/trunk/src Developers: jeroen

Login name:
jeroen
Total Commits:
1964 (9.2%)
Lines of Code:
87783 (21.7%)
Most Recent Commit:
2006-06-12 16:45

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Activity by Hour of Day for jeroen

Activity by Day of Week for jeroen

Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 1964 (100.0%) 87783 (100.0%) 44.6
Packages/ModelCreation/Core/Fields/ 307 (15.6%) 19663 (22.4%) 64.0
Core/Algorithms/Fields/ 139 (7.1%) 12421 (14.1%) 89.3
Packages/CardioWave/Core/Model/ 49 (2.5%) 5582 (6.4%) 113.9
Packages/CardioWave/Core/XML/ 55 (2.8%) 3146 (3.6%) 57.2
Packages/ModelCreation/Dataflow/GUI/ 101 (5.1%) 2805 (3.2%) 27.7
Packages/CardioWave/Dataflow/Modules/DiscreteMultiDomain/ 53 (2.7%) 2702 (3.1%) 50.9
Packages/ModelCreation/Dataflow/XML/ 210 (10.7%) 2443 (2.8%) 11.6
Packages/MatlabInterface/MatlabLibrary/bem/ 17 (0.9%) 2340 (2.7%) 137.6
Core/Algorithms/Math/ 14 (0.7%) 2294 (2.6%) 163.8
Packages/ModelCreation/Core/DataStreaming/ 10 (0.5%) 2204 (2.5%) 220.4
Packages/CardioWave/Dataflow/GUI/ 58 (3.0%) 1938 (2.2%) 33.4
Packages/ModelCreation/Core/Numeric/ 41 (2.1%) 1914 (2.2%) 46.6
Packages/ModelCreation/Core/Datatypes/ 20 (1.0%) 1841 (2.1%) 92.0
Core/Algorithms/Numeric/ 21 (1.1%) 1717 (2.0%) 81.7
Packages/CardioWave/Dataflow/Modules/ContinuousBiDomain/ 19 (1.0%) 1670 (1.9%) 87.8
Packages/ModelCreation/Dataflow/Modules/FieldsData/ 52 (2.6%) 1641 (1.9%) 31.5
Core/Algorithms/Util/ 21 (1.1%) 1563 (1.8%) 74.4
Packages/ModelCreation/Dataflow/Modules/FieldsGeometry/ 41 (2.1%) 1453 (1.7%) 35.4
Core/Util/ 30 (1.5%) 1426 (1.6%) 47.5
Core/Algorithms/Regression/ 15 (0.8%) 1284 (1.5%) 85.6
Packages/ModelCreation/Core/Util/ 21 (1.1%) 1135 (1.3%) 54.0
Core/Datatypes/ 38 (1.9%) 1101 (1.3%) 28.9
Packages/ModelCreation/Core/Converter/ 29 (1.5%) 1095 (1.2%) 37.7
Packages/CardioWave/Dataflow/XML/ 67 (3.4%) 1043 (1.2%) 15.5
Core/Algorithms/Converter/ 14 (0.7%) 1039 (1.2%) 74.2
Packages/CardiacVis/Core/Algorithms/Fields/ 9 (0.5%) 909 (1.0%) 101.0
Core/Geom/ 9 (0.5%) 863 (1.0%) 95.8
Packages/ModelCreation/Dataflow/Modules/FieldsCreate/ 47 (2.4%) 810 (0.9%) 17.2
Packages/ModelCreation/Core/Algorithms/ 38 (1.9%) 752 (0.9%) 19.7
Core/Algorithms/DataIO/ 8 (0.4%) 735 (0.8%) 91.8
Packages/ModelCreation/Core/DataIO/ 13 (0.7%) 702 (0.8%) 54.0
Packages/MatlabInterface/nets/ 4 (0.2%) 559 (0.6%) 139.7
Core/Basis/ 35 (1.8%) 541 (0.6%) 15.4
StandAlone/regression/ 3 (0.2%) 515 (0.6%) 171.6
Packages/ModelCreation/Dataflow/Modules/FiniteElements/ 28 (1.4%) 475 (0.5%) 16.9
Packages/ModelCreation/Dataflow/Modules/Math/ 28 (1.4%) 450 (0.5%) 16.0
Packages/ModelCreation/Dataflow/Modules/Converter/ 19 (1.0%) 431 (0.5%) 22.6
Packages/ModelCreation/Dataflow/Modules/DataStreaming/ 8 (0.4%) 424 (0.5%) 53.0
Packages/ModelCreation/Dataflow/Modules/Time/ 2 (0.1%) 419 (0.5%) 209.5
Packages/CardioWave/Dataflow/Modules/Model/ 15 (0.8%) 304 (0.3%) 20.2
Packages/CardiacVis/Dataflow/Modules/FieldsCreate/ 7 (0.4%) 217 (0.2%) 31.0
Packages/ModelCreation/Dataflow/Modules/TensorVectorMath/ 8 (0.4%) 179 (0.2%) 22.3
Packages/ModelCreation/Dataflow/Modules/FieldsExample/ 11 (0.6%) 177 (0.2%) 16.0
Core/Algorithms/Visualization/ 3 (0.2%) 139 (0.2%) 46.3
Core/Geometry/ 5 (0.3%) 101 (0.1%) 20.2
Dataflow/Network/ 3 (0.2%) 88 (0.1%) 29.3
Packages/MatlabInterface/Core/Datatypes/ 18 (0.9%) 81 (0.1%) 4.5
Packages/CardiacVis/Dataflow/XML/ 2 (0.1%) 75 (0.1%) 37.5
Packages/CardiacVis/Dataflow/GUI/ 2 (0.1%) 49 (0.1%) 24.5
Dataflow/Modules/Fields/ 3 (0.2%) 28 (0.0%) 9.3
Packages/ModelCreation/Dataflow/Modules/DataIO/ 6 (0.3%) 27 (0.0%) 4.5
Packages/CardiacVis/Core/Datatypes/ 1 (0.1%) 26 (0.0%) 26.0
Dataflow/Modules/String/ 2 (0.1%) 21 (0.0%) 10.5
Packages/CardioWave/Core/Datatypes/ 7 (0.4%) 19 (0.0%) 2.7
Packages/CardiacVis/Dataflow/Modules/ 1 (0.1%) 19 (0.0%) 19.0
Core/GUI/ 2 (0.1%) 17 (0.0%) 8.5
Packages/ModelCreation/Dataflow/Modules/DataInfo/ 4 (0.2%) 16 (0.0%) 4.0
Packages/MatlabInterface/Dataflow/Modules/DataIO/ 21 (1.1%) 16 (0.0%) 0.7
Packages/CardiacVis/Dataflow/ 1 (0.1%) 16 (0.0%) 16.0
Packages/CardiacVis/Core/ 1 (0.1%) 16 (0.0%) 16.0
Packages/CardiacVis/Core/Algorithms/ 1 (0.1%) 15 (0.0%) 15.0
Packages/CardioWave/Dataflow/Modules/DataIO/ 3 (0.2%) 14 (0.0%) 4.6
Packages/CardiacVis/ 1 (0.1%) 10 (0.0%) 10.0
Packages/ModelCreation/Dataflow/Modules/SelectionMask/ 9 (0.5%) 9 (0.0%) 1.0
Core/Algorithms/ 6 (0.3%) 8 (0.0%) 1.3
Packages/ModelCreation/Dataflow/Modules/ 7 (0.4%) 7 (0.0%) 1.0
Dataflow/Modules/Visualization/ 3 (0.2%) 7 (0.0%) 2.3
Packages/ModelCreation/Core/ 7 (0.4%) 6 (0.0%) 0.8
Packages/MatlabInterface/Dataflow/GUI/ 2 (0.1%) 6 (0.0%) 3.0
Packages/CardioWave/Dataflow/Modules/ 5 (0.3%) 4 (0.0%) 0.8
Packages/BioPSE/Dataflow/Modules/LeadField/ 1 (0.1%) 4 (0.0%) 4.0
Packages/CardioWave/Dataflow/Modules/CreateModel/ 17 (0.9%) 3 (0.0%) 0.1
Packages/CardioWave/Dataflow/Modules/Tools/ 5 (0.3%) 2 (0.0%) 0.4
Packages/CardioWave/Core/ 3 (0.2%) 2 (0.0%) 0.6
Core/Persistent/ 2 (0.1%) 2 (0.0%) 1.0
StandAlone/ 2 (0.1%) 1 (0.0%) 0.5
Packages/ModelCreation/Dataflow/Modules/Script/ 2 (0.1%) 1 (0.0%) 0.5
Packages/ModelCreation/Dataflow/Modules/FieldsProperty/ 2 (0.1%) 1 (0.0%) 0.5
Packages/CardioWave/Dataflow/Modules/Math/ 4 (0.2%) 1 (0.0%) 0.2
Packages/CardioWave/Core/Algorithms/ 2 (0.1%) 1 (0.0%) 0.5
Dataflow/Modules/DataIO/ 3 (0.2%) 1 (0.0%) 0.3
Dataflow/GUI/ 3 (0.2%) 1 (0.0%) 0.3
Core/Bundle/ 2 (0.1%) 1 (0.0%) 0.5
StandAlone/utils/ 2 (0.1%) 0 (0.0%) 0.0
StandAlone/convert/ 2 (0.1%) 0 (0.0%) 0.0
Packages/MatlabInterface/nets/example_fields/ 33 (1.7%) 0 (0.0%) 0.0
Packages/MatlabInterface/nets/data/ 5 (0.3%) 0 (0.0%) 0.0
Packages/MatlabInterface/Dataflow/XML/ 12 (0.6%) 0 (0.0%) 0.0
Core/Containers/ 2 (0.1%) 0 (0.0%) 0.0

Activity of jeroen

Most Recent Commits

jeroen 2006-06-12 16:45 Rev.: 34471

Fixed regression test

18 lines of code changed in 1 file:

  • StandAlone/regression: TEST_FieldsAlgo.cc (+18 -6)
jeroen 2006-06-12 16:44 Rev.: 34470

Added speed ups in BuildFEMatrix, for regular grids (need to compute Jacobians only once as each element is the same). Added LogFile support for regression tests and fixed the regression testing program

1362 lines of code changed in 24 files:

  • Core/Algorithms/DataIO: DataIOAlgo.cc (+15 -1)
  • Core/Algorithms/Fields: DomainBoundary.cc (new), DomainBoundary.h (new), FieldsAlgo.cc (+16), FieldsAlgo.h (+5)
  • Core/Algorithms/Math: BuildFEMatrix.h (+446 -154)
  • Core/Basis: HexTrilinearLgn.h (new), PrismLinearLgn.h (new)
  • Core/Datatypes: HexVolMesh.h (new)
  • Core/Util: LogFile.cc (new 75), LogFile.h (new 76), RegressionReporter.cc (+14 -2), RegressionReporter.h (+7), sub.mk (+1)
jeroen 2006-06-09 12:57 Rev.: 34453

Series of bug fixes and first version of regression test for the core algorithms (currently limited), but will expand this soon to include most algorithms. Fixed HexVolMesh to do degenerate elements properly this time. First series of test indicated a series of problems in the algorithms fixed these here. To run the regression tests one still needs to have example files and gold standards. We will be setting up that directory shortly. Added the ability in the algorithms to compile dynamic files and delete them afterwards, so it is not a burden on the filing system. This now happens automatically when the algorithm detects that the ProgressReporter is of the class RegressionReporter. This automatically triggers the dynamic compilation system to build those libs on-the-fly but remove them afterwards

1445 lines of code changed in 92 files:

  • Core/Algorithms/DataIO: DataIOAlgo.cc (+38), DataIOAlgo.h (+3)
  • Core/Algorithms/Fields: ClearAndChangeFieldBasis.cc (+2), ClipBySelectionMask.cc (+2), ConvertToTetVol.cc (new), ConvertToTetVol.h (new), ConvertToTriSurf.cc (+3 -1), DistanceField.cc (+9 -1), DomainBoundary.cc (+4), FieldBoundary.h (new), FieldDataElemToNode.cc (+2), FieldDataNodeToElem.cc (+2), GatherFields.cc (+2), GetFieldData.cc (new), GetFieldDataMinMax.cc (new), GetFieldInfo.cc (+2), IsInsideField.cc (new), LinkToCompGridByDomain.cc (new), MappingMatrixToField.cc (new), MergeFields.cc (new), ScaleField.cc (new), SetFieldData.cc (new), SplitByConnectedRegion.cc (new), SplitFieldByDomain.cc (+2), ToPointCloud.cc (+2), TransformField.cc (+2), Unstructure.cc (+1 -3)
  • Core/Algorithms/Regression: CompareFields.cc (+1 -1), CompareFields.h (new), RegressionAlgo.cc (+250), RegressionAlgo.h (+7 -1), sub.mk (+2 -1)
  • Core/Algorithms/Util: FieldInformation.cc (+110), FieldInformation.h (new)
  • Core/Datatypes: CurveMesh.h (new), HexVolMesh.h (+268 -96), PropertyManager.h (new), QuadSurfMesh.h (+99 -16)
  • Core/Geometry: Tensor.cc (new)
  • Core/Persistent: Pstreams.cc (+2)
  • Core/Util: DynamicLoader.cc (new), RegressionReporter.cc (+2)
  • Packages/MatlabInterface/Core/Datatypes: matfiledefs.h (new)
  • Packages/ModelCreation/Core/Algorithms: ArrayEngine.cc (+17 -15), ArrayEngine.h (new), TVMMath.h (+1 -1)
  • Packages/ModelCreation/Dataflow/Modules/FieldsData: CreateFieldData.cc (new)
  • StandAlone: sub.mk (new)
  • StandAlone/regression: TEST_FieldsAlgo.cc (+445), sub.mk (+52)
jeroen 2006-05-31 21:48 Rev.: 34371

Fix a stupid problem in get_faces, the orginal function querried an inverse face, however this was corrected with the overhead in the face_table_, with this removed this became a problem, but is fixed now

4 lines of code changed in 1 file:

  • Core/Datatypes: HexVolMesh.h (+4 -4)
jeroen 2006-05-29 21:23 Rev.: 34352

Adding preparations for Regression testing: added comaprison functions for dataflow objects. Modified Dynamic compilation so it has an option to compile load and destroy the library, to prevent the on-the-fly-lib directory to grow out of control when testing whether dynamically compilled algorithms work. Fixed HexVolMesh to deal with degenerate meshes and started to better optimize this mesh to use less memory (still need to finish this as table sizes can be shrunk even more). Added a RegressionReporter to store all the information during regression testing. Fixed the Finite Element Code to deal with degenerate elements (Comparison with Tetsn and Prisms show that Hexahedral elements with degenerate nodes can act as tetrahedrals or prisms and still generate the proper stiffness matrix). Fixed the visualization so degenerate elements show upm properly (fixed the order of the faces of these degenerate elements so the three unique element nodes are always returned first when quering a face). Still need to upgrade the quadsurfmesh to also support degenerate elements. Field boundary now also supports degenerate elements as the number of faces returned per element can now vary with the actual number of faces. Next to do: generate degenerate meshes with tets, piramids, prisms and hexahedral and test which algorithms fail and fix those.

1552 lines of code changed in 35 files:

  • Core/Algorithms: sub.mk (new)
  • Core/Algorithms/Converter: ConverterAlgo.cc (new), ConverterAlgo.h (new)
  • Core/Algorithms/Fields: ApplyMappingMatrix.cc (new), FieldBoundary.cc (+2), Unstructure.cc (+4)
  • Core/Algorithms/Math: BuildFEMatrix.h (+23 -8)
  • Core/Algorithms/Regression: CompareFields.cc (+90), CompareFields.h (+219), RegressionAlgo.cc (+587), RegressionAlgo.h (+63), share.h (new 11), sub.mk (+48)
  • Core/Algorithms/Util: AlgoLibrary.h (+1), DynamicAlgo.h (+1), FieldInformation.cc (+10), FieldInformation.h (+4)
  • Core/Bundle: Bundle.h (+1 -1)
  • Core/Datatypes: HexVolMesh.h (+262 -94)
  • Core/Util: DynamicCompilation.h (+10), DynamicLoader.cc (+8 -1), DynamicLoader.h (new), RegressionReporter.cc (+115), RegressionReporter.h (+70), sub.mk (+2 -1)
jeroen 2006-05-18 21:34 Rev.: 34285

Fix the MatlabBundlesWriter so we have an option to write a strutured matrix or a numeric matrix. Fixed the StreamMatrix function to use weights for row vectors and added a few sanity checks in the function.

68 lines of code changed in 9 files:

  • Dataflow/GUI: Module.tcl (+1 -1)
  • Packages/MatlabInterface/Dataflow/GUI: MatlabBundlesWriter.tcl (+6 -6)
  • Packages/MatlabInterface/Dataflow/Modules/DataIO: MatlabBundlesWriter.cc (+13 -1)
  • Packages/ModelCreation/Core/DataStreaming: StreamMatrix.cc (new)
  • Packages/ModelCreation/Dataflow/Modules/DataStreaming: StreamMatrix.cc (new)
jeroen 2006-05-18 15:06 Rev.: 34281

Adding functionality to stream time adaptive signals. TimeToWeights takes in a vector with times and creates the weights of the nearest timeframes and does a linear interpolation. This module serves as input for StreamMatrix which has a port with weights that describe how multiple columns or rows need to be combined into one. Note: the weights here are not compatible yet with MatrixSelectVector, that module uses a custom system to do a sparse matrix. StreamMatrix and TimeToWeights use the default sparse matrix to define weights.

653 lines of code changed in 11 files:

  • Packages/ModelCreation/Dataflow/GUI: TimeToWeights.tcl (new 188), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules: sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/Converter: MatrixToField.cc (-2)
  • Packages/ModelCreation/Dataflow/Modules/DataStreaming: StreamMatrix.cc (+3 -3)
  • Packages/ModelCreation/Dataflow/Modules/Time: TimeToWeights.cc (new 391), sub.mk (new 28)
  • Packages/ModelCreation/Dataflow/XML: TimeToWeights.xml (new 41)
jeroen 2006-05-15 11:34 Rev.: 34229

Adding a different stimulus model

1073 lines of code changed in 27 files:

  • Packages/CardioWave/Core/Model: ModelAlgo.cc (changed), sub.mk (changed)
  • Packages/CardioWave/Dataflow/GUI: CBDAddBlockStimulus.tcl (del), CBDAddStimulus.tcl (new 120), DMDAddBlockStimulus.tcl (del), DMDAddStimulus.tcl (new 69), DMDAddStimulusSeries.tcl (new 75), sub.mk (changed), tclIndex (new)
  • Packages/CardioWave/Dataflow/Modules/ContinuousBiDomain: CBDAddBlockStimulus.cc (del), CBDAddStimulus.cc (new 216), sub.mk (changed)
  • Packages/CardioWave/Dataflow/Modules/DiscreteMultiDomain: DMDAddBlockStimulus.cc (del), DMDAddStimulus.cc (new 215), DMDAddStimulusSeries.cc (new 221), sub.mk (new)
  • Packages/CardioWave/Dataflow/XML: CBDAddBlockStimulus.xml (del), CBDAddStimulus.xml (new 51), DMDAddBlockStimulus.xml (del), DMDAddStimulus.xml (new 51), DMDAddStimulusSeries.xml (new 55)
jeroen 2006-05-15 11:25 Rev.: 34227

Adding a plugin to matrix reader that reads Nrrd compatible files directly as matrices. This way the model creation effeort will not depend on anything in the Teem Package

170 lines of code changed in 5 files:

  • Packages/ModelCreation/Core/Datatypes: NrrdToMatrix_Plugin.cc (new 170), Startup.cc (new), sub.mk (new)
jeroen 2006-05-13 01:48 Rev.: 34223

updates

0 lines of code changed in 6 files:

  • Packages/ModelCreation/Dataflow/GUI: DomainBoundary.tcl (new), FieldInfo.tcl (new)
  • Packages/ModelCreation/Dataflow/Modules/FieldsCreate: DomainBoundary.cc (changed)
jeroen 2006-05-13 01:47 Rev.: 34222

Updates to algorithms

352 lines of code changed in 10 files:

  • Core/Algorithms/Fields: ConvertToTriSurf.h (+26 -19), DomainBoundary.cc (+79), DomainBoundary.h (+216 -3), FieldsAlgo.cc (+11 -4), FieldsAlgo.h (+1 -1), SplitByConnectedRegion.h (new), Unstructure.h (+5 -18)
jeroen 2006-05-08 17:08 Rev.: 34169

Merge my algorithms from the ModelCreation package to Core/Algorithms so they are available for everyone. I added four directories to Core/Algorithms: Math for mathematical operations (mirrors Math in module tree), this currently has the FE code, Fields: my version of the field algorithms, these contain new ones and old ones with bug fixes to get my CardioWave stuff to work, Converter: Converter algorithms a series of converters to deal with conversion between Matrices, Nrrds and Fields, DataIO: gui less version for writing and reading in SCIRun files using PersistentIO or the Plug-ins. All the algorithms are grouped into libraries with one main header file: Algorithms/Math/MathAlgo.h Algorithms/Fields/FieldsAlgo.h Algorithms/DataIO/DataIOAlgo.h Algorithms/Converter/ConverterAlgo.h. Each library needs to be initialised with the ProgressReporter after which all the dynamic compilation is hidden from the user. I put all the algorithms in a separate namespace call SCIRunAlgo to avoid possible conflicts between class names. Similarly all the dynamic files will start with the word ALGO, to avoid duplication of filenames created by the current set of modules. --Jeroen

13371 lines of code changed in 308 files:

  • Core/Algorithms: sub.mk (+1)
  • Core/Algorithms/Converter: ConverterAlgo.cc (+314), ConverterAlgo.h (+83), MatricesToDipoleField.cc (+117), MatricesToDipoleField.h (new 48), MatrixToField.cc (new 97), MatrixToField.h (+48), NrrdToField.cc (+236), NrrdToField.h (new 48), share.h (new 11), sub.mk (new 28)
  • Core/Algorithms/DataIO: DataIOAlgo.cc (+579), DataIOAlgo.h (+87), sub.mk (+13 -6)
  • Core/Algorithms/Fields: ApplyMappingMatrix.cc (+93), ApplyMappingMatrix.h (new 172), ClearAndChangeFieldBasis.cc (+92), ClearAndChangeFieldBasis.h (new 142), ClipBySelectionMask.cc (+81), ClipBySelectionMask.h (new 287), ConvertToTetVol.cc (+101), ConvertToTetVol.h (+459), ConvertToTriSurf.cc (+103), ConvertToTriSurf.h (+385), DistanceField.cc (+356), DistanceField.h (new 748), DomainBoundary.cc (+111), DomainBoundary.h (+286), FieldBoundary.cc (+109), FieldBoundary.h (+224), FieldCount.cc (del), FieldCount.h (del), FieldDataElemToNode.cc (+95), FieldDataElemToNode.h (new 209), FieldDataNodeToElem.cc (+94), FieldDataNodeToElem.h (new 217), FieldsAlgo.cc (+345 -2), FieldsAlgo.h (+200 -13), GatherFields.cc (+160), GatherFields.h (+190), GetFieldData.cc (+71), GetFieldData.h (new 341), GetFieldDataMinMax.cc (+73), GetFieldDataMinMax.h (+127), GetFieldInfo.cc (+70), GetFieldInfo.h (new 74), IsInsideField.cc (+88), IsInsideField.h (new 153), LinkFieldBoundary.cc (new 83), LinkFieldBoundary.h (new 611), LinkToCompGrid.cc (+136), LinkToCompGrid.h (new 47), LinkToCompGridByDomain.cc (+88), LinkToCompGridByDomain.h (new 193), MappingMatrixToField.cc (+87), MappingMatrixToField.h (new 147), MergeFields.cc (+168), MergeFields.h (new 392), ScaleField.cc (+78), ScaleField.h (new 117), SetFieldData.cc (+120), SetFieldData.h (new 765), SplitByConnectedRegion.cc (+92), SplitByConnectedRegion.h (+248), SplitFieldByDomain.cc (+88), SplitFieldByDomain.h (new 203), ToPointCloud.cc (+11 -9), ToPointCloud.h (new), TransformField.cc (+118), TransformField.h (new 363), Unstructure.cc (+100), Unstructure.h (+186), sub.mk (new)
  • Core/Algorithms/Math: BuildFEMatrix.cc (+5 -2), BuildFEMatrix.h (+3 -1), MathAlgo.cc (+3 -2), MathAlgo.h (new)
  • Dataflow/Modules/Fields: FieldInfo.cc (+13 -13), TransformData2.cc (+7 -15), TransformData3.cc (+8 -17)
  • Dataflow/Modules/Visualization: ShowField.cc (+7 -15)
  • Packages/BioPSE/Dataflow/Modules/LeadField: BuildElemLeadField.cc (+4 -6)
  • Packages/CardiacVis/Core/Algorithms/Fields: TriSurfPhaseFilter.cc (new)
  • Packages/CardiacVis/Dataflow/Modules/FieldsCreate: TracePoints.cc (+2 -2), sub.mk (+1 -1)
  • Packages/CardioWave/Core/Model: ModelAlgo.cc (+38 -11), ModelAlgo.h (+1 -2), sub.mk (+3 -3)
  • Packages/CardioWave/Dataflow/Modules/ContinuousBiDomain: CBDAddBlockStimulus.cc (new 2), CBDAddMembrane.cc (new), CBDAddReference.cc (new), CBDCreateSimulation.cc (new), sub.mk (+3 -3)
  • Packages/CardioWave/Dataflow/Modules/DiscreteMultiDomain: DMDAddBlockStimulus.cc (new 136), DMDAddMembrane.cc (+4 -4), DMDAddReference.cc (new), DMDConductionVelocity.cc (new), DMDCreateSimulation.cc (-1), sub.mk (+3 -3)
  • Packages/CardioWave/Dataflow/Modules/Model: BuildStimulusTable.cc (new), BuildStimulusTableByElement.cc (+2 -2), sub.mk (+1 -1)
  • Packages/ModelCreation/Core: sub.mk (-2)
  • Packages/ModelCreation/Core/Algorithms: ArrayObjectFieldAlgo.cc (+62 -1), ArrayObjectFieldAlgo.h (new)
  • Packages/ModelCreation/Core/Converter: ConverterAlgo.cc (del), ConverterAlgo.h (del), MatricesToDipoleField.cc (del), MatricesToDipoleField.h (del), MatrixToField.cc (del), MatrixToField.h (del), NrrdToField.cc (del), NrrdToField.h (del), sub.mk (del)
  • Packages/ModelCreation/Core/DataIO: DataIOAlgo.cc (del), DataIOAlgo.h (del), sub.mk (del)
  • Packages/ModelCreation/Core/Datatypes: Startup.cc (-4), sub.mk (+2 -2)
  • Packages/ModelCreation/Core/Fields: ApplyMappingMatrix.cc (del), ApplyMappingMatrix.h (del), ClearAndChangeFieldBasis.cc (del), ClearAndChangeFieldBasis.h (del), ClipBySelectionMask.cc (del), ClipBySelectionMask.h (del), ConvertToTetVol.cc (del), ConvertToTetVol.h (del), ConvertToTriSurf.cc (del), ConvertToTriSurf.h (del), DistanceField.cc (del), DistanceField.h (del), DistanceToField.cc (del), DistanceToField.h (del), DomainBoundary.cc (del), DomainBoundary.h (del), ExampleFields.cc (new), ExampleFields.h (-4), FieldBoundary.cc (del), FieldBoundary.h (del), FieldDataElemToNode.cc (del), FieldDataElemToNode.h (del), FieldDataNodeToElem.cc (del), FieldDataNodeToElem.h (del), FieldsAlgo.cc (del), FieldsAlgo.h (del), GetFieldData.cc (del), GetFieldData.h (del), GetFieldInfo.cc (del), GetFieldInfo.h (del), IsInsideField.cc (del), IsInsideField.h (del), LinkFieldBoundary.cc (del), LinkFieldBoundary.h (del), LinkToCompGridByDomain.cc (del), LinkToCompGridByDomain.h (del), MappingMatrixToField.cc (del), MappingMatrixToField.h (del), MergeFields.cc (del), MergeFields.h (del), Precompile.cc (del), Precompile.h (del), ScaleField.cc (del), ScaleField.h (del), SetFieldData.cc (del), SetFieldData.h (del), SplitByConnectedRegion.cc (del), SplitByConnectedRegion.h (del), SplitFieldByDomain.cc (del), SplitFieldByDomain.h (del), ToPointCloud.cc (del), ToPointCloud.h (del), TransformField.cc (del), TransformField.h (del), Unstructure.cc (del), Unstructure.h (del), sub.mk (new)
  • Packages/ModelCreation/Core/Numeric: BuildFEMatrix.cc (del), BuildFEMatrix.h (del), LinearTetFEM.cc (del), LinearTetFEM.h (del), NumericAlgo.cc (del), NumericAlgo.h (del), sub.mk (del)
  • Packages/ModelCreation/Core/Util: AlgoLibrary.h (del), AlgoList.h (del), DynamicAlgo.h (del), FieldInformation.cc (del), FieldInformation.h (del), sub.mk (del)
  • Packages/ModelCreation/Dataflow/GUI: CollectFields.tcl (new 33), SetFieldData.tcl (new 29), sub.mk (+2)
  • Packages/ModelCreation/Dataflow/Modules/Converter: MatricesToDipoleField.cc (+2 -2), MatrixToField.cc (+7 -19), NrrdToField.cc (+6 -23), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/DataInfo: FieldInfo.cc (new)
  • Packages/ModelCreation/Dataflow/Modules/FieldsCreate: ClipFieldByFunction.cc (+3 -9), ClipFieldBySelectionMask.cc (new), CollectFields.cc (new 130), DomainBoundary.cc (+2 -2), MergeFields.cc (+2 -2), SplitFieldByConnectedRegion.cc (+2 -2), SplitFieldByDomain.cc (+3 -4), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/FieldsData: DistanceToBoundary.cc (new), DistanceToField.cc (new), FieldDataElemToNode.cc (+8 -54), FieldDataNodeToElem.cc (new), GetFieldData.cc (new 68), IsInsideField.cc (new), MappingMatrixToField.cc (new), SetFieldData.cc (new 74), SignedDistanceToField.cc (+2 -3), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/FieldsExample: SphericalSurface.cc (+4 -4), sub.mk (+3 -2)
  • Packages/ModelCreation/Dataflow/Modules/FieldsGeometry: ComputeFieldNodes.cc (new), ComputeFieldsNodes.cc (+2 -2), ConvertToPointCloud.cc (+7 -19), ConvertToTetVol.cc (+6 -19), ConvertToTriSurf.cc (+7 -19), LinkFieldBoundary.cc (new), MergeNodes.cc (new), ScaleField.cc (new), Unstructure.cc (+7 -20), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/FiniteElements: BuildFEMatrix.cc (+1 -1), LinkToCompGrid.cc (+2 -2), LinkToCompGridByDomain.cc (new), sub.mk (new)
  • Packages/ModelCreation/Dataflow/Modules/Math: ApplyColumnOperation.cc (new), ApplyRowOperation.cc (+1 -1), CuthillMcKee.cc (+1 -1), ResizeMatrix.cc (new), ReverseCuthillMcKee.cc (new), sub.mk (new)
  • Packages/ModelCreation/Dataflow/XML: CollectFields.xml (new 35), FieldDataElemToNode.xml (-4), FieldDataNodeToElem.xml (-4), GetFieldData.xml (new 29), SetFieldData.xml (new 35)
jeroen 2006-05-08 14:42 Rev.: 34163

Fix the compilation of RenderField.h for the MaskedLatVolMesh. I still need to fix the algorithm to do the topology for the mesh, but it will now use the old renderer again for this mesh.

23 lines of code changed in 3 files:

  • Core/Algorithms/Visualization: RenderField.h (+16)
  • Core/Datatypes: MaskedLatVolMesh.h (new)
jeroen 2006-05-07 16:47 Rev.: 34150

Added a mode to display the data contained in the cells of volumetric meshes using two-sided triangles and quadrilaterals. For shared faces each side is given the color representing the data in the cell, for outward facing faces they are colored on both sides with the color, the one of the cell they are bordering. This way one can use the clipping planes to check segmentations of unstructured mesh, without the need of doing a full volume rendering.

122 lines of code changed in 1 file:

  • Core/Algorithms/Visualization: RenderField.h (+122 -10)
jeroen 2006-05-07 16:43 Rev.: 34149

Adding new Geometry objects to deal with faces that are colored different in the front and the back. The current implementation uses culling to first draw the front of all the faces in the object and then draw the back of the objects. This way in between we can switch dataset and color both faces differently. This functionality is intended to display data located at cells. As each part of the face is part of a different cell they get colored differently.

863 lines of code changed in 9 files:

  • Core/Geom: GeomOpenGL.cc (+284), GeomQuads.cc (new), GeomQuads.h (new), GeomTriangles.cc (new), GeomTriangles.h (+47)
jeroen 2006-05-07 16:39 Rev.: 34148

Fix a bug: Standalone uses integers that are not typed Node::index_type, which is causing problems when I added additional functionality to get_elems().

0 lines of code changed in 2 files:

  • StandAlone/utils: RemoveConnectedFaces.cc (new)
jeroen 2006-05-07 16:37 Rev.: 34147

Adding functions to find element indices based on the Edge of Face index. This functionality is needed for volumetric meshes to find the colors that are assigned in the renderer to faces when assuming constant data on the elements. Fixed or added these functions to all mesh classes (still need to complete TriSurfmesh and QuadSurfMesh).

257 lines of code changed in 14 files:

  • Core/Datatypes: CurveMesh.h (+5), HexVolMesh.h (+37 -1), ImageMesh.h (+33), LatVolMesh.h (new), PointCloudMesh.h (+5), PrismVolMesh.h (+9), QuadSurfMesh.h (+7), ScanlineMesh.h (+4), TetVolMesh.h (+35 -3), TriSurfMesh.h (+5)
jeroen 2006-05-05 19:21 Rev.: 34143

Fixes to do deal with changes in Core

4 lines of code changed in 2 files:

  • Packages/CardioWave/Core/Model: ModelAlgo.cc (+3 -3), sub.mk (+1 -1)
jeroen 2006-05-05 19:20 Rev.: 34142

Add a new package to help with the needs of Alexey Zaitsev, a collaborator at CVRTI. These tools include reconstructions and visualizations of phase of the cardiac cycle as a function of time

1347 lines of code changed in 20 files:

  • Packages/CardiacVis: sub.mk (new 10)
  • Packages/CardiacVis/Core: sub.mk (new 16)
  • Packages/CardiacVis/Core/Algorithms: sub.mk (new 15)
  • Packages/CardiacVis/Core/Algorithms/Fields: FieldsAlgo.cc (new 52), FieldsAlgo.h (new 54), TracePoints.cc (new 86), TracePoints.h (new 184), TriSurfPhaseFilter.cc (+100), TriSurfPhaseFilter.h (new 402), sub.mk (new 29)
  • Packages/CardiacVis/Core/Datatypes: sub.mk (new 26)
  • Packages/CardiacVis/Dataflow: sub.mk (new 16)
  • Packages/CardiacVis/Dataflow/GUI: TracePoints.tcl (new 26), sub.mk (new 23)
  • Packages/CardiacVis/Dataflow/Modules: sub.mk (new 19)
  • Packages/CardiacVis/Dataflow/Modules/FieldsCreate: TracePoints.cc (+100), TriSurfPhaseFilter.cc (new 82), sub.mk (+32)
  • Packages/CardiacVis/Dataflow/XML: TracePoints.xml (new 35), TriSurfPhaseFilter.xml (new 40)
jeroen 2006-05-05 19:18 Rev.: 34141

Updates to fix the changes I made in Core/Algorithms. Renamed a couple of modules to better represent the functionality. Remove Cardiac Visualization tools developed for CVRTI.

3888 lines of code changed in 107 files:

  • Packages/ModelCreation/Core: sub.mk (+1 -1)
  • Packages/ModelCreation/Core/Converter: ConverterAlgo.cc (+16 -67), ConverterAlgo.h (+3), MatricesToDipoleField.cc (new 116), MatricesToDipoleField.h (new 47), MatrixToField.cc (new 97), MatrixToField.h (new 47), NrrdToField.cc (new 235), NrrdToField.h (new 47), sub.mk (+4 -1)
  • Packages/ModelCreation/Core/DataIO: DataIOAlgo.cc (+217 -5), DataIOAlgo.h (new), sub.mk (new)
  • Packages/ModelCreation/Core/DataStreaming: StreamDataMatrix.h (del), StreamMatrix.cc (+627 -188), StreamMatrix.h (+9 -10), sub.mk (new 26)
  • Packages/ModelCreation/Core/Datatypes: TimeDataFile.cc (del), TimeDataFile.h (del)
  • Packages/ModelCreation/Core/Fields: ApplyMappingMatrix.cc (new 1), ApplyMappingMatrix.h (new), BuildMembraneTable.cc (del), BuildMembraneTable.h (del), ClearAndChangeFieldBasis.cc (new 1), ClipBySelectionMask.cc (new 39), ClipBySelectionMask.h (new 31), CompartmentBoundary.cc (del), CompartmentBoundary.h (del), ConvertToTetVol.cc (new 1), ConvertToTriSurf.cc (new 1), DistanceField.cc (new 3), DistanceToField.cc (new 1), DomainBoundary.cc (new 114), DomainBoundary.h (new 286), FieldBoundary.cc (new 25), FieldDataElemToNode.cc (new 45), FieldDataElemToNode.h (new 285), FieldDataNodeToElem.cc (new 48), FieldDataNodeToElem.h (new 235), FieldsAlgo.cc (new 210), FieldsAlgo.h (new 8), GetFieldData.cc (new 24), GetFieldData.h (new 25), IsInsideField.cc (new 1), LinkFieldBoundary.cc (new 106), LinkToCompGridByDomain.cc (new 1), MappingMatrixToField.cc (new 19), MergeFields.cc (new 12), NrrdToField.h (del), ScaleField.cc (new 1), SetFieldData.cc (new 30), SetFieldData.h (new 40), SplitByConnectedRegion.cc (new 1), SplitFieldByElementData.cc (del), SplitFieldByElementData.h (del), ToPointCloud.cc (new 15), TracePoints.cc (del), TracePoints.h (del), TransformField.cc (new 2), TriSurfPhaseFilter.cc (del), TriSurfPhaseFilter.h (del), Unstructure.cc (new 3), sub.mk (+1 -4)
  • Packages/ModelCreation/Dataflow/GUI: StreamMatrix.tcl (+346 -3)
  • Packages/ModelCreation/Dataflow/Modules/Converter: MatrixToField.cc (+2 -2), NrrdToField.cc (+2 -2)
  • Packages/ModelCreation/Dataflow/Modules/DataStreaming: StreamMatrix.cc (+338 -16), sub.mk (+3 -1)
  • Packages/ModelCreation/Dataflow/Modules/FieldsCreate: DomainBoundary.cc (+1 -1)
  • Packages/ModelCreation/Dataflow/Modules/FieldsData: TriSurfPhaseFilter.cc (del), sub.mk (-1)
  • Packages/ModelCreation/Dataflow/Modules/FiniteElements: BuildFEMatrix.cc (+2 -2), sub.mk (+1 -1)
  • Packages/ModelCreation/Dataflow/Modules/Math: ApplyColumnOperation.cc (+2 -2), ApplyRowOperation.cc (+2 -2), CuthillMcKee.cc (+2 -2), ResizeMatrix.cc (+2 -2), ReverseCuthillMcKee.cc (+2 -2), sub.mk (+1 -1)
  • Packages/ModelCreation/Dataflow/XML: ColorMap2Writer.xml (new), ColorMapWriter.xml (+6), FieldWriter.xml (new), MatrixWriter.xml (+6), PathWriter.xml (new), SplitFieldByConnectedRegion.xml (new), SplitFieldByDomain.xml (+4 -3), StringWriter.xml (+9 -2), TriSurfPhaseFilter.xml (del), Unstructure.xml (new)

(82 more)

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