Merge branch 'master' into dev

Author: arnaudbore

.github/workflows/make_binaries.yml

@@ -11,7 +11,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-13, ubuntu-20.04, windows-latest] # not using latest based on https://github.com/Nuitka/Nuitka/issues/2240#issuecomment-1564030218
+        os: [macos-15, ubuntu-24.04, windows-2025] # not using latest based on https://github.com/Nuitka/Nuitka/issues/2240#issuecomment-1564030218
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/publish_doc.yaml

@@ -37,7 +37,7 @@ jobs:
         run: echo "::set-output name=dir::$(pip cache dir)"
 
       - name: Cache dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-doc.txt') }}

.github/workflows/tests.yml

@@ -10,10 +10,10 @@ jobs:
       matrix:
         # https://help.github.com/articles/virtual-environments-for-github-actions
         platform:
-          - ubuntu-latest  # ubuntu-22.04
-          - macos-13  # macOS-13 -
-          - windows-latest  # windows-2022
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+          - ubuntu-24.04  # ubuntu-24.04
+          - macos-15  # macOS-15
+          - windows-2025  # windows-2025
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4

dcm2bids/acquisition.py

@@ -284,6 +284,8 @@ def dstSidecarData(self, idList):
                                         f"will be made "
                                         f"for json file '{self.dstFile}.json' "
                                         "with this id.")
+                    elif isinstance(val, str) and not val:
+                        data.pop(key, None)
                     else:
                         values.append(idList.get(val, val))
                         if values[-1] != val:
@@ -308,9 +310,8 @@ def dstSidecarData(self, idList):
 
             if len(flat_value_list) == 1:
                 data[key] = flat_value_list[0]
-            else:
+            elif flat_value_list:
                 data[key] = flat_value_list
-
         return data
 
     @staticmethod

dcm2bids/cli/dcm2bids.py

@@ -26,41 +26,52 @@ def _build_arg_parser():
 
     p.add_argument("-d", "--dicom_dir",
                    required=True, nargs="+",
-                   help="DICOM directory(ies) or archive(s) (" +
-                        DEFAULT.arch_extensions + ").")
+                   help="Path to one or more directories or archives"
+                        f" ({DEFAULT.arch_extensions}) containing the DICOM files for a"
+                        " single participant and session to be converted to BIDS."
+                    )
 
     p.add_argument("-p", "--participant",
                    required=True,
-                   help="Participant ID.")
+                   help="Participant ID to be used in the BIDS dataset filenames"
+                        " (e.g. sub-<PARTICIPANT>)."
+    )
 
     p.add_argument("-s", "--session",
                    required=False,
                    default=DEFAULT.cli_session,
-                   help="Session ID. [%(default)s]")
+                   help="Session ID to be used in the BIDS dataset filenames"
+                        " (e.g. ses-<SESSION>). If not provided, no session"
+                        " entity will be added to the BIDS filenames."
+                   )
 
     p.add_argument("-c", "--config",
                    required=True,
-                   help="JSON configuration file (see example/config.json).")
+                   help="JSON configuration that specifies additional parameters for"
+                        " BIDS conversion. See the documentation for more information:"
+                        f" \nhttps://unfmontreal.github.io/Dcm2Bids/{__version__}/how-to/create-config-file/"  # noqa: E501
+                )
 
     p.add_argument("-o", "--output_dir",
                    required=False,
                    default=DEFAULT.output_dir,
-                   help="Output BIDS directory. [%(default)s]")
+                   help="Output BIDS directory. Defaults to the current working directory."
+                )
 
     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]")
+                   " Default is [%(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]")
+                        " Default is [%(default)s]")
 
     p.add_argument("--bids_validate",
                    action='store_true',
@@ -87,7 +98,9 @@ def _build_arg_parser():
                    required=False,
                    default=DEFAULT.cli_log_level,
                    choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
-                   help="Set logging level to the console. [%(default)s]")
+                   help="Set logging level to the console." 
+                        " The default level is [%(default)s]"
+                )
 
     p.add_argument("-v", "--version",
                    action="version",

dcm2bids/cli/dcm2bids_helper.py

@@ -2,7 +2,7 @@
 
 """
 Converts DICOM files to NIfTI files including their JSON sidecars in a
-temporary directory which can be inspected to make a dc2mbids config file.
+temporary directory which can be inspected to make a dcm2bids config file.
 """
 import argparse
 import logging

dcm2bids/sidecar.py

@@ -297,7 +297,6 @@ def compare(name, pattern):
                 if not self.case_sensitive:
                     name = name.lower()
                     pattern = pattern.lower()
-
                 return fnmatch(name, pattern)
 
         def compare_list(name, pattern):
@@ -396,10 +395,21 @@ def compare_float(name, pattern):
 
             elif isinstance(name, list):
                 result.append(compare_list(name, pattern))
+<<<<<<< HEAD
             elif name:
                 result.append(compare(name, pattern))
             else:
                 result.append(False)
+=======
+            else:
+                # If criteria is empty and key not found in json
+                if not name and not pattern:
+                    result.append(True)
+                elif name and pattern:
+                    result.append(compare(name, pattern))
+                else:
+                    result.append(False)
+>>>>>>> master
 
         return all(result)
 

dcm2bids/utils/tools.py

@@ -49,6 +49,10 @@ def check_github_latest(github_repo, timeout=3):
                        "your machine is probably not connected to the Internet.")
         logger.debug(f"Reason {e.reason}")
         return "no_internet"
+    except TimeoutError as e:
+        logger.warning(f"Timeout")
+        logger.debug(f"Socket timeout: {e}")
+        return "no_internet"
     else:
         content = json.loads(response.read())
         return content["tag_name"]

dcm2bids/utils/utils.py

@@ -7,14 +7,15 @@
 from pathlib import Path
 from subprocess import Popen, PIPE
 
+from dcm2bids.version import __version__
 
 class DEFAULT(object):
     """ Default values of the package"""
 
     doc = "Documentation at https://unfmontreal.github.io/Dcm2Bids/"
 
     link_bids_validator = "https://github.com/bids-standard/bids-validator#quickstart"
-    link_doc_intended_for = "https://unfmontreal.github.io/Dcm2Bids/docs/tutorial/first-steps/#populating-the-config-file"
+    link_doc_intended_for = f"https://unfmontreal.github.io/Dcm2Bids/{__version__}/tutorial/first-steps/#populating-the-config-file"  # noqa: E501
 
     # cli dcm2bids
     cli_session = ""

docs/how-to/create-config-file.md

@@ -56,7 +56,8 @@
       },
       "sidecar_changes": {
         "TaskName": "learning",
-        "IntendedFor": "id_task_learning"
+        "IntendedFor": "id_task_learning",
+        ""
       }
     }
   ]
@@ -99,6 +100,20 @@ the value of `SeriesDescription` of a sidecar. `AXIAL_T2_SPACE` will be a match,
 prefer to also match with the filename of the sidecar. Note that filename are
 subject to change depending on the dcm2niix version in use.
 
+In some cases, a user may want to select a criterion based on a key that must not exist
+in the list of sidecars[^1]. To validate that this key is absent, the user should provide
+an empty pattern.
+
+Example:
+
+```json
+{
+  "criteria": {
+    "EchoNumber": ""
+  }
+}
+```
+
 You can enter several criteria. **All criteria must match** for a description to
 be linked to a sidecar.
 
@@ -156,20 +171,23 @@ custom_entities could also be combined with extractors. See
 
 ## sidecar_changes, id and IntendedFor
 
-Optional field to change or add information in a sidecar.
+Optional field to change, delete or add information in a sidecar.
 
-:warning: `IntendedFor` is now considered a sidecar_changes.
+:warning: `IntendedFor` is now considered a sidecar_changes and does support list.
 
 Example:
 
 ```json
 {
   "sidecar_changes": {
+    "AcquisitionDuration": "",
     "IntendedFor": "task_rest"
   }
 }
 ```
 
+If you want to delete a key in a sidecar you can set it to an empty string.
+
 If you want to add an `IntendedFor` entry or any extra sidecar linked to a
 specific file, you will need to set an id to the corresponding description and
 put the same id with `IntendedFor`.