oceanproc 1.3.1__tar.gz → 1.3.3__tar.gz

{oceanproc-1.3.1 → oceanproc-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.3.1
+Version: 1.3.3
 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-1.3.1 → oceanproc-1.3.3}/oceanproc/ocean_proc.py

@@ -103,7 +103,7 @@ 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 v1.3.1')
+    parser.add_argument("--version", action="version", version='%(prog)s v1.3.3')
     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")
 
@@ -157,11 +157,13 @@ 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("--topup_config", "--topup-config", "-tc", type=ExistingFile, dest="topup_config",
+                             help="Path to a TOPUP config file.")
     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 
@@ -170,7 +172,7 @@ def main():
                              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. 
@@ -296,7 +298,7 @@ def main():
     ignore_list = ["tmp_dcm2bids"]
     if (bids_path / ".bidsignore").is_file():
         with open(bids_path / ".bidsignore", "r") as f:
-            ignore_list.extend(f.readlines())
+            ignore_list.extend([l.strip() for l in f.readlines()])
     ignore_list = list(set(ignore_list))
     other_sub_paths = [
       p.name for p in bids_path.glob("sub-*") 

{oceanproc-1.3.1 → oceanproc-1.3.3}/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__)
@@ -31,8 +32,12 @@ infant_defaults = SimpleNamespace(
 )
 
 # Preprocessing arguments that need to have their paths binded when running docker
-mount_opts = {"fs_subjects_dir",
-                  "derivatives"}
+mount_opts = {
+    "fs_subjects_dir",
+    "derivatives",
+    "topup_config"
+}
+
 
 @debug_logging
 def run_preprocessing(subject:str,
@@ -68,7 +73,7 @@ def run_preprocessing(subject:str,
     :raise RuntimeError: If preprocessing throws an error, or exits with a non-zero exit code.
     """
     def clean_up(): return shutil.rmtree(work_path) if remove_work_folder else None
-   
+
     log_linebreak()
     logger.info(f"####### Starting {title} #######\n")
     if not bids_path.exists():
@@ -80,12 +85,19 @@ def run_preprocessing(subject:str,
     bids_mount = "/data"
     derivs_mount = "/out"
     work_mount = "/work"
-    
+
     if flags.apptainer:
         cmd_prelude = f"apptainer run --nv --cleanenv --no-mount cwd --pwd {work_mount}"
         mount_flag = "-B"
-    else: 
+    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 = []
@@ -118,7 +130,7 @@ def run_preprocessing(subject:str,
                             -w {work_mount} --verbose
                             {additional_mount_args}
                             {option_chain}"""
-    
+
     success = True
     try:
         run_subprocess(preproc_command, title=title)
@@ -132,6 +144,7 @@ def run_preprocessing(subject:str,
 
     return success
 
+
 @debug_logging
 def add_fd_plot_to_report(subject:str,
                           session:str,
@@ -222,7 +235,7 @@ def add_fd_plot_to_report(subject:str,
                 # Add the new elements into the file
                 logger.debug(f" inserting the new html elements into the {title} report")
                 confounds_plot_div.insert_after(fd_plot_div)
-            else: 
+            else:
                 confounds_plot_reference_div = confounds_plot_div.find_next_sibling("div", class_="elem-filename")
                 fd_plot_reference_div = copy.copy(confounds_plot_reference_div)
                 fd_plot_reference_div.a["href"] = "./" + rel_path
@@ -244,9 +257,9 @@ def insert_dummy_frames(subject:str,
                         session:str,
                         dscan_dir:Path,
                         bids_layout:BIDSLayout):
-    
+
     dscans_suffix = "dscans"
-    dscans_path_pattern = "sub-{subject}[/ses-{session}]/{datatype<func|meg|beh>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<"+dscans_suffix+">}{extension<.tsv|.json>|.tsv}"
+    dscans_path_pattern = "sub-{subject}[/ses-{session}]/{datatype<func|meg|beh>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<" + dscans_suffix + ">}{extension<.tsv|.json>|.tsv}"
 
     log_linebreak()
     logger.info(f"####### Inserting Dummy Scans #######\n")
@@ -298,27 +311,27 @@ def insert_dummy_frames(subject:str,
         frame_list = []
         dscans_index = 0
         for f in range(num_bold_frames):
-            copy_dex = f-1 if f > 0 else f
+            copy_dex = f - 1 if f > 0 else f
             while dscans_list[dscans_index] != 0:
                 frame_list.append(bold_data[:,:,:,copy_dex])
                 dscans_index += 1
             frame_list.append(bold_data[:,:,:,f])
             dscans_index += 1
             # check if end of run needs to be extended
-            if (f == num_bold_frames-1) and (dscans_index < len(dscans_list)):
+            if (f == num_bold_frames - 1) and (dscans_index < len(dscans_list)):
                 while dscans_index < len(dscans_list):
                     frame_list.append(bold_data[:,:,:,f])
                     dscans_index += 1
 
         if len(frame_list) != len(dscans_list):
             exit_program_early(f"Something went wrong when creating dummy scans, lengths do not match. bold frames: {len(frame_list)}, dscan length: {len(dscans_list)}")
-        
+
         # save new image
         extended_bold_data = np.stack(frame_list, axis=3)
         extended_bold_img = bold_img.__class__(extended_bold_data, header=bold_img.header, affine=bold_img.affine)
         logger.info(f"  saving extended bold image")
         nib.save(extended_bold_img, bfile.path)
-    
+
 
 @debug_logging
 def process_data(subject:str,
@@ -356,23 +369,23 @@ def process_data(subject:str,
     preproc_title = "NiBabies" if flags.infant else "fMRIPrep"
 
     preproc_success = run_preprocessing(subject=subject,
-                      session=session if flags.infant else None,
-                      bids_path=bids_path,
-                      derivs_path=derivs_path,
-                      work_path=work_path,
-                      license_file=license_file,
-                      image_name=image_name,
-                      title=preproc_title,
-                      option_chain=option_chain,
-                      additional_mounts=additional_mounts,
-                      remove_work_folder=remove_work_folder)
-    
+                                        session=session if flags.infant else None,
+                                        bids_path=bids_path,
+                                        derivs_path=derivs_path,
+                                        work_path=work_path,
+                                        license_file=license_file,
+                                        image_name=image_name,
+                                        title=preproc_title,
+                                        option_chain=option_chain,
+                                        additional_mounts=additional_mounts,
+                                        remove_work_folder=remove_work_folder)
+
     if preproc_success:
         add_fd_plot_to_report(subject=subject,
-                            session=session,
-                            derivs_path=derivs_path,
-                            title=preproc_title)
-    
+                              session=session,
+                              derivs_path=derivs_path,
+                              title=preproc_title)
+
     paths_to_update = []
     paths_to_update.extend(sorted(derivs_path.glob(f"sub-{subject}*")))
     paths_to_update.extend(sorted(derivs_path.glob(f"sourcedata/*/sub-{subject}*")))
@@ -380,14 +393,14 @@ def process_data(subject:str,
         if out_path.exists():
             # update file permissions for preprocessing outputs
             update_permissions(
-                permissions=flags.file_permissions, 
-                path=out_path, 
+                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"]
+    other_paths = [derivs_path / "dataset_description.json", derivs_path / "logs"]
     for op in other_paths:
         if op.exists() and (op.stat().st_uid == flags.uid):
             update_permissions(
@@ -396,15 +409,15 @@ def process_data(subject:str,
                 recursive=True,
                 group=flags.permissions_group
             )
-            
+
     # update file permisions for working directory files
     update_permissions(
-        permissions=flags.file_permissions, 
-        path=work_path, 
+        permissions=flags.file_permissions,
+        path=work_path,
         recursive=True,
         group=flags.permissions_group,
         quiet=True
     )
-    
+
     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-1.3.1 → oceanproc-1.3.3}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.3.1"
+version = "1.3.3"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"