Add support for FreeSurfer

setup.py

@@ -26,6 +26,9 @@ def get_version(rel_path: str) -> str:
     author_email='[email protected]',
     url='https://github.com/FNNDSC/pl-visual-dataset',
     packages=['visualdataset'],
+    package_data={
+        'visualdataset': ['colormaps/*']
+    },
     install_requires=['chris_plugin'],
     license='MIT',
     entry_points={

visualdataset/__main__.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import os.path
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 from pathlib import Path
 
@@ -13,12 +14,14 @@
 parser = ArgumentParser(description='Prepares a dataset for use with the ChRIS_ui '
                                     '"Visual Datasets" feature.',
                         formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('--matchers', type=str, required=True,
+parser.add_argument('--mode', type=str, default='file', choices=['file', 'string', 'freesurfer-7.3.3'],
+                    help='File matching and option selection mode. file=accept JSON files from '
+                         '--matchers and --options. string=accept JSON strings from --matchers and --options. '
+                         'freesurfer=built-in support for the FreeSurfer output files.')
+parser.add_argument('--matchers', type=str,
                     help='Regular expressions used to assign tags to files')
 parser.add_argument('--options', type=str,
                     help='Metadata to go with tag sets')
-parser.add_argument('-s', '--string-args', action='store_true',
-                    help='Interpret --matchers and --options as data instead of paths')
 parser.add_argument('--first-run-files', type=str, default='[]',
                     help='List of files to show on first run, '
                          'as a stringified JSON list of paths relative to inputdir')
@@ -39,10 +42,14 @@
     min_cpu_limit='1000m',
 )
 def main(options: Namespace, inputdir: Path, outputdir: Path):
-    matchers, tag_options = parse_args(options.matchers, options.options,
-                                       None if options.string_args else inputdir)
+    matchers, tag_options = parse_args(inputdir, options.mode, options.matchers, options.options)
     first_run_files = _LIST_ADAPTER.validate_json(options.first_run_files)
     first_run_tags = _DICT_ADAPTER.validate_json(options.first_run_tags)
+
+    if not first_run_files and options.mode.lower().startswith('freesurfer'):
+        if t1 := next(filter(os.path.isfile, inputdir.rglob('T1.mgz')), None):
+            first_run_files.append(str(t1.relative_to(inputdir)))
+
     print(DISPLAY_TITLE, flush=True)
     brain_dataset(inputdir, outputdir, matchers, tag_options, first_run_files, first_run_tags, options.readme)
 

visualdataset/brain_dataset.py

@@ -1,6 +1,8 @@
+import shutil
 import sys
 from pathlib import Path
-from typing import Sequence, Optional, Mapping, Set
+from typing import Sequence, Optional, Mapping, Set, Iterator
+import importlib.resources
 
 from tqdm import tqdm
 
@@ -39,6 +41,8 @@ def brain_dataset(
               'for the files of --first-run-files')
         sys.exit(1)
 
+    copy_colormaplabel_files(options, input_dir, output_dir)
+
     with tqdm(index, desc='Writing outputs') as pbar:
         for file in pbar:
             output_path = output_dir / file.path
@@ -91,3 +95,32 @@ def find_first_run_files(
             print(f'File was not matched: {file}')
             sys.exit(1)
     return first_run_index_nums
+
+
+def copy_colormaplabel_files(options: Sequence[OptionsLink], input_dir: Path, output_dir: Path):
+    for file in colormaplabel_files_of(options):
+        shutil.copy(resolve_colormaplabel(file, input_dir), output_dir / file)
+
+
+def resolve_colormaplabel(file: str, input_dir: Path) -> Path:
+    """
+    If ``file`` is found in ``input_dir``, return its path.
+    Else, look for the file in this package's files.
+    """
+    path = input_dir / file
+    if path.is_file():
+        return path
+    trav = importlib.resources.files(__package__).joinpath('colormaps', file)
+    if trav.is_file():
+        with importlib.resources.as_file(trav) as trav_path:
+            return trav_path
+    print(f'colormapLabel not found: "{file}"')
+    sys.exit(1)
+
+
+def colormaplabel_files_of(options: Sequence[OptionsLink]) -> Iterator[str]:
+    return filter(lambda x: x is not None, map(colormaplabel_of, options))
+
+
+def colormaplabel_of(option: OptionsLink) -> Optional[str]:
+    return option.options.get('niivue_defaults', {}).get('colormapLabelFile', None)

visualdataset/json_arg_parser.py

@@ -7,16 +7,23 @@
 
 from visualdataset.args_types import Matcher
 from visualdataset.manifest import OptionsLink
+from visualdataset.wellknown import FREESURFER_MATCHERS, FREESURFER_OPTIONS
 
 
-def parse_args(matchers: str | None, options: str | None, input_dir: Path | None,
+def parse_args(input_dir: Path, mode: str, matchers: str | None, options: str | None
                ) -> tuple[Sequence[Matcher], Sequence[OptionsLink]]:
-    if input_dir:
+    mode = mode.lower()
+    if mode.startswith('freesurfer'):
+        return FREESURFER_MATCHERS, FREESURFER_OPTIONS
+    if mode == 'file':
         matchers_str = '[]' if matchers is None else (input_dir / matchers).read_text()
         options_str = '[]' if options is None else (input_dir / options).read_text()
-    else:
+    elif mode == 'string':
         matchers_str = '[]' if matchers is None else matchers
         options_str = '[]' if options is None else options
+    else:
+        print(f'Unsupported option --mode={mode}')
+        sys.exit(1)
     matchers_list = deserialize_list(matchers_str, Matcher, '--matchers')
     options_list = deserialize_list(options_str, OptionsLink, '--options')
     return matchers_list, options_list

visualdataset/wellknown/__init__.py

@@ -0,0 +1,2 @@
+from visualdataset.wellknown.freesurfer import FREESURFER_MATCHERS, FREESURFER_OPTIONS
+

visualdataset/wellknown/freesurfer.py

@@ -0,0 +1,82 @@
+"""
+See https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
+"""
+
+from typing import Sequence
+
+from visualdataset.args_types import Matcher
+from visualdataset.manifest import OptionsLink
+from visualdataset.options import ChrisViewerFileOptions, NiivueVolumeSettings
+
+FREESURFER_MATCHERS: Sequence[Matcher] = [
+    Matcher(key='type', value='T1 MRI', regex=r'mri/T1\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='name', value='T1 MRI', regex=r'mri/T1\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='type', value='T1 MRI', regex=r'mri/brainmask\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='name', value='brain', regex=r'mri/brainmask\.(mgz|nii|nii\.gz)$'),
+
+    Matcher(key='type', value='labels', regex=r'mri/wmparc\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='labels', value='White Matter Parcellation', regex=r'mri/wmparc\.(mgz|nii|nii\.gz)$'),
+
+    Matcher(key='type', value='labels', regex=r'mri/aparc\.a2009s\+aseg\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='labels', value='Destrieux Atlas Parcellation', regex=r'mri/aparc\.a2009s\+aseg\.(mgz|nii|nii\.gz)$'),
+
+    Matcher(key='type', value='labels',
+            regex=r'mri/aparc\.DKTatlas\+aseg(\.(orig|deep|deep\.withCC))?\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='labels', value='DKTatlas',
+            regex=r'mri/aparc\.DKTatlas\+aseg(\.(orig|deep|deep\.withCC))?\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='program', value='FreeSurfer',
+            regex=r'mri/aparc\.DKTatlas\+aseg\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='program', value='FastSurfer',
+            regex=r'mri/aparc\.DKTatlas\+aseg\.deep(\.withCC)?\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='withCC', value='yes',
+            regex=r'mri/aparc\.DKTatlas\+aseg\.deep\.withCC\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='withCC', value='no',
+            regex=r'mri/aparc\.DKTatlas\+aseg\.deep\.(mgz|nii|nii\.gz)$'),
+    Matcher(key='orig', value='yes',
+            regex=r'mri/aparc\.DKTatlas\+aseg\.orig\.(mgz|nii|nii\.gz)$')
+]
+
+FREESURFER_OPTIONS: Sequence[OptionsLink] = [
+    OptionsLink(
+        match={'type': 'T1 MRI'},
+        options=ChrisViewerFileOptions(niivue_defaults=NiivueVolumeSettings(colormap='gray'))
+    ),
+    OptionsLink(
+        match={'name': 'T1 MRI'},
+        options=ChrisViewerFileOptions(name='T1 MRI')
+    ),
+    OptionsLink(
+        match={'name': 'brain'},
+        options=ChrisViewerFileOptions(name='Extracted brain (skull-stripped)')
+    ),
+    OptionsLink(
+        match={'type': 'labels'},
+        options=ChrisViewerFileOptions(
+            niivue_defaults=NiivueVolumeSettings(colormapLabelFile='FreeSurferColorLUT.v7.3.3.json')
+        )
+    ),
+    OptionsLink(
+        match={'labels': 'White Matter Parcellation'},
+        options=ChrisViewerFileOptions(name='White Matter Parcellation')
+    ),
+    OptionsLink(
+        match={'labels': 'Destrieux Atlas Parcellation'},
+        options=ChrisViewerFileOptions(name='Destrieux Atlas Parcellation')
+    ),
+    OptionsLink(
+        match={'labels': 'DKTatlas', 'program': 'FreeSurfer'},
+        options=ChrisViewerFileOptions(name='Desikan-Killiany Atlas')
+    ),
+    OptionsLink(
+        match={'labels': 'DKTatlas', 'program': 'FastSurfer', 'withCC': 'yes'},
+        options=ChrisViewerFileOptions(name='Desikan-Killiany Atlas (FastSurfer, with corpus callosum)')
+    ),
+    OptionsLink(
+        match={'labels': 'DKTatlas', 'program': 'FastSurfer', 'withCC': 'no'},
+        options=ChrisViewerFileOptions(name='Desikan-Killiany Atlas (FastSurfer)')
+    ),
+    OptionsLink(
+        match={'labels': 'DKTatlas', 'orig': 'yes'},
+        options=ChrisViewerFileOptions(name='Desikan-Killiany Atlas (original)')
+    ),
+]