work-around for bxh/imagemagick problem on mountain/lion

workAround-installBxhOnMountainLion.sh

#!/bin/bash
#
# workAround-installBxhOnMountainLion.sh
# [email protected]
#
# As of May 2013, the shipping version of BXH/XCEDE tools for OS X includes broken imagemagick:
#
#       $ bin/fmriqa_generate.pl ~/test.bxh ~/testQA
#       Trying int16 data type (instead of input uint16 datatype).
#       Checking for overflow...
#       dyld: Library not loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libclparser.dylib
#         Referenced from: /Users/stowler/Downloads/bxh/bin/montage
#         Reason: image not found
#       dyld: Library not loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libclparser.dylib
#         Referenced from: /Users/stowler/Downloads/bxh/bin/convert
#         Reason: image not found
#       ...(snip)...
#
#       $ bin/convert ~/Downloads/rose.jpg ~/Downloads/rose.png
#       dyld: Library not loaded: /Users/gadde/install/ImageMagick-6.7.1-6/lib/libMagickCore.4.dylib
#
#
# A temporary fix: install local imagemagick and symlink to it. 
#
# In four steps:


# Step 1/4: install imagemagick via macports:
sudo port install imagemagick 


# Step 2/4: manualy download most recent bxh/xcede release from nitrc: http://www.nitrc.org/projects/bxh_xcede_tools
# ls -l ~/Downloads/bxh_xcede_tools-*.tgz


# Step 3/4: unpack and install bxh/xcede:
#
# ...first declare the bxh version as it appears in the download filename:
bxhVersion=1.10.7

# ...then unpack, install, and substitute for broken imagemagick binaries: 
cd ~/Downloads
tar -zxvf bxh_xcede_tools-${bxhVersion}-MacOSX.i686.tgz
sudo mv bxh_xcede_tools-${bxhVersion}-MacOSX.i686 /usr/local/
sudo ln -s /usr/local/bxh_xcede_tools-${bxhVersion}-MacOSX.i686 /usr/local/bxh
sudo mv /usr/local/bxh/bin/convert /usr/local/bxh/bin/orig_convert
sudo mv /usr/local/bxh/bin/montage /usr/local/bxh/bin/orig_montage
sudo ln -s /opt/local/bin/convert /usr/local/bxh/bin/convert
sudo ln -s /opt/local/bin/montage /usr/local/bxh/bin/montage
ls -al /usr/local/bxh/bin/convert
ls -al /usr/local/bxh/bin/montage


# Step 4/4: For system-wide access, configure the environment via /etc/bashrc :
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):

editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER 
# added some BXH/XCEDE environment statements:
BXHDIR=/usr/local/bxh
PATH=\${BXHDIR}/bin:\${PATH}
export BXHDIR PATH
#------------------------------------------
EOF