Fixed imglob's print statements in FSL (used by eddy_correct)

Author: slimnsour

.docker/fsl-6.0/bin/imglob

@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+#   imglob - expand list of image filenames
+#   Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
+#   Copyright (C) 2009 University of Oxford 
+#   Part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   [email protected]
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+#   LICENCE
+#   
+#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
+#   Oxford (the "Software")
+#   
+#   The Software remains the property of the University of Oxford ("the
+#   University").
+#   
+#   The Software is distributed "AS IS" under this Licence solely for
+#   non-commercial use in the hope that it will be useful, but in order
+#   that the University as a charitable foundation protects its assets for
+#   the benefit of its educational and research purposes, the University
+#   makes clear that no condition is made or to be implied, nor is any
+#   warranty given or to be implied, as to the accuracy of the Software,
+#   or that it will be suitable for any particular purpose or for use
+#   under any specific conditions. Furthermore, the University disclaims
+#   all responsibility for the use which is made of the Software. It
+#   further disclaims any liability for the outcomes arising from using
+#   the Software.
+#   
+#   The Licensee agrees to indemnify the University and hold the
+#   University harmless from and against any and all claims, damages and
+#   liabilities asserted by third parties (including claims for
+#   negligence) which arise directly or indirectly from the use of the
+#   Software or the sale of any products based on the Software.
+#   
+#   No part of the Software may be reproduced, modified, transmitted or
+#   transferred in any form or by any means, electronic or mechanical,
+#   without the express permission of the University. The permission of
+#   the University is not required if the said reproduction, modification,
+#   transmission or transference is done without financial return, the
+#   conditions of this Licence are imposed upon the receiver of the
+#   product, and all original and amended source code is included in any
+#   transmitted product. You may be held legally responsible for any
+#   copyright infringement that is caused or encouraged by your failure to
+#   abide by these terms and conditions.
+#   
+#   You are not permitted under this Licence to use this Software
+#   commercially. Use for which any financial return is received shall be
+#   defined as commercial use, and includes (1) integration of all or part
+#   of the source code or the Software into a product for sale or license
+#   by or on behalf of Licensee to third parties or (2) use of the
+#   Software or any derivative of it for research with the final aim of
+#   developing software products for sale or license to a third party or
+#   (3) use of the Software or any derivative of it for research with the
+#   final aim of developing non-software products for sale or license to a
+#   third party, or (4) use of the Software to provide any service to an
+#   external organisation for which payment is received. If you are
+#   interested in using the Software commercially, please contact Isis
+#   Innovation Limited ("Isis"), the technology transfer company of the
+#   University, to negotiate a licence. Contact details are:
+#   [email protected] quoting reference DE/9564.
+
+import sys
+import os
+import glob
+
+setAvailable=True
+if sys.version_info < (2, 4):
+   import sets
+   from sets import Set
+   setAvailable=False
+
+def usage():
+    print("Usage: $0 [-extension/extensions] <list of names>")
+    print("       -extension for one image with full extension")
+    print("       -extensions for image list with full extensions")
+    sys.exit(1)
+
+def isImage(input,allExtensions):       #Returns whether an input filename has an image extension ( and the basename and extension pair )
+    for extension in allExtensions:
+       if input[-len(extension):] == extension:
+          return True, input[:-len(extension)], extension
+    return False, input, ''
+
+def removeImageExtension(input,allExtensions):
+    return isImage(input,allExtensions)[1]
+
+if len(sys.argv) <= 1:
+    usage()
+
+deleteExtensions=True
+primaryExtensions=['.nii.gz', '.nii', '.hdr.gz', '.hdr']
+secondaryExtensions=['.img.gz', '.img']
+allExtensions=primaryExtensions+secondaryExtensions
+validExtensions=primaryExtensions
+startingArg=1
+
+if sys.argv[1] == "-extensions":
+   validExtensions=allExtensions
+   deleteExtensions=False
+   startingArg=2
+if sys.argv[1] == "-extension":
+   deleteExtensions=False
+   startingArg=2
+    
+filelist=[]
+for arg in range(startingArg, len(sys.argv)):
+#      if isImage(sys.argv[arg],allExtensions)[0]:          #These enable a "pedantic" style mode currently not used
+#         filelist.extend(glob.glob(sys.argv[arg]))
+#      else:
+#         for currentExtension in validExtensions:
+#            filelist.extend(glob.glob(sys.argv[arg]+currentExtension))
+    for currentExtension in validExtensions:
+       filelist.extend(glob.glob(removeImageExtension(sys.argv[arg],allExtensions)+currentExtension))
+
+if deleteExtensions:
+    for file in range(0, len(filelist)):
+        filelist[file]=removeImageExtension(filelist[file],allExtensions)
+if setAvailable:
+   filelist=list(set(filelist))
+else:
+   filelist=list(Set(filelist))
+filelist.sort()
+
+for file in range(0, len(filelist)):
+    print(filelist[file], end=' ')
+    if file < len(filelist)-1:
+       print(" ", end=' ')

Dockerfile

@@ -93,6 +93,7 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
 ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
 
 COPY .docker/fsl-6.0/bin/topup /usr/share/fsl/5.0/bin/topup
+COPY .docker/fsl-6.0/bin/imglob /usr/share/fsl/5.0/bin/imglob
 COPY .docker/fsl-6.0/lib/* /usr/lib/fsl/5.0/
 
 # Installing ANTs 2.3.3 (NeuroDocker build)