nipreps · oesteban · Apr 16, 2024 · Apr 13, 2024 · Apr 15, 2024 · Apr 15, 2024
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -11,6 +11,7 @@
 All configuration values have a default; values that are commented out
 serve to show the default.
 """
+
 import os
 
 from packaging.version import Version

diff --git a/mriqc/__init__.py b/mriqc/__init__.py
@@ -25,6 +25,7 @@
 :abbr:`IQMs (image quality metrics)` to used in :abbr:`QAPs (quality
 assessment protocols)` for :abbr:`MRI (magnetic resonance imaging)`.
 """
+
 from mriqc._version import __version__
 
 __copyright__ = 'Copyright 2022, The NiPreps Developers'

diff --git a/mriqc/_warnings.py b/mriqc/_warnings.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Manipulate Python warnings."""
+
 import logging
 import sys
 
@@ -64,12 +65,15 @@ def __init__(self, datefmt=None, colored=True, **kwargs):
     def format(self, record):
         reset = CONSOLE_COLORS['reset'] if self._colored else ''
         self._style._fmt = (
-            '%(message)s' if record.levelno == 26
+            '%(message)s'
+            if record.levelno == 26
             else LOGGER_FMT.format(
                 color=CONSOLE_COLORS.get(
                     record.levelno,
                     CONSOLE_COLORS['reset'],
-                ) if self._colored else '',
+                )
+                if self._colored
+                else '',
                 reset=reset,
             )
         )

diff --git a/mriqc/bin/abide2bids.py b/mriqc/bin/abide2bids.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """ABIDE2BIDS download tool."""
+
 from __future__ import annotations
 
 import errno
@@ -50,12 +51,8 @@ def main():
     )
     g_input = parser.add_argument_group('Inputs')
     g_input.add_argument('-i', '--input-abide-catalog', action='store', required=True)
-    g_input.add_argument(
-        '-n', '--dataset-name', action='store', default='ABIDE Dataset'
-    )
-    g_input.add_argument(
-        '-u', '--nitrc-user', action='store', default=os.getenv('NITRC_USER')
-    )
+    g_input.add_argument('-n', '--dataset-name', action='store', default='ABIDE Dataset')
+    g_input.add_argument('-u', '--nitrc-user', action='store', default=os.getenv('NITRC_USER'))
     g_input.add_argument(
         '-p',
         '--nitrc-password',

diff --git a/mriqc/bin/dfcheck.py b/mriqc/bin/dfcheck.py
@@ -23,6 +23,7 @@
 """
 Compares pandas dataframes by columns.
 """
+
 import sys
 from argparse import ArgumentParser, RawTextHelpFormatter
 from pathlib import Path
@@ -39,9 +40,7 @@ def read_iqms(feat_file):
     feat_file = Path(feat_file)
 
     if feat_file.suffix == '.csv':
-        x_df = pd.read_csv(
-            feat_file, index_col=False, dtype={col: str for col in BIDS_COMP}
-        )
+        x_df = pd.read_csv(feat_file, index_col=False, dtype={col: str for col in BIDS_COMP})
         # Find present bids bits and sort by them
         bids_comps_present = list(set(x_df.columns) & set(BIDS_COMP))
         bids_comps_present = [bit for bit in BIDS_COMP if bit in bids_comps_present]
@@ -58,9 +57,7 @@ def read_iqms(feat_file):
                 pass
     else:
         bids_comps_present = ['subject_id']
-        x_df = pd.read_csv(
-            feat_file, index_col=False, sep='\t', dtype={'bids_name': str}
-        )
+        x_df = pd.read_csv(feat_file, index_col=False, sep='\t', dtype={'bids_name': str})
         x_df = x_df.sort_values(by=['bids_name'])
         x_df['subject_id'] = x_df.bids_name.str.lstrip('sub-')
         x_df = x_df.drop(columns=['bids_name'])
@@ -134,9 +131,7 @@ def main():
         tst_keep = np.sum(tst_rows.isin(ref_rows).values.ravel().tolist())
         print(tst_keep)
 
-    diff = ~np.isclose(
-        ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance
-    )
+    diff = ~np.isclose(ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance)
     if np.any(diff):
         # ne_stacked = pd.DataFrame(data=diff, columns=ref_names).stack()
         # ne_stacked = np.isclose(ref_df[ref_names], tst_df[ref_names]).stack()

diff --git a/mriqc/bin/fs2gif.py b/mriqc/bin/fs2gif.py
@@ -23,6 +23,7 @@
 """
 Batch export freesurfer results to animated gifs.
 """
+
 import os
 import os.path as op
 import subprocess as sp
@@ -129,10 +130,7 @@ def main():
                 )
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
-                tclfp.write(
-                    f'    SaveTIFF [format "{tmp_sub}/{subid}-'
-                    '%03d.tif" $i]\n'
-                )
+                tclfp.write(f'    SaveTIFF [format "{tmp_sub}/{subid}-' '%03d.tif" $i]\n')
                 tclfp.write('    incr i\n')
                 tclfp.write('}\n')
                 tclfp.write('QuitMedit\n')
@@ -175,15 +173,10 @@ def main():
                     'for { set slice %d } { $slice < %d } { incr slice } {'
                     % (bbox_min[2], bbox_max[2])
                 )
-                tclfp.write(
-                    '    SetZoomCenter %d %d $slice\n'
-                    % (center[0] + 30, center[1] - 10)
-                )
+                tclfp.write('    SetZoomCenter %d %d $slice\n' % (center[0] + 30, center[1] - 10))
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
-                tclfp.write(
-                    f'    SaveTIFF [format "{tmp_sub}/{subid}-lh-%03d.tif" $i]\n'
-                )
+                tclfp.write(f'    SaveTIFF [format "{tmp_sub}/{subid}-lh-%03d.tif" $i]\n')
                 tclfp.write('    incr i\n')
                 tclfp.write('}\n')
                 tclfp.write('QuitMedit\n')
@@ -205,15 +198,10 @@ def main():
                     'for { set slice %d } { $slice < %d } { incr slice } {'
                     % (bbox_min[2], bbox_max[2])
                 )
-                tclfp.write(
-                    '    SetZoomCenter %d %d $slice\n'
-                    % (center[0] - 30, center[1] - 10)
-                )
+                tclfp.write('    SetZoomCenter %d %d $slice\n' % (center[0] - 30, center[1] - 10))
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
-                tclfp.write(
-                    f'    SaveTIFF [format "{tmp_sub}/{subid}-rh-%03d.tif" $slice]\n'
-                )
+                tclfp.write(f'    SaveTIFF [format "{tmp_sub}/{subid}-rh-%03d.tif" $slice]\n')
                 tclfp.write('    incr i\n')
                 tclfp.write('}\n')
                 tclfp.write('QuitMedit\n')

diff --git a/mriqc/bin/messages.py b/mriqc/bin/messages.py
@@ -20,20 +20,12 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-ABIDE_SUBJECT_FETCHED = (
-    'Successfully processed subject {subject_id} from site {site_name}'
-)
+ABIDE_SUBJECT_FETCHED = 'Successfully processed subject {subject_id} from site {site_name}'
 ABIDE_TEMPORAL_WARNING = 'WARNING: Error deleting temporal files: {message}'
-BIDS_LABEL_MISSING = (
-    'Participant label(s) not found in the BIDS root directory: {label}'
-)
-BIDS_GROUP_SIZE = (
-    'Group size should be at least 0 (i.e. all participants assigned to same group).'
-)
+BIDS_LABEL_MISSING = 'Participant label(s) not found in the BIDS root directory: {label}'
+BIDS_GROUP_SIZE = 'Group size should be at least 0 (i.e. all participants assigned to same group).'
 CLF_CAPTURED_WARNING = 'Captured warning ({category}): {message}'
-CLF_CLASSIFIER_MISSING = (
-    'No training samples were given, and the --load-classifier option {info}.'
-)
+CLF_CLASSIFIER_MISSING = 'No training samples were given, and the --load-classifier option {info}.'
 CLF_SAVED_RESULTS = 'Results saved as {path}.'
 CLF_TRAIN_LOAD_ERROR = 'Errors ({n_errors}) loading training set: {errors}.'
 CLF_WRONG_PARAMETER_COUNT = 'Wrong number of parameters.'

diff --git a/mriqc/bin/nib_hash.py b/mriqc/bin/nib_hash.py
@@ -23,6 +23,7 @@
 """
 Extracts the sha hash of the contents of a nifti file.
 """
+
 from argparse import ArgumentParser, RawTextHelpFormatter
 from hashlib import sha1
 

diff --git a/mriqc/bin/subject_wrangler.py b/mriqc/bin/subject_wrangler.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """BIDS-Apps subject wrangler."""
+
 import glob
 import os.path as op
 from argparse import ArgumentParser, RawTextHelpFormatter
@@ -124,9 +125,7 @@ def main():
 
         if list(set(subject_list) - set(all_subjects)):
             non_exist = list(set(subject_list) - set(all_subjects))
-            missing_label_error = messages.BIDS_LABEL_MISSING.format(
-                label=' '.join(non_exist)
-            )
+            missing_label_error = messages.BIDS_LABEL_MISSING.format(label=' '.join(non_exist))
             raise RuntimeError(missing_label_error)
 
     if not opts.no_randomize:

diff --git a/mriqc/cli/parser.py b/mriqc/cli/parser.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Parser."""
+
 import re
 
 from mriqc import config
@@ -42,10 +43,9 @@ def _parse_participant_labels(value):
     ['s060']
 
     """
-    return sorted({
-        re.sub(r'^sub-', '', item.strip())
-        for item in re.split(r'\s+', f'{value}'.strip())
-    })
+    return sorted(
+        {re.sub(r'^sub-', '', item.strip()) for item in re.split(r'\s+', f'{value}'.strip())}
+    )
 
 
 def _build_parser():
@@ -176,10 +176,13 @@ def _bids_filter(value):
         'identifier (the sub- prefix can be removed).',
     )
     g_bids.add_argument(
-        '--bids-filter-file', action='store', type=Path, metavar='PATH',
+        '--bids-filter-file',
+        action='store',
+        type=Path,
+        metavar='PATH',
         help='a JSON file describing custom BIDS input filter using pybids '
-             '{<suffix>:{<entity>:<filter>,...},...} '
-             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)'
+        '{<suffix>:{<entity>:<filter>,...},...} '
+        '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)',
     )
     g_bids.add_argument(
         '--session-id',
@@ -280,7 +283,7 @@ def _bids_filter(value):
         action='store_true',
         default=True,
         help="Cast the input data to float32 if it's represented in higher precision "
-        "(saves space and improves performance).",
+        '(saves space and improves performance).',
     )
     g_perfm.add_argument(
         '--pdb',
@@ -333,8 +336,7 @@ def _bids_filter(value):
         '--no-sub',
         default=False,
         action='store_true',
-        help="Turn off submission of anonymized quality metrics "
-        "to MRIQC's metrics repository.",
+        help="Turn off submission of anonymized quality metrics to MRIQC's metrics repository.",
     )
     g_outputs.add_argument(
         '--email',
@@ -423,15 +425,13 @@ def _bids_filter(value):
         '--deoblique',
         action='store_true',
         default=False,
-        help='Deoblique the functional scans during head motion correction '
-        'preprocessing.',
+        help='Deoblique the functional scans during head motion correction preprocessing.',
     )
     g_func.add_argument(
         '--despike',
         action='store_true',
         default=False,
-        help='Despike the functional scans during head motion correction '
-        'preprocessing.',
+        help='Despike the functional scans during head motion correction preprocessing.',
     )
     g_func.add_argument(
         '--start-idx',
@@ -491,18 +491,16 @@ def parse_args(args=None, namespace=None):
 
     config.loggers.init()
 
-    _log_file = (
-        Path(opts.output_dir)
-        / 'logs'
-        / f'mriqc-{config.execution.run_uuid}.log'
-    )
+    _log_file = Path(opts.output_dir) / 'logs' / f'mriqc-{config.execution.run_uuid}.log'
     _log_file.parent.mkdir(exist_ok=True, parents=True)
     _handler = FileHandler(_log_file)
-    _handler.setFormatter(_LogFormatter(
-        fmt=LOGGER_FMT.format(color='', reset=''),
-        datefmt=DATE_FMT,
-        colored=False,
-    ))
+    _handler.setFormatter(
+        _LogFormatter(
+            fmt=LOGGER_FMT.format(color='', reset=''),
+            datefmt=DATE_FMT,
+            colored=False,
+        )
+    )
     config.loggers.default.addHandler(_handler)
 
     extra_messages = ['']
@@ -521,7 +519,7 @@ def parse_args(args=None, namespace=None):
             output_dir=opts.output_dir,
             analysis_level=opts.analysis_level,
             extra_messages='\n'.join(extra_messages),
-        )
+        ),
     )
     config.from_dict(vars(opts))
 
@@ -535,9 +533,7 @@ def parse_args(args=None, namespace=None):
         if _plugin:
             config.nipype.plugin = _plugin
             config.nipype.plugin_args = plugin_settings.get('plugin_args', {})
-            config.nipype.nprocs = config.nipype.plugin_args.get(
-                'nprocs', config.nipype.nprocs
-            )
+            config.nipype.nprocs = config.nipype.plugin_args.get('nprocs', config.nipype.nprocs)
 
     # Load BIDS filters
     if opts.bids_filter_file:
@@ -575,13 +571,12 @@ def parse_args(args=None, namespace=None):
     config.execution.init()
 
     participant_label = [
-        d.name[4:] for d in config.execution.bids_dir.glob('sub-*')
-        if d.is_dir() and d.exists()
+        d.name[4:] for d in config.execution.bids_dir.glob('sub-*') if d.is_dir() and d.exists()
     ]
 
     if config.execution.participant_label is not None:
         selected_label = set(config.execution.participant_label)
-        if (missing_subjects := selected_label - set(participant_label)):
+        if missing_subjects := selected_label - set(participant_label):
             parser.error(
                 "One or more participant labels were not found in the BIDS directory: "
                 f"{', '.join(missing_subjects)}."
@@ -604,23 +599,19 @@ def parse_args(args=None, namespace=None):
         session_id=config.execution.session_id,
         task=config.execution.task_id,
         group_echos=True,
-        bids_filters={
-            mod: config.execution.bids_filters.get(mod, {})
-            for mod in lc_modalities
-        },
-        queries={mod: DEFAULT_BIDS_QUERIES[mod] for mod in lc_modalities}
+        bids_filters={mod: config.execution.bids_filters.get(mod, {}) for mod in lc_modalities},
+        queries={mod: DEFAULT_BIDS_QUERIES[mod] for mod in lc_modalities},
     )
 
     # Drop empty queries
-    bids_dataset = {
-        mod: files for mod, files in bids_dataset.items() if files
-    }
+    bids_dataset = {mod: files for mod, files in bids_dataset.items() if files}
     config.workflow.inputs = bids_dataset
 
     # Check the query is not empty
     if not list(config.workflow.inputs.values()):
         ffile = (
-            '(--bids-filter-file was not set)' if not opts.bids_filter_file
+            '(--bids-filter-file was not set)'
+            if not opts.bids_filter_file
             else f"(with '--bids-filter-file {opts.bids_filter_file}')"
         )
         parser.error(
@@ -636,8 +627,7 @@ def parse_args(args=None, namespace=None):
     }
     if unknown_mods:
         parser.error(
-            'MRIQC is unable to process the following modalities: '
-            f'{", ".join(unknown_mods)}.'
+            f'MRIQC is unable to process the following modalities: {", ".join(unknown_mods)}.'
         )
 
     # Estimate the biggest file size / leave 1GB if some file does not exist (datalad)
-Original file line number
+Diff line change
@@ Expand Up / @@ -23,6 +23,7 @@ @@
     """
     Extracts the sha hash of the contents of a nifti file.
     """
     from argparse import ArgumentParser, RawTextHelpFormatter
     from hashlib import sha1
@@ Expand Down @@