Convert CLIs to subcommands in modelarrayio CLI (#27)

Author: tsalo

docs/examples/plot_fixel_workflow.py

@@ -98,7 +98,7 @@
 #     # activate your conda environment first
 #     conda activate <env_name>
 #
-#     confixel \
+#     modelarrayio mif-to-h5 \
 #         --index-file      /home/username/myProject/data/FD/index.mif \
 #         --directions-file /home/username/myProject/data/FD/directions.mif \
 #         --cohort-file     /home/username/myProject/data/cohort_FD.csv \
@@ -118,7 +118,7 @@
 #
 # .. code-block:: console
 #
-#     fixelstats_write \
+#     modelarrayio h5-to-mif \
 #         --index-file      /home/username/myProject/data/FD/index.mif \
 #         --directions-file /home/username/myProject/data/FD/directions.mif \
 #         --cohort-file     /home/username/myProject/data/cohort_FD.csv \
@@ -144,7 +144,7 @@
 #
 # .. code-block:: console
 #
-#     confixel --help
-#     fixelstats_write --help
+#     modelarrayio mif-to-h5 --help
+#     modelarrayio h5-to-mif --help
 #
 # or in the :doc:`/usage` page of this documentation.

docs/examples/plot_voxel_workflow.py

@@ -104,7 +104,7 @@
 #     # activate your conda environment first
 #     conda activate <env_name>
 #
-#     convoxel \
+#     modelarrayio nifti-to-h5 \
 #         --group-mask-file /home/username/myProject/data/group_mask.nii.gz \
 #         --cohort-file     /home/username/myProject/data/cohort_FA.csv \
 #         --output-hdf5     /home/username/myProject/data/FA.h5
@@ -121,7 +121,7 @@
 #
 # .. code-block:: console
 #
-#     volumestats_write \
+#     modelarrayio h5-to-nifti \
 #         --group-mask-file /home/username/myProject/data/group_mask.nii.gz \
 #         --cohort-file     /home/username/myProject/data/cohort_FA.csv \
 #         --analysis-name   mylm \
@@ -177,7 +177,7 @@
 #
 # .. code-block:: console
 #
-#     convoxel --help
-#     volumestats_write --help
+#     modelarrayio nifti-to-h5 --help
+#     modelarrayio h5-to-nifti --help
 #
 # or in the :doc:`/usage` page of this documentation.

docs/usage.rst

@@ -3,60 +3,60 @@ Usage
 #####
 
 
-********
-confixel
-********
+**********
+mif-to-h5
+**********
 
 .. argparse::
-   :ref: modelarrayio.cli.mif_to_h5.get_parser
-   :prog: confixel
-   :func: get_parser
+   :ref: modelarrayio.cli.mif_to_h5._parse_mif_to_h5
+   :prog: modelarrayio mif-to-h5
+   :func: _parse_mif_to_h5
 
 
-********
-convoxel
-********
+**********
+nifti-to-h5
+**********
 
 .. argparse::
-   :ref: modelarrayio.cli.nifti_to_h5.get_parser
-   :prog: convoxel
-   :func: get_parser
+   :ref: modelarrayio.cli.nifti_to_h5._parse_nifti_to_h5
+   :prog: modelarrayio nifti-to-h5
+   :func: _parse_nifti_to_h5
 
 
-********
-concifti
-********
+**********
+cifti-to-h5
+**********
 
 .. argparse::
-   :ref: modelarrayio.cli.cifti_to_h5.get_parser
-   :prog: concifti
-   :func: get_parser
+   :ref: modelarrayio.cli.cifti_to_h5._parse_cifti_to_h5
+   :prog: modelarrayio cifti-to-h5
+   :func: _parse_cifti_to_h5
 
 
-****************
-fixelstats_write
-****************
+**********
+h5-to-mif
+**********
 
 .. argparse::
-   :ref: modelarrayio.cli.h5_to_mif.get_parser
-   :prog: fixelstats_write
-   :func: get_parser
+   :ref: modelarrayio.cli.h5_to_mif._parse_h5_to_mif
+   :prog: modelarrayio h5-to-mif
+   :func: _parse_h5_to_mif
 
-*****************
-volumestats_write
-*****************
+***********
+h5-to-nifti
+***********
 
 .. argparse::
-   :ref: modelarrayio.cli.h5_to_nifti.get_parser
-   :prog: volumestats_write
-   :func: get_parser
+   :ref: modelarrayio.cli.h5_to_nifti._parse_h5_to_nifti
+   :prog: modelarrayio h5-to-nifti
+   :func: _parse_h5_to_nifti
 
 
-****************
-ciftistats_write
-****************
+***********
+h5-to-cifti
+***********
 
 .. argparse::
-   :ref: modelarrayio.cli.h5_to_cifti.get_parser
-   :prog: ciftistats_write
-   :func: get_parser
+   :ref: modelarrayio.cli.h5_to_cifti._parse_h5_to_cifti
+   :prog: modelarrayio h5-to-cifti
+   :func: _parse_h5_to_cifti

pyproject.toml

@@ -67,12 +67,7 @@ Repository = "https://github.com/PennLINC/ModelArrayIO"
 Documentation = "https://modelarrayio.readthedocs.io"
 
 [project.scripts]
-confixel = "modelarrayio.cli.mif_to_h5:main"
-convoxel = "modelarrayio.cli.nifti_to_h5:main"
-concifti = "modelarrayio.cli.cifti_to_h5:main"
-fixelstats_write = "modelarrayio.cli.h5_to_mif:main"
-volumestats_write = "modelarrayio.cli.h5_to_nifti:main"
-ciftistats_write = "modelarrayio.cli.h5_to_cifti:main"
+modelarrayio = "modelarrayio.cli.main:main"
 
 #
 # Hatch

src/modelarrayio/cli/cifti_to_h5.py

@@ -204,7 +204,55 @@ def _process_scalar_job(scalar_name, source_files):
         return 0
 
 
-def get_parser():
+def cifti_to_h5_main(
+    cohort_file,
+    backend='hdf5',
+    output_hdf5='fixelarray.h5',
+    output_tiledb='arraydb.tdb',
+    storage_dtype='float32',
+    compression='gzip',
+    compression_level=4,
+    shuffle=True,
+    chunk_voxels=0,
+    target_chunk_mb=2.0,
+    tdb_compression='zstd',
+    tdb_compression_level=5,
+    tdb_shuffle=True,
+    tdb_tile_voxels=0,
+    tdb_target_tile_mb=2.0,
+    tdb_workers=None,
+    scalar_columns=None,
+    s3_workers=1,
+    log_level='INFO',
+):
+    """Entry point for the ``modelarrayio cifti-to-h5`` command."""
+    logging.basicConfig(
+        level=getattr(logging, str(log_level).upper(), logging.INFO),
+        format='[%(levelname)s] %(name)s: %(message)s',
+    )
+    return cifti_to_h5(
+        cohort_file=cohort_file,
+        backend=backend,
+        output_hdf5=output_hdf5,
+        output_tiledb=output_tiledb,
+        storage_dtype=storage_dtype,
+        compression=compression,
+        compression_level=compression_level,
+        shuffle=shuffle,
+        chunk_voxels=chunk_voxels,
+        target_chunk_mb=target_chunk_mb,
+        tdb_compression=tdb_compression,
+        tdb_compression_level=tdb_compression_level,
+        tdb_shuffle=tdb_shuffle,
+        tdb_tile_voxels=tdb_tile_voxels,
+        tdb_target_tile_mb=tdb_target_tile_mb,
+        tdb_workers=tdb_workers,
+        scalar_columns=scalar_columns,
+        s3_workers=s3_workers,
+    )
+
+
+def _parse_cifti_to_h5():
     parser = argparse.ArgumentParser(
         description='Create a hdf5 file of CIDTI2 dscalar data',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -228,15 +276,3 @@ def get_parser():
     )
     add_s3_workers_arg(parser)
     return parser
-
-
-def main():
-    parser = get_parser()
-    args = parser.parse_args()
-    kwargs = vars(args)
-    log_level = kwargs.pop('log_level')
-    logging.basicConfig(
-        level=getattr(logging, str(log_level).upper(), logging.INFO),
-        format='[%(levelname)s] %(name)s: %(message)s',
-    )
-    return cifti_to_h5(**kwargs)

src/modelarrayio/cli/h5_to_cifti.py

@@ -90,33 +90,34 @@ def h5_to_cifti(example_cifti, in_file, analysis_name, output_dir):
             temp_nifti2_1mpvalue.to_filename(out_cifti_1mpvalue)
 
 
-def main():
-    """Write the contents of an hdf5 file to a cifti directory."""
-    parser = get_parser()
-    args = parser.parse_args()
-
-    if os.path.exists(args.output_dir):
+def h5_to_cifti_main(
+    analysis_name,
+    in_file,
+    output_dir,
+    cohort_file=None,
+    example_cifti=None,
+):
+    """Entry point for the ``modelarrayio h5-to-cifti`` command."""
+    if os.path.exists(output_dir):
         print('WARNING: Output directory exists')
-    os.makedirs(args.output_dir, exist_ok=True)
+    os.makedirs(output_dir, exist_ok=True)
 
-    # Get an example cifti
-    example_cifti = args.example_cifti
     if example_cifti is None:
         logger.warning(
             'No example cifti file provided, using the first cifti file from the cohort file'
         )
-        cohort_df = pd.read_csv(args.cohort_file)
+        cohort_df = pd.read_csv(cohort_file)
         example_cifti = cohort_df['source_file'][0]
 
     h5_to_cifti(
         example_cifti=example_cifti,
-        in_file=args.in_file,
-        analysis_name=args.analysis_name,
-        output_dir=args.output_dir,
+        in_file=in_file,
+        analysis_name=analysis_name,
+        output_dir=output_dir,
     )
 
 
-def get_parser():
+def _parse_h5_to_cifti():
     parser = argparse.ArgumentParser(
         description='Create a directory with cifti results from an hdf5 file',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,

src/modelarrayio/cli/h5_to_mif.py

@@ -92,36 +92,32 @@ def h5_to_mif(example_mif, in_file, analysis_name, output_dir):
             nifti2_to_mif(temp_nifti2_1mpvalue, out_mif_1mpvalue)
 
 
-def main():
-    parser = get_parser()
-    args = parser.parse_args()
-
-    if os.path.exists(args.output_dir):
+def h5_to_mif_main(index_file, directions_file, cohort_file, analysis_name, in_file, output_dir):
+    """Entry point for the ``modelarrayio h5-to-mif`` command."""
+    if os.path.exists(output_dir):
         print('WARNING: Output directory exists')
-    os.makedirs(args.output_dir, exist_ok=True)
+    os.makedirs(output_dir, exist_ok=True)
 
-    # Copy in the index and directions
     shutil.copyfile(
-        args.directions_file,
-        os.path.join(args.output_dir, os.path.basename(args.directions_file)),
+        directions_file,
+        os.path.join(output_dir, os.path.basename(directions_file)),
     )
     shutil.copyfile(
-        args.index_file,
-        os.path.join(args.output_dir, os.path.basename(args.index_file)),
+        index_file,
+        os.path.join(output_dir, os.path.basename(index_file)),
     )
 
-    # Get an example mif file
-    cohort_df = pd.read_csv(args.cohort_file)
+    cohort_df = pd.read_csv(cohort_file)
     example_mif = cohort_df['source_file'][0]
     h5_to_mif(
         example_mif=example_mif,
-        in_file=args.in_file,
-        analysis_name=args.analysis_name,
-        output_dir=args.output_dir,
+        in_file=in_file,
+        analysis_name=analysis_name,
+        output_dir=output_dir,
     )
 
 
-def get_parser():
+def _parse_h5_to_mif():
     parser = argparse.ArgumentParser(
         description='Create a fixel directory from an hdf5 file',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,

src/modelarrayio/cli/h5_to_nifti.py

@@ -126,18 +126,28 @@ def _decode_names(arr):
             output_img_1mpvalue.to_filename(out_file_1mpvalue)
 
 
-def main():
-    parser = get_parser()
-    args = parser.parse_args()
-
-    if os.path.exists(args.output_dir):
+def h5_to_nifti_main(
+    group_mask_file,
+    analysis_name,
+    in_file,
+    output_dir,
+    output_extension='.nii.gz',
+):
+    """Entry point for the ``modelarrayio h5-to-nifti`` command."""
+    if os.path.exists(output_dir):
         print('WARNING: Output directory exists')
-    os.makedirs(args.output_dir, exist_ok=True)
-
-    h5_to_nifti(*vars(args))
+    os.makedirs(output_dir, exist_ok=True)
+
+    h5_to_nifti(
+        in_file=in_file,
+        analysis_name=analysis_name,
+        group_mask_file=group_mask_file,
+        output_extension=output_extension,
+        output_dir=output_dir,
+    )
 
 
-def get_parser():
+def _parse_h5_to_nifti():
     parser = argparse.ArgumentParser(
         description='Convert statistical results from an hdf5 file to a volume data (NIfTI file)',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -150,13 +160,6 @@ def get_parser():
         required=True,
         type=IsFile,
     )
-    parser.add_argument(
-        '--cohort-file',
-        '--cohort_file',
-        help='Path to a csv with demographic info and paths to data.',
-        required=True,
-        type=IsFile,
-    )
     parser.add_argument(
         '--analysis-name',
         '--analysis_name',
@@ -180,6 +183,7 @@ def get_parser():
     parser.add_argument(
         '--output-ext',
         '--output_ext',
+        dest='output_extension',
         help=(
             'The extension for output volume data. '
             'Options are .nii.gz (default) and .nii. Please provide the prefix dot.'