[ENH] Update Filename Entity Order

.gitignore

@@ -29,6 +29,7 @@ dist/
 .idea/
 .env
 .envrc
+.devcontainer/devcontainer.json
 
 # Additional
 .ipynb_checkpoints/

petprep/cli/run.py

@@ -74,7 +74,12 @@ def main():
     # CRITICAL Call build_workflow(config_file, retval) in a subprocess.
     # Because Python on Linux does not ever free virtual memory (VM), running the
     # workflow construction jailed within a process preempts excessive VM buildup.
-    if 'pdb' not in config.execution.debug:
+    # Skip multiprocessing if debugging (pdb) or if running under a debugger
+
+    is_debugging = (
+        'pdb' in config.execution.debug or hasattr(sys, 'gettrace') and sys.gettrace() is not None
+    )
+    if not is_debugging:
         with Manager() as mgr:
             retval = mgr.dict()
             p = Process(target=build_workflow, args=(str(config_file), retval))

petprep/data/nipreps.json

@@ -153,15 +153,21 @@
       "name": "cohort",
       "pattern": "[_/\\\\]+cohort-0*(\\d+)",
       "dtype": "int"
+    },
+    {
+      "name": "seg",
+      "pattern": "[_/\\\\]+seg-([a-zA-Z0-9+]+)"
     }
   ],
   "default_path_patterns": [
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_label-{label}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_desc-{desc}]_{suffix<dseg>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix<morph>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|boldmap|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
@@ -187,11 +193,11 @@
     "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
     "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE|pet>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix<timeseries|regressors|tacs>|timeseries}{extension<.json|.tsv>|.tsv}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE|pet>}{extension<.html|.svg>|.svg}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dwi|epi|epiref|pet>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|boldmap|pet>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<pet>}{extension<.html|.svg|.png>|.html}"
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix<dwi|epi|epiref|pet>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix<bold|boldmap|pet>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix<pet>}{extension<.html|.svg|.png>|.html}"
   ]
 }

petprep/interfaces/__init__.py

@@ -1,7 +1,11 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+from json import loads
+
 from niworkflows.interfaces.bids import DerivativesDataSink as _DDSink
 
+from petprep.utils.bids import load_data
+
 from .cifti import GeneratePetCifti
 from .motion import MotionPlot
 from .reports import AtlasROIsReport
@@ -10,6 +14,10 @@
 
 class DerivativesDataSink(_DDSink):
     out_path_base = ''
+    _petprep_spec = loads(load_data.readable('nipreps.json').read_text())
+    _config_entities = frozenset({e['name'] for e in _petprep_spec['entities']})
+    _config_entities_dict = _petprep_spec['entities']
+    _file_patterns = tuple(_petprep_spec['default_path_patterns'])
 
 
 __all__ = (

petprep/workflows/pet/outputs.py

@@ -201,7 +201,6 @@ def init_func_fit_reports_wf(
                 desc='ref',
                 label=ref_name,
                 datatype='figures',
-                allowed_entities=('label',),
             ),
             name='ds_report_refmask',
             run_without_submitting=True,
@@ -362,7 +361,6 @@ def init_func_fit_reports_wf(
                 label=ref_name,
                 suffix='pet',
                 datatype='figures',
-                allowed_entities=('label',),
             ),
             name='ds_pet_t1_refmask_report',
         )
@@ -573,7 +571,6 @@ def init_ds_refmask_wf(
             suffix='mask',
             desc='ref',
             label=ref_name,
-            allowed_entities=('label',),
             compress=True,
         ),
         name='ds_refmask',
@@ -1060,7 +1057,6 @@ def init_refmask_report_wf(
             desc='ref',
             label=ref_name,
             datatype='figures',
-            allowed_entities=('label',),
             suffix='pet',
         ),
         name='ds_report_refmask',

petprep/workflows/pet/reference_mask.py

@@ -74,7 +74,6 @@ def init_pet_refmask_wf(
             base_directory=config.execution.petprep_dir,
             label=ref_mask_name,
             desc='ref',
-            allowed_entities=('label',),
             suffix='morph',
             extension='.tsv',
             datatype='anat',

petprep/workflows/pet/segmentation.py

@@ -182,7 +182,6 @@ def _build_nodes(
         DerivativesDataSink(
             base_directory=config.execution.petprep_dir,
             seg=seg,
-            allowed_entities=('seg',),
             suffix='dseg',
             extension='.nii.gz',
             compress=True,
@@ -233,7 +232,6 @@ def _build_nodes(
         DerivativesDataSink(
             base_directory=config.execution.petprep_dir,
             seg=seg,
-            allowed_entities=('seg',),
             suffix='dseg',
             extension='.tsv',
             datatype='anat',
@@ -247,7 +245,6 @@ def _build_nodes(
         DerivativesDataSink(
             base_directory=config.execution.petprep_dir,
             seg=seg,
-            allowed_entities=('seg',),
             suffix='morph',
             extension='.tsv',
             datatype='anat',

petprep/workflows/pet/tests/test_fit.py

@@ -359,8 +359,9 @@ def test_refmask_report_connections(bids_root: Path, tmp_path: Path, pvc_method)
         ds_tacs = wf.get_node('ds_ref_tacs')
         assert ds_tacs.inputs.label == 'cerebellum'
         assert 'label' in ds_tacs.interface._allowed_entities
-        assert 'seg' not in ds_tacs.interface._allowed_entities
-        assert not hasattr(ds_tacs.inputs, 'seg')
+        assert 'seg' in ds_tacs.interface._config_entities
+        assert hasattr(ds_tacs.inputs, 'seg')
+        assert ds_tacs.inputs.seg is Undefined
         assert ds_tacs.inputs.desc == 'preproc'
         edge_tacs = wf._graph.get_edge_data(wf.get_node('pet_ref_tacs_wf'), ds_tacs)
         assert ('outputnode.timeseries', 'in_file') in edge_tacs['connect']