threads / discuss / 28518

Merge seems to overwrite unstaged local changes

Subject: Merge seems to overwrite unstaged local changes

## tl;dr

6 messages between Sep 28, 2011 and Jan 10, 2012.

replies: 5people: 4as markdown or json

Sebastian Schuberth· Sep 28, 2011, 14:08 UTC · lore

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 <file>..." to update what will be committed) # (use "git checkout -- <file>..." 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
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$ 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· Sep 28, 2011, 15:25 UTC · re: Sebastian Schuberth · lore

Re: Merge seems to overwrite unstaged local changes

Sebastian Schuberth <sschuberth@gmail.com> 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· Sep 29, 2011, 13:07 UTC · re: Junio C Hamano · lore

Re: Merge seems to overwrite unstaged local changes

On Wed, Sep 28, 2011 at 17:25, Junio C Hamano <gitster@pobox.com> wrote:

Show 5 quoted lines

>> ... 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· Oct 6, 2011, 13:27 UTC · re: Sebastian Schuberth · lore

Re: Merge seems to overwrite unstaged local changes

On 29.09.2011 15:07, Sebastian Schuberth wrote:

Show 9 quoted lines

>> 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· Oct 6, 2011, 15:35 UTC · re: Sebastian Schuberth · lore

Re: Merge seems to overwrite unstaged local changes

Sebastian Schuberth <sschuberth@gmail.com> writes:

Show 21 quoted lines

> 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· Jan 10, 2012, 14:08 UTC · re: Jakub Narebski · lore

Another casualty

3 hours-worth of work just got whacked by this bug. Unimpressed :-(

Could have been worse I suppose. Thanks for the confirmation.

<Goes to update Git>