oceanproc 1.2.0__tar.gz → 1.2.2__tar.gz

{oceanproc-1.2.0 → oceanproc-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.2.0
+Version: 1.2.2
 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-1.2.0 → oceanproc-1.2.2}/oceanproc/bids_wrapper.py

@@ -182,19 +182,6 @@ def run_dcm2niix(source_dir:Path,
         exit_program_early(f"Problem running '{title}'.",
                            exit_func=clean_up_func if clean_up_func else None)
 
-    # Delete or move extra files from short runs
-    files_to_remove = list(tmp_nifti_dir.glob("*a.nii.gz")) + list(tmp_nifti_dir.glob("*a.json")) + list(tmp_nifti_dir.glob(f"10[0-9][0-9]_{source_dir.name}*"))
-    if flags.debug:
-        unused_files_dir = tmp_nifti_dir.parent / f"{tmp_nifti_dir.name}_unused"
-        unused_files_dir.mkdir(exist_ok=True)
-        logger.debug(f"moving some unused files and files created from shortened runs to directory {unused_files_dir}")
-        for f in files_to_remove:
-            shutil.move(f.resolve(), (unused_files_dir / f.name).resolve())
-    else:
-        logger.info(f"removing some unused files and files created from shortened runs :\n  {[str(f) for f in files_to_remove]}")
-        for f in files_to_remove:
-            os.remove(f)
-
 
 def get_usability_from_file(usability_file:Path):
     quality_pairs = {}
@@ -310,7 +297,8 @@ def dicom_to_bids(subject:str,
                   nifti:bool = False,
                   skip_validate:bool = False,
                   skip_prompt:bool = False,
-                  session_index:int = 0):
+                  session_index:int = 0,
+                  keep_all_niftis:bool = False):
     """
     Facilitates the conversion of DICOM data into NIFTI data in BIDS format, and the removal of data marked 'unusable'.
 
@@ -346,32 +334,71 @@ def dicom_to_bids(subject:str,
         else:
             return
 
-    tmp_path = bids_dir / f"tmp_dcm2bids/sub-{subject}_ses-{session}"
+    tmp_nifti_path = bids_dir / f"tmp_dcm2bids/sub-{subject}_ses-{session}"
 
     def clean_up(quiet=False):
         try:
-            logger.debug(f"removing the temporary directory used by dcm2bids: {tmp_path}")
-            shutil.rmtree(tmp_path)
+            logger.debug(f"removing the temporary directory used by dcm2bids: {tmp_nifti_path}")
+            shutil.rmtree(tmp_nifti_path)
         except Exception:
             if not quiet:
-                logger.warning(f"There was a problem deleting the temporary directory at {tmp_path}")
+                logger.warning(f"There was a problem deleting the temporary directory at {tmp_nifti_path}")
 
-    nifti_path = None
     clean_up(quiet=True)
     if not nifti:
         run_dcm2niix(source_dir=source_dir,
-                     tmp_nifti_dir=tmp_path)
-        nifti_path = tmp_path
+                     tmp_nifti_dir=tmp_nifti_path)
     else:
-        nifti_path = source_dir
+        # 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())
+
+
+    # filter out know 'weird' files that can be created during conversion
+    if not keep_all_niftis:
+        files_to_remove = []
+        short_runs = list(tmp_nifti_path.glob("[!.]*[a-z].nii*")) + list(tmp_nifti_path.glob("[!.]*[a-z].json"))
+        for sr in short_runs:
+            suffix = None
+            if sr.name.endswith(".nii.gz"):
+                suffix = ".nii.gz"
+            elif sr.name.endswith(".nii"):
+                suffix = ".nii"
+            elif sr.name.endswith(".json"):
+                suffix = ".json"
+            else:
+                continue
+            if (sr.parent / f"{sr.name.removesuffix(suffix)[:-1]}{suffix}").exists():
+                files_to_remove.append(sr)
+
+        for jf in tmp_nifti_path.glob("[!.]*.json"):
+            with open(jf, "r") as f:
+                jd = json.load(f)
+                if int(jd["SeriesNumber"]) > 1000:
+                    files_to_remove.extend(list(tmp_nifti_path.glob(f"{jf.stem}.*")))
+
+        if len(files_to_remove) > 0:
+            logger.info("filtering out NIFTI files")
+            file_list_string = '\n\t'.join([str(f) for f in files_to_remove])
+            if flags.debug:
+                unused_files_dir = tmp_nifti_path.parent / f"{tmp_nifti_path.name}_unused"
+                unused_files_dir.mkdir(exist_ok=True)
+                logger.debug(f"moving some unused files and files created from shortened runs to directory {unused_files_dir}:\n\t{file_list_string}")
+                for f in files_to_remove:
+                    shutil.move(f.resolve(), (unused_files_dir / f.name).resolve())
+            else:
+                file_list_string = '\n\t'.join([str(f) for f in files_to_remove])
+                logger.info(f"removing some unused files and files created from shortened runs :\n\t{file_list_string}")
+                for f in files_to_remove:
+                    os.remove(f)
 
-    add_information_to_sidecar(nifti_dir=nifti_path,
+    add_information_to_sidecar(nifti_dir=tmp_nifti_path,
                                usability_file=usability_file,
                                session_number=session_index)
 
     run_dcm2bids(subject=subject,
                  session=session,
-                 nifti_dir=nifti_path,
+                 nifti_dir=tmp_nifti_path,
                  bids_output_dir=bids_dir,
                  config_file=bids_config,
                  nordic_config=nordic_config,

{oceanproc-1.2.0 → oceanproc-1.2.2}/oceanproc/ocean_proc.py

@@ -121,6 +121,8 @@ def main():
                              help="The path to the second dcm2bids config file to use for this subject and session. This implies that the session contains NORDIC data")
     config_args.add_argument("--nifti", action=argparse.BooleanOptionalAction,
                              help="Flag to specify that the source directory contains files of type NIFTI (.nii/.jsons) instead of DICOM")
+    config_args.add_argument("--keep_all_niftis", action=argparse.BooleanOptionalAction,
+                             help="Oceanproc will try its best to remove 'weird' NIFTI files that can be introduced during conversion from DICOM. This flag specifies that oceanproc should not do that and keep all of the files instead.")
     config_args.add_argument("--anat_only", action=argparse.BooleanOptionalAction,
                              help="Flag to specify only anatomical images should be processed.")
     config_args.add_argument("--fd_spike_threshold", "-fd", type=float, default=0.9,
@@ -258,7 +260,8 @@ def main():
                 nifti=args.nifti,
                 skip_validate=args.skip_bids_validation,
                 skip_prompt=index > 0,
-                session_index=index
+                session_index=index,
+                keep_all_niftis=args.keep_all_niftis
             )
             if index > 0:
                 extend_session(subject=args.subject,

{oceanproc-1.2.0 → oceanproc-1.2.2}/oceanproc/preprocessing_wrapper.py

@@ -76,9 +76,14 @@ def run_preprocessing(subject:str,
         exit_program_early(f"Bids path {bids_path} does not exist.")
     elif not derivs_path.exists():
         exit_program_early(f"Derivatives path {derivs_path} does not exist.")
+
+    license_mount = "/opt/freesurfer/license.txt"
+    bids_mount = "/data"
+    derivs_mount = "/out"
+    work_mount = "/work"
     
     if flags.apptainer:
-        cmd_prelude = "apptainer run --nv --cleanenv --no-mount cwd"
+        cmd_prelude = f"apptainer run --nv --cleanenv --no-mount cwd --pwd {work_mount}"
         mount_flag = "-B"
     else:
         uid = Popen(["id", "-u"], stdout=PIPE).stdout.read().decode("utf-8").strip()
@@ -104,10 +109,6 @@ def run_preprocessing(subject:str,
     additional_mount_paths = " ".join(additional_mount_paths)
     additional_mount_args = " ".join(additional_mount_args)
 
-    license_mount = "/opt/freesurfer/license.txt"
-    bids_mount = "/data"
-    derivs_mount = "/out"
-    work_mount = "/work"
     preproc_command = f"""{cmd_prelude}
                             {mount_flag} {license_file.resolve()}:{license_mount}:ro
                             {mount_flag} {bids_path.resolve()}:{bids_mount}:ro
@@ -256,16 +257,27 @@ def insert_dummy_frames(subject:str,
     for bfile in func_files:
         if not Path(bfile.path).exists:
             continue
+
         # Find the dscans file for bold run
+        try_find = True
         dscans_entities = bids_layout.parse_file_entities(bfile.path) | {"suffix":dscans_suffix, "extension":".tsv"}
-        dscans_bids_path = bids_layout.build_path(dscans_entities, path_patterns=[dscans_path_pattern], validate=False)
-        dscans_file = sorted(dscan_dir.glob(Path(dscans_bids_path).name))
-        if len(dscans_file) > 1:
-            exit_program_early(f"Found more than one dscans file for bold run {bfile} --> {dscans_file}")
-        elif len(dscans_file) == 0:
+        while try_find:
+            dscans_bids_path = bids_layout.build_path(dscans_entities, path_patterns=[dscans_path_pattern], validate=False)
+            dscans_file = sorted(dscan_dir.glob(Path(dscans_bids_path).name))
+            if len(dscans_file) > 1:
+                exit_program_early(f"Found more than one dscans file for bold run {bfile} --> {dscans_file}")
+            elif len(dscans_file) == 1:
+                try_find = False
+            if ("echo" in dscans_entities) and try_find:
+                del dscans_entities["echo"]
+            else:
+                try_find = False
+
+        if len(dscans_file) == 0:
             logger.info(f"Did not find any dscans files for bold run: {bfile}, file will remain unmodified.")
             continue
-        dscans_file = dscans_file[0]
+        else:
+            dscans_file = dscans_file[0]
         logger.info(f"found dscans file <{dscans_file.name}> for bold run <{bfile.filename}>")
 
         dscans_list = pd.read_csv(dscans_file, sep="\t").loc[:, "dummy_scan"].to_numpy().astype(np.int32)

{oceanproc-1.2.0 → oceanproc-1.2.2}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.2.0"
+version = "1.2.2"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"