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Update docs with preferred markdown heading 1 style

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
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imikejackson committed May 11, 2019
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Showing with 467 additions and 395 deletions.
  1. +2 −2 Documentation/FilterTemplate.md
  2. +2 −3 Documentation/ReferenceManual/1_UsingDREAM3D/[C]_CreatingPipeline.md
  3. +2 −3 Documentation/ReferenceManual/1_UsingDREAM3D/[D]_ImportExportPipelines copy.md
  4. +2 −2 Documentation/ReferenceManual/2_Tutorials/CroppingData.md
  5. +2 −2 Documentation/ReferenceManual/2_Tutorials/EBSDReconstruction.md
  6. +2 −2 Documentation/ReferenceManual/2_Tutorials/SurfaceMeshing.md
  7. +2 −2 Documentation/ReferenceManual/2_Tutorials/SyntheticSinglePhase.md
  8. +2 −2 Documentation/ReferenceManual/3_SupportedFileFormats/H5EbsdFile.md
  9. +2 −3 Documentation/ReferenceManual/4_AuxiliaryTools/DevHelper.md
  10. +2 −2 Documentation/ReferenceManual/5_ReleaseNotes/ReleaseNotes_6_0_0.md
  11. +2 −2 Documentation/ReferenceManual/5_ReleaseNotes/ReleaseNotes_6_1_0.md
  12. +2 −2 Documentation/ReferenceManual/5_ReleaseNotes/ReleaseNotes_6_2_0.md
  13. +2 −2 Documentation/ReferenceManual/5_ReleaseNotes/ReleaseNotes_6_3_0.md
  14. +2 −2 Documentation/ReferenceManual/6_Developer/Out_Of_Date/Compiling_External_Libraries.md
  15. +2 −3 Documentation/ReferenceManual/6_Developer/Out_Of_Date/DataCheck.md
  16. +2 −3 Documentation/ReferenceManual/6_Developer/Out_Of_Date/Execute.md
  17. +2 −2 Documentation/ReferenceManual/6_Developer/Out_Of_Date/Versioning.md
  18. +2 −2 Documentation/ReferenceManual/6_Developer/SDKInstall.md
  19. +2 −3 Documentation/ReferenceManual/6_Developer/WritingAFilter.md
  20. +2 −2 Source/Plugins/EMMPM/Documentation/EMMPMFilters/EMMPMFilter.md
  21. +2 −2 Source/Plugins/EMMPM/Documentation/EMMPMFilters/MultiEmmpmFilter.md
  22. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindBoundaryCells.md
  23. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindBoundingBoxFeatures.md
  24. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindFeatureCentroids.md
  25. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindFeaturePhases.md
  26. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindFeaturePhasesBinary.md
  27. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/FindSurfaceFeatures.md
  28. +2 −2 Source/Plugins/Generic/Documentation/GenericFilters/GenerateVectorColors.md
  29. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/AbaqusHexahedronWriter.md
  30. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/AbaqusSurfaceMeshWriter.md
  31. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/AvizoRectilinearCoordinateWriter.md
  32. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/AvizoUniformCoordinateWriter.md
  33. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/DxReader.md
  34. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/DxWriter.md
  35. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/GBCDTriangleDumper.md
  36. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/GoldfeatherReader.md
  37. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/H5VoxelFileReader.md
  38. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/ImportAvxmMDSim.md
  39. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/LammpsFileWriter.md
  40. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/LosAlamosFFTWriter.md
  41. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/NodesTrianglesToStl.md
  42. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/NodesTrianglesToVtk.md
  43. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/PhReader.md
  44. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/PhWriter.md
  45. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/ReadStlFile.md
  46. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/SPParksDumpReader.md
  47. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/SPParksSitesWriter.md
  48. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/SurfaceMeshToNonconformalVtk.md
  49. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/SurfaceMeshToVtk.md
  50. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/VASPReader.md
  51. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/VisualizeGBCDGMT.md
  52. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/VisualizeGBCDPoleFigure.md
  53. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/VtkRectilinearGridWriter.md
  54. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/VtkStructuredPointsReader.md
  55. +2 −2 Source/Plugins/ImportExport/Documentation/ImportExportFilters/WriteStlFile.md
  56. +2 −2 ...s/OrientationAnalysis/Documentation/OrientationAnalysisFilters/BadDataNeighborOrientationCheck.md
  57. +2 −2 ...Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ChangeAngleRepresentation.md
  58. +2 −2 ...lugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ConvertHexGridToSquareGrid.md
  59. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ConvertOrientations.md
  60. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/CreateEnsembleInfo.md
  61. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/EbsdToH5Ebsd.md
  62. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/EnsembleInfoReader.md
  63. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindAvgCAxes.md
  64. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindAvgOrientations.md
  65. +2 −2 ...ce/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindBasalLoadingFactor.md
  66. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindBoundaryStrengths.md
  67. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindCAxisLocations.md
  68. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindDistsToCharactGBs.md
  69. +2 −2 ...ntationAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureNeighborCAxisMisalignments.md
  70. +2 −2 ...tionAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureReferenceCAxisMisorientations.md
  71. +2 −2 ...ientationAnalysis/Documentation/OrientationAnalysisFilters/FindFeatureReferenceMisorientations.md
  72. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindGBCD.md
  73. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindGBCDMetricBased.md
  74. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindGBPDMetricBased.md
  75. +2 −2 ...gins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindKernelAvgMisorientations.md
  76. +2 −2 ...rientationAnalysis/Documentation/OrientationAnalysisFilters/FindLocalAverageCAxisMisalignments.md
  77. +2 −2 ...e/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindMicroTextureRegions.md
  78. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindMisorientations.md
  79. +2 −2 .../Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindOrientationFieldCurl.md
  80. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindSchmids.md
  81. +2 −2 ...ugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindSlipTransmissionMetrics.md
  82. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindTwinBoundaries.md
  83. +2 −2 ...ins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/FindTwinBoundarySchmidFactors.md
  84. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateEulerColors.md
  85. +2 −3 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateFZQuaternions.md
  86. +2 −2 ...e/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateFaceIPFColoring.md
  87. +2 −2 ...rientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateFaceMisorientationColoring.md
  88. +2 −2 ...ationAnalysis/Documentation/OrientationAnalysisFilters/GenerateFaceSchuhMisorientationColoring.md
  89. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateIPFColors.md
  90. +2 −2 ...e/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/GenerateRodriguesColors.md
  91. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/INLWriter.md
  92. +2 −2 ...ns/OrientationAnalysis/Documentation/OrientationAnalysisFilters/NeighborOrientationCorrelation.md
  93. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/OrientationUtility.md
  94. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadAngData.md
  95. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadCtfData.md
  96. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadH5Ebsd.md
  97. +2 −2 ...onAnalysis/Documentation/OrientationAnalysisFilters/ReplaceElementAttributesWithNeighborValues.md
  98. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/RotateEulerRefFrame.md
  99. +2 −3 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/Stereographic3D.md
  100. +2 −2 .../Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/WriteIPFStandardTriangle.md
  101. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/WritePoleFigure.md
  102. +2 −2 Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/YSChoiAbaqusReader.md
  103. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/ConvertColorToGrayScale.md
  104. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/DetectEllipsoids.md
  105. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateBadData.md
  106. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateCoordinationNumber.md
  107. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/ErodeDilateMask.md
  108. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/FillBadData.md
  109. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/FindProjectedImageStatistics.md
  110. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/FindRelativeMotionBetweenSlices.md
  111. +2 −3 Source/Plugins/Processing/Documentation/ProcessingFilters/FixNonmanifoldVoxels.md
  112. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/InitializeData.md
  113. +2 −2 Source/Plugins/Processing/Documentation/ProcessingFilters/RemoveFlaggedFeatures.md
  114. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsFeature.md
  115. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsFeatureCentroid.md
  116. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsList.md
  117. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsMisorientation.md
  118. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/AlignSectionsMutualInformation.md
  119. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/CAxisSegmentFeatures.md
  120. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/ComputeFeatureRect.md
  121. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/EBSDSegmentFeatures.md
  122. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/GroupMicroTextureRegions.md
  123. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/IdentifyMicroTextureRegions.md
  124. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/MergeColonies.md
  125. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/MergeTwins.md
  126. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/ScalarSegmentFeatures.md
  127. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/SineParamsSegmentFeatures.md
  128. +2 −2 Source/Plugins/Reconstruction/Documentation/ReconstructionFilters/VectorSegmentFeatures.md
  129. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/AppendImageGeometryZSlice.md
  130. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/ChangeResolution.md
  131. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/ExtractFlaggedFeatures.md
  132. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/NearestPointFuseRegularGrids.md
  133. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/RegularGridSampleSurfaceMesh.md
  134. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/RegularizeZSpacing.md
  135. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/RotateSampleRefFrame.md
  136. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/SampleSurfaceMeshSpecifiedPoints.md
  137. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/UncertainRegularGridSampleSurfaceMesh.md
  138. +2 −2 Source/Plugins/Sampling/Documentation/SamplingFilters/WarpRegularGrid.md
  139. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/CalculateArrayHistogram.md
  140. +2 −3 Source/Plugins/Statistics/Documentation/StatisticsFilters/ComputeMomentInvariants2D.md
  141. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/CorrelateValuesWithVectorDirection.md
  142. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindAvgScalarValueForFeatures.md
  143. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindBoundaryElementFractions.md
  144. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindDifferenceMap.md
  145. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindEllipsoidError.md
  146. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindEuclideanDistMap.md
  147. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindFeatureClustering.md
  148. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindFeatureHistogram.md
  149. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindLargestCrossSections.md
  150. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNeighborhoods.md
  151. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNeighbors.md
  152. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindNumFeatures.md
  153. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindRadialDist.md
  154. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSaltykovSizes.md
  155. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindShapes.md
  156. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSizes.md
  157. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindSlicetoSliceRotations.md
  158. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FindVolFractions.md
  159. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FitCorrelatedFeatureData.md
  160. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/FitFeatureData.md
  161. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/GenerateEnsembleStatistics.md
  162. +2 −2 Source/Plugins/Statistics/Documentation/StatisticsFilters/QuiltCellData.md
  163. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FeatureFaceCurvatureFilter.md
  164. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomCentroids.md
  165. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomNeighbors.md
  166. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomShapes.md
  167. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/FindTriangleGeomSizes.md
  168. +2 −2 Source/Plugins/SurfaceMeshing/Documentation/SurfaceMeshingFilters/GenerateGeometryConnectivity.md
  169. +44 −48 Tools/SandboxTool.cpp
  170. +1 −1 Tools/SandboxTool/Sandbox.h
  171. +86 −0 Tools/SandboxTool/UpdateMDHeader.hpp
@@ -1,5 +1,5 @@
Name of Filter
=============
# Name of Filter #


## Group (Subgroup) ##

@@ -1,5 +1,5 @@
Creating a Pipeline
=========
# Creating a Pipeline #


In DREAM.3D, the user processes their data by creating what is known as a **Pipeline** which is constructed out of a series of **Filters**. By chaining together a series of **Filters**, the underlying data structure is processed and modified in quick succession. The user should be aware that all processing on the data is done **in place**, i.e., there is only a single copy of the data resident in memory at any one time. While this reduces the overall memory footprint, the user will have to be aware that their data may be modified from its original form. To help the user avoid accidentally overwriting data, all objects at a given hierarchy level in the [data structure](@ref datastructure) are not allowed to share the same name. For example, a data structure can have an **Attribute Matrix** named _foo_ that holds an **Attribute Array** named _bar_, but if the user tries to create a new **Attribute Matrix** named _foo_, an error will be presented in the **Pipeline Error Table**. The user _is allowed_ to create another **Attribute Array** named _bar_, however, as long as that **Attribute Array** belongs to a different **Attribute Matrix**. In other words, no two children of a given data structure object can share the same name!

@@ -20,4 +20,3 @@ Once you've translated your data into the DREAM.3D ontology, you can start think

After you've constructed the analysis portion of a **Pipeline**, you'll probably want to export your new data structure to your disk. Again, the [Supported File Formats](@ref supportedfileformats) section explains what sorts of files you can export. In particular, the native .dream3d file format is very useful, since it was designed to handle the abstract data structure. Also, the file is based on open source [HDF5](https://www.hdfgroup.org/HDF5/), meaning anyone can read the data!

Over time, you'll probably want to start saving your **Pipelines** so you can streamline the **Pipeline** creation process or share your workflow. The [Saving & Opening Pipelines](@ref importexportsavepipeline) section gives more details on this process.
@@ -1,5 +1,5 @@
Saving & Opening Pipelines
=========
# Saving & Opening Pipelines #


A current **Pipeline** in the **Pipeline View** can be saved to the disk by selecting the _Save_ option in the _File_ menu. Once saved to the disk, the files can be **Bookmarked** for quick access. For more information on **Bookmarks**, visit the [user interface](@ref userinterface) section. A saved **Pipeline** file can be opened by choosing the _Open..._ option in the _File_ menu and selecting the desired **Pipeline** file.

@@ -91,4 +91,3 @@ The .json file format is an open standard that most scripting languages, such as

The .dream3d file format is a binary file based on [HDF5](https://www.hdfgroup.org/HDF5/). More specific information about this file format can be found in the [Native DREAM.3D File Format](@ref nativedream3d) section. The .dream3d format is also how the data structure objects are stored to disk. Whenever a user writes a new DREAM.3D file, the **Pipeline** used to create it will be written into the .dream3d file alongside the data structure objects. This means that the data structure is always accompanied by the workflow that was used to create it, adding _provenance_ to the data. If you select a .dream3d file from the _Open_ option of the _File_ menu, the **Pipeline** from within that .dream3d file will be extracted and opened in a new window. This allows users to recover the workflow used to create a particular DREAM.3D file. Additionally, a .dream3d file can be dragged from the file system and dropped into the **Pipeline View**. The user is then asked if they would like to extract the **Pipeline** from the file or read the data structure objects out of the file into the current **Pipeline**.

Note that if you select to save a **Pipeline** file as a .dream3d file, the resulting .dream3d file will **only** have the current **Pipeline** in it, not any of the data structure. To save the actual data structure along with the **Pipeline**, you must run the [Write DREAM.3D Data File](@ref datacontainerwriter) **Filter**.
@@ -1,5 +1,5 @@
Cropping Data
========
# Cropping Data #


Cropping data in DREAM.3D can help reduce the time for processing by removing data that the user decides should not be analyzed. The **Filter** that accomplishes this task is the [Crop Image Geometry](@ref cropimagegeometry) **Filter**. Note that since this **Filter** uses 3D voxel indices as the minimum and maximum values that define the region of interest, it will _only_ work on **Image Geometries**. The easiest way to work through cropping the data is to initially run a **Pipeline** that writes out a .dream3d file and then load the .xdmf file into [ParaView](http://www.paraview.org). In the _Information_ tab, ParaView will display the extents of the data. For this example, note that the data extent in voxels is [(0, 164), (0, 172), (0, 39)] and in real space units (microns) is [(0, 16.4), (0, 13.8), (0, 9.75)]. These units correspond to a resolution of (0.1, 0.08, 0.25).

@@ -1,5 +1,5 @@
3D Orientation Data Reconstruction
========
# 3D Orientation Data Reconstruction #


This tutorial uses a **Prebuilt Pipeline** to reconstruct a 3D data set of a Ni based superalloy called the "Small IN100" data set. This data set was collected by M. Uchic et. al. at the Air Force Research Laboratory (AFRL) and is provided to the DREAM.3D community as a learning tool. The data set consists of 117 slices of EBSD data where each slice is 189 x 201 scan points.

@@ -1,5 +1,5 @@
Surface Meshing
========
# Surface Meshing #


Creating a surface mesh in DREAM.3D can currently be accomplished by using the [Quick Surface Mesh](@ref quicksurfacemesh) **Filter**. This **Filter** will surface mesh a set of **Features** that exists on an **Image Geometry**. For example, you could mesh a structure [created synthetically](@ref tutorialsyntheticsingle), or mesh a structure [reconstructed from a serial sectioning experiment](@ref tutorialebsdreconstruction). The [Quick Surface Mesh](@ref quicksurfacemesh) **Filter** is "quick" because it simply draws triangles across the voxel faces of an **Image Geometry**. Thus, the result of the **Filter** is a **Triangle Geometry** where the boundaries between **Features** are defined by connected triangles. Note that this means that any given triangle is shared by _two_ **Features**.

@@ -1,5 +1,5 @@
Synthetic Microstructure Generation
=========
# Synthetic Microstructure Generation #


This tutorial uses a **Prebuilt Pipeline** to explain the concepts behind _sythentic microstructure_ generation in DREAM.3D. Begin by finding the **Prebuilt Pipeline** <i>(01) Single Cubic Phase Equiaxed</i> in the **Prebuilt Pipelines View** and double click on it. This will open that **Pipeline** in a new DREAM.3D window. In order to generate a synthetic microstructure, DREAM.3D needs a set of statistics that define the stochastic properties of the structure. In this case, the statistics have been generated _synthetically_ using the [StatsGenerator](@ref statsgeneratorfilter) **Filter**. To learn how to generate your own microstructure statistics, visit the [StatsGenerator documentation](@ref statsgeneratorfilter).

@@ -1,5 +1,5 @@
H5EBSD Data File Specification
================
# H5EBSD Data File Specification #


DREAM.3D can store EBSD data from multiple vendors in a data file using the [HDF5](http://www.hdfgroup.org) file format library. Although the general layout of the HDF5 file is the same between vendors, there are details that are _not_ the same between vendors, because each vendor chooses to save different types of data. The top level datasets that deal with the basic volume information is the same for every file.

@@ -1,5 +1,5 @@
DevHelper
========
# DevHelper #


**DevHelper** is a developer tool that allows the user to generate the _skeleton_ code necessary to create a new **Plugin** or **Filter**. **DevHelper** _does not_ create a functioning **Filter** automatically, and _is not_ a development environment. Instead, it streamlines the development process by auto-generating most of the "boiler plate" code that is necessary for a working **Plugin** or **Filter**.

@@ -74,4 +74,3 @@ The **FilterMaker** tab contains all the elements needed to create a new **Filte
8. Use the combo box in the right pane to look at each file's contents for accuracy. The **Filter** parameters in the table in the left pane should be created and initialized in the code in the right pane.
9. When everything is correct, press the _Generate_ button.

The **Filter** now exists in the top level plugin folder that was specified in the _Plugin Directory_ field. Additionally, the _SourceList.cmake_ file for that **Plugin** is automatically updated with the new **Filter**.
@@ -1,5 +1,5 @@
Version 6.0.0 Release Notes
===========
# Version 6.0.0 Release Notes #


These release notes summarize the major changes for each officially released version of DREAM.3D. The official bug report is located at the [DREAM.3D GitHub issues page](https://github.com/DREAM3D/DREAM3D/issues).

@@ -1,5 +1,5 @@
Version 6.1.0 Release Notes
===========
# Version 6.1.0 Release Notes #


These release notes summarize the major changes for each officially released version of DREAM.3D. The official bug report is located at the [DREAM.3D GitHub issues page](https://github.com/DREAM3D/DREAM3D/issues).

@@ -1,5 +1,5 @@
Version 6.2.0 Release Notes
===========
# Version 6.2.0 Release Notes #


These release notes summarize the major changes for each officially released version of DREAM.3D. The official bug report is located at the [DREAM.3D GitHub issues page](https://github.com/DREAM3D/DREAM3D/issues).

@@ -1,5 +1,5 @@
Version 6.3.0 Release Notes
===========
# Version 6.3.0 Release Notes #


These release notes summarize the major changes for each officially released version of DREAM.3D. The official bug report is located at the [DREAM.3D GitHub issues page](https://github.com/DREAM3D/DREAM3D/issues).

@@ -1,5 +1,5 @@
Compiling External Libraries
========
# Compiling External Libraries #


# Online SDK Installation Tutorial #

@@ -1,5 +1,5 @@
The DataCheck Function
========
# The DataCheck Function #


Intro goes here...

@@ -15,4 +15,3 @@ Some examples of common sanity checks:
- Arrays needed by the filter currently exist when this filter is running.
- Created arrays' tuple dimensions match their attribute matrix's tuple dimensions.
- Values that cannot be negative should be positive, and vice versa.
- The value that was input into the filter is in range. (i.e. An unsigned 8-bit integer array should be initialized only with values between 0-255).
@@ -1,5 +1,5 @@
The Execute Function
========
# The Execute Function #


Intro here...

@@ -10,4 +10,3 @@ Intro here...

The **execute()** function runs when the user actually starts the pipeline. This function contains the code that actually accomplishes the filter's intended objective.

To learn more about execute(), see [The Execute Function](#theexecutefunction).
@@ -1,5 +1,5 @@
Versioning
========
# Versioning #


The DREAM.3D version scheme is a set of 4 values. The first 3 values are integers while the last value is the first part of a SHA1 hash. An example is the following:

@@ -1,5 +1,5 @@
Installing the DREAM.3D SDK
========
# Installing the DREAM.3D SDK #


<a name="prerequisites">
## Prerequisites ##
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Writing A Filter
========
# Writing A Filter #


Developers can write new filters for DREAM.3D to accomplish their own objectives. There are several major functions that every new filter must implement to work with DREAM.3D's filter interface.

@@ -155,4 +155,3 @@ The **getter functions** allow the filter to procure various values for other ar
**getCompiledLibraryName()**: The *Compiled Library Name* (or the *Compiled Plugin Name* in the image above) is the name of the plugin group that this filter is categorized in.

---
**Previous Page**: [Creating a Filter](http://dream3d.bluequartz.net/binaries/Help/DREAM3D/creating_a_filter.html)
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EM/MPM
=============
# EM/MPM #


## Group (Subgroup) ##

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Multi-Array EM/MPM
=============
# Multi-Array EM/MPM #


## Group (Subgroup) ##

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Find Boundary Cells (Image)
=============
# Find Boundary Cells (Image) #


## Group (Subgroup) ##

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Find Biased Features (Bounding Box)
=============
# Find Biased Features (Bounding Box) #


## Group (Subgroup) ##

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Find Feature Centroids
=============
# Find Feature Centroids #


## Group (Subgroup) ##

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Find Feature Phases
=============
# Find Feature Phases #


## Group (Subgroup) ##

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Find Feature Phases Binary
=============
# Find Feature Phases Binary #


## Group (Subgroup) ##

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Find Surface Features
=============
# Find Surface Features #


## Group (Subgroup) ##

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Generate Vector Colors
=============
# Generate Vector Colors #


## Group (Subgroup) ##

@@ -1,5 +1,5 @@
Abaqus Hexahedron Exporter
=============
# Abaqus Hexahedron Exporter #


## Group (Subgroup) ##

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Export Abaqus Surface Mesh
=============
# Export Abaqus Surface Mesh #


## Group (Subgroup) ##

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Avizo Rectilinear Coordinate Writer
======
# Avizo Rectilinear Coordinate Writer #


## Group (Subgroup) ##

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Avizo Uniform Coordinate Writer
===========
# Avizo Uniform Coordinate Writer #


## Group (Subgroup) ##

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Read Dx File (Feature Ids)
=============
# Read Dx File (Feature Ids) #


## Group (Subgroup) ##

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Write Dx File (Feature Ids)
=============
# Write Dx File (Feature Ids) #


## Group (Subgroup) ##

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Write GBCD Triangles File
=============
# Write GBCD Triangles File #


## Group (Subgroup) ##

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Goldfeather Reader
======
# Goldfeather Reader #

[TOC]

## Group (Subgroup) ##
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Read Legacy DREAM.3D H5voxel File
=======
# Read Legacy DREAM.3D H5voxel File #


## Group (Subgroup) ##

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ImportAvxmMDSim
=============
# ImportAvxmMDSim #


## Group (Subgroup) ##

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Lammps File Writer
======
# Lammps File Writer #


## Group (Subgroup) ##

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Los Alamos FFT Writer
=============
# Los Alamos FFT Writer #


## Group (Subgroup) ##

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Convert Nodes & Triangles To STL Files
=============
# Convert Nodes & Triangles To STL Files #


## Group (Subgroup) ##

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Nodes & Triangles To Vtk File
=============
# Nodes & Triangles To Vtk File #


## Group (Subgroup) ##

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Read Ph File (Feature Ids)
=============
# Read Ph File (Feature Ids) #


## Group (Subgroup) ##

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Write Ph File (Feature Ids)
=============
# Write Ph File (Feature Ids) #


## Group (Subgroup) ##

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Read STL File
=============
# Read STL File #


## Group (Subgroup) ##

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