# Merge seems to overwrite unstaged local changes 6 messages from 2011-09-28 to 2012-01-10. Participants: Sebastian Schuberth, Junio C Hamano, Jakub Narebski, Chris Hatton. Thread: https://gitlist.dev/t/28518 ## Sebastian Schuberth, 2011-09-28 14:08 Subject: Merge seems to overwrite unstaged local changes Message-ID: URL: https://gitlist.dev/e/j5v9r7%24fi1%241%40dough.gmane.org ``` Hi, although it is good practice to have a clean working tree before pulling / merging, my understanding of "In particular, the local modifications you had before you started merge will stay the same and the index entries for them stay as they were, i.e. matching HEAD." from [1] is that my local unstaged changes to a file known to Git should not get lost during a merge (especially if there a no conflicts in the file that's modified locally). It seems I can reproduce a case where this is not true. Here's what I do: # Checkout a branch $ git co -b marianne 45e0d23bf1a6bf62e3317a691385e0f1a7b279ea $ git status # On branch marianne nothing to commit (working directory clean) $ git log --oneline hxprofile1d/HxComputeProfileAlongAxis.cpp 45e0d23 hxprofile1d: [Fix] errors according to move of files 3509d94 hxprofile1d: moved files from package hxneuralnetwork to hxprofile1d # Add some stuff to the end of the existing file. $ vim hxprofile1d/HxComputeProfileAlongAxis.cpp $ git status # On branch marianne # Changes not staged for commit: # (use "git add ..." to update what will be committed) # (use "git checkout -- ..." to discard changes in working directory) # # modified: hxprofile1d/HxComputeProfileAlongAxis.cpp # no changes added to commit (use "git add" and/or "git commit -a") $ git merge 569e443faf5ae773af1c8eedfefa41ebfd066171 Removing cgal/BuildCGAL.sh Auto-merging hxcortexinsilico/QxCorticalColumnTool.cpp Auto-merging hxcortexinsilico/QxCorticalColumnTool.h Removing hxneuralnetwork/QxAddFilesDialog.cpp Removing hxneuralnetwork/QxAddFilesDialog.h Removing hxneuralnetwork/QxAddFilesDialogUI.ui Auto-merging hxneuralnetwork/SelectionPredicateCellTypeIsTest.cpp Removing hxneuralnetwork/SelectionPredicateHasCellTypeName.cpp Removing hxneuralnetwork/SelectionPredicateHasCellTypeName.h Removing hxneuralnetwork/SelectionPredicateHasCellTypeNameTest.h Auto-merging hxneuralnetwork/share/resources/hxneuralnetwork.rc Auto-merging hxneuralnetwork/share/resources/test_hxneuralnetwork.rc Auto-merging hxneuronkernels/HxLandmarksInSurface.h Auto-merging hxneuronkernels/MeasurementFunctions.h Merge made by recursive. cgal/BuildCGAL.sh | 153 ---- cgal/BuildCGALforLinux.sh | 94 ++ cgal/Package | 11 +- hx2d3drecon/Reg2d3dFunctionalEdgeNormal.cpp | 5 +- .../ConnectEndNodesToSomaOperationSet.cpp | 0 .../ConnectEndNodesToSomaOperationSet.h | 0 hxcortexinsilico/Package | 27 + .../QxCorticalColumnTool.cpp | 5 +- .../QxCorticalColumnTool.h | 10 +- .../QxCorticalColumnTool.ui | 0 hxcortexinsilico/hxcortexinsilicoAPI.h | 14 + .../share/png/CorticalColumnTool.png | Bin 326 -> 326 bytes .../share/resources/hxcortexinsilico.rc | 9 + hxcrosscorrelation/CCR.cpp | 415 +++++++++ hxcrosscorrelation/CCR.h | 111 +++ hxcrosscorrelation/CCR_hollowCylinder.cpp | 209 +++++ hxcrosscorrelation/CCR_hollowCylinder.h | 80 ++ hxcrosscorrelation/CCR_hollowSphere.cpp | 164 ++++ hxcrosscorrelation/CCR_hollowSphere.h | 69 ++ hxcrosscorrelation/CCR_plane.cpp | 196 ++++ hxcrosscorrelation/CCR_plane.h | 77 ++ hxcrosscorrelation/CCR_rotation.cpp | 131 +++ hxcrosscorrelation/CCR_rotation.h | 64 ++ hxcrosscorrelation/CCR_scale.cpp | 59 ++ hxcrosscorrelation/CCR_scale.h | 55 ++ hxcrosscorrelation/CCR_solidCylinder.cpp | 197 ++++ hxcrosscorrelation/CCR_solidCylinder.h | 76 ++ hxcrosscorrelation/CCR_solidSphere.cpp | 153 ++++ hxcrosscorrelation/CCR_solidSphere.h | 66 ++ hxcrosscorrelation/CrossCorrelation.cpp | 442 +++++++++ hxcrosscorrelation/CrossCorrelation.h | 103 +++ hxcrosscorrelation/CrossCorrelation_cuda.cu | 208 +++++ hxcrosscorrelation/DataSplitter.cpp | 339 +++++++ hxcrosscorrelation/DataSplitter.h | 85 ++ hxcrosscorrelation/HxCCRShow.cpp | 79 ++ hxcrosscorrelation/HxCCRShow.h | 50 + hxcrosscorrelation/HxCrossCorrelation.cpp | 316 +++++++ hxcrosscorrelation/HxCrossCorrelation.h | 81 ++ hxcrosscorrelation/HxDataToSpreadsheet.cpp | 100 ++ hxcrosscorrelation/HxDataToSpreadsheet.h | 58 ++ hxcrosscorrelation/HxHollowCylinderToCCR.cpp | 199 ++++ hxcrosscorrelation/HxHollowCylinderToCCR.h | 61 ++ hxcrosscorrelation/HxHollowSphereToCCR.cpp | 148 +++ hxcrosscorrelation/HxHollowSphereToCCR.h | 59 ++ hxcrosscorrelation/HxPlaneToCCR.cpp | 166 ++++ hxcrosscorrelation/HxPlaneToCCR.h | 60 ++ .../HxReferenceIndicesToData_scalar.cpp | 84 ++ .../HxReferenceIndicesToData_scalar.h | 49 + .../HxReferenceIndicesToData_vector.cpp | 88 ++ .../HxReferenceIndicesToData_vector.h | 50 + hxcrosscorrelation/HxSolidCylinderToCCR.cpp | 194 ++++ hxcrosscorrelation/HxSolidCylinderToCCR.h | 61 ++ hxcrosscorrelation/HxSolidSphereToCCR.cpp | 143 +++ hxcrosscorrelation/HxSolidSphereToCCR.h | 59 ++ hxcrosscorrelation/Package | 7 + hxcrosscorrelation/doc/HxCCRShow.doc | 29 + .../doc/HxCCRShow_selectReference.png | Bin 0 -> 2071 bytes hxcrosscorrelation/doc/HxCrossCorrelation.doc | 65 ++ .../doc/HxCrossCorrelation_GPUDevice.png | Bin 0 -> 2327 bytes .../doc/HxCrossCorrelation_GPUMemory.png | Bin 0 -> 1956 bytes .../doc/HxCrossCorrelation_blockSize.png | Bin 0 -> 2012 bytes .../doc/HxCrossCorrelation_nrBlocks.png | Bin 0 -> 2149 bytes .../doc/HxCrossCorrelation_timerThreshold.png | Bin 0 -> 1404 bytes hxcrosscorrelation/doc/HxDataToSpreadSheet.doc | 30 + .../doc/HxDataToSpreadSheet_threshold.png | Bin 0 -> 1296 bytes hxcrosscorrelation/doc/HxHollowCylinderToCCR.doc | 123 +++ .../HxHollowCylinderToCCR_cylinderParameter.png | Bin 0 -> 4826 bytes .../doc/HxHollowCylinderToCCR_defineForeground.png | Bin 0 -> 4561 bytes .../doc/HxHollowCylinderToCCR_defineForground.png | Bin 0 -> 1918 bytes .../doc/HxHollowCylinderToCCR_increment.png | Bin 0 -> 2800 bytes .../doc/HxHollowCylinderToCCR_maskParameter.png | Bin 0 -> 4708 bytes .../doc/HxHollowCylinderToCCR_options.png | Bin 0 -> 4923 bytes .../doc/HxHollowCylinderToCCR_psiRange.png | Bin 0 -> 3649 bytes .../doc/HxHollowCylinderToCCR_smoothing.png | Bin 0 -> 2483 bytes .../doc/HxHollowCylinderToCCR_thetaRange.png | Bin 0 -> 3660 bytes .../doc/HxHollowCylinderToCCR_tiltAngles.png | Bin 0 -> 3577 bytes .../doc/HxHollowCylinderToCCR_tiltAxis.png | Bin 0 -> 2909 bytes .../doc/HxHollowCylinderToCCR_tiltType.png | Bin 0 -> 3667 bytes .../doc/HxHollowCylinderToCCR_voxelSize.png | Bin 0 -> 3218 bytes hxcrosscorrelation/doc/HxHollowSphereToCCR.doc | 94 ++ .../doc/HxHollowSphereToCCR_defineForground.png | Bin 0 -> 1918 bytes .../doc/HxHollowSphereToCCR_increment.png | Bin 0 -> 1406 bytes .../doc/HxHollowSphereToCCR_options.png | Bin 0 -> 2335 bytes .../doc/HxHollowSphereToCCR_scaleRange.png | Bin 0 -> 1773 bytes .../doc/HxHollowSphereToCCR_smoothing.png | Bin 0 -> 1255 bytes .../doc/HxHollowSphereToCCR_sphereParameter.png | Bin 0 -> 1977 bytes .../doc/HxHollowSphereToCCR_tiltAngles.png | Bin 0 -> 1810 bytes .../doc/HxHollowSphereToCCR_tiltAxis.png | Bin 0 -> 1831 bytes .../doc/HxHollowSphereToCCR_tiltType.png | Bin 0 -> 2018 bytes .../doc/HxHollowSphereToCCR_voxelSize.png | Bin 0 -> 1331 bytes hxcrosscorrelation/doc/HxPlaneToCCR.doc | 105 +++ .../doc/HxPlaneToCCR_defineForground.png | Bin 0 -> 1918 bytes hxcrosscorrelation/doc/HxPlaneToCCR_increment.png | Bin 0 -> 1406 bytes hxcrosscorrelation/doc/HxPlaneToCCR_options.png | Bin 0 -> 2335 bytes .../doc/HxPlaneToCCR_planeParameter.png | Bin 0 -> 2574 bytes hxcrosscorrelation/doc/HxPlaneToCCR_psiRange.png | Bin 0 -> 1728 bytes .../doc/HxPlaneToCCR_subdivision.png | Bin 0 -> 1255 bytes hxcrosscorrelation/doc/HxPlaneToCCR_thetaRange.png | Bin 0 -> 1748 bytes hxcrosscorrelation/doc/HxPlaneToCCR_tiltAngles.png | Bin 0 -> 1810 bytes hxcrosscorrelation/doc/HxPlaneToCCR_tiltAxis.png | Bin 0 -> 1831 bytes hxcrosscorrelation/doc/HxPlaneToCCR_tiltType.png | Bin 0 -> 2018 bytes hxcrosscorrelation/doc/HxPlaneToCCR_voxelSize.png | Bin 0 -> 1331 bytes .../doc/HxReferenceIndicesToData_scalar.doc | 27 + .../doc/HxReferenceIndicesToData_vector.doc | 28 + hxcrosscorrelation/doc/HxSolidCylinderToCCR.doc | 121 +++ .../doc/HxSolidCylinderToCCR_cylinderParameter.png | Bin 0 -> 4867 bytes .../doc/HxSolidCylinderToCCR_defineForeground.png | Bin 0 -> 4561 bytes .../doc/HxSolidCylinderToCCR_defineForground.png | Bin 0 -> 1918 bytes .../doc/HxSolidCylinderToCCR_increment.png | Bin 0 -> 2800 bytes .../doc/HxSolidCylinderToCCR_maskParameter.png | Bin 0 -> 4769 bytes .../doc/HxSolidCylinderToCCR_options.png | Bin 0 -> 4923 bytes .../doc/HxSolidCylinderToCCR_psiRange.png | Bin 0 -> 3649 bytes .../doc/HxSolidCylinderToCCR_smoothing.png | Bin 0 -> 2483 bytes .../doc/HxSolidCylinderToCCR_thetaRange.png | Bin 0 -> 3660 bytes .../doc/HxSolidCylinderToCCR_tiltAngles.png | Bin 0 -> 3577 bytes .../doc/HxSolidCylinderToCCR_tiltAxis.png | Bin 0 -> 2909 bytes .../doc/HxSolidCylinderToCCR_tiltType.png | Bin 0 -> 3667 bytes .../doc/HxSolidCylinderToCCR_voxelSize.png | Bin 0 -> 3218 bytes hxcrosscorrelation/doc/HxSolidSphereToCCR.doc | 93 ++ .../doc/HxSolidSphereToCCR_defineForground.png | Bin 0 -> 1918 bytes .../doc/HxSolidSphereToCCR_increment.png | Bin 0 -> 1406 bytes .../doc/HxSolidSphereToCCR_options.png | Bin 0 -> 2335 bytes .../doc/HxSolidSphereToCCR_scaleRange.png | Bin 0 -> 1773 bytes .../doc/HxSolidSphereToCCR_smoothing.png | Bin 0 -> 1255 bytes .../doc/HxSolidSphereToCCR_sphereParameter.png | Bin 0 -> 1699 bytes .../doc/HxSolidSphereToCCR_tiltAngles.png | Bin 0 -> 1810 bytes .../doc/HxSolidSphereToCCR_tiltAxis.png | Bin 0 -> 1831 bytes .../doc/HxSolidSphereToCCR_tiltType.png | Bin 0 -> 2018 bytes .../doc/HxSolidSphereToCCR_voxelSize.png | Bin 0 -> 1331 bytes hxcrosscorrelation/hxcrosscorrelationWinDLLAPI.h | 19 + .../share/resources/hxcrosscorrelation.rc | 74 ++ .../script-objects/TraceFilamentsAndFilter.scro | 82 ++- hxlineextraction/HxAngularDistribution.cpp | 272 ++++++ hxlineextraction/HxAngularDistribution.h | 75 ++ hxlineextraction/HxExtractLines.cpp | 951 ++++++++++++++++++++ hxlineextraction/HxExtractLines.h | 239 +++++ hxlineextraction/HxLinesetToSpreadSheet.cpp | 100 ++ hxlineextraction/HxLinesetToSpreadSheet.h | 51 ++ hxlineextraction/Package | 10 + hxlineextraction/doc/HxAngularDistribution.doc | 17 + hxlineextraction/doc/HxExtractLines.doc | 122 +++ hxlineextraction/doc/HxExtractLines_.png | Bin 0 -> 153 bytes .../doc/HxExtractLines_advancedMenu.png | Bin 0 -> 1465 bytes .../doc/HxExtractLines_cocircularity.png | Bin 0 -> 2227 bytes .../doc/HxExtractLines_coneAutoParameter.png | Bin 0 -> 1908 bytes hxlineextraction/doc/HxExtractLines_distance.png | Bin 0 -> 2006 bytes .../doc/HxExtractLines_getLabelFields.png | Bin 0 -> 2483 bytes hxlineextraction/doc/HxExtractLines_linearity.png | Bin 0 -> 2081 bytes hxlineextraction/doc/HxExtractLines_maskRadius.png | Bin 0 -> 1486 bytes .../doc/HxExtractLines_minCorrelation.png | Bin 0 -> 2287 bytes .../doc/HxExtractLines_minLineLength.png | Bin 0 -> 1450 bytes hxlineextraction/doc/HxExtractLines_radius.png | Bin 0 -> 1355 bytes hxlineextraction/doc/HxExtractLines_scale.png | Bin 0 -> 1387 bytes .../doc/HxExtractLines_searchConeAngle.png | Bin 0 -> 1613 bytes .../doc/HxExtractLines_searchConeSize.png | Bin 0 -> 1710 bytes .../doc/HxExtractLines_similThreshold.png | Bin 0 -> 2172 bytes .../doc/HxExtractLines_similarityFactors.png | Bin 0 -> 2628 bytes .../doc/HxExtractLines_timerThreshold.png | Bin 0 -> 1972 bytes hxlineextraction/doc/HxLineSetToSpreadSheet.doc | 17 + hxlineextraction/hxlineextractionWinDLLAPI.h | 19 + .../share/resources/hxlineextraction.rc | 17 + hxneuralnetwork/ASTToQueryVisitor.cpp | 55 +- hxneuralnetwork/ASTToQueryVisitor.h | 12 +- hxneuralnetwork/ASTVisitorTest.cpp | 54 +- hxneuralnetwork/ASTVisitorTest.h | 9 +- hxneuralnetwork/AbstractSyntaxTree.cpp | 55 +- hxneuralnetwork/AbstractSyntaxTree.h | 35 +- hxneuralnetwork/AbstractSyntaxTreeVisitor.h | 10 +- hxneuralnetwork/HxCreateMorphologyGallery.cpp | 199 +++-- hxneuralnetwork/HxCreateMorphologyGallery.h | 30 +- hxneuralnetwork/HxNeuralNetworkAnalyzer.cpp | 75 ++- hxneuralnetwork/HxNeuralNetworkAnalyzer.h | 14 +- hxneuralnetwork/HxNeuralNetworkAnalyzerTest.cpp | 2 +- hxneuralnetwork/HxNeuralNetworkSubApp.cpp | 14 +- hxneuralnetwork/HxNeuronDistributorTest.cpp | 10 +- hxneuralnetwork/MorphologyManager.cpp | 64 +- hxneuralnetwork/MorphologyManager.h | 11 +- hxneuralnetwork/MorphologyManagerTest.cpp | 37 +- hxneuralnetwork/MorphologyManagerTest.h | 1 + hxneuralnetwork/NeuralNetworkDSLParser.l | 10 +- hxneuralnetwork/NeuralNetworkDSLParser.y | 84 ++- hxneuralnetwork/NeuralNetworkDSLParserTest.cpp | 33 +- hxneuralnetwork/NeuralNetworkDSLParserTest.h | 11 +- hxneuralnetwork/Package | 3 - hxneuralnetwork/PrintASTVisitor.cpp | 27 +- hxneuralnetwork/PrintASTVisitor.h | 9 +- hxneuralnetwork/QxAddFilesDialog.cpp | 55 -- hxneuralnetwork/QxAddFilesDialog.h | 30 - hxneuralnetwork/QxAddFilesDialogUI.ui | 85 -- hxneuralnetwork/SelectionPredicateCellTypeIs.cpp | 42 + hxneuralnetwork/SelectionPredicateCellTypeIs.h | 24 + ...st.cpp => SelectionPredicateCellTypeIsTest.cpp} | 11 +- hxneuralnetwork/SelectionPredicateCellTypeIsTest.h | 18 + .../SelectionPredicateHasCellTypeName.cpp | 27 - .../SelectionPredicateHasCellTypeName.h | 21 - .../SelectionPredicateHasCellTypeNameTest.h | 18 - hxneuralnetwork/SelectionPredicateTreeNode.cpp | 21 +- hxneuralnetwork/SelectionPredicateTreeNode.h | 16 +- hxneuralnetwork/SelectionQuery.cpp | 26 +- hxneuralnetwork/SelectionQuery.h | 25 +- hxneuralnetwork/SelectionQueryExecutor.cpp | 73 ++- hxneuralnetwork/SelectionQueryExecutorTest.cpp | 73 ++- hxneuralnetwork/SelectionQueryExecutorTest.h | 6 +- hxneuralnetwork/SelectionQueryManager.cpp | 2 +- hxneuralnetwork/SelectionQueryResult.cpp | 13 + hxneuralnetwork/SelectionQueryResult.h | 4 + hxneuralnetwork/TestHelpers.cpp | 16 +- hxneuralnetwork/share/resources/hxneuralnetwork.rc | 17 - .../share/resources/test_hxneuralnetwork.rc | 2 +- .../HxLandmarksInSurface.cpp | 0 .../HxLandmarksInSurface.h | 4 +- .../MeasurementFunctions.cpp | 0 .../MeasurementFunctions.h | 4 +- hxneuronkernels/Package | 1 + hxneuronkernels/share/resources/hxneuronkernels.rc | 5 + hxoptimizeactiveshape2/GlobalOptimizeFunc.cpp | 435 ++++++++-- hxoptimizeactiveshape2/GlobalOptimizeFunc.h | 51 +- hxoptimizeactiveshape2/GridSamples.cpp | 2 +- hxoptimizeactiveshape2/HxGlobalOptimize.cpp | 8 +- hxoptimizeactiveshape2/HxTestParameters.cpp | 4 +- hxrabbitct/HxRabbitCTRunner.cpp | 54 +- hxrabbitct/HxRabbitCTRunner.h | 5 +- hxrabbitct/Package | 2 - hxscanconvert/Bresenham.cpp | 152 ++++ hxscanconvert/Bresenham.h | 31 + hxscanconvert/HxScanConvert.cpp | 202 +++++ hxscanconvert/HxScanConvert.h | 83 ++ hxscanconvert/HxScanConvertCylinder.cpp | 110 +++ hxscanconvert/HxScanConvertCylinder.h | 37 + hxscanconvert/HxScanConvertCylinderHollow.cpp | 165 ++++ hxscanconvert/HxScanConvertCylinderHollow.h | 37 + hxscanconvert/HxScanConvertPlane.cpp | 111 +++ hxscanconvert/HxScanConvertPlane.h | 37 + hxscanconvert/HxScanConvertSphere.cpp | 97 ++ hxscanconvert/HxScanConvertSphere.h | 36 + hxscanconvert/HxScanConvertSphereHollow.cpp | 155 ++++ hxscanconvert/HxScanConvertSphereHollow.h | 36 + hxscanconvert/Package | 10 + hxscanconvert/ScanConvert.cpp | 477 ++++++++++ hxscanconvert/ScanConvert.h | 125 +++ hxscanconvert/ScanConvertCylinder.cpp | 159 ++++ hxscanconvert/ScanConvertCylinder.h | 51 ++ hxscanconvert/ScanConvertPlane.cpp | 99 ++ hxscanconvert/ScanConvertPlane.h | 56 ++ hxscanconvert/ScanConvertSphere.cpp | 76 ++ hxscanconvert/ScanConvertSphere.h | 49 + hxscanconvert/hxscanconvertWinDLLAPI.h | 19 + hxscanconvert/share/resources/hxscanconvert.rc | 24 + .../HxSetSpatialGraphInterfaceImpl.cpp | 2 +- hxspatialgraphset/HxSetSpatialGraphInterfaceImpl.h | 2 +- hxspatialgraphset/HxSpatialGraphSet.cpp | 4 +- hxspatialgraphset/HxSpatialGraphSet.h | 4 +- hxspatialgraphset/HxSpatialGraphSetLegend.cpp | 45 +- hxspatialgraphset/HxSpatialGraphSetLegend.h | 3 +- hxspatialgraphset/HxSpatialGraphSetView.cpp | 92 ++- hxspatialgraphset/HxSpatialGraphSetView.h | 15 +- .../QxSpatialGraphSetViewSelectionDialog.cpp | 43 +- hxtemplatematching/HxRadonTransform.cpp | 4 +- hxtensor3d/HxExtractTensorSlice.cpp | 92 ++- hxtensor3d/HxExtractTensorSlice.h | 9 + hxtensor3d/HxStructureTensor.cpp | 4 +- hxtensor3dSegmentation/Package | 2 +- hxtensordisplay/HxTensorGlyphDisplay.cpp | 418 +++++++++ hxtensordisplay/HxTensorGlyphDisplay.h | 132 +++ hxtensordisplay/Package | 37 +- hxtensordisplay/share/resources/hxtensordisplay.rc | 6 + .../hxtensordisplay/HxTensorGlyphDisplay-Frag.glsl | 69 ++ .../hxtensordisplay/HxTensorGlyphDisplay-Geom.glsl | 154 ++++ .../HxTensorGlyphDisplay-Vertex.glsl | 293 ++++++ hxtensordisplay2d/HxTensorGlyphDisplay2D.cpp | 151 ++-- hxtensordisplay2d/HxTensorGlyphDisplay2D.h | 54 +- hxtomtools/HxAverageSlices.cpp | 114 +++ hxtomtools/HxAverageSlices.h | 61 ++ hxtomtools/HxRemoveSmallSurfaces.cpp | 247 +++++ hxtomtools/HxRemoveSmallSurfaces.h | 73 ++ hxtomtools/Package | 10 + hxtomtools/doc/HxAverageSlices.doc | 27 + hxtomtools/doc/HxAverageSlices_numSlices.png | Bin 0 -> 1603 bytes hxtomtools/doc/HxRemoveSmallSurfaces.doc | 28 + .../doc/HxRemoveSmallSurfaces_surfaceSize.png | Bin 0 -> 1614 bytes hxtomtools/hxtomtoolsWinDLLAPI.h | 19 + hxtomtools/share/resources/hxtomtools.rc | 11 + 282 files changed, 14158 insertions(+), 1084 deletions(-) delete mode 100755 cgal/BuildCGAL.sh create mode 100755 cgal/BuildCGALforLinux.sh rename {hxneuralnetwork => hxcortexinsilico}/ConnectEndNodesToSomaOperationSet.cpp (100%) rename {hxneuralnetwork => hxcortexinsilico}/ConnectEndNodesToSomaOperationSet.h (100%) create mode 100644 hxcortexinsilico/Package rename {hxneuralnetwork => hxcortexinsilico}/QxCorticalColumnTool.cpp (99%) rename {hxneuralnetwork => hxcortexinsilico}/QxCorticalColumnTool.h (96%) rename {hxneuralnetwork => hxcortexinsilico}/QxCorticalColumnTool.ui (100%) create mode 100644 hxcortexinsilico/hxcortexinsilicoAPI.h rename {hxneuralnetwork => hxcortexinsilico}/share/png/CorticalColumnTool.png (100%) create mode 100644 hxcortexinsilico/share/resources/hxcortexinsilico.rc create mode 100644 hxcrosscorrelation/CCR.cpp create mode 100644 hxcrosscorrelation/CCR.h create mode 100644 hxcrosscorrelation/CCR_hollowCylinder.cpp create mode 100644 hxcrosscorrelation/CCR_hollowCylinder.h create mode 100644 hxcrosscorrelation/CCR_hollowSphere.cpp create mode 100644 hxcrosscorrelation/CCR_hollowSphere.h create mode 100644 hxcrosscorrelation/CCR_plane.cpp create mode 100644 hxcrosscorrelation/CCR_plane.h create mode 100644 hxcrosscorrelation/CCR_rotation.cpp create mode 100644 hxcrosscorrelation/CCR_rotation.h create mode 100644 hxcrosscorrelation/CCR_scale.cpp create mode 100644 hxcrosscorrelation/CCR_scale.h create mode 100644 hxcrosscorrelation/CCR_solidCylinder.cpp create mode 100644 hxcrosscorrelation/CCR_solidCylinder.h create mode 100644 hxcrosscorrelation/CCR_solidSphere.cpp create mode 100644 hxcrosscorrelation/CCR_solidSphere.h create mode 100644 hxcrosscorrelation/CrossCorrelation.cpp create mode 100644 hxcrosscorrelation/CrossCorrelation.h create mode 100644 hxcrosscorrelation/CrossCorrelation_cuda.cu create mode 100644 hxcrosscorrelation/DataSplitter.cpp create mode 100644 hxcrosscorrelation/DataSplitter.h create mode 100644 hxcrosscorrelation/HxCCRShow.cpp create mode 100644 hxcrosscorrelation/HxCCRShow.h create mode 100644 hxcrosscorrelation/HxCrossCorrelation.cpp create mode 100644 hxcrosscorrelation/HxCrossCorrelation.h create mode 100644 hxcrosscorrelation/HxDataToSpreadsheet.cpp create mode 100644 hxcrosscorrelation/HxDataToSpreadsheet.h create mode 100644 hxcrosscorrelation/HxHollowCylinderToCCR.cpp create mode 100644 hxcrosscorrelation/HxHollowCylinderToCCR.h create mode 100644 hxcrosscorrelation/HxHollowSphereToCCR.cpp create mode 100644 hxcrosscorrelation/HxHollowSphereToCCR.h create mode 100644 hxcrosscorrelation/HxPlaneToCCR.cpp create mode 100644 hxcrosscorrelation/HxPlaneToCCR.h create mode 100644 hxcrosscorrelation/HxReferenceIndicesToData_scalar.cpp create mode 100644 hxcrosscorrelation/HxReferenceIndicesToData_scalar.h create mode 100644 hxcrosscorrelation/HxReferenceIndicesToData_vector.cpp create mode 100644 hxcrosscorrelation/HxReferenceIndicesToData_vector.h create mode 100644 hxcrosscorrelation/HxSolidCylinderToCCR.cpp create mode 100644 hxcrosscorrelation/HxSolidCylinderToCCR.h create mode 100644 hxcrosscorrelation/HxSolidSphereToCCR.cpp create mode 100644 hxcrosscorrelation/HxSolidSphereToCCR.h create mode 100644 hxcrosscorrelation/Package create mode 100644 hxcrosscorrelation/doc/HxCCRShow.doc create mode 100644 hxcrosscorrelation/doc/HxCCRShow_selectReference.png create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation.doc create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation_GPUDevice.png create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation_GPUMemory.png create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation_blockSize.png create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation_nrBlocks.png create mode 100644 hxcrosscorrelation/doc/HxCrossCorrelation_timerThreshold.png create mode 100644 hxcrosscorrelation/doc/HxDataToSpreadSheet.doc create mode 100644 hxcrosscorrelation/doc/HxDataToSpreadSheet_threshold.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR.doc create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_cylinderParameter.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_defineForeground.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_defineForground.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_increment.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_maskParameter.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_options.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_psiRange.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_smoothing.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_thetaRange.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_tiltAngles.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_tiltAxis.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_tiltType.png create mode 100644 hxcrosscorrelation/doc/HxHollowCylinderToCCR_voxelSize.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR.doc create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_defineForground.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_increment.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_options.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_scaleRange.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_smoothing.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_sphereParameter.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_tiltAngles.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_tiltAxis.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_tiltType.png create mode 100644 hxcrosscorrelation/doc/HxHollowSphereToCCR_voxelSize.png create mode 100644 hxcrosscorrelation/doc/HxPlaneToCCR.doc create mode 100644 hxcrosscorrelation/doc/HxPlaneToCCR_defineForground.png create mode 100644 hxcrosscorrelation/doc/HxPlaneToCCR_increment.png create mode 100644 hxcrosscorrelation/doc/HxPlaneToCCR_options.png create mode 100644 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create mode 100644 hxneuralnetwork/SelectionPredicateCellTypeIs.h rename hxneuralnetwork/{SelectionPredicateHasCellTypeNameTest.cpp => SelectionPredicateCellTypeIsTest.cpp} (66%) create mode 100644 hxneuralnetwork/SelectionPredicateCellTypeIsTest.h delete mode 100644 hxneuralnetwork/SelectionPredicateHasCellTypeName.cpp delete mode 100644 hxneuralnetwork/SelectionPredicateHasCellTypeName.h delete mode 100644 hxneuralnetwork/SelectionPredicateHasCellTypeNameTest.h rename {hxneuralnetwork => hxneuronkernels}/HxLandmarksInSurface.cpp (100%) rename {hxneuralnetwork => hxneuronkernels}/HxLandmarksInSurface.h (92%) rename {hxneuralnetwork => hxneuronkernels}/MeasurementFunctions.cpp (100%) rename {hxneuralnetwork => hxneuronkernels}/MeasurementFunctions.h (83%) create mode 100644 hxscanconvert/Bresenham.cpp create mode 100644 hxscanconvert/Bresenham.h create mode 100644 hxscanconvert/HxScanConvert.cpp create mode 100644 hxscanconvert/HxScanConvert.h create mode 100644 hxscanconvert/HxScanConvertCylinder.cpp create mode 100644 hxscanconvert/HxScanConvertCylinder.h create mode 100644 hxscanconvert/HxScanConvertCylinderHollow.cpp create mode 100644 hxscanconvert/HxScanConvertCylinderHollow.h create mode 100644 hxscanconvert/HxScanConvertPlane.cpp create mode 100644 hxscanconvert/HxScanConvertPlane.h create mode 100644 hxscanconvert/HxScanConvertSphere.cpp create mode 100644 hxscanconvert/HxScanConvertSphere.h create mode 100644 hxscanconvert/HxScanConvertSphereHollow.cpp create mode 100644 hxscanconvert/HxScanConvertSphereHollow.h create mode 100644 hxscanconvert/Package create mode 100644 hxscanconvert/ScanConvert.cpp create mode 100644 hxscanconvert/ScanConvert.h create mode 100644 hxscanconvert/ScanConvertCylinder.cpp create mode 100644 hxscanconvert/ScanConvertCylinder.h create mode 100644 hxscanconvert/ScanConvertPlane.cpp create mode 100644 hxscanconvert/ScanConvertPlane.h create mode 100644 hxscanconvert/ScanConvertSphere.cpp create mode 100644 hxscanconvert/ScanConvertSphere.h create mode 100644 hxscanconvert/hxscanconvertWinDLLAPI.h create mode 100644 hxscanconvert/share/resources/hxscanconvert.rc create mode 100644 hxtensordisplay/HxTensorGlyphDisplay.cpp create mode 100644 hxtensordisplay/HxTensorGlyphDisplay.h create mode 100644 hxtensordisplay/share/shaders/hxtensordisplay/HxTensorGlyphDisplay-Frag.glsl create mode 100644 hxtensordisplay/share/shaders/hxtensordisplay/HxTensorGlyphDisplay-Geom.glsl create mode 100644 hxtensordisplay/share/shaders/hxtensordisplay/HxTensorGlyphDisplay-Vertex.glsl create mode 100644 hxtomtools/HxAverageSlices.cpp create mode 100644 hxtomtools/HxAverageSlices.h create mode 100644 hxtomtools/HxRemoveSmallSurfaces.cpp create mode 100644 hxtomtools/HxRemoveSmallSurfaces.h create mode 100644 hxtomtools/Package create mode 100644 hxtomtools/doc/HxAverageSlices.doc create mode 100644 hxtomtools/doc/HxAverageSlices_numSlices.png create mode 100644 hxtomtools/doc/HxRemoveSmallSurfaces.doc create mode 100644 hxtomtools/doc/HxRemoveSmallSurfaces_surfaceSize.png create mode 100644 hxtomtools/hxtomtoolsWinDLLAPI.h create mode 100644 hxtomtools/share/resources/hxtomtools.rc $ git status # On branch marianne nothing to commit (working directory clean) Do, although there were no conflicts during the merge, and the merge does not seem to touch hxprofile1d/HxComputeProfileAlongAxis.cpp, the local changes in that file are gone. I'm seeing this on Linux and Windows, with versions 1.7.4.3 and 1.7.6. I'd say this is not expected, or am I missing something? [1] http://manpages.ubuntu.com/manpages/oneiric/man1/git-merge.1.html -- Sebastian Schuberth ``` ## Junio C Hamano, 2011-09-28 15:25 Subject: Re: Merge seems to overwrite unstaged local changes Message-ID: <7vaa9o1yf7.fsf@alter.siamese.dyndns.org> URL: https://gitlist.dev/e/7vaa9o1yf7.fsf%40alter.siamese.dyndns.org In-Reply-To: ``` Sebastian Schuberth writes: > ... I'm seeing this on Linux and Windows, with versions 1.7.4.3 and 1.7.6. There recently have been quite a change in merge-recursive implementation and it would be really nice if you can try this again with the tip of 'master' before 1.7.7 final ships. Thanks. ``` ## Sebastian Schuberth, 2011-09-29 13:07 Subject: Re: Merge seems to overwrite unstaged local changes Message-ID: URL: https://gitlist.dev/e/CAHGBnuNrhtyq1tfok3p9YHAVbfo9T7BO3ZOUy%2B8YvNE9Mmhjhg%40mail.gmail.com In-Reply-To: <7vaa9o1yf7.fsf@alter.siamese.dyndns.org> ``` On Wed, Sep 28, 2011 at 17:25, Junio C Hamano wrote: >> ... I'm seeing this on Linux and Windows, with versions 1.7.4.3 and 1.7.6. > > There recently have been quite a change in merge-recursive implementation > and it would be really nice if you can try this again with the tip of > 'master' before 1.7.7 final ships. The unstaged changes do not seem to get lost during the merge anymore when using git version 1.7.7.rc3.4.g8d714 on Linux. I guess that somewhat confirms that there's a bug in git < 1.7.7. I'll write a word of warning to our in-house git users that they should always commit before merging ... -- Sebastian Schuberth ``` ## Sebastian Schuberth, 2011-10-06 13:27 Subject: Re: Merge seems to overwrite unstaged local changes Message-ID: <4E8DACCC.2050302@gmail.com> URL: https://gitlist.dev/e/4E8DACCC.2050302%40gmail.com In-Reply-To: ``` On 29.09.2011 15:07, Sebastian Schuberth wrote: >> There recently have been quite a change in merge-recursive implementation >> and it would be really nice if you can try this again with the tip of >> 'master' before 1.7.7 final ships. > > The unstaged changes do not seem to get lost during the merge anymore > when using git version 1.7.7.rc3.4.g8d714 on Linux. I guess that > somewhat confirms that there's a bug in git< 1.7.7. I'll write a word > of warning to our in-house git users that they should always commit > before merging ... It seems I'm not the only one who lost code due to this bug. For a more detailed analysis see this blog post: http://benno.id.au/blog/2011/10/01/git-recursive-merge-broken As it turns out, my use case also involves a rename of the file in which changes were lost. And just like for the blog's author it somewhat concerns me and shakes my confidence in Git for how long this severe bug slipped through undetected. -- Sebastian Schuberth ``` ## Jakub Narebski, 2011-10-06 15:35 Subject: Re: Merge seems to overwrite unstaged local changes Message-ID: URL: https://gitlist.dev/e/m3zkhe16bu.fsf%40localhost.localdomain In-Reply-To: <4E8DACCC.2050302@gmail.com> ``` Sebastian Schuberth writes: > On 29.09.2011 15:07, Sebastian Schuberth wrote: > >>> There recently have been quite a change in merge-recursive implementation >>> and it would be really nice if you can try this again with the tip of >>> 'master' before 1.7.7 final ships. >> >> The unstaged changes do not seem to get lost during the merge anymore >> when using git version 1.7.7.rc3.4.g8d714 on Linux. I guess that >> somewhat confirms that there's a bug in git< 1.7.7. I'll write a word >> of warning to our in-house git users that they should always commit >> before merging ... > > It seems I'm not the only one who lost code due to this bug. For a > more detailed analysis see this blog post: > > http://benno.id.au/blog/2011/10/01/git-recursive-merge-broken > > As it turns out, my use case also involves a rename of the file in > which changes were lost. And just like for the blog's author it > somewhat concerns me and shakes my confidence in Git for how long this > severe bug slipped through undetected. Khmmm... perhaps Mercurial was right in its transaction-based atomicity (that allows to safely merge even if there are local changes; not theough that I have doubts if it is sane behavior) ;-) I wonder if it would be possible to get some Comp. Sci. student, or graduate, or postdoc, to analyse formally the recursive merge algorithm. And to *prove* that it is correct (or not). -- Jakub Narębski ``` ## Chris Hatton, 2012-01-10 14:08 Subject: Another casualty Message-ID: URL: https://gitlist.dev/e/loom.20120110T150742-201%40post.gmane.org In-Reply-To: ``` 3 hours-worth of work just got whacked by this bug. Unimpressed :-( Could have been worse I suppose. Thanks for the confirmation. ```