12.46. Read Oxford Instr. EBSD Data (.ctf)

Group (Subgroup)

IO (Input)

Description

This filter reads a single .ctf file (the EBSD scan format written by Oxford Instruments / HKL Channel 5 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).

The user should be aware that simply reading the file and then performing operations that depend on a correct crystal reference frame (the axes fixed to the crystal lattice) and sample reference frame (the axes fixed to the physical specimen) will be undefined, inaccurate and/or wrong. To bring the crystal and sample reference frames into coincidence, rotations may need to be applied to the data. An excellent reference for this is the following PDF file: http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf

Fig. 1: An EBSD orientation is the rotation (Euler angles) between the sample reference frame (specimen axes) and the crystal reference frame (lattice axes). Import conventions may require realigning the sample frame with Rotate Sample Reference Frame and/or the crystal frame with Rotate Euler Reference Frame.

Multi-Slice (3D) .ctf Files

If the file header declares more than one slice (ZCells > 1), the created Image Geometry is sized X × Y × Z and the slice thickness is taken from the header’s ZStep key (a missing or zero ZStep defaults to 1.0). Single-slice (2D) files produce a geometry with a z-extent of 1.

Unindexed Points (Phase 0)

Points the acquisition software could not index (“zero solutions”) carry a phase value of 0 in the .ctf file, and this filter preserves that value in the Phases array. (Legacy DREAM3D 6.5 remapped these points to phase 1, silently assigning them to a real phase — see the migration notes below.) To mask unindexed points, threshold on Error = 0 (see below) or on Phases > 0.

Default HKL Transformations

If the data has come from a HKL acquisition system and the settings of the acquisition software were in the default modes, then the following reference frame transformations need to be performed. These rotations can be applied with Rotate Sample Reference Frame and Rotate Euler Reference Frame:

Sample Reference Frame: 180^o about the <010> Axis
Crystal Reference Frame: None

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 Error = 0.

Memory Requirements

While the filter executes, the reader’s per-column buffers and the created Attribute Arrays are resident simultaneously: peak memory is roughly 88 bytes per scan point for a standard 11-column file (about 4.4 GB for a 50-million-point map). Files carrying optional columns (Z, GrainIndex, GrainRandomColour) cost about 4 bytes per point more for each extra column.

Radians and Degrees

Most 2D .ctf files store their angles in degrees, whereas DREAM3D-NX expects radians. The filter provides an option to convert the Euler angles to radians, turned on by default. The user is encouraged to create an IPF (Inverse Pole Figure) image of their EBSD data to confirm whether this option actually needs to be enabled.

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 .ctf file on disk.

The Axis Alignment Issue for Hexagonal Symmetry (Advanced) [1]

The issue with hexagonal materials is the alignment of the Cartesian coordinate system used for calculations with the crystal coordinate system (the Bravais lattice).
In one convention (e.g. EDAX.TSL), the x-axis, i.e. [1,0,0], is aligned with the crystal a1 axis, i.e. the [2,-1,-1,0] direction. In this case, the y-axis is aligned with the [0,1,-1,0] direction. (Green Axis in Figure 1)
In the other convention, (e.g. Oxford Instr, Univ. Metz software), the x-axis, i.e. [1,0,0], is aligned with the crystal [1,0,-1,0] direction. In this case, the y-axis is aligned with the [-1,2,-1,0] direction. (Red Axis in Figure 1)
This is important because texture analysis can lead to an ambiguity as to the alignment of [2,-1,-1,0] versus [1,0,-1,0], with apparent 30 Degree shifts in the data.
Caution: it appears that the axis alignment is a choice that must be made when installing TSL software so determination of which convention is in use must be made on a case-by-case basis. It is fixed to the y-convention in the HKL software.
The main clue that something is wrong in a conversion is that either the 2110 & 1010 pole figures are transposed, or that a peak in the inverse pole figure that should be present at 2110 has shifted over to 1010.
DREAM3D-NX uses the TSL/EDAX convention.
The result of this is that the filter will by default add 30 degrees to the third Euler angle (phi2) of every point belonging to a hexagonal (6/mmm) phase when reading Oxford Instr (.ctf) files. Unindexed (Phase 0) points are never shifted. This can be disabled by the user if necessary.

Figure 1

Figure 1: showing TSL and Oxford Instr. conventions. EDAX/TSL is in Green. Oxford Instr. is in Red.

Input Parameter(s)

Parameter Name	Parameter Type	Description
Input File	FileSystemPath	The input .ctf file path
Convert Euler Angles to Radians	Bool	Whether or not to convert the Euler angles to Radians
Convert Hexagonal X-Axis to EDAX Standard	Bool	Whether or not to convert a Hexagonal phase to the EDAX standard for x-axis alignment

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.

Migration Notes from DREAM3D 6.5

Documented behavioral differences from legacy DREAM3D 6.5 are maintained as Deviation entries in the source tree at src/Plugins/OrientationAnalysis/vv/deviations/ReadCtfDataFilter.md. In brief: unindexed points keep their phase value of 0 (legacy remapped them to 1, and consequently also applied the hexagonal +30° shift to them), and malformed .ctf files that crashed legacy DREAM3D are rejected with descriptive errors.

Example Pipelines

TxCopper_Exposed
TxCopper_Unexposed

License & Copyright

Please see the description file distributed with this Plugin

References

[1] Rollett, A.D. Lecture Slides located at http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf

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.