cnda_dl 0.1.0__tar.gz

cnda_dl-0.1.0/LICENSE

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+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

cnda_dl-0.1.0/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.1
+Name: cnda_dl
+Version: 0.1.0
+Summary: A command line utility for downloading fMRI data from CNDA
+Author-Email: Ramone Agard <agardr@wustl.edu>, Joey Scanga <joeyscanga92@gmail.com>
+Requires-Python: <4.0,>=3.9
+Requires-Dist: matplotlib>=3.7.2
+Requires-Dist: matplotlib-inline>=0.1.6
+Requires-Dist: progressbar2>=4.4.2
+Requires-Dist: pyxnat>=1.6.2
+Description-Content-Type: text/markdown
+
+# Dev installation
+
+Ensure `uv` is installed:
+
+```
+which uv
+```
+
+If not, this can be installed following instructions [here](https://docs.astral.sh/uv/getting-started/installation/).
+
+Then run:
+
+```
+git clone https://github.com/washu-ocean/cnda-dl.git
+cd cnda-dl
+uv sync
+```

cnda_dl-0.1.0/README.md

@@ -0,0 +1,17 @@
+# Dev installation
+
+Ensure `uv` is installed:
+
+```
+which uv
+```
+
+If not, this can be installed following instructions [here](https://docs.astral.sh/uv/getting-started/installation/).
+
+Then run:
+
+```
+git clone https://github.com/washu-ocean/cnda-dl.git
+cd cnda-dl
+uv sync
+```

cnda_dl-0.1.0/cnda_dl/.ruff_cache/.gitignore

@@ -0,0 +1,2 @@
+# Automatically created by ruff.
+*

cnda_dl-0.1.0/cnda_dl/.ruff_cache/CACHEDIR.TAG

@@ -0,0 +1 @@
+Signature: 8a477f597d28d172789f06886806bc55

cnda_dl-0.1.0/cnda_dl/cli.py

@@ -0,0 +1,481 @@
+#!/usr/bin/env python
+
+'''
+Script to download MRI sessions from the CNDA
+Authors:
+    Joey Scanga (scanga@wustl.edu)
+    Ramone Agard (rhagard@wustl.edu)
+'''
+
+from glob import glob
+from matplotlib.ticker import EngFormatter
+from pathlib import Path
+from pyxnat import Interface
+import pyxnat
+import argparse
+import logging
+import os
+import progressbar
+import shlex
+import shutil
+import hashlib
+import subprocess
+import sys
+import xml.etree.ElementTree as et
+import zipfile
+import datetime
+
+default_log_format = "%(levelname)s:%(funcName)s: %(message)s"
+sout_handler = logging.StreamHandler(stream=sys.stdout)
+logging.basicConfig(level=logging.INFO,
+                    handlers=[sout_handler],
+                    format=default_log_format)
+
+logger = logging.getLogger()
+
+
+def handle_dir_creation(dir_path: Path):
+    '''
+    Creates (or doesn't create) directories specified in the arguments, if any are still needed.
+
+    :param dir_title: how the directory is denoted in prompt messages
+    :type dir_title: str
+    :param dir_path: string representing path to new directory
+    :type dir_path: str
+    '''
+    prompt_chosen = False
+    while not prompt_chosen:
+        ans = input(f"input directory does not exist: {dir_path}. \nCreate one? (y/n)\n")
+        ans = ans.lower()
+
+        if len(ans) != 1 or ans not in 'yn':
+            logger.info("Invalid response.")
+        elif ans == 'y':
+            dir_path.mkdir(parents=True)
+            prompt_chosen = True
+            logger.info(f"new directory created at {dir_path}.")
+        elif ans == 'n':
+            logger.info("Chose to not create a new directory. Aborting...")
+            sys.exit(0)
+        else:
+            logger.info("Invalid response.")
+
+
+def download_xml(central: Interface,
+                 subject_id: str,
+                 project_id: str,
+                 file_path: Path):
+
+    logger.info("Downloading session xml...")
+    sub = central.select(f"/projects/{project_id}/subjects/{subject_id}")
+    with open(file_path, "w") as f:
+        f.write(sub.get().decode())
+    return True
+
+
+def retrieve_experiment(central: Interface,
+                        session: str,
+                        experiment_id: bool = False,
+                        project_id: str = None) -> pyxnat.jsonutil.JsonTable:
+
+    query_params = {}
+    if project_id:
+        query_params['project_id'] = project_id
+    if experiment_id:
+        query_params['experiment_id'] = session
+    else:
+        query_params['subject_label'] = session
+
+    return central.array.mrsessions(**query_params)
+
+
+def get_xml_scans(xml_file: Path,
+                  quality_pair: bool = False) -> dict:
+
+    xml_tree = et.parse(xml_file)
+    prefix = "{" + str(xml_tree.getroot()).split("{")[-1].split("}")[0] + "}"
+    scan_xml_entries = xml_tree.getroot().find(
+        f"./{prefix}experiments/{prefix}experiment/{prefix}scans"
+    )
+    if quality_pair:
+        return {s.get("ID"): s.find(f"{prefix}quality").text
+                for s in scan_xml_entries}
+    return scan_xml_entries
+
+
+def download_experiment_dicoms(session_experiment: pyxnat.jsonutil.JsonTable,
+                               central: Interface,
+                               session_dicom_dir: Path,
+                               xml_file_path: Path,
+                               scan_number_start: str = None,
+                               skip_unusable: bool = False):
+
+    project_id = session_experiment["project"]
+    exp_id = session_experiment['ID']
+
+    # parse the xml file for the scan quality information
+    quality_pairs = get_xml_scans(xml_file=xml_file_path,
+                                  quality_pair=True)
+
+    # retrieve the list of scans for this session
+    scans = central.select(f"/projects/{project_id}/experiments/{exp_id}/scans/*/").get()
+    scans.sort()
+    logger.info(f"Found {len(scans)} scans for this session")
+
+    # truncate the scan list if a starting point was given
+    if scan_number_start:
+        assert scan_number_start in scans, "Specified scan number does not exist for this session/experiment"
+        sdex = scans.index(scan_number_start)
+        scans = scans[sdex:]
+        logger.info(f"Downloading scans for this session starting from series {scan_number_start}")
+
+    # remove the unusable scans from the list if skipping is requested
+    if skip_unusable:
+        scans = [s for s in scans if quality_pairs[s] != "unusable"]
+        logger.info(f"The following scans were marked 'unusable' and will not be downloaded: \n\t {[s for s,q in quality_pairs.items() if q=='unusable']}")
+
+    # Get total number of files
+    total_file_count, cur_file_count = 0, 0
+    for s in scans:
+        files = central.select(f"/projects/{project_id}/experiments/{exp_id}/scans/{s}/resources/files").get("")
+        total_file_count += len(files)
+    logger.info(f"Total number of files: {total_file_count}")
+
+    # So log message does not interfere with format of the progress bar
+    logger.removeHandler(sout_handler)
+    downloaded_files = set()
+    zero_size_files = set()
+    fmt = EngFormatter('B')
+
+    # Download the session files
+    with progressbar.ProgressBar(max_value=total_file_count, redirect_stdout=True) as bar:
+        for s in scans:
+            logger.info(f"  Downloading scan {s}...")
+            print(f"Downloading scan {s}...")
+            series_path = session_dicom_dir / s / "DICOM"
+            series_path.mkdir(parents=True, exist_ok=True)
+            files = central.select(f"/projects/{project_id}/experiments/{exp_id}/scans/{s}/resources/files").get("")
+            for f in files:
+                cur_file_count += 1
+                add_file = True
+                file_name = series_path / f._uri.split("/")[-1]
+                file_size = fmt(int(f.size())) if f.size() else fmt(0)
+                file_info = f"File {f.attributes()['Name']}, {file_size} ({cur_file_count} out of {total_file_count})"
+                print("\t" + file_info)
+                logger.info("\t" + file_info)
+                if not f.size():
+                    msg = "\t-- File is empty"
+                    if file_name in downloaded_files:
+                        msg += " -- another copy was already downloaded, skipping download of this file"
+                        add_file = False
+                    else:
+                        zero_size_files.add(file_name)
+                    print(msg)
+                    logger.info(msg)
+                elif file_name in zero_size_files:
+                    zero_size_files.remove(file_name)
+                if add_file:
+                    f.get(file_name)
+                    downloaded_files.add(file_name)
+                bar.update(cur_file_count)
+    logger.addHandler(sout_handler)
+    logger.info("Dicom download complete \n")
+    if len(zero_size_files) > 0:
+        logger.warning(f"The following downloaded files contained no data:\n{[f.label() for f in zero_size_files]} \nCheck these files for unintended missing data!")
+
+
+def download_nordic_zips(session: str,
+                         central: Interface,
+                         session_experiment: pyxnat.jsonutil.JsonTable,
+                         session_dicom_dir: Path) -> list[Path]:
+    dat_dir_list = []
+    project_id = session_experiment["project"]
+    exp_id = session_experiment['ID']
+
+    def __digests_identical(zip_path: Path,
+                            cnda_file: pyxnat.core.resources.File):
+        if zip_path.is_file():  # Compare digests of zip on CNDA to see if we need to redownload
+            with zip_path.open("rb") as f:
+                if hashlib.md5(f.read()).hexdigest() == cnda_file.attributes()['digest']:  # digests match
+                    return True
+        return False
+
+    # check for zip file from NORDIC sessions
+    nordic_volumes = central.select(f"/projects/{project_id}/experiments/{exp_id}/resources/NORDIC_VOLUMES/files").get("")
+    logger.info(f"Found {len(nordic_volumes)} 'NORDIC_VOLUMES' for this session")
+    for nv in nordic_volumes:
+        zip_path = session_dicom_dir / nv._uri.split("/")[-1]
+        if not __digests_identical(zip_path, nv):
+            logger.info(f"Downloading {zip_path.name}...")
+            nv.get(zip_path)
+        unzip_path = zip_path.parent / zip_path.stem
+        with zipfile.ZipFile(zip_path, "r") as zip_ref:
+            logger.info(f"Unzipping to {unzip_path}...")
+            zip_ref.extractall(unzip_path)
+        dat_dir_list.append(unzip_path)
+
+    return dat_dir_list
+
+
+def dat_dcm_to_nifti(session: str,
+                     dat_directory: Path,
+                     xml_file_path: Path,
+                     session_dicom_dir: Path,
+                     nifti_path: Path,
+                     skip_short_runs: bool = False):
+    # check if the required program is on the current PATH
+    can_convert = False
+    unconverted_series = set()
+    error_series = set()
+    if shutil.which('dcmdat2niix') is not None:
+        can_convert = True
+        nifti_path.mkdir(parents=True, exist_ok=True)
+        logger.info(f"Combined .dcm & .dat files (.nii.gz format) will be stored at: {nifti_path}")
+    else:
+        logger.warning("dcmdat2niix not installed or has not been added to the PATH. Cannot convert data files into NIFTI")
+
+    # find all of the scans that are in the dicom directory for this session
+    downloaded_scans = [p.name.split("/")[-1] for p in session_dicom_dir.glob("*")
+                        if (p / "DICOM").exists()]
+    downloaded_scans.sort()
+
+    # create a map of downloaded scan IDs to UIDs to later match with the UIDs in the .dat files
+    xml_scans = get_xml_scans(xml_file=xml_file_path)
+    # [:-6] is to ignore the trailing '.0.0.0' at the end of the UID string
+    uid_to_id = {s.get("UID")[:-6]:s.get("ID") for s in xml_scans if s.get("ID") in downloaded_scans}
+
+    # collect all of the .dat files and map them to their UIDs
+    dat_files = list(dat_directory.glob("*.dat"))
+    uid_to_dats = {uid: [d for d in dat_files if uid in d.name] for uid in uid_to_id.keys()}
+
+    for uid, dats in uid_to_dats.items():
+        series_id = uid_to_id[uid]
+        series_path = session_dicom_dir / series_id / "DICOM"
+        for dat in dats:
+            # if (series_path / dat.name).is_file():
+            #     (series_path / dat.name).unlink()
+            shutil.move(dat.resolve(), series_path.resolve())
+
+        # Either there are no accompanying dats, or they were already in the series directory
+        if len(dats) == 0:
+            dats = list(series_path.glob("*.dat"))
+
+        dcms = list(series_path.glob("*.dcm"))
+        logger.info(f"length of dats: {len(dats)}")
+        logger.info(f"length of dcms: {len(dcms)}")
+
+        # if we cannot convert to NIFTI then continue
+        if not can_convert:
+            continue
+
+        # check if there's a mismatch between number of .dcm and .dat files (indicative of run that stopped prematurely)
+        if (len(dats) != 0) and (len(dats) != len(dcms)):
+            logger.warning(f"WARNING: number of .dat and .dcm files mismatched for series {series_id} with UID {uid}.")
+            logger.warning("This mismatch may indicate that one of your runs has ended early")
+            if skip_short_runs:
+                logger.warning("skipping running dcmdat2niix \n")
+                unconverted_series.add(series_id)
+                continue
+            elif (len(dcms) == len(dats) + 1) and len(dcms) > 1:
+                logger.info("Attempting to remove the extra dcm file, and convert the remaing data")
+                last_dcm = glob(f"{series_path}/*-{len(dcms)}-*.dcm")
+                if len(last_dcm) == 1:
+                    logger.info(f"Removing the mismatched dicom: {last_dcm[0]}")
+                    os.remove(last_dcm[0])
+                else:
+                    logger.warning("Could not find the mismatched dicom")
+
+        # run the dcmdat2niix subprocess
+        logger.info(f"Running dcmdat2niix on series {series_id}...")
+        dcmdat2niix_cmd = shlex.split(f"dcmdat2niix -ba n -z o -w 1 -o {nifti_path} {series_path}")
+        with subprocess.Popen(dcmdat2niix_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) as p:
+            while p.poll() is None:
+                for line in p.stdout:
+                    logger.info(line.decode("utf-8", "ignore"))
+            if p.poll() == 0:
+                logger.info(f"dcmdat2niix complete for series {series_id} \n")
+            else:
+                logger.error(f"dcmdat2niix ended with a nonzero exit code for series {series_id} \n")
+                error_series.add(series_id)
+
+    if len(unconverted_series) > 0:
+        logger.warning(f"""
+        The following series for session:{session} were
+        not converted to NIFTI beause the '--skip_short_runs'
+        option was selected
+        {unconverted_series}\n""")
+
+    if len(error_series) > 0:
+        logger.warning(f"""
+        The following series for session:{session} encountered
+        an error while being converted to NIFTI. This can be due
+        to corrupted dat files (.dat files with zero or very little
+        data) or if they are Physiolog acquisitions. Check these
+        series for possible causes.
+        {error_series}\n""")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="cnda-dl",
+        description="download cnda data directly to wallace",
+    )
+    parser.add_argument('session_list',
+                        nargs="+",
+                        help="List of either subject labels or experiment ids, separated by spaces.")
+    parser.add_argument("-d", "--dicom_dir", type=Path,
+                        help="Path to the directory the dicom files should be downloaded to.",
+                        required=True)
+    parser.add_argument("-x", "--xml_dir", type=Path,
+                        help="Path to the directory the session xml file should be downloaded to. If not specified, defaults to path stored in -d.")
+    parser.add_argument("-e", "--experiment_id",
+                        help="Query by CNDA experiment identifier (default is to query by experiment 'label', which may be ambiguous)",
+                        action='store_true')
+    parser.add_argument("-p", "--project_id",
+                        help="Specify the project ID to narrow down search. Recommended if the session list is not eperiment ids.")
+    parser.add_argument("-s", "--scan_number",
+                        help="Select the scan number to start the download from (may be used when only ONE session/experiment is specified)")
+    parser.add_argument("-n", "--ignore_nordic_volumes",
+                        help="Don't download a NORDIC_VOLUMES folder from CNDA if it exists.",
+                        action='store_true')
+    parser.add_argument("--map_dats", type=Path,
+                        help="""The path to a directory containting .dat files you wish to pair with DICOM files. Using this argument
+                        means that all data is already available locally and the script will only pair Dat files to DICOMs and
+                        run dcmdat2niix""")
+    parser.add_argument("--log_dir", type=Path,
+                        help="Points to a specified directory that will store the log file. Will not make the directory if it doesn't exist.")
+    parser.add_argument("-ssr","--skip_short_runs",
+                        action="store_true",
+                        help="Flag to indicate that runs stopped short should not be converted to NIFTI")
+    parser.add_argument("--skip_unusable",
+                        help="Don't download any scans marked as 'unusable' in the XML",
+                        action='store_true')
+    parser.add_argument("--dats_only",
+                        help="Skip downloading DICOMs, only try to pull .dat files",
+                        action='store_true')
+    args = parser.parse_args()
+
+    # validate argument inputs
+    if args.log_dir:
+        if not args.log_dir.is_dir():
+            parser.error(f"'--log_dir' directory does not exist: {args.log_dir}")
+    else:
+        args.log_dir = Path.home() / ".local" / "share" / "cnda-dl" / "logs"
+        args.log_dir.mkdir(parents=True, exist_ok=True)
+    log_path = args.log_dir / f"cnda-dl_{datetime.datetime.now().strftime('%m-%d-%y_%I:%M%p')}.log"
+
+    if args.scan_number and len(args.session_list) > 1:
+        parser.error("'--scan_number' can only be specified when there is only one session/experiment to download")
+
+    if args.map_dats and not args.map_dats.is_dir():
+        parser.error(f"'--map_dats' directory does not exist: {args.map_dats}")
+
+    # set up file logging
+    file_handler = logging.FileHandler(log_path)
+    file_handler.setFormatter(logging.Formatter(default_log_format))
+    logger.addHandler(file_handler)
+    logger.addHandler(sout_handler)
+
+    logger.info("Starting cnda-dl...")
+    logger.info(f"Log will be stored at {log_path}")
+
+    # set up data paths
+    session_list = args.session_list
+    dicom_path = args.dicom_dir
+    if hasattr(args, 'xml_dir') and args.xml_dir is not None:
+        xml_path = args.xml_dir
+    else:
+        xml_path = dicom_path
+
+    if not dicom_path.is_dir():
+        handle_dir_creation(dicom_path)
+    if not xml_path.is_dir():
+        handle_dir_creation(xml_path)
+
+    # set up CNDA connection
+    central = None
+    if not args.map_dats:
+        central = Interface(server="https://cnda.wustl.edu/")
+
+    # main loop
+    for session in session_list:
+        xml_file_path = xml_path / f"{session}.xml"
+        session_dicom_dir = dicom_path / session
+
+        # if only mapping is needed
+        if args.map_dats:
+            # map the .dat files to the correct scans and convert the files to NIFTI
+            nifti_path = dicom_path / f"{session}_nii"
+            try:
+                dat_dcm_to_nifti(session=session,
+                                 dat_directory=args.map_dats,
+                                 xml_file_path=xml_file_path,
+                                 session_dicom_dir=session_dicom_dir,
+                                 nifti_path=nifti_path,
+                                 skip_short_runs=args.skip_short_runs)
+            except Exception:
+                logger.exception(f"Error moving the .dat files to the appropriate scan directories and converting to NIFTI for session: {session}")
+            continue
+
+        # download the experiment data
+        logger.info(f"Starting download of session {session}...")
+
+        # try to retrieve the experiment corresponding to this session
+        exp = None
+        try:
+            exp = retrieve_experiment(central=central,
+                                      session=session,
+                                      experiment_id=args.experiment_id,
+                                      project_id=args.project_id)
+            if len(exp) == 0:
+                raise RuntimeError("ERROR: CNDA query returned JsonTable object of length 0, meaning there were no results found with the given search parameters.")
+            elif len(exp) > 1:
+                raise RuntimeError("ERROR: CNDA query returned JsonTable object of length >1, meaning there were multiple results returned with the given search parameters.")
+
+        except Exception:
+            logger.exception("Error retrieving the experiment from the given parameters. Double check your inputs or enter more specific parameters.")
+            continue
+
+        # download the xml for this session
+        download_xml(central=central,
+                     subject_id=exp["xnat:mrsessiondata/subject_id"],
+                     project_id=exp["project"],
+                     file_path=xml_file_path)
+        # try to download the files for this experiment
+        if not args.dats_only:
+            try:
+                download_experiment_dicoms(session_experiment=exp,
+                                           central=central,
+                                           session_dicom_dir=session_dicom_dir,
+                                           xml_file_path=xml_file_path,
+                                           scan_number_start=args.scan_number,
+                                           skip_unusable=args.skip_unusable)
+            except Exception:
+                logger.exception(f"Error downloading the experiment data from CNDA for session: {session}")
+                continue
+
+        # if we are not skipping the NORDIC files
+        if not args.ignore_nordic_volumes:
+            # try to download NORDIC related files and convert raw data to NIFTI
+            try:
+                nordic_dat_dirs = download_nordic_zips(session=session,
+                                                       central=central,
+                                                       session_experiment=exp,
+                                                       session_dicom_dir=session_dicom_dir)
+                nifti_path = dicom_path / f"{session}_nii"
+                for nordic_dat_path in nordic_dat_dirs:
+                    dat_dcm_to_nifti(session=session,
+                                     dat_directory=nordic_dat_path,
+                                     xml_file_path=xml_file_path,
+                                     session_dicom_dir=session_dicom_dir,
+                                     nifti_path=nifti_path,
+                                     skip_short_runs=args.skip_short_runs)
+            except Exception:
+                logger.exception(f"Error downloading 'NORDIC_VOLUMES' and converting to NIFTI for session: {session}")
+                continue
+
+    logger.info("\n...Downloads Complete")
+
+
+if __name__ == "__main__":
+    main()

cnda_dl-0.1.0/pyproject.toml

@@ -0,0 +1,38 @@
+[tool.pdm.dev-dependencies]
+dev = [
+    "pytest<9.0.0,>=8.2.2",
+]
+
+[tool.pdm.build]
+includes = []
+
+[build-system]
+requires = [
+    "pdm-backend",
+]
+build-backend = "pdm.backend"
+
+[project]
+authors = [
+    { name = "Ramone Agard", email = "agardr@wustl.edu" },
+    { name = "Joey Scanga", email = "joeyscanga92@gmail.com" },
+]
+requires-python = "<4.0,>=3.9"
+dependencies = [
+    "matplotlib>=3.7.2",
+    "matplotlib-inline>=0.1.6",
+    "progressbar2>=4.4.2",
+    "pyxnat>=1.6.2",
+]
+name = "cnda_dl"
+version = "0.1.0"
+description = "A command line utility for downloading fMRI data from CNDA"
+readme = "README.md"
+
+[project.scripts]
+cnda-dl = "cnda_dl.cli:main"
+
+[dependency-groups]
+dev = [
+    "pytest<9.0.0,>=8.2.2",
+]