spm12Batch_Global

#
# Copyright Robert C. Welsh, Ann Arbor MI 2005-2016
# 	    	      	     Salt Lake City, UT, 2016-2021
#
# No warranty or guarantee made. USE AT OWN RISK.
#
# To make this work at your site you need to change the 
# definition of "topDIR" below. Point to the parent directory
# of the spm12 and spm12Batch directories. In our local installation
# the directories "spm12" and "spm12Batch" and "spm12_patch"
# live side-by-side under the same parent. If you wish something different 
# than that then you will need "bash" knowledge greater than novice.
#
#
#  Things that you need to change to make it work locally (search for these below):
#
#  topDIR
#  LOCALOWNER
#  MATLAB
#  TemplateImageFile      (we have our own)
#  MAILRECPT
#
#
# ** INSTALLATION VARIABLE TO CHECK
#
#      SPM12B1     -- points to your local SPM12 installation directory
#      SPM12B2     -- automatically defined
#      SPM12B3     -- automatically defined
#
#      SANDBOXTOP  -- top directory of the sandbox directory
#
#      SANDBOXUSE  -- string that is passed to a grep command to determine
#                     if a sandbox should be used. See the Documentation/
#                     about why a sandbox is used.
#
#      MATLAB      -- where MATLAB is found. If in your path it will be okay, but for
#                     Mac OS X it is looking in the Applications/ folder, so make sure
#                     it points to the correct. It will point to the actual binary
#                     image and not just the ".app" folder.
#
#      LOGSPM12BATCHUSAGE --
#                     Set to something other than 1 for logging of usage. The usage
#                     goes into spm12Batch/Usage. All users must have write access
#                     to that sub-folder.
#
# ** End of Job Email
#
#     If you system has postfix enabled for sending out email, you can configure the system
#     to send emails to the user when the job has finished. In the past I have been
#     successful with also sending text messages to phones.
#
# ** Other software needed
#
#    YOU NEED TO MAKE SURE TO HAVE FSL, ANTs, ANIMA, AFNI installed and in your path
#
# ** Installation check
#
#    Run the command spm12Batch_CheckInstall which will look for executables.
#
# ** Daisy Chain -- experts
# 
# Using standard error exit codes as shown in
# https://www.freebsd.org/cgi/man.cgi?query=sysexits&apropos=0&sektion=0&manpath=FreeBSD%204.3-RELEASE&format=html
#
# 78  = misconfiguration
# 77  = no permission
# 74  = I/O error
# 69  = command not supported yet
# 66  = input file does not exist
# 65  = input data was incorrect
# 64  = command issued incorrectly
#
# -----------------------------------------------------------------------------

# Added some proper error returns when failing due to error.

COPYRIGHTENDYEAR=`date +%Y`
COPYRIGHT="Copyright Robert C. Welsh, 2005-${COPYRIGHTENDYEAR}, Version"

# There can be a recursive call accidentally, so don't allow.

if [ -z "${SPM12BATCHGLOBAL_CALLED}" ]
then

    echo
    echo Initializing spm12 Batch
    echo

# Are we logging usage? Set to something other than 1 to not log.
# The logs do into the spm12Batch/Usage directory

LOGSPM12BATCHUSAGE=1

# Bring in out function to determine whether something
# is a number or not.
    
    . ${thisDir}/isnumber.sh
    
#
# SOME GLOBAL THINGS TO CHANGE ACCORDING TO SITE
#    

    # Since the path is set to this command, then
    # the code will use the following to define
    # some internal variables needed.
     
    curdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
    topDIR="$( cd $curdir/.. && pwd )"

# ----------VERY CRUCIAL TO DEFINE THESE CORRECTLY

# You must point to SPM12 !!!
    
    SPM12B1=/Users/rcwelsh/Software/SPM12/spm12_r7771

    # Are we running on mnemosyne?
    if [ -d /erato ]
    then
        SPM12B1=/erato/mnemosyne/Software/SPM/spm12_r7771
    fi

# This is Robert Welsh's UNIX batch interface to spm12
    
    SPM12B2=${topDIR}/spm12Batch
    
# This must point to the place where the SPM12 patch is locally. 
    
    SPM12B3=${SPM12B2}/matlabScripts
    
    AUXPATH=${SPM12B2}/spm12_patch
    
#
# If the sandbox is populated then we copy files to local disk for processing
# and then copy back after completion. This will increase performance
# of processing of warpfMRI and smoothfMRI
#

    SANDBOXHOST=`echo $HOSTNAME | awk -F. '{print $1}' | awk -F- '{print $1}'`
    HOSTTYPE=`uname`
    if [ "${HOSTTYPE}" == "Darwin" ]
    then
	SANDBOXTOP=${HOME}/sandbox
    else
	SANDBOXTOP=/home/sandbox
    fi
     
    SANDBOX=${SANDBOXTOP}/${SANDBOXHOST}/sandbox/

# list the devices that require the use of the sandbox

    SANDBOXUSE="-e erato"

#
# You should put in the user id of the person
# that locally manages this software.
#
    
    LOCALOWNER=rcwelsh
    
#
# Mail job will be sent to your user name at the institutionname
# Please set the instituion email server name here.
    
    MAILRECPT=utah.edu
    
#
# Default email address to send messages to, on the linux machines
# use the currently logged in user as the name, on machines with a common
# analysis login you will need to set to a unique person.
#
    
    DEFAULTUSER=${USER}
    
#
#****
#   Where to find the template image to normalize to.
#   This is site DEPENDENT!!!!
    
    TemplateImageDir=${SPM12B1}/toolbox/OldNorm
    TemplateImageFile=T1.nii
    
    TemplateImage=${TemplateImageDir}/${TemplateImageFile}
    
# And finally, you need to point to matlab
        
    OSTYPE=`uname`

    if [ "${OSTYPE}" == "Darwin" ]
    then
        # Use the latest MATLAB we can find, but this should be static for stability.
        MATLAB=/Applications/MATLAB_R2020b.app/bin/matlab    # added 2020-03-12
    else
        MATLAB=`which matlab`
    	if [ -d /erato ]
    	then
	   MATLAB=/home/Software/MATLAB/R2020b/bin/matlab
    	fi
    fi
#    
# Only allow author to execute code during switch.
# If the current user is the localowner then they may
# execute the software.
    
    if [ -e "${thisDir}/.${LOCALOWNER}.Only" ]
    then
	if [ ! "${USER}" == "${LOCALOWNER}" ]
	then
	    echo
	    echo " Currently disabled during switch to new version."
	    echo
            # return the error code of EX_NOPERM
	    SPM12BATCH_ERROR_CODE=77
	    . ${thisDir}/auxiliary/exit_w_removal
	else
	    echo
	    echo " AUTHORIZED USER."
	    echo
	fi
    fi
    
# Done with author check
    
# Now check the critical components are here.
    
    for CRITICALCOMPONENT in $topDIR $SPM12B1 $SPM12B2 $SPM12B3
    do	
	if [ ! -z "${CRITICALCOMPONENT}" ]
	then
	    if [ ! -d ${CRITICALCOMPONENT} ]
	    then
		echo 
		echo " FATAL ERROR - CHECK THE INSTALL"
		echo	
		echo " The directory :"
		echo	
		echo "     ${CRITICALCOMPONENT}"
		echo
		echo " does not exist."
		# error EX_CONFIG
	        SPM12BATCH_ERROR_CODE=78
	        . ${thisDir}/auxiliary/exit_w_removal
	    fi
	fi
    done
    
# Make sure we have access to matlab
    
    if [ ! -e "${MATLAB}" ]
    then
	echo
	echo " FATAL ERROR - CHECK THE INSTALL"
	echo 
	echo " I can not find matlab: "
	echo
	echo "       $MATLAB"
	echo
	# EX_CONFIG error
	SPM12BATCH_ERROR_CODE=78
	. ${thisDir}/auxiliary/exit_w_removal
    fi
    
# Now fix on whether we are on 64bit machine or 32bit machine
    
# Not sure if we need this, we really should be using
# the 64 bit version.
    
    ARCH=`uname -m`
    
#if [ "${ARCH}" == "x86_64" ]
#then
#	MATLAB="linux32 ${MATLAB}"
#fi
    
# Well, if we got this far then software seems to be installed
# ok.
    
# Now start building the automatic scripts. Some of these variables are from the parent shell script that
# has sourced this code block.
    
# We can build the names for the scripts right here.
    
# Put in a little more protection for the 
# naming of the script files. On linux we can request 
# the nanosecond timing and then take the first two (most significan digits)

# On MAC OS X we just have to suck it up and hope there are no
# clashes of file names. In general it shoudl not happen as
# the script builing has a forced delay of 1 second in it.

# For MAC OS X we just throw a 3-digit random number on it.

    if [ "${OSTYPE}" == "Darwin" ]
    then   
       theDate=`date +%y%m%d_%H_%M_%S`
       # Need to seed with process ID, else we get the same number
       RANDOM=$$
       THERANDOM=$RANDOM
       theRandom=`echo $THERANDOM | awk '{printf "%05d",$1}'`
       theDate=${theDate}_${theRandom:0:3}
       theYearMonth=`date +%Y_%m`
    else
       # On LINUX we can get the nano-second clock as well.
       theDate=`date +%y%m%d_%H_%M_%S_%N`
       theDate=${theDate:0:19}
       theYearMonth=`date +%Y_%m`
    fi
    
    HOSTCOMPUTER=`echo $HOSTNAME | awk -F. '{print $1}' | sed 's/-/_/g'`

    # grab part of host name.
    if (( ${#HOSTCOMPUTER} > 8 ))
    then
	HOSTCOMPUTER=${HOSTCOMPUTER:0:8}
    fi
    
    SCRIPTNAME=${thisCommand}_${theDate}_${USER}_${HOSTCOMPUTER}
    
    MATLABDIR=matlabScripts/spm12Batch/${thisCommand}/${theYearMonth}
    
    UMBatchMaster=`pwd`
    
    FULLSCRIPTNAME=${UMBatchMaster}/${MATLABDIR}/${SCRIPTNAME}
    
    GENERICRUNDIR=run_
    
fi

SPM12BATCHGLOBAL_CALLED=YES

# # # # # # # # # # # # #
# 
# Function Definitions
#
# # # # # # # # # # # # #

# define out debug output function

# to use debugout then do 'debugout "string" D'

function debugout()
{
    if ! [ -z "$1" ]
    then
	if ! [ -z "$2" ]
	then
	    if  [ $2 == "D" ] || [ $2 == 'd' ]
	    then
		echo $1
	    fi
        fi
    fi
}

# A function to return NIFTI file information to the screen.

function NIFTIINFO()
{
    printf "         ${2} ${1} \t\t:"
    for DIM in dim1 dim2 dim3
    do
	INFO=`fslinfo ${1} | grep -v pix | grep ${DIM} | awk '{print $2}'`
	echo -n "${INFO} x "
    done
    INFO=`fslinfo ${1} | grep -v pix | grep dim4 | awk '{print $2}'`
    echo "${INFO}"		    
}

#
# Globals all done.
#