diff --git a/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
index 09083d3d41..b776190c3d 100644
--- a/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
@@ -13,12 +13,10 @@ This **Filter** will read a single .h5 file into a new **Image Geometry**, allow
|-------|
||
-
| User interface AFTER setting the "Z Spacing" and selecting files. |
|-------|
||
-
## Notes About Reference Frames
The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. The recommended filters are:
@@ -28,8 +26,15 @@ The user should be aware that simply reading the file then performing operations
If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, the following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
-+ Sample Reference Frame: 180o about the <010> Axis
+ Crystal Reference Frame: 90o about the <001> Axis
++ Sample Reference Frame: 180o about the <010> Axis
+
+### Important Consideration for Sample Reference Frame
+
+If the user is importing more than a single slice from the HDF5 file and using the "Rotate Sample Reference Frame" filter,
+the user should **CHECK** the option **ON** for "Perform Slice By Slice Transform".
+
+## Thresholding out Unindexed Scan Points
The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The [Threshold Objects](../MultiThresholdObjects/index.html) **Filter** can be used to define this *mask* by thresholding on values such as *Confidence Index* > xx or *Image Quality* > desired quality.
diff --git a/src/Plugins/OrientationAnalysis/pipelines/ImportEdaxOIMData.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/ImportEdaxOIMData.d3dpipeline
index 52604253c8..56c5a96610 100644
--- a/src/Plugins/OrientationAnalysis/pipelines/ImportEdaxOIMData.d3dpipeline
+++ b/src/Plugins/OrientationAnalysis/pipelines/ImportEdaxOIMData.d3dpipeline
@@ -1,7 +1,6 @@
{
"isDisabled": false,
- "name": "ImportEdaxOIMData.d3dpipeline",
- "pinnedParams": [],
+ "name": "Untitled Pipeline",
"pipeline": [
{
"args": {
@@ -13,11 +12,19 @@
0.0,
0.0
],
- "read_pattern_data": true,
+ "read_pattern_data": false,
"selected_scan_names": {
- "input_file_path": "Data/OrientationAnalysis/EdaxOIMData.h5",
+ "input_file_path": "Data/Hikari_Ni_Sequence.h5",
"scan_names": [
- "Scan 1"
+ "Scan 1",
+ "Scan 2",
+ "Scan 3",
+ "Scan 4",
+ "Scan 5",
+ "Scan 6",
+ "Scan 7",
+ "Scan 8",
+ "Scan 9"
],
"stacking_order": 0
},
@@ -30,6 +37,70 @@
},
"isDisabled": false
},
+ {
+ "args": {
+ "cell_euler_angles_array_path": "ImageGeom/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": "",
+ "remove_original_geometry": true,
+ "rotate_slice_by_slice": true,
+ "rotation_axis": [
+ 0.0,
+ 1.0,
+ 0.0,
+ 180.0
+ ],
+ "rotation_matrix": [
+ [
+ 1.0,
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 1.0,
+ 0.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 0.0,
+ 1.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
+ ]
+ ],
+ "rotation_representation": 0,
+ "selected_image_geometry": "ImageGeom"
+ },
+ "comments": "",
+ "filter": {
+ "name": "complex::RotateSampleRefFrameFilter",
+ "uuid": "d2451dc1-a5a1-4ac2-a64d-7991669dcffc"
+ },
+ "isDisabled": false
+ },
{
"args": {
"export_file_path": "Data/Output/Examples/EdaxOIMData.dream3d",
@@ -43,5 +114,5 @@
"isDisabled": false
}
],
- "workflowParams": []
-}
+ "version": 1
+}
\ No newline at end of file
diff --git a/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline
index 1cff377aa2..c0f5f27661 100644
--- a/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline
+++ b/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline
@@ -1,7 +1,6 @@
{
"isDisabled": false,
- "name": "ReadAng.d3dpipeline",
- "pinnedParams": [],
+ "name": "Untitled Pipeline",
"pipeline": [
{
"args": {
@@ -10,12 +9,99 @@
"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": {
+ "cell_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": 1,
+ "inverted": false,
+ "type": "array",
+ "union": 0,
+ "value": 0.1
+ }
+ ],
+ "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",
@@ -30,6 +116,7 @@
],
"use_good_voxels": false
},
+ "comments": "",
"filter": {
"name": "complex::GenerateIPFColorsFilter",
"uuid": "64cb4f27-6e5e-4dd2-8a03-0c448cb8f5e6"
@@ -37,5 +124,5 @@
"isDisabled": false
}
],
- "workflowParams": []
-}
+ "version": 1
+}
\ No newline at end of file
diff --git a/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline
index 85a9ce6b59..c0dd481341 100644
--- a/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline
+++ b/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline
@@ -1,7 +1,6 @@
{
"isDisabled": false,
- "name": "ReadCTF.d3dpipeline",
- "pinnedParams": [],
+ "name": "Untitled Pipeline",
"pipeline": [
{
"args": {
@@ -12,26 +11,106 @@
"edax_hexagonal_alignment": false,
"input_file": "Data/T12-MAI-2010/fw-ar-IF1-aptr12-corr.ctf"
},
+ "comments": "",
"filter": {
"name": "complex::ReadCtfDataFilter",
"uuid": "7751923c-afb9-4032-8372-8078325c69a4"
},
"isDisabled": false
},
+ {
+ "args": {
+ "created_image_geometry": "",
+ "remove_original_geometry": true,
+ "rotate_slice_by_slice": false,
+ "rotation_axis": [
+ 0.0,
+ 1.0,
+ 0.0,
+ 180.0
+ ],
+ "rotation_matrix": [
+ [
+ 1.0,
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 1.0,
+ 0.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 0.0,
+ 1.0,
+ 0.0
+ ],
+ [
+ 0.0,
+ 0.0,
+ 0.0,
+ 1.0
+ ]
+ ],
+ "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/Error",
+ "comparison": 2,
+ "inverted": false,
+ "type": "array",
+ "union": 0,
+ "value": 0.0
+ }
+ ],
+ "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",
- "good_voxels_array_path": "",
+ "good_voxels_array_path": "DataContainer/Cell Data/Mask",
"reference_dir": [
0.0,
0.0,
1.0
],
- "use_good_voxels": false
+ "use_good_voxels": true
},
+ "comments": "",
"filter": {
"name": "complex::GenerateIPFColorsFilter",
"uuid": "64cb4f27-6e5e-4dd2-8a03-0c448cb8f5e6"
@@ -39,5 +118,5 @@
"isDisabled": false
}
],
- "workflowParams": []
-}
+ "version": 1
+}
\ No newline at end of file