Add bids-validator option

dcm2bids/cli/dcm2bids.py

@@ -38,6 +38,12 @@ def _build_arg_parser():
                    default=DEFAULT.cliOutputDir,
                    help="Output BIDS directory. [%(default)s]")
 
+    p.add_argument("--bids_validate",
+                   action='store_true',
+                   help="If set, once your conversion is done it"
+                        " will check if your output folder is BIDS valid. [%(default)s]\n"
+                        f"bids-validator needs to be installed check: {DEFAULT.link_bids_validator}")
+
     p.add_argument("--forceDcm2niix",
                    action="store_true",
                    help="Overwrite previous temporary dcm2niix "

dcm2bids/dcm2bids_gen.py

@@ -43,6 +43,7 @@ def __init__(
         participant,
         config,
         output_dir=DEFAULT.outputDir,
+        bids_validate=DEFAULT.bids_validate,
         session=DEFAULT.session,
         clobber=DEFAULT.clobber,
         forceDcm2niix=DEFAULT.forceDcm2niix,
@@ -56,6 +57,7 @@ def __init__(
         self.config = load_json(valid_path(config, type="file"))
         self.participant = Participant(participant, session)
         self.clobber = clobber
+        self.bids_validate = bids_validate
         self.forceDcm2niix = forceDcm2niix
         self.logLevel = log_level
 
@@ -71,6 +73,8 @@ def __init__(
         self.logger.info("session: %s", self.participant.session)
         self.logger.info("config: %s", os.path.realpath(config))
         self.logger.info("BIDS directory: %s", os.path.realpath(output_dir))
+        self.logger.info("Validate BIDS: %s", self.bids_validate)
+
 
     @property
     def dicomDirs(self):
@@ -134,6 +138,17 @@ def run(self):
             acq.setDstFile()
             intendedForList = self.move(acq, intendedForList)
 
+        if self.bids_validate:
+            try:
+                self.logger.info(f"Validate if { self.output_dir} is BIDS valid.")
+                self.logger.info("Use bids-validator version: ")
+                run_shell_command(['bids-validator', '-v'])
+                run_shell_command(['bids-validator', self.bidsDir])
+            except:
+                self.logger.info("The bids-validator does not seem to work properly. "
+                                 "The bids-validator may not been installed on your computer. "
+                                 f"Please check: https://github.com/bids-standard/bids-validator#quickstart.")
+
     def move(self, acquisition, intendedForList):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
@@ -186,63 +201,4 @@ def move(self, acquisition, intendedForList):
             if intendedFile not in intendedForList[acquisition.indexSidecar]:
                 intendedForList[acquisition.indexSidecar].append(intendedFile)
 
-        return intendedForList
-
-
-def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.EPILOG,
-                                formatter_class=argparse.RawTextHelpFormatter)
-
-    p.add_argument("-d", "--dicom_dir",
-                   type=Path, 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="",
-                   help="Session ID.")
-
-    p.add_argument("-c", "--config",
-                   type=Path,
-                   required=True,
-                   help="JSON configuration file (see example/config.json).")
-
-    p.add_argument("-o", "--output_dir",
-                   required=False,
-                   type=Path,
-                   default=Path.cwd(),
-                   help="Output BIDS directory. (Default: %(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]")
-
-    return p
-
-
-def main():
-    """Let's go"""
-    parser = _build_arg_parser()
-    args = parser.parse_args()
-
-    app = Dcm2BidsGen(**vars(args))
-    return app.run()
-
-
-if __name__ == "__main__":
-    sys.exit(main())
+        return intendedForList

dcm2bids/utils/utils.py

@@ -13,6 +13,8 @@ class DEFAULT(object):
 
     doc = "Documentation at https://unfmontreal.github.io/Dcm2Bids/"
 
+    link_bids_validator = "https://github.com/bids-standard/bids-validator#quickstart"
+
     # cli dcm2bids
     cliSession = ""
     cliOutputDir = os.getcwd()
@@ -21,6 +23,7 @@ class DEFAULT(object):
     # dcm2bids.py
     outputDir = Path.cwd()
     session = ""  # also Participant object
+    bids_validate = False
     clobber = False
     forceDcm2niix = False
     defaceTpl = None

docs/get-started/install.md

@@ -277,7 +277,7 @@ usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c
                 [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
 Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-dcm2bids 2.1.7
+dcm2bids 3.0.0
 
 options:
   -h, --help            show this help message and exit
@@ -292,6 +292,8 @@ options:
   -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                         Output BIDS directory, Default: current directory
                         (/home/sam/dcm2bids-proj)
+  --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
+                        bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
   --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
   --clobber             Overwrite output if it exists
   -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}

docs/tutorial/first-steps.md

@@ -83,7 +83,7 @@ You can test it with any command but a safe way is to use the `--help` command.
                     [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
     Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-    dcm2bids 2.1.7
+    dcm2bids 3.0.0
 
     options:
     -h, --help            show this help message and exit
@@ -98,6 +98,8 @@ You can test it with any command but a safe way is to use the `--help` command.
     -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                             Output BIDS directory, Default: current directory
                             (/home/sam)
+    --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
+                          bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
     --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
@@ -951,7 +953,7 @@ command.
                     [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
     Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-    dcm2bids 2.1.7
+    dcm2bids 3.0.0
 
     options:
     -h, --help            show this help message and exit
@@ -965,6 +967,8 @@ command.
                             JSON configuration file (see example/config.json)
     -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                             Output BIDS directory, Default: current directory (/home/sam/dcm2bids-tutorial/bids_project)
+    --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
+                          bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
     --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}

requirements-doc.txt

@@ -13,51 +13,51 @@ filelock==3.6.0
 future==0.18.3
 ghp-import==2.0.2
 gitdb==4.0.9
-GitPython==3.1.29
+GitPython==3.1.30
 hug==2.6.1
 idna==3.3
 importlib-metadata==4.11.3
 ipython==8.10.0
 jedi==0.18.1
 Jinja2==3.1.1
 livereload==2.6.3
-Mako==1.2.2
+Mako==1.2.3
 Markdown==3.3.6
 MarkupSafe==2.1.1
 matplotlib-inline==0.1.3
 mergedeep==1.3.4
 mike==1.1.2
-mkdocs==1.2.4
+mkdocs==1.3.0
 mkdocs-git-authors-plugin==0.6.4
 mkdocs-git-revision-date-localized-plugin==1.0.1
 mkdocs-git-revision-date-plugin==0.3.2
 mkdocs-material==7.3.0
 mkdocs-material-extensions==1.0.3
-packaging==21.3
+packaging==23.1
 parso==0.8.3
-pdocs==1.1.1
+pdocs==1.2.0
 pexpect==4.8.0
 pickleshare==0.7.5
 platformdirs==2.5.1
 pluggy==1.0.0
-portray==1.7.0
+portray==1.8.0
 prompt-toolkit==3.0.30
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py==1.11.0
-Pygments==2.11.2
-pymdown-extensions==7.1
+Pygments==2.12.0
+pymdown-extensions==10.0
 pyparsing==3.0.8
 python-dateutil==2.8.2
 pytz==2022.1
 PyYAML==6.0
 pyyaml_env_tag==0.1
-requests==2.27.1
+requests==2.31.0
 six==1.16.0
 smmap==5.0.0
 stack-data==0.2.0
 toml==0.10.2
-tornado==6.1
+tornado==6.3.2
 tox==3.25.0
 traitlets==5.1.1
 urllib3==1.26.9