oceanproc 1.3.0__tar.gz → 1.3.2__tar.gz

{oceanproc-1.3.0 → oceanproc-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.3.0
+Version: 1.3.2
 Summary: MRI preprocessing for WUSTL Ocean labs
 Author-Email: Ramone Agard <rhagard@wustl.edu>, Joey Scanga <joeyscanga92@gmail.com>
 Requires-Python: <3.13,>=3.10

{oceanproc-1.3.0 → oceanproc-1.3.2}/oceanproc/ocean_proc.py

@@ -103,10 +103,9 @@ def main():
         epilog="An arguments file can be accepted with @FILEPATH.\nAny additional arguments not listed in the help message will be passed to the preprocessing subprocess.",
         allow_abbrev=False
     )
-    parser.add_argument("--version", action="version", version='%(prog)s v1.3.0')
+    parser.add_argument("--version", action="version", version='%(prog)s v1.3.2')
     session_args = parser.add_argument_group("Session Specific")
     config_args = parser.add_argument_group("Configuration Arguments", "These arguments are saved to a file if the '--export_args' option is used")
-    parser.register("type", "Full-Path", lambda p: Path(p).resolve())
 
     session_args.add_argument("--subject", "-su", required=True,
                               help="The identifier of the subject to preprocess")
@@ -158,20 +157,20 @@ def main():
                              help="framewise displacement threshold (in mm) to determine outlier framee (Default is 0.9).")
     config_args.add_argument("--skip_bids_validation", action=argparse.BooleanOptionalAction,
                              help="Specifies skipping BIDS validation (only enabled for fMRIprep step)")
-    config_args.add_argument("--fs_subjects_dir", "-fs", type=ExistingDir,
+    config_args.add_argument("--fs_subjects_dir", "--fs-subjects-dir", "-fs", type=ExistingDir, dest="fs_subjects_dir",
                              help="The path to the directory that contains previous FreeSurfer outputs/derivatives to use for fMRIPrep. If empty, this is the path where new FreeSurfer outputs will be stored.")
     config_args.add_argument("--allow_uneven_fmap_groups", action="store_true",
                              help="Flag to allow for automated fieldmap pairing when there's more AP- than PA-encoded fieldmaps, or vice versa (will still error out if at least one of each is not present.)")
-    config_args.add_argument("--extract_best_fmap", action="store_true",
+    config_args.add_argument("--extract_best_fmap", action=argparse.BooleanOptionalAction,
                              help="Flag to specify that the lowest variance fieldmap volume should be extracted from each fieldmap, and used for distortion correction (opposed to all volumes being used)")
     config_args.add_argument("--dscans_path", type=ExistingDir,
                              help="""The path to the directory containing 'dscans' files for inserting dummy scans into bold runs. Must be named exactly as corresponding bold image except with 'dscans' as 
                              the suffix and '.tsv' as the extension. Contents of the file must be a column, titled 'dummy_scan', with ones and zeros. Ones denote which frames should be dummy scans.""")
-    config_args.add_argument("--precomputed_derivatives", "-pd", type="Full-Path", dest="derivatives", nargs="*",
+    config_args.add_argument("--precomputed_derivatives", "-pd", type=ExistingDir, dest="derivatives", nargs="+",
                              help="A list of paths to any BIDS-style precomputed derivatives that should be used in preprocessing. (Ex. /path/to/bibsnet)")
     config_args.add_argument("--work_dir", "-w", type=ExistingDir, required=True,
                              help="The path to the working directory used to store intermediate files")
-    config_args.add_argument("--fs_license", "-l", type=ExistingFile, required=True,
+    config_args.add_argument("--fs_license", "--fs-license-file", "-l", type=ExistingFile, dest="fs_license", required=True,
                              help="The path to the license file for the local installation of FreeSurfer")
     config_args.add_argument("--image_version", "-iv", default=None,
                              help=f"""The version of fmriprep to use; It is reccomended that an entire study use the same version. 
@@ -185,9 +184,9 @@ def main():
     config_args.add_argument("--bibsnet_work", "-bw", type=ExistingDir,
                              help="The path to the working directory used to store intermediate files for BIBSnet")
     config_args.add_argument("--permissions_group", "-g", type=ValidGroup, default=default_user_group,
-                             help=f"The user group that should own all of the created files. (Default is for the current user is '{default_user_group}'")
+                             help=f"The user group that should own all of the created files. (Default for the current user is '{default_user_group}')")
     config_args.add_argument("--file_permissions", "-fp", type=ValidPermissions, default=default_file_permissions,
-                             help=f"The file permissions that all output files should have, represented in numeric format. (Default permissions is '{default_file_permissions}'")
+                             help=f"The file permissions that all output files should have, represented in numeric format. (Default permissions is '{default_file_permissions}')")
     args, unknown_args = parser.parse_known_args()
 
     if args.infant:

{oceanproc-1.3.0 → oceanproc-1.3.2}/oceanproc/preprocessing_wrapper.py

@@ -13,6 +13,7 @@ import nibabel as nib
 import json
 import os
 import copy
+import subprocess
 from types import SimpleNamespace
 
 logger = logging.getLogger(__name__)
@@ -86,6 +87,13 @@ def run_preprocessing(subject:str,
         mount_flag = "-B"
     else: 
         cmd_prelude = f"docker run --rm -i -u {flags.uid}:{flags.gid}"
+        import grp
+        mygids = (
+            grp.getgrnam(groupname).gr_gid for groupname in 
+            subprocess.run('groups', capture_output=True).stdout.decode().strip().split()
+        )
+        for mygid in mygids:
+            cmd_prelude += f" --group-add {mygid} "
         mount_flag = "-v"
 
     additional_mount_paths = []
@@ -377,13 +385,14 @@ def process_data(subject:str,
     paths_to_update.extend(sorted(derivs_path.glob(f"sub-{subject}*")))
     paths_to_update.extend(sorted(derivs_path.glob(f"sourcedata/*/sub-{subject}*")))
     for out_path in paths_to_update:
-        # update file permissions for preprocessing outputs
-        update_permissions(
-            permissions=flags.file_permissions, 
-            path=out_path, 
-            recursive=True,
-            group=flags.permissions_group
-        )
+        if out_path.exists():
+            # update file permissions for preprocessing outputs
+            update_permissions(
+                permissions=flags.file_permissions, 
+                path=out_path, 
+                recursive=True,
+                group=flags.permissions_group
+            )
         
     # check other top-level files
     other_paths = [derivs_path/"dataset_description.json", derivs_path/"logs"]
@@ -406,4 +415,4 @@ def process_data(subject:str,
     )
     
     if not preproc_success:
-        exit_program_early(f"Program '{preproc_title}' has run into an error.")
+        exit_program_early(f"Program '{preproc_title}' has run into an error.")

{oceanproc-1.3.0 → oceanproc-1.3.2}/oceanproc/segmentation_wrapper.py

@@ -128,12 +128,13 @@ def segment_anatomical(subject:str,
     paths_to_update = sorted(derivs_path.glob(f"bibsnet/sub-{subject}*"))
     paths_to_update.extend(sorted(work_path.glob(f"*/sub-{subject}*")))
     for out_path in paths_to_update:
-        # update file permissions for segmentation outputs and working files
-        update_permissions(
-            permissions=flags.file_permissions, 
-            path=out_path, 
-            recursive=True,
-            group=flags.permissions_group)
+        if out_path.exists():
+            # update file permissions for segmentation outputs and working files
+            update_permissions(
+                permissions=flags.file_permissions, 
+                path=out_path, 
+                recursive=True,
+                group=flags.permissions_group)
         
     # check other top-level files
     other_paths = [derivs_path/"dataset_description.json"]

{oceanproc-1.3.0 → oceanproc-1.3.2}/oceanproc/utils.py

@@ -239,10 +239,11 @@ def prepare_subprocess_logging(this_logger,
 
 
 @debug_logging
-def run_subprocess(cmd: str, title: str, log_output=True):
+def run_subprocess(cmd: str, title: str, log_output=True, quiet=False):
     split_cmd = shlex.split(cmd)
     logger.info(f"running '{title}' with the following command: \n{' '.join(split_cmd)}\n")
     prepare_subprocess_logging(logger)
+    ecode = 0
     with Popen(split_cmd, stdout=PIPE, stderr=PIPE) as p:
         while p.poll() == None:
             if log_output:
@@ -251,9 +252,11 @@ def run_subprocess(cmd: str, title: str, log_output=True):
                 for line in p.stderr:
                     logger.info(line.decode("utf-8", "ignore"))
         prepare_subprocess_logging(logger, stop=True)
+        ecode = p.poll()
         p.kill()
-        if (ecode:=p.poll()) != 0:
+        if (ecode != 0) and (not quiet):
             raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code <{ecode}>.")
+    return ecode
 
 
 def log_linebreak():
@@ -412,8 +415,8 @@ def update_permissions(permissions:str, path:Path, recursive=False, group=None,
         raise ValueError(f"Did not receive a valid path: <{path}>")
     
     chmod_cmd = f"chmod {'-R' if recursive else ''} {permissions} {path.resolve()}"
-    run_subprocess(cmd=chmod_cmd, title="chmod", log_output=False)
+    run_subprocess(cmd=chmod_cmd, title="chmod", log_output=False, quiet=True)
 
     if group is not None:
         chgrp_cmd = f"chgrp {'-R' if recursive else ''} {group} {path.resolve()}"
-        run_subprocess(cmd=chgrp_cmd, title="chgrp", log_output=False)
+        run_subprocess(cmd=chgrp_cmd, title="chgrp", log_output=False, quiet=True)

{oceanproc-1.3.0 → oceanproc-1.3.2}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.3.0"
+version = "1.3.2"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"