Tweaks for pylint testing

- Fixed issues in blend and convert_bruker scripts - Added bypass comments to prevent pylint erros in specific locations where the behaviour is intended; this includes library functions that are not invoked within that particular library file, but may be used elsewhere. - Minor tweaks to run_pylint script.
jdtournier · Aug 16, 2017 · f2e91c8 · f2e91c8
1 parent ccaf0cd
commit f2e91c8
Show file tree

Hide file tree

Showing 11 changed files with 87 additions and 45 deletions.
diff --git a/bin/blend b/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)
+  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)
 
 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)
diff --git a/bin/convert_bruker b/bin/convert_bruker
@@ -62,13 +62,15 @@ with open (sys.argv[2], 'w') as f:
     f.write (',' + str(mat_size[2]))
   else:
     try:
-      dummy = nslices
+      #pylint: disable=pointless-statement
+      nslices
       f.write (',' + str(nslices))
     except:
       pass
 
   try:
-    dummy = nacq
+    #pylint: disable=pointless-statement
+    nacq
     f.write (',' + str(nacq))
   except:
     pass
@@ -78,12 +80,14 @@ with open (sys.argv[2], 'w') as f:
     f.write (',' + str(res[2]))
   else:
     try:
-      dummy = slicethick
+      #pylint: disable=pointless-statement
+      slicethick
       f.write (',' + str(slicethick))
     except:
       pass
   try:
-    dummy = nacq
+    #pylint: disable=pointless-statement
+    nacq
     f.write (',')
   except:
     pass
@@ -101,21 +105,25 @@ with open (sys.argv[2], 'w') as f:
 
   f.write ('\nlayout: +0,+1')
   try:
-    dummy = nslices
+    #pylint: disable=pointless-statement
+    nslices
     f.write (',+2')
   except:
     pass
   try:
-    dummy = nacq
+    #pylint: disable=pointless-statement
+    nacq
     f.write (',+3')
   except:
     pass
 
   f.write ('\nfile: ' + sys.argv[1] + '\n')
 
   try:
-    dummy = bvec
-    dummy = bval
+    #pylint: disable=pointless-statement
+    bvec
+    #pylint: disable=pointless-statement
+    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')
   except:

diff --git a/lib/mrtrix3/algorithm.py b/lib/mrtrix3/algorithm.py
@@ -14,6 +14,7 @@ def _algorithmsPath():
 
 
 # This function needs to be safe to run in order to populate the help page; that is, no app initialisation has been run
+#pylint: disable=unused-variable
 def getList():
   import os
   from mrtrix3 import app
@@ -32,6 +33,7 @@ def getList():
 # Note: This function essentially duplicates the current state of app.cmdline in order for command-line
 #   options common to all algorithms of a particular script to be applicable once any particular sub-parser
 #   is invoked. Therefore this function must be called _after_ all such options are set up.
+#pylint: disable=unused-variable
 def initialise():
   import importlib, pkgutil
   from mrtrix3 import app, path
@@ -46,7 +48,7 @@ def initialise():
 
 
 
-
+#pylint: disable=unused-variable
 def getModule(name):
   import sys
   from mrtrix3 import path

diff --git a/lib/mrtrix3/app.py b/lib/mrtrix3/app.py
@@ -27,6 +27,7 @@
 args = ''
 cmdline = None
 config = { }
+#pylint: disable=unused-variable
 force = False
 
 
@@ -44,7 +45,9 @@
 of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 For more details, see http://www.mrtrix.org/.'''
+#pylint: disable=unused-variable
 _lastFile = ''
+#pylint: disable=unused-variable
 _nthreads = None
 _tempDir = ''
 _verbosity = 1 # 0 = quiet; 1 = default; 2 = info; 3 = debug
@@ -73,7 +76,7 @@
 
 
 
-
+#pylint: disable=unused-variable
 def init(author, synopsis):
   import os, signal
   global cmdline, config
@@ -103,6 +106,7 @@ def init(author, synopsis):
 
 
 
+#pylint: disable=unused-variable
 def parse():
   import os, sys
   global args, cmdline
@@ -166,7 +170,7 @@ def parse():
 
 
 
-
+#pylint: disable=unused-variable
 def checkOutputPath(path):
   import os
   global args, force
@@ -188,7 +192,7 @@ def checkOutputPath(path):
 
 
 
-
+#pylint: disable=unused-variable
 def makeTempDir():
   import os, random, string, sys
   global args, config
@@ -224,6 +228,7 @@ def makeTempDir():
 
 
 
+#pylint: disable=unused-variable
 def gotoTempDir():
   import os
   global _tempDir
@@ -235,6 +240,7 @@ def gotoTempDir():
 
 
 
+#pylint: disable=unused-variable
 def complete():
   import os, shutil, sys
   global _cleanup, _tempDir, _workingDir
@@ -257,7 +263,6 @@ def complete():
 
 
 
-
 # A set of functions and variables for printing various information at the command-line.
 clearLine = ''
 colourClear = ''
@@ -267,13 +272,15 @@ def complete():
 colourExec = ''
 colourWarn = ''
 
+#pylint: disable=unused-variable
 def console(text):
   import os, sys
   global colourClear, colourConsole
   global _verbosity
   if _verbosity:
     sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + colourConsole + text + colourClear + '\n')
 
+#pylint: disable=unused-variable
 def debug(text):
   import inspect, os, sys
   global colourClear, colourDebug
@@ -299,6 +306,7 @@ def debug(text):
     origin = funcname + ' (from ' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')'
   sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + colourDebug + '[DEBUG] ' + origin + ': ' + text + colourClear + '\n')
 
+#pylint: disable=unused-variable
 def error(text):
   import os, sys
   global colourClear, colourError
@@ -308,6 +316,7 @@ def error(text):
   complete()
   sys.exit(1)
 
+#pylint: disable=unused-variable
 def warn(text):
   import os, sys
   global colourClear, colourWarn
@@ -368,18 +377,22 @@ def __init__(self, *args_in, **kwargs_in):
       standard_options.add_argument('-debug', action='store_true', help='Display additional debugging information over and above the output of -info')
       self.flagMutuallyExclusiveOptions( [ 'quiet', 'info', 'debug' ] )
 
+  #pylint: disable=unused-variable
   def addCitation(self, condition, reference, is_external):
     self._citationList.append( (condition, reference) )
     if is_external:
       self._externalCitations = True
 
+  #pylint: disable=unused-variable
   def addDescription(self, text):
     self._description.append(text)
 
+  #pylint: disable=unused-variable
   def setCopyright(self, text):
     self._copyright = text
 
   # Mutually exclusive options need to be added before the command-line input is parsed
+  #pylint: disable=unused-variable
   def flagMutuallyExclusiveOptions(self, options, required=False):
     import sys
     if not isinstance(options, list) or not isinstance(options[0], str):
@@ -820,6 +833,7 @@ def done(self):
 
 
 # Return a boolean flag to indicate whether or not script is being run on a Windows machine
+#pylint: disable=unused-variable
 def isWindows():
   import platform
   system = platform.system().lower()

diff --git a/lib/mrtrix3/file.py b/lib/mrtrix3/file.py
@@ -6,6 +6,7 @@
 #   that is no longer required by the script. If the script has been instructed to retain
 #   all temporaries, the resource will be retained; if not, it will be deleted (in particular
 #   to dynamically free up storage space used by the script).
+#pylint: disable=unused-variable
 def delTemporary(path):
   import shutil, os
   from mrtrix3 import app
@@ -30,6 +31,7 @@ def delTemporary(path):
 
 
 # Make a directory if it doesn't exist; don't do anything if it does already exist
+#pylint: disable=unused-variable
 def makeDir(path):
   import errno, os
   from mrtrix3 import app
@@ -45,6 +47,7 @@ def makeDir(path):
 
 # Get an appropriate location and name for a new temporary file
 # Note: Doesn't actually create a file; just gives a unique name that won't over-write anything
+#pylint: disable=unused-variable
 def newTempFile(suffix):
   import os, random, string, sys
   from mrtrix3 import app
@@ -87,6 +90,7 @@ def newTempFile(suffix):
 # Initially, checks for the file once every 1/1000th of a second; this gradually
 #   increases if the file still doesn't exist, until the program is only checking
 #   for the file once a minute.
+#pylint: disable=unused-variable
 def waitFor(path):
   import os, time
   from mrtrix3 import app

diff --git a/lib/mrtrix3/fsl.py b/lib/mrtrix3/fsl.py
@@ -6,6 +6,7 @@
 #   this depends on both whether or not the user has requested that the CUDA
 #   version of eddy be used, and the various names that this command could
 #   conceivably be installed as.
+#pylint: disable=unused-variable
 def eddyBinary(cuda):
   import os
   from mrtrix3 import app
@@ -53,6 +54,7 @@ def eddyBinary(cuda):
 #   makes it more convenient to locate these commands.
 # Note that if FSL 4 and 5 are installed side-by-side, the approach taken in this
 #   function will select the version 5 executable.
+#pylint: disable=unused-variable
 def exeName(name):
   from mrtrix3 import app
   from distutils.spawn import find_executable
@@ -71,6 +73,7 @@ def exeName(name):
 #   FSL commands will generate based on the suffix() function, the FSL binaries themselves
 #   ignore the FSLOUTPUTTYPE environment variable. Therefore, the safest approach is:
 # Whenever receiving an output image from an FSL command, explicitly search for the path
+#pylint: disable=unused-variable
 def findImage(name):
   import os
   from mrtrix3 import app
@@ -90,6 +93,7 @@ def findImage(name):
 #   stored in 'FSLOUTPUTTYPE'. This may even override a filename extension provided
 #   to the relevant command. Therefore use this function to 'guess' what the names
 #   of images provided by FSL commands will be.
+#pylint: disable=unused-variable
 def suffix():
   import os
   from mrtrix3 import app

diff --git a/lib/mrtrix3/image.py b/lib/mrtrix3/image.py
@@ -3,6 +3,7 @@
 #   data, rather than trying to duplicate support for all possible image formats natively
 #   in Python.
 
+#pylint: disable=unused-variable
 def check3DNonunity(image_path):
   from mrtrix3 import app
   dim = header(image_path).size
@@ -43,6 +44,7 @@ def __init__(self, image_path):
            self.format or not self.datatype or not self.transform:
       app.error('Error in reading header information from file \'' + image_path + '\'')
 
+#pylint: disable=unused-variable
 def header(image_path):
   result = _Header(image_path)
   return result
@@ -54,6 +56,7 @@ def header(image_path):
 # Therefore, provide this function to execute mrinfo and get just the information of
 #   interest. Note however that parsing the output of mrinfo e.g. into list / numerical
 #   form is not performed by this function.
+#pylint: disable=unused-variable
 def mrinfo(image_path, field):
   import subprocess
   from mrtrix3 import app, run
@@ -71,6 +74,7 @@ def mrinfo(image_path, field):
 
 # Check to see whether the fundamental header properties of two images match
 # Inputs can be either _Header class instances, or file paths
+#pylint: disable=unused-variable
 def match(image_one, image_two):
   import math
   from mrtrix3 import app
@@ -107,6 +111,7 @@ def match(image_one, image_two):
 
 # TODO Change mask_path to instead receive a string of additional command-line options
 #   (that way, -allvolumes can be used)
+#pylint: disable=unused-variable
 def statistic(image_path, stat, mask_path = ''):
   import subprocess
   from mrtrix3 import app, run