Merge pull request #1232 from MRtrix3/dev

Tag 3.0_RC3

.gitignore

@@ -22,6 +22,7 @@ build.*
 /configure.log
 /build.log
 /core/version.cpp
+/src/exec_version.cpp
 /src/project_version.h
 /lib/mrtrix3/_version.py
 /test/src/project_version.h

.travis.yml

@@ -1,30 +1,133 @@
-sudo: false
 language: cpp
+cache:
+ apt: true
+ packages: true
+ directories:
+ - $HOME/.cache/pip
 addons:
  apt:
  sources:
  - ubuntu-toolchain-r-test
+ - llvm-toolchain-trusty-6.0
  packages:
+ - g++-7
+ - clang-6.0
  - zlib1g-dev
  - libqt4-opengl-dev
- - g++-4.8
  - python3
-compiler:
- - clang
-env:
- - py=python2
- - py=python3
-install: 
- - export NUMBER_OF_PROCESSORS=4
- - export PATH=`pwd`/release/bin:`pwd`/scripts:${PATH}
- - export EIGEN_CFLAGS=-I`pwd`/../eigen
- - (cd ..; hg clone --insecure https://bitbucket.org/eigen/eigen/; cd eigen; hg update 3.3)
+ - python-pip
+ - python3-pip
+matrix:
+ include:
+ #################################################
+ # Run a single OSX job to test compilation only #
+ #################################################
+ - os: osx
+ env: CFLAGS="-Werror" TRAVIS_CXX=clang++ py=python test=build
+ ###############################################
+ # All subsequent tests are performed on Linux #
+ ###############################################
+ #####################################################################
+ # Build binaries, run tests and check documentation: Clang, Python3 #
+ # (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
+ #######################################################################
+ # 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
+ #######################################################################
+ # Generate documentation through Sphinx; Use both Python2 and Python3 #
+ #######################################################################
+ - os: linux
+ env: py=python2 test=sphinx
+ - os: linux
+ env: py=python3 test=sphinx
+ ###########################################################
+ # Run the check_syntax script; only needs to be done once #
+ ###########################################################
+ - os: linux
+ env: test=syntax
+ ##############################################
+ # Run PyLint tests; both Python2 and Python3 #
+ ##############################################
+ - os: linux
+ env: py=python2 test=pylint
+ - os: linux
+ env: py=python3 test=pylint
+install:
+ ##################################################
+ # OSX build requires explicit installation of QT #
+ ##################################################
+ - |
+ if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+ brew install qt5
+ brew link --force qt5
+ fi
+ #########################################
+ # Installation requirements for MRtrix3 #
+ #########################################
+ - export NUMBER_OF_PROCESSORS=2
+ - export PATH=`pwd`/bin:${PATH}
+ - export PYTHONPATH=`pwd`/lib:${PYTHONPATH}
+ - |
+ if [[ "${test}" == "sphinx" ]]; then
+ if [[ "${py}" == "python2" ]]; then
+ pip install urllib3[secure];
+ pip install --user recommonmark sphinx sphinx-rtd-theme;
+ else
+ pip3 install --user recommonmark sphinx sphinx-rtd-theme;
+ fi
+ fi
+ - |
+ if [[ "${test}" == "pylint" ]]; then
+ if [[ "${py}" == "python2" ]]; then
+ pip install --user pylint;
+ else
+ pip3 install --user pylint;
+ fi
+ fi
+ - |
+ if [[ "${test}" == "build" || "${test}" == "run" ]]; then
+ export EIGEN_CFLAGS=-I`pwd`/../eigen;
+ (cd ..; hg clone https://bitbucket.org/eigen/eigen/; cd eigen; hg update 3.3);
+ fi
+before_script:
+ #######################################################################################################################
+ # TravisCI sets CXX based on what it thinks the compiler should be; therefore we need to set it as late as possible #
+ # Since this is not needed for the installation section, only for the travis.sh script, moved this to "before_script" #
+ #######################################################################################################################
+ - |
+ if [[ -n "${TRAVIS_CXX}" ]]; then
+ export CXX=${TRAVIS_CXX}
+ fi
 script:
- - ./check_memalign && $py ./configure -assert && $py ./build -nowarnings && ./run_tests
-
-after_failure: 
- - cat memalign.log
- - cat configure.log
- - cat build.log
- - cat testing.log
+ - ./travis.sh
+before_cache:
+ - rm -f $HOME/.cache/pip/log/debug.log
+after_failure:
+ - |
+ case "${test}" in # CLICK HERE TO FIND REPORTED ERRORS
+ "sphinx")
+ cat sphinx.log
+ ;;
+ "syntax")
+ cat syntax.log
+ ;;
+ "pylint")
+ cat pylint.log
+ ;;
+ "build")
+ cat configure.log
+ cat build.log
+ ;;
+ *)
+ cat configure.log
+ cat build.log
+ cat testing.log
+ cat gitdiff.log
+ esac
  - sleep 10

bin/5ttgen

@@ -11,7 +11,7 @@
 
 # Make the corresponding MRtrix3 Python libraries available
 import inspect, os, sys
-lib_folder = os.path.realpath(os.path.abspath(os.path.join(os.path.split(inspect.getfile(inspect.currentframe()))[0], os.pardir, 'lib')))
+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)
@@ -46,10 +46,11 @@ app.gotoTempDir()
 
 alg.execute()
 
-(stdout,stderr) = run.command('5ttcheck result.mif', False)
-if len(stderr) and 'ERROR' in stderr:
- app.warn('Generated image does not perfectly conform to 5TT format')
+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.force else ''))
+run.command('mrconvert result.mif ' + path.fromUser(app.args.output, True) + (' -force' if app.forceOverwrite else ''))
 app.complete()
-

bin/average_response

@@ -1,19 +1,18 @@
 #!/usr/bin/env python
 import sys
-import string
 
-def errorMessage (msg):
- print (msg)
+def errorMessage(msg):
+ sys.stderr.write(msg + '\n')
  exit(1)
 
 if len(sys.argv) < 3 :
- print("example usage: average_response input_response1.txt input_response2.txt input_response3.txt ... output_average_response.txt")
+ sys.stderr.write("example usage: average_response input_response1.txt input_response2.txt input_response3.txt ... output_average_response.txt\n")
  exit(1)
 
 num_bvals = 0
 num_coeff = 0
 num_subjects = len(sys.argv) - 2
-print ("Number of subjects: " + str(num_subjects))
+sys.stdout.write("Number of subjects: " + str(num_subjects) + '\n')
 
 for i in range(1, num_subjects + 1):
  with open(sys.argv[i], 'r') as f:
@@ -23,17 +22,18 @@ for i in range(1, num_subjects + 1):
  num_coeff = len(lines[0].split())
  for l in lines:
  if len(l.split()) != num_coeff:
- errorMessage ("Error in file " + sys.argv[i] + ": multi-shell response functions must have the same number of coefficients per b-value (line)")
+ errorMessage("Error in file " + sys.argv[i] + ": multi-shell response functions must have the same number of coefficients per b-value (line)")
  else:
  if len(lines) != num_bvals:
- errorMessage ("Error in file " + sys.argv[i] + ": Input files do not contain the same number of b-values")
+ errorMessage("Error in file " + sys.argv[i] + ": Input files do not contain the same number of b-values")
  for l in lines:
  if len(l.split()) != num_coeff:
- errorMessage ("Error in file " + sys.argv[i] + ": multi-shell response functions must have the same number of coefficients per b-value (line)")
+ errorMessage("Error in file " + sys.argv[i] + ": multi-shell response functions must have the same number of coefficients per b-value (line)")
 
-print ("Number of b-values: " + str(num_bvals))
+sys.stdout.write("Number of b-values: " + str(num_bvals) + '\n')
 
-average_response = [[0 for x in range(num_coeff)] for y in range(num_bvals)] 
+# Can't use multiplication operator in outer loop since it duplicates by reference rather than value
+average_response = [[0] * num_coeff for _ in range(num_bvals)] #pylint: disable=unused-variable
 for i in range(1, num_subjects + 1):
  with open(sys.argv[i], 'r') as f:
  lines = f.readlines()
@@ -44,7 +44,7 @@ for i in range(1, num_subjects + 1):
 
 f = open(sys.argv[len(sys.argv)-1], 'w')
 line_out = ''
-for l in range(num_bvals): 
+for l in range(num_bvals):
  line_out = ''
  for c in range(0, num_coeff):
  line_out = line_out + "{0:.5f}".format(average_response[l][c]) + ' '

bin/blend

@@ -1,14 +1,12 @@
 #!/usr/bin/env python2
 import os
 import sys
-import string
-import math
 
 if len(sys.argv) <= 1:
-  print 'A script to blend two sets of movie frames together with a desired overlap.'
-  print 'The input arguments are two folders containing the movie frames (eg. output from the MRview screenshot tool), and the desired number of overlapping frames.'
-  print 'eg: blend folder1 folder2 20 output_folder'
-  sys.exit(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('eg: blend folder1 folder2 20 output_folder\n')
+ sys.exit(1)
 
 input_folder1 = sys.argv[1]
 input_folder2 = sys.argv[2]
@@ -18,19 +16,17 @@ num_overlap = int(sys.argv[3])
 output_folder = sys.argv[4]
 
 if not os.path.exists(output_folder):
-  os.mkdir(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):
- 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 (i > (len(file_list1) - num_overlap)) and (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) 
-
-
+ 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 i > (len(file_list1) - num_overlap) and 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)

bin/convert_bruker

@@ -3,7 +3,7 @@
 import sys, os.path
 
 if len (sys.argv) != 3:
- print ("usage: convert_bruker 2dseq header.mih")
+ sys.stderr.write("usage: convert_bruker 2dseq header.mih\n")
  sys.exit (0)
 
 
@@ -12,21 +12,21 @@ if len (sys.argv) != 3:
  #sys.exit (1)
 
 if not sys.argv[2].endswith ('.mih'):
- print ("expected .mih suffix as the second argument")
+ sys.stderr.write("expected .mih suffix as the second argument\n")
  sys.exit (1)
 
 with open (os.path.join (os.path.dirname (sys.argv[1]), 'reco')) as f:
- lines = f.read().split ('##$'); 
+ lines = f.read().split ('##$')
 
 with open (os.path.join (os.path.dirname (sys.argv[1]), '../../acqp')) as f:
- lines += f.read().split ('##$');
+ lines += f.read().split ('##$')
 
 with open (os.path.join (os.path.dirname (sys.argv[1]), '../../method')) as f:
- lines += f.read().split ('##$');
+ lines += f.read().split ('##$')
 
 
 for line in lines:
- line = line.lower();
+ line = line.lower()
  if line.startswith ('reco_size='):
  mat_size = line.splitlines()[1].split()
  print ('mat_size', mat_size)
@@ -62,28 +62,28 @@ with open (sys.argv[2], 'w') as f:
  f.write (',' + str(mat_size[2]))
  else:
  try:
- nslices
+ nslices #pylint: disable=pointless-statement
  f.write (',' + str(nslices))
  except:
  pass
- 
+
  try:
- nacq
+ nacq #pylint: disable=pointless-statement
  f.write (',' + str(nacq))
  except:
  pass
 
- f.write ('\nvox: ' + str(res[0]) + ',' + str(res[1]));
- if len(res) > 2: 
- f.write (',' + str(res[2]));
+ f.write ('\nvox: ' + str(res[0]) + ',' + str(res[1]))
+ if len(res) > 2:
+ f.write (',' + str(res[2]))
  else:
  try:
- slicethick
+ slicethick #pylint: disable=pointless-statement
  f.write (',' + str(slicethick))
  except:
  pass
  try:
- nacq
+ nacq #pylint: disable=pointless-statement
  f.write (',')
  except:
  pass
@@ -101,24 +101,22 @@ with open (sys.argv[2], 'w') as f:
 
  f.write ('\nlayout: +0,+1')
  try:
- nslices
+ nslices #pylint: disable=pointless-statement
  f.write (',+2')
  except:
  pass
  try:
- nacq
+ nacq #pylint: disable=pointless-statement
  f.write (',+3')
  except:
  pass
 
- f.write ('\nfile: ' + sys.argv[1] + '\n') 
+ f.write ('\nfile: ' + sys.argv[1] + '\n')
 
  try:
- bvec
- bval
- for n in range (0, len (bval)):
- f.write ('dw_scheme: ' + bvec[3*n] + ',' + bvec[3*n+1] + ',' + str(-float(bvec[3*n+2])) + ',' + bval[n] + '\n')
+ assert len(bvec) == 3*len(bval)
+ bvec = [ bvec[n:n+3] for n in range(0,len(bval),3) ]
+ for direction, value in zip(bvec, bval):
+ f.write ('dw_scheme: ' + direction[0] + ',' + direction[1] + ',' + str(-float(direction[2])) + ',' + value + '\n')
  except:
  pass
-
-