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ENH: Add proper sample and crystal reference frame rotations to pipelines #734

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Oct 9, 2023
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ENH: Add proper sample and crystal reference frame rotations to pipelines #734

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11 changes: 8 additions & 3 deletions src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,10 @@ This **Filter** will read a single .h5 file into a new **Image Geometry**, allow
|-------|
|![](Images/ReadEDAXH5_1.png)|


| User interface AFTER setting the "Z Spacing" and selecting files. |
|-------|
|![](Images/ReadEDAXH5_2.png)|


## 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:
Expand All @@ -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: 180<sup>o</sup> about the <010> Axis
+ Crystal Reference Frame: 90<sup>o</sup> about the <001> Axis
+ Sample Reference Frame: 180<sup>o</sup> 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.

Expand Down
85 changes: 78 additions & 7 deletions src/Plugins/OrientationAnalysis/pipelines/ImportEdaxOIMData.d3dpipeline
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
{
"isDisabled": false,
"name": "ImportEdaxOIMData.d3dpipeline",
"pinnedParams": [],
"name": "Untitled Pipeline",
"pipeline": [
{
"args": {
Expand All @@ -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
},
Expand All @@ -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",
Expand All @@ -43,5 +114,5 @@
"isDisabled": false
}
],
"workflowParams": []
}
"version": 1
}
95 changes: 91 additions & 4 deletions src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
{
"isDisabled": false,
"name": "ReadAng.d3dpipeline",
"pinnedParams": [],
"name": "Untitled Pipeline",
"pipeline": [
{
"args": {
Expand All @@ -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",
Expand All @@ -30,12 +116,13 @@
],
"use_good_voxels": false
},
"comments": "",
"filter": {
"name": "complex::GenerateIPFColorsFilter",
"uuid": "64cb4f27-6e5e-4dd2-8a03-0c448cb8f5e6"
},
"isDisabled": false
}
],
"workflowParams": []
}
"version": 1
}
91 changes: 85 additions & 6 deletions src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
{
"isDisabled": false,
"name": "ReadCTF.d3dpipeline",
"pinnedParams": [],
"name": "Untitled Pipeline",
"pipeline": [
{
"args": {
Expand All @@ -12,32 +11,112 @@
"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"
},
"isDisabled": false
}
],
"workflowParams": []
}
"version": 1
}