Grain ID (Feature ID) Grouping based on Orientation & Neighboring Grains
Issac Loo
Michael Jackson
Let’s take a step back and figure out what data you have and in what format? DREAM.3D is able to import ASCII files, raw binary files, text files and HDF5 files that are NOT organized how DREAM.3D expects. What form of input data do you have.
Once we know that then please let us know what you are wanting to do with the data. Are you wanting to segment the data? Did you make up the Crystal Structure data yourself? Are you sure it is correct? If there is a mismatch between the crystal structure and the actual data that may show up as incorrect results.
The existing GrainId values: Do they start at zero and are contiguous to the maximum value? Actually, they _could_ start at 1 but they MUST be contiguous from 1 to the max value with NO gaps.
There is a filter called “Segment Grains (Scalar)” that might work better for you since you already have GrainIds. Running this filter would ensure that the FeatureIds are contiguous and start at the proper value. What format are your quaternions? w<x,y,z> or <x,y,z>w. DREAM3D only likes <x,y,z>w style of Quats. You would have to convert them if they are w<x,y,z>
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Michael Jackson | Owner, President
BlueQuartz Software
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Issac Loo
On Tuesday, June 19, 2018 at 4:24:09 PM UTC-5, Michael Jackson wrote:
Let’s take a step back and figure out what data you have and in what format? DREAM.3D is able to import ASCII files, raw binary files, text files and HDF5 files that are NOT organized how DREAM.3D expects. What form of input data do you have.
Once we know that then please let us know what you are wanting to do with the data. Are you wanting to segment the data? Did you make up the Crystal Structure data yourself? Are you sure it is correct? If there is a mismatch between the crystal structure and the actual data that may show up as incorrect results.
The existing GrainId values: Do they start at zero and are contiguous to the maximum value? Actually, they _could_ start at 1 but they MUST be contiguous from 1 to the max value with NO gaps.
There is a filter called “Segment Grains (Scalar)” that might work better for you since you already have GrainIds. Running this filter would ensure that the FeatureIds are contiguous and start at the proper value. What format are your quaternions? w<x,y,z> or <x,y,z>w. DREAM3D only likes <x,y,z>w style of Quats. You would have to convert them if they are w<x,y,z>
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Michael Jackson | Owner, President
BlueQuartz Software
Michael Jackson
I would be interested in obtaining a sample file in the hopes that we could find funding to write a proper reader for the data or at least have an example pipeline showing how to get the data into/out-of DREAM.3D
Now to answer your questions: I would skip the Phase information and use the “Create Ensemble Info” filter to manually generate the phase information so that you know it is correct. Please refer to http://www.dream3d.io/#Filters/OrientationAnalysis_Filters/CreateEnsembleInfo/index.html#create-ensemble-info-createensembleinfo for the Laue Group class values that DREAM.3D uses. For space group 225 you would want Cubic-High.
What algorithm did you use to convert the Rodrigues to Quaternions? Was your reference frame correct when you did the conversion? DREAM.3D can do the conversion for you using the “Convert Orientation Representation” filter which is thoroughly tested and vetted among an international group of authors. http://muri.materials.cmu.edu/wp-content/uploads/2015/06/RotationPaperRevised.pdf See Appendix A. The conversions can be found here: https://github.com/BlueQuartzSoftware/DREAM3D/blob/develop/Source/OrientationLib/OrientationMath/OrientationTransforms.hpp
My guess is that using 225 for the Laue group was messing up the segmentation. Once you get the proper phase information you should be able to use the Segment by Misorientation to create a new set of Grain Ids.
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Michael Jackson | Owner, President
BlueQuartz Software
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Michael Jackson
26,133,822 voxels that have 59,340 unique “GrainId” values which are clustered into 175,846 features.
This can happen when distinct groups or clusters of voxels that are NOT connected to each other share the same “GrainId” value. I was thinking initially to have you just create the proper Feature AttributeMatrix but DREAM.3D assumes that each cluster will have a unique FeatureId so using the “GrainId” data is just not going to work. If I instead use the Rodrigues vector as the orientation data, after correcting for proper sample-crystal transformation and some cleanup where I force grains to have at least 25 voxels I get around 20,000 grains which at first glance seems reasonable. Once you get a segmentation and pre/post processing figured out you can run both morphological and crystallographic statistics and see what that produces.
I will include a starting pipeline that has some of these filters prepopulated. You will need to adjust the paths in the json file to suit your system. You will also need to use a nightly build of DREAM.3D starting on JUNE 28 2018. Those can be found at http://dream3d.bluequartz.net/binaries/experimental/ as I developed a few new filters while I was analyzing the data that are related to the orientation transformation.
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Mike Jackson