From 882e055612b07e359f553796bbe90b29495d9e37 Mon Sep 17 00:00:00 2001
From: Samuel Guay <samuel.guay@umontreal.ca>
Date: Fri, 22 Apr 2022 14:10:13 -0400
Subject: [PATCH] Change argparse default + improve suffix handling

---
 dcm2bids/dcm2bids.py | 18 +++++++++---------
 dcm2bids/utils.py    | 16 +++++++---------
 2 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/dcm2bids/dcm2bids.py b/dcm2bids/dcm2bids.py
index b2a174bc..ea305c2b 100644
--- a/dcm2bids/dcm2bids.py
+++ b/dcm2bids/dcm2bids.py
@@ -134,8 +134,8 @@ 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))
 
             dstFile.parent.mkdir(parents = True, exist_ok = True)
 
@@ -153,9 +153,9 @@ def move(self, acquisition, intendedForList):
             # 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:
@@ -166,9 +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)
@@ -199,7 +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",
@@ -210,8 +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",
diff --git a/dcm2bids/utils.py b/dcm2bids/utils.py
index 4ee02fa1..d487157f 100644
--- a/dcm2bids/utils.py
+++ b/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)