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[ENH] Add possibility for the user to custom the skipped interfaces #63

Merged
merged 32 commits into from
Dec 22, 2020
Merged

[ENH] Add possibility for the user to custom the skipped interfaces #63

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5f4566e
Merge branch 'master' into v2.0.1-dev
pdedumast Dec 5, 2020
fe65ed3
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 7, 2020
0fc8535
STYLE: Improve JSON file visibility with indent.
pdedumast Dec 9, 2020
00b1322
ENH: Wrap mialsrtkImageReconstruction --noreg option to skip SVR.
pdedumast Dec 9, 2020
d14d0c4
ENH: SVR registration is skipped if specified in JSON parameters
pdedumast Dec 9, 2020
a791ae6
ENH: Refinement of HR mask is optional.
pdedumast Dec 9, 2020
60652b6
STYLE: Renamed HR mask refinement node.
pdedumast Dec 9, 2020
993819f
TEST: Update test-01 list of outputs
pdedumast Dec 9, 2020
041cad5
TEST: Update test-02 list of outputs
pdedumast Dec 9, 2020
382eea6
DOC: Update input participants_params.json example [skip ci]
pdedumast Dec 9, 2020
037ac0d
DOC: Update documentation of AnatomicalPipeline inputs
pdedumast Dec 9, 2020
a57ef59
ENH: NLM denoising preprocessing is optional
pdedumast Dec 9, 2020
5297eec
DOC: Update documentation related to NLM denoising skipping
pdedumast Dec 9, 2020
d95f10d
ENH: Automatic stacks ordering can be done on a pre-selection of stacks.
pdedumast Dec 9, 2020
b60218e
DOC: Update documentation related to stacks ordering
pdedumast Dec 9, 2020
c61894a
TEST: Adapt participants_param.json for stacks ordering for automatic…
pdedumast Dec 9, 2020
b6d1420
TEST: Update test-01 list of outputs
pdedumast Dec 10, 2020
97508da
TEST: Update test-02 list of outputs
pdedumast Dec 10, 2020
33844a9
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 10, 2020
7538d4c
Merge branch 'v2.0.1-dev' into 27_custom_skipped_interfaces
pdedumast Dec 10, 2020
8d82f1e
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 11, 2020
06028d0
Merge branch 'v2.0.1-dev' into 27_custom_skipped_interfaces
pdedumast Dec 11, 2020
4cdcf5a
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 11, 2020
6d60e61
Merge branch 'v2.0.1-dev' into 27_custom_skipped_interfaces
pdedumast Dec 11, 2020
f9cc28c
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 14, 2020
3df73ab
Merge branch 'v2.0.1-dev' into 27_custom_skipped_interfaces
pdedumast Dec 14, 2020
99eea6e
TEST: Update output for test03
pdedumast Dec 14, 2020
2b6ec7b
TEST: Update outputs test 04
pdedumast Dec 14, 2020
b549fd4
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
pdedumast Dec 22, 2020
ecf3502
Fix merge conflicts
pdedumast Dec 22, 2020
b50060f
ENH: Custom interfaces parameters must be gathered in a unique dictio…
pdedumast Dec 22, 2020
8c082cc
DOC: Custom interfaces dictionary documentation
pdedumast Dec 22, 2020
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50 changes: 25 additions & 25 deletions .circleci/test-01_outputs.txt
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Expand Up @@ -40,92 +40,97 @@ nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/result_nlmDenoise.pklz
nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/sub-01_run-1_T2w_nlm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/sub-01_run-3_T2w_nlm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/sub-01_run-5_T2w_nlm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/sub-01_run-6_T2w_nlm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/result_srtkCorrectSliceIntensity01_nlm.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/sub-01_run-1_T2w_nlm_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/sub-01_run-3_T2w_nlm_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/sub-01_run-5_T2w_nlm_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01_nlm/sub-01_run-6_T2w_nlm_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/result_srtkCorrectSliceIntensity01.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/sub-01_run-1_T2w_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/sub-01_run-3_T2w_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/sub-01_run-5_T2w_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity01/sub-01_run-6_T2w_uni.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/result_srtkCorrectSliceIntensity02_nlm.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/sub-01_run-1_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/sub-01_run-3_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/sub-01_run-5_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02_nlm/sub-01_run-6_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/result_srtkCorrectSliceIntensity02.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/sub-01_run-1_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/sub-01_run-3_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/sub-01_run-5_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkCorrectSliceIntensity02/sub-01_run-6_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/result_srtkHistogramNormalization_nlm.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/sub-01_run-1_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/sub-01_run-3_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/sub-01_run-5_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization_nlm/sub-01_run-6_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/result_srtkHistogramNormalization.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/sub-01_run-1_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/sub-01_run-3_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/sub-01_run-5_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHistogramNormalization/sub-01_run-6_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkHRMask/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHRMask/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHRMask/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkHRMask/result_srtkHRMask.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkHRMask/SRTV_sub-01_3V_rad1_srMask.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/_inputs.pklz
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nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/result_srtkImageReconstruction.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/SDI_sub-01_3V_rad1.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/sub-01_run-1_T2w_nlm_uni_bcorr_histnorm_transform_3V.txt
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/sub-01_run-3_T2w_nlm_uni_bcorr_histnorm_transform_3V.txt
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/sub-01_run-5_T2w_nlm_uni_bcorr_histnorm_transform_3V.txt
nipype/sub-01/rec-1/srr_pipeline/srtkImageReconstruction/sub-01_run-6_T2w_nlm_uni_bcorr_histnorm_transform_3V.txt
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01_nlm/_inputs.pklz
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nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01_nlm/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01_nlm/result_srtkIntensityStandardization01_nlm.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01_nlm/sub-01_run-1_T2w_nlm_uni_bcorr.nii.gz
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nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/result_srtkIntensityStandardization01.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/sub-01_run-1_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/sub-01_run-3_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization01/sub-01_run-5_T2w_uni_bcorr.nii.gz
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nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/_inputs.pklz
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nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/result_srtkIntensityStandardization02_nlm.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/sub-01_run-1_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/sub-01_run-3_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/sub-01_run-5_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02_nlm/sub-01_run-6_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/result_srtkIntensityStandardization02.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/sub-01_run-1_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/sub-01_run-3_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/sub-01_run-5_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkIntensityStandardization02/sub-01_run-6_T2w_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/result_srtkMaskImage01.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/sub-01_run-1_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/sub-01_run-3_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/sub-01_run-5_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage01/sub-01_run-6_T2w_nlm_uni_bcorr_histnorm.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage02/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage02/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkMaskImage02/_report/report.rst
Expand All @@ -136,18 +141,13 @@ nipype/sub-01/rec-1/srr_pipeline/srtkN4BiasFieldCorrection/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkN4BiasFieldCorrection/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkN4BiasFieldCorrection/result_srtkN4BiasFieldCorrection.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkN4BiasFieldCorrection/SRTV_sub-01_3V_rad1_gbcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkRefineHRMaskByIntersection/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkRefineHRMaskByIntersection/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkRefineHRMaskByIntersection/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkRefineHRMaskByIntersection/result_srtkRefineHRMaskByIntersection.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkRefineHRMaskByIntersection/sub-01_T2w_uni_bcorr_histnorm_srMask.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/_report/report.rst
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/result_srtkSliceBySliceCorrectBiasField.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/sub-01_run-1_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/sub-01_run-3_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/sub-01_run-5_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceCorrectBiasField/sub-01_run-6_T2w_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/_report/report.rst
Expand All @@ -156,8 +156,8 @@ nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_ru
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-1_T2w_nlm_uni_n4bias.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-3_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-3_T2w_nlm_uni_n4bias.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-5_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-5_T2w_nlm_uni_n4bias.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-6_T2w_nlm_uni_bcorr.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkSliceBySliceN4BiasFieldCorrection/sub-01_run-6_T2w_nlm_uni_n4bias.nii.gz
nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_inputs.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_node.pklz
nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
Expand All @@ -178,9 +178,9 @@ pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-1_T2w_desc-brain_mask.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-3_id-1_desc-preprocSDI_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-3_id-1_desc-preprocSR_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-3_T2w_desc-brain_mask.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-5_id-1_desc-preprocSDI_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-5_id-1_desc-preprocSR_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSDI_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSR_T2w.nii.gz
pymialsrtk-2.0.1-dev/sub-01/anat/sub-01_run-6_T2w_desc-brain_mask.nii.gz
pymialsrtk-2.0.1-dev/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
pymialsrtk-2.0.1-dev/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
pymialsrtk-2.0.1-dev/sub-01/xfm/sub-01_run-5_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
pymialsrtk-2.0.1-dev/sub-01/xfm/sub-01_run-6_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
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