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DREAM.3D User Manual and Filter Reference

1. Prebuilt Pipelines DREAMSD provides several Prebuilt Pipelines that can aid the new user in getting started with DREAMSD Simply double clicking a preset will clear any current filters in the pipeline area and populate the pipeline area with the filters from the Pipeline Preset Favorite Pipelines After the user builds a pipeline that they may want to save for later the user can use the Pipeline menu and select the Add Favorite menu to save that specific pipeline configuration If at a future point in time the user wants to remove the favorite from the Favorites list they user can select from the Add Favorite menu and choose Remove Favorite to remove it from the list Add Favorite 8 Rename Favorite SER Remove Favorite Clear k Additional shortcuts are available by right clicking on the Favorite Pipelines tree item which will display a contextual menu to create a new favorite pipeline entry Wy Favorite Pinelines The user can also rename a Favorite Pipeline entry by right clicking on the entry item and selecting the desired action The only valid characters that can be used are AlphaNumeric the underscore and the dash CurvatureTestl CurvatureTest2 k 3 3 o Goldfeather C Rename Favorite R GrainCurvatur Remove Favorite o i IN100 Mesh Test RAPP Conant Tart The user should also note that simply selecting a Favorite Pipeline from the list will display the filters in order of operation in the Fil
2. These arrays have default names given to them which are defined in DREAM3DLib Common Constants h const std string SurfaceMeshNodes SurfaceMeshNodes const std string SurfaceMeshTriangles SurfaceMeshTriangles In order to stay consistent with the VoxelDataContainer and its terminology DREAMSD refers to Vertex Attributes as Cell data and Triangle Attributes as Field data There are also convenience methods that are named set PointData setFaceData andsetEdgeData thatmap loosely to the Cell Field and Ensemble syntax of the VoxelDataContainer Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 40 Tutorials In the filter documentation the following terminology will be used e Vertex Array Refers to the shared vertex array stored in the Sur f faceMeshDataContainer e Triangle Array Refers to the triangle array stored in the SurfaceMeshDataContainer Edge Array Refers to the edge array stored in the Sur f aceMeshDataContainer Edge Data Update with algorithm to generate Unique Edge Ids Surface Meshing Tutorial For this tutorial we are going to be using a pre made DREAMSD data file The file is simply a Single Phase Synthetic Structure that was quickly generated using the Synthetic Microstructure Creation abilities of DREAMS3D There are other options that exist to create a surface mesh One can read in a Ph or Dx file use the Raw Binary Reader to read in the Raw Grain Ids from a binary
3. DREAM3D Reference Manual by Doxygen 52 WEE Primary Phase Size Distribution Omega 3 Distributions Angle Axis iw h k l7 Weight MRD 4t Ye La P Load List From File e Some Message about how the data was generated Auxiliary Tools Untitled dream3d Primary Phase Shape Distributions Neighbor Distributions ODF Axis ODF 0 2 0 15 Freq ce 0 05 10 20 30 40 50 60 70 Misorientation Angle w Angle D this is the angle of the misorientation to increase in weight Axis D this is the axis of the misorientation to increase in weight If the crystal structure being used for the phase is Hexagonal then this axis is in the 3 index orthogonal convention not the true hkil convention Weight D this is the weight in units of MRD multiples of random of the entered misorientation Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 9 1 Stats Generator 83 Axis ODF Tab Untitled h5stats x Primary Phase Primary Phase Size Distribution Omega 3 Distributions Shape Distributions Neighbor Distributions ODF Axis ODF Euler 1 Euler 2 Euler 3 Weight Sigma By default if no custom rows are entered then a completely random ODF will be generated JP x Load List From File Adding rows to this table results in those texture values being integrated into the random Calculate ODF ODF data A Axis B Axis C Axis sV
4. Group FACE DATA Group Normals Dataset Centroids Dataset Curvature Dataset IPFColor Dataset FIELD DATA Group AvgCurvature Dataset MeanWidth Dataset ENSEMBLE DATA Group GBCD Dataset In the above we show how a surface mesh is stored For more information on the actual data structure of the surface mesh please see the Surface Meshing Tutorial NOTE DREAMSD is perfectly capable of storing BOTH the voxel data and the surface mesh data in the same file if the user so desires This allows all the data to stay together and more easily shared among collaborators Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 7 2 H5EBSD Data File Specification 25 7 2 H5EBSD Data File Specification Introduction The EBSD Data from multiple vendors is stored in a data file using the HDF5 file format library While the general layout of the HDF5 file is the same between vendors there are details that are NOT the same between vendors because each vendors chooses to save different types of data The top level datasets that deal with the basic volume information is the same for every file Orientations Reference Frames and Coordinate Systems DREAM 3D s origin follows the sample coordinate system so that the physical location of the O row and O column voxel should visually appear in the lower left corner of a computer graphics display Sample Coordinate System White over
5. Raw Binary Files Dx files Limited Subset e H5Ebsd files e Ph files Vtk file Structured Points e DREAMSD Native Files Supported Output File Types Avizo Rectilinear Coordinate e Avizo Uniform Coordinate Writer H5EBSD files DREAMSD Native files e Dx files Limited Subset e Ph files SPParks file e STL Files StereoLithography Format e VTK Rectilinear Grid Voxel Based Data VIK Polydata Surfacemesh Based Data VTK Polydata Solidmesh Based Data INL CSV File of Voxel attributes Nodes Triangles from Surfacemesh e CSV File of Field Values Please take a look at each of the various filters that read or write those files for notes on each type of file Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 8 Tutorials DREAMSD is capable of a wide variety of reconstruction data analysis and synthetic microstructure which can present issues to the new user with regards to how to get started constructing a working pipeline In these sections a few sample pipelines are presented which will allow the new user to get started quickly 3D Orientation Data Reconstruction This tutorial describes how to reconstruct EBSD data into a 3D Voxel based volume and visualize the results with ParaView Synthetic Microstructure Generation This tutorial shows the user how to create a pipeline that will generate a single phase equiaxed synthetic microstructure from a set of sta
6. Tab 4 The Pipeline Area 3c DREAM3D Filter Library amp Generic amp 10 amp Add Orientation Noise ASEEN Align Sections Feature Centroid gt amp Processing 35 Align Sections Feature gt amp Reconstruction Align Sections List gt amp sampling 35 Align Sections Misorientation gt d Statistics d Align Sections Mutual Information gt d SurfaceMeshing d amp Avizo Rectilin oordinate Writer amp SyntheticBuilding amp Avizo unform r Writer vy E Prebuilt Pipelines amp Change Resol iah 4 Ebsd 3D Reconstruc E Fleis Data 4 x Statistics amp Convert Euler Angles ynthetic Single Pha d Convert Hexagonal Grid Data to Squi Synthetic Primary Convert Nodes amp Triangles To STL Fi Yui Favorite Pipelines amp Convert Nodes amp Triangles To Vtk E Drag filters here to build t amp Create Cell Array From Field Array Crop Volume amp Delete Arrays Errors Warnings Filter Name Error Description Error Code 14 Overview of the User Interface The Filter Library Area 1 This area of the user interface is broken into 3 basic groups Filter Library Prebuilt Pipelines and Favorite Pipelines The Filter Library section contains the various groups that the filters are organized into The user can click a specific group and just the filters associated with that group will be displayed in the Filter List area of the user interface
7. file or have an already existing set of Grain Ids from a DREAMSD pipeline that segmented the grains for you DREAM3D File tmp SurfaceMeshTutorial dream3d _Select X Dim 64 X Res 0 15 X Origin O Voxel Volume Info Y Dim 6 amp 4 Y Res 0 15 Y Origin O Z Dim 64 ZRes 0 15 Y Origin O V Read Voxel Data Read Surface Mesh Read Solid Mesh Weaseeeic e Surface Mesh Data Solid Mesh Data Cell Data Field Data Ensemble Data ole CrystalStructures NumFields PhaseTypes EulerAngles Active Grainlds IPFColor Phases AvgQuats EulerAngles NeighborList ShapeTypes Delete Temp Files vi Iteration Steps Default Lambda Triple Line Lambda Quad Points Lambda Outer Points Lambda 0 Outer Triple Line Lambda Outer Quad Points Lambda Write Voxel Data Write SurfaceMesh Data v Write Xdmf File XML Wrapper M Output File tmp SurfaceMeshTutorial Mesh dream3d Save s Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen Start by adding the Read DREAMSD Data File filter Select the file that you just downloaded an then only check the Grainlds data under the Cell Data section This will ensure that this is the only data that is loaded from the file Since creating the mesh can take large amounts of memory we only want to load the data necessary Next add in the M3C Surface Meshing Slice at a time filter which will create the actual surface mesh Leave the option
8. more phases are added by scaling the current total of all the phases fractions to 1 in case the user s total is not equal to 1 when finished Select Phase Type this specifies the type of the phase Currently the two types of phases are Primary and Precipitate Note that there must be at least one Primary phase before any Precipitate phase can be created or the Synthetic Builder will fail Fraction of Precipitate on Boundary if the phase type is set to Precipitate then the user must specify the number fraction of the precipitates that are located on grain boundaries of the primary phase This value will be scaled to 1 if the userOs value is larger than 1 The value is keyed to 1 for Primary phases Create Data This locks in the values the user has entered and populates the other tabs with default values The user can move through the other tabs and change any default values if desired Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 48 Auxiliary Tools Omega3 Tab Untitled h5stats Wy Primary Phase Size Distribution s n 91 94 Shape Distributions Neighbor Distributions ODF Axis ODF Beta Distribution Bin Alpha Beta Color 1 64872 5 1 darkblue 2 14872 5 1 2 66667 darkcyan 2 64872 5 2 4 33333 darkgolden 3 14872 5 3 6 darkgray 3 64872 5 4 7 66667 darkgreen 4 14872 55 9 33333 darkgrey Bin this column is calculated from
9. that have been created For those uses importing data from other sources the sections on the various file formats will be of interest Finally the Filter Documentation lists each of the filters that the user can utilize in their workflows Welcome to DREAM 3D an open and modular software package that allows users to reconstruct instantiate quan tify mesh handle and visualize microstructure digitally The core software package has four 4 major functionalities First a series of EBSD data files either TSL ang or HKL ctf or images bmp jpeg tif or png can be read and packed into a single HDF5 data file in order to reduce data size and clutter The sections can be aligned cleaned reconstructed segmented and statistically characterized otatistics either synthetically created or from real data can be used to generate a statistically equivelent microstructure The reconstructed volumes and the synthetic volumes can be surfaced meshed to allow the models to be moved into FEM or other simulations DREAMSD makes the reconstruction of 3D EBSD data simple and straight forward The development of more features is always on going and the DREAM3D development team welcomes your feed back whether you are first time user or seasoned user Brief History and Acknowledgements DREAM 3D Data Structure Supported File Formats Overview of the User Interface Creating a Pipeline Import Export amp Favorite Pipelines filterdocumentat
10. to Delete Temp Files checked on The files are in a binary format meant for debugging if things go wrong during the meshing After we get the surface mesh we could simply write out a DREAMSD file or a VTK legacy file but we are selecting to also smooth the surface mesh to prepare it for other analysis In order to smooth the mesh we now add the Laplacian Smoothing Filter which takes 7 arguments The first argument is the number of iterations of smoothing to use The remaining 6 arguments are 2 sets of 3 arguments where you can set the lambda value for the bulk nodes triple line nodes and quad point nodes for both the inside triangles and those triangles that touch the outer surface of the model The user should understand that a side effect of the Laplacian smoothing algorithm is shrinkage of the actual value due to movement of the nodes f enough iterations are run and all 6 arguments have valid value 0 to 1 then the volume can collapse on itself This is why we have the 6 arguments to alleviate some of the shrinkage by pinning the outer shell of triangles in place and only allowing the internal triangles to move We can also allow the bulk triangles to move more than the triple line or quad point nodes Finally after the Smoothing filter add a Write DREAMSD Data File filter Be sure to check the option to write the SurfaceMesh Data and also make sure the Write Xdmf File is also checked After smoothing the mesh can be viewed with ParaView
11. user to change colors of the curves for image creation or easier identification during stats generation Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 50 Auxiliary Tools Neighbor Distribution Tab Untitled h5stats wre Primary Phase Size Distribution Shape Distributions SSI Mosca ODF Axis ODF Omega 3 Distributions Log Normal Distribution Bin Average StdDev Color 1 64872 2 07944 0 4 darkblue 2 14872 2 30259 0 366667 darkcyan 2 64872 2 48491 0 333333 darkgolden 3 14872 2 63906 0 3 darkgray 3 64872 2 77259 0 266667 darkgreen E 4 14872 2 89037 0 233333 E H ncs 20 30 40 50 Number of Grains within 1 diameter Bin this column is calculated from the size distribution and cannot be changed Alpha this is the alpha parameter of a Power Law distribution this is the exponent of a Power Law Distribution Beta this is the beta parameter of a Power Law distribution Color this allows the user to change colors of the curves for image creation or easier identification during stats generation Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen ODF Tab Untitled h5stats Primary Phase Primary Phase Size Distribution Omega 3 Distributions Shape Distributions Neighbor Distributions ODF Axis ODF Euler 1 Euler 2 Euler 3 Weight Si
12. value for the header ome emm LatticeAngles H5T NATIVE FLOAT Contains value for the header entry Lattice Angles in a 1x3 array LatticeDimensions H5T NATIVE FLOAT Contains value for the header entry Lattice Dimensions in a 1x3 array LaueGroup H5T NATIVE INT32 Contains value for the header entry LaueGroup plus an H5T STRING Attribute which is the string name of the Laue Group for example Hexagonal High 6 mmm SpaceGroup H5T NATIVE INT32 Contains value for the header Po OT om PhaseName H5T STRING Contains value for the header Stacking Order Discussion The Stacking Order refers to the order in which the z slices are stacked together when they are read from the file The enumerations are also in the EbsdLibConstanis h header file As a further explanation if the ordering is Low To High then the slice with the lowest number is positioned at Z 0 in 3D Cartesian space For example if your data set is numbered from 23 to 86 with file names of the form Slice 023 ang and you select Low To High then the data inside of file Slice 023 ang will be positioned at Z 0 during any method that has to deal with the data The opposite of this is if the user were to select to have their data High to Low in which case the file with name Slice 086 ang will be positioned at Z 0 and the file with name Slice 023 ang will be positioned at Z 64 7 3 XDMF For Visualization Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by
13. with IPF coloring with a 001 reference direction Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 38 Tutorials Mf ParaView 3 98 1 64 bit o B UW Ww ec SF A RSE wt R D DD Tre B Qa amp Giro Magnitude Surface ges c ESL jum B8Soos hosooduss ss 20 m Faout n ES E builtin NIEJE 3p E m Bn o a Small IN100 xdmf Properties Information eo Properties Apply Q Reset X Delete r 3 ET LUIUr IPFColor Magnitude E Show s Edit Res CubeAxes Visible Edit Representation Surface Map Scalars Interpolate ScalaPS efore Mapping Opacity Pl Interpolation Gouraud Line Width 1 M CUR Follow Frontface Translation 0 lo lo Scale 1 1 1 Orientation 0 lo lo Origin 0 lo lo a saa P Figure 8 3 ParaView OverView 8 3 Surface Meshing Tutorial Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen Surface Mesh Definitions Creating a surface mesh in DREAMSD can be accomplished in several ways There are a pair of filters Multi Material Marching Cubes Slice at a Time and Quick Surface Mesh that will generate a triangular based mesh of the primary Field for you The terminology of the underlying data structures is something that the user should understand so that they can be well informed We start ou
14. 0 Z Min Plane OQ X Max Column 80 Y Max Row 125 Z Max Plane Renumber Grains VI After the filter executes the data from the volume of interest is cropped out T Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 43 44 Tutorials Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 9 Auxiliary Tools Stats Generator A discussion of the helper tool for generating uer defined statistics for building synthetic structures in DREAM 3D 9 1 Stats Generator Introduction In order to allow the user to quickly generate a set of statistics that can be used to create a synthetic microstructure the StatsGenerator program was created Using this program the user can generate the necessary statistics that describe a microstructure and save those statistics to a DREAMSD file that can then be used in a DREAMSD pipeline to generate a synthetic microstructure The main features are Describe the grain size distribution via a simple Gaussian distribution Select from several preset microstructure types Define the Omega 3 Distributions Define the Shape distributions Define the Neighbor distributions Define a Crystallographic Texture through ODF parameters Define the MDF through various parameters Define the Axis ODF for the grains e Add as many phases as the user needs e Define each phase according to several presets Primary Precip
15. 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER Supported File Formats DREAMSD supports the reading from and writing to a number of different file formats from data acquisition systems to visualization systems The various file formats are discussed in this section Native DREAMSD File Format A discussion of the native DREAMSD file format based on HDF5 H5EBSD Data File Specification A discussion of the H5EBSD file format XDMF For Visualization How to use the Xdmf wrapper for visualizing data with ParaView Import amp Export File Formats This sections lists the various file formats that can be used as import and export of data 7 1 Native DREAMSD File Format HDF5 DREAM3D uses the HDF5 as its native file format which means that ANY software package capable of reading an HDF5 file can read a DREAMSD file HDF5 stores data in a hierarchical format with complete descriptors for the data stored in the file HDF5 is open source and a number of tools exist that allow a user to view and manipulate HDF5 data files Once such tool is the free HDFView from The HDF Group which is a java based program that can view and edit HDF5 data files Each array is stored as an individual data set in HDF5 under one of several different types of DataContainer storage groups e Voxel DataContainer e SurfaceMesh DataContainer SolidMesh DataContainer Depending on the type of data created the actual data array that a use
16. 98 1 64 bit p B SS oa S lyk Bee wt RO d P me B Qa amp PFColor Magnitude Surface eS ae A 42 9sc595oszooduwess eo Pipeline Browser Geese B builtin NL S8 3D 6 mB8no a Small IN100 xdmf Properties Information eo o Properties Apply Reset 3X Delete T 3 ES tour IPFColor Magnitude E Show s Edit amp Res CubeAxes Visible Edit Representation Surface Map Scalars Interpolate ScalaPS efore Mapping Opacity 1 Interpolation Gouraud Line Width 1 pata Follow Frontface epresentation Translation 0 lo lo Scale 1 n 1 Orientation 0 lo lo Origin 0 lo lo E O Figure 8 1 3D Reconstruction of EBSD Orientation Data 8 2 Synthetic Microstructure Generation Launch DREAMSD and create the pipeline that is displayed in the following image Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 36 Tutorials HDFS Stats File hared Data SyntheticStructures SinglePhase SingleEquiaxed h5 stats Voxel Dims Spacing micron Shape Types 256 X 0 1500 IB Ellipsoid 256 ly 01500 7 256 0 1500 G Estimated No Grains 5158 Periodic Boundary O Write Goal Attributes Goal Attribute CSV File Do Maximum Number of Iterations Swaps 1
17. Contains value for the header Author H5T STRING Contains value for the header JobMode H5T STRING Contains value for the header XCells H5T NATIVE INT32 Contains value for the header YCells H5T NATIVE INT32 Contains value for the header XStep H5T NATIVE FLOAT Contains value for the header YStep H5T NATIVE FLOAT Contains value for the header ZStep H5T NATIVE FLOAT Contains value for the header ZCells H5T NATIVE FLOAT Contains value for the header AcgE1 H5T NATIVE FLOAT Contains value for the header AcqE2 H5T NATIVE FLOAT Contains value for the header AcqES3 H5T NATIVE FLOAT Contains value for the header entry AcgE3 Generated on Wed Apr 3 2013 11 03 23 for DREAMSD Reference Manual by Doxygen 30 Supported File Formats Mag H5T NATIVE INT32 Contains value for the header emia Coverage H5T NATIVE INT32 Contains value for the header o oiro o Device H5T NATIVE INT32 Contains value for the header Cor O e O KV H5T NATIVE INT32 Contains value for the header Co To jy e TiltAngle H5T NATIVE FLOAT Contains value for the header me id TiltAxis H5T NATIVE FLOAT Contains value for the header BINNEN ddl Phases H5G GROUP Group that contains a subgroup for each phase where the name of each subgroup is simply the index of the phase starting at 1 HKL ctf Phase Group Specification Name HDF Type Comment H5T STRING Contains value for the header MM PS Internal1 H5T STRING Contains value for the header BU emma Internal2 H5T STRING Contains
18. DREAM 3D User Manual and Filter Reference DREAMSD Development Team dream3d bluequartz net June 10 2013 Contents Table of Contents 3 Brief History and Acknowledgements 5 DREAM 3D Data Structure 9 Overview of the User Interface 13 Creating a Pipeline 17 Import Export amp Favorite Pipelines 21 Supported File Formats 23 7 1 Native DREAMSD File Format 2 2 2 2 2 22 2525252 2 25 225 23 7 2 HSEBSD Data File Specification 45eee 99 se HRA RR EE E ESSO S RE e RS 25 7 XDMF For Visualization uu Eos how ae ew ESE RE HESS a 30 7 4 Import amp Export File Formats llle sess sss 32 Tutorials 33 8 1 3D Orientation Data Reconstruction 2 2 lll rn 33 8 2 Synthetic Microstructure Generation 2 lll rrr 35 8 3 Surface Meshing Tutorial 45 2 ko REA E XR RR Eo RE 38 8 4 Cropping Data Tutorial 4uns xw cx S h A sia Pe See DEE EG 42 Auxiliary Tools 45 SB OB Cenaa eoo eo om o wok o m RR UE ORO R REPRE ERE EE REE OY Ro ox os 45 10 Created Array Index 55 CONTENTS Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 1 Table of Contents The DREAMSD Rererence Manual contains all the information to start using DREAMSD quickly The user is urged to read through the short introduction to get a basic idea of how to use DREAMSD For a really quick start the user is referred to the various tutorials
19. Doxygen 7 3 XDMF For Visualization 31 Introduction XDMF is an XML file that describes either a regular grid or unstructured grid data set where the data can be stored in an HDF5 Binary or with the xml file itself The user is can find out more information for this format at the Xdmf website DREAMSD will optionally write out an Xdmf file when writing a DREAMSD Data file so that users can view the processed data easily using the free ParaView application In prior versions of DREAMSD the only way to view the data was to write out a legacy VTK file which can be slow and simply duplicates much of the data that is stored in the dream3d file This is a waste of space and not memory efficient when it comes to ParaView loading the data from the legacy vtk file Properties Information e Properties gt ee Se O Reset 3 Delete JC Properties Small IN100 xdmf Point Arrays v Cell Arrays Al Confidence Index M f EulerAngles wi da Fit M f GoodVoxels Mi f Grainlds Mi E IPFColor Mi f Image Quality Mi f Phases Mi di Quats Mi f SEM Signal Sets Blocks Hierarchy v Blocks Eil Voxel DataContainer C Uncheck Selected Blocks Check Selected Blocks Uncheck selected BIOCKS Stride 1 1 1 By using an Xdmf wrapper file the user can selectively load just the data that they are interested in viewing This saves time loading the data and more important
20. TIVE FLOAT Contains all the Phi data in a 1D Array with length equal to the total number of points Phi2 H5T NATIVE FLOAT Contains all the Phi2 data in a 1D Array with length equal to the total number of points Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 7 2 H5EBSD Data File Specification 27 X Position H5T NATIVE FLOAT Contains all the X position data in a 1D Array with length equal to the total number of points Y Position H5T NATIVE FLOAT Contains all the Y position data in a 1D Array with length equal to the total number of points Image Quality H5T NATIVE FLOAT Contains all the Image Quality data in a 1D Array with length equal to the total number of points Confidence Index H5T NATIVE FLOAT Contains all the Confidence Index data in a 1D Array with length equal to the total number of points PhaseData H5T NATIVE INT32 Contains all the PhaseData data in o a 1D Array with length equal to the total number of points SEM Signal H5T NATIVE FLOAT Contains all the SEM Signal data in a 1D Array with length equal to the total number of points Fit H5T NATIVE FLOAT Contains all the Fit of Solution data in a 1D Array with length equal to the total number of points TSL ang Header Group Specification Name HDF Type OriginalFile H5T STRING Path to the ang file that was AS mote OriginalHeader H5T STRING Contains the original header from PRM TO impna ae o TEM PIXperUM H5T NATIVE FLOAT Cont
21. Voxels CellData e Single Threshold Cell Data Processing Threshold e Multi Threshold Cell Data Processing Threshold e Segment Fields Misorientation Reconstruction Segmentation e Segment Fields C Axis Misorientation Reconstruction Segmentation GrainAvgCAxisMisorientations FieldData e Find Field Reference C Axis Misorientations Statistics gt Crystallographic GrainAvgMisorientations FieldData e Find Field Reference Misorientations Statistics Crystallographic Grainlds CellData e Read Dx File Grain Ids I0 gt Input e Read Legacy DREAM 3D H5Voxel File lO Input e Read Ph File Grain Ids I0 gt Input e Read YS Choi Abaqus Vtk Output File lO gt Input Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 58 Created Array Index e Read Vtk File STRUCTURED POINTS Grain Ids Only lO Input e Segment Fields Misorientation Reconstruction Segmentation e Segment Fields Scalar Reconstruction Segmentation e Segment Fields C Axis Misorientation Reconstruction Segmentation GrainReferenceCAxisMisorientations CellData Find Field Reference C Axis Misorientations Statistics gt Crystallographic GrainReferenceMisorientations CellData e Find Field Reference Misorientations Statistics Crystallographic IPFColor CellData e Generate IPF Colors Generic gt Crystallography KernelAverageMisorientations CellData e Find Ker
22. X Reference Direction 0 Y Reference Direction 0 Z Reference Direction 1 Write Voxel Data MI Write SurfaceMesh Data Write Xdmf File XML Wrapper vi Output File tmp out dream3d Save As Figure 8 2 DREAMSD Gui showing complete pipeline Note that you need to fill out the Voxel Dims and the Spacing with NON Zero values in order for the generation to Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 8 2 Synthetic Microstructure Generation 37 complete successfully Pipeline nitialize Synthetic Volume 256 Voxels in X Y amp Z 0 15 micron resolution in X Y amp Z Pack Primary Phases e Find Number of Fields Find Surface Grains Match Crystallography Generate IPF Colors Optional This filter is Optional t will generate actual colors corresponding to the standard IPF Color Triangle e Write DREAMSD Data File 111 001 101 Notes Be sure to properly select the h5stats or dream3d input file and properly select an output file to save the data We will save the data as a dream3d file with the XDMF file wrapper enabled Make sure you do NOT name the output file the same as the input file or it will get over written Visualization From ParaView open the xdmf file and select the Grain Ids and IPFColors data sets then click the Apply button The microstructure should look something like below which is shown
23. ains value for the header POM o x star H5T NATIVE FLOAT Contains value for the header ma eae a O y star H5T NATIVE FLOAT Contains value for the header Por ITS RARE z star H5T NATIVE FLOAT Contains value for the header pe eye WorkingDistance H5T NATIVE FLOAT Contains value for the header ee DD o ElasticConstants H5T STRING Contains value for the header ET epo o GRID H5T STRING Contains value for the header ee E XSTEP H5T NATIVE FLOAT Contains value for the header A o emp YSTEP H5T NATIVE FLOAT Contains value for the header o emyyster NCOLS ODD H5T NATIVE INT32 Contains value for the header CS TD emyNCOISQDD oo NCOLS EVEN H5T NATIVE INT32 Contains value for the header TETE TS emyNCOISEEN oo NROWS H5T NATIVE INT32 Contains value for the header entry NROWS Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 28 Supported File Formats OPERATOR H5T STRING Contains value for the header SAMPLEID H5T STRING Contains value for the header SCANID H5T STRING Contains value for the header Phases H5G GROUP Group that contains a subgroup for each phase where the name of each subgroup is simply the index of the phase starting at 1 TSL ang Phase Group Specification Name HDFSTyp Value hklFamilies H5G GROUP Contains all the HKL Family information where the number of datasetscontained in this group is the number of HKL Families TSL ang HKLFamily Group Specification HDF5 Type Value Bas
24. as seen in the image below See the DREAMSD documentation for more details on the exact storage layout of the mesh within the DREAMSD data file lll ParaView 3 98 1 64 bit o P B Ww c GF MBAR SE Ot amp o d P DA OX mo T E ga L Solid Color Outline Tm x ix sd st sz 2 68 6 lU 9 OUS v9 0 o li Ww m w x oo Pon tows ESTES ES E builtin BS 3p 8 menm gt SurfaceMeshTutorial_Mesh xdmf a Clips Properties Information o0 Properties Apply Reset Delete Search go Properties SurfaceMeshTutorial Mesh xdmf A Point Arrays SurfaceMeshNodeType Y Cell Arrays V f Triangle Field O V fj Triangle Field 1 Sets Blocks Hierarchy v Blocks V SurfaceMesh DataContainer Check Selected Blocks Uncheck Selected Blocks Stride 1 Ih Ih Display UnstructuredGridRepresentation Color Q Solid Color A E Show s Edit gt Rescale Figure 8 4 Mesh Generated from DREAM3D Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 42 Tutorials 8 4 Cropping Data Tutorial Cropping data in DREAMSD can help reduce the time to process data by removing data that the user decides should not be processed The filter uses the 3D Voxel index as the minimum and maximum values to use for the region of interest The easiest way to work through the data is to initially run a pip
25. cal User Interfaces GUIs common data structures and documentation for the tools developed in the research effort of Groeber and Ghosh 2009 201 1 After the initial phase of development 2011 Jackson and Groeber approached Rollett Lee Sintay Chan and Tucker and proposed the unification of the parallel efforts The Rollett group accepted the proposal and graciously made available all of their algorithms and source code It was at this point that DREAM 3D was named and the vision for the software was truly solidified Over the next couple years 2011 2013 additional researchers contributed code for extending capabilites of DR EAM 3D Specifically the grain boundary centric tools of Dave Rowenhorst Naval Research Laboratory and Greg Rohrer Carnegie Mellon University greatly augmented the functionality of the package By 2013 Jackson and Groeber had fully documented the tools created a Software Developers Kit SDK and generated tools for adding plugins to the package making the software package readily usable and extensible Funding Sources Parts of DREAM 3D were written under US Air Force AFRL Contract FA8650 07 D 5800 and Navy Research Labs NRL Contract N00173 07 C 2068 Many others have contributed to the code including the following Major Contributing Institutions BlueQuartz Software Specializing in Software Tools for the Scientist Carnegie Mellon SIATE UNIVERSITY List of Code Contributors CC and Visi
26. d c Weights and Spreads Weights and Spreads Sub Tab Euler 1 3 D these are the Euler angles that define an orientation that the user would like to increase in weight Weight D this is the weight in MRD multiples of random to be assigned to the orientation listed Sigma D this is the spread to use in blurring out the orientation chosen The value corresponds to the number of bins in Rodrigues orientation space it takes for the MRD value entered in the Weight column to reduce to 0 0 decreasing quadratically from the bin of the entered orientation Calculate ODF D this builds the ODF and then creates pole figures PFs for the user to inspect Pole Figure PF Sub Tabs There are three pole figures formed which correspond to the location of the 3 principal axes of the grains to be generated i e a gt b gt c Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 54 Auxiliary Tools Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen cHAPTER 10 Created Array Index Active FieldData Minimum Number of Neighbors Filter Processing Cleanup e Minimum Size Filter All Phases Processing Cleanup e Minimum Size Filter Per Phase Processing Cleanup e Segment Fields Misorientation Reconstruction Segmentation e Segment Fields Scalar Reconstruction Segmentation e Segment Fields C Axis Misorientation Reconstruction Segmentation e Mer
27. during the actual execution of the processing pipeline DREAM3D v amp Filter Library amp Generic oo PR amp EEE TES gt Io amp Add Orientation Noise gt amp eee 35 Align Sections Feature Centroid d Processing 35 Align Sections Feature di Reconstruction Align Sections List gt amp Sampling amp Align Sections Misorientation gt amp AES 35 Align Sections Mutual Information gt amp SurfaceMeshing amp Avizo Rectilin coordinate Writer a amp SyntheticBuilding amp Avizo utomgloranae Writer v Prebuilt Pipelines Change Resolution 4 Ebsd 3D Reconstruc amp Clear Data 4 4 Statistics amp Convert Euler Angles Convert Hexagonal Grid Data to Squi n ih d Convert Nodes amp Triangles To STL Fi Favorite Pipelines db Convert Nodes amp Triangles To Vtk Drag filters here to build amp Create Cell Array From Field Array Crop Volume db Delete Arrays 4 Synthetic Single Pha a Synthetic Primary E Errors Warnings Filter Name Error Description Error Code 3 980 TT L co Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen CHAPTER 5 Creating a Pipeline In DREAMSD the user processes their data by creating what is known as a Pipeline which is constructed out of a series of Filt
28. ections_SurfaceMeshFace size 0 das ArraySelections_SurfaceMeshEdge size 0 ArraySelections_SolidMeshPoint size 0 4 ArraySelections_SolidMeshFace size 0 p ArraySelections_SolidMeshEnsemble size 0 1 Filter Name MultiThresholdCells OutputArrayName GoodVoxels ComparisonInputs size 2 ComparisonInputs 1 ArrayName Image Quality 22 Import Export amp Favorite Pipelines A4 ComparisonInputs 1 CompOperator 1 ComparisonInputs 1 CompValue 120 ComparisonInputs 2 ArrayName Confidence Index ComparisonInputsN2NCompOperator 1 ComparisonInputs 2 CompValue 0 100000001490116 2 Filter Name IdentifySample 3 Filter Name AlignSectionsFeatureCentroid UseReferenceSlice true ReferenceSlice 0 Creating a Favorite Pipeline If the user creates a pipeline that they intend to use several times then they may want to save the pipeline to the Favorites area This can simply be accomplished by using the Pipeline menu and selecting the Add Favorite If the user wants to remove a favorite at any time they simply need to select the Remove Favorite menu item Add Favorite Rename Favorite Remove Favorite Clear k Clearing the Pipeline As a convenience for those situations where the user has created a large pipeline and they would like to delete every filter from the pipeline the Pipeline Menu also has a menu item to remove every filter from a pipeline and an associated keyboard short cut Generated on Wed Apr 3
29. ed at the Edge level Calculated values i e Curvatures Coordination etc these calculated values are typically values associ ated with the connectivity or geometry of the mesh or structure itself Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen Face Cell Field 11 Map of attributes associated with surface patches Measured values data is not typically measured at the Face level Calculated values i e Bounding Field Ids Normals Curvature etc these calculated values are typically IDs to the higher level maps Field and Ensemble related to gradients of the measured values values associated with the connectivity or geometry of the mesh or structure itself or relationships to values calculated in the higher level maps Map of attributes associated with single datapoints often these datapoints are not truly volumes but rather point probe measurements that are homogenized over the volume nearest to each probe point Measured values i e Orientation Chemistry Greyscale etc typically this is the level at which most data is actually acquired Calculated values i e Field Ids Kernel Avg Misorientation Euclidean Distance etc these calculated values are typically IDs to the higher level maps Field and Ensemble related to gradients of the measured values or relationships to values calculated in the higher level maps Map of attributes associated with sets of datapoi
30. ed on Index of the family If Custom See Below there are 4 families then there are 4 data sets with names O 1 2 and 3 typedef struct int h n int k n int 1 n int sl n float diffractionIntensity n int s2 n HKLFamily_t HKL Specification This section details the data to be imported from a ctf file into the h5ebsd file HKL ctf Data Group Specification 1D Array of Values where the number of elements in the array is equal to the total number of points per 2D Slice Name HDF5 Type Value Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 7 2 H5EBSD Data File Specification 29 HET NATIVE INT32 E HST NATIVE FLOAT E Y H5T NATIVE FLOAT Z H5T NATIVE FLOAT Note that this ONLY appears in a 3D ctf data file HIST NATIVE INT32 ESC Emr HSLNATVEINT2 o SOS S SCSCS Euler1 H5T NATIVE FLOAT In 2D files these are in Degrees In E E Euler H5T NATIVE FLOAT In 2D files these are in Degrees In Euler3 H5T NATIVE FLOAT In 2D files these are in Degrees In T E E BD HSTNATVEINTE O BS HSLNATMMETNIS Gud HSTNATME NIS GrinRandomCouR HST NATVEUNTB oOo Oo GrinRandomCouG HSI NATME UNTB o HKL ctf Header Specification Name HDF Type Value OriginalFile H5T STRING Path to the ctf file that was OriginalHeader H5T STRING Contains the original header from Prj H5T STRING
31. eline that writes out a dream3d file and load the xdmf file into ParaView Then in the nformation 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 Microns is 0 16 4 0 13 8 0 9 75 which corresponds to a resolution of 0 1 0 08 0 25 Amin Ymax Xmax Ymax ah Rmin Y min all Xmax Ymig The display in ParaView shows the values in Microns so we need to convert those to Voxels Or just estimate if that is good enough Again for this example we want to crop out a section from 2 8 in X and 4 10 in Y and all of Z Extents X Extent Oto 164 dimension 165 Y Extent Oto 172 dimension 173 Z Extent Oto 39 dimension 40 Bounds X range Oto 16 4 delta 16 4 Y range Oto 13 8 delta 13 8 Z range Oto 9 75 delta 9 75 Tien The general formula to figure this out is the following Micron Resolution Voxel Micron Voxel Applying this to our sample data gives the following table Example Calculation for Min Max Voxels for Cropping 2101 20 8 0 1 80 4 0 08 50 10 0 08 125 0 0 25 0 9 75 0 25 39 1 We subtract 1 from the max Z value because the internal arrays are Zero Based Entering these values into the Crop Volume filter gives us the following Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 8 4 Cropping Data Tutorial X Min Column Y Min Row 5
32. ers By chaining together a series of filters the data is processed in quick succession and can ultimately be saved to a number of different file formats 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 Building a Pipeline In order the build a pipeline the user can either double click on a particular filter or drag the filter from the Filter List into the Pipeline Area DREAMSD Search di Add Bad Data L amp Add Orientation Noise T 2 Align Sections Feature Centroi db Align Sections Feature 35 Align Sections List 5 Align Sections Misorientation 35 Align Sections Mutual Informa A Avizo Rectilinear Coordinate W amp Avizo Uniform Coordinate Wad Change Resolution amp Clear Data amp Convert Euler Angles Convert Hexagonal Grid Data t d Convert Nadas amp Triannlas Tn 1 v a zz zB ation Errors Warnings isorientation Filter Jh red Arrays Created Arrays Authors nsecutive serial sections by determining F a Go i The user can place multiple filters into the pipeline to generate a workflow of data input analysis and data output 18 Creating a Pipeline filters The user can reorder the filters by simply using drag and drop of a selected filter in the pipeline and moving it into a new position in the p
33. ge Twins Reconstruction Grouping Reconstruct Prior Beta Grains Reconstruction gt Grouping Identify MicroTexture C Axis Misorientation Reconstruction gt Grouping Crop Volume Sampling gt Croping Cutting Pack Primary Phases SyntheticBuilding gt Packing Insert Precipitate Phases SyntheticBuilding Packing e Establish Matrix Phase SyntheticBuilding Packing AspectRatios FieldData e Find Field Shapes Statistics Morphological AvgCAxes FieldData e Find Average C Axis Orientations Statistics gt Crystallographic AvgQuats FieldData e Read YS Choi Abaqus Vtk Output File lO gt Input e Find Field Average Orientations Statistics gt Crystallographic e Match Crystallography SyntheticBuilding gt Crystallography Jumble Orientations SyntheticBuilding gt Crystallography 56 Created Array Index AxisEulerAngles FieldData e Find Field Shapes Statistics Morphological e Pack Primary Phases SyntheticBuilding Packing Insert Precipitate Phases SyntheticBuilding Packing AxisLengths FieldData e Find Field Shapes Statistics Morphological Pack Primary Phases SyntheticBuilding gt Packing Insert Precipitate Phases SyntheticBuilding Packing BiasedFields FieldData e Find Biased Fields Bounding Box Generic gt Spatial Centroids FieldData e Find Field Centroids Generic gt Misc Pack Primary Phases SyntheticBuilding gt Packing I
34. gma 90 35 45 750 3 _ By default if no custom rows are entered then a completely random ODF will be generated da x Load List From File Adding rows to this table results in those texture values being integrated into the random Calculate ODF ODF data lt 001 gt 011 111 Weights and Spreads Sub Tab Euler 1 3 these are the Euler angles that define an orientation that the user would like to increase in weight Weight this is the weight in MRD multiples o Sigma this is the spread to use in blurring out the orientation chosen The value corresponds to the number of bins in Rodrigues orientation space it takes for the MRD value entered in the Weight column to reduce to 0 0 decreasing quadratically from the bin of the entered orientation e Calculate ODF this builds the ODF and then creates pole figures PFs for the user to inspect Pole Figure PF Sub Tabs here are three PFs formed for each of the crystal structures that can be chosen though they are of different directions for the different crystal structures MDF Sub Tab This sub tab will display the baseline MDF for the generated ODF The implemented algorithm proceeds by randomly sampling pairs of orientations from the ODF and calculating the misorientation axis angle only Only the angle is plotted in the misorientation distribution plot The user can also add axis angle pairs to increase in weight Generated on Wed Apr 3 2013 11 03 23 for
35. gned to generate a random equiaxed microstructure Rolled this populates the statistic tabs with data that is designed to generate a rolled microstructure with elongated grains with user defined aspect ratios Aspect Ratio 1 this is the aspect ratio between the dimensions of the grains in the rolling direction and transverse direction respectively Aspect Ratio 2 this is the aspect ratio between the dimensions of the grains in the rolling direction and normal direction respectively This value must be larger than Aspect Ratio 1 or the default values will be wrong Phase Properties this is the area where the user can enter information about the phase for which statistics are currently being generated The Plus Button allows the user to add a phase the Minus Button allows the user to remove a phase and the Wheel Button allows the user to edit the currently selected phase Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 9 1 Stats Generator 47 amo Phase Properties Select Crystal Structure Hexagonal Fraction Calculated Phase Fraction 0 0 Select Phase Type Primary Fraction of Precipitate on Boundary Y Cancel Select Crystal Structure this allows the user to specify the crystal structure of the phase Currently the two options are Cubic and Hexagonal Fraction this is the volume fraction of the phase The Calculated Phase Fraction is updated as
36. gt Stacking Order Low To High Euler Transformation Recommended 270 2 001 Start Slice 1 B End Slice 117 B Use Recommended Transformations i Cell Data Field Data Ensemble Data M Confidence Index EulerAngles Fit Image Quality Phases SEM Signal vi CrystalStructures MaterialName Output Array Name GoodVoxels Select Arrays to Threshold Field Image Quality Confidence Index Misorientation Tolerance Degrees 5 Misorientation Tolerance Degrees so Reference Direction 0 0 1 Write Voxel Data vi Write SurfaceMesh Data Write Xdmf File XML Wrapper vi Output File tmp Data SmalllN100 dream3d 8 2 Synthetic Microstructure Generation 35 After running the pipeline Pa xaView can be used to display the generated Xdmf file There are a few options within ParaView that need to be set in order to show the encoded IPF colors otherwise ParaView will create a random color table for the visualization 1 Set the representation to Surface 2 Set the color by to PFColor 3 Click the little gear icon to show the advanced options 4 Uncheck the Map Scalars and Interpolate Scalars After all of these options are set the visualized volume will display with the encoded IPF Colors The user is free to use what ever coloring scheme they would like for example coloring by the phase or Grain Id will also show grain boundaries Mi ParaView 3
37. imilarity For the example above the Cells are grouped to identify Fields i e grains by applying a criterion of similar crystallographic orientation i e neighboring Cells with similar orientation are said to belong to the same Field The Fields are then grouped to identify Ensembles by a criterion of similar phase i e all grains of the same phase in the dataset are said to belong to the same Ensemble The grouping criteria are at the discretion of the user because these additional levels are not required for description of the structure but rather are organizational levels for describing the information that lives on the structure At each level DREAM 3D creates a Map to store information data about the individual elements at that level Additional information about the maps of the DREAM 3D data structure and typical data are given below Vertex Map of attributes associated with single points Measured values i e Orientation Chemistry Greyscale etc generally measured data is not represented at the Vertex level but the user could choose to store measured values at the Vertices rather than the more typical Cell centered convention Calculated values i e Curvatures Coordination etc these calculated values are typically values associ ated with the connectivity or geometry of the mesh or structure itself Edge Map of attributes associated with edges of Faces Measured values data is not typically measur
38. ion Created Array Index Tutorials Auxiliary Tools Table of Contents Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 2 Brief History and Acknowledgements History of DREAM 3D The history of DREAM 3D is rooted in two parallel research efforts he first was the graduate research project of Michael Groeber under the advisement of Dr Somnath Ghosh at The Ohio State University 2003 2007 The key developments under this project were the creation of many of DREAM 3D s current filters for reconstructing serial section experimental datasets quantifying microstruc tural features in 3D and generating statistically equivalent microstructures The second research effort was carried out by the research group of Tony Rollett at Carnegie Mellon Uni versity over a number of graduate student projects see names below and years 72000 2011 The key developments under these projects were the development of a synthetic microstructure builder microstruc ture clean up tools surface mesh generation and quantification tools for microstructural features The tools developed under these efforts generally remained as command line executables with limited portability due to lacking documentation In an effort to extend the capabilites of these tools to the larger materials community Dr Chris Woodward of the Air Force Research Laboratory AFRL funded Mike Jackson of BlueQuartz Software to create Graphi
39. ipeline As filters are placed into the pipeline a basic error checking algorithm called the Preflight is executed on the entire pipeline During the preflight stage the pipeline will have each filter check its input parameters and the availability of required data arrays Figure 2 shows a pipeline ready to execute with no errors LKEAIM SLI Use Reference Slice iv Reference Slice Misorientation Tolerance Degrees 5s Minimum Allowed Grain Size Pixels Grain lds Array Name Grainids T Cell Phase Array Name Phases Field Phase Array Name Phases A Click to Misorientation Tolerance Degrees remove To remove a filter from the pipeline the user can simply use the mouse to click the small X icon in the upper left corner of the filter If the preflight did not complete successfully the user will see the offending filters show a red outline and red title area This indicates that one or more of the input parameters have an error or the filter requires data that will not be available at that point in the pipeline By looking at the error table the user can read the error message from the pipeline and act accordingly An example pipeline with errors is shown in figure 4 Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen P Wy ouriacemesning gt amp SyntheticBuilding v f Prebuilt Pipelines a Ebsd 3D Reconstruc x Statistics Synthetic Single Pha Synthetic Primary YW Favor
40. itate Transformation Matrix Boundary 46 Auxiliary Tools Size Distribution Tab Eg Primary Phase Omega 3 Distributions Shape Distributions Neighbor Distributions ODF Axis ODF Log Normal Distribution Size Distribution 0 015 q 0 01 P s 5 5 c E Td e 5 6 0 005 E 5 t i o 5 E 0 O 1 5 2 2 5 3 3 5 4 4 5 Mu 1 0 Min Sigma Cut Off Value 5 q Ur min o Sigma 0 1 Max Sigma Cut Off Value 5 a n maz a Bins to be Created 6 Bin Step Size 0 5000 Preset Statistic Models Default al Create Data Mu This is the average value of the lognormal grain size distribution Sigma This is the standard deviation of the lognormal grain size distribution Sigma Cut Off Value This allows the user to truncate the distribution to remove very large grains Bin Step Size This is the size of bin to use in segregating the grains into size classes for correlating other statistics to grain size Note that the Bins to be Created is displayed in the bottom left corner Preset Statistic Models This allows the user to select a morphological type of microstructure to populate the default data Default this populates the statistic tabs with generic random data that may not create a ObuildableO microstructure This option should only be used if the user is going to enter the values on all the statistics tabs themselves Equiaxed this populates the statistic tabs with data that is desi
41. ite Pipelines Filter Name 1 Segment Grains Misorientation 2 Find Field Phases 3 Minimum Size Filter All Phases 9 A co Errors Warnings Error Description An array with name Phases in the CellData grouping does not exist ai is required for this filter to execute An array with name Phases in the CellData grouping does not exist ai is required for this filter to execute The current array with name GoodVoxels is not valid for the internal array named Phases for th filter The preflight failed for one or more reasons Check additional err Kererence 5Ilice U Misorientation Tolerance Degrees 5 Minimum Allowed Grain Size Pixels 12 Grain Ids Array Name Grainlds s Cell Phase Array Name l GoodVoxels m Field Phase Array Name l Phases t 19 Once the errors are resolved the user can now execute the pipeline and generate the outputs Because the DREA M3D native file format stores the complete state of the data arrays the user can use this idea to add checkpoints to the pipeline in the case of a long running pipeline Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 20 Creating a Pipeline Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 6 Import Export amp Favorite Pipelines Saving and Loading a Predefined Pipeline DREAM3D allows the user to Export and Import pipe
42. laid with EBSD Coordinate System Yellow Commercial EBSD acquisition systems do not typically follow this convention and DREAM 3D needs input from the user so that the proper transformations to the data can be applied during the Reconstruction and other analysis Commercial EBSD software packages allow for some initial transformations of the data in which case the DREA M 3D environment does not have any way of determining if those transformations have already occured During the import process the user is asked a few questions regarding the orientation of their EBSD data in relation to the sample coordinate system Currently there are 3 items that must be answered otherwise undefined behavior may occur during any of the analysis algorithms Some Commercial EBSD acquisition systems allow for a scan rotation which rotates the sample coordinate system 180 degrees around the Z axis Should we rotate the Euler angles to bring them in line with the sample reference frame HDF5 File Layout HDF5 Root Level Layout Specification H5Ebsd Specification Root Level Datasets and Group Attribute Name FileVersion Current Value 4 Name HDFS Type Index H5T NATIVE INT32 List of all Slice index values Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 26 Supported File Formats EulerTransformationAngle H5T NATIVE FLOAT EMT EulerTransformationAngle H5T NATIVE FLOAT ILL Manufacturer H5T STRING The Manufact
43. lines via the File menu and the Save Pipeline and Open Pipeline menu items The pipeline files are saved in the x ini file format popular among many other programs This file format is a simple text file with delineated sections with Key Value entries This makes the sharing of Pipelines mostly transparent between users If a pipeline has filters that require files to be read from or written to and the pipeline file is passed to another user that does not have those same paths then the new user may have to make the adjustments inside of DREAMSD after the pipeline is loaded Open Pipeline 0 Save Pipeline 3 5 Recent Files k e b EI The following is a partial listing of a 3D EBSD reconstruction pipeline saved as a pipeline file PipelineBuilder Number Filters 15 Name Reconstruction 0 Filter Name ReadH5Ebsd InputFile Users Shared Data Ang Data Small IN100 Output Small IN100 h5ebsd ZStartIndex 1 ZEndlIndex 117 UseTransformations false ArraySelections_VoxelCell size 4 ArraySelections_VoxelCell 1 VoxelCell Confidence Index ArraySelections_VoxelCell 2 VoxelCell EulerAngles ArraySelections VoxelCellN3NVoxelCell Image Quality ArraySelections_VoxelCell 4 VoxelCell Phases ArraySelections_VoxelField size 0 p ArraySelections VoxelEnsembleNsize 2 das ArraySelections_VoxelEnsemble 1 VoxelEnsemble CrystalStructures ArraySelections_VoxelEnsemble 2 VoxelEnsemble MaterialName 4 ArraySelections_SurfaceMeshPoint size 0 ArraySel
44. ly reduces the amount of memory needed to load store and view the data Note It is a REQUIREMENT that the Xdmf file and the DREAMBD file are in the same directory because paths in the XDMF file refer to data stored in the DREAMSD file The XML files are typically a few kilobytes in size and are therefor a huge savings over writing the VTK file for the same data XDMF Example Contents Below is an example of what an Xdmf file might contain lt xml version 1 0 gt lt DOCTYPE Xdmf SYSTEM Xdmf dtd gt lt Xdmf xmlns xi http www w3 org 2003 XInclude Version 2 2 gt lt Domain gt Grid Name Voxel DataContainer GridType Uniform gt lt Topology TopologyType 3DCoRectMesh Dimensions 183 885 1025 gt lt Topology gt Geometry Type ORIGIN DXDYDZ gt Dataltem Pormat kXML Dimensions 3 gt 0 0 D Dataltem Datarte em Formate xML Dimensions 32 gt 1 1 l Datartem Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 32 Supported File Formats lt Geometry gt Attribute Name ImageData AttributeType Scalar Center Cell gt Dataltem Format HDF Dimensions 182 884 1024 NumberType UChar Precision 1 gt out dream3d VoxelDataContainer CELL DATA ImageData lt Dataltem gt lt Attribute gt lt Grid gt lt Domain gt lt Xdmf gt 7 4 Import amp Export File Formats Supported Input File Types e TSL ang files HKL ctf files e HEDM mic files e
45. nel Average Misorientations Statistics Crystallographic NearestNeighbors CellData e Find Euclidean Distance Map Statistics Morphological NeighborList Field Find Field Neighbors Statistics gt Morphological Neighborhoods FieldData e Find Field Neighborhoods Statistics gt Morphological Pack Primary Phases SyntheticBuilding gt Packing Insert Precipitate Phases SyntheticBuilding Packing NumCells FieldData e Find Field Sizes Statistics gt Morphological Insert Precipitate Phases SyntheticBuilding Packing NumFields EnsembleData Find Number of Fields Statistics gt Morphological Insert Precipitate Phases SyntheticBuilding Packing Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 59 NumNeighbors FieldData Find Field Neighbors Statistics gt Morphological Omega3s FieldData e Find Field Shapes Statistics Morphological e Pack Primary Phases SyntheticBuilding Packing Insert Precipitate Phases SyntheticBuilding Packing Parentlds CellData e Merge Twins Reconstruction Grouping Reconstruct Prior Beta Grains Reconstruction gt Grouping Identify MicroTexture C Axis Misorientation Reconstruction gt Grouping Parentlds FieldData e Merge Twins Reconstruction Grouping Reconstruct Prior Beta Grains Reconstruction gt Grouping Identify MicroTexture C Axis Misorientation Reconstructi
46. nsert Precipitate Phases SyntheticBuilding Packing CrystalStructures EnsembleData e Read Ensemble Info File lO gt Input e Read Legacy DREAM 3D H5Voxel File lO Input e Read YS Choi Abaqus Vtk Output File lO gt Input EquivalentDiameters FieldData e Find Field Sizes Statistics gt Morphological Pack Primary Phases SyntheticBuilding gt Packing Insert Precipitate Phases SyntheticBuilding Packing EulerAngles CellData e Read Field Info File lO gt Input e Read Legacy DREAM 3D H5Voxel File lO gt Input e Read YS Choi Abaqus Vtk Output File lO gt Input e Match Crystallography SyntheticBuilding gt Crystallography Jumble Orientations SyntheticBuilding gt Crystallography Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 57 EulerAngles FieldData e Read Field Info File lO gt Input e Find Field Average Orientations Statistics gt Crystallographic e Match Crystallography SyntheticBuilding gt Crystallography Jumble Orientations SyntheticBuilding gt Crystallography EulerColor CellData Generate Euler Colors Generic gt Misc FlatlmageData CellData Flatten Image Processing gt Image GBEuclideanDistances CellData e Find Euclidean Distance Map Statistics Morphological GoodFields FieldData Single Threshold Field Data Processing gt Threshold e Multi Threshold Field Data Processing Threshold Good
47. nts generally elements in this map are sets of contiguous Cells that have some aspect of similarity often in their measured values i e orientation chemistry greyscale etc Measured values i e Avg Stresses Avg Strains etc some measurement techniques are capable of measuring values averaged over an entire Field i e High Energy Diffraction Microscopy Calculated values i e Avg Orientation Size Shape No of Neighbors etc generally there is little measured data at this level and these values are calculated from averaging the measured data from the Cells that constitute each Field or geometrically describing the size and or shape of the set of Cells Ensemble Map of attributes associated with sets of Fields Measured Set values i e Crystal Structure Phase Type etc measured values at the Ensemble level are usually user defined parameters during the data collection or during analysis within DREAM 3D Calculated values i e Size Distribution No of Fields ODF etc these values are typically descriptions of the distribution of values from the lower level Field map Generated on Wed Apr 3 2013 11 03 23 for DREAMSD Reference Manual by Doxygen 12 DREAM 3D Data Structure Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 4 Overview of the User Interface DREAMSD has 4 main areas of its user interface 1 The Filter Library 2 he Filter List 3 The Errors
48. on gt Grouping PhaseTypes EnsembleData e Read Ensemble Info File lO gt Input e Read Legacy DREAM 3D H5Voxel File lO Input Phases CellData e Read Field Info File lO gt Input e Read Legacy DREAM 3D H5Voxel File lO Input e Read YS Choi Abaqus Vtk Output File lO gt Input Phases FieldData e Find Field Phases Generic gt Misc e Read Field Info File lO gt Input Pack Primary Phases SyntheticBuilding Packing Insert Precipitate Phases SyntheticBuilding Packing e Establish Matrix Phase SyntheticBuilding Packing Poles FieldData e Find Schmid Factors Statistics gt Crystallographic Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 60 Created Array Index QPEuclideanDistances CellData e Find Euclidean Distance Map Statistics Morphological Quats CellData Find Cell Quaternions Generic gt Crystallography e Read YS Choi Abaqus Vtk Output File lO gt Input Schmids FieldData e Find Schmid Factors Statistics Crystallographic SharedSurfaceAreaList Field Find Field Neighbors Statistics gt Morphological SlipSystems FieldData e Find Schmid Factors Statistics Crystallographic SurfaceFields FieldData e Find Surface Fields Generic gt Spatial e Read YS Choi Abaqus Vtk Output File lO gt Input Find Field Neighbors Statistics gt Morphological SurfaceMeshNodeType VertexData e M3C Surface Me
49. on Contributors VC Air Force Research Laboratory AFRL e Dr Michael A Groeber VC CC e Dr Adam Pilchak VC CC Dr Megna Shah VC CC Dr Michael Uchic VC Dr Chris Woodward VC Dr Dennis Dimiduk VC BlueQuartz Software Mr Michael A Jackson VC CC Ohio State University Johns Hopkins University e Dr Somnath Ghosh VC Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen Carnegie Mellon University Dr Tony Rollett VC CC e Dr Greg Rohrer CC Dr Marc De Graef CC e Dr Sukbin Lee CC e Dr Joe Tucker CC e Dr Lisa Chan CC e Dr Stephen Sintay CC e Dr Abhijeet Brahme CC e Dr David Saylor CC e Dr Joe Fridy CC Dr Patrick Callahan CC Dr Shlomo Taasan CC Navy Research Laboratory NRL Dr Dave Rowenhorst VC CC Other Insitituations Mr Joey Kleingers CC SOCHE Mr Jarrell Waggoner CC Univ South Carolina Generated on Wed Apr 3 2013 11 03 23 for DREAMSD Reference Manual by Doxygen Brief History and Acknowledgements Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen CHAPTER 3 DREAM 3D Data Structure DREAMSD uses a data structure that is based on the concepts of combinatorial topology and common methods for describing mesh structures Any topological network in 2 or 3 D can be decribed with a the foll
50. owing hierarchy Vertex Point dim 0 Edge Curve dim 1 limited by points dim 0 Volume Face Space dim3 Surface dim 2 limited by Faces dim 2 limited by Edges dim 1 If the mesh or network is 2 D then the Volume element does not exist and the Face element is the highest level element For typical voxel based data the voxels are the Volume elements and are referred to within DREAM 3D as Cells Similarly in a surface mesh with triangular patches the triangles are the Face elements and are referred 10 DREAM 3D Data Structure to within DREAM 3D as Faces This topology is required to describe the mesh or structure of the data itself and is not cannot be adjusted defined by the user However once the topology of the structure is set the user can begin grouping topological elements into higher level features of the structure Below is an example of this grouping for a voxel based dataset of a polycrystalline metal p is A Pais L Li l Size E N l Am EZ H Z7 CT NN t e v Cell Data So 100 000s 1 000 000s e A AN 100s 1 000s 100s 1 0005 of Cells Ensemble Data 1s 100s 1 000s of Fields DREAM 3D uses two additional levels above the topological levels required to define the structure of the data These two levels are called Field and Ensemble These levels allow the user to group topological elements together based on criteria of s
51. r may be interested in may be stored in various subgroups in the HDF5 file For example with a Voxel Data Container there are six 6 types of Data Vertex Edge Face Cell Field and Ensemble Arrays created for each type are stored in subgroups For example with Voxel based data the following HDF5 group organization is used e VoxelDataContainer Group DIMENSIONS Dataset 24 Supported File Formats ORIGIN Dataset SPACING Dataset VERTEX_DATA Group EDGE DATA Group FACE DATA Group CELL DATA Group Grainlds Dataset EulerAngles Dataset IPFColors Dataset FIELD DATA Group Phases Dataset AvgEulerAngle Dataset ENSEMBLE DATA Group CrystalStructures Dataset MaterialName Dataset In the above example we have shown a number of data arrays for each group type The user should note that the data sets shown in the above example are hypothetical and may or may not appear in data sets that the user generates With a SurfaceMesh Data Container there are only five 5 types of Data Vertex Edge Face Field and Ensemble The missing type of Data in the SurfaceMesh is the Cell This is because the SurfaceMesh is a 2 D feature and thus the Face is the Cell and thus a level can be ommitted SurfaceMeshDataContainer Group Faces Dataset Vertices Dataset VERTEX DATA Group VertexNormal Dataset EDGE DATA
52. s Feature Centroid b amp Statistics b ln Align Sections Feature 3 Align Sections List Align Sections Misorientation 35 Align Sections Mutual Information d SurfaceMeshing amp SyntheticBuildi amp Avizo Rectilin oordinate Writer METUS NEA amp Avizo Uniform gf6ordinate Writer Prebuiit Pipelines 35 Change Resolution 4 Ebsd 3D Reconstruc amp Clear Data 4 Statistics 4 Synthetic Single Pha 4 Synthetic Primary Favorite Pipelines amp Convert Euler Angles Convert Hexagonal Grid Data to Squi Aa Convert Nodes amp Triangles To STL Fi Convert Nodes amp Triangles To Vtk Drag filters here to build amp Create Cell Array From Field Array Crop Volume db Delete Arrays E Errors Warnings Filter Name Error Description Error Code 3 l Td co Pipeline Area Area 4 This area is where the user will construct their pipeline by either double clicking on a filter in the filter list area or dragging a filter from the filter list and dropping the filter into the pipeline area Filters in this section can be Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen 16 Overview of the User Interface rearranged by simply dragging the filter into a new location As the user updates the pipeline a process called the Preflight will be executed to make sure that the pipeline will have all the necessary data available
53. shing Slice at a time SurfaceMeshing Generation SurfaceVoxels CellData e Find Boundary Cells Generic Spatial Find Field Neighbors Statistics gt Morphological TJEuclideanDistances CellData e Find Euclidean Distance Map Statistics Morphological Volumes FieldData Find Field Shapes Statistics gt Morphological e Find Field Sizes Statistics Morphological e Pack Primary Phases SyntheticBuilding Packing e Match Crystallography SyntheticBuilding gt Crystallography Insert Precipitate Phases SyntheticBuilding Packing Generated on Wed Apr 3 2013 11 03 23 for DREAM3D_Reference_Manual by Doxygen
54. t by defining a triangle T which we will call a Face Each Triangle has 3 Vertex VO V1 V2 which are referred to as a Point Vertex and or Node interchangeably within DREAMSD A k These data structures are declared in DREAMSD in the following code typedef struct Float t pos 3 Vert t typedef struct signed int verts 3 Face t DREAMSD stores all the vertices in a single array DREAMSD has the notion of a shared vertex list where each vertex is only listed once in the vertex list Each Triangle is then created by referencing 3 indexes out of the vertex list to form the 3 points of the triangle Vertex amp Triangle Attributes DREAMBD filters can attach attributes to each vertex or triangle These attributes can be scalar or vector of any nu merical type Some attributes are dependent on the winding of the triangle From OpenGL the normal is computed via a right hand rule and so proper triangle winding is important when visualizing the mesh and also is important to some filters such as the Grain Face Curvature Filter This is why there are filters such as Reverse Triangle Winding and Verify Triangle Winding in order to ensure proper winding and normal cal culations Surface Mesh Data Container To support the creation and manipulation of a surface mesh DREAMSD introduced a new data container type called the SurfaceMeshDataContainer and have as its core properties the shared vertex array and triangle array
55. ter List area Getting Help for a Filter The user can Right Click in the title area of the filter to display a menu where the user can select the Show Filter Help menu selection The user s default web browser will be opened to the page containing the documentation for the current filter Generated on Wed Apr 3 2013 11 03 23 for DREAM3D Reference Manual by Doxygen 15 E depor Goninon Fine o HER Show Filter Help q Orientation Source Data Input Directory Users Shared Data Ang Remove Filter Total Files Found 117 Filter List Area 2 This section lists the filters that are associated with a specific group that is selected in the Filter Library area If the Filter Library is itself selected then all filters will be shown in this list The user typically will select a filter from this list and drag it over to the pipeline area Errors amp Warnings Tab Area 3 This area displays any errors and or warnings associated with the filter if it is actively being used in a pipeline The display of the errors can be toggled on and off by pressing the appropriate buttons Also clicking the xx xx icon will display all of the help including filter reference tutorials and user manual in the users default web browser Jain DREAM3D v amp Filter Library Search sss amp Generic d Add Bad Data amp 10 di Add Orientation Noise d Imagelmport amp Processing 35 Reconstruction amp Sampling Align Section
56. the size distribution and cannot be changed e Alpha this is the alpha parameter of a Beta distribution Omega 3 is normalized and can only be between 0 and 1 so the Beta distribution is a good fit Beta this is the beta parameter of the Beta distribution Color this allows the user to change colors of the curves for image creation or easier identification during stats generation Generated on Wed Apr 3 2013 11 03 23 for DREAMS3D Reference Manual by Doxygen 9 1 Stats Generator Shape Distribution Tab EEE Primary Phase Size Distribution Omega 3 Distributions Shape Distributions Untitled h5stats _ Primary Phase 49 Neighbor Distributions ODF Axis ODF Beta Distribution Frequency Bin Alpha Beta Color 1 64872 5 1 darkblue 2 14872 5 1 2 66667 darkcyan 2 64872 Do 5 2 4 33333 darkgolden 3 14872 5 3 6 darkgray Beta Distribution Bin Alpha Beta Color 1 64872 3 1 darkblue 2 14872 S1 2 66667 darkcyan 2 64872 5 2 4 33333 darkgolden 3 14872 5 3 6 darkgray Bin this column is calculated from the size distribution and cannot be changed Frequency Alpha this is the alpha parameter of a Beta distribution B A C A and C B are normalized and can only be between 0 and 1 so the Beta distribution is a good fit Beta this is the beta parameter of the Beta distribution Color this allows the
57. tistics generated with StatsGenerator Surface Meshing Tutorial This tutorial serves as an introduction to creating a triangle based surface mesh from a 3D voxel volume Background information on the terminology used in the filters is also presented Cropping Data Tutorial This tutorial shows how to use ParaView to crop volumes of data using the Crop Volume filter 8 1 3DOrientation Data Reconstruction With the advent of 3D EBSD data collection systems the visualization of the collected data is typically the first order of business Using the sample data set Small IN100 which is a Nickel based super alloy we can use DREAMSD to build a 3D reconstruction of the 2D slices The order of operations for this type of work flow is the following 1 Convert the Orientation Data toan H5Ebsd based archive file 2 Read H5Ebsd file 3 Determine which voxels are considered good 4 Find the Quaternions for each Cell 5 Align the sections using a Misorientation Alignment filter 6 Segment the grains using a Misorientation Algorithm 7 Generate the IPF Inverse Pole Figure colors based on the Euler Angles 8 Write out a DREAM3D data file with optional Xdmf file 34 Tutorials EBSD HDFS File Jsers Shared Data Ang Data Small IN100 Output Small IN100 h5ebsd X Dim 189 X Res 0 25 Minimum Slice EBSD Manufacturer Y Dim 201 Y Res 0 25 Maximum Slice 117 Dim 117 Res 025 TSL Sample Transformation Recommended 180 lt 010
58. urer currently is e O s Max X Points H5T NATIVE INT64 The maximum number of X points C OT fesmpegd oo Max Y Points H5T NATIVE INT64 The maximum number of Y points CS RTT Times o o SampleTransformationAngle H5T NATIVE FLOAT pU SampleTransformationAngle H5T NATIVE FLOAT E Stacking Order H5T NATIVE UINT32 Defines which slice corresponds to the Z 0 in the coordinate system Optional Attribute of type H5T STRING with Name Name and Value Low To High or High To Low X Resolution H5T NATIVE FLOAT Resolution between sample points eee nite etbon o o Y Resolution H5T NATIVE FLOAT Resolution between sample points eee mfevdidon oo Z Resolution H5T NATIVE FLOAT Resolution between slices in the Z Tn E ZEndIndex H5T NATIVE INT64 otarting Slice index ZStartindex H5T NATIVE INT64 Ending Slice index inclusive Slice Data organized by Slice index Slice Group Specification Each Slice is grouped into its own H5G GROUP with the Name of the group simply the index of the slice Within each slice group are 2 more groups with names Data and Header Name HDFSType H5G GROUP Contains all the data columns H5G GROUP Contains all the header entries TSL Specification This section details the data to be imported from a ang file into the n5ebsd file TSL ang Data Group Specification Name HDF Type H5T NATIVE FLOAT Contains all the Phi1 data in a 1D Array with length equal to the total number of points H5T NA

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