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WIP: refactoring of the code base#226

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fedorov wants to merge 118 commits intoQIICR:masterQIICR/dcmqi:masterfrom fedorov:frame-handling-refactoringfedorov/dcmqi:frame-handling-refactoringCopy head branch name to clipboard

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Commits on Jul 5, 2017

• WIP: refactoring of the multiframe conversion implementation

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• BUG: initialize modality from the source dataset

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• ENH: a different shot at refactoring

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• ENH: adding functionality - temp commit

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• ENH: more updates

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• ENH: checkpointing updates to the branch

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• BUG: fix API typo fixed in dcmtk

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• BUG: add docker_entry removed by accident in ff52820

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• BUG: return value

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• ENH: checkpoint commit

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• checkpoint

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• ENH: fix compile errors, initialize common instance module

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• ENH: fixing issues identified by tests

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• circle_ci another dummy

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• ENH: fix more issues

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• BUG: fixing wrong initialization of DPMParametricMapIOD

  

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• ENH: adding refactored code for paramap from DCM to itk

  

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• ENH: added region and origin to ImageVolumeGeometry getITKRepresentation

  

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• ENH: initialize meta information from DCM into internal data structure

  

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• ENH: complete initialization of meta information from DCM

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• ENH: adaption to changes in QIICR#271

  

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• ENH: added initialization of derivation image FG

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• ENH: added initialization of the frame content

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• ENH: fix initialization of the composite context

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• ENH: add RWVM FG

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• ENH: fix RWVM FG segfault

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• ENH: replace temporary codes with standard ones

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• ENH: fix initialization of PM

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• BUG: fix initialization of the ITK PM output geometry

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• ENH: added reminder comment to revisit modality initialization

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• BUG: initialize modality from the source dataset

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• ENH: adding refactored code for paramap from DCM to itk

  

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• ENH: added first step for segmentation dcm to itk

  

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• ENH: reading segmentAttributes into metadata

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• ENH: ctests for dcm segmentation 2 itk succeed

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• ENH: extraction of more methods

  

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• STYLE: and uncommented code

  

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• BUG: updates to account for standard updates

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• BUG: initialize origin from ITK image

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• BUG: fix initialization of ReferencedSeriesSequence

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• BUG: pass the initialized derivation FG to addFrame()

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• ENH: initialize DerivationCode from input JSON

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• BUG: initialize series-specific attributes from JSON

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• BUG: fix initialization of DerivationImageSequence

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• touch to trigger circleci build

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Commits on Jul 24, 2017

• ENH: add codecov badge

  

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• BUG: do not cache codecov build directory

  

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• ENH: switch to 3-clause BSD license

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• ENH: update license wording in README

  

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• STYLE: fix typo

  

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• ENH: further simplify mentioning of the license

  

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• WIP: adding attribute to link segmentAttributes sub-arrays to specific files

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• ENH: make mkdir happy if the directory exists

  

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• BUG: reduce intensity tolerance test parameter

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• ENH: finalize file order mapping

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• BUG: add segmentAttributesFileMapping

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• BUG: fix duplicate test name

  

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• ENH: updated dcmtk version

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• WIP: refactoring of the multiframe conversion implementation

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• ENH: fixed extent computation for both paramap and seg (issue QIICR#275)

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• ENH: reusing initializeVolumeGeometry and reorganizing

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• ENH: added comment for computation of extent including reference

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• ENH: separated matching frames with segmentId/slice and writing segment images

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• ENH: renamed method, removed some comments and simplified

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• ENH: added method for creating CodeSequenceMacro from metadata attribute

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• ENH: fixed type and renamed type ShortImageType to ShortITKImageType

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• ENH: added missing type change

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• ENH: factored out creation of itkimage from frames

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Commits on Jul 28, 2017

• ENH: started initialization from itk to DICOM for segmentations

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• ENH: proceeding with further extraction and generalizing code

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• WIP: refactoring of the multiframe conversion implementation

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• BUG: initialize modality from the source dataset

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• ENH: a different shot at refactoring

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• ENH: adding functionality - temp commit

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• ENH: more updates

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• ENH: checkpointing updates to the branch

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• BUG: fix API typo fixed in dcmtk

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• BUG: add docker_entry removed by accident in ff52820

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• BUG: return value

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• ENH: checkpoint commit

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• checkpoint

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• ENH: fix compile errors, initialize common instance module

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• ENH: fixing issues identified by tests

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• circle_ci another dummy

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• ENH: fix more issues

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• BUG: fixing wrong initialization of DPMParametricMapIOD

  

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• ENH: adding refactored code for paramap from DCM to itk

  

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• ENH: added region and origin to ImageVolumeGeometry getITKRepresentation

  

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• ENH: initialize meta information from DCM into internal data structure

  

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• ENH: complete initialization of meta information from DCM

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• ENH: adaption to changes in QIICR#271

  

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• ENH: added initialization of derivation image FG

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• ENH: added initialization of the frame content

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• ENH: fix initialization of the composite context

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• ENH: add RWVM FG

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• ENH: fix RWVM FG segfault

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• ENH: replace temporary codes with standard ones

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• ENH: fix initialization of PM

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• BUG: fix initialization of the ITK PM output geometry

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• ENH: added reminder comment to revisit modality initialization

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• BUG: initialize modality from the source dataset

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• ENH: adding refactored code for paramap from DCM to itk

  

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• ENH: added first step for segmentation dcm to itk

  

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• ENH: reading segmentAttributes into metadata

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• ENH: ctests for dcm segmentation 2 itk succeed

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• ENH: extraction of more methods

  

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• STYLE: and uncommented code

  

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• BUG: updates to account for standard updates

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• BUG: initialize origin from ITK image

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• BUG: fix initialization of ReferencedSeriesSequence

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• BUG: pass the initialized derivation FG to addFrame()

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• ENH: initialize DerivationCode from input JSON

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• BUG: initialize series-specific attributes from JSON

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• BUG: fix initialization of DerivationImageSequence

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• touch to trigger circleci build

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• Merge branch 'frame-handling-refactoring' into rebased-frame-handling-refactoring

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Commits on Jul 30, 2017

• Merge pull request #5 from che85/rebased-frame-handling-refactoring

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• ENH: ignore node_modules

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