Merge remote-tracking branch 'origin/dev' into mrcolour

Conflicts:
	testing/data
	testing/tests/mrconvert

.gitignore

@@ -31,6 +31,7 @@ build.*
 /dev/
 /bin/
 /tmp/
+/.vscode/
 .cproject
 .idea
 .project
@@ -43,6 +44,7 @@ build.*
 *.creator.user
 *.files
 *.includes
+*.code-workspace
 /debug/
 /assert/
 testing.log

.travis.yml

@@ -8,15 +8,16 @@ addons:
   apt:
     sources:
       - ubuntu-toolchain-r-test
-      - llvm-toolchain-trusty-6.0
+      - llvm-toolchain-xenial-8
     packages:
-      - g++-7
-      - clang-6.0
+      - g++-9
+      - clang-8
       - zlib1g-dev
       - libqt4-opengl-dev
       - python3
       - python-pip
       - python3-pip
+      - python3-setuptools
 matrix:
   include:
     #################################################
@@ -32,13 +33,13 @@ matrix:
     # (Note: Run this one first, since it'll be the longest job)        #
     #####################################################################
     - os: linux
-      env: CFLAGS="-Werror" TRAVIS_CXX=clang++-6.0 py=python3 test=run
+      env: CFLAGS="-Werror" TRAVIS_CXX=clang++-8 py=python3 test=run
     #######################################################################
     # Build binaries (without optimisation): GCC, Python2                 #
     # (Also ensures both Python 2 and 3 are tested for configure & build) #
     #######################################################################
     - os: linux
-      env: CFLAGS="-Werror" TRAVIS_CXX=g++-7 py=python2 test=build
+      env: CFLAGS="-Werror" TRAVIS_CXX=g++-9 py=python2 test=build
     #######################################################################
     # Generate documentation through Sphinx; Use both Python2 and Python3 #
     #######################################################################
@@ -78,9 +79,9 @@ install:
     if [[ "${test}" == "sphinx" ]]; then
         if [[ "${py}" == "python2" ]]; then
             pip install urllib3[secure];
-            pip install --user recommonmark sphinx sphinx-rtd-theme;
+            pip install --user recommonmark sphinx sphinx-rtd-theme typing;
         else
-            pip3 install --user recommonmark sphinx sphinx-rtd-theme;
+            pip3 install --user recommonmark sphinx sphinx-rtd-theme typing;
         fi
     fi
   - |
@@ -95,7 +96,7 @@ install:
     fi
   - |
     if [[ "${test}" == "build" || "${test}" == "run" ]]; then
-        export EIGEN_CFLAGS=-I`pwd`/../eigen;
+        export EIGEN_CFLAGS="-idirafter `pwd`/../eigen";
         ( cd ..; git clone https://github.com/eigenteam/eigen-git-mirror.git eigen; cd eigen; git checkout branches/3.3 )
     fi
 before_script:

bin/5ttgen

@@ -9,47 +9,50 @@
 #   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 #pylint: disable=no-name-in-module
 
-from mrtrix3 import algorithm, app, run
+  cmdline.set_author('Robert E. Smith ([email protected])')
+  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\'.')
 
-app.init('Robert E. Smith ([email protected])', '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 = 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')
 
-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')
+  # Import the command-line settings for all algorithms found in the relevant directory
+  algorithm.usage(cmdline)
 
-# Import the command-line settings for all algorithms found in the relevant directory
-algorithm.initialise()
 
-app.parse()
 
-# Find out which algorithm the user has requested
-alg = algorithm.getModule(app.args.algorithm)
+def execute(): #pylint: disable=unused-variable
+  from mrtrix3 import algorithm, app, run #pylint: disable=no-name-in-module
 
-app.checkOutputPath(app.args.output)
-alg.checkOutputPaths()
+  # Find out which algorithm the user has requested
+  alg = algorithm.get_module(app.ARGS.algorithm)
 
-app.makeTempDir()
-alg.getInputs()
-app.gotoTempDir()
+  alg.check_output_paths()
 
-alg.execute()
+  app.make_scratch_dir()
+  alg.get_inputs()
+  app.goto_scratch_dir()
 
-stderr = run.command('5ttcheck result.mif')[1]
-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()
 
-app.complete()
+  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)
+
+
+
+
+
+
+# Execute the script
+import mrtrix3
+mrtrix3.execute() #pylint: disable=no-member

bin/blend

@@ -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)