12.40. Read EDAX OIMAnalysis Data (.h5)

Group (Subgroup)

IO (Input)

Description

This filter reads a single .h5 file (the HDF5-based EBSD export from EDAX OIM Analysis software) into a new Image Geometry. Reading the file directly lets the data be used immediately by other filters, instead of having to first build an intermediate .h5ebsd file. A Cell Attribute Matrix (per-pixel data) and an Ensemble Attribute Matrix (per-phase data) are created to hold the imported EBSD information. The user currently has no control over the names of the created Attribute Arrays.

The scan stores an orientation at every pixel as three Euler angles (three angles, in the Bunge Z-X-Z convention, describing how the measured crystal at that pixel is rotated relative to the sample). When stacking multiple slices into a 3D volume, the Z Spacing parameter sets the out-of-plane distance between adjacent slices in microns, and the Origin parameter sets the location of the volume’s corner in microns.

User interface before entering a proper "Z Spacing" value and selecting which scans to include.

User interface AFTER setting the "Z Spacing" and selecting files.

Notes About Reference Frames

The user should be aware that simply reading the file then performing operations that are dependent on the proper crystal reference frame (the axes fixed to the crystal lattice) and sample reference frame (the axes fixed to the physical specimen) will be undefined or simply wrong. To bring the crystal and sample reference frames into coincidence, rotations may need to be applied to the data. The recommended filters are:

If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, the following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:

Crystal Reference Frame: 90^o about the <001> Axis
Sample Reference Frame: 180^o about the <010> Axis

Important Consideration for Sample Reference Frame

If the user is importing more than a single slice from the HDF5 file and using the Rotate Sample Reference Frame filter, the user should CHECK the option ON for “Perform Slice By Slice Transform”.

Thresholding out Unindexed Scan Points

The user also may want to assign un-indexed pixels to be ignored by flagging them as “bad”. The Multi-Threshold Objects filter can be used to define this mask by thresholding on values such as Confidence Index > xx or Image Quality > desired quality. Confidence Index and Image Quality are per-pixel metrics that describe how reliable each individual measurement is.

Downstream Processing

Once the reference frames are correct, the imported Euler angles are typically converted to other orientation representations (quaternions, and so on) with Convert Orientation Representation before computing misorientations, segmenting grains, or generating pole figures.

Required Input Sources

None — this filter reads directly from a .h5 file on disk.

Input Parameter(s)

Parameter Name	Parameter Type	Parameter Notes	Description
Scan Names	orientationanalysis.OEMEbsdScanSelection		The name of the scan in the .h5 file. EDAX can store multiple scans in a single file
Origin	Vector of Float32 Values	Order=x,y,z	The origin of the volume
Z Spacing (Microns)	Scalar Value	Float32	The spacing in microns between each layer.
Import Pattern Data	Bool		Whether or not to import the pattern data

Output Image Geometry

Parameter Name	Parameter Type	Parameter Notes	Description
Image Geometry	DataGroupCreation		The path to the created Image Geometry

Output Cell Attribute Matrix

Parameter Name	Parameter Type	Parameter Notes	Description
Cell Attribute Matrix	DataObjectName		The name of the cell data attribute matrix for the created Image Geometry

Output Ensemble Attribute Matrix

Parameter Name	Parameter Type	Parameter Notes	Description
Ensemble Attribute Matrix	DataObjectName		The Attribute Matrix where the phase information is stored.

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.