "union": 0
+        },
+        "created_data_path": "Mask",
+        "created_mask_type": 10,
+        "custom_false_value": 0.0,
+        "custom_true_value": 1.0,
+        "use_custom_false_value": false,
+        "use_custom_true_value": false
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::MultiThresholdObjects",
+        "uuid": "4246245e-1011-4add-8436-0af6bed19228"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "cell_euler_angles_array_path": "DataContainer/Cell Data/EulerAngles",
+        "cell_ipf_colors_array_name": "IPFColors",
+        "cell_phases_array_path": "DataContainer/Cell Data/Phases",
+        "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures",
+        "mask_array_path": "",
+        "reference_dir": [
+          0.0,
+          0.0,
+          1.0
+        ],
+        "use_mask": false
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::GenerateIPFColorsFilter",
+        "uuid": "64cb4f27-6e5e-4dd2-8a03-0c448cb8f5e6"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "array_thresholds": {
+          "inverted": false,
+          "thresholds": [
+            {
+              "array_path": "DataContainer/Cell Data/Y Position",
+              "comparison": 1,
+              "inverted": false,
+              "type": "array",
+              "union": 0,
+              "value": 25.0
+            }
+          ],
+          "type": "collection",
+          "union": 0
+        },
+        "created_data_path": "Mask Y Pos",
+        "created_mask_type": 10,
+        "custom_false_value": 0.0,
+        "custom_true_value": 1.0,
+        "use_custom_false_value": false,
+        "use_custom_true_value": false
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::MultiThresholdObjects",
+        "uuid": "4246245e-1011-4add-8436-0af6bed19228"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "array_handling": 0,
+        "included_data_array_paths": [
+          "DataContainer/Cell Data/Confidence Index",
+          "DataContainer/Cell Data/EulerAngles",
+          "DataContainer/Cell Data/Fit",
+          "DataContainer/Cell Data/IPFColors",
+          "DataContainer/Cell Data/Image Quality",
+          "DataContainer/Cell Data/Phases",
+          "DataContainer/Cell Data/SEM Signal",
+          "DataContainer/Cell Data/X Position",
+          "DataContainer/Cell Data/Y Position",
+          "DataContainer/Cell Data/Mask"
+        ],
+        "input_geometry_path": "DataContainer",
+        "mask_array_path": "DataContainer/Cell Data/Mask Y Pos",
+        "output_shared_vertex_list_name": "SharedVertexList",
+        "output_vertex_attr_matrix_name": "VertexData",
+        "output_vertex_geometry_path": "Vertex Geometry",
+        "use_mask": true
+      },
+      "comments": "This filter will only create vertices where the Y Position was below a threshold set in the previous filter. The filter will move the arrays to the newly created vertext geometry",
+      "filter": {
+        "name": "complex::ExtractVertexGeometryFilter",
+        "uuid": "621a71ca-124b-4471-ad1a-02f05ffba099"
+      },
+      "isDisabled": false
+    }
+  ],
+  "version": 1
+}