Merge pull request MRtrix3#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
-
-