Merge pull request #314 from UNFmontreal/dev

Update master to 3.2.0

.github/workflows/codespell.yml

@@ -3,9 +3,9 @@ name: Codespell
 
 on:
   push:
-    branches: [master]
+    branches: [master, dev]
   pull_request:
-    branches: [master]
+    branches: [master, dev]
 
 permissions:
   contents: read

.github/workflows/coverage.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python 3.11
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: "3.11"
     - name: Install dependencies

.github/workflows/make_binaries.yml

@@ -19,7 +19,7 @@ jobs:
       # Check-out repository
       - uses: actions/checkout@v3
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11' # Version range or exact version of a Python version to use, using SemVer's version range syntax
           architecture: 'x64' # optional x64 or x86. Defaults to x64 if not specified
@@ -95,4 +95,4 @@ jobs:
           files: |
             download/artifact/*
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/publish_doc.yaml

@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - master
+      - dev
     tags:
       - '[0-9]+.[0-9]+.[0-9]+'
   release:
@@ -22,7 +23,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
@@ -50,6 +51,7 @@ jobs:
           dcm2bids -h > docs_helper/help.txt
           dcm2bids_helper -h > docs_helper/helper.txt
           dcm2bids_scaffold -h > docs_helper/help_scaffold.txt
+          echo "export VERSION=$(dcm2bids -v | awk '/dcm2bids/ {print $3}')" > docs_helper/version.txt
 
       - name: Set git credentials
         run: |
@@ -76,8 +78,9 @@ jobs:
           mike deploy -p ${{ github.ref_name }}
 
       - name: Deploy dev version
-        if: ${{ github.ref == 'refs/heads/master' }}
+        if: ${{ github.ref == 'refs/heads/dev' }}
         run: |
           VERSION=$(dcm2bids -v | awk '/dcm2bids/ {print $3}')
-          echo "Version: $VERSION"
-          mike deploy -p $VERSION dev -u
+          echo "Version: ${VERSION}-dev"
+          mike delete dev
+          mike deploy -p dev

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.gitignore

@@ -139,3 +139,4 @@ tests/data/*
 docs_helper/help.txt
 docs_helper/help_scaffold.txt
 docs_helper/helper.txt
+docs_helper/version.txt

Dockerfile

@@ -0,0 +1,57 @@
+# Conda image for installing FSL tools
+FROM continuumio/miniconda3 AS build
+
+# Install FSL tools with conda
+COPY environment.yml /tmp/environment.yml
+RUN conda env create -f /tmp/environment.yml
+
+# Install and use conda-pack
+RUN conda install -c conda-forge conda-pack
+RUN conda-pack -n fsl -o /tmp/env.tar && \
+  mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
+  rm /tmp/env.tar
+RUN /venv/bin/conda-unpack
+
+# Runtime image for executing FSL tools
+FROM debian:stable AS runtime
+
+# Copy the conda env from previous stage
+COPY --from=build /venv /venv
+
+# Point to conda executables
+ENV PATH="/venv/bin:$PATH"
+
+# Set FSL variables
+ENV FSLDIR="/venv" 
+ENV FSLCONFDIR="${FSLDIR}/config"
+ENV FSLOUTPUTTYPE="NIFTI"
+ENV FSLMULTIFILEQUIT="TRUE"
+ENV FSLTCLSH="${FSLDIR}/bin/fsltclsh"
+ENV FSLWISH="${FSLDIR}/bin/fslwish"
+ENV FSLGECUDAQ="cuda.q"
+
+# Update and install some utils
+RUN apt-get -y update && apt-get -y install dc wget npm unzip
+
+# Fetch data
+RUN wget -P ${FSLDIR}/data https://git.fmrib.ox.ac.uk/fsl/data_standard/-/raw/master/MNI152_T1_1mm_brain.nii.gz
+
+# Install bids-validator
+RUN npm install -g bids-validator
+
+# Install dcm2niix
+WORKDIR /
+RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
+RUN unzip dcm2niix_lnx.zip
+RUN mv dcm2niix /usr/bin/
+
+# Install dcm2bids
+
+WORKDIR /
+ADD . /dcm2bids
+WORKDIR /dcm2bids
+RUN pip install -e .
+
+RUN pip install pydeface
+
+ENTRYPOINT ["dcm2bids"]

README.md

@@ -48,7 +48,8 @@ Please take a look at the [documentation][dcm2bids-doc] to:
 
 * [Learn about bids][bids-spec] with some dataset [examples][bids-examples]
 * [Install dcm2bids][dcm2bids-install]
-* [Follow the tutorial][dcm2bids-tutorial]
+* [Use docker and Apptainer/Singularity][dcm2bids-container]
+* [Follow the tutorials][dcm2bids-tutorial]
 * [Seek for more advanced usage][dcm2bids-advanced]
 
 ## Issues and Questions
@@ -68,6 +69,7 @@ Before posting your question, you may want to first browse through questions tha
 [dcm2bids-install]: https://unfmontreal.github.io/Dcm2Bids/latest/get-started/install/
 [dcm2bids-tutorial]: https://unfmontreal.github.io/Dcm2Bids/latest/tutorial/first-steps/#tutorial-first-steps
 [dcm2bids-advanced]: https://unfmontreal.github.io/Dcm2Bids/latest/advanced/
+[dcm2bids-container]: https://unfmontreal.github.io/Dcm2Bids/latest/how-to/container/
 [dcm2bids-upgrade]: https://unfmontreal.github.io/Dcm2Bids/dev/upgrade/
 [dcm2bids-issues]: https://github.com/UNFmontreal/Dcm2Bids/issues
 [dcm2niix-install]: https://github.com/rordenlab/dcm2niix#install

dcm2bids/acquisition.py

@@ -4,6 +4,7 @@
 
 import logging
 from os.path import join as opj
+from os import sep
 
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.version import __version__
@@ -30,6 +31,8 @@ def __init__(
         id=None,
         src_sidecar=None,
         sidecar_changes=None,
+        bids_uri=None,
+        do_not_reorder_entities=None,
         **kwargs
     ):
         self.logger = logging.getLogger(__name__)
@@ -43,6 +46,8 @@ def __init__(
         self.suffix = suffix
         self.custom_entities = custom_entities
         self.src_sidecar = src_sidecar
+        self.bids_uri = bids_uri
+        self.do_not_reorder_entities = do_not_reorder_entities
 
         if sidecar_changes is None:
             self.sidecar_changes = {}
@@ -156,8 +161,8 @@ def setExtraDstFile(self, new_entities):
         """
         Return:
             The destination filename formatted following
-            the v1.8.0 BIDS entity key table
-            https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
+            the v1.9.0 BIDS entity key table
+            https://bids-specification.readthedocs.io/en/v1.9.0/99-appendices/04-entity-table.html
         """
 
         if self.custom_entities.strip() == "":
@@ -196,11 +201,14 @@ def setExtraDstFile(self, new_entities):
                                 "compliant. Make sure you know what "
                                 "you are doing.")
 
-        if current_name != new_name:
-            self.logger.warning(
-                f"""✅ Filename was reordered according to BIDS entity table order:
-                from:   {current_name}
-                to:     {new_name}""")
+        if not self.do_not_reorder_entities:
+            if current_name != new_name:
+                self.logger.warning(
+                    f"""✅ Filename was reordered according to BIDS entity table order:
+                    from:   {current_name}
+                    to:     {new_name}""")
+        else:
+            new_name = current_name
 
         self.extraDstFile = opj(self.participant.directory,
                                 self.datatype,
@@ -210,8 +218,8 @@ def setDstFile(self):
         """
         Return:
             The destination filename formatted following
-            the v1.8.0 BIDS entity key table
-            https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
+            the v1.9.0 BIDS entity key table
+            https://bids-specification.readthedocs.io/en/v1.9.0/99-appendices/04-entity-table.html
         """
         current_name = self.participant.prefix + self.build_suffix
         new_name = ''
@@ -241,13 +249,15 @@ def setDstFile(self):
                                 "compliant. Make sure you know what "
                                 "you are doing.")
 
-        if current_name != new_name:
-            self.logger.warning(
-                f"""✅ Filename was reordered according to BIDS entity table order:
-                from:   {current_name}
-                to:     {new_name}""")
+        self.dstFile = current_name
+        if not self.do_not_reorder_entities:
+            if current_name != new_name:
+                self.logger.warning(
+                    f"""✅ Filename was reordered according to BIDS entity table order:
+                    from:   {current_name}
+                    to:     {new_name}""")
+                self.dstFile = new_name
 
-        self.dstFile = new_name
 
     def dstSidecarData(self, idList):
         """
@@ -277,10 +287,16 @@ def dstSidecarData(self, idList):
                     else:
                         values.append(idList.get(val, val))
                         if values[-1] != val:
-                            if isinstance(values[-1], list):
-                                values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
+                            if self.bids_uri == DEFAULT.bids_uri:
+                                if isinstance(values[-1], list):
+                                    values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
+                                else:
+                                    values[-1] = "bids::" + values[-1]
                             else:
-                                values[-1] = "bids::" + values[-1]
+                                if isinstance(values[-1], list):
+                                    values[-1] = [img_dest.replace(self.participant.name + sep, "") for img_dest in values[-1]]
+                                else:
+                                    values[-1] = values[-1].replace(self.participant.name + sep, "")
 
             # handle if nested list vs str
             flat_value_list = []

dcm2bids/cli/dcm2bids.py

@@ -47,12 +47,21 @@ def _build_arg_parser():
                    default=DEFAULT.output_dir,
                    help="Output BIDS directory. [%(default)s]")
 
-    p.add_argument("--auto_extract_entities",
+    g = p.add_mutually_exclusive_group()
+    g.add_argument("--auto_extract_entities",
                    action='store_true',
                    help="If set, it will automatically try to extract entity"
                    "information [task, dir, echo] based on the suffix and datatype."
                    " [%(default)s]")
 
+    g.add_argument("--do_not_reorder_entities",
+                   action='store_true',
+                   help="If set, it will not reorder entities according to the relative "
+                        "ordering indicated in the BIDS specification and use the "
+                        "order defined in custom_entities by the user.\n"
+                        "Cannot be used with --auto_extract_entities. "
+                        " [%(default)s]")
+
     p.add_argument("--bids_validate",
                    action='store_true',
                    help="If set, once your conversion is done it "
@@ -120,6 +129,7 @@ def main():
     logger.info(f"config: {os.path.realpath(args.config)}")
     logger.info(f"BIDS directory: {os.path.realpath(args.output_dir)}")
     logger.info(f"Auto extract entities: {args.auto_extract_entities}")
+    logger.info(f"Reorder entities: {not args.do_not_reorder_entities}")
     logger.info(f"Validate BIDS: {args.bids_validate}\n")
 
     app = Dcm2BidsGen(**vars(args)).run()

dcm2bids/cli/dcm2bids_helper.py

@@ -15,7 +15,6 @@
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.utils.tools import dcm2niix_version, check_latest
 from dcm2bids.utils.logger import setup_logging
-from dcm2bids.utils.args import assert_dirs_empty
 from dcm2bids.version import __version__
 
 
@@ -59,12 +58,22 @@ def main():
     """Let's go"""
     parser = _build_arg_parser()
     args = parser.parse_args()
-    out_dir = Path(args.output_dir)
-    log_file = (Path(DEFAULT.output_dir)
-                / DEFAULT.tmp_dir_name
-                / "log"
-                / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
 
+    out_dir = Path(args.output_dir)
+    if args.output_dir != parser.get_default('output_dir'):
+        out_dir = (Path(args.output_dir)
+                   / DEFAULT.tmp_dir_name
+                   / DEFAULT.helper_dir)
+
+        log_file = (Path(args.output_dir)
+                    / DEFAULT.tmp_dir_name
+                    / "log"
+                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
+    else:
+        log_file = (Path(DEFAULT.output_dir)
+                    / DEFAULT.tmp_dir_name
+                    / "log"
+                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
     if args.nest:
         if isinstance(args.nest, str):
             log_file = Path(
@@ -94,8 +103,6 @@ def main():
     check_latest("dcm2bids")
     check_latest("dcm2niix")
 
-    assert_dirs_empty(parser, args, out_dir)
-
     app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)
 
     rsl = app.run(force=args.overwrite)