[ENH] Refactorisation - Major API upgrade

.github/workflows/coverage.yml

@@ -8,19 +8,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python 3.7
+    - name: Set up Python 3.10.11
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.10.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements-test.txt
         pip install .
     - name: Run coverage
       run: pytest --cov --cov-report=xml
-    - name: Upload coverage  
-      uses: codecov/codecov-action@v1
+    - name: Upload coverage
+      uses: codecov/codecov-action@v3
       if: always()
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish_doc.yaml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.10.4"
+          python-version: "3.10.11"
       - name: Upgrade pip
         run: |
           # install pip=>20.1 to use "pip cache dir"

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
           - ubuntu-latest  # ubuntu-18.04
           - macos-latest  # macOS-10.14
           - windows-latest  # windows-2019
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, 3.10.11]
 
     steps:
     - uses: actions/checkout@v1

README.md

@@ -12,6 +12,8 @@ Your friendly DICOM converter.
 
 
 [![PyPI version badge](https://img.shields.io/pypi/v/dcm2bids?logo=pypi&logoColor=white)](https://pypi.org/project/dcm2bids)
+[![PyPI - Downloads](https://static.pepy.tech/badge/dcm2bids)](https://pypi.org/project/dcm2bids)
+
 [![Anaconda-Server Badge](https://img.shields.io/conda/vn/conda-forge/dcm2bids?logo=anaconda&logoColor=white)](https://anaconda.org/conda-forge/dcm2bids)
 [![Docker container badge](https://img.shields.io/docker/v/unfmontreal/dcm2bids?label=docker&logo=docker&logoColor=white)](https://hub.docker.com/r/unfmontreal/dcm2bids)
 

dcm2bids/__init__.py

@@ -1,15 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-dcm2bids
---------
-
-Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-"""
-
-
-from .dcm2bids import Dcm2bids
-from .scaffold import scaffold
-from .version import __version__
-
-__all__ = ["__version__", "Dcm2bids", "scaffold"]

dcm2bids/structure.py → dcm2bids/acquisition.py

@@ -4,96 +4,9 @@
 
 import logging
 from os.path import join as opj
-from future.utils import iteritems
-from .utils import DEFAULT
-from .version import __version__
 
-
-class Participant(object):
-    """ Class representing a participant
-
-    Args:
-        name (str): Label of your participant
-        session (str): Optional label of a session
-    """
-
-    def __init__(self, name, session=DEFAULT.session):
-        self._name = ""
-        self._session = ""
-
-        self.name = name
-        self.session = session
-
-    @property
-    def name(self):
-        """
-        Returns:
-            A string 'sub-<subject_label>'
-        """
-        return self._name
-
-    @name.setter
-    def name(self, name):
-        """ Prepend 'sub-' if necessary"""
-        if name.startswith("sub-"):
-            self._name = name
-
-        else:
-            self._name = "sub-" + name
-
-    @property
-    def session(self):
-        """
-        Returns:
-            A string 'ses-<session_label>'
-        """
-        return self._session
-
-    @session.setter
-    def session(self, session):
-        """ Prepend 'ses-' if necessary"""
-        if session.strip() == "":
-            self._session = ""
-
-        elif session.startswith("ses-"):
-            self._session = session
-
-        else:
-            self._session = "ses-" + session
-
-    @property
-    def directory(self):
-        """ The directory of the participant
-
-        Returns:
-            A path 'sub-<subject_label>' or
-            'sub-<subject_label>/ses-<session_label>'
-        """
-        if self.hasSession():
-            return opj(self.name, self.session)
-        else:
-            return self.name
-
-    @property
-    def prefix(self):
-        """ The prefix to build filenames
-
-        Returns:
-            A string 'sub-<subject_label>' or
-            'sub-<subject_label>_ses-<session_label>'
-        """
-        if self.hasSession():
-            return self.name + "_" + self.session
-        else:
-            return self.name
-
-    def hasSession(self):
-        """ Check if a session is set
-
-        Returns:
-            Boolean
-        """
-        return self.session.strip() != DEFAULT.session
+from dcm2bids.utils.utils import DEFAULT
+from dcm2bids.version import __version__
 
 
 class Acquisition(object):
@@ -313,7 +226,7 @@ def dstSidecarData(self, descriptions, intendedForList):
                 data["IntendedFor"] = intendedValue
 
         # sidecarChanges
-        for key, value in iteritems(self.sidecarChanges):
+        for key, value in self.sidecarChanges.items():
             data[key] = value
 
         return data

dcm2bids/cli/dcm2bids.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
+"""
+
+import argparse
+
+from dcm2bids.dcm2bids_gen import Dcm2BidsGen
+from dcm2bids.utils.tools import check_latest
+from dcm2bids.utils.utils import DEFAULT
+from dcm2bids.version import __version__
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
+                                formatter_class=argparse.RawTextHelpFormatter)
+
+    p.add_argument("-d", "--dicom_dir",
+                   required=True, nargs="+",
+                   help="DICOM directory(ies).")
+
+    p.add_argument("-p", "--participant",
+                   required=True,
+                   help="Participant ID.")
+
+    p.add_argument("-s", "--session",
+                   required=False,
+                   default=DEFAULT.cliSession,
+                   help="Session ID. [%(default)s]")
+
+    p.add_argument("-c", "--config",
+                   required=True,
+                   help="JSON configuration file (see example/config.json).")
+
+    p.add_argument("-o", "--output_dir",
+                   required=False,
+                   default=DEFAULT.cliOutputDir,
+                   help="Output BIDS directory. [%(default)s]")
+
+    p.add_argument("--forceDcm2niix",
+                   action="store_true",
+                   help="Overwrite previous temporary dcm2niix "
+                        "output if it exists.")
+
+    p.add_argument("--clobber",
+                   action="store_true",
+                   help="Overwrite output if it exists.")
+
+    p.add_argument("-l", "--log_level",
+                   required=False,
+                   default=DEFAULT.cliLogLevel,
+                   choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+                   help="Set logging level. [%(default)s]")
+
+    p.add_argument("-v", "--version",
+                   action="version",
+                   version=f"dcm2bids version:\t{__version__}\nBased on BIDS version:\t{DEFAULT.bids_version}",
+                   help="Report dcm2bids version and the BIDS version.")
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    check_latest()
+    check_latest("dcm2niix")
+
+    app = Dcm2BidsGen(**vars(args))
+    return app.run()
+
+
+if __name__ == "__main__":
+    main()

dcm2bids/helper.py → dcm2bids/cli/dcm2bids_helper.py

@@ -3,28 +3,25 @@
 """helper module"""
 
 import argparse
-import os
-from pathlib import Path
-import sys
+from os.path import join as opj
 
-from dcm2bids.dcm2niix import Dcm2niix
-from dcm2bids.utils import DEFAULT, assert_dirs_empty
+from dcm2bids.dcm2niix_gen import Dcm2niixGen
+from dcm2bids.utils.args import assert_dirs_empty
+from dcm2bids.utils.utils import DEFAULT
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.EPILOG,
+    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
                                 formatter_class=argparse.RawTextHelpFormatter)
 
     p.add_argument("-d", "--dicom_dir",
-                   type=Path,
                    required=True, nargs="+",
                    help="DICOM files directory.")
 
     p.add_argument("-o", "--output_dir",
-                   required=False, default=Path.cwd(),
-                   type=Path,
-                   help="Output BIDS directory. "
-                        "(Default: %(default)s)")
+                   required=False, default=DEFAULT.cliOutputDir,
+                   help="Output BIDS directory."
+                        " (Default: %(default)s)")
 
     p.add_argument('--force',
                    dest='overwrite', action='store_true',
@@ -37,13 +34,17 @@ def main():
     """Let's go"""
     parser = _build_arg_parser()
     args = parser.parse_args()
-    out_folder = args.output_dir / DEFAULT.tmpDirName / DEFAULT.helperDir
+
+    out_folder = opj(args.output_dir, 'tmp_dcm2bids', 'helper')
     assert_dirs_empty(parser, args, out_folder)
-    app = Dcm2niix(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)
+
+    app = Dcm2niixGen(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)
     rsl = app.run()
-    print(f"Example in: {out_folder}")
+    print("Example in:")
+    print(opj(args.output_dir, DEFAULT.tmpDirName, DEFAULT.helperDir))
+
     return rsl
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    main()

dcm2bids/cli/dcm2bids_scaffold.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+    Create basic BIDS files and directories.
+
+    Based on the material provided by
+    https://github.com/bids-standard/bids-starter-kit
+"""
+
+
+import argparse
+import datetime
+import logging
+import os
+from os.path import join as opj
+
+from dcm2bids.utils.io import write_txt
+from dcm2bids.utils.args import add_overwrite_arg, assert_dirs_empty
+from dcm2bids.utils.utils import DEFAULT
+from dcm2bids.utils.scaffold import bids_starter_kit
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
+                                formatter_class=argparse.RawTextHelpFormatter)
+
+    p.add_argument("-o", "--output_dir",
+                   required=False,
+                   default=DEFAULT.cliOutputDir,
+                   help="Output BIDS directory. Default: [%(default)s]")
+
+    add_overwrite_arg(p)
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    assert_dirs_empty(parser, args, args.output_dir)
+
+    for _ in ["code", "derivatives", "sourcedata"]:
+        os.makedirs(opj(args.output_dir, _), exist_ok=True)
+
+    logging.info("The files used to create your BIDS directory comes from"
+                 "https://github.com/bids-standard/bids-starter-kit")
+    # CHANGES
+    write_txt(opj(args.output_dir, "CHANGES"),
+              bids_starter_kit.CHANGES.replace('DATE',
+                                               datetime.date.today().strftime("%Y-%m-%d")))
+
+    # dataset_description
+    write_txt(opj(args.output_dir, "dataset_description"),
+              bids_starter_kit.dataset_description.replace("BIDS_VERSION",
+                                                           DEFAULT.bids_version))
+
+    # participants.json
+    write_txt(opj(args.output_dir, "participants.json"),
+              bids_starter_kit.participants_json)
+
+    # participants.tsv
+    write_txt(opj(args.output_dir, "participants.tsv"),
+              bids_starter_kit.participants_tsv)
+
+    # README
+    write_txt(opj(args.output_dir, "README"),
+              bids_starter_kit.README)
+
+
+if __name__ == "__main__":
+    main()