12.42. Read GrainMapper3D File
Group (Subgroup)
Readers
Description
This filter reads Version 4 and Version 5 GrainMapper3D HDF5 (.h5) files. GrainMapper3D is XNovo Technology’s lab diffraction-contrast-tomography (LabDCT) reconstruction software, used to reconstruct 3D crystallographic grain maps from laboratory X-ray measurements.
Euler data is read in radians.
The Image Geometry that is produced is in units of millimeters. This differs from the micron length-unit assumption made by many downstream DREAM3D-NX filters (for example, size and spacing computations). Be aware of this difference when chaining this reader into a pipeline.
The user has the opportunity to create DREAM3D-NX compatible Orientation Data and Phase data. See below.
Parameter Discussion
GrainMapper3D orientation convention is the same as used by MTEX, and the inverse of that adapted by DREAM3D-NX. This requires certain modifications to the orientation related data (Rodrigues and Quaternions) when being read from the file. These modifications ensure that when DREAM3D computes orientation related data, the correct results will be output.
Specifically, the Rodrigues vector will be converted into a 4 component and the conjugate computed. The quaternion order will be changed from wxyz to xyzw and the conjugate will be computed.
PhaseId data will be converted to int32 (when the Create Compatible Phase Data option is checked) to make that data immediately compatible with DREAM3D-NX’s filters.
IPF (inverse pole figure) colors can be stored in the file as either uint8 or float32 values. To immediately view the IPF colors that came from the file, the user should check the box for Create Compatible IPFColor Data, which converts any float32 color data to uint8.
Special Notes
The IPF colors (if any) that are read in from the file are NOT compatible with the IPF color legends provided by DREAM3D-NX or EBSDLib. There are two distinct options at play, and they should not be confused:
Create Compatible IPFColor Data only re-types the colors that were already computed by GrainMapper3D so they can be displayed; it does not recompute them against DREAM3D-NX’s legends.
To obtain IPF colors that match the DREAM3D-NX / EBSDLib legends, run Compute IPF Colors downstream on the imported orientation data. Alternatively, the user can obtain the matching IPF legends from XNovo.
Use Compute IPF Colors if you need to specifically understand the crystallographic orientations using DREAM3D-NX’s color conventions.
Required Input Sources
None. This filter reads directly from a .h5 GrainMapper3D file and creates the Image Geometry, Cell data, and Ensemble data itself.
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Input File |
FileSystemPath |
The input .hdf5 file path |
|
Create Compatible Phase Data |
Bool |
Native Phases data value is uint8. Convert to Int32 for better filter compatibility |
|
Create Compatible Orientation Data |
Bool |
Orientation data such as Quaternions and Rodrigues vectors will be converted to be DREAM3D-NX compatible |
|
Create Compatible IPFColor Data |
Bool |
If the IPF Color data is float32, it will be converted to uint8 |
LabDCT Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Read LabDCT Data |
Bool |
Read the LabDCT Data |
|
Image Geometry |
DataGroupCreation |
The path to the created Image Geometry |
|
Cell Attribute Matrix |
DataObjectName |
The name of the cell data attribute matrix for the created Image Geometry |
|
Ensemble Attribute Matrix |
DataObjectName |
The Attribute Matrix where the phase information is stored. |
AbsorptionCT Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Read AbsorptionCT Data |
Bool |
Read the AbsorptionCT data |
|
Image Geometry |
DataGroupCreation |
The path to the created Image Geometry |
|
Cell Attribute Matrix |
DataObjectName |
The name of the cell data attribute matrix for the created Image Geometry |
References
Example Pipelines
License & Copyright
Please see the description file distributed with this Plugin
DREAM3D-NX Help
If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.