Python: Initial fixes to piped image support on Windows

python/mrtrix3/app.py

@@ -601,6 +601,9 @@ def __format__(self, _):
 #   (which itself through __new__() / __init__() could be Posix or Windows)
 #   and a desired augmentation that provides additional functions
 # TODO Can this be made a callable?
+# TODO Trouble with exposing this outside of the Parser is that
+#   as soon as one of the member functions is called,
+#   the returned type will no longer be derived from _QuoteEscapedPath
 def make_quote_escaped_path_object(base_class, *args):
   abspath = pathlib.Path(WORKING_DIR, *args).resolve()
   super_class = type(abspath)
@@ -663,21 +666,21 @@ class _UserInPathExtras(_QuoteEscapedPath):
     def __init__(self, *args, **kwargs):
       super().__init__(self, *args, **kwargs)
     def check_input(self, item_type='path'):
-      if not self.exists():
+      if not super().exists(): # pylint: disable=no-member
         raise argparse.ArgumentTypeError(f'Input {item_type} "{self}" does not exist')
   class _UserFileInPathExtras(_UserInPathExtras):
     def __init__(self, *args, **kwargs):
       super().__init__(self, *args, **kwargs)
     def check_input(self): # pylint: disable=arguments-differ
       super().check_input('file')
-      if not self.is_file():
+      if not super().is_file(): # pylint: disable=no-member
         raise argparse.ArgumentTypeError(f'Input path "{self}" is not a file')
   class _UserDirInPathExtras(_UserInPathExtras):
     def __init__(self, *args, **kwargs):
       super().__init__(self, *args, **kwargs)
     def check_input(self): # pylint: disable=arguments-differ
       super().check_input('directory')
-      if not self.is_dir():
+      if not super().is_dir(): # pylint: disable=no-member
         raise argparse.ArgumentTypeError(f'Input path "{self}" is not a directory')
 
   # Various callable types for use as argparse argument types
@@ -832,8 +835,8 @@ def __call__(self, input_value):
       input_value = sys.stdin.readline().strip()
       if shutil.which('cygpath.exe'):
         try:
-          new_path = subprocess.run(['cygpath.exe', '-m', input_value], check=True, capture_output=True, text=True).stdout.strip()
-          debug(f'stdin contents to cygpath.exe: {input_value} -> {new_path}\n')
+          new_path = subprocess.run(['cygpath.exe', '-u', input_value], check=True, capture_output=True, text=True).stdout.strip()
+          debug(f'stdin contents to cygpath.exe: {input_value} -> {new_path}')
           abspath = make_quote_escaped_path_object(_QuoteEscapedPath, new_path)
         except subprocess.CalledProcessError:
           warn(f'Error converting input piped image path {input_value} using cygpath;'

python/mrtrix3/commands/dwi2response/dhollander.py

@@ -14,7 +14,7 @@
 # For more details, see http://www.mrtrix.org/.
 
 
-import math, shlex, shutil
+import math, shutil
 from mrtrix3 import CONFIG, MRtrixError
 from mrtrix3 import app, image, run
 
@@ -303,8 +303,7 @@ def execute(): #pylint: disable=unused-variable
       app.warn('Single-fibre WM response function selection algorithm "tax" will not honour requested WM voxel percentage')
     run.command(f'dwi2response {app.ARGS.wm_algo} dwi.mif _respsfwmss.txt -mask refined_wm.mif -voxels voxels_sfwm.mif'
                 + ('' if app.ARGS.wm_algo == 'tax' else (' -number ' + str(voxsfwmcount)))
-                + ' -scratch ' + shlex.quote(app.SCRATCH_DIR)
-                + recursive_cleanup_option,
+                + f' -scratch {app.SCRATCH_DIR}{recursive_cleanup_option}',
                 show=False)
   else:
     app.console('   Selecting WM single-fibre voxels using built-in (Dhollander et al., 2019) algorithm')

python/mrtrix3/commands/dwi2response/msmt_5tt.py

@@ -138,13 +138,11 @@ def execute(): #pylint: disable=unused-variable
   if not app.ARGS.sfwm_fa_threshold:
     app.console(f'Selecting WM single-fibre voxels using "{app.ARGS.wm_algo}" algorithm')
     run.command(f'dwi2response {app.ARGS.wm_algo} dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif'
-                ' -scratch %s' % shlex.quote(app.SCRATCH_DIR)
-                + recursive_cleanup_option)
+                f' -scratch {app.SCRATCH_DIR}{recursive_cleanup_option}')
   else:
     app.console(f'Selecting WM single-fibre voxels using "fa" algorithm with a hard FA threshold of {app.ARGS.sfwm_fa_threshold}')
     run.command(f'dwi2response fa dwi.mif wm_ss_response.txt -mask wm_mask.mif -threshold {app.ARGS.sfwm_fa_threshold} -voxels wm_sf_mask.mif'
-                ' -scratch %s' % shlex.quote(app.SCRATCH_DIR)
-                + recursive_cleanup_option)
+                f' -scratch {app.SCRATCH_DIR}{recursive_cleanup_option}')
 
   # Check for empty masks
   wm_voxels  = image.statistics('wm_sf_mask.mif', mask='wm_sf_mask.mif').count

python/mrtrix3/commands/dwinormalise/group.py

@@ -140,7 +140,7 @@ def __init__(self, filename, prefix, mask_filename = ''):
                  in_path,
                  wm_mask_warped_path,
                  dwi_normalised_path])
-    run.command(['mrconvert', dwi_normalised_path, app.ARGS.output_dir / i.filename],
+    run.command(['mrconvert', dwi_normalised_path, app.make_quote_escaped_path_object(app.ARGS.output_dir, i.filename)],
                 mrconvert_keyval=in_path,
                 force=app.FORCE_OVERWRITE)
     app.cleanup([warp_path, fa_path, wm_mask_warped_path, dwi_normalised_path])