From 2ee998cf10e58bf9621eb81a9551ddd66b07836c Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Wed, 3 Jul 2024 16:51:34 -0400 Subject: [PATCH 1/4] [ENH] Update dependencies in docker image (#768) --- .circleci/config.yml | 2 +- Dockerfile | 2 +- pyproject.toml | 8 +- qsiprep/config.py | 2 +- ...rix_multishell_msmt_pyafq_tractometry.json | 4 +- qsiprep/data/pipelines/pyafq_tractometry.json | 4 +- .../data/pyafq_recon_external_trk_outputs.txt | 182 +++++++-------- .../tests/data/pyafq_recon_full_outputs.txt | 221 +++++++++--------- qsiprep/tests/utils.py | 2 +- qsiprep/utils/sloppy_recon.py | 3 +- qsiprep/workflows/recon/base.py | 2 +- 11 files changed, 215 insertions(+), 217 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b5c93f69..59ec4dfb 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,7 +4,7 @@ orbs: .dockersetup: &dockersetup docker: - - image: pennbbl/qsiprep_build:24.4.29 + - image: pennbbl/qsiprep_build:24.7.1 working_directory: /src/qsiprep runinstall: &runinstall diff --git a/Dockerfile b/Dockerfile index 66fbaa95..7cf9afc4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,7 @@ RUN pip install build RUN apt-get update && \ apt-get install -y --no-install-recommends git -FROM pennbbl/qsiprep_build:24.4.29 +FROM pennbbl/qsiprep_build:24.7.1 # Install qsiprep COPY . /src/qsiprep diff --git a/pyproject.toml b/pyproject.toml index 3ce8c5bf..ca22085f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ license = {file = "LICENSE"} requires-python = ">=3.10" dependencies = [ 'importlib_resources; python_version < "3.11"', - "dipy <= 1.5.0", + "dipy>=1.8.0,<1.9.0", "dmri-amico == 1.5.4", "fury", "indexed_gzip <= 1.8.7", @@ -27,13 +27,13 @@ dependencies = [ "networkx ~= 2.8.8", "nibabel <= 5.2.0", "nilearn == 0.10.1", - "nipype <= 1.8.6", + "nipype == 1.8.6", "niworkflows >=1.9,<= 1.10", "numpy <= 1.26.3", "pandas < 2.0.0", "psutil <= 5.9.8", - "pyAFQ <= 1.3.2", - "pybids < 0.16.1", + "pyAFQ == 1.3.2", + "pybids", "pyyaml", "scikit-image", "scikit-learn <= 1.4.0", diff --git a/qsiprep/config.py b/qsiprep/config.py index 9fcd07cf..c626db68 100644 --- a/qsiprep/config.py +++ b/qsiprep/config.py @@ -498,7 +498,7 @@ def init(cls): "stimuli", "sourcedata", "models", - re.compile(r"^\."), + re.compile(r"\/\.\w+|^\.\w+"), # hidden files re.compile(r"sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|func|eeg|ieeg|meg|perf)"), ] if cls.participant_label and cls.bids_database_dir is None: diff --git a/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json b/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json index 2582b507..9decefb6 100644 --- a/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json +++ b/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json @@ -83,7 +83,7 @@ "dist_to_waypoint": "", "rng": "", "return_idx": false, - "presegment_bundle_dict": "", + "presegment_bundle_dict": null, "presegment_kwargs": "{}", "filter_by_endpoints": true, "dist_to_atlas": 4, @@ -104,7 +104,7 @@ "csd_tau": 0.1, "gtol": 0.01, "brain_mask_definition": "", - "bundle_info": "", + "bundle_info": null, "reg_template_spec": "mni_T1", "mapping_definition": "", "reg_subject_spec": "power_map", diff --git a/qsiprep/data/pipelines/pyafq_tractometry.json b/qsiprep/data/pipelines/pyafq_tractometry.json index 050ec401..67074e9c 100644 --- a/qsiprep/data/pipelines/pyafq_tractometry.json +++ b/qsiprep/data/pipelines/pyafq_tractometry.json @@ -47,7 +47,7 @@ "dist_to_waypoint": "", "rng": "", "return_idx": false, - "presegment_bundle_dict": "", + "presegment_bundle_dict": null, "presegment_kwargs": "{}", "filter_by_endpoints": true, "dist_to_atlas": 4, @@ -68,7 +68,7 @@ "csd_tau": 0.1, "gtol": 0.01, "brain_mask_definition": "", - "bundle_info": "", + "bundle_info": null, "reg_template_spec": "mni_T1", "mapping_definition": "", "reg_subject_spec": "power_map", diff --git a/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt b/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt index b42ab633..8f4e8e8c 100644 --- a/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt +++ b/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt @@ -27,98 +27,96 @@ qsirecon-PYAFQ/sub-ABCD qsirecon-PYAFQ/sub-ABCD/dwi qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ROIs -qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ROIs/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi_space-subject_desc-ARCL1end_mask.json -qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ROIs/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi_space-subject_desc-ARCL1end_mask.nii.gz -qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ROIs/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi_space-subject_desc-ARCL1include_mask.json 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+qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi +qsiprep +qsiprep/sub-ABCD.html +qsiprep/sub-ABCD +qsiprep/logs +qsiprep/logs/CITATION.tex +qsiprep/logs/CITATION.bib +qsiprep/logs/CITATION.md +qsiprep/logs/CITATION.html +qsiprep/dataset_description.json +qsiprep/dwiqc.json diff --git a/qsiprep/tests/utils.py b/qsiprep/tests/utils.py index 8e54ee05..c46f1fda 100644 --- a/qsiprep/tests/utils.py +++ b/qsiprep/tests/utils.py @@ -1,12 +1,12 @@ """Utility functions for tests.""" +import lzma import os import tarfile from glob import glob from gzip import GzipFile from io import BytesIO -import lzma import requests from nipype import logging diff --git a/qsiprep/utils/sloppy_recon.py b/qsiprep/utils/sloppy_recon.py index 94b670d8..c1e4cf38 100644 --- a/qsiprep/utils/sloppy_recon.py +++ b/qsiprep/utils/sloppy_recon.py @@ -30,7 +30,8 @@ def make_sloppy(spec): ("MRTrix3", "global_tractography"): {"niters": 10000}, ("pyAFQ", "pyafq_tractometry"): { "mapping_definition": 'AffMap(affine_kwargs={"level_iters": [10, 10, 10]})', - "bundle_info": '["SLF_L", "ARC_L", "CST_L", "CST_R"]', + "bundle_info": 'default18_bd()["Left Superior Longitudinal", "Left Arcuate", ' + '"Left Corticospinal", "Right Corticospinal"]', "n_seeds": 10000, "random_seeds": True, "export": "all_bundles_figure", diff --git a/qsiprep/workflows/recon/base.py b/qsiprep/workflows/recon/base.py index 5cd56f8e..914de5bc 100644 --- a/qsiprep/workflows/recon/base.py +++ b/qsiprep/workflows/recon/base.py @@ -239,7 +239,7 @@ def init_single_subject_recon_wf(subject_id): (recon_full_inputs[dwi_file], dwi_recon_wfs[dwi_file], [(trait, "inputnode." + trait) for trait in recon_workflow_input_fields]), - (anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep" \ + (anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep" else anat_ingress_nodes[dwi_file], dwi_individual_anatomical_wfs[dwi_file], [(f"outputnode.{trait}", f"inputnode.{trait}") From d18ff0f16f265de68d8b1ef40fac393e5c57b1b1 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Mon, 8 Jul 2024 16:31:39 -0400 Subject: [PATCH 2/4] [CI] add optional bundles (#771) add optional bundles --- qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt diff --git a/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt b/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt new file mode 100644 index 00000000..b8631086 --- /dev/null +++ b/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt @@ -0,0 +1,2 @@ +qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html +qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk From 5192009f89a81730ae70183ddef057cb597f52f6 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Mon, 8 Jul 2024 17:15:57 -0400 Subject: [PATCH 3/4] [CI] Update expected AFQ outputs again --- qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt | 2 ++ qsiprep/tests/data/pyafq_recon_full_outputs.txt | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt b/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt index b8631086..2043c227 100644 --- a/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt +++ b/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt @@ -1,2 +1,4 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk +qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk +qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html diff --git a/qsiprep/tests/data/pyafq_recon_full_outputs.txt b/qsiprep/tests/data/pyafq_recon_full_outputs.txt index dd5285dd..f5e2361c 100644 --- a/qsiprep/tests/data/pyafq_recon_full_outputs.txt +++ b/qsiprep/tests/data/pyafq_recon_full_outputs.txt @@ -9,7 +9,6 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_desc-seed_mask.nii.gz qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi.html -qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinalviz_dwi.html qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/sub-ABCD_acq-10per000_space-subject_desc-template_dwi.json @@ -103,7 +102,6 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.json qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinal_tractography.trk qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.trk -qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi qsiprep qsiprep/sub-ABCD.html From 555556cc5dd1d0862adbb2efdc5ca9487ba9e548 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Tue, 9 Jul 2024 09:19:06 -0400 Subject: [PATCH 4/4] [FIX] CI test file checking --- qsiprep/tests/utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/qsiprep/tests/utils.py b/qsiprep/tests/utils.py index c46f1fda..9b9c9161 100644 --- a/qsiprep/tests/utils.py +++ b/qsiprep/tests/utils.py @@ -121,7 +121,9 @@ def check_generated_files(qsiprep_dir, output_list_file, optional_output_list_fi if found_not_expected: msg += "\nFound but not expected:\n\t" msg += "\n\t".join(found_not_expected) - raise ValueError(msg) + + if msg: + raise ValueError(msg) def reorder_expected_outputs():