ImageConversion.sh

#!/bin/bash


#./ImageConversion.sh ../Data/SNAP-154443-0011.zvi

#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.



# extract extension in the filename and save it in $EXT
LEN=$(echo ${#1})
LAST=$(($LEN-3))
EXT=$(echo $1 | cut -c $(($LEN-2))-) 
FILENAME=$(echo ${1%.*}) #filename path
#echo $EXT
#echo $FILENAME

# just to make sure it: TO BE COMPLETED!!
rm -rf $FILENAME

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

# writes the metadata information into txt file
./bioformatsTools/showinf -nopix $1 > $FILENAME_metadata.txt


function metadataConversion {

#This function takes input metadata and converts it to MegaCapture metadata formatted file.
#metadataConversion.sh converts metadata from an input image file to a MegaCapture (.meg) metadata format.

#The command has three (3) required inputs in specific order:

#1) metadata file (e.g. log.txt)
#2) name of the .meg output file you want without the extension (e.g. datetest)
#3) the extension of the input image data that defines the format of the input metadata file (e.g. zvi)

cp MegaCaptureFormatFile.meg MegaCaptureFormat.meg

INPUTFILE=$1

MEGAFILENAME=$2

EXTENSION=$3

	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 [ "$EXTENSION" == "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

	# 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' $INPUTFILE > 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/${LSM[${i}]}:/${MEG[${i}]}/" input.tmp > ext.tmp

                mv ext.tmp input.tmp

        done

        cp input.tmp aftercolon.tmp


 

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' $INPUTFILE > 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

	
	cp input.tmp afterexposuretime.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

	cp input.tmp aftercolon.tmp
	





#	echo ${ZVI[@]}
#	EXT=("${ZVT[@]}")
#	echo ${EXT[@]}
		
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 > mega.meg
		mv mega.meg MegaCaptureFormat.meg
		
	done
	
	cp MegaCaptureFormat.meg switchfeilds.meg	

	# 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 > tmp.meg
	mv tmp.meg MegaCaptureFormat.meg


	for k in {7..9}
	do
	
		# Locates the parameters of Time points, z slice, and channel and keeps their parameter values in DIM

		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))


	#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 image-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %4.4u $t)-ch$(printf %2.2u $c)-zs$(printf %4.4u $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 > new.meg

				mv new.meg MegaCaptureFormat.meg
				
				mv image-PL00-CO00-RO00-ZT00-YT00-XT00-TM$t-ch$c-zs$z.png $2-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %4.4u $t)-ch$(printf %2.2u $c)-zs$(printf %4.4u $z).png

                                #convert to grayscale png
                                convert $2-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %4.4u $t)-ch$(printf %2.2u $c)-zs$(printf %4.4u $z).png -colorspace Gray $2-PL00-CO00-RO00-ZT00-YT00-XT00-TM$(printf %4.4u $t)-ch$(printf %2.2u $c)-zs$(printf %4.4u $z).png

			done
                    
		done

	done
	
	
	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" $1 | cut -c 1-19 > DATETIME.txt
	sed "s/^DateTime.*$/DateTime $(cat DATETIME.txt)/g" MegaCaptureFormat.meg > $2.meg

	rm loopedMegaCaptureFormat.meg input.tmp DATETIME.txt MegaCaptureFormat.meg aftercolon.tmp switchfeilds.meg   


}






metadataConversion $FILENAME_metadata.txt $FILENAME $EXT



mkdir $FILENAME
mv $FILENAME.meg $FILENAME*.png $FILENAME