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imikejackson committed Jan 9, 2018
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  1. +4 −0 Source/Plugins/EMMPM/Documentation/EMMPMFilters/EMMPMFilter.md
  2. +4 −0 Source/Plugins/EMMPM/Documentation/EMMPMFilters/MultiEmmpmFilter.md
  3. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindBoundaryCells.md
  4. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindBoundingBoxFeatures.md
  5. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindFeatureCentroids.md
  6. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindFeaturePhases.md
  7. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindFeaturePhasesBinary.md
  8. +2 −0 Source/Plugins/Generic/Documentation/GenericFilters/FindSurfaceFeatures.md
  9. +4 −0 Source/Plugins/Generic/Documentation/GenericFilters/GenerateVectorColors.md
  10. +6 −0 Source/Plugins/IO/Documentation/IOFilters/AbaqusHexahedronWriter.md
  11. +5 −0 Source/Plugins/IO/Documentation/IOFilters/AbaqusSurfaceMeshWriter.md
  12. +5 −0 Source/Plugins/IO/Documentation/IOFilters/AvizoRectilinearCoordinateWriter.md
  13. +4 −0 Source/Plugins/IO/Documentation/IOFilters/AvizoUniformCoordinateWriter.md
  14. +1 −0 Source/Plugins/IO/Documentation/IOFilters/DxReader.md
  15. +9 −0 Source/Plugins/IO/Documentation/IOFilters/DxWriter.md
  16. +6 −0 Source/Plugins/IO/Documentation/IOFilters/FeatureInfoReader.md
  17. +4 −0 Source/Plugins/IO/Documentation/IOFilters/GBCDTriangleDumper.md
  18. +3 −0 Source/Plugins/IO/Documentation/IOFilters/GoldfeatherReader.md
  19. +4 −0 Source/Plugins/IO/Documentation/IOFilters/H5VoxelFileReader.md
  20. +1 −0 Source/Plugins/IO/Documentation/IOFilters/LammpsFileWriter.md
  21. +7 −0 Source/Plugins/IO/Documentation/IOFilters/LosAlamosFFTWriter.md
  22. +5 −0 Source/Plugins/IO/Documentation/IOFilters/NodesTrianglesToStl.md
  23. +7 −0 Source/Plugins/IO/Documentation/IOFilters/NodesTrianglesToVtk.md
  24. +5 −0 Source/Plugins/IO/Documentation/IOFilters/PhReader.md
  25. +4 −0 Source/Plugins/IO/Documentation/IOFilters/PhWriter.md
  26. +4 −0 Source/Plugins/IO/Documentation/IOFilters/ReadStlFile.md
  27. +5 −0 Source/Plugins/IO/Documentation/IOFilters/SPParksDumpReader.md
  28. +4 −0 Source/Plugins/IO/Documentation/IOFilters/SPParksSitesWriter.md
  29. +5 −0 Source/Plugins/IO/Documentation/IOFilters/SurfaceMeshToNonconformalVtk.md
  30. +4 −0 Source/Plugins/IO/Documentation/IOFilters/SurfaceMeshToVtk.md
  31. +3 −0 Source/Plugins/IO/Documentation/IOFilters/VASPReader.md
  32. +5 −0 Source/Plugins/IO/Documentation/IOFilters/VisualizeGBCDGMT.md
  33. +5 −0 Source/Plugins/IO/Documentation/IOFilters/VisualizeGBCDPoleFigure.md
  34. +4 −0 Source/Plugins/IO/Documentation/IOFilters/VtkRectilinearGridWriter.md
  35. +5 −0 Source/Plugins/IO/Documentation/IOFilters/VtkStructuredPointsReader.md
  36. +4 −0 Source/Plugins/IO/Documentation/IOFilters/WriteStlFile.md
  37. +6 −0 Source/Plugins/ImageIO/Documentation/ImageIOFilters/ImportImageStack.md
  38. +2 −0 Source/Plugins/ImageIO/Documentation/ImageIOFilters/ImportVectorImageStack.md
  39. +5 −0 Source/Plugins/ImageIO/Documentation/ImageIOFilters/WriteImages.md
  40. +4 −0 ...s/OrientationAnalysis/Documentation/OrientationAnalysisFilters/BadDataNeighborOrientationCheck.md
  41. +5 −0 ...Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ChangeAngleRepresentation.md
  42. +6 −0 ...lugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ConvertHexGridToSquareGrid.md
  43. +1 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ConvertOrientations.md
  44. +5 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/CreateEnsembleInfo.md
  45. +9 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/EMsoftSO3Sampler.md
  46. +13 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/EbsdToH5Ebsd.md
  47. +5 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/EnsembleInfoReader.md
  48. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindAvgCAxes.md
  49. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindAvgOrientations.md
  50. +2 −0 ...ce/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindBasalLoadingFactor.md
  51. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindBoundaryStrengths.md
  52. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindCAxisLocations.md
  53. +2 −0 ...ntationAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureNeighborCAxisMisalignments.md
  54. +4 −0 ...tionAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureReferenceCAxisMisorientations.md
  55. +4 −0 ...ientationAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureReferenceMisorientations.md
  56. +4 −0 ...gins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindKernelAvgMisorientations.md
  57. +3 −0 ...rientationAnalysis/Documentation/OrientationAnalysisFilters/FindLocalAverageCAxisMisalignments.md
  58. +3 −0 ...e/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindMicroTextureRegions.md
  59. +3 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindMisorientations.md
  60. +3 −0 .../Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindOrientationFieldCurl.md
  61. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindSchmids.md
  62. +4 −0 ...ugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindSlipTransmissionMetrics.md
  63. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindTwinBoundaries.md
  64. +4 −0 ...ins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindTwinBoundarySchmidFactors.md
  65. +2 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateEulerColors.md
  66. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateIPFColors.md
  67. +10 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/INLWriter.md
  68. +4 −0 ...ns/OrientationAnalysis/Documentation/OrientationAnalysisFilters/NeighborOrientationCorrelation.md
  69. +2 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/OrientationUtility.md
  70. +6 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadAngData.md
  71. +3 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadCtfData.md
  72. +5 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadEdaxH5Data.md
  73. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadH5Ebsd.md
  74. +5 −0 ...onAnalysis/Documentation/OrientationAnalysisFilters/ReplaceElementAttributesWithNeighborValues.md
  75. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/RotateEulerRefFrame.md
  76. +6 −0 .../Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/WriteIPFStandardTriangle.md
  77. +4 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/WritePoleFigure.md
  78. +1 −0 ...Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/WriteStatsGenOdfAngleFile.md
  79. +2 −0 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/YSChoiAbaqusReader.md
  80. +4 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateBadData.md
  81. +4 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateCoordinationNumber.md
  82. +5 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateMask.md
  83. +5 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/FillBadData.md
  84. +3 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/FindProjectedImageStatistics.md
  85. +3 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/FindRelativeMotionBetweenSlices.md
  86. +4 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/IdentifySample.md
  87. +4 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/InitializeData.md
  88. +4 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/MinNeighbors.md
  89. +5 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/MinSize.md
  90. +5 −0 Source/Plugins/Processing/Documentation/ProcessingFilters/RemoveFlaggedFeatures.md
  91. +5 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsFeature.md
  92. +5 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsFeatureCentroid.md
  93. +6 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsList.md
  94. +5 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsMisorientation.md
  95. +5 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsMutualInformation.md
  96. +4 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/CAxisSegmentFeatures.md
  97. +2 −1 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/ComputeFeatureRect.md
  98. +4 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/EBSDSegmentFeatures.md
  99. +3 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/GroupMicroTextureRegions.md
  100. +3 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/IdentifyMicroTextureRegions.md
  101. +4 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/MergeColonies.md
  102. +4 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/MergeTwins.md
  103. +4 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/ScalarSegmentFeatures.md
  104. +3 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/SineParamsSegmentFeatures.md
  105. +6 −0 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/VectorSegmentFeatures.md
  106. +1 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/AppendImageGeometryZSlice.md
  107. +3 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/ChangeResolution.md
  108. +3 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/CropImageGeometry.md
  109. +5 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/ExtractFlaggedFeatures.md
  110. +5 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/NearestPointFuseRegularGrids.md
  111. +4 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/RegularGridSampleSurfaceMesh.md
  112. +4 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/RegularizeZSpacing.md
  113. +4 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/RotateSampleRefFrame.md
  114. +3 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/SampleSurfaceMeshSpecifiedPoints.md
  115. +4 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/UncertainRegularGridSampleSurfaceMesh.md
  116. +4 −0 Source/Plugins/Sampling/Documentation/SamplingFilters/WarpRegularGrid.md
  117. +9 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/CalculateArrayHistogram.md
  118. +1 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/CorrelateValuesWithVectorDirection.md
  119. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindAvgScalarValueForFeatures.md
  120. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindBoundaryElementFractions.md
  121. +4 −1 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindDifferenceMap.md
  122. +3 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindEllipsoidError.md
  123. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindFeatureClustering.md
  124. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindFeatureHistogram.md
  125. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindLargestCrossSections.md
  126. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNeighborhoods.md
  127. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNeighbors.md
  128. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNumFeatures.md
  129. +5 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindRadialDist.md
  130. +3 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSaltykovSizes.md
  131. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindShapes.md
  132. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSizes.md
  133. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSlicetoSliceRotations.md
  134. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSurfaceAreaToVolume.md
  135. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindVolFractions.md
  136. +3 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FitCorrelatedFeatureData.md
  137. +4 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/FitFeatureData.md
  138. +3 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/GenerateEnsembleStatistics.md
  139. +3 −0 Source/Plugins/Statistics/Documentation/StatisticsFilters/QuiltCellData.md
  140. +2 −1 Source/Plugins/StatsGenerator/Documentation/StatsGeneratorFilters/GeneratePrecipitateStatsData.md
  141. +2 −1 Source/Plugins/StatsGenerator/Documentation/StatsGeneratorFilters/GeneratePrimaryStatsData.md
  142. +4 −1 Source/Plugins/StatsGenerator/Documentation/StatsGeneratorFilters/StatsGeneratorFilter.md
  143. +11 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindDistsToCharactGBs.md
  144. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindGBCD.md
  145. +10 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindGBCDMetricBased.md
  146. +10 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindGBPDMetricBased.md
  147. +4 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomCentroids.md
  148. +4 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomNeighbors.md
  149. +4 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomShapes.md
  150. +4 −1 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomSizes.md
  151. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/GenerateFaceIPFColoring.md
  152. +4 −0 .../Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/GenerateFaceMisorientationColoring.md
  153. +2 −0 ...ins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/GenerateFaceSchuhMisorientationColoring.md
  154. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/GenerateGeometryConnectivity.md
  155. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/LaplacianSmoothing.md
  156. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/M3CSliceBySlice.md
  157. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/MovingFiniteElementSmoothing.md
  158. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/QuickSurfaceMesh.md
  159. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/ReverseTriangleWinding.md
  160. +4 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/SharedFeatureFaceFilter.md
  161. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/TriangleAreaFilter.md
  162. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/TriangleCentroidFilter.md
  163. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/TriangleDihedralAngleFilter.md
  164. +5 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/TriangleNormalFilter.md
  165. +6 −0 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/VerifyTriangleWinding.md
  166. +5 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/AddBadData.md
  167. +5 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/AddOrientationNoise.md
  168. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/EstablishMatrixPhase.md
  169. +3 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/EstablishShapeTypes.md
  170. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/InitializeSyntheticVolume.md
  171. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/InsertAtoms.md
  172. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/InsertPrecipitatePhases.md
  173. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/JumbleOrientations.md
  174. +6 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/MatchCrystallography.md
  175. +4 −0 Source/Plugins/SyntheticBuilding/Documentation/SyntheticBuildingFilters/PackPrimaryPhases.md
  176. +7 −51 Tools/FilterParameterTool.cpp
@@ -2,14 +2,17 @@ EM/MPM {#emmpmfilter}
=============
## Group (Subgroup) ##
Reconstruction (Segmentation)
## Description ##
This **Filter** performs the EM/MPM segmentation algorithm on an **Attribute Array** representing a grayscale image. The EM/MPM algorithm employs an advanced expectation maximization routine over Gaussian mixtures to determine an image segmeneation into a defined number of classes. The segmented image will be stored into a new **Attribute Array** with a user definable name. Note that the created segmentation will have **Cell** labels defining the class membership. Thus, the labels will be unsigned 8 bit integers, matching the incoming grayscale image. These labels can be considered **Feature** Ids for the purposes of most DREAM.3D analysis routines. However, DREAM.3D assumes that **Feature** Ids are signed 32 bit integers. It may therefore be required to use the [Convert Attribute Data Type](ConvertData.html "") **Filter** to convert the segmented image labels from unsigned 8 bit integers to signed 32 bit integers for further analysis.
**It is highly recommended that users consult references [1], [2], [3], and [4] for details on the impact of particular parameters on the EM/MPM algorithm.**
## Parameters ##
| Name | Type | Description |
|------------------|------|-------------|
| Number of Classes | int32_t | The number of classes in which to segment the image |
@@ -26,6 +29,7 @@ This **Filter** performs the EM/MPM segmentation algorithm on an **Attribute Arr
| Use 1-Based Values | bool | Use 1-based values instead of 0-based values |
## Required Geometry ##
Image
## Required Objects ##
@@ -2,14 +2,17 @@ Multi-Array EM/MPM {#multiemmpmfilter}
=============
## Group (Subgroup) ##
Reconstruction (Segmentation)
## Description ##
This **Filter** performs the EM/MPM algorithm on a selected number of **Atribute Arrays**, representing grayscale images, that all belong to the same **Cell Attribute Matrix**. The user may select any number of **Attribute Arrays** to segment. The _Select/Deselect All_ button can used to automatically select all **Attribute Arrays** in a given **Attribute Matrix**. The segmented images will be stored into a newly created **Cell Attribute Matrix** where the name of each output array will be the a user defined _prefix_ plus the original name of the input array. For information regarding the operation of the EM/MPM algorithm and the meaning of the parameters, please refer to the documentation for the [EM/MPM](EMMPMFilter.html "") **Filter**.
This **Filter** contains an additional option to use the last mu (mean) and sigma (variance) values calculated on the current array as the initialization values for the next **Attribute Array** to process. Using this can help the EM/MPM algorithm achieve subjectively "better" segmentations by starting the algorithm at values that should be close to the ending values. This option should _only_ be used if all of the images are "similar" to one another (e.g., a montage/tiled data set or a 3D stack of images). If the input **Attribute Arrays** are qualitatively different, using this option can have negative effects on the accuracy of the final segmented images.
## Input Parameters ##
| Name | Type | Description |
|------------------|------|-------------|
| Number of Classes | int32_t | The number of classes in which to segment the image |
@@ -28,6 +31,7 @@ This **Filter** contains an additional option to use the last mu (mean) and sigm
| Output Array Name Prefix | String | Prefix to apply to the output segmented arrays |
## Required Geometry ##
Image
## Required Objects ##
@@ -2,9 +2,11 @@ Find Boundary Cells (Image) {#findboundarycells}
=============
## Group (Subgroup) ##
Generic (Spatial)
## Description ##
This **Filter** determines, for each **Cell**, the number of neighboring **Cells** that are owned by a different **Feature**. The algorithm for determining this is as follows:
1. Identify the **Feature** to which a **Cell** belongs
@@ -13,11 +15,13 @@ This **Filter** determines, for each **Cell**, the number of neighboring **Cells
4. Repeat 1-3 for all **Cells**
## Parameters ##
| Name | Type | Description |
|------------------|------|-------------|
| Ignore Feature 0 | bool | Do not use feature 0 |
## Required Geometry ##
Image
## Required Objects ##
@@ -2,9 +2,11 @@ Find Biased Features (Bounding Box) {#findboundingboxfeatures}
=============
## Group (Subgroup) ##
Generic (Spatial)
## Description ##
This **Filter** determines which **Features** are _biased_ by the outer surfaces of the sample. Larger **Features** are more likely to intersect the outer surfaces and thus it is not sufficient to only note which **Features** touch the outer surfaces of the sample. Denoting which **Features** are biased is important so that they may be excluded from any statistical analyses. The algorithm for determining whether a **Feature** is _biased_ is as follows:
1. The _centroids_ of all **Features** are calculated
@@ -19,11 +21,13 @@ By definition of the box, no **Feature** that intersects an outer surface of the
*Note:* This **Filter** is a modification of an algorithm from Dave Rowenhorst (Naval Research Laboratory).
## Parameters ##
| Name | Type | Description |
|------------------|------|-------------|
| Apply Phase by Phase | int32_t | Whether to apply the biased **Features** algorithm per **Ensemble** |
## Required Geometry ##
Image
## Required Objects ##
@@ -2,15 +2,19 @@ Find Feature Centroids {#findfeaturecentroids}
=============
## Group (Subgroup) ##
Generic (Misc)
## Description ##
This **Filter** calculates the _centroid_ of each **Feature** by determining the average X, Y, and Z position of all the **Cells** belonging to the **Feature**. Note that **Features** that intersect the outer surfaces of the sample will still have _centroids_ calculated, but they will be _centroids_ of the truncated part of the **Feature** that lies inside the sample.
## Parameters ##
None
## Required Geometry ##
Image
## Required Objects ##
@@ -2,15 +2,19 @@ Find Feature Phases {#findfeaturephases}
=============
## Group (Subgroup) ##
Generic (Misc)
## Description ##
This **Filter** determines the **Ensemble** of each **Feature** by querying the **Ensemble** of the **Elements** that belong to the **Feature**. Note that it is assumed that all **Elements** belonging to a **Feature** are of the same **Feature**, and thus any **Element** can be used to determine the **Ensemble** of the **Feature** that owns that **Element**.
## Parameters ##
None
## Required Geometry ##
Not Applicable
## Required Objects ##
@@ -2,17 +2,21 @@ Find Feature Phases Binary {#findfeaturephasesbinary}
=============
## Group (Subgroup) ##
Generic (Misc)
## Description ##
This **Filter** assigns an **Ensemble** Id number to binary data. The *true* **Cells** will be **Ensemble** 1, and *false* **Cells** will be **Ensemble** 0. This **Filter** is generally useful when the **Cell Ensembles** were not known ahead of time. For example, if an image is segmented into precipitates and non-precipitates, this **Filter** will assign the precipitates to **Ensemble** 1, and the non-precipitates to **Ensemble** 0.
Additionally, this **Filter** creates an **Ensemble Attribute Matrix** to hold ensemble data.
## Parameters ##
None
## Required Geometry ##
Image
## Required Objects ##
@@ -2,9 +2,11 @@ Find Surface Features {#findsurfacefeatures}
=============
## Group (Subgroup) ##
Generic (Spatial)
## Description ##
This **Filter** determines whether a **Feature** touches an outer surface of the sample. This is accomplished by simply querying the **Feature** owners of the **Cells** that sit at either . Any **Feature** that owns one of those **Cells** is said to touch an outer surface and all other **Features** are said to not touch an outer surface of the sample.
@@ -2,17 +2,21 @@ Generate Vector Colors {#generatevectorcolors}
=============
## Group (Subgroup) ##
Generic (Crystallography)
## Description ##
This **Filter** generates a color for each **Element** based on the vector assigned to that **Element** in the input vector data. The color scheme assigns a unique color to all points on the unit hemisphere using a HSV-like scheme.
## Parameters ##
| Name | Type | Description |
|------------------|------|---------|
| Apply to Good Voxels Only (Bad Voxels Will Be Black) | bool | Whether or not to assign colors to *bad* voxels or leave them black |
## Required Geometry ##
Not Applicable
## Required Objects ##
@@ -2,12 +2,15 @@ Abaqus Hexahedron Exporter {#abaqushexahedronwriter}
=============
## Group (Subgroup) ##
IO (Output)
## Description ##
This **Filter** produces the basic five Abaqus .inp files for input into the Abaqus analysis tool. The files created are: xxx.inp (the master file), xxx_nodes.inp, xxx_elems.inp, xxx_elset.inp and xxx_sects.inp. This **Filter** is based on a Python script developed by Matthew W. Priddy (Ga. Tech., early 2015).
### Example Output ###
The master file:
*Heading
@@ -110,6 +113,7 @@ The _sects.inp file:
## Parameters ##
| Name | Type | Description |
|------------------|------|------------------------|
| Hour Glass Stiffness | int32_t | Only recommended if using C3D8R elements |
@@ -119,6 +123,7 @@ The _sects.inp file:
## Required Geometry ##
Image
## Required Objects ##
@@ -128,6 +133,7 @@ Image
| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
## Created Objects ##
None
## License & Copyright ##
@@ -2,9 +2,11 @@ Export Abaqus Surface Mesh {#abaqussurfacemeshwriter}
=============
## Group (Subgroup) ##
IO (Output)
## Description ##
This **Filter** writes an Abaqus file that is a surface mesh using S3 Elements. There are 3 sections to this INP File: Nodes, Elements and Sets of Elements for each **Feature**. This file represents a triangular based mesh with 'shell' elements. No boundary elements are written. The element type selected is TRI_ELEMENT_TYPE "SFM3D3" for the triangles.
**This file is an experimental output from DREAM.3D. The user is responsible for verifying all elements in Abaqus.**
@@ -30,11 +32,13 @@ This **Filter** writes an Abaqus file that is a surface mesh using S3 Elements.
…..
## Parameters ##
| Name | Type | Description |
|------------------|------|--------------------|
| Output File | File Path | The output path for the .inp file |
## Required Geometry ##
Triangle
## Required Objects ##
@@ -44,6 +48,7 @@ Triangle
| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
## Created Objects ##
None
## License & Copyright ##
@@ -2,6 +2,7 @@ Avizo Rectilinear Coordinate Writer {#avizorectilinearcoordinatewriter}
======
## Group (Subgroup) ##
IO (Output)
## Description ##
@@ -32,21 +33,25 @@ This filter writes out a native Avizo Rectilinear Coordinate data file. Values s
…..
## Parameters ##
| Name | Type | Description |
|------|------| ----------- |
| Output File | File Path | Amira Mesh .am file created|
| Write Binary File | Boolean | Binary file created, if checked |
## Required Geometry ##
Image / Rectilinear Grid
## Required Objects ##
| Type | Default Name | Type | Component Dimensions | Description |
|------|--------------|-------------|---------|-----|
| Cell | FeatureIds | Ids (Int) that specify to which **Feature** each **Cell** belongs. | (1) | Filters Known to Create Data: Segment Features (Misorientation, C-Axis Misorientation, Scalar) (Reconstruction), Read Dx File (IO), Read Ph File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)
## Created Objects ##
None
## License & Copyright ##
@@ -2,6 +2,7 @@ Avizo Uniform Coordinate Writer {#avizouniformcoordinatewriter}
===========
## Group (Subgroup) ##
IO (Output)
## Description ##
@@ -33,13 +34,15 @@ This filter writes out a native Avizo Uniform Coordinate data file. Values shoul
…..
## Parameters ##
| Name | Type | Description |
|------|------| ----------- |
| Output File | File Path | Amira Mesh .am file created|
| Write Binary File | Boolean | Binary file created, if checked |
## Required Geometry ##
Image / Rectilinear Grid
@@ -51,6 +54,7 @@ Image / Rectilinear Grid
## Created Objects ##
None
@@ -53,6 +53,7 @@ This **Filter** reads from a Dx file. This is a file in a format generated using
_See: [the opendx site](http://www.opendx.org)_ for more information.
## Parameters ##
| Name | Type | Description |
|------|------| ----------- |
| Input File | File Path | The input .dx file path |
@@ -19,21 +19,26 @@ The .dx file:
# at [0 0 0], and the deltas are 1 in the first and third dimensions, and
# 2 in the second dimension
#
object 1 class gridpositions counts 118 202 190
origin 0 0 0
delta 1 0 0
delta 0 1 0
delta 0 0 1
#
# object 2 are the regular connections
#
object 2 class gridconnections counts 118 202 190
#
# object 3 are the data, which are in a one-to-one correspondence with
# the positions ("dep" on positions). The positions increment in the order
# "last index varies fastest", i.e. (x0, y0, z0), (x0, y0, z1), (x0, y0, z2),
# (x0, y1, z0), etc.
#
object 3 class array type int rank 0 items 4444713 data follows
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
…..
@@ -46,15 +51,19 @@ The .dx file with a surface layer:
delta 0 1 0
delta 0 0 1
#
# object 2 are the regular connections
#
object 2 class gridconnections counts 120 204 192
#
# object 3 are the data, which are in a one-to-one correspondence with
# the positions ("dep" on positions). The positions increment in the order
# "last index varies fastest", i.e. (x0, y0, z0), (x0, y0, z1), (x0, y0, z2),
# (x0, y1, z0), etc.
#
object 3 class array type int rank 0 items 4613987 data follows
-3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3
…..
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