Merge pull request #163 from SamGuay/fix_windows_paths-patch

Fix windows paths patch

dcm2bids/dcm2bids.py

@@ -80,31 +80,17 @@ def dicomDirs(self):
     @dicomDirs.setter
     def dicomDirs(self, value):
 
-        if isinstance(value, list):
-            dicom_dirs = value
-        else:
-            dicom_dirs = [value]
+        dicom_dirs = value if isinstance(value, list) else [value]
 
-        valid_dirs = []
-        for _dir in dicom_dirs:
-            valid_dirs.append(valid_path(_dir, "folder"))
+        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__)
@@ -148,29 +134,28 @@ 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:
@@ -181,9 +166,9 @@ def move(self, acquisition, intendedForList):
                 cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
                 run_shell_command(cmd)
 
-                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + ext)
+                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + "".join(ext))
 
-            elif ext == ".json":
+            elif ".json" in ext:
                 data = acquisition.dstSidecarData(self.config["descriptions"],
                                                   intendedForList)
                 save_json(dstFile, data)
@@ -214,7 +199,7 @@ def _build_arg_parser():
 
     p.add_argument("-s", "--session",
                    required=False,
-                   default=DEFAULT.cliSession,
+                   default="",
                    help="Session ID.")
 
     p.add_argument("-c", "--config",
@@ -225,8 +210,8 @@ def _build_arg_parser():
     p.add_argument("-o", "--output_dir",
                    required=False,
                    type=Path,
-                   default=DEFAULT.cliOutputDir,
-                   help="Output BIDS directory, [%(default)s]")
+                   default=Path.cwd(),
+                   help="Output BIDS directory. (Default: %(default)s)")
 
     p.add_argument("--forceDcm2niix",
                    action="store_true",

dcm2bids/dcm2niix.py

@@ -4,6 +4,7 @@
 
 import logging
 import os
+from pathlib import Path
 import shlex
 import shutil
 from glob import glob
@@ -41,11 +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

dcm2bids/helper.py

@@ -21,10 +21,10 @@ def _build_arg_parser():
                    help="DICOM files directory.")
 
     p.add_argument("-o", "--output_dir",
-                   required=False, default=DEFAULT.cliOutputDir,
+                   required=False, default=Path.cwd(),
                    type=Path,
-                   help="Output BIDS directory."
-                        " (Default: %(default)s)")
+                   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/structure.py

@@ -251,12 +251,12 @@ def setDstFile(self):
             self.logger.warning("Entity \"{}\"".format(list(current_dict.keys())) +
                                 " is not a valid BIDS entity.")
 
-        new_name += f"_{'_'.join(suffix_list)}"  # Allow multiple single key (without value)
+        new_name += f"_{'_'.join(suffix_list)}"  # Allow multiple single keys (without value)
 
         if len(suffix_list) != 1:
             self.logger.warning("There was more than one suffix found "
-                                f"({suffix_list}). this is not BIDS "
-                                "compliant. Make sure you know what"
+                                f"({suffix_list}). This is not BIDS "
+                                "compliant. Make sure you know what "
                                 "you are doing.")
 
         if current_name != new_name:

dcm2bids/utils.py

@@ -17,14 +17,12 @@ class DEFAULT(object):
     """ Default values of the package"""
 
     # cli dcm2bids
-    cliSession = ""
-    cliOutputDir = os.getcwd()
     cliLogLevel = "INFO"
     EPILOG="Documentation at https://github.com/unfmontreal/Dcm2Bids"
 
     # dcm2bids.py
-    outputDir = cliOutputDir
-    session = cliSession  # also Participant object
+    outputDir = Path.cwd()
+    session = ""  # also Participant object
     clobber = False
     forceDcm2niix = False
     defaceTpl = None
@@ -67,7 +65,7 @@ def load_json(filename):
 
 
 def save_json(filename, data):
-    with open(filename, "w") as f:
+    with filename.open("w") as f:
         json.dump(data, f, indent=4)
 
 
@@ -133,14 +131,14 @@ def valid_path(in_path, type="folder"):
     if isinstance(in_path, str):
         in_path = Path(in_path)
 
-    if type=='folder':
+    if type == 'folder':
         if in_path.is_dir() or in_path.parent.is_dir():
-            return str(in_path)
+            return in_path
         else:
             raise NotADirectoryError(in_path)
-    elif type=="file":
+    elif type == "file":
         if in_path.is_file():
-            return str(in_path)
+            return in_path
         else:
             raise FileNotFoundError(in_path)
 
@@ -163,25 +161,30 @@ def assert_dirs_empty(parser, args, required):
         If true, create the directory if it does not exist.
     """
     def check(path):
-        if os.path.isdir(path):
-            if not args.overwrite:
-                parser.error(
-                    f"Output directory {path} isn't empty, so some files "
-                    "could be overwritten or deleted.\nRerun the command with "
-                    "--force option to overwrite existing output files.")
-            else:
-                for the_file in os.listdir(path):
-                    file_path = os.path.join(path, the_file)
-                    try:
-                        if os.path.isfile(file_path):
-                            os.unlink(file_path)
-                        elif os.path.isdir(file_path):
-                            shutil.rmtree(file_path)
-                    except Exception as e:
-                        print(e)
-
-    if isinstance(required, str):
-        required = [required]
+        if not path.is_dir():
+            return
+
+        if not any(path.iterdir()):
+            return
+
+        if not args.overwrite:
+            parser.error(
+                f"Output directory {path} isn't empty, so some files "
+                "could be overwritten or deleted.\nRerun the command with "
+                "--force option to overwrite existing output files.")
+        else:
+            for the_file in path.iterdir():
+                file_path = path / the_file
+                try:
+                    if file_path.is_file():
+                        file_path.unlink()
+                    elif file_path.is_dir():
+                        shutil.rmtree(file_path)
+                except Exception as e:
+                    print(e)
+
+    if isinstance(required, str) or isinstance(required, Path):
+        required = [Path(required)]
 
     for cur_dir in required:
         check(cur_dir)