ThreadedImageConversion.sh

#!/bin/bash

#ImageConversion.sh has one input parameter: the path-to-file to be converted to megacapture format.  
#It must include the the appropriate .lsm or .zvi extension.
#Creates folder with same name as input file and same path with the .meg metadata and the corresponding .png image files.
#./ImageConversion.sh ../Data/SNAP-154443-0011.zvi

# extract extension in the filename and save it in $EXT
a=$1
xpath=${a%/*} 
xbase=${a##*/}
xext=${xbase##*.}
xpref=${xbase%.*}
NumberOfThreads=$2
echo "Bash version ${BASH_VERSION}..."
echo path=${xpath};
echo pref=${xpref};
echo ext=${xext};

#LEN=$(echo ${#1})
#LAST=$(($LEN-3))

# just to make sure no similar folder exists
rm -rf ${xpath}/${xpref}
mkdir ${xpath}/${xpref}

# writes the metadata information into txt file
./bioformatsTools/showinf -nopix $1 > ${xpath}/${xpref}_metadata.txt

NumberOfPlanes=$(grep "Image count = " ${xpath}/${xpref}_metadata.txt  | cut -c 16-)
#echo ${NumberOfPlanes}
Increment=$((${NumberOfPlanes}/${NumberOfThreads}))
#echo ${Increment}

# generates all png files from the input file
for iter in $(eval echo {1..${NumberOfThreads}})
do
  start=$((${Increment}*(${iter}-1)))
  stop=$(($start+${Increment}-1))
  if [ "${iter}" -eq "${NumberOfThreads}" ]
  then
    stop=$NumberOfPlanes
  fi
  ./bioformatsTools/bfconvert -range ${start} ${stop} $1 ${xpath}/${xpref}/${xpref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM%t-ch%c-zs%z.png &
done
wait

# generates all png files from the input file
#./bioformatsTools/bfconvert $1 ${xpath}/${xpref}/${xpref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM%t-ch%c-zs%z.png

function ConvertToGrayscale {

  path=$1
  pref=$2
  TM=$3
  CH=$4
  ZS=$5
  NumberOfThreads=$6
  Start=$7

	#first is TM
	for t in $(eval echo {0..${TM}})
	do
		#second is CH
		for c in $(eval echo {0..${CH}})
		do		
			#third is ZS
			for z in $(eval echo {${Start}..${ZS}..${NumberOfThreads}})
			do
        #convert to grayscale png and use 0 padded subscripts for time, z, ch
        convert ${path}/${pref}/${pref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM$t-ch$c-zs$z.png -colorspace Gray ${path}/${pref}/${pref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %04d $t)-ch$(printf %02d $c)-zs$(printf %04d $z).png
        # delete original image
        rm ${path}/${pref}/${pref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM$t-ch$c-zs$z.png

			done                    
		done
	done
}

function WriteMegacaptureImagePart {

  path=$1
  pref=$2
  ext=$3
  TM=$4
  CH=$5
  ZS=$6

	#first is TM
	for t in $(eval echo {0..${TM}})
	do
		#second is CH
		for c in $(eval echo {0..${CH}})
		do		
			#third is ZS
			for z in $(eval echo {0..${ZS}})
			do

				# prints these image lines with looped number for TM, ch, zs in 0001, 01, 0001 number format
				echo -e "\
<Image>\n\
Filename ${pref}-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %04d $t)-ch$(printf %02d $c)-zs$(printf %04d $z).png\n\
DateTime 2009-11-05 09:44:11\n\
StageX 1000\n\
StageY -1000\n\
Pinhole 44.216\n\
</Image>" > loopedMegaCaptureFormat.meg
				
				cat MegaCaptureFormat.meg loopedMegaCaptureFormat.meg > Meg.meg
				mv Meg.meg MegaCaptureFormat.meg

			done                    
		done
	done
}


function metadataConversion {
#This function takes input metadata and converts it to MegaCapture metadata formatted file.
#The command has three (3) required inputs in specific order:

#1) Path to image file
#2) Prefix of image file (filename without extension)
#3) Extension (lsm or zvi)

  cp MegaCaptureFormatFile.meg MegaCaptureFormat.meg

  path=$1
  pref=$2
  ext=$3
  NumberOfThreads=$4

  METADATAFILE=$1/$2_metadata.txt

	MEG[1]="TimeInterval"
  #MEG[1]="Objective"
  MEG[2]="VoxelSizeX"
  MEG[3]="VoxelSizeY"
  MEG[4]="VoxelSizeZ"
  MEG[5]="DimensionX"
  MEG[6]="DimensionY"
  MEG[7]="DimensionTM"
  MEG[8]="DimensionZS"
  MEG[9]="DimensionCH"
  MEG[10]="ChannelColor00"
  MEG[11]="ChannelColor01"
  MEG[12]="ChannelColor02"
  MEG[13]="ChannelDepth"


if [ "${ext}" == "lsm" ]
then

  LSM[1]="TimeInterval"
  #LSM[1]="Recording #1 Objective"
  LSM[2]="VoxelSizeX"
  LSM[3]="VoxelSizeY"
  LSM[4]="VoxelSizeZ"
  LSM[5]="DimensionX"
  LSM[6]="DimensionY"
  LSM[7]="SizeT"
  LSM[8]="SizeZ"
  LSM[9]="SizeC"
  LSM[10]="DataChannel #1 Color"
  LSM[11]="DataChannel #2 Color"
  LSM[12]="DataChannel #3 Color"
  LSM[13]="Valid bits per pixel"


  # Delete parameters that get confused with DimensionX and DimensionY
	sed -e 's/DimensionXT/DXT/g' -e 's/DimensionYT/DYT/g' -e 's/DimensionZT/DZT/g' MegaCaptureFormat.meg > Meg.meg
  mv Meg.meg MegaCaptureFormat.meg

	# Rearrange SizeT, SizeZ, SizeC and Valid bits per pixel to fit format of rest of parameters
	sed -e 's/\tSizeT =/SizeT:/g' -e 's/\tSizeZ =/SizeZ:/g' -e 's/\tSizeC =/SizeC:/g' -e 's/\tValid bits per pixel =/Valid bits per pixel:/g' ${METADATAFILE} > input.tmp

  for i in {1..13}
  do
    # Replaces elements in vector ending in colon with elements in vector MEG in tmp file input.tmp which$
    sed "s/${LSM[${i}]}:/${MEG[${i}]}/" input.tmp > ext.tmp
    mv ext.tmp input.tmp
  done

elif [ "$EXTENSION" == "zvi" ]
then

	#BlackValue: 0.0
	#WhiteValue: 0.03571428571428571
	#Exposure Time [ms]: 32000.0
	
    	ZVI[1]="Exposure Time"
        #ZVI[1]="Recording #1 Objective"
        ZVI[2]="Scale Factor for X"
        ZVI[3]="Scale Factor for Y"
        ZVI[4]="Scale Factor for Z"
        ZVI[5]="Width"
        ZVI[6]="Height"
        ZVI[7]="SizeT"
        ZVI[8]="SizeZ"
        ZVI[9]="SizeC"
        ZVI[10]="WhiteValue"
        ZVI[11]="BlackValue"
        ZVI[12]="DataChannel #3 Color"
        ZVI[13]="Valid bits per pixel"

	sed -e 's/DimensionXT/DXT/g' -e 's/DimensionYT/DYT/g' -e 's/DimensionZT/DZT/g' MegaCaptureFormat.meg > Meg.meg
	sed -e 's/\tSizeT =/SizeT:/g' -e 's/\tSizeZ =/SizeZ:/g' -e 's/\tSizeC =/SizeC:/g' -e 's/\tValid bits per pixel =/Valid bits per pixel:/g' ${METADATAFILE} > input.tmp
	sed -e 's/\tWidth =/Width:/g' -e 's/\tHeight =/Height:/g' input.tmp > in.tmp
	sed 's/Exposure Time \[ms\]/Exposure Time/g' in.tmp > input.tmp
	sed "s/(.*)$//g" input.tmp > in.tmp
	
	mv in.tmp input.tmp

	# calculates TimeInterval by multiplying exposure time [ms] by number of time points and dividing by 1000
	EXPOSURETIME_MS=$(grep "${ZVI[1]}" input.tmp  | cut -c 15-)
	EXP=$(echo ${EXPOSURETIME_MS%.*})
	EXPOSURETIME_S=$(($EXP/1000))

	DIMTM=$(grep "${ZVI[7]}" input.tmp  | cut -c 8-)
	TIMEINTERVAL=$(($EXPOSURETIME_S*$DIMTM))

	sed "s/^Exposure Time.*$/Exposure Time: $TIMEINTERVAL/g" input.tmp > in.tmp

	mv in.tmp input.tmp
  mv Meg.meg MegaCaptureFormat.meg

  for i in {1..13}
  do
    # Replaces elements in vector ending in colon with elements in vector MEG in tmp file input.tmp which$
    sed "s/${ZVI[${i}]}:/${MEG[${i}]}/" input.tmp > ext.tmp
    mv ext.tmp input.tmp
  done
		
else
  echo "This is an unsupported file extension!!!"
fi	
	

	for j in {1..13}
	do
		# Replaces lines in MegaCaptureFormat.meg with the converted lines in the tmp metadata format file input.tmp
		sed "s/$(grep ^${MEG[${j}]} MegaCaptureFormat.meg)/$(grep ^${MEG[${j}]} input.tmp)/" MegaCaptureFormat.meg > Meg.meg
		mv Meg.meg MegaCaptureFormat.meg
	done

	# NOTE: both .lsm and .zvi have these fields in common, so they are in this loop.  These are changed from DimensionXT to DXT and back to DimensionXT so they are
	# not confused with the other fields that begin with Dimension
	
	sed -e 's/DXT/DimensionXT/g' -e 's/DYT/DimensionYT/g' -e 's/DZT/DimensionZT/g' MegaCaptureFormat.meg > Meg.meg
	mv Meg.meg MegaCaptureFormat.meg

	# Locates the parameters of Time points, z slice, and channel and keeps their parameter values in DIM
	for k in {7..9}
	do
		DIM[${k}]=$(grep "${MEG[${k}]}" MegaCaptureFormat.meg  | cut -c 13-)     	
	done

	
	# 7 is TM, 8 is ZS, 9 is CH
	TM=$((${DIM[7]}-1))
	ZS=$((${DIM[8]}-1))
	CH=$((${DIM[9]}-1))

  LastThread=$(($NumberOfThreads-1))
  WriteMegacaptureImagePart ${path} ${pref} ${ext} ${TM} ${CH} ${ZS} &
	for start in $(eval echo {0..${LastThread}})
	do
    ConvertToGrayscale ${path} ${pref} ${TM} ${CH} ${ZS}	 ${NumberOfThreads} ${start} &
  done
	wait

	sed '/^$/d' MegaCaptureFormat.meg > tmp.tmp
	mv tmp.tmp MegaCaptureFormat.meg
	
	# aquires date and time of input metadata file and replaces old date and time everywhere in MegaCaptureFormat.meg 

	stat -c "%y" ${METADATAFILE} | cut -c 1-19 > DATETIME.txt
	sed "s/^DateTime.*$/DateTime $(cat DATETIME.txt)/g" MegaCaptureFormat.meg > ${path}/${pref}/${pref}.meg

	rm loopedMegaCaptureFormat.meg input.tmp DATETIME.txt MegaCaptureFormat.meg   
}

metadataConversion ${xpath} ${xpref} ${xext} ${NumberOfThreads}