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WIP: refactoring of the code base #226

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d45f860
WIP: refactoring of the multiframe conversion implementation
fedorov Mar 10, 2017
9266df0
BUG: initialize modality from the source dataset
fedorov Mar 11, 2017
5fbb7f1
ENH: a different shot at refactoring
fedorov Mar 14, 2017
65f336f
ENH: adding functionality - temp commit
fedorov Mar 16, 2017
7a84538
ENH: more updates
fedorov Mar 21, 2017
c531da9
ENH: checkpointing updates to the branch
fedorov Apr 8, 2017
90fa8d8
BUG: fix API typo fixed in dcmtk
fedorov May 5, 2017
d852e12
BUG: add docker_entry removed by accident in ff52820
fedorov May 5, 2017
e8c04ca
BUG: return value
fedorov May 5, 2017
13e805b
ENH: checkpoint commit
fedorov May 14, 2017
c092ec5
checkpoint
fedorov May 22, 2017
18d6d8d
ENH: fix compile errors, initialize common instance module
fedorov Jun 22, 2017
46d567b
ENH: fixing issues identified by tests
fedorov Jun 22, 2017
1ea1416
circle_ci another dummy
fedorov Jun 23, 2017
92745e3
ENH: fix more issues
fedorov Jun 23, 2017
2ba7583
BUG: fixing wrong initialization of DPMParametricMapIOD
che85 Jun 27, 2017
04fe695
ENH: adding refactored code for paramap from DCM to itk
che85 Jun 28, 2017
426fd9f
ENH: added region and origin to ImageVolumeGeometry getITKRepresentation
che85 Jun 28, 2017
01f8e5d
ENH: initialize meta information from DCM into internal data structure
che85 Jun 28, 2017
88ac52e
ENH: complete initialization of meta information from DCM
che85 Jun 28, 2017
2e46ce3
ENH: adaption to changes in https://github.com/QIICR/dcmqi/pull/271
che85 Jun 29, 2017
7937ed4
ENH: added initialization of derivation image FG
fedorov Jun 30, 2017
abdeb77
ENH: added initialization of the frame content
fedorov Jun 30, 2017
65eeb7e
ENH: fix initialization of the composite context
fedorov Jun 30, 2017
6baea74
ENH: add RWVM FG
fedorov Jun 30, 2017
1796e80
ENH: fix RWVM FG segfault
fedorov Jun 30, 2017
5a1a721
ENH: replace temporary codes with standard ones
fedorov Jun 30, 2017
f0997cd
ENH: fix initialization of PM
fedorov Jun 30, 2017
f3c29d5
BUG: fix initialization of the ITK PM output geometry
fedorov Jun 30, 2017
634e88c
ENH: added reminder comment to revisit modality initialization
fedorov Jun 30, 2017
685a4a8
BUG: initialize modality from the source dataset
fedorov Mar 11, 2017
6797a00
ENH: adding refactored code for paramap from DCM to itk
che85 Jun 28, 2017
97317bc
ENH: added first step for segmentation dcm to itk
che85 Jun 29, 2017
44d6ee3
ENH: reading segmentAttributes into metadata
che85 Jun 29, 2017
0796fc6
ENH: ctests for dcm segmentation 2 itk succeed
che85 Jun 30, 2017
97ba967
ENH: extraction of more methods
che85 Jun 30, 2017
759607e
STYLE: and uncommented code
che85 Jun 30, 2017
7fa1185
BUG: updates to account for standard updates
fedorov Jul 3, 2017
1ec643f
BUG: initialize origin from ITK image
fedorov Jul 3, 2017
3d206ac
BUG: fix initialization of ReferencedSeriesSequence
fedorov Jul 3, 2017
f5bef13
BUG: pass the initialized derivation FG to addFrame()
fedorov Jul 3, 2017
2043c7e
ENH: initialize DerivationCode from input JSON
fedorov Jul 3, 2017
7c0303a
BUG: initialize series-specific attributes from JSON
fedorov Jul 5, 2017
f4d0ca4
BUG: fix initialization of DerivationImageSequence
fedorov Jul 5, 2017
49ed047
touch to trigger circleci build
fedorov Jul 5, 2017
e4e4b11
ENH: add codecov badge
fedorov Jul 7, 2017
e74ed7a
BUG: do not cache codecov build directory
fedorov Jul 10, 2017
da677e5
ENH: switch to 3-clause BSD license
fedorov Jul 14, 2017
7b9431a
ENH: update license wording in README
fedorov Jul 14, 2017
f2be20e
STYLE: fix typo
fedorov Jul 14, 2017
150d32f
ENH: further simplify mentioning of the license
fedorov Jul 14, 2017
a51201f
WIP: adding attribute to link segmentAttributes sub-arrays to specifi…
fedorov Jul 17, 2017
7846113
ENH: make mkdir happy if the directory exists
fedorov Jul 18, 2017
a9a76be
BUG: reduce intensity tolerance test parameter
fedorov Jul 18, 2017
53ce662
ENH: finalize file order mapping
fedorov Jul 18, 2017
3012939
BUG: add segmentAttributesFileMapping
fedorov Jul 18, 2017
735be00
BUG: fix duplicate test name
fedorov Jul 18, 2017
261ad20
ENH: updated dcmtk version
che85 Jul 20, 2017
5753ee4
WIP: refactoring of the multiframe conversion implementation
fedorov Mar 10, 2017
882e54d
ENH: fixed extent computation for both paramap and seg (issue #275)
che85 Jul 7, 2017
c3ba545
ENH: reusing initializeVolumeGeometry and reorganizing
che85 Jul 7, 2017
a06b391
ENH: added comment for computation of extent including reference
che85 Jul 7, 2017
4cc12cf
ENH: separated matching frames with segmentId/slice and writing segme…
che85 Jul 11, 2017
6f582f3
ENH: renamed method, removed some comments and simplified
che85 Jul 11, 2017
78c404c
ENH: added method for creating CodeSequenceMacro from metadata attribute
che85 Jul 11, 2017
0b7878a
ENH: fixed type and renamed type ShortImageType to ShortITKImageType
che85 Jul 11, 2017
92e56c2
ENH: added missing type change
che85 Jul 11, 2017
b740f93
ENH: factored out creation of itkimage from frames
che85 Jul 12, 2017
1f440f0
ENH: started initialization from itk to DICOM for segmentations
che85 Jul 28, 2017
e702155
ENH: proceeding with further extraction and generalizing code
che85 Jul 28, 2017
86013eb
WIP: refactoring of the multiframe conversion implementation
fedorov Mar 10, 2017
9340926
BUG: initialize modality from the source dataset
fedorov Mar 11, 2017
ab76d22
ENH: a different shot at refactoring
fedorov Mar 14, 2017
ad10310
ENH: adding functionality - temp commit
fedorov Mar 16, 2017
92df603
ENH: more updates
fedorov Mar 21, 2017
4a6c043
ENH: checkpointing updates to the branch
fedorov Apr 8, 2017
cf43663
BUG: fix API typo fixed in dcmtk
fedorov May 5, 2017
01d38ee
BUG: add docker_entry removed by accident in ff52820
fedorov May 5, 2017
ad1dbea
BUG: return value
fedorov May 5, 2017
b20726a
ENH: checkpoint commit
fedorov May 14, 2017
d1ed723
checkpoint
fedorov May 22, 2017
a58ab73
ENH: fix compile errors, initialize common instance module
fedorov Jun 22, 2017
a2b5dfb
ENH: fixing issues identified by tests
fedorov Jun 22, 2017
8a27285
circle_ci another dummy
fedorov Jun 23, 2017
5a33a86
ENH: fix more issues
fedorov Jun 23, 2017
c524783
BUG: fixing wrong initialization of DPMParametricMapIOD
che85 Jun 27, 2017
ee8832e
ENH: adding refactored code for paramap from DCM to itk
che85 Jun 28, 2017
8944b6c
ENH: added region and origin to ImageVolumeGeometry getITKRepresentation
che85 Jun 28, 2017
1682bd0
ENH: initialize meta information from DCM into internal data structure
che85 Jun 28, 2017
49b676f
ENH: complete initialization of meta information from DCM
che85 Jun 28, 2017
e396019
ENH: adaption to changes in https://github.com/QIICR/dcmqi/pull/271
che85 Jun 29, 2017
d420bab
ENH: added initialization of derivation image FG
fedorov Jun 30, 2017
3448569
ENH: added initialization of the frame content
fedorov Jun 30, 2017
9a6d06c
ENH: fix initialization of the composite context
fedorov Jun 30, 2017
4091f63
ENH: add RWVM FG
fedorov Jun 30, 2017
7a27b02
ENH: fix RWVM FG segfault
fedorov Jun 30, 2017
53e7d68
ENH: replace temporary codes with standard ones
fedorov Jun 30, 2017
9648bde
ENH: fix initialization of PM
fedorov Jun 30, 2017
5391f64
BUG: fix initialization of the ITK PM output geometry
fedorov Jun 30, 2017
69308f6
ENH: added reminder comment to revisit modality initialization
fedorov Jun 30, 2017
08e5464
BUG: initialize modality from the source dataset
fedorov Mar 11, 2017
d500882
ENH: adding refactored code for paramap from DCM to itk
che85 Jun 28, 2017
51d45c7
ENH: added first step for segmentation dcm to itk
che85 Jun 29, 2017
ae28c47
ENH: reading segmentAttributes into metadata
che85 Jun 29, 2017
672ac9f
ENH: ctests for dcm segmentation 2 itk succeed
che85 Jun 30, 2017
7c6ec67
ENH: extraction of more methods
che85 Jun 30, 2017
4faeb3f
STYLE: and uncommented code
che85 Jun 30, 2017
c6732a3
BUG: updates to account for standard updates
fedorov Jul 3, 2017
e2d95ef
BUG: initialize origin from ITK image
fedorov Jul 3, 2017
02564da
BUG: fix initialization of ReferencedSeriesSequence
fedorov Jul 3, 2017
4006d1b
BUG: pass the initialized derivation FG to addFrame()
fedorov Jul 3, 2017
855cdbf
ENH: initialize DerivationCode from input JSON
fedorov Jul 3, 2017
0dc80e0
BUG: initialize series-specific attributes from JSON
fedorov Jul 5, 2017
6c48bb0
BUG: fix initialization of DerivationImageSequence
fedorov Jul 5, 2017
ec36add
touch to trigger circleci build
fedorov Jul 5, 2017
d2b2711
Merge branch 'frame-handling-refactoring' into rebased-frame-handling…
che85 Jul 28, 2017
5fd0a5d
Merge pull request #5 from che85/rebased-frame-handling-refactoring
fedorov Jul 30, 2017
6ccf62d
ENH: ignore node_modules
fedorov Jul 30, 2017
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ENH: initialize DerivationCode from input JSON
  • Loading branch information
fedorov committed Jul 5, 2017
commit 2043c7eaaa5b48f580af68965c0623bfbcd33ffd
11 changes: 9 additions & 2 deletions libsrc/ParametricMapObject.cpp
Original file line number Diff line number Diff line change
@@ -488,8 +488,15 @@ int ParametricMapObject::initializeFrames(vector<set<dcmqi::DICOMFrame,dcmqi::DI
perFrameFGs.push_back(fgfc);

if(!slice2frame[sliceNumber].empty()){
// TODO: read derivation code from metadata, if available, and pass instead of the default
addDerivationItemToDerivationFG(fgder, slice2frame[sliceNumber]);
if(metaDataJson.isMember("DerivationCode")){
CodeSequenceMacro purposeOfReference = CodeSequenceMacro("121322","DCM","Source image for image processing operation");
CodeSequenceMacro derivationCode = CodeSequenceMacro(metaDataJson["DerivationCode"]["CodeValue"].asCString(),
metaDataJson["DerivationCode"]["CodingSchemeDesignator"].asCString(),
metaDataJson["DerivationCode"]["CodeMeaning"].asCString());
addDerivationItemToDerivationFG(fgder, slice2frame[sliceNumber], purposeOfReference, derivationCode);
} else {
addDerivationItemToDerivationFG(fgder, slice2frame[sliceNumber]);
}
perFrameFGs.push_back(fgder);
}