OrientationAnalysis Filter API

This is the documentation for all filters included in the OrientationAnalysis module. These filters can be used by importing the appropriate module. Each filter is contained in the module:

import orientationanalysis
# Instantiate and execute a filter from the module
result = orientationanalysis.SomeFilterName.execute(...)

Align Sections (Misorientation)

class OrientationAnalysis.AlignSectionsMisorientationFilter

This Filter attempts to align consecutive ‘sections’ perpendicular to the Z-direction of the sample by determining the position that results in the minimum amount of misorientation between Cells directly above-below each other. The algorithm of this Filter is as follows:

Link to the full online documentation for AlignSectionsMisorientationFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Alignment File Path

alignment_shift_file_name

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Selected Image Geometry

input_image_geometry_path

Cell Mask Array

mask_array_path

Misorientation Tolerance (Degrees)

misorientation_tolerance

Cell Quaternions

quats_array_path

Use Mask Array

use_mask

Write Alignment Shift File

write_alignment_shifts
Execute(data_structure, alignment_shift_file_name, cell_phases_array_path, crystal_structures_array_path, input_image_geometry_path, mask_array_path, misorientation_tolerance, quats_array_path, use_mask, write_alignment_shifts)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • alignment_shift_file_name (nx.FileSystemPathParameter) – The output file path where the user would like the shifts applied to the section to be written.

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • input_image_geometry_path (nx.GeometrySelectionParameter) – The target geometry

  • mask_array_path (nx.ArraySelectionParameter) – Path to the DataArray Mask

  • misorientation_tolerance (nx.Float32Parameter) – Tolerance used to decide if Cells above/below one another should be considered to be the same. The value selected should be similar to the tolerance one would use to define Features (i.e., 2-10 degrees)

  • quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation

  • use_mask (nx.BoolParameter) – Whether to remove some Cells from consideration in the alignment process

  • write_alignment_shifts (nx.BoolParameter) – Whether to write the shifts applied to each section to a file

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Align Sections (Mutual Information)

class OrientationAnalysis.AlignSectionsMutualInformationFilter

This Filter segments each 2D slice, creating Feature Ids that are used when determining the mutual information between neighboring slices. The slices are shifted relative to one another until the position of maximum mutual information is determined for each section. The Feature Ids are temporary, they apply to this Filter only and are not related to the Feature Ids generated in other Filters. The algorithm of this Filter is listed below:

Link to the full online documentation for AlignSectionsMutualInformationFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Alignment File Path

alignment_shift_file_name

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Selected Image Geometry

input_image_geometry_path

Cell Mask Array

mask_array_path

Misorientation Tolerance

misorientation_tolerance

Cell Quaternions

quats_array_path

Use Mask Array

use_mask

Write Alignment Shift File

write_alignment_shifts
Execute(data_structure, alignment_shift_file_name, cell_phases_array_path, crystal_structures_array_path, input_image_geometry_path, mask_array_path, misorientation_tolerance, quats_array_path, use_mask, write_alignment_shifts)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • alignment_shift_file_name (nx.FileSystemPathParameter) – The output file path where the user would like the shifts applied to the section to be written. Only needed if Write Alignment Shifts File is checked.

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Cell belongs.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble.

  • input_image_geometry_path (nx.GeometrySelectionParameter) – The target geometry

  • mask_array_path (nx.ArraySelectionParameter) – Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked.

  • misorientation_tolerance (nx.Float32Parameter) – Tolerance used to decide if Cells above/below one another should be considered to be the same. The value selected should be similar to the tolerance one would use to define Features (i.e., 2-10 degrees).

  • quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation.

  • use_mask (nx.BoolParameter) – Whether to remove some Cells from consideration in the alignment process.

  • write_alignment_shifts (nx.BoolParameter) – Whether to write the shifts applied to each section to a file.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Neighbor Orientation Comparison (Bad Data)

class OrientationAnalysis.BadDataNeighborOrientationCheckFilter

This Filter compares the orientations of bad Cells with their neighbor Cells. If the misorientation is below a user defined tolerance for a user defined number of neighbor Cells , then the bad Cell will be changed to a good Cell.

Link to the full online documentation for BadDataNeighborOrientationCheckFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Image Geometry

input_image_geometry_path

Cell Mask Array

mask_array_path

Misorientation Tolerance (Degrees)

misorientation_tolerance

Required Number of Neighbors

number_of_neighbors

Cell Quaternions

quats_array_path
Execute(data_structure, cell_phases_array_path, crystal_structures_array_path, input_image_geometry_path, mask_array_path, misorientation_tolerance, number_of_neighbors, quats_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Segment Features (C-Axis Misalignment)

class OrientationAnalysis.CAxisSegmentFeaturesFilter

This Filter segments the Features by grouping neighboring Cells that satisfy the C-axis misalignment tolerance, i.e., have misalignment angle less than the value set by the user. The C-axis misalignment refers to the angle between the <001> directions (C-axis in the hexagonal system) that is present between neighboring Cells. The process by which the Features are identified is given below and is a standard burn algorithm.

Link to the full online documentation for CAxisSegmentFeaturesFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Active

active_array_name

Feature Attribute Matrix

cell_feature_attribute_matrix_name

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_array_name

Image Geometry

input_image_geometry_path

Cell Mask Array

mask_array_path

C-Axis Misorientation Tolerance (Degrees)

misorientation_tolerance

Cell Quaternions

quats_array_path

Randomize Feature Ids

randomize_feature_ids

Use Mask Array

use_mask
Execute(data_structure, active_array_name, cell_feature_attribute_matrix_name, cell_phases_array_path, crystal_structures_array_path, feature_ids_array_name, input_image_geometry_path, mask_array_path, misorientation_tolerance, quats_array_path, randomize_feature_ids, use_mask)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • active_array_name (nx.DataObjectNameParameter) – Specifies if the Feature is still in the sample (true if the Feature is in the sample and false if it is not). At the end of the Filter, all Features will be Active

  • cell_feature_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the created feature attribute matrix

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_ids_array_name (nx.DataObjectNameParameter) – Specifies to which Feature each Cell belongs

  • input_image_geometry_path (nx.GeometrySelectionParameter) – The path to the input image geometry

  • mask_array_path (nx.ArraySelectionParameter) – Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked

  • misorientation_tolerance (nx.Float32Parameter) – Tolerance (in degrees) used to determine if neighboring Cells belong to the same Feature

  • quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation

  • randomize_feature_ids (nx.BoolParameter) – Specifies whether to randomize the feature ids

  • use_mask (nx.BoolParameter) – Specifies whether to use a boolean array to exclude some Cells from the Feature identification process

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Convert EDAX Hex Grid to Square Grid (.ang)

class OrientationAnalysis.ConvertHexGridToSquareGridFilter

This Filter will convert TSL .ang files on hexagonal grids to TSL .ang files on square grids by means of interpolation between points. Note that the resulting square grid .ang files may have more or less rows of data and that some data may be interpolated based on its neighbor data. By default, the spacing of the square grid will be the spacing between columns in the hexagonal grid.

Link to the full online documentation for ConvertHexGridToSquareGridFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Generated File List

generated_file_list

Input File

input_path

Convert Multiple Files

multiple_files

Output Directory

output_path

Output Prefix

output_prefix

Spacing

spacing
Execute(data_structure, generated_file_list, input_path, multiple_files, output_path, output_prefix, spacing)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Convert Orientation Representation

class OrientationAnalysis.ConvertOrientationsFilter

This Filter generates a new orientation representation (see Data Layout Table below) for each Element, given the Input Orientation Representation for the Element. The following table lists the various orientation representations that are supported. DREAM3D is capable of converting between any representation with some caveats.

Link to the full online documentation for ConvertOrientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Input Orientations

input_orientation_array_path

Input Orientation Type

input_representation_index

Output Orientations

output_orientation_array_name

Output Orientation Type

output_representation_index
Execute(data_structure, input_orientation_array_path, input_representation_index, output_orientation_array_name, output_representation_index)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • input_orientation_array_path (nx.ArraySelectionParameter) – The complete path to the incoming orientation representation data array

  • input_representation_index (nx.ChoicesParameter) – Specifies the incoming orientation representation

  • output_orientation_array_name (nx.DataObjectNameParameter) – The name of the data array with the converted orientation representation

  • output_representation_index (nx.ChoicesParameter) – Specifies to which orientation representation to convert the incoming data

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Convert Quaternion Order

class OrientationAnalysis.ConvertQuaternionFilter

Internally DREAM.3D assumes that a quaternion is laid out in the order such that < x, y, z >, w or Vector-Scalar ordering. Codes and algorithms external to DREAM.3D may store quaternions in the opposite or Scalar-Vector order (w < x,y,z >). This filter will allow the user to easily convert imported Quaternions into the representation that DREAM.3D expects.

Link to the full online documentation for ConvertQuaternionFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Conversion Type

conversion_index

Delete Original Data

delete_original_data

Input Quaternions

input_data_array_path

Output Quaternions

output_data_array_name
Execute(data_structure, conversion_index, delete_original_data, input_data_array_path, output_data_array_name)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • conversion_index (nx.ChoicesParameter) – The conversion type: To Scalar Vector=0, To Vector Scalar=1

  • delete_original_data (nx.BoolParameter) – Should the original quaternions array be deleted from the DataStructure

  • input_data_array_path (nx.ArraySelectionParameter) – Specifies the quaternions to convert

  • output_data_array_name (nx.DataObjectNameParameter) – The DataPath to the converted quaternions

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Create Ensemble Info

class OrientationAnalysis.CreateEnsembleInfoFilter

This Filter allows the user to enter basic crystallographic information about each phase. The Laue class, Phase Type, and Phase Name can all be entered by the user. The information is stored in an EnsembleAttributeMatrix. These values are needed to allow the calculation of certain kinds of crystallographic statistics on the volume, if they have not already been provided by some other means. Each row in the table lists the Crystal Structure, Phase Type, and Phase Name. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:

Link to the full online documentation for CreateEnsembleInfoFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_path

Crystal Structures

crystal_structures_array_name

Created Ensemble Info

ensemble

Phase Names

phase_names_array_name

Phase Types

phase_types_array_name
Execute(data_structure, cell_ensemble_attribute_matrix_path, crystal_structures_array_name, ensemble, phase_names_array_name, phase_types_array_name)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_ensemble_attribute_matrix_path (nx.DataGroupCreationParameter) – The complete path to the attribute matrix in which to store the ensemble phase data arrays

  • crystal_structures_array_name (nx.DataObjectNameParameter) – The name of the data array representing the crystal structure for each Ensemble

  • ensemble (nx.EnsembleInfoParameter) – The values with which to populate the crystal structures, phase types, and phase names data arrays. Each row corresponds to an ensemble phase.

  • phase_names_array_name (nx.DataObjectNameParameter) – The name of the string array representing the phase names for each Ensemble

  • phase_types_array_name (nx.DataObjectNameParameter) – The name of the data array representing the phase types for each Ensemble

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Segment Features (Misorientation)

class OrientationAnalysis.EBSDSegmentFeaturesFilter

This Filter segments the Features by grouping neighboring Cells that satisfy the misorientation tolerance, i.e., have misorientation angle less than the value set by the user. The process by which the Features are identified is given below and is a standard burn algorithm.

Link to the full online documentation for EBSDSegmentFeaturesFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Active

active_array_name

Feature Attribute Matrix

cell_feature_attribute_matrix_name

Cell Mask Array

cell_mask_array_path

Cell Phases

cell_phases_array_path

Cell Quaternions

cell_quats_array_path

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_array_name

Input Grid Geometry

input_image_geometry_path

Misorientation Tolerance (Degrees)

misorientation_tolerance

Randomize Feature IDs

randomize_features

Use Mask Array

use_mask
Execute(data_structure, active_array_name, cell_feature_attribute_matrix_name, cell_mask_array_path, cell_phases_array_path, cell_quats_array_path, crystal_structures_array_path, feature_ids_array_name, input_image_geometry_path, misorientation_tolerance, randomize_features, use_mask)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • active_array_name (nx.DataObjectNameParameter) – The name of the array which specifies if the Feature is still in the sample (true if the Feature is in the sample and false if it is not). At the end of the Filter, all Features will be Active

  • cell_feature_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the created cell feature attribute matrix

  • cell_mask_array_path (nx.ArraySelectionParameter) – Path to the data array that specifies if the Cell is to be counted in the algorithm

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • cell_quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_ids_array_name (nx.DataObjectNameParameter) – Specifies to which Feature each Cell belongs.

  • input_image_geometry_path (nx.GeometrySelectionParameter) – DataPath to input Grid Geometry

  • misorientation_tolerance (nx.Float32Parameter) – Tolerance (in degrees) used to determine if neighboring Cells belong to the same Feature

  • randomize_features (nx.BoolParameter) – Specifies if feature IDs should be randomized during calculations

  • use_mask (nx.BoolParameter) – Specifies whether to use a boolean array to exclude some Cells from the Feature identification process

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Import Orientation File(s) to H5EBSD

class OrientationAnalysis.EbsdToH5EbsdFilter

This Filter will convert orientation data obtained from Electron Backscatter Diffraction (EBSD) experiments into a single file archive based on the HDF5 file specification. See the Supported File Formats section below for information on file compatibility. This Filter is typically run as a single Filter Pipeline to perform the conversion. All subsequent Pipelines should then use the Read H5EBSD File Filter to import the H5EBSD file into DREAM.3D for analysis, as opposed to re-importing the raw EBSD files. The primary purpose of this Filter is to import a stack of data that forms a 3D volume. If the user wishes to import a single data file, then the Filters Read EDAX EBSD Data (.ang), Read EDAX EBSD Data (.h5), or Read Oxford Instr. EBSD Data (.ctf) should be used for EDAX .ang, EDAX .h5, or Oxford .ctf files, respectively.

Link to the full online documentation for EbsdToH5EbsdFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Input File List

input_file_list_object

Output H5Ebsd File

output_file_path

Reference Frame Options

reference_frame_index

Stacking Order

stacking_order_index

Z Spacing (Microns)

z_spacing
Execute(data_structure, input_file_list_object, output_file_path, reference_frame_index, stacking_order_index, z_spacing)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • input_file_list_object (nx.GeneratedFileListParameter) – The values that are used to generate the input file list. See GeneratedFileListParameter for more information.

  • output_file_path (nx.FileSystemPathParameter) – The path to the generated .h5ebsd file

  • reference_frame_index (nx.ChoicesParameter) – The reference frame transformation. 0=EDAX(.ang), 1=Oxford(.ctf), 2=No/Unknown Transformation, 3=HEDM-IceNine

  • stacking_order_index (nx.ChoicesParameter) – The order the files should be placed into the

  • z_spacing (nx.Float32Parameter) – The spacing between each slice of data

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Average C-Axis Orientations

class OrientationAnalysis.FindAvgCAxesFilter

This Filter determines the average C-axis location of each Feature by the following algorithm:

Link to the full online documentation for FindAvgCAxesFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average C-Axes

avg_c_axes_array_name

Feature Attribute Matrix

cell_feature_attribute_matrix_path

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_array_path

Cell Quaternions

quats_array_path
Execute(data_structure, avg_c_axes_array_name, cell_feature_attribute_matrix_path, cell_phases_array_path, crystal_structures_array_path, feature_ids_array_path, quats_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Average Orientations

class OrientationAnalysis.FindAvgOrientationsFilter

This Filter determines the average orientation of each Feature by the following algorithm:

Link to the full online documentation for FindAvgOrientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Euler Angles

avg_euler_angles_array_name

Average Quaternions

avg_quats_array_name

Feature Attribute Matrix

cell_feature_attribute_matrix_path

Cell Feature Ids

cell_feature_ids_array_path

Cell Phases

cell_phases_array_path

Cell Quaternions

cell_quats_array_path

Crystal Structures

crystal_structures_array_path
Execute(data_structure, avg_euler_angles_array_name, avg_quats_array_name, cell_feature_attribute_matrix_path, cell_feature_ids_array_path, cell_phases_array_path, cell_quats_array_path, crystal_structures_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Boundary Strength Metrics

class OrientationAnalysis.FindBoundaryStrengthsFilter

This Filter calculates the same metrics as in the Find Neighbor Slip Transmission Metrics Filter. However, this Filter stores the values in the Face Attribute Matrix of a Triangle Geometry. The algorithm the Filter uses is as follows:

Link to the full online documentation for FindBoundaryStrengthsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Quaternions

avg_quats_array_path

Crystal Structures

crystal_structures_array_path

Phases

feature_phases_array_path

Loading Direction (XYZ)

loading

F1s

surface_mesh_f1s_array_name

F1spts

surface_mesh_f1spts_array_name

F7s

surface_mesh_f7s_array_name

Face Labels

surface_mesh_face_labels_array_path

mPrimes

surface_meshm_primes_array_name
Execute(data_structure, avg_quats_array_path, crystal_structures_array_path, feature_phases_array_path, loading, surface_mesh_f1s_array_name, surface_mesh_f1spts_array_name, surface_mesh_f7s_array_name, surface_mesh_face_labels_array_path, surface_meshm_primes_array_name)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find C-Axis Locations

class OrientationAnalysis.FindCAxisLocationsFilter

This Filter determines the direction <u,v,w> of the C-axis for each Element by applying the quaternion of the Element to the <001> direction, which is the C-axis for Hexagonal materials. This will tell where the C-axis of the Element sits in the sample reference frame.

Link to the full online documentation for FindCAxisLocationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

C-Axis Locations

c_axis_locations_array_name

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Quaternions

quats_array_path
Execute(data_structure, c_axis_locations_array_name, cell_phases_array_path, crystal_structures_array_path, quats_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Neighbor C-Axis Misalignments

class OrientationAnalysis.FindFeatureNeighborCAxisMisalignmentsFilter

This Filter determines, for each Feature, the C-axis misalignments with the Features that are in contact with it. The C-axis misalignments are stored as a list (for each Feature) of angles (in degrees).

Link to the full online documentation for FindFeatureNeighborCAxisMisalignmentsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average C-Axis Misalignments

avg_c_axis_misalignments_array_name

Average Quaternions

avg_quats_array_path

C-Axis Misalignment List

c_axis_misalignment_list_array_name

Crystal Structures

crystal_structures_array_path

Phases

feature_phases_array_path

Find Average Misalignment Per Feature

find_avg_misals

Neighbor List

neighbor_list_array_path
Execute(data_structure, avg_c_axis_misalignments_array_name, avg_quats_array_path, c_axis_misalignment_list_array_name, crystal_structures_array_path, feature_phases_array_path, find_avg_misals, neighbor_list_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_c_axis_misalignments_array_name (nx.DataObjectNameParameter) – Number weighted average of neighbor C-axis misalignments. Only created if Find Average Misalignment Per Feature is checked

  • avg_quats_array_path (nx.ArraySelectionParameter) – Defines the average orientation of the Feature in quaternion representation

  • c_axis_misalignment_list_array_name (nx.DataObjectNameParameter) – List of the C-axis misalignment angles (in degrees) with the contiguous neighboring Features for a given Feature

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Feature belongs

  • find_avg_misals (nx.BoolParameter) – Whether the average of the C-axis misalignments with the neighboring Features should be stored for each Feature

  • neighbor_list_array_path (nx.NeighborListSelectionParameter) – List of the contiguous neighboring Features for a given Feature

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Reference C-Axis Misalignments

class OrientationAnalysis.FindFeatureReferenceCAxisMisorientationsFilter

This Filter calculates the misorientation angle between the C-axis of each Cell within a Feature and the average C-axis for that Feature and stores that value for each Cell. The average and standard deviation of those values for all Cells belonging to the same Feature is also stored for each Feature.

Link to the full online documentation for FindFeatureReferenceCAxisMisorientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average C-Axes

avg_c_axes_array_path

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Average C-Axis Misorientations

feature_avg_c_axis_misorientations_array_name

Cell Feature Ids

feature_ids_array_path

Feature Reference C-Axis Misorientations

feature_reference_c_axis_misorientations_array_name

Feature Stdev C-Axis Misorientations

feature_stdev_c_axis_misorientations_array_name

Image Geometry

input_image_geometry_path

Cell Quaternions

quats_array_path
Execute(data_structure, avg_c_axes_array_path, cell_phases_array_path, crystal_structures_array_path, feature_avg_c_axis_misorientations_array_name, feature_ids_array_path, feature_reference_c_axis_misorientations_array_name, feature_stdev_c_axis_misorientations_array_name, input_image_geometry_path, quats_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_c_axes_array_path (nx.ArraySelectionParameter) – The direction of the Feature’s C-axis in the sample reference frame

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_avg_c_axis_misorientations_array_name (nx.DataObjectNameParameter) – Average of the Feature Reference CAxis Misorientation values for all of the Cells that belong to the Feature

  • feature_ids_array_path (nx.ArraySelectionParameter) – Data Array that specifies to which Feature each Element belongs

  • feature_reference_c_axis_misorientations_array_name (nx.DataObjectNameParameter) – Misorientation angle (in degrees) between Cell’s C-axis and the C-axis of the Feature that owns that Cell

  • feature_stdev_c_axis_misorientations_array_name (nx.DataObjectNameParameter) – Standard deviation of the Feature Reference CAxis Misorientation values for all of the Cells that belong to the Feature

  • input_image_geometry_path (nx.GeometrySelectionParameter) – The path to the input image geometry

  • quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Reference Misorientations

class OrientationAnalysis.FindFeatureReferenceMisorientationsFilter

This Filter calculates the misorientation angle between each Cell within a Feature and a reference orientation for that Feature. The user can choose the reference orientation to be used for the Features from a drop-down menu. The options for the reference orientation are the average orientation of the Feature or the orientation of the Cell that is furthest from the boundary of the Feature.

Link to the full online documentation for FindFeatureReferenceMisorientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Quaternions

avg_quats_array_path

Feature Attribute Matrix

cell_feature_attribute_matrix_path

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Average Misorientations

feature_avg_misorientations_array_name

Cell Feature Ids

feature_ids_path

Feature Reference Misorientations

feature_reference_misorientations_array_name

Boundary Euclidean Distances

gb_euclidean_distances_array_path

Cell Quaternions

quats_array_path

Reference Orientation

reference_orientation_index
Execute(data_structure, avg_quats_array_path, cell_feature_attribute_matrix_path, cell_phases_array_path, crystal_structures_array_path, feature_avg_misorientations_array_name, feature_ids_path, feature_reference_misorientations_array_name, gb_euclidean_distances_array_path, quats_array_path, reference_orientation_index)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_quats_array_path (nx.ArraySelectionParameter) – Specifies the average orientation of the Feature in quaternion representation (, w). Only required if the reference orientation is selected to be the average of the Feature

  • cell_feature_attribute_matrix_path (nx.AttributeMatrixSelectionParameter) – The path to the cell feature attribute matrix

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_avg_misorientations_array_name (nx.DataObjectNameParameter) – The name of the array containing the average of the Feature reference misorientation values for all of the Cells that belong to the Feature

  • feature_ids_path (nx.ArraySelectionParameter) – Specifies to which Feature each cell belongs

  • feature_reference_misorientations_array_name (nx.DataObjectNameParameter) – The name of the array containing the misorientation angle (in degrees) between Cell’s orientation and the reference orientation of the Feature that owns that Cell

  • gb_euclidean_distances_array_path (nx.ArraySelectionParameter) – Distance the Cells are from the boundary of the Feature they belong to. Only required if the reference orientation is selected to be the orientation at the Feature centroid

  • quats_array_path (nx.ArraySelectionParameter) – Specifies the orientation of the Cell in quaternion representation

  • reference_orientation_index (nx.ChoicesParameter) – Specifies the reference orientation to use when comparing to each Cell

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find GBCD

class OrientationAnalysis.FindGBCDFilter

This Filter computes the 5D grain boundary character distribution (GBCD) for a Triangle Geometry, which is the relative area of grain boundary for a given misorientation and normal. The GBCD can be visualized by using either the Write GBCD Pole Figure (GMT) or the Write GBCD Pole Figure (VTK) Filters.

Link to the full online documentation for FindGBCDFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Crystal Structures

crystal_structures_array_path

Face Ensemble Attribute Matrix

face_ensemble_attribute_matrix_name

Average Euler Angles

feature_euler_angles_array_path

Phases

feature_phases_array_path

GBCD

gbcd_array_name

GBCD Spacing (Degrees)

gbcd_resolution

Triangle Geometry

input_triangle_geometry_path

Face Areas

surface_mesh_face_areas_array_path

Face Labels

surface_mesh_face_labels_array_path

Face Normals

surface_mesh_face_normals_array_path
Execute(data_structure, crystal_structures_array_path, face_ensemble_attribute_matrix_name, feature_euler_angles_array_path, feature_phases_array_path, gbcd_array_name, gbcd_resolution, input_triangle_geometry_path, surface_mesh_face_areas_array_path, surface_mesh_face_labels_array_path, surface_mesh_face_normals_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • face_ensemble_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the created face ensemble attribute matrix

  • feature_euler_angles_array_path (nx.ArraySelectionParameter) – Array specifying three angles defining the orientation of the Feature in Bunge convention (Z-X-Z)

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which phase each Feature belongs

  • gbcd_array_name (nx.DataObjectNameParameter) – 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere

  • gbcd_resolution (nx.Float32Parameter) – The resolution in degrees for the GBCD calculation

  • input_triangle_geometry_path (nx.GeometrySelectionParameter) – Path to the triangle geometry for which to calculate the GBCD

  • surface_mesh_face_areas_array_path (nx.ArraySelectionParameter) – Array specifying the area of each Face

  • surface_mesh_face_labels_array_path (nx.ArraySelectionParameter) – Array specifying which Features are on either side of each Face

  • surface_mesh_face_normals_array_path (nx.ArraySelectionParameter) – Array specifying the normal of each Face

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find GBCD (Metric-Based Approach)

class OrientationAnalysis.FindGBCDMetricBasedFilter

This Filter computes a section through the five-dimensional grain boundary distirbution for a fixed misorientation. An example of such a section is shown in Fig. 1. Differently than Find GBCD Filter, which uses a method based on partition of the boundary space into bins, this Filter implements an alternative metric-based approach described by K. Glowinski and A. Morawiec in Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)

Link to the full online documentation for FindGBCDMetricBasedFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Limiting Distances

chosen_limit_dists_index

Crystal Structures

crystal_structures_array_path

Output Distribution File

dist_output_file

Output Distribution Errors File

err_output_file

Exclude Triangles Directly Neighboring Triple Lines

exclude_triple_lines

Average Euler Angles

feature_euler_angles_array_path

Phases

feature_phases_array_path

Triangle Geometry

input_triangle_geometry_path

Fixed Misorientation

misorientation_rotation

Node Types

node_types_array_path

Number of Sampling Points (on a Hemisphere)

num_sampl_pts

Phase of Interest

phase_of_interest

Save Relative Errors Instead of Their Absolute Values

save_relative_err

Face Areas

surface_mesh_face_areas_array_path

Face Labels

surface_mesh_face_labels_array_path

Face Normals

surface_mesh_face_normals_array_path

Feature Face Labels

surface_mesh_feature_face_labels_array_path
Execute(data_structure, chosen_limit_dists_index, crystal_structures_array_path, dist_output_file, err_output_file, exclude_triple_lines, feature_euler_angles_array_path, feature_phases_array_path, input_triangle_geometry_path, misorientation_rotation, node_types_array_path, num_sampl_pts, phase_of_interest, save_relative_err, surface_mesh_face_areas_array_path, surface_mesh_face_labels_array_path, surface_mesh_face_normals_array_path, surface_mesh_feature_face_labels_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • chosen_limit_dists_index (nx.ChoicesParameter) – The max angles from within which boundary segments are selected for the misorientations and plane inclinations

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • dist_output_file (nx.FileSystemPathParameter) – The output distribution file path (extension .dat, GMT format)

  • err_output_file (nx.FileSystemPathParameter) – The output distribution errors file path (extension .dat, GMT format)

  • exclude_triple_lines (nx.BoolParameter) – If checked, only interiors of Faces are included in GBCD

  • feature_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Feature in Bunge convention (Z-X-Z)

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which phase each Feature belongs

  • input_triangle_geometry_path (nx.GeometrySelectionParameter) – The complete path to the triangle geometry

  • misorientation_rotation (nx.VectorFloat32Parameter) – Axis-angle representation of the misorientation of interest. Angle value should be in degrees.

  • node_types_array_path (nx.ArraySelectionParameter) – Specifies the type of node in the Geometry

  • num_sampl_pts (nx.Int32Parameter) – The approximate number of sampling directions

  • phase_of_interest (nx.Int32Parameter) – Index of the Ensemble for which to compute GBCD; boundaries having grains of this phase on both its sides will only be taken into account

  • save_relative_err (nx.BoolParameter) – Whether or not to save the distribution errors as relative (if exceeds 100%, then rounded down) or absolute

  • surface_mesh_face_areas_array_path (nx.ArraySelectionParameter) – Specifies the area of each Face

  • surface_mesh_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which Features are on either side of each Face

  • surface_mesh_face_normals_array_path (nx.ArraySelectionParameter) – Specifies the normal of each Face

  • surface_mesh_feature_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which original Features are on either side of each boundary Feature

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find GBPD (Metric-Based Approach)

class OrientationAnalysis.FindGBPDMetricBasedFilter

This Filter computes the grain boundary plane distribution (GBPD) like that shown in Fig. 1. It should be noted that most GBPDs presented so far in literature were obtained using a method based on partition of the grain boundary space into bins, similar to that implemented in the Find GBCD Filter. This Filter calculates the GBPD using an alternative approach adapted from the one included in the Find GBCD (Metric-based Approach) Filter and described by K. Glowinski and A. Morawiec in Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014). Briefly, the GBPD is probed at evenly distributed sampling directions (similarly to Find GBCD (Metric-based Approach) Filter) and areas of mesh segments with their normal vectors deviated by less than a limiting angle &rho;<sub>p</sub> from a given direction are summed. If n*<sub>S</sub> is the number of crystal symmetry transformations, each boundary plane segment is represented by up to 4 &times; *n*<sub>S</sub> equivalent vectors, and all of them are processed. It is enough to sample the distribution at directions corresponding to the standard stereographic triangle (or, in general, to a fundamental region corresponding to a considered crystallographic point group); values at remaining points are obtained based on crystal symmetries. After summing the boundary areas, the distribution is normalized. First, the values at sampling vectors are divided by the total area of all segments. Then, in order to express the distribution in the conventional units, i.e., multiples of random distribution (MRDs), the obtained fractional values are divided by the volume *v = (A n<sub>S</sub>) / (4&pi;), where A is the area of a spherical cap determined by &rho;<sub>p</sub>.

Link to the full online documentation for FindGBPDMetricBasedFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Crystal Structures

crystal_structures_array_path

Output Distribution File

dist_output_file

Output Distribution Errors File

err_output_file

Exclude Triangles Directly Neighboring Triple Lines

exclude_triple_lines

Average Euler Angles

feature_euler_angles_array_path

Phases

feature_phases_array_path

Triangle Geometry

input_triangle_geometry_path

Limiting Distance [deg.]

limit_dist

Node Types

node_types_array_path

Number of Sampling Points (on a Hemisphere)

num_sampl_pts

Phase of Interest

phase_of_interest

Save Relative Errors Instead of Their Absolute Values

save_relative_err

Face Areas

surface_mesh_face_areas_array_path

Face Labels

surface_mesh_face_labels_array_path

Face Normals

surface_mesh_face_normals_array_path

Feature Face Labels

surface_mesh_feature_face_labels_array_path
Execute(data_structure, crystal_structures_array_path, dist_output_file, err_output_file, exclude_triple_lines, feature_euler_angles_array_path, feature_phases_array_path, input_triangle_geometry_path, limit_dist, node_types_array_path, num_sampl_pts, phase_of_interest, save_relative_err, surface_mesh_face_areas_array_path, surface_mesh_face_labels_array_path, surface_mesh_face_normals_array_path, surface_mesh_feature_face_labels_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • dist_output_file (nx.FileSystemPathParameter) – The output distribution file path (extension .dat, GMT format)

  • err_output_file (nx.FileSystemPathParameter) – The output distribution errors file path (extension .dat, GMT format)

  • exclude_triple_lines (nx.BoolParameter) – If checked, only interiors of Faces are included in GBCD

  • feature_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Feature in Bunge convention (Z-X-Z)

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which phase each Feature belongs

  • input_triangle_geometry_path (nx.GeometrySelectionParameter) – The complete path to the triangle geometry

  • limit_dist (nx.Float32Parameter) – The max angle from within which mesh segments are selected

  • node_types_array_path (nx.ArraySelectionParameter) – Specifies the type of node in the Geometry

  • num_sampl_pts (nx.Int32Parameter) – The approximate number of sampling directions

  • phase_of_interest (nx.Int32Parameter) – Index of the Ensemble for which to compute GBPD; boundaries having grains of this phase on both its sides will only be taken into account

  • save_relative_err (nx.BoolParameter) – Whether or not to save the distribution errors as relative (if exceeds 100%, then rounded down) or absolute

  • surface_mesh_face_areas_array_path (nx.ArraySelectionParameter) – Specifies the area of each Face

  • surface_mesh_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which Features are on either side of each Face

  • surface_mesh_face_normals_array_path (nx.ArraySelectionParameter) – Specifies the normal of each Face

  • surface_mesh_feature_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which original Features are on either side of each boundary Feature

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Kernel Average Misorientations

class OrientationAnalysis.FindKernelAvgMisorientationsFilter

This Filter determines the Kernel Average Misorientation (KAM) for each Cell. The user can select the size of the kernel to be used in the calculation. The kernel size entered by the user is the radius of the kernel (i.e., entering values of 1, 2, 3 will result in a kernel that is 3, 5, and 7 Cells in size in the X, Y and Z directions, respectively). The algorithm for determination of KAM is as follows:

Link to the full online documentation for FindKernelAvgMisorientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_path

Selected Image Geometry

input_image_geometry_path

Kernel Average Misorientations

kernel_average_misorientations_array_name

Kernel Radius

kernel_size

Cell Quaternions

quats_array_path
Execute(data_structure, cell_phases_array_path, crystal_structures_array_path, feature_ids_path, input_image_geometry_path, kernel_average_misorientations_array_name, kernel_size, quats_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Neighbor Misorientations

class OrientationAnalysis.FindMisorientationsFilter

This Filter determines, for each Feature, the misorientations with each of the Features that are in contact with it. The misorientations are stored as a list (for each Feature) of angles (in degrees). The axis of the misorientation is not stored by this Filter.

Link to the full online documentation for FindMisorientationsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Misorientations

avg_misorientations_array_name

Feature Average Quaternions

avg_quats_array_path

Crystal Structures

crystal_structures_array_path

Feature Phases

feature_phases_array_path

Find Average Misorientation Per Feature

find_avg_misors

Misorientation List

misorientation_list_array_name

Feature Neighbor List

neighbor_list_array_path
Execute(data_structure, avg_misorientations_array_name, avg_quats_array_path, crystal_structures_array_path, feature_phases_array_path, find_avg_misors, misorientation_list_array_name, neighbor_list_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_misorientations_array_name (nx.DataObjectNameParameter) – The name of the array containing the number weighted average of neighbor misorientations.

  • avg_quats_array_path (nx.ArraySelectionParameter) – Defines the average orientation of the Feature in quaternion representation

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Feature belongs

  • find_avg_misors (nx.BoolParameter) – Specifies if the average of the misorienations with the neighboring Features should be stored for each Feature

  • misorientation_list_array_name (nx.DataObjectNameParameter) – The name of the data object containing the list of the misorientation angles with the contiguous neighboring Features for a given Feature

  • neighbor_list_array_path (nx.NeighborListSelectionParameter) – List of the contiguous neighboring Features for a given Feature

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Schmid Factors

class OrientationAnalysis.FindSchmidsFilter

This Filter calculates the Schmid factor of each Feature given its average orientation and a user defined loading axis. The Schmid Factor is the combination of the component of the axial force F that lies parallel to the slip direction and the component that lies perpendicular to the slip plane. The equation for the Schmid Factor is given as:

Link to the full online documentation for FindSchmidsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Quaternions

avg_quats_array_path

Crystal Structures

crystal_structures_array_path

Phases

feature_phases_array_path

Lambdas

lambdas_array_name

Loading Direction

loading_direction

Override Default Slip System

override_system

Phis

phis_array_name

Poles

poles_array_name

Schmids

schmids_array_name

Slip Direction

slip_direction

Slip Plane

slip_plane

Slip Systems

slip_systems_array_name

Store Angle Components of Schmid Factor

store_angle_components
Execute(data_structure, avg_quats_array_path, crystal_structures_array_path, feature_phases_array_path, lambdas_array_name, loading_direction, override_system, phis_array_name, poles_array_name, schmids_array_name, slip_direction, slip_plane, slip_systems_array_name, store_angle_components)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_quats_array_path (nx.ArraySelectionParameter) – Specifies the average orienation of each Feature in quaternion representation

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • lambdas_array_name (nx.DataObjectNameParameter) – The name of the array containing the angle between tensile axis and slip direction.

  • loading_direction (nx.VectorFloat32Parameter) – The loading axis for the sample

  • override_system (nx.BoolParameter) – Allows the user to manually input the slip plane and slip direction

  • phis_array_name (nx.DataObjectNameParameter) – The name of the array containing the angle between tensile axis and slip plane normal.

  • poles_array_name (nx.DataObjectNameParameter) – The name of the array specifying the crystallographic pole that points along the user defined loading direction

  • schmids_array_name (nx.DataObjectNameParameter) – The name of the array containing the value of the Schmid factor for the most favorably oriented slip system (i.e., the one with the highest Schmid factor)

  • slip_direction (nx.VectorFloat32Parameter) – Vector defining the slip direction.

  • slip_plane (nx.VectorFloat32Parameter) – Vector defining the slip plane normal.

  • slip_systems_array_name (nx.DataObjectNameParameter) – The name of the array containing the enumeration of the slip system that has the highest Schmid factor

  • store_angle_components (nx.BoolParameter) – Whether to store the angle components for each Feature

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Shapes

class OrientationAnalysis.FindShapesFilter

This Filter calculates the second-order moments of each Feature in order to determine the principal axis lengths, principal axis directions, aspect ratios and moment invariant Omega3s. The principal axis lengths are those of a “best-fit” ellipsoid. The algorithm for determining the moments and these values is as follows:

Link to the full online documentation for FindShapesFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Aspect Ratios

aspect_ratios_array_name

Axis Euler Angles

axis_euler_angles_array_name

Axis Lengths

axis_lengths_array_name

Feature Centroids

centroids_array_path

Cell Feature Ids

feature_ids_path

Selected Image Geometry

input_image_geometry_path

Omega3s

omega3s_array_name

Volumes

volumes_array_name
Execute(data_structure, aspect_ratios_array_name, axis_euler_angles_array_name, axis_lengths_array_name, centroids_array_path, feature_ids_path, input_image_geometry_path, omega3s_array_name, volumes_array_name)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Neighbor Slip Transmission Metrics

class OrientationAnalysis.FindSlipTransmissionMetricsFilter

This Filter calculates a suite of slip transmission metrics that are related to the alignment of slip directions and planes across Feature boundaries. The algorithm for calculation of these metrics is as follows:

Link to the full online documentation for FindSlipTransmissionMetricsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Quaternions

avg_quats_array_path

Crystal Structures

crystal_structures_array_path

F1 List

f1_list_array_name

F1spt List

f1spt_list_array_name

F7 List

f7_list_array_name

Phases

feature_phases_array_path

mPrime List

m_prime_list_array_name

Neighbor List

neighbor_list_array_path
Execute(data_structure, avg_quats_array_path, crystal_structures_array_path, f1_list_array_name, f1spt_list_array_name, f7_list_array_name, feature_phases_array_path, m_prime_list_array_name, neighbor_list_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Find Feature Shapes from Triangle Geometry

class OrientationAnalysis.FindTriangleGeomShapesFilter

This Filter calculates the second-order moments of each enclosed Feature in a Triangle Geometry. Thesecond-order moments allow for the determination of the principal axis lengths, principal axis directions, aspectratios and moment invariant Omega3s. The principal axis lengths are those of a “best-fit” ellipsoid. The algorithmfor determining the moments and these values is as follows:

Link to the full online documentation for FindTriangleGeomShapesFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Aspect Ratios

aspect_ratios_array_name

Axis Euler Angles

axis_euler_angles_array_name

Axis Lengths

axis_lengths_array_name

Face Feature Centroids

centroids_array_path

Face Labels

face_labels_array_path

Face Feature Attribute Matrix

feature_attribute_matrix_path

Triangle Geometry

input_triangle_geometry_path

Omega3s

omega3s_array_name

Face Feature Volumes

volumes_array_path
Execute(data_structure, aspect_ratios_array_name, axis_euler_angles_array_name, axis_lengths_array_name, centroids_array_path, face_labels_array_path, feature_attribute_matrix_path, input_triangle_geometry_path, omega3s_array_name, volumes_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Reduce Orientations to Fundamental Zone

class OrientationAnalysis.GenerateFZQuaternionsFilter

This Filter reduces input orientations (Quaternions) into the fundamental zone for the given Laue group.

Link to the full online documentation for GenerateFZQuaternionsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Input Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Input Quaternions

input_quats_array_path

Input Mask [Optional]

mask_array_path

Created FZ Quaternions

output_fz_quats_array_name

Apply to Good Elements Only (Bad Elements Will Be Black)

use_mask
Execute(data_structure, cell_phases_array_path, crystal_structures_array_path, input_quats_array_path, mask_array_path, output_fz_quats_array_name, use_mask)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_phases_array_path (nx.ArraySelectionParameter) – The phases of the data. The data should be the indices into the Crystal Structures Data Array.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • input_quats_array_path (nx.ArraySelectionParameter) – The input quaternions to convert.

  • mask_array_path (nx.ArraySelectionParameter) – Optional Mask array where valid data is TRUE or 1.

  • output_fz_quats_array_name (nx.DataObjectNameParameter) – The name of the array containing the Quaternion that represents an orientation within the fundamental zone for each Element

  • use_mask (nx.BoolParameter) – Whether to assign a black color to ‘bad’ Elements

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate IPF Colors (Face)

class OrientationAnalysis.GenerateFaceIPFColoringFilter

This Filter generates a pair of colors for each Triangle in a Triangle Geometry based on the inverse pole figure (IPF) color scheme for the present crystal structure. Each Triangle has 2 colors since any Face sits at a boundary between 2 Features for a well-connected set of Features that represent _grains_. The reference direction used for the IPF color generation is the _normal_ of the Triangle.

Link to the full online documentation for GenerateFaceIPFColoringFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Crystal Structures

crystal_structures_array_path

Average Euler Angles

feature_euler_angles_array_path

Phases

feature_phases_array_path

IPF Colors

surface_mesh_face_ipf_colors_array_name

Face Labels

surface_mesh_face_labels_array_path

Face Normals

surface_mesh_face_normals_array_path
Execute(data_structure, crystal_structures_array_path, feature_euler_angles_array_path, feature_phases_array_path, surface_mesh_face_ipf_colors_array_name, surface_mesh_face_labels_array_path, surface_mesh_face_normals_array_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Feature in Bunge convention (Z-X-Z)

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which phase each Feature belongs

  • surface_mesh_face_ipf_colors_array_name (nx.DataObjectNameParameter) – A set of two RGB color schemes encoded as unsigned chars for each Face

  • surface_mesh_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which Features are on either side of each Face

  • surface_mesh_face_normals_array_path (nx.ArraySelectionParameter) – Specifies the normal of each Face

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate Feature Face Misorientation (Face)

class OrientationAnalysis.GenerateFeatureFaceMisorientationFilter

This Filter generates a 3 component vector for each Triangle in a Triangle Geometry that is the axis-angle of the misorientation associated with the Features that lie on either side of the Triangle. The axis is normalized, so if the magnitude of the vector is viewed, it will be the misorientation angle in degrees.

Link to the full online documentation for GenerateFeatureFaceMisorientationFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Quaternions

avg_quats_array_path

Crystal Structures

crystal_structures_array_path

Phases

feature_phases_array_path

Face Labels

surface_mesh_face_labels_array_path

Misorientation Colors

surface_mesh_face_misorientation_colors_array_name
Execute(data_structure, avg_quats_array_path, crystal_structures_array_path, feature_phases_array_path, surface_mesh_face_labels_array_path, surface_mesh_face_misorientation_colors_array_name)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • avg_quats_array_path (nx.ArraySelectionParameter) – Specifies the average orientation of each Feature in quaternion representation

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which phase each Feature belongs

  • surface_mesh_face_labels_array_path (nx.ArraySelectionParameter) – Specifies which Features are on either side of each Face

  • surface_mesh_face_misorientation_colors_array_name (nx.DataObjectNameParameter) – A set of RGB color schemes encoded as floats for each Face

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate GBCD Pole Figure

class OrientationAnalysis.GenerateGBCDPoleFigureFilter

This Filter creates a pole figure from the Grain Boundary Character Distribution (GBCD) data. The user must select the relevant phase for which to generate the pole figure by entering the phase index.

Link to the full online documentation for GenerateGBCDPoleFigureFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix Name

cell_attribute_matrix_name

Cell MRD Array Name

cell_intensity_array_name

Crystal Structures

crystal_structures_array_path

Input GBCD

gbcd_array_path

Misorientation Angle-Axis

misorientation_rotation

Output Image Dimension

output_image_dimension

Image Geometry

output_image_geometry_path

Phase of Interest

phase_of_interest
Execute(data_structure, cell_attribute_matrix_name, cell_intensity_array_name, crystal_structures_array_path, gbcd_array_path, misorientation_rotation, output_image_dimension, output_image_geometry_path, phase_of_interest)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the cell attribute matrix for the created image geometry

  • cell_intensity_array_name (nx.DataObjectNameParameter) – The name of the created cell intensity data array

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • gbcd_array_path (nx.ArraySelectionParameter) – 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere

  • misorientation_rotation (nx.VectorFloat32Parameter) – Angle-Axis values for drawing GBCD

  • output_image_dimension (nx.Int32Parameter) – The value to use for the dimensions for the image geometry

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created image geometry

  • phase_of_interest (nx.Int32Parameter) – Index of the Ensemble for which to plot the pole figure

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate IPF Colors

class OrientationAnalysis.GenerateIPFColorsFilter

This Filter will generate inverse pole figure (IPF) colors for cubic, hexagonal or trigonal crystal structures. The user can enter the Reference Direction, which defaults to [001]. The Filter also has the option to apply a black color to all “bad” Elements, as defined by a boolean mask array, which can be generated using the Threshold Objects Filter.

Link to the full online documentation for GenerateIPFColorsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Euler Angles

cell_euler_angles_array_path

IPF Colors

cell_ipf_colors_array_name

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Mask Array

mask_array_path

Reference Direction

reference_dir

Use Mask Array

use_mask
Execute(data_structure, cell_euler_angles_array_path, cell_ipf_colors_array_name, cell_phases_array_path, crystal_structures_array_path, mask_array_path, reference_dir, use_mask)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)

  • cell_ipf_colors_array_name (nx.DataObjectNameParameter) – The name of the array containing the RGB colors encoded as unsigned chars for each Element

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • mask_array_path (nx.ArraySelectionParameter) – Path to the data array used to define Elements as good or bad.

  • reference_dir (nx.VectorFloat32Parameter) – The reference axis with respect to compute the IPF colors

  • use_mask (nx.BoolParameter) – Whether to assign a black color to ‘bad’ Elements

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate Quaternion Conjugate

class OrientationAnalysis.GenerateQuaternionConjugateFilter

This filter will generate the transpose of a [1x4] Quaternion laid out in memory such that < x, y, z >, w. This can behandy when the user wants to convert the orientation transformation to an opposite effect. The algorihtm will calculatethe conjugate of each quaternion in the array of input quaternions

Link to the full online documentation for GenerateQuaternionConjugateFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Delete Original Data

delete_original_data

Quaternions

input_quats_data_path

Created Quaternion Conjugate

output_data_array_name
Execute(data_structure, delete_original_data, input_quats_data_path, output_data_array_name)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Merge Twins

class OrientationAnalysis.MergeTwinsFilter

THIS FILTER ONLY WORKS ON CUBIC-HIGH (m3m) Laue Classes.

Link to the full online documentation for MergeTwinsFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Active

active_array_name

Angle Tolerance (Degrees)

angle_tolerance

Average Quaternions

avg_quats_array_path

Axis Tolerance (Degrees)

axis_tolerance

Parent Ids

cell_parent_ids_array_name

Contiguous Neighbor List

contiguous_neighbor_list_array_path

Feature Attribute Matrix

created_feature_attribute_matrix_name

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_path

Parent Ids

feature_parent_ids_array_name

Phases

feature_phases_array_path

Non-Contiguous Neighbor List

non_contiguous_neighbor_list_array_path

Stored Seed Value Array Name

seed_array_name

Seed Value

seed_value

Use Non-Contiguous Neighbors

use_non_contiguous_neighbors

Use Seed for Random Generation

use_seed
Execute(data_structure, active_array_name, angle_tolerance, avg_quats_array_path, axis_tolerance, cell_parent_ids_array_name, contiguous_neighbor_list_array_path, created_feature_attribute_matrix_name, crystal_structures_array_path, feature_ids_path, feature_parent_ids_array_name, feature_phases_array_path, non_contiguous_neighbor_list_array_path, seed_array_name, seed_value, use_non_contiguous_neighbors, use_seed)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • active_array_name (nx.DataObjectNameParameter) – The name of the array specifying if the Feature is still in the sample (true if the Feature is in the sample and false if it is not). At the end of the Filter, all Features will be Active

  • angle_tolerance (nx.Float32Parameter) – Tolerance allowed when comparing the angle part of the axis-angle representation of the misorientation

  • avg_quats_array_path (nx.ArraySelectionParameter) – Specifies the average orientation of each Feature in quaternion representation

  • axis_tolerance (nx.Float32Parameter) – Tolerance allowed when comparing the axis part of the axis-angle representation of the misorientation

  • cell_parent_ids_array_name (nx.DataObjectNameParameter) – The name of the array specifying to which parent each cell belongs

  • contiguous_neighbor_list_array_path (nx.NeighborListSelectionParameter) – List of contiguous neighbors for each Feature.

  • created_feature_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the created cell feature attribute matrix

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • feature_ids_path (nx.ArraySelectionParameter) – Specifies to which Feature each cell belongs

  • feature_parent_ids_array_name (nx.DataObjectNameParameter) – The name of the array specifying to which parent each Feature belongs

  • feature_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • non_contiguous_neighbor_list_array_path (nx.NeighborListSelectionParameter) – List of non-contiguous neighbors for each Feature.

  • seed_array_name (nx.DataObjectNameParameter) – Name of array holding the seed value

  • seed_value (nx.UInt64Parameter) – The seed fed into the random generator

  • use_non_contiguous_neighbors (nx.BoolParameter) – Whether to use a list of non-contiguous or contiguous neighbors for each feature when merging

  • use_seed (nx.BoolParameter) – When true the user will be able to put in a seed for random generation

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Neighbor Orientation Correlation

class OrientationAnalysis.NeighborOrientationCorrelationFilter

This Filter first identifies all Cells that have a confidence index below the minimum set by the user. Then, for each of those Cells, their neighboring Cells are checked to determine the number of neighbor Cells with orientations different than the reference Cell by more than the user defined misorientation tolerance. In addition the neighboring Cells are compared with each other to determine the number of neighboring Cells that have the same orientation (again within the user defined tolerance). The Cleanup Level set by the user is then used to determine which Cells are replaced. If a level of 5 is set, then at least 5 of the neighboring Cells must be different than the reference Cell and at least 5 of the neighboring Cells must be the same as each other (and so on for other Cleanup Level). If a Cell meets the replacement criteria, then all of its attributes are replaced with the attributes of one of the neighboring Cells that are the same as each other.

Link to the full online documentation for NeighborOrientationCorrelationFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Phases

cell_phases_array_path

Confidence Index

correlation_array_path

Crystal Structures

crystal_structures_array_path

Attribute Arrays to Ignore

ignored_data_array_paths

Image Geometry

input_image_geometry_path

Cleanup Level

level

Minimum Confidence Index

min_confidence

Misorientation Tolerance (Degrees)

misorientation_tolerance

Cell Quaternions

quats_array_path
Execute(data_structure, cell_phases_array_path, correlation_array_path, crystal_structures_array_path, ignored_data_array_paths, input_image_geometry_path, level, min_confidence, misorientation_tolerance, quats_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read EDAX EBSD Data (.ang)

class OrientationAnalysis.ReadAngDataFilter

This Filter will read a single .ang file into a new Image Geometry, allowing the immediate use of Filters on the data instead of having to generate the intermediate .h5ebsd file. A Cell Attribute Matrix and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created Attribute Arrays. 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.

Link to the full online documentation for ReadAngDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Input File

input_file

Image Geometry

output_image_geometry_path
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, input_file, output_image_geometry_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read Oxford Instr. EBSD Data (.ctf)

class OrientationAnalysis.ReadCtfDataFilter

This Filter will read a single .ctf file into a new Image Geometry, allowing the immediate use of Filters on the data instead of having to generate the intermediate .h5ebsd file. A Cell Attribute Matrix and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created Attribute Arrays. 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, inaccurate and/or wrong. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. An excellant reference for this is the following PDF file:http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf

Link to the full online documentation for ReadCtfDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Convert Euler Angles to Radians

degrees_to_radians

Convert Hexagonal X-Axis to EDAX Standard

edax_hexagonal_alignment

Input File

input_file

Image Geometry

output_image_geometry_path
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, degrees_to_radians, edax_hexagonal_alignment, input_file, output_image_geometry_path)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the cell data attribute matrix for the created Image Geometry

  • cell_ensemble_attribute_matrix_name (nx.DataObjectNameParameter) – The Attribute Matrix where the phase information is stored.

  • degrees_to_radians (nx.BoolParameter) – Whether or not to convert the Euler angles to Radians

  • edax_hexagonal_alignment (nx.BoolParameter) – Whether or not to convert a Hexagonal phase to the EDAX standard for x-axis alignment

  • input_file (nx.FileSystemPathParameter) – The input .ctf file path

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created Image Geometry

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read Ensemble Info File

class OrientationAnalysis.ReadEnsembleInfoFilter

This Filter reads in information about the crystal structure and phase types of all the Features that are contained in a Cell based volume. These values are needed to allow the calculation of statistics on the volume, if they have not already been provided by some other means. The format of the input file is a simple ASCII text file with the extension .ini or .txt. The first group in the file is the name [EnsembleInfo] in square brackets with the key Number_Phases=*number of phases* that are contained in the volume. Subsequent groups in the file list the Phase Number, Crystal Structure and Phase Type. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:

Link to the full online documentation for ReadEnsembleInfoFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Crystal Structures

crystal_structures_array_name

Input Ensemble Info File

input_file

Data Container

parent_group_path

Phase Types

phase_types_array_name
Execute(data_structure, cell_ensemble_attribute_matrix_name, crystal_structures_array_name, input_file, parent_group_path, phase_types_array_name)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read H5EBSD File

class OrientationAnalysis.ReadH5EbsdFilter

This Filter reads from the .h5ebsd file that was generated with the Import Orientation File(s) to H5EBSD Filter.

Link to the full online documentation for ReadH5EbsdFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Image Geometry

output_image_geometry_path

Import H5Ebsd File

read_h5_ebsd_object
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, output_image_geometry_path, read_h5_ebsd_object)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read Bruker Nano Esprit Data (.h5)

class OrientationAnalysis.ReadH5EspritDataFilter

This Filter will read a single .h5 file into a new Image Geometry, allowing the immediate use of Filters on the data instead of having to generate the intermediate .h5ebsd file. A Cell Attribute Matrix and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created Attribute Arrays.

Link to the full online documentation for ReadH5EspritDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Convert Euler Angles to Radians

degrees_to_radians

Origin

origin

Image Geometry

output_image_geometry_path

Import Pattern Data

read_pattern_data

Scan Names

selected_scan_names

Z Spacing (Microns)

z_spacing
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, degrees_to_radians, origin, output_image_geometry_path, read_pattern_data, selected_scan_names, z_spacing)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the cell data attribute matrix for the created Image Geometry

  • cell_ensemble_attribute_matrix_name (nx.DataObjectNameParameter) – The Attribute Matrix where the phase information is stored.

  • degrees_to_radians (nx.BoolParameter) – Whether or not to convert the euler angles to radians

  • origin (nx.VectorFloat32Parameter) – The origin of the volume

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created Image Geometry

  • read_pattern_data (nx.BoolParameter) – Whether or not to import the pattern data

  • selected_scan_names (nx.OEMEbsdScanSelectionParameter) – The name of the scan(s) in the .h5 file. Esprit can store multiple scans in a single file

  • z_spacing (nx.Float32Parameter) – The spacing in microns between each layer.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read EDAX OIMAnalysis Data (.h5)

class OrientationAnalysis.ReadH5OimDataFilter

This Filter will read a single .h5 file into a new Image Geometry, allowing the immediate use of Filters on the data instead of having to generate the intermediate .h5ebsd file. A Cell Attribute Matrix and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created Attribute Arrays.

Link to the full online documentation for ReadH5OimDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Origin

origin

Image Geometry

output_image_geometry_path

Import Pattern Data

read_pattern_data

Scan Names

selected_scan_names

Z Spacing (Microns)

z_spacing
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, origin, output_image_geometry_path, read_pattern_data, selected_scan_names, z_spacing)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the cell data attribute matrix for the created Image Geometry

  • cell_ensemble_attribute_matrix_name (nx.DataObjectNameParameter) – The Attribute Matrix where the phase information is stored.

  • origin (nx.VectorFloat32Parameter) – The origin of the volume

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created Image Geometry

  • read_pattern_data (nx.BoolParameter) – Whether or not to import the pattern data

  • selected_scan_names (nx.OEMEbsdScanSelectionParameter) – The name of the scan in the .h5 file. EDAX can store multiple scans in a single file

  • z_spacing (nx.Float32Parameter) – The spacing in microns between each layer.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Read Oxford Aztec Data (.h5oina)

class OrientationAnalysis.ReadH5OinaDataFilter

This filter will read data from a single .h5oina file into a new Image Geometry, allowing the immediate use of**Filters** on the data instead of having to generate the intermediate .h5ebsd file. A Cell Attribute Matrix and**Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no controlover the names of the created Attribute Arrays.

Link to the full online documentation for ReadH5OinaDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Attribute Matrix

cell_attribute_matrix_name

Ensemble Attribute Matrix

cell_ensemble_attribute_matrix_name

Convert Phase Data to Int32

convert_phase_to_int32

Convert Hexagonal X-Axis to EDAX Standard

edax_hexagonal_alignment

Origin

origin

Image Geometry

output_image_geometry_path

Import Pattern Data

read_pattern_data

Scan Names

selected_scan_names

Z Spacing (Microns)

z_spacing
Execute(data_structure, cell_attribute_matrix_name, cell_ensemble_attribute_matrix_name, convert_phase_to_int32, edax_hexagonal_alignment, origin, output_image_geometry_path, read_pattern_data, selected_scan_names, z_spacing)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_attribute_matrix_name (nx.DataObjectNameParameter) – The name of the cell data attribute matrix for the created Image Geometry

  • cell_ensemble_attribute_matrix_name (nx.DataObjectNameParameter) – The Attribute Matrix where the phase information is stored.

  • convert_phase_to_int32 (nx.BoolParameter) – Native Phases data value is uint8. Convert to Int32 for better filter compatibility

  • edax_hexagonal_alignment (nx.BoolParameter) – Whether or not to convert a Hexagonal phase to the EDAX standard for x-axis alignment

  • origin (nx.VectorFloat32Parameter) – The origin of the volume

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created Image Geometry

  • read_pattern_data (nx.BoolParameter) – Whether or not to import the pattern data

  • selected_scan_names (nx.OEMEbsdScanSelectionParameter) – The name of the scan in the .h5oina file. Oxford can store multiple scans in a single file

  • z_spacing (nx.Float32Parameter) – The spacing in microns between each layer.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Rodrigues Convertor

class OrientationAnalysis.RodriguesConvertorFilter

This filter will convert a 3 component Rodrigues vector into a 4 component vector that DREAM.3D expects in itsequations and algorithms. The algorithm is the following:

Link to the full online documentation for RodriguesConvertorFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Delete Original Data

delete_original_data

Input Rodrigues Vectors

input_data_array_path

Converted Rodrigues Data Array

output_data_array_name
Execute(data_structure, delete_original_data, input_data_array_path, output_data_array_name)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • delete_original_data (nx.BoolParameter) – Should the original Rodrigues data array be deleted from the DataStructure

  • input_data_array_path (nx.ArraySelectionParameter) – Specifies the Rodrigues data to convert

  • output_data_array_name (nx.DataObjectNameParameter) – The DataArray name of the converted Rodrigues vectors

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Rotate Euler Reference Frame

class OrientationAnalysis.RotateEulerRefFrameFilter

This Filter performs a passive rotation (Right hand rule) of the Euler Angles about a user defined axis. The reference frame is being rotated and thus the Euler Angles necessary to represent the same orientation must change to account for the new reference frame. The user can set an angle and an axis to define the rotation of the reference frame.

Link to the full online documentation for RotateEulerRefFrameFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Input Euler Angles

euler_angles_array_path

Rotation Axis-Angle [<ijk>w]

rotation_axis_angle
Execute(data_structure, euler_angles_array_path, rotation_axis_angle)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Cell in Bunge convention (Z-X-Z)

  • rotation_axis_angle (nx.VectorFloat32Parameter) – Axis-Angle in sample reference frame to rotate about.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Write GBCD Pole Figure (GMT 5)

class OrientationAnalysis.WriteGBCDGMTFileFilter

This Filter creates a .dat file that can be used in conjunction with GMT to generate a grain boundary character distribution (GBCD) pole figure. The user must select the relevant phase for which to write the pole figure by entering the phase index.

Link to the full online documentation for WriteGBCDGMTFileFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Crystal Structures

crystal_structures_array_path

GBCD

gbcd_array_path

Misorientation Axis-Angle

misorientation_rotation

Output GMT File

output_file

Phase of Interest

phase_of_interest
Execute(data_structure, crystal_structures_array_path, gbcd_array_path, misorientation_rotation, output_file, phase_of_interest)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • gbcd_array_path (nx.ArraySelectionParameter) – 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere

  • misorientation_rotation (nx.VectorFloat32Parameter) – Axis-Angle pair values for drawing GBCD

  • output_file (nx.FileSystemPathParameter) – The output .dat file path

  • phase_of_interest (nx.Int32Parameter) – Index of the Ensemble for which to plot the pole figure

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Write GBCD Triangles File

class OrientationAnalysis.WriteGBCDTriangleDataFilter

This Filter writes relevant information about the Grain Boundary Character Distribution (GBCD) on an existing set of triangles. The information written includes the inward and outward Euler angles, normals, and areas for each triangle. The file format was originally defined by Prof. Greg Rohrer (CMU).

Link to the full online documentation for WriteGBCDTriangleDataFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Average Euler Angles

feature_euler_angles_array_path

Output File

output_file

Face Areas

surface_mesh_face_areas_array_path

Face Labels

surface_mesh_face_labels_array_path

Face Normals

surface_mesh_face_normals_array_path
Execute(data_structure, feature_euler_angles_array_path, output_file, surface_mesh_face_areas_array_path, surface_mesh_face_labels_array_path, surface_mesh_face_normals_array_path)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Write INL File

class OrientationAnalysis.WriteINLFileFilter

This Filter writes out Cell data from an Image Geometry to a file format used by the Idaho National Laboratory (INL). The format is columnar and space delimited, with header lines denoted by the “#” character. The columns are the following:

Link to the full online documentation for WriteINLFileFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Euler Angles

cell_euler_angles_array_path

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Cell Feature Ids

feature_ids_array_path

Image Geometry

input_image_geometry_path

Material Names

material_name_array_path

Number of Features

num_features_array_path

Output File

output_file
Execute(data_structure, cell_euler_angles_array_path, cell_phases_array_path, crystal_structures_array_path, feature_ids_array_path, input_image_geometry_path, material_name_array_path, num_features_array_path, output_file)
Parameters:
Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Generate and Write Pole Figure Images

class OrientationAnalysis.WritePoleFigureFilter

This Filter creates a standard crystallographic pole figure image for each Ensemble (phase)in a selected Data Container. The Filter uses Euler angles in radians and requires the crystal structures and material names for each Ensemble array and the corresponding Ensemble Ids on the Cells. The Filter also optionally can use a mask array to determine which Cells are valid for the pole figure computation.

Link to the full online documentation for WritePoleFigureFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Cell Euler Angles

cell_euler_angles_array_path

Cell Phases

cell_phases_array_path

Crystal Structures

crystal_structures_array_path

Pole Figure Type

generation_algorithm_index

Image Layout

image_layout_index

Pole Figure File Prefix

image_prefix

Image Size (Square Pixels)

image_size

Lambert Image Size (Pixels)

lambert_size

Mask Array

mask_array_path

Material Name

material_name_array_path

Number of Colors

num_colors

Output Image Geometry

output_image_geometry_path

Output Directory Path

output_path

Save Output as Image Geometry

save_as_image_geometry

Figure Title

title

Use Mask Array

use_mask

Write Pole Figure as Image

write_image_to_disk
Execute(data_structure, cell_euler_angles_array_path, cell_phases_array_path, crystal_structures_array_path, generation_algorithm_index, image_layout_index, image_prefix, image_size, lambert_size, mask_array_path, material_name_array_path, num_colors, output_image_geometry_path, output_path, save_as_image_geometry, title, use_mask, write_image_to_disk)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each cell belongs

  • crystal_structures_array_path (nx.ArraySelectionParameter) – Enumeration representing the crystal structure for each Ensemble

  • generation_algorithm_index (nx.ChoicesParameter) – The type of pole figure generated. 0=Color, 1=Discrete

  • image_layout_index (nx.ChoicesParameter) – How to layout the 3 pole figures. 0=Horizontal, 1=Vertical, 2=Square

  • image_prefix (nx.StringParameter) – The prefix to apply to each generated pole figure. Each Phase will have its own pole figure.

  • image_size (nx.Int32Parameter) – The number of pixels that define the height and width of each output pole figure

  • lambert_size (nx.Int32Parameter) – The height/width of the internal Lambert Square that is used for interpolation

  • mask_array_path (nx.ArraySelectionParameter) – DataPath to the input Mask DataArray

  • material_name_array_path (nx.DataPathSelectionParameter) – DataPath to the input DataArray that holds the material names

  • num_colors (nx.Int32Parameter) – The number of colors to use for the Color Intensity pole figures

  • output_image_geometry_path (nx.DataGroupCreationParameter) – The path to the created Image Geometry

  • output_path (nx.FileSystemPathParameter) – This is the path to the directory where the pole figures will be created. One file for each phase.

  • save_as_image_geometry (nx.BoolParameter) – Save the generated pole figure as an ImageGeometry

  • title (nx.StringParameter) – The title to place at the top of the Pole Figure

  • use_mask (nx.BoolParameter) – Should the algorithm use a mask array to remove non-indexed points

  • write_image_to_disk (nx.BoolParameter) – Should the filter write the pole figure plots to a file.

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult

Write StatsGenerator ODF Angle File

class OrientationAnalysis.WriteStatsGenOdfAngleFileFilter

This Filter is used in a workflow where the user would like to generate a synthetic microstructure with an ODF that matches (as closely as possible) an existing experimental data set or other data set that is being mimicked. The basic workflow is the following:

Link to the full online documentation for WriteStatsGenOdfAngleFileFilter

Mapping of UI display to python named argument

UI Display

Python Named Argument

Euler Angles

cell_euler_angles_array_path

Phases

cell_phases_array_path

Convert to Degrees

convert_to_degrees

Delimiter

delimiter_index

Mask Array

mask_array_path

Output File

output_file

Default Sigma

sigma

Only Write Good Elements

use_mask

Default Weight

weight
Execute(data_structure, cell_euler_angles_array_path, cell_phases_array_path, convert_to_degrees, delimiter_index, mask_array_path, output_file, sigma, use_mask, weight)
Parameters:

  • data_structure (DataStructure) – The DataStructure object that holds the data to be processed.

  • cell_euler_angles_array_path (nx.ArraySelectionParameter) – Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)

  • cell_phases_array_path (nx.ArraySelectionParameter) – Specifies to which Ensemble each Element belongs

  • convert_to_degrees (nx.BoolParameter) – Whether to convert the Euler angles from radians to degrees. If the Euler angles are already in degrees, this option will ‘convert’ the data again, resulting in garbage orientations!

  • delimiter_index (nx.ChoicesParameter) – The delimiter separating the data

  • mask_array_path (nx.ArraySelectionParameter) – Used to define Elements as good or bad. Only required if Only Write Good Elements is checked

  • output_file (nx.FileSystemPathParameter) – The output angles file path

  • sigma (nx.Int32Parameter) – This value will be used for the Sigma column

  • use_mask (nx.BoolParameter) – Whether to only write the Euler angles for those elements denoted as true in the supplied mask array

  • weight (nx.Float32Parameter) – This value will be used for the Weight column

Returns:

Returns a nx.IFilter.ExecuteResult object that holds any warnings and/or errors that were encountered during execution.

Return type:

nx.IFilter.ExecuteResult