asladc_batch.bash

#!/bin/bash
#
# asladc_batch.bash
#
# Copyright 2008 Rudolph Pienaar
# Massachusetts General Hospital
#
# GPL v2
#

# "include" the set of common script functions
source common.bash

declare -i Gi_verbose=0
declare -i Gb_forceStage=1
declare -i Gb_loopOverride=0
declare -i Gb_useCluster=0

G_TABLEFILE="-x"
G_DICOMINPUTDIR="-x"
G_DICOMINPUTFILE="-x"
G_LOOPCOUNT="1"

G_CLUSTERSCHED="mosrun -b -q -e -E "


G_SYNOPSIS="

 NAME

	asladc_batch.bash

 SYNOPSIS

	asladc_batch.bash	-t <batchTableFile>                  	\\
                                [-C]                                    \\ 
				[-l <loopOverride>]			\\
                                [-v <verbosity>]

 DESCRIPTION

	'asladc_batch.bash' is a batch controller for a set of 
	'asladc_b0_process.bash' runs. Given a <batchTableFile> that contains 
	a set of runs to process, step through each run in the table.

 BATCH TABLE
 
        The <batchTable> contains a table denoting a set of runs.

        A set of common command line arguments can be defined in a line
        starting with the text 'DEFAULTCOM', followed by a '=',
        followed by the command line options themselves.
        
        Usually the DICOM data to be processed is grouped together as a
        set of study-specific directories stored in a base directory. This
        base directory can be specified with the command 'DEFAULTDIR'.

        The table itself comprises a semi-colon delimted set of three 
        columns:

	<DICOMDIR>;<ASLseriesFile>;<ADCseriesFile>;<B0seriesFile>;<DIRsuffix>

	where:

	    <DICOMDIR>      	: The directory containing the study.
	    <ASLseriesFile> 	: A single file in the ASL series.
	    <ADCseriesFile> 	: A single file in the ADC series.
	    <B0seriesFile>  	: A single file in the B0  series.
	    <DIRsuffix>		: An output suffix that is appended
				  to processed *dirnames*.

        The <DIRsuffix> denotes a descriptive suffix for the acutal directory
        housing the final post-processing run, typically <MRID><DIRsuffix>, and
        also specifies the log directory suffix in the original DICOMDIR.

 ARGUMENTS

	-v <level> (Optional)
	Verbosity level. A value of '10' is a good choice here.
	
	-l <loopOverride> (Optional)
	If specified, only loop over the first <loopOverride> entries
	in the <batchTable>. This is provided so that new entries to
	an already processed <batchTableFile> can be selected, provided
	of course that these new entries appear at the *beginning* of the
	process specification.

        -t <batchTableFile>
        The table file to process.

 PRECONDITIONS
	
	o A FreeSurfer 'std' or 'dev' environment.

        o 'asladc_b0_process.bash' and related.

 POSTCONDITIONS

        o Each line of the batch table is interpreted and passed to a 
          spawned 'asladc_b0_process' process.

 HISTORY

	03 April 2009
	o Initial design and coding.
"

###\\\
# Globals are in capital letters. Immutable globals are prefixed by 'G'.
###///


# Actions
A_noTableFileArg="checking on -t <batchTableFile> argument"
A_noTableFile="checking on the table file"
A_noDicomDir="checking on input DICOM directory"
A_noDicomFile="checking on input DICOM directory / file"
A_stageRun="running a stage in the processing pipeline"

# Error messages
EM_noTableFileArg="it seems as though you didn't specify a -t <batchTableFile>."
EM_noTableFile="I couldn't access the file. Does it exist? Do you have access rights?"
EM_noDicomDir="I couldn't access the input DICOM dir. Does it exist?"
EM_noDicomFile="I couldn't find any DICOM *dcm files. Do any exist?"
EM_stageRun="I encountered an error processing this stage."

# Error codes

EC_noTableFile=41
EC_noDicomDir=50
EC_noTableFileArg=51
EC_noDicomFile=52
EC_stageRun=30

# Defaults
D_whatever=

###\\\
# Function definitions
###///

###\\\
# Process command options
###///

while getopts v:t:l:C option ; do
	case "$option"
	in
		v) 	Gi_verbose=$OPTARG		;;
		t)	G_TABLEFILE=$OPTARG		;;
                C)      Gb_useCluster=1                 ;;
		l)	G_LOOPCOUNT=$OPTARG
			let Gb_loopOverride=1		;;
		\?) synopsis_show
		    exit 0;;
	esac
done

verbosity_check

echo ""
cprint  "hostname"      "[ $(hostname) ]"

## Check on script preconditions
REQUIREDFILES="common.bash asladc_b0_process.bash"

for file in $REQUIREDFILES ; do
        printf "%40s"   "Checking for $file"
        file_checkOnPath $file || fatal fileCheck
done

## Check on input table file 
statusPrint     "Checking -t <batchTableFile>"
if [[ "$G_TABLEFILE" == "-x" ]] ; then fatal noTableFileArg ; fi
ret_check $?
statusPrint     "Checking <batchTableFile>"
fileExist_check $G_TABLEFILE || fatal noTableFile
topDir=$(pwd)
G_LOGDIR=$(dirname $G_TABLEFILE)
cd ${topDir}/${G_LOGDIR}
G_LOGDIR=$(pwd)
G_TABLEFILE=${G_LOGDIR}/$G_TABLEFILE
BASETABLE=$(basename $G_TABLEFILE)
cd $LOGDIR

DATE=$(date)

## Main processing start
STAMPLOG=${G_LOGDIR}/${G_SELF}.log
stage_stamp "Init | ($(pwd); $BASETABLE) $G_SELF $*" $STAMPLOG

G_TABLEFILEPARSED=$(cat $G_TABLEFILE | grep -v \#)

DEFAULTDIR=$(echo "$G_TABLEFILEPARSED"   | grep DEFAULTDIR       | awk -F \= '{print $2}')
DEFAULTCOM=$(echo "$G_TABLEFILEPARSED"   | grep DEFAULTCOM       | awk -F \= '{print $2}')
DEFAULTMAIL=$(echo "$G_TABLEFILEPARSED"  | grep DEFAULTMAIL      | awk -F \= '{print $2}')
TABLE=$(cat $G_TABLEFILE | grep -v \# | grep -v DEFAULT | sed '/^$/d' )

MAILCOM=""
if (( ${#DEFAULTMAIL} )) ; then
  MAILCOM="-M $DEFAULTMAIL"
fi
declare -i lineNum=1
declare -i totalLines=0
declare -i b_OKDIR
declare -i b_OKFILE
totalLines=$(echo "$TABLE" | wc -l)
if (( Gb_loopOverride )) ; then
    let totalLines=$G_LOOPCOUNT
fi
for LINE in $TABLE ; do
  b_OKDIR=1
  b_OKFILE=1
  cprint        "Preparing run"         "[ $lineNum / $totalLines ]"
  STAGE="batchRun_$lineNum/$totalLines"
  RUNDIR=$(echo $LINE | awk -F \; '{print $1}')
  G_DICOMINPUTDIR=${DEFAULTDIR}/$RUNDIR
  G_ASLINPUTFILE=$(echo $LINE | awk -F \; '{print $2}')
  G_ADCINPUTFILE=$(echo $LINE | awk -F \; '{print $3}')
  G_B0INPUTFILE=$(echo $LINE  | awk -F \; '{print $4}')
  DIRSUFFIX=$(echo $LINE      | awk -F \; '{print $5}')
  statusPrint     "Checking on <dicomInputDir>"
  dirExist_check $G_DICOMINPUTDIR || b_OKDIR=0
  statusPrint     "Checking on <ASLFile>"
  fileExist_check ${G_DICOMINPUTDIR}/${G_ASLINPUTFILE} || b_OKFILE=0
  statusPrint     "Checking on <ADCFile>"
  fileExist_check ${G_DICOMINPUTDIR}/${G_ADCINPUTFILE} || b_OKFILE=0
  statusPrint     "Checking on <B0File>"
  fileExist_check ${G_DICOMINPUTDIR}/${G_B0INPUTFILE}  || b_OKFILE=0
  STAGERUN=stage_run_bg
  if (( !Gb_useCluster )) ; then
    STAGERUN=stage_run
    G_CLUSTERSCHED="" 
  fi
  if (( b_OKDIR && b_OKFILE )) ; then
    STAGECMD="$G_CLUSTERSCHED asladc_b0_process.bash    \
              $DEFAULTCOM                               \
              $MAILCOM                                  \
              -R $DIRSUFFIX                             \
              -D $G_DICOMINPUTDIR                       \
              -S $G_ASLINPUTFILE			\
	      -C $G_ADCINPUTFILE			\
	      -B $G_B0INPUTFILE"
#     echo $STAGECMD
    echo ""
    $STAGERUN "$STAGE" "$STAGECMD"                      \
        "${G_LOGDIR}/${G_SELF}.std"                     \
        "${G_LOGDIR}/${G_SELF}.err"			\
#       || fatal stageRun
  else
    statusPrint "Invalid run spec"
  fi
  lineNum=$(expr $lineNum + 1)
  if (( Gb_loopOverride && lineNum > G_LOOPCOUNT )) ; then break; fi
done

lineNum=$(expr $lineNum - 1)
STAGE="($BASETABLE) Normal termination -- processed $lineNum / $totalLines"
stage_stamp "$STAGE" $STAMPLOG

printf "%40s" "Cleaning up"
shut_down 0