Merge pull request #2406 from MRtrix3/dev_update

dev update

Author: jdtournier

.github/ISSUE_TEMPLATE/bug_report.md

@@ -34,7 +34,7 @@ Please provide the following information:
 **Advanced debugging information (if applicable)**
 
 -  In case of a critical error such as "segmentation fault", please generate
-   and report the backtrace as described [here](https://mrtrix.readthedocs.io/en/latest/troubleshooting/advanced_debugging.html).
+   and report the backtrace as described [here](https://community.mrtrix.org/t/advanced-debugging-of-mrtrix3-binaries).
 
 - For issues with `mrview`, please provide:
 

CONTRIBUTING.md

@@ -145,9 +145,17 @@ to be provided in subsequent sections of this document.
 
    -  If only making changes to the *MRtrix3* *documentation*, then the
       appropriate base branch will depend upon the nature of the changes
-      being proposed and the urgency of the update. In this scenario,
-      please generate an [Issue](https://github.com/MRtrix3/mrtrix3/issues)
-      to facilitate communication with the core development team.
+      being proposed and the urgency of the update. For instance, if providing
+      a minor correction to spelling / grammar, or fixing an erroneous
+      hyperlink, then a direct merge to `master` is likely appropriate.
+      Conversely, if the changes are non-trivial, and it makes more sense for
+      the changes to be made as part of an *MRtrix3* update rather than
+      immediately, then `dev` may be the more appropriate base branch. If
+      the answer to this question in the context of your proposed changes is
+      unclear to you, then please generate an [Issue](https://github.com/MRtrix3/mrtrix3/issues)
+      to facilitate direct discussion with the *MRtrix3* core development
+      team (ideally before commencing the implementation of changes, as
+      incorrect selection can sometimes be laborious to resolve later).
 
 1. Generate one or more Git commits that apply your proposed changes to
    the repository.

README.md

@@ -1,6 +1,7 @@
 # MRtrix
 
 [![Build Status](https://github.com/MRtrix3/mrtrix3/workflows/checks/badge.svg)](https://github.com/MRtrix3/mrtrix3/actions)
+[![@MRtrix3](http://img.shields.io/twitter/follow/MRtrix3.svg?style=social)](https://twitter.com/MRtrix3)
 
 *MRtrix3* can be installed / run through multiple avenues:
 - [Direct download](https://www.mrtrix.org/download/) through mechanisms tailored for different OS platforms;

bin/blend

@@ -20,7 +20,9 @@ import sys
 
 if len(sys.argv) <= 1:
   sys.stderr.write('A script to blend two sets of movie frames together with a desired overlap.\n')
-  sys.stderr.write('The input arguments are two folders containing the movie frames (eg. output from the MRview screenshot tool), and the desired number of overlapping frames.\n')
+  sys.stderr.write('The input arguments are two folders containing the movie frames '
+                   '(eg. output from the MRview screenshot tool), and the desired number '
+                   'of overlapping frames.\n')
   sys.stderr.write('eg: blend folder1 folder2 20 output_folder\n')
   sys.exit(1)
 
@@ -42,7 +44,9 @@ for i in range(NUM_OUTPUT_FRAMES):
   if len(FILE_LIST_1) - NUM_OVERLAP < i < len(FILE_LIST_1):
     i2 = i - (len(FILE_LIST_1) - NUM_OVERLAP) - 1
     blend_amount = 100 * float(i2 + 1) / float(NUM_OVERLAP)
-    os.system('convert ' + INPUT_FOLDER_1 + '/' + FILE_LIST_1[i] + ' ' + INPUT_FOLDER_2 + '/' + FILE_LIST_2[i2] + ' -alpha on -compose blend  -define compose:args=' + str(blend_amount) + ' -gravity South  -composite ' + OUTPUT_FOLDER + '/' + file_name)
+    os.system('convert ' + INPUT_FOLDER_1 + '/' + FILE_LIST_1[i] + ' ' + INPUT_FOLDER_2 \
+        + '/' + FILE_LIST_2[i2] + ' -alpha on -compose blend  -define compose:args=' \
+        + str(blend_amount) + ' -gravity South  -composite ' + OUTPUT_FOLDER + '/' + file_name)
   if i >= (len(FILE_LIST_1)):
     i2 = i - (len(FILE_LIST_1) - NUM_OVERLAP) - 1
     os.system('cp -L ' + INPUT_FOLDER_2 + '/' + FILE_LIST_2[i2] + ' ' + OUTPUT_FOLDER + '/' + file_name)

bin/dwi2response

@@ -103,19 +103,20 @@ def execute(): #pylint: disable=unused-variable
 
   app.goto_scratch_dir()
 
-  if app.ARGS.mask:
-    # Check that the brain mask is appropriate
-    mask_header = image.Header('mask.mif')
-    if mask_header.size()[:3] != image.Header('dwi.mif').size()[:3]:
-      raise MRtrixError('Dimensions of provided mask image do not match DWI')
-    if not (len(mask_header.size()) == 3 or (len(mask_header.size()) == 4 and mask_header.size()[3] == 1)):
-      raise MRtrixError('Provided mask image needs to be a 3D image')
-  else:
-    app.console('Computing brain mask (dwi2mask)...')
-    run.command('dwi2mask ' + CONFIG.get('Dwi2maskAlgorithm', 'legacy') + ' dwi.mif mask.mif', show=False)
-
-  if not image.statistics('mask.mif', mask='mask.mif').count:
-    raise MRtrixError(('Provided' if app.ARGS.mask else 'Generated') + ' mask image does not contain any voxels')
+  if alg.supports_mask():
+    if app.ARGS.mask:
+      # Check that the brain mask is appropriate
+      mask_header = image.Header('mask.mif')
+      if mask_header.size()[:3] != image.Header('dwi.mif').size()[:3]:
+        raise MRtrixError('Dimensions of provided mask image do not match DWI')
+      if not (len(mask_header.size()) == 3 or (len(mask_header.size()) == 4 and mask_header.size()[3] == 1)):
+        raise MRtrixError('Provided mask image needs to be a 3D image')
+    else:
+      app.console('Computing brain mask (dwi2mask)...')
+      run.command('dwi2mask ' + CONFIG.get('Dwi2maskAlgorithm', 'legacy') + ' dwi.mif mask.mif', show=False)
+
+    if not image.statistics('mask.mif', mask='mask.mif').count:
+      raise MRtrixError(('Provided' if app.ARGS.mask else 'Generated') + ' mask image does not contain any voxels')
 
   # From here, the script splits depending on what estimation algorithm is being used
   alg.execute()

bin/dwicat

@@ -17,7 +17,7 @@
 
 
 
-import json
+import json, shutil
 
 
 
@@ -36,7 +36,7 @@ def usage(cmdline): #pylint: disable=unused-variable
 
 
 def execute(): #pylint: disable=unused-variable
-  from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
+  from mrtrix3 import CONFIG, MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
   from mrtrix3 import app, image, path, run #pylint: disable=no-name-in-module, import-outside-toplevel
 
   num_inputs = len(app.ARGS.inputs)
@@ -45,13 +45,26 @@ def execute(): #pylint: disable=unused-variable
 
   # check input data
   def check_header(header):
-    if len(header.size()) != 4:
-      raise MRtrixError('Image "' + header.name() + '" is not a 4D image series')
+    if len(header.size()) > 4:
+      raise MRtrixError('Image "' + header.name() + '" contains more than 4 dimensions')
     if not 'dw_scheme' in header.keyval():
       raise MRtrixError('Image "' + header.name() + '" does not contain a gradient table')
-    num_grad_lines = len(header.keyval()['dw_scheme'])
-    if num_grad_lines != header.size()[3]:
-      raise MRtrixError('Number of lines in gradient table for image "' + header.name() + '" (' + str(num_grad_lines) + ') does not match number of volumes (' + str(header.size()[3]) + ')')
+    dw_scheme = header.keyval()['dw_scheme']
+    try:
+      if isinstance(dw_scheme[0], list):
+        num_grad_lines = len(dw_scheme)
+      elif (isinstance(dw_scheme[0], ( int, float))) and len(dw_scheme) >= 4:
+        num_grad_lines = 1
+      else:
+        raise MRtrixError
+    except (IndexError, MRtrixError):
+      raise MRtrixError('Image "' + header.name() + '" contains gradient table of unknown format') # pylint: disable=raise-missing-from
+    if len(header.size()) == 4:
+      num_volumes = header.size()[3]
+      if num_grad_lines != num_volumes:
+        raise MRtrixError('Number of lines in gradient table for image "' + header.name() + '" (' + str(num_grad_lines) + ') does not match number of volumes (' + str(num_volumes) + ')')
+    elif not (num_grad_lines == 1 and len(dw_scheme) >= 4 and dw_scheme[3] <= float(CONFIG.get('BZeroThreshold', 10.0))):
+      raise MRtrixError('Image "' + header.name() + '" is 3D, and cannot be validated as a b=0 volume')
 
   first_header = image.Header(path.from_user(app.ARGS.inputs[0], False))
   check_header(first_header)
@@ -87,7 +100,12 @@ def execute(): #pylint: disable=unused-variable
 
   # extract b=0 volumes within each input series
   for index in range(0, num_inputs):
-    run.command('dwiextract ' + str(index) + 'in.mif ' + str(index) + 'b0.mif -bzero')
+    infile = str(index) + 'in.mif'
+    outfile = str(index) + 'b0.mif'
+    if len(image.Header(infile).size()) > 3:
+      run.command('dwiextract ' + infile + ' ' + outfile + ' -bzero')
+    else:
+      run.function(shutil.copyfile, infile, outfile)
 
   mask_option = ' -mask_input mask.mif -mask_target mask.mif' if app.ARGS.mask else ''
 

bin/dwifslpreproc

@@ -847,7 +847,7 @@ def execute(): #pylint: disable=unused-variable
           app.cleanup(se_epi_path)
           se_epi_path = new_se_epi_path
           new_dwi_path = os.path.splitext(dwi_path)[0] + '_pad' + str(axis) + '.mif'
-          run.command('mrconvert ' + dwi_path + ' -coord ' + str(axis) + ' ' + str(axis_size-1) + ' - | mrcat ' + dwi_path + ' - ' + new_dwi_path + ' -axis ' + str(axis))
+          run.command('mrconvert ' + dwi_path + ' -coord ' + str(axis) + ' ' + str(axis_size-1) + ' -clear dw_scheme - | mrcat ' + dwi_path + ' - ' + new_dwi_path + ' -axis ' + str(axis))
           app.cleanup(dwi_path)
           dwi_path = new_dwi_path
           dwi_post_eddy_crop_option += ' -coord ' + str(axis) + ' 0:' + str(axis_size-1)

build

@@ -534,7 +534,8 @@ cpp = cpp_flags = ld = ld_flags = ld_lib = ld_lib_flags = eigen_cflags = qt_cfla
 
 try:
   log ('reading configuration from "' + config_file + '"...' + os.linesep)
-  exec (codecs.open (config_file, mode='r', encoding='utf-8').read()) # pylint: disable=exec-used,consider-using-with
+  with codecs.open (config_file, mode='r', encoding='utf-8') as f:
+    exec (f.read()) # pylint: disable=exec-used
 except IOError:
   fail ('''no configuration file found!
 please run "./configure" prior to invoking this script

cmd/dwiextract.cpp

@@ -67,6 +67,8 @@ void usage ()
 void run()
 {
   auto input_image = Image<float>::open (argument[0]);
+  if (input_image.ndim() < 4)
+    throw Exception ("Epected input image to contain more than three dimensions");
   auto grad = DWI::get_DW_scheme (input_image);
 
   // Want to support non-shell-like data if it's just a straight extraction

configure

@@ -344,8 +344,8 @@ class TempFile:
   def __exit__(self, exception_type, value, traceback):
     try:
       os.unlink (self.name)
-    except OSError as excp: # pylint: disable=redefined-outer-name
-      log ('error deleting temporary file "' + self.name + '": ' + excp.strerror)
+    except OSError as excp_local:
+      log ('error deleting temporary file "' + self.name + '": ' + excp_local.strerror)
 
 
 
@@ -359,8 +359,8 @@ class DeleteAfter:
   def __exit__(self, exception_type, value, traceback):
     try:
       os.unlink (self.name)
-    except OSError as excp: # pylint: disable=redefined-outer-name
-      log ('error deleting temporary file "' + self.name + '": ' + excp.strerror)
+    except OSError as excp_local:
+      log ('error deleting temporary file "' + self.name + '": ' + excp_local.strerror)
 
 
 class TempDir:
@@ -380,8 +380,8 @@ class TempDir:
           os.unlink (fullpath)
       os.rmdir (self.name)
 
-    except OSError as excp: # pylint: disable=redefined-outer-name
-      log ('error deleting temporary folder "' + self.name + '": ' + excp.strerror)
+    except OSError as excp_local:
+      log ('error deleting temporary folder "' + self.name + '": ' + excp_local.strerror)
 
 
 
@@ -522,7 +522,8 @@ def execute (cmd, exception, raise_on_non_zero_exit_code = True, cwd = None):
     log ('error invoking command "' + cmd[0] + '": ' + excp_local.strerror + '\n>>\n\n')
     raise exception from excp_local
   except Exception as excp_local:
-    error ('unexpected exception of type ' + type(excp_local).__name__ + ': ' + str(excp_local) + configure_log_hint)
+    error ('unexpected exception of type ' + type(excp_local).__name__ + ': ' + str(excp_local) +  configure_log_hint)
+    raise exception from excp_local
   else:
     if raise_on_non_zero_exit_code and process.returncode != 0:
       raise exception (stderr)
@@ -663,8 +664,8 @@ def compile_check (full_name, name, cflags, ldflags, code, cflags_env=None, cfla
     error ('''runtime error!
 
    Unable to configure ''' + name + configure_log_hint)
-  except Exception as excp: # pylint: disable=redefined-outer-name
-    error ('unexpected exception of type ' + type(excp).__name__ + ': ' + str(excp) +  configure_log_hint)
+  except Exception as excp_local:
+    error ('unexpected exception of type ' + type(excp_local).__name__ + ': ' + str(excp_local) +  configure_log_hint)