oceanproc 1.3.2__tar.gz → 1.3.4__tar.gz

{oceanproc-1.3.2 → oceanproc-1.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.3.2
+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-1.3.2 → 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-1.3.2 → 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-1.3.2 → 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",
@@ -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 v1.3.2')
+    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")
 
@@ -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")
@@ -159,6 +159,8 @@ def main():
                              help="Specifies skipping BIDS validation (only enabled for fMRIprep step)")
     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=argparse.BooleanOptionalAction,
@@ -172,8 +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")
@@ -233,7 +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
@@ -253,7 +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}")
@@ -284,23 +287,24 @@ 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():
         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-*") 
-      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))
@@ -352,7 +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(
@@ -362,7 +365,6 @@ def main():
             bids_layout=bids_layout
         )
 
-
     ##### Run fMRIPrep or NiBabies #####
     all_opts = dict(args._get_kwargs())
 

{oceanproc-1.3.2 → oceanproc-1.3.4}/oceanproc/preprocessing_wrapper.py

@@ -32,8 +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,
@@ -69,7 +73,15 @@ 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
-   
+
+    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():
@@ -81,15 +93,15 @@ 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 
+            grp.getgrnam(groupname).gr_gid for groupname in
             subprocess.run('groups', capture_output=True).stdout.decode().strip().split()
         )
         for mygid in mygids:
@@ -103,12 +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)
@@ -126,7 +140,7 @@ def run_preprocessing(subject:str,
                             -w {work_mount} --verbose
                             {additional_mount_args}
                             {option_chain}"""
-    
+
     success = True
     try:
         run_subprocess(preproc_command, title=title)
@@ -140,6 +154,7 @@ def run_preprocessing(subject:str,
 
     return success
 
+
 @debug_logging
 def add_fd_plot_to_report(subject:str,
                           session:str,
@@ -230,7 +245,7 @@ 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
@@ -252,9 +267,9 @@ 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")
@@ -306,27 +321,27 @@ 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,
@@ -364,23 +379,23 @@ 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}*")))
@@ -388,14 +403,14 @@ 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(
@@ -404,15 +419,15 @@ 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.")

{oceanproc-1.3.2 → oceanproc-1.3.4}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.3.2"
+version = "1.3.4"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"