Merge remote-tracking branch 'upstream/dev'

Merge current MRtrix3 dev branch for MRtrix3Tissue v1.0.0 release

Also update core/version.h for corresponding 3Tissue_v1.0.0 tag

Also update README.md tag checkout example to 3Tissue_v1.0.0

Author: thijsdhollander

.travis.yml

@@ -23,7 +23,7 @@ matrix:
     # Run a single OSX job to test compilation only #
     #################################################
     - os: osx
-      env: CFLAGS="-Werror" TRAVIS_CXX=clang++ py=python test=build
+      env: CFLAGS="-Werror" TRAVIS_CXX=clang++ HOMEBREW_LOGS=$HOME/homebrew-logs HOMEBREW_TEMP=$HOME/homebrew-temp py=python test=build
     ###############################################
     # All subsequent tests are performed on Linux #
     ###############################################
@@ -64,6 +64,7 @@ install:
   ##################################################
   - |
     if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+        brew update
         brew install qt5
         brew link --force qt5
     fi
@@ -85,6 +86,7 @@ install:
   - |
     if [[ "${test}" == "pylint" ]]; then
         if [[ "${py}" == "python2" ]]; then
+            pip install --user --upgrade setuptools;
             pip install --user pylint;
         else
             pip3 install --user --upgrade setuptools;

README.md

@@ -64,7 +64,7 @@ MRtrix3Tissue is a fork of the MRtrix3 project. It adds capabilities for 3-Tissu
 
 You can build a particular release of MRtrix3Tissue by checking out the corresponding _tag_, and using the same procedure as above to build it:
 
-    git checkout 3Tissue_v0.1.0
+    git checkout 3Tissue_v1.0.0
 
     ./configure
 

appveyor.yml

@@ -5,6 +5,22 @@ configuration: Release
 clone_folder: c:\msys64\mrtrix3
 shallow_clone: false
 
+init:
+  - git config --global core.autocrlf input
+
 build_script:
-  - cmd: echo "empty build to allow passing on master branch"
+  - cmd: C:\msys64\msys2_shell.cmd -mingw64 -here -defterm -no-start -c "pacman -S --noconfirm bc mingw-w64-x86_64-diffutils mingw-w64-x86_64-eigen3 mingw-w64-x86_64-fftw mingw-w64-x86_64-libtiff mingw-w64-x86_64-qt5 python > pacman.log" || (appveyor PushArtifact %APPVEYOR_BUILD_FOLDER%/pacman.log & EXIT 1)
+  - cmd: C:\msys64\msys2_shell.cmd -mingw64 -here -defterm -no-start -c "python --version"
+  - cmd: C:\msys64\msys2_shell.cmd -mingw64 -here -defterm -no-start -c "./configure -assert" || (appveyor PushArtifact %APPVEYOR_BUILD_FOLDER%/configure.log & EXIT 1)
+  - cmd: C:\msys64\msys2_shell.cmd -mingw64 -here -defterm -no-start -c "./build -nowarnings -nopaginate" || (appveyor PushArtifact %APPVEYOR_BUILD_FOLDER%/build.log & EXIT 1)
+
+test_script:
+  - cmd: C:\msys64\msys2_shell.cmd -mingw64 -here -defterm -no-start -c "./run_tests" || (appveyor PushArtifact %APPVEYOR_BUILD_FOLDER%/testing.log & EXIT 1)
+
+artifacts:
+  - path: pacman.log
+  - path: config
+  - path: configure.log
+  - path: build.log
+  - path: testing.log
 

bin/5ttgen

@@ -9,48 +9,57 @@
 #   defining the appropriate functions; 5ttgen will automatically make that algorithm available at the command-line
 
 
-# Make the corresponding MRtrix3 Python libraries available
-import inspect, os, sys
-lib_folder = os.path.realpath(os.path.join(os.path.dirname(os.path.realpath(inspect.getfile(inspect.currentframe()))), os.pardir, 'lib'))
-if not os.path.isdir(lib_folder):
-  sys.stderr.write('Unable to locate MRtrix3 Python libraries')
-  sys.exit(1)
-sys.path.insert(0, lib_folder)
 
+def usage(cmdline): #pylint: disable=unused-variable
+  from mrtrix3 import algorithm
+
+  cmdline.set_author('Robert E. Smith (robert.smith@florey.edu.au)')
+  cmdline.set_synopsis('Generate a 5TT image suitable for ACT')
+  cmdline.add_citation('Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938')
+  cmdline.add_description('5ttgen acts as a \'master\' script for generating a five-tissue-type (5TT) segmented tissue image suitable for use in Anatomically-Constrained Tractography (ACT). A range of different algorithms are available for completing this task. When using this script, the name of the algorithm to be used must appear as the first argument on the command-line after \'5ttgen\'. The subsequent compulsory arguments and options available depend on the particular algorithm being invoked.')
+  cmdline.add_description('Each algorithm available also has its own help page, including necessary references; e.g. to see the help page of the \'fsl\' algorithm, type \'5ttgen fsl\'.')
+
+  common_options = cmdline.add_argument_group('Options common to all 5ttgen algorithms')
+  common_options.add_argument('-nocrop', action='store_true', default=False, help='Do NOT crop the resulting 5TT image to reduce its size (keep the same dimensions as the input image)')
+  common_options.add_argument('-sgm_amyg_hipp', action='store_true', default=False, help='Represent the amygdalae and hippocampi as sub-cortical grey matter in the 5TT image')
+
+  # Import the command-line settings for all algorithms found in the relevant directory
+  algorithm.usage(cmdline)
 
-from mrtrix3 import algorithm, app, path, run
 
-app.init('Robert E. Smith (robert.smith@florey.edu.au)', 'Generate a 5TT image suitable for ACT')
-app.cmdline.addCitation('', 'Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938', False)
-app.cmdline.addDescription('5ttgen acts as a \'master\' script for generating a five-tissue-type (5TT) segmented tissue image suitable for use in Anatomically-Constrained Tractography (ACT). A range of different algorithms are available for completing this task. When using this script, the name of the algorithm to be used must appear as the first argument on the command-line after \'5ttgen\'. The subsequent compulsory arguments and options available depend on the particular algorithm being invoked.')
-app.cmdline.addDescription('Each algorithm available also has its own help page, including necessary references; e.g. to see the help page of the \'fsl\' algorithm, type \'5ttgen fsl\'.')
 
-common_options = app.cmdline.add_argument_group('Options common to all 5ttgen algorithms')
-common_options.add_argument('-nocrop', action='store_true', default=False, help='Do NOT crop the resulting 5TT image to reduce its size (keep the same dimensions as the input image)')
-common_options.add_argument('-sgm_amyg_hipp', action='store_true', default=False, help='Represent the amygdalae and hippocampi as sub-cortical grey matter in the 5TT image')
+def execute(): #pylint: disable=unused-variable
+  from mrtrix3 import algorithm, run
 
-# Import the command-line settings for all algorithms found in the relevant directory
-algorithm.initialise()
+  # Find out which algorithm the user has requested
+  alg = algorithm.get_module(app.ARGS.algorithm)
 
-app.parse()
+  alg.check_output_paths()
 
-# Find out which algorithm the user has requested
-alg = algorithm.getModule(app.args.algorithm)
+  app.make_scratch_dir()
+  alg.get_inputs()
+  app.goto_scratch_dir()
 
-app.checkOutputPath(app.args.output)
-alg.checkOutputPaths()
+  alg.execute()
 
-app.makeTempDir()
-alg.getInputs()
-app.gotoTempDir()
+  stderr = run.command('5ttcheck result.mif').stderr
+  if '[WARNING]' in stderr:
+    app.warn('Generated image does not perfectly conform to 5TT format:')
+    for line in stderr.splitlines():
+      app.warn(line)
 
-alg.execute()
 
-stderr = run.command('5ttcheck result.mif')[1]
-if stderr:
-  app.warn('Generated image does not perfectly conform to 5TT format:')
-  for line in stderr:
-    app.warn(line)
 
-run.command('mrconvert result.mif ' + path.fromUser(app.args.output, True) + (' -force' if app.forceOverwrite else ''))
-app.complete()
+
+
+
+# Make the corresponding MRtrix3 Python libraries available
+import inspect, os, sys
+LIB_FOLDER = os.path.realpath(os.path.join(os.path.dirname(os.path.realpath(inspect.getfile(inspect.currentframe()))), os.pardir, 'lib'))
+if not os.path.isdir(LIB_FOLDER):
+  sys.stderr.write('Unable to locate MRtrix3 Python libraries')
+  sys.exit(1)
+sys.path.insert(0, LIB_FOLDER)
+# Execute the script
+from mrtrix3 import app
+app.execute()

bin/average_response

@@ -8,25 +8,25 @@ if len(sys.argv) <= 1:
   sys.stderr.write('eg: blend folder1 folder2 20 output_folder\n')
   sys.exit(1)
 
-input_folder1 = sys.argv[1]
-input_folder2 = sys.argv[2]
-file_list1 = sorted(os.listdir(input_folder1))
-file_list2 = sorted(os.listdir(input_folder2))
-num_overlap =  int(sys.argv[3])
-output_folder = sys.argv[4]
+INPUT_FOLDER_1 = sys.argv[1]
+INPUT_FOLDER_2 = sys.argv[2]
+FILE_LIST_1 = sorted(os.listdir(INPUT_FOLDER_1))
+FILE_LIST_2 = sorted(os.listdir(INPUT_FOLDER_2))
+NUM_OVERLAP = int(sys.argv[3])
+OUTPUT_FOLDER = sys.argv[4]
 
-if not os.path.exists(output_folder):
-  os.mkdir(output_folder)
+if not os.path.exists(OUTPUT_FOLDER):
+  os.mkdir(OUTPUT_FOLDER)
 
-total_num_output_frames = len(file_list1) + len(file_list2) - num_overlap
-for i in range(total_num_output_frames):
+NUM_OUTPUT_FRAMES = len(FILE_LIST_1) + len(FILE_LIST_2) - NUM_OVERLAP
+for i in range(NUM_OUTPUT_FRAMES):
   file_name = 'frame' + '%0*d' % (5, i) + '.png'
-  if i <= len(file_list1) - num_overlap:
-    os.system('cp -L ' + input_folder1 + '/' + file_list1[i] + ' ' + output_folder + '/' + file_name)
-  if len(file_list1) - num_overlap < i < len(file_list1):
-    i2 = i - (len(file_list1) - num_overlap) - 1
-    blend_amount = 100 * float(i2 + 1) / float(num_overlap)
-    os.system('convert ' + input_folder1 + '/' + file_list1[i] + ' ' + input_folder2 + '/' + file_list2[i2] + ' -alpha on -compose blend  -define compose:args=' + str(blend_amount) + ' -gravity South  -composite ' + output_folder + '/' + file_name)
-  if i >= (len(file_list1)):
-    i2 = i - (len(file_list1) - num_overlap) - 1
-    os.system('cp -L ' + input_folder2 + '/' + file_list2[i2] + ' ' + output_folder + '/' + file_name)
+  if i <= len(FILE_LIST_1) - NUM_OVERLAP:
+    os.system('cp -L ' + INPUT_FOLDER_1 + '/' + FILE_LIST_1[i] + ' ' + OUTPUT_FOLDER + '/' + file_name)
+  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)
+  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)