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| 1 | +#!/usr/bin/env python |
| 2 | +# imglob - expand list of image filenames |
| 3 | +# Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group |
| 4 | +# Copyright (C) 2009 University of Oxford |
| 5 | +# Part of FSL - FMRIB's Software Library |
| 6 | +# http://www.fmrib.ox.ac.uk/fsl |
| 7 | + |
| 8 | +# |
| 9 | +# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
| 10 | +# Imaging of the Brain), Department of Clinical Neurology, Oxford |
| 11 | +# University, Oxford, UK |
| 12 | +# |
| 13 | +# |
| 14 | +# LICENCE |
| 15 | +# |
| 16 | +# FMRIB Software Library, Release 5.0 (c) 2012, The University of |
| 17 | +# Oxford (the "Software") |
| 18 | +# |
| 19 | +# The Software remains the property of the University of Oxford ("the |
| 20 | +# University"). |
| 21 | +# |
| 22 | +# The Software is distributed "AS IS" under this Licence solely for |
| 23 | +# non-commercial use in the hope that it will be useful, but in order |
| 24 | +# that the University as a charitable foundation protects its assets for |
| 25 | +# the benefit of its educational and research purposes, the University |
| 26 | +# makes clear that no condition is made or to be implied, nor is any |
| 27 | +# warranty given or to be implied, as to the accuracy of the Software, |
| 28 | +# or that it will be suitable for any particular purpose or for use |
| 29 | +# under any specific conditions. Furthermore, the University disclaims |
| 30 | +# all responsibility for the use which is made of the Software. It |
| 31 | +# further disclaims any liability for the outcomes arising from using |
| 32 | +# the Software. |
| 33 | +# |
| 34 | +# The Licensee agrees to indemnify the University and hold the |
| 35 | +# University harmless from and against any and all claims, damages and |
| 36 | +# liabilities asserted by third parties (including claims for |
| 37 | +# negligence) which arise directly or indirectly from the use of the |
| 38 | +# Software or the sale of any products based on the Software. |
| 39 | +# |
| 40 | +# No part of the Software may be reproduced, modified, transmitted or |
| 41 | +# transferred in any form or by any means, electronic or mechanical, |
| 42 | +# without the express permission of the University. The permission of |
| 43 | +# the University is not required if the said reproduction, modification, |
| 44 | +# transmission or transference is done without financial return, the |
| 45 | +# conditions of this Licence are imposed upon the receiver of the |
| 46 | +# product, and all original and amended source code is included in any |
| 47 | +# transmitted product. You may be held legally responsible for any |
| 48 | +# copyright infringement that is caused or encouraged by your failure to |
| 49 | +# abide by these terms and conditions. |
| 50 | +# |
| 51 | +# You are not permitted under this Licence to use this Software |
| 52 | +# commercially. Use for which any financial return is received shall be |
| 53 | +# defined as commercial use, and includes (1) integration of all or part |
| 54 | +# of the source code or the Software into a product for sale or license |
| 55 | +# by or on behalf of Licensee to third parties or (2) use of the |
| 56 | +# Software or any derivative of it for research with the final aim of |
| 57 | +# developing software products for sale or license to a third party or |
| 58 | +# (3) use of the Software or any derivative of it for research with the |
| 59 | +# final aim of developing non-software products for sale or license to a |
| 60 | +# third party, or (4) use of the Software to provide any service to an |
| 61 | +# external organisation for which payment is received. If you are |
| 62 | +# interested in using the Software commercially, please contact Isis |
| 63 | +# Innovation Limited ("Isis"), the technology transfer company of the |
| 64 | +# University, to negotiate a licence. Contact details are: |
| 65 | +# [email protected] quoting reference DE/9564. |
| 66 | + |
| 67 | +import sys |
| 68 | +import os |
| 69 | +import glob |
| 70 | + |
| 71 | +setAvailable=True |
| 72 | +if sys.version_info < (2, 4): |
| 73 | + import sets |
| 74 | + from sets import Set |
| 75 | + setAvailable=False |
| 76 | + |
| 77 | +def usage(): |
| 78 | + print("Usage: $0 [-extension/extensions] <list of names>") |
| 79 | + print(" -extension for one image with full extension") |
| 80 | + print(" -extensions for image list with full extensions") |
| 81 | + sys.exit(1) |
| 82 | + |
| 83 | +def isImage(input,allExtensions): #Returns whether an input filename has an image extension ( and the basename and extension pair ) |
| 84 | + for extension in allExtensions: |
| 85 | + if input[-len(extension):] == extension: |
| 86 | + return True, input[:-len(extension)], extension |
| 87 | + return False, input, '' |
| 88 | + |
| 89 | +def removeImageExtension(input,allExtensions): |
| 90 | + return isImage(input,allExtensions)[1] |
| 91 | + |
| 92 | +if len(sys.argv) <= 1: |
| 93 | + usage() |
| 94 | + |
| 95 | +deleteExtensions=True |
| 96 | +primaryExtensions=['.nii.gz', '.nii', '.hdr.gz', '.hdr'] |
| 97 | +secondaryExtensions=['.img.gz', '.img'] |
| 98 | +allExtensions=primaryExtensions+secondaryExtensions |
| 99 | +validExtensions=primaryExtensions |
| 100 | +startingArg=1 |
| 101 | + |
| 102 | +if sys.argv[1] == "-extensions": |
| 103 | + validExtensions=allExtensions |
| 104 | + deleteExtensions=False |
| 105 | + startingArg=2 |
| 106 | +if sys.argv[1] == "-extension": |
| 107 | + deleteExtensions=False |
| 108 | + startingArg=2 |
| 109 | + |
| 110 | +filelist=[] |
| 111 | +for arg in range(startingArg, len(sys.argv)): |
| 112 | +# if isImage(sys.argv[arg],allExtensions)[0]: #These enable a "pedantic" style mode currently not used |
| 113 | +# filelist.extend(glob.glob(sys.argv[arg])) |
| 114 | +# else: |
| 115 | +# for currentExtension in validExtensions: |
| 116 | +# filelist.extend(glob.glob(sys.argv[arg]+currentExtension)) |
| 117 | + for currentExtension in validExtensions: |
| 118 | + filelist.extend(glob.glob(removeImageExtension(sys.argv[arg],allExtensions)+currentExtension)) |
| 119 | + |
| 120 | +if deleteExtensions: |
| 121 | + for file in range(0, len(filelist)): |
| 122 | + filelist[file]=removeImageExtension(filelist[file],allExtensions) |
| 123 | +if setAvailable: |
| 124 | + filelist=list(set(filelist)) |
| 125 | +else: |
| 126 | + filelist=list(Set(filelist)) |
| 127 | +filelist.sort() |
| 128 | + |
| 129 | +for file in range(0, len(filelist)): |
| 130 | + print(filelist[file], end=' ') |
| 131 | + if file < len(filelist)-1: |
| 132 | + print(" ", end=' ') |
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