Python CLI changes for Windows image piping

core/formats/pipe.cpp

@@ -42,7 +42,8 @@ std::unique_ptr<ImageIO::Base> Pipe::read(Header &H) const {
     SignalHandler::mark_file_for_deletion(H.name());
 
   if (!Path::has_suffix(H.name(), ".mif"))
-    throw Exception("MRtrix only supports the .mif format for command-line piping");
+    throw Exception("MRtrix only supports the .mif format for command-line piping"
+                    " (received \"" + H.name() + "\")");
 
   std::unique_ptr<ImageIO::Base> original_handler(mrtrix_handler.read(H));
   std::unique_ptr<ImageIO::Pipe> io_handler(new ImageIO::Pipe(std::move(*original_handler)));

python/mrtrix3/commands/dwi2mask/b02template.py

@@ -128,7 +128,7 @@ def check_ants_executable(cmdname):
   check_ants_executable(ANTS_REGISTERFULL_CMD if mode == 'full' else ANTS_REGISTERQUICK_CMD)
   check_ants_executable(ANTS_TRANSFORM_CMD)
   if app.ARGS.ants_options:
-    ants_options_as_path = app.Parser.make_userpath_object(app.Parser._UserPathExtras, app.ARGS.ants_options) # pylint: disable=protected-access
+    ants_options_as_path = app.FSQEPath(app.ARGS.ants_options)
     if ants_options_as_path.is_file():
       run.function(shutil.copyfile, ants_options_as_path, 'ants_options.txt')
       with open('ants_options.txt', 'r', encoding='utf-8') as ants_options_file:

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

@@ -15,7 +15,7 @@
 
 import os
 from mrtrix3 import MRtrixError
-from mrtrix3 import app, image, path, run, utils
+from mrtrix3 import app, image, path, run
 
 
 FA_THRESHOLD_DEFAULT = 0.4
@@ -97,7 +97,7 @@ def __init__(self, filename, prefix, mask_filename = ''):
 
   app.activate_scratch_dir()
 
-  utils.make_dir('fa')
+  os.makedirs('fa')
   progress = app.ProgressBar('Computing FA images', len(input_list))
   for i in input_list:
     run.command(['dwi2tensor', os.path.join(app.ARGS.input_dir, i.filename), '-mask', os.path.join(app.ARGS.mask_dir, i.mask_filename), '-', '|',
@@ -122,22 +122,28 @@ def __init__(self, filename, prefix, mask_filename = ''):
   run.command(f'mrthreshold fa_template.mif -abs {app.ARGS.fa_threshold} template_wm_mask.mif')
 
   progress = app.ProgressBar('Intensity normalising subject images', len(input_list))
-  utils.make_dir(app.ARGS.output_dir)
-  utils.make_dir('wm_mask_warped')
+  app.ARGS.output_dir.mkdir()
+  os.makedirs('wm_mask_warped')
+  os.makedirs('dwi_normalised')
   for i in input_list:
-    run.command(['mrtransform', 'template_wm_mask.mif', os.path.join('wm_mask_warped', f'{i.prefix}.mif'),
+    in_path = os.path.join(app.ARGS.input_dir, i.filename)
+    warp_path = os.path.join('warps', f'{i.prefix}.mif')
+    fa_path = os.path.join('fa', f'{i.prefix}.mif')
+    wm_mask_warped_path = os.path.join('wm_mask_warped', f'{i.prefix}.mif')
+    dwi_normalised_path = os.path.join('dwi_normalised', f'{i.prefix}.mif')
+    run.command(['mrtransform', 'template_wm_mask.mif', wm_mask_warped_path,
                  '-interp', 'nearest',
-                 '-warp_full', os.path.join('warps', f'{i.prefix}.mif'),
+                 '-warp_full', warp_path,
                  '-from', '2',
-                 '-template', os.path.join('fa', f'{i.prefix}.mif')])
+                 '-template', fa_path])
     run.command(['dwinormalise', 'manual',
-                 os.path.join(app.ARGS.input_dir, i.filename),
-                 os.path.join('wm_mask_warped', f'{i.prefix}.mif'),
-                 'temp.mif'])
-    run.command(['mrconvert', 'temp.mif', os.path.join(app.ARGS.output_dir, i.filename)],
-                mrconvert_keyval=os.path.join(app.ARGS.input_dir, i.filename),
+                 in_path,
+                 wm_mask_warped_path,
+                 dwi_normalised_path])
+    run.command(['mrconvert', dwi_normalised_path, app.ARGS.output_dir / i.filename],
+                mrconvert_keyval=in_path,
                 force=app.FORCE_OVERWRITE)
-    os.remove('temp.mif')
+    app.cleanup([warp_path, fa_path, wm_mask_warped_path, dwi_normalised_path])
     progress.increment()
   progress.done()
 

python/mrtrix3/commands/population_template/execute.py

@@ -54,8 +54,8 @@ def execute(): #pylint: disable=unused-variable
   app.ARGS.template = []
   for i_contrast in range(n_contrasts):
     inargs = (input_output[i_contrast*2], input_output[i_contrast*2+1])
-    app.ARGS.input_dir.append(app.Parser.make_userpath_object(app.Parser._UserPathExtras, inargs[0])) # pylint: disable=protected-access
-    app.ARGS.template.append(app.Parser.make_userpath_object(app.Parser._UserOutPathExtras, inargs[1])) # pylint: disable=protected-access
+    app.ARGS.input_dir.append(app.Parser.UserInPath(inargs[0]))
+    app.ARGS.template.append(app.Parser.UserOutPath(inargs[1]))
   # Perform checks that otherwise would have been done immediately after command-line parsing
   #   were it not for the inability to represent input-output pairs in the command-line interface representation
   for output_path in app.ARGS.template:
@@ -366,7 +366,7 @@ def execute(): #pylint: disable=unused-variable
 
   if use_masks:
     os.mkdir('mask_transformed')
-  write_log = (app.VERBOSITY >= 2)
+  write_log = app.VERBOSITY >= 2
   if write_log:
     os.mkdir('log')
 

python/mrtrix3/commands/population_template/usage.py

@@ -34,8 +34,7 @@
 
 class SequenceDirectoryOut(app.Parser.CustomTypeBase):
   def __call__(self, input_value):
-    return [app.Parser.make_userpath_object(app.Parser._UserDirOutPathExtras, item) # pylint: disable=protected-access \
-            for item in input_value.split(',')]
+    return [app.Parser.UserDirOutPath(item) for item in input_value.split(',')]
   @staticmethod
   def _legacytypestring():
     return 'SEQDIROUT'

python/mrtrix3/commands/population_template/utils.py

@@ -13,7 +13,7 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-import csv, math, os, re, shutil, sys
+import csv, math, os, re, shutil
 from mrtrix3 import MRtrixError
 from mrtrix3 import app, image, path, run, utils
 from . import IMAGEEXT
@@ -33,10 +33,7 @@ def copy(src, dst, follow_symlinks=True): # pylint: disable=unused-variable
   """
   if os.path.isdir(dst):
     dst = os.path.join(dst, os.path.basename(src))
-  if sys.version_info[0] > 2:
-    shutil.copyfile(src, dst, follow_symlinks=follow_symlinks)   # pylint: disable=unexpected-keyword-arg
-  else:
-    shutil.copyfile(src, dst)
+  shutil.copyfile(src, dst, follow_symlinks=follow_symlinks) # pylint: disable=unexpected-keyword-arg
   return dst
 
 
@@ -52,16 +49,16 @@ def check_linear_transformation(transformation, cmd, max_scaling=0.5, max_shear=
     return True
   data = utils.load_keyval(f'{transformation}decomp')
   run.function(os.remove, f'{transformation}decomp')
-  scaling = [float(value) for value in data['scaling']]
+  scaling = [float(value) for value in data['scaling'].split()]
   if any(a < 0 for a in scaling) or any(a > (1 + max_scaling) for a in scaling) or any(
       a < (1 - max_scaling) for a in scaling):
     app.warn(f'large scaling ({scaling})) in {transformation}')
     good = False
-  shear = [float(value) for value in data['shear']]
+  shear = [float(value) for value in data['shear'].split()]
   if any(abs(a) > max_shear for a in shear):
     app.warn(f'large shear ({shear}) in {transformation}')
     good = False
-  rot_angle = float(data['angle_axis'][0])
+  rot_angle = float(data['angle_axis'].split()[0])
   if abs(rot_angle) > max_rot:
     app.warn(f'large rotation ({rot_angle}) in {transformation}')
     good = False

python/mrtrix3/fsl.py

@@ -13,14 +13,19 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-import os, shutil
+import os, pathlib, shutil
 from mrtrix3 import MRtrixError
 
 
 
 
 _SUFFIX = ''
 
+IMAGETYPE2SUFFIX = {'NIFTI': '.nii',
+                    'NIFTI_GZ': '.nii.gz',
+                    'NIFTI_PAIR': '.img',
+                    'NIFTI_PAIR_GZ': None}
+
 
 
 # Functions that may be useful for scripts that interface with FMRIB FSL tools
@@ -30,8 +35,8 @@
 #   the output files to appear.
 def check_first(prefix, structures): #pylint: disable=unused-variable
   from mrtrix3 import app, path #pylint: disable=import-outside-toplevel
-  vtk_files = [ prefix + '-' + struct + '_first.vtk' for struct in structures ]
-  existing_file_count = sum(os.path.exists(filename) for filename in vtk_files)
+  vtk_files = [ pathlib.Path(f'{prefix}-{struct}_first.vtk') for struct in structures ]
+  existing_file_count = sum(vtk_file.exists() for vtk_file in vtk_files)
   if existing_file_count != len(vtk_files):
     if 'SGE_ROOT' in os.environ and os.environ['SGE_ROOT']:
       app.console('FSL FIRST job may have been run via SGE; '
@@ -43,7 +48,7 @@ def check_first(prefix, structures): #pylint: disable=unused-variable
       app.DO_CLEANUP = False
       raise MRtrixError('FSL FIRST has failed; '
                         f'{"only " if existing_file_count else ""}{existing_file_count} of {len(vtk_files)} structures were segmented successfully '
-                        f'(check {os.path.join(app.SCRATCH_DIR, "first.logs")})')
+                        f'(check {app.SCRATCH_DIR / "first.logs"})')
 
 
 
@@ -64,15 +69,17 @@ def eddy_binary(cuda): #pylint: disable=unused-variable
     #   select the one with the highest version number
     binaries = [ ]
     for directory in os.environ['PATH'].split(os.pathsep):
-      if os.path.isdir(directory):
-        for entry in os.listdir(directory):
-          if entry.startswith('eddy_cuda'):
-            binaries.append(entry)
+      directory = pathlib.Path(directory)
+      try:
+        for entry in directory.glob('eddy_cuda*'):
+          binaries.append(entry)
+      except OSError:
+        pass
     max_version = 0.0
-    exe_path = ''
+    exe_path = None
     for entry in binaries:
       try:
-        version = float(entry.lstrip('eddy_cuda'))
+        version = float(entry.stem.lstrip('eddy_cuda'))
         if version > max_version:
           max_version = version
           exe_path = entry
@@ -113,21 +120,26 @@ def exe_name(name): #pylint: disable=unused-variable
 
 
 # In some versions of FSL, even though we try to predict the names of image files that
-#   FSL commands will generate based on the suffix() function, the FSL binaries themselves
-#   ignore the FSLOUTPUTTYPE environment variable. Therefore, the safest approach is:
-# Whenever receiving an output image from an FSL command, explicitly search for the path
+#   FSL commands will generate based on the suffix() function,
+#   the FSL binaries themselves ignore the FSLOUTPUTTYPE environment variable.
+# Therefore, the safest approach is:
+#   Whenever receiving an output image from an FSL command,
+#   explicitly search for the path
 def find_image(name): #pylint: disable=unused-variable
   from mrtrix3 import app #pylint: disable=import-outside-toplevel
-  prefix = os.path.join(os.path.dirname(name), os.path.basename(name).split('.')[0])
-  if os.path.isfile(prefix + suffix()):
-    app.debug(f'Image at expected location: "{prefix}{suffix()}"')
-    return f'{prefix}{suffix()}'
+  prefix = pathlib.PurePath(name)
+  prefix = prefix.parent / prefix.name.split('.')[0]
+  expected = prefix.with_suffix(suffix())
+  if expected.is_file():
+    app.debug(f'Image at expected location: {expected}')
+    return expected
   for suf in ['.nii', '.nii.gz', '.img']:
-    if os.path.isfile(f'{prefix}{suf}'):
-      app.debug(f'Expected image at "{prefix}{suffix()}", '
-                f'but found at "{prefix}{suf}"')
-      return f'{prefix}{suf}'
-  raise MRtrixError(f'Unable to find FSL output file for path "{name}"')
+    candidate = prefix.with_suffix(suf)
+    if candidate.is_file():
+      app.debug(f'Expected image at {expected}, '
+                f'but found at {candidate}')
+      return candidate
+  raise MRtrixError(f'Unable to find FSL output image for path {name}')
 
 
 
@@ -141,26 +153,20 @@ def suffix(): #pylint: disable=unused-variable
   if _SUFFIX:
     return _SUFFIX
   fsl_output_type = os.environ.get('FSLOUTPUTTYPE', '')
-  if fsl_output_type == 'NIFTI':
-    app.debug('NIFTI -> .nii')
-    _SUFFIX = '.nii'
-  elif fsl_output_type == 'NIFTI_GZ':
-    app.debug('NIFTI_GZ -> .nii.gz')
-    _SUFFIX = '.nii.gz'
-  elif fsl_output_type == 'NIFTI_PAIR':
-    app.debug('NIFTI_PAIR -> .img')
-    _SUFFIX = '.img'
-  elif fsl_output_type == 'NIFTI_PAIR_GZ':
-    raise MRtrixError('MRtrix3 does not support compressed NIFTI pairs; '
-                      'please change FSLOUTPUTTYPE environment variable')
-  elif fsl_output_type:
-    app.warn('Unrecognised value for environment variable FSLOUTPUTTYPE '
-             f'("{fsl_output_type}"): '
-             'Expecting compressed NIfTIs, but FSL commands may fail')
-    _SUFFIX = '.nii.gz'
+  if fsl_output_type in IMAGETYPE2SUFFIX:
+    _SUFFIX = IMAGETYPE2SUFFIX[fsl_output_type]
+    if _SUFFIX is None:
+      raise MRtrixError(f'MRtrix3 does not support FSL output image type "{fsl_output_type}; '
+                        'please change FSLOUTPUTTYPE environment variable')
+    app.debug(f'{fsl_output_type} -> {_SUFFIX}')
   else:
-    app.warn('Environment variable FSLOUTPUTTYPE not set; '
-             'FSL commands may fail, '
-             'or script may fail to locate FSL command outputs')
     _SUFFIX = '.nii.gz'
+    if fsl_output_type:
+      app.warn('Unrecognised value for environment variable FSLOUTPUTTYPE '
+              f'("{fsl_output_type}"): '
+              'executed FSL commands may fail')
+    else:
+      app.warn('Environment variable FSLOUTPUTTYPE not set; '
+               'FSL commands may fail, '
+               'or this script may fail to locate FSL command outputs')
   return _SUFFIX