Test collect_derivatives function (#29)

* Work on collect_derivatives. * Work on queries. * Work on collect_derivatives. * Tests look good now. Will still fail. * Update conftest.py * Work on raw vs. derivative collection. * Update test_utils_bids.py * Update bids.py * Try this. * Fix style issues. * Update utils.py * Update conftest.py * Update test_utils_bids.py * Update test_utils_bids.py * Don't index metadata. * Update test_utils_bids.py * Update test_utils_bids.py * Fix up entrypoint and imports. * Keep fixing. * Update. * Fix some stuff. * Keep trying to fix. * Update base.py * Get it building at least. * Remove reporting nodes. * Whoops! * Fix more stuff. * Get the workflow to run all the way through. * Fix style issues. * Update confounds.py
nipreps · May 16, 2024 · 741c099 · 741c099
1 parent e6134df
commit 741c099
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diff --git a/Dockerfile b/Dockerfile
@@ -230,7 +230,7 @@ ENV IS_DOCKER_8395080871=1
 
 RUN ldconfig
 WORKDIR /tmp
-ENTRYPOINT ["/opt/conda/envs/fmripost_aroma/bin/fmripost_aroma"]
+ENTRYPOINT ["/opt/conda/envs/fmripost_aroma/bin/fmripost-aroma"]
 
 ARG BUILD_DATE
 ARG VCS_REF

diff --git a/docs/spaces.rst b/docs/spaces.rst
@@ -37,7 +37,7 @@ stereotactic coordinate system.
 The most extended standard space for fMRI analyses is generally referred to MNI.
 For instance, to instruct *fMRIPost-AROMA* to use the MNI template brain distributed with
 FSL as coordinate reference the option will read as follows: ``--output-spaces MNI152NLin6Asym``.
-By default, *fMRIPost-AROMA* uses ``MNI152NLin2009cAsym`` as spatial-standardization reference.
+By default, *fMRIPost-AROMA* uses ``MNI152NLin6Asym`` as spatial-standardization reference.
 Valid template identifiers (``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, etc.) come from
 the `TemplateFlow repository <https://github.com/templateflow/templateflow>`__.
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -59,7 +59,7 @@ Issues = "https://github.com/nipreps/fmripost-aroma/issues"
 Source = "https://github.com/nipreps/fmripost-aroma"
 
 [project.scripts]
-fmripost-aroma = "fmripost_aroma.cli:aroma"
+fmripost-aroma = "fmripost_aroma.cli.run:main"
 
 [tool.hatch.metadata]
 allow-direct-references = true

diff --git a/src/fmripost_aroma/cli/parser.py b/src/fmripost_aroma/cli/parser.py
@@ -195,7 +195,6 @@ def _bids_filter(value, parser):
         '--derivatives',
         action=ToDict,
         metavar='PACKAGE=PATH',
-        type=str,
         nargs='+',
         help=(
             'Search PATH(s) for pre-computed derivatives. '
@@ -332,6 +331,17 @@ def _bids_filter(value, parser):
         default=False,
         help='Skip generation of HTML and LaTeX formatted citation with pandoc',
     )
+    g_outputs.add_argument(
+        '--aggregate-session-reports',
+        dest='aggr_ses_reports',
+        action='store',
+        type=PositiveInt,
+        default=4,
+        help=(
+            "Maximum number of sessions aggregated in one subject's visual report. "
+            'If exceeded, visual reports are split by session.'
+        ),
+    )
 
     g_aroma = parser.add_argument_group('Options for running ICA_AROMA')
     g_aroma.add_argument(
@@ -347,7 +357,7 @@ def _bids_filter(value, parser):
     )
     g_aroma.add_argument(
         '--error-on-warnings',
-        dest='error_on_aroma_warnings',
+        dest='err_on_warn',
         action='store_true',
         default=False,
         help=(
@@ -361,6 +371,7 @@ def _bids_filter(value, parser):
         nargs='+',
         choices=['aggr', 'nonaggr', 'orthaggr'],
         default=None,
+        dest='denoise_method',
         help='Denoising method to apply, if any.',
     )
 
@@ -530,6 +541,9 @@ def parse_args(args=None, namespace=None):
     work_dir = config.execution.work_dir
     version = config.environment.version
 
+    if config.execution.fmripost_aroma_dir is None:
+        config.execution.fmripost_aroma_dir = output_dir
+
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory
@@ -569,7 +583,7 @@ def parse_args(args=None, namespace=None):
         validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
     # Setup directories
-    config.execution.log_dir = config.execution.fmriprep_dir / 'logs'
+    config.execution.log_dir = config.execution.fmripost_aroma_dir / 'logs'
     # Check and create output and working directories
     config.execution.log_dir.mkdir(exist_ok=True, parents=True)
     work_dir.mkdir(exist_ok=True, parents=True)

diff --git a/src/fmripost_aroma/cli/run.py b/src/fmripost_aroma/cli/run.py
@@ -204,8 +204,6 @@ def main():
             )
         errno = 0
     finally:
-        from pkg_resources import resource_filename as pkgrf
-
         # Code Carbon
         if config.execution.track_carbon:
             emissions: float = tracker.stop()
@@ -217,11 +215,9 @@ def main():
 
         # Generate reports phase
         failed_reports = generate_reports(
-            config.execution.participant_label,
-            config.execution.fmripost_aroma_dir,
-            config.execution.run_uuid,
-            config=pkgrf('fmripost_aroma', 'data/reports-spec.yml'),
-            packagename='fmripost_aroma',
+            subject_list=config.execution.participant_label,
+            output_dir=config.execution.fmripost_aroma_dir,
+            run_uuid=config.execution.run_uuid,
         )
         write_derivative_description(
             config.execution.bids_dir, config.execution.fmripost_aroma_dir
@@ -233,7 +229,7 @@ def main():
                 'Report generation failed for %d subjects' % failed_reports,
                 level='error',
             )
-        sys.exit(int((errno + failed_reports) > 0))
+        sys.exit(int((errno + len(failed_reports)) > 0))
 
 
 def migas_exit() -> None:

diff --git a/src/fmripost_aroma/cli/workflow.py b/src/fmripost_aroma/cli/workflow.py
@@ -36,14 +36,13 @@ def build_workflow(config_file, retval):
     """Create the Nipype Workflow that supports the whole execution graph."""
     from pathlib import Path
 
+    from fmriprep.utils.bids import check_pipeline_version
+    from fmriprep.utils.misc import check_deps
     from niworkflows.utils.bids import collect_participants
-    from niworkflows.utils.misc import check_valid_fs_license
     from pkg_resources import resource_filename as pkgrf
 
     from fmripost_aroma import config
     from fmripost_aroma.reports.core import generate_reports
-    from fmripost_aroma.utils.bids import check_pipeline_version
-    from fmripost_aroma.utils.misc import check_deps
     from fmripost_aroma.workflows.base import init_fmripost_aroma_wf
 
     config.load(config_file)
@@ -92,11 +91,9 @@ def build_workflow(config_file, retval):
     if config.execution.reports_only:
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         retval['return_code'] = generate_reports(
-            config.execution.participant_label,
-            config.execution.fmripost_aroma_dir,
-            config.execution.run_uuid,
-            config=pkgrf('fmripost_aroma', 'data/reports-spec.yml'),
-            packagename='fmripost_aroma',
+            subject_list=config.execution.participant_label,
+            output_dir=config.execution.fmripost_aroma_dir,
+            run_uuid=config.execution.run_uuid,
         )
         return retval
 
@@ -112,37 +109,10 @@ def build_workflow(config_file, retval):
     if config.execution.derivatives:
         init_msg += [f'Searching for derivatives: {config.execution.derivatives}.']
 
-    if config.execution.fs_subjects_dir:
-        init_msg += [f"Pre-run FreeSurfer's SUBJECTS_DIR: {config.execution.fs_subjects_dir}."]
-
     build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
 
     retval['workflow'] = init_fmripost_aroma_wf()
 
-    # Check for FS license after building the workflow
-    if not check_valid_fs_license():
-        from fmripost_aroma.utils.misc import fips_enabled
-
-        if fips_enabled():
-            build_log.critical(
-                """\
-ERROR: Federal Information Processing Standard (FIPS) mode is enabled on your system. \
-FreeSurfer (and thus fMRIPost-AROMA) cannot be used in FIPS mode. \
-Contact your system administrator for assistance."""
-            )
-        else:
-            build_log.critical(
-                """\
-ERROR: a valid license file is required for FreeSurfer to run. \
-fMRIPost-AROMA looked for an existing license file at several paths, in this order: \
-1) command line argument ``--fs-license-file``; \
-2) ``$FS_LICENSE`` environment variable; and \
-3) the ``$FREESURFER_HOME/license.txt`` path. \
-Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html"""
-            )
-        retval['return_code'] = 126  # 126 == Command invoked cannot execute.
-        return retval
-
     # Check workflow for missing commands
     missing = check_deps(retval['workflow'])
     if missing:

diff --git a/src/fmripost_aroma/config.py b/src/fmripost_aroma/config.py
@@ -225,13 +225,15 @@ def load(cls, settings, init=True, ignore=None):
         for k, v in settings.items():
             if k in ignore or v is None:
                 continue
+
             if k in cls._paths:
                 if isinstance(v, list | tuple):
                     setattr(cls, k, [Path(val).absolute() for val in v])
                 elif isinstance(v, dict):
                     setattr(cls, k, {key: Path(val).absolute() for key, val in v.items()})
                 else:
                     setattr(cls, k, Path(v).absolute())
+
             elif hasattr(cls, k):
                 setattr(cls, k, v)
 
@@ -250,17 +252,24 @@ def get(cls):
         for k, v in cls.__dict__.items():
             if k.startswith('_') or v is None:
                 continue
+
             if callable(getattr(cls, k)):
                 continue
+
             if k in cls._paths:
                 if isinstance(v, list | tuple):
                     v = [str(val) for val in v]
+                elif isinstance(v, dict):
+                    v = {key: str(val) for key, val in v.items()}
                 else:
                     v = str(v)
+
             if isinstance(v, SpatialReferences):
                 v = ' '.join(str(s) for s in v.references) or None
+
             if isinstance(v, Reference):
                 v = str(v) or None
+
             out[k] = v
         return out
 
@@ -533,7 +542,7 @@ def _process_value(value):
 class workflow(_Config):
     """Configure the particular execution graph of this workflow."""
 
-    err_on_warn = None
+    err_on_warn = False
     """Cast AROMA warnings to errors."""
     melodic_dim = None
     """Number of ICA components to be estimated by MELODIC
@@ -729,8 +738,8 @@ def init_spaces(checkpoint=True):
         spaces.checkpoint()
 
     # Add the default standard space if not already present (required by several sub-workflows)
-    if 'MNI152NLin2009cAsym' not in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        spaces.add(Reference('MNI152NLin2009cAsym', {}))
+    if 'MNI152NLin6Asym' not in spaces.get_spaces(nonstandard=False, dim=(3,)):
+        spaces.add(Reference('MNI152NLin6Asym', {}))
 
     # Ensure user-defined spatial references for outputs are correctly parsed.
     # Certain options require normalization to a space not explicitly defined by users.