oceanproc 1.3.3__tar.gz → 1.3.4__tar.gz

{oceanproc-1.3.3 → oceanproc-1.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.3.3
+Version: 1.3.4
 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-1.3.3 → oceanproc-1.3.4}/oceanproc/bids_wrapper.py

@@ -74,7 +74,8 @@ def run_dcm2bids(subject:str,
                  bids_output_dir:Path,
                  config_file:Path,
                  nordic_config:Path = None,
-                 skip_validate:bool = False):
+                 skip_validate:bool = False,
+                 keep_part_files: bool = False):
     """
     Run dcm2bids with a given set of parameters.
 
@@ -128,11 +129,12 @@ def run_dcm2bids(subject:str,
             run_subprocess(nordic_run_command, title=title)
 
             # Clean up NORDIC files
-            separate_nordic_files = bids_output_dir.glob(f"sub-{subject}/ses-{session}/func/*_part-*")
-            logger.debug("removing the old nordic files that are not needed after mag-phase combination :")
-            for f in separate_nordic_files:
-                logger.debug(f"deleting file: {f}")
-                os.remove(f)
+            if not keep_part_files:
+                separate_nordic_files = bids_output_dir.glob(f"sub-{subject}/ses-{session}/func/*_part-*")
+                logger.debug("removing the old nordic files that are not needed after mag-phase combination :")
+                for f in separate_nordic_files:
+                    logger.debug(f"deleting file: {f}")
+                    os.remove(f)
 
     except (Exception, KeyboardInterrupt) as e:
         prepare_subprocess_logging(logger, stop=True)
@@ -141,6 +143,7 @@ def run_dcm2bids(subject:str,
 
     return True
 
+
 @debug_logging
 def run_dcm2niix(source_dir:Path,
                  tmp_nifti_dir:Path):
@@ -178,7 +181,7 @@ def run_dcm2niix(source_dir:Path,
         prepare_subprocess_logging(logger, stop=True)
         logger.exception(e, stack_info=True)
         return False
-    
+
     return True
 
 
@@ -271,7 +274,7 @@ def extend_session(subject:str,
             continue
         run_nums = [f.entities['run'] for f in similar_files if 'run' in f.entities]
         max_bids_run = 1 if len(run_nums) == 0 else int(max(run_nums))
-        tmp_ent['run'] = f"{(max_bids_run+tmp_run_num):02d}"
+        tmp_ent['run'] = f"{(max_bids_run + tmp_run_num):02d}"
         tmp_new_path = bids_layout.build_path(tmp_ent)
         logger.info(f"moving file: {tmp_file.path} to: {tmp_new_path}")
         shutil.move(tmp_file.path, tmp_new_path)
@@ -297,7 +300,8 @@ def dicom_to_bids(subject:str,
                   skip_validate:bool = False,
                   skip_prompt:bool = False,
                   session_index:int = 0,
-                  keep_all_niftis:bool = False):
+                  keep_all_niftis:bool = False,
+                  keep_part_files:bool = False):
     """
     Facilitates the conversion of DICOM data into NIFTI data in BIDS format, and the removal of data marked 'unusable'.
 
@@ -350,7 +354,7 @@ def dicom_to_bids(subject:str,
         nii_success = run_dcm2niix(source_dir=source_dir,
                                    tmp_nifti_dir=tmp_nifti_path)
     else:
-        # copy current niftis to tmp_nifti_path 
+        # copy current niftis to tmp_nifti_path
         logger.info(f"copying the source NIFTI files to tmp directory, {tmp_nifti_path}")
         shutil.copytree(source_dir.resolve(), tmp_nifti_path.resolve())
 
@@ -361,7 +365,7 @@ def dicom_to_bids(subject:str,
         recursive=True,
         group=flags.permissions_group
     )
-    
+
     if not nii_success:
         exit_program_early(f"Problem running 'dcm2niix'")
 
@@ -408,13 +412,14 @@ def dicom_to_bids(subject:str,
                                session_number=session_index)
 
     dcm2bids_success = run_dcm2bids(subject=subject,
-                 session=session,
-                 nifti_dir=tmp_nifti_path,
-                 bids_output_dir=bids_dir,
-                 config_file=bids_config,
-                 nordic_config=nordic_config,
-                 skip_validate=skip_validate)
-    
+                                    session=session,
+                                    nifti_dir=tmp_nifti_path,
+                                    bids_output_dir=bids_dir,
+                                    config_file=bids_config,
+                                    nordic_config=nordic_config,
+                                    skip_validate=skip_validate,
+                                    keep_part_files=keep_part_files)
+
     update_permissions(
         permissions=flags.file_permissions,
         path=sub_ses_bids_dir,

{oceanproc-1.3.3 → oceanproc-1.3.4}/oceanproc/group_series.py

@@ -50,7 +50,7 @@ def get_func_from_bids(bids_layout: BIDSLayout,
                        session:str,
                        groupings: list[dict[str:set]]):
 
-    func_files = bids_layout.get(subject=subject, session=session, suffix="bold", datatype="func", extension="nii.gz")
+    func_files = bids_layout.get(subject=subject, session=session, suffix="bold", datatype="func", extension=["nii.gz","nii"])
     if len(func_files) == 0:
         exit_program_early("Could not find any functional BOLD files for this subject and session.")
 

{oceanproc-1.3.3 → oceanproc-1.3.4}/oceanproc/ocean_proc.py

@@ -94,7 +94,7 @@ def main():
 
     default_user_group = grp.getgrgid(os.getgid()).gr_name
     default_file_permissions = "771"
-    
+
     parser = OceanParser(
         prog="oceanproc",
         description="Ocean Labs adult MRI preprocessing",
@@ -141,7 +141,7 @@ def main():
     config_args.add_argument("--derivs_path", "-d", type=ExistingDir, required=True,
                              help="The path to the BIDS formated derivatives directory for this subject")
     config_args.add_argument("--derivs_subfolder", "-ds", default=None,
-                             help=f"""The subfolder in the derivatives directory where bids style outputs should be stored. 
+                             help=f"""The subfolder in the derivatives directory where bids style outputs should be stored.
                                   The default is {adult_defaults.derivs_subfolder} or {infant_defaults.derivs_subfolder} if the '--infant' flag is set.""")
     config_args.add_argument("--bids_config", "-c", type=ExistingFile, required=True,
                              help="The path to the dcm2bids config file to use for this subject and session")
@@ -174,8 +174,10 @@ def main():
                              help="The path to the working directory used to store intermediate files")
     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("--keep_part_files", action=argparse.BooleanOptionalAction,
+                             help="Don't automatically remove 'part-mag' and 'part-phase' files after running dcm2bids.")
     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. 
+                             help=f"""The version of fmriprep to use; It is reccomended that an entire study use the same version.
                                   The default is {adult_defaults.image_version} or {infant_defaults.image_version} if the '--infant' flag is set.""")
     config_args.add_argument("--infant", "-I", action=argparse.BooleanOptionalAction,
                              help="Flag to specify that NiBabies should be used instead of fMRIPrep")
@@ -235,7 +237,7 @@ def main():
     if args.debug_mode:
         flags.debug = True
         logger.setLevel(logging.DEBUG)
-    
+
     flags.file_permissions = args.file_permissions
     flags.permissions_group = args.permissions_group
     flags.gid = grp.getgrnam(flags.permissions_group).gr_gid
@@ -255,7 +257,6 @@ def main():
             logger.exception(e)
             exit_program_early(e)
 
-
     # log the input arguments
     for k,v in (dict(args._get_kwargs())).items():
         logger.info(f" {k} : {v}")
@@ -286,14 +287,15 @@ def main():
                 skip_validate=args.skip_bids_validation,
                 skip_prompt=index > 0,
                 session_index=index,
-                keep_all_niftis=args.keep_all_niftis
+                keep_all_niftis=args.keep_all_niftis,
+                keep_part_files=args.keep_part_files
             )
             if index > 0:
                 extend_session(subject=args.subject,
                                session=args.session,
                                tmp_dir=bids_path,
                                bids_dir=args.bids_path)
-                
+
     # create a bids layout object
     ignore_list = ["tmp_dcm2bids"]
     if (bids_path / ".bidsignore").is_file():
@@ -301,8 +303,8 @@ def main():
             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-*") 
-      if not f"sub-{args.subject}".startswith(p.name) and p.is_dir()  # 'startswith' to account for pybids regexifying after the end of subject name
+        p.name for p in bids_path.glob("sub-*")
+        if not f"sub-{args.subject}".startswith(p.name) and p.is_dir()  # 'startswith' to account for pybids regexifying after the end of subject name
     ]
     ignore_list.extend(other_sub_paths)
     bids_layout = BIDSLayout(args.bids_path, validate=False, indexer=BIDSLayoutIndexer(ignore=ignore_list, validate=False))
@@ -354,7 +356,6 @@ def main():
         if not bibsnet_path.exists():
             exit_program_early(f"Cannot find the outputs for BIBSnet at the path {bibsnet_path}")
 
-
     ##### Insert dummy scans in requested #####
     if args.dscans_path:
         insert_dummy_frames(
@@ -364,7 +365,6 @@ def main():
             bids_layout=bids_layout
         )
 
-
     ##### Run fMRIPrep or NiBabies #####
     all_opts = dict(args._get_kwargs())
 

{oceanproc-1.3.3 → oceanproc-1.3.4}/oceanproc/preprocessing_wrapper.py

@@ -74,6 +74,14 @@ def run_preprocessing(subject:str,
     """
     def clean_up(): return shutil.rmtree(work_path) if remove_work_folder else None
 
+    def make_mount_path(path_to_mount:str|Path, mount_key:int):
+        mount_path = f"/deriv{mount_key}"
+        path_to_mount = Path(path_to_mount)
+        if path_to_mount.is_file():
+            suffix = "".join(path_to_mount.suffixes)
+            mount_path += suffix
+        return mount_path
+
     log_linebreak()
     logger.info(f"####### Starting {title} #######\n")
     if not bids_path.exists():
@@ -107,12 +115,14 @@ def run_preprocessing(subject:str,
         arg_vals = [k]
         if isinstance(v, list):
             for sub_v in v:
-                additional_mount_paths.append(f"{mount_flag} {sub_v.resolve()}:/deriv{mount_dex}")
-                arg_vals.append(f"/deriv{mount_dex}")
+                mount_path = make_mount_path(sub_v, mount_dex)
+                additional_mount_paths.append(f"{mount_flag} {sub_v.resolve()}:{mount_path}")
+                arg_vals.append(mount_path)
                 mount_dex += 1
         else:
-            additional_mount_paths.append(f"{mount_flag} {v.resolve()}:/deriv{mount_dex}")
-            arg_vals.append(f"/deriv{mount_dex}")
+            mount_path = make_mount_path(v, mount_dex)
+            additional_mount_paths.append(f"{mount_flag} {v.resolve()}:{mount_path}")
+            arg_vals.append(mount_path)
             mount_dex += 1
         additional_mount_args.append(" ".join(arg_vals))
     additional_mount_paths = " ".join(additional_mount_paths)

{oceanproc-1.3.3 → oceanproc-1.3.4}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.3.3"
+version = "1.3.4"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"