Fix windows paths

dcm2bids/dcm2bids.py

@@ -1,20 +1,25 @@
 # -*- coding: utf-8 -*-
 
-"""dcm2bids module"""
+"""
+Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
+"""
 
 import argparse
 import logging
 import os
+from pathlib import Path
 import platform
 import sys
 from datetime import datetime
 from glob import glob
-from .dcm2niix import Dcm2niix
-from .logger import setup_logging
-from .sidecar import Sidecar, SidecarPairing
-from .structure import Participant
-from .utils import DEFAULT, load_json, save_json, run_shell_command, splitext_
-from .version import __version__, check_latest, dcm2niix_version
+
+from dcm2bids.dcm2niix import Dcm2niix
+from dcm2bids.logger import setup_logging
+from dcm2bids.sidecar import Sidecar, SidecarPairing
+from dcm2bids.structure import Participant
+from dcm2bids.utils import (DEFAULT, load_json, save_json,
+                            splitext_, run_shell_command, valid_path)
+from dcm2bids.version import __version__, check_latest, dcm2niix_version
 
 
 class Dcm2bids(object):
@@ -47,8 +52,8 @@ def __init__(
         self._dicomDirs = []
 
         self.dicomDirs = dicom_dir
-        self.bidsDir = output_dir
-        self.config = load_json(config)
+        self.bidsDir = valid_path(output_dir, type="folder")
+        self.config = load_json(valid_path(config, type="file"))
         self.participant = Participant(participant, session)
         self.clobber = clobber
         self.forceDcm2niix = forceDcm2niix
@@ -74,37 +79,18 @@ def dicomDirs(self):
 
     @dicomDirs.setter
     def dicomDirs(self, value):
-        if isinstance(value, list):
-            dicom_dirs = value
-        else:
-            dicom_dirs = [value]
-
-        dir_not_found = []
-        for _dir in dicom_dirs:
-            if os.path.isdir(_dir):
-                pass
-            else:
-                dir_not_found.append(_dir)
 
-        if dir_not_found:
-            raise FileNotFoundError(dir_not_found)
+        dicom_dirs = value if isinstance(value, list) else [value]
 
-        self._dicomDirs = dicom_dirs
+        valid_dirs = [valid_path(_dir, "folder") for _dir in dicom_dirs]
+
+        self._dicomDirs = valid_dirs
 
     def set_logger(self):
         """ Set a basic logger"""
-        logDir = os.path.join(self.bidsDir, DEFAULT.tmpDirName, "log")
-        logFile = os.path.join(
-            logDir,
-            "{}_{}.log".format(
-                self.participant.prefix, datetime.now().isoformat().replace(":", "")
-            ),
-        )
-
-        # os.makedirs(logdir, exist_ok=True)
-        # python2 compatibility
-        if not os.path.exists(logDir):
-            os.makedirs(logDir)
+        logDir = self.bidsDir / DEFAULT.tmpDirName / "log"
+        logFile = logDir / f"{self.participant.prefix}_{datetime.now().isoformat().replace(':', '')}.log"
+        logDir.mkdir(parents=True, exist_ok=True)
 
         setup_logging(self.logLevel, logFile)
         self.logger = logging.getLogger(__name__)
@@ -148,40 +134,41 @@ def move(self, acquisition, intendedForList):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
 
-            _, ext = splitext_(srcFile)
-            dstFile = os.path.join(self.bidsDir, acquisition.dstRoot + ext)
+            ext = Path(srcFile).suffixes
+            dstFile = (self.bidsDir / acquisition.dstRoot).with_suffix("".join(ext))
 
-            if not os.path.exists(os.path.dirname(dstFile)):
-                os.makedirs(os.path.dirname(dstFile))
+            dstFile.parent.mkdir(parents = True, exist_ok = True)
 
             # checking if destination file exists
-            if os.path.isfile(dstFile):
+            if dstFile.exists():
                 self.logger.info("'%s' already exists", dstFile)
 
                 if self.clobber:
-                    self.logger.info("Overwriting because of 'clobber' option")
+                    self.logger.info("Overwriting because of --clobber option")
 
                 else:
-                    self.logger.info("Use clobber option to overwrite")
+                    self.logger.info("Use --clobber option to overwrite")
                     continue
 
             # it's an anat nifti file and the user using a deface script
             if (
                 self.config.get("defaceTpl")
-                and acquisition.dataType == "anat"
+                and acquisition.dataType == "func"
                 and ".nii" in ext
-            ):
+                ):
                 try:
                     os.remove(dstFile)
                 except FileNotFoundError:
                     pass
                 defaceTpl = self.config.get("defaceTpl")
-                cmd = defaceTpl.format(srcFile=srcFile, dstFile=dstFile)
 
+                cmd = [w.replace('srcFile', srcFile) for w in defaceTpl]
+                cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
                 run_shell_command(cmd)
-                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + ext)
 
-            elif ext == ".json":
+                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + "".join(ext))
+
+            elif ".json" in ext:
                 data = acquisition.dstSidecarData(self.config["descriptions"],
                                                   intendedForList)
                 save_json(dstFile, data)
@@ -198,102 +185,56 @@ def move(self, acquisition, intendedForList):
         return intendedForList
 
 
-def get_arguments():
-    """Load arguments for main"""
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        description="""
-Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
-dcm2bids {}""".format(
-            __version__
-        ),
-        epilog="""
-            Documentation at https://github.com/unfmontreal/Dcm2Bids
-            """,
-    )
-
-    parser.add_argument(
-        "-d", "--dicom_dir", required=True, nargs="+", help="DICOM directory(ies)"
-    )
-
-    parser.add_argument("-p", "--participant", required=True, help="Participant ID")
-
-    parser.add_argument(
-        "-s", "--session", required=False, default=DEFAULT.cliSession, help="Session ID"
-    )
-
-    parser.add_argument(
-        "-c",
-        "--config",
-        required=True,
-        help="JSON configuration file (see example/config.json)",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--output_dir",
-        required=False,
-        default=DEFAULT.cliOutputDir,
-        help="Output BIDS directory, Default: current directory ({})".format(
-            DEFAULT.cliOutputDir
-        ),
-    )
-
-    parser.add_argument(
-        "--forceDcm2niix",
-        required=False,
-        action="store_true",
-        help="Overwrite previous temporary dcm2niix output if it exists",
-    )
-
-    parser.add_argument(
-        "--clobber",
-        required=False,
-        action="store_true",
-        help="Overwrite output if it exists",
-    )
-
-    parser.add_argument(
-        "-l",
-        "--log_level",
-        required=False,
-        default=DEFAULT.cliLogLevel,
-        choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
-        help="Set logging level",
-    )
-
-    parser.add_argument(
-        "-a",
-        "--anonymizer",
-        required=False,
-        action="store_true",
-        help="""
-        This option no longer exists from the script in this release.
-        See:https://github.com/unfmontreal/Dcm2Bids/blob/master/README.md#defaceTpl""",
-    )
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.EPILOG,
+                                formatter_class=argparse.RawTextHelpFormatter)
 
-    args = parser.parse_args()
-    return args
+    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"""
-    args = get_arguments()
-
-    if args.anonymizer:
-        print(
-            """
-        The anonymizer option no longer exists from the script in this release
-        It is still possible to deface the anatomical nifti images
-        Please add "defaceTpl" key in the congifuration file
-
-        For example, if you use the last version of pydeface, add:
-        "defaceTpl": "pydeface --outfile {dstFile} {srcFile}"
-        It is a template string and dcm2bids will replace {srcFile} and {dstFile}
-        by the source file (input) and the destination file (output)
-        """
-        )
-        return 1
+    parser = _build_arg_parser()
+    args = parser.parse_args()
 
     check_latest()
     check_latest("dcm2niix")

dcm2bids/dcm2niix.py

@@ -4,6 +4,8 @@
 
 import logging
 import os
+from pathlib import Path
+import shlex
 import shutil
 from glob import glob
 from .utils import DEFAULT, run_shell_command
@@ -40,11 +42,9 @@ def outputDir(self):
         Returns:
             A directory to save all the output files of dcm2niix
         """
-        if self.participant:
-            tmpDir = self.participant.prefix
-        else:
-            tmpDir = DEFAULT.helperDir
-        return os.path.join(self.bidsDir, DEFAULT.tmpDirName, tmpDir)
+        tmpDir = self.participant.prefix if self.participant else DEFAULT.helperDir
+
+        return self.bidsDir / DEFAULT.tmpDirName / tmpDir
 
     def run(self, force=False):
         """ Run dcm2niix if necessary
@@ -95,8 +95,8 @@ def execute(self):
         """ Execute dcm2niix for each directory in dicomDirs
         """
         for dicomDir in self.dicomDirs:
-            commandTpl = "dcm2niix {} -o {} {}"
-            cmd = commandTpl.format(self.options, self.outputDir, dicomDir)
+            cmd = ['dcm2niix', *shlex.split(self.options),
+                   '-o', self.outputDir, dicomDir]
             output = run_shell_command(cmd)
 
             try:

dcm2bids/helper.py

@@ -4,27 +4,27 @@
 
 import argparse
 import os
+from pathlib import Path
 import sys
-from .dcm2niix import Dcm2niix
-from .utils import DEFAULT, assert_dirs_empty
 
-EPILOG = """
-    Documentation at https://github.com/unfmontreal/Dcm2Bids
-    """
+from dcm2bids.dcm2niix import Dcm2niix
+from dcm2bids.utils import DEFAULT, assert_dirs_empty
 
 
 def _build_arg_parser():
-    p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
+    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 files directory.")
 
     p.add_argument("-o", "--output_dir",
-                   required=False, default=DEFAULT.cliOutputDir,
-                   help="Output BIDS directory."
-                        " (Default: %(default)s)")
+                   required=False, default=Path.cwd(),
+                   type=Path,
+                   help="Output BIDS directory. "
+                        "(Default: %(default)s)")
 
     p.add_argument('--force',
                    dest='overwrite', action='store_true',
@@ -37,12 +37,11 @@ def main():
     """Let's go"""
     parser = _build_arg_parser()
     args = parser.parse_args()
-    out_folder = os.path.join(args.output_dir, 'tmp_dcm2bids', 'helper')
+    out_folder = args.output_dir / DEFAULT.tmpDirName / DEFAULT.helperDir
     assert_dirs_empty(parser, args, out_folder)
     app = Dcm2niix(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)
     rsl = app.run()
-    print("Example in:")
-    print(os.path.join(args.output_dir, DEFAULT.tmpDirName, DEFAULT.helperDir))
+    print(f"Example in: {out_folder}")
     return rsl
 
 

dcm2bids/sidecar.py

@@ -86,7 +86,7 @@ class SidecarPairing(object):
     """
     Args:
         sidecars (list): List of Sidecar objects
-        descriptions (list): List of dictionnaries describing acquisitions
+        descriptions (list): List of dictionaries describing acquisitions
     """
 
     def __init__(self, sidecars, descriptions, searchMethod=DEFAULT.searchMethod,
@@ -146,7 +146,7 @@ def caseSensitive(self, value):
     def build_graph(self):
         """
         Test all the possible links between the list of sidecars and the
-        description dictionnaries and build a graph from it
+        description dictionaries and build a graph from it
         The graph is in a OrderedDict object. The keys are the Sidecars and
         the values are a list of possible descriptions