sci/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_coll...

diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
--- fsl.orig/src/fslio/imln	2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imln	1969-12-31 19:00:00.000000000 -0500
@@ -1,90 +0,0 @@
-#!/bin/sh
-
-#   imln - make symbolic link(s) to image file(s)
-#
-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-#   Copyright (C) 1999-2004 University of Oxford
-#
-#   Part of FSL - FMRIB's Software Library
-#   http://www.fmrib.ox.ac.uk/fsl
-#   fsl@fmrib.ox.ac.uk
-#
-#   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 6.0 (c) 2018, The University of
-#   Oxford (the "Software")
-#
-#   The Software remains the property of the Oxford University Innovation
-#   ("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 Oxford
-#   University Innovation ("OUI"), the technology transfer company of the
-#   University, to negotiate a licence. Contact details are:
-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-if [ $# -lt 2 ] ; then
-  echo "Usage: $0 <file1> <file2>"
-  echo "  Makes a link (called file2) to file1"
-  echo "  NB: filenames can be basenames or include an extension"
-  exit 1;
-fi
-
-f1=`${FSLDIR}/bin/remove_ext $1`;
-f2=`${FSLDIR}/bin/remove_ext $2`;
-
-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi
-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi
-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi
-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi
-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi
-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi
-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi
-
diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
--- fsl.orig/src/fslio/imrm	2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imrm	1969-12-31 19:00:00.000000000 -0500
@@ -1,83 +0,0 @@
-#!/bin/sh
-
-#   imrm - remove image files
-#
-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-#   Copyright (C) 1999-2004 University of Oxford
-#
-#   Part of FSL - FMRIB's Software Library
-#   http://www.fmrib.ox.ac.uk/fsl
-#   fsl@fmrib.ox.ac.uk
-#
-#   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 6.0 (c) 2018, The University of
-#   Oxford (the "Software")
-#
-#   The Software remains the property of the Oxford University Innovation
-#   ("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 Oxford
-#   University Innovation ("OUI"), the technology transfer company of the
-#   University, to negotiate a licence. Contact details are:
-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-if [ $# -lt 1 ] ; then
-  echo "Usage: $0 <list of image names to remove>"
-  echo "NB: filenames can be basenames or not"
-  exit 1;
-fi
-
-for f in $@ ; do
-  fn=`${FSLDIR}/bin/remove_ext $f`;
-  # do the rm silently
-  /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
-done
-
diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
--- fsl.orig/src/fslio/imtest	2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imtest	1969-12-31 19:00:00.000000000 -0500
@@ -1,118 +0,0 @@
-#!/bin/sh
-
-#   imtest - test to see if a valid image file exists with this name (root)
-#
-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-#   Copyright (C) 1999-2004 University of Oxford
-#
-#   Part of FSL - FMRIB's Software Library
-#   http://www.fmrib.ox.ac.uk/fsl
-#   fsl@fmrib.ox.ac.uk
-#
-#   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 6.0 (c) 2018, The University of
-#   Oxford (the "Software")
-#
-#   The Software remains the property of the Oxford University Innovation
-#   ("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 Oxford
-#   University Innovation ("OUI"), the technology transfer company of the
-#   University, to negotiate a licence. Contact details are:
-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-# return 0 if no image exists or 1 if the image exists
-
-if [ $# -lt 1 ] ; then
- echo "0";
- exit;
-fi
-
-inputfile=$1
-
-
-
-for i in 1 2 3 4 5 6 7 8 9 10 11 12
-do
-if [ -h $inputfile ] ; then
-inputfile=`readlink $inputfile`;
-fi
-done
-
-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
-
-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
-  echo "1";
-  exit;
-fi
-
-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
-  echo "1";
-  exit;
-fi
-
-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
-  # return 0 here as no header exists and no single image means no image!
-  echo "0";
-  exit;
-fi
-
-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
-  # return 0 here as no img file exists and no single image means no image!
-  echo "0";
-  exit;
-fi
-
-# only gets to here if there was a hdr and an img file
-
-echo "1";
-exit;
-