OBJS = \
	ConvertAmicasJPEG2000FilesetToDicom.class \
	NIfTI1ToDicom.class \
	NIfTI1Header.class \
	NIfTI1Exception.class \
	NRRDToDicom.class \
	NRRDHeader.class \
	NRRDException.class \
	RawRGBInformation.class \
	RawRGBToDicomMultiFrame.class

all:	${OBJS}

PATHTOROOT = ../../..

include ${PATHTOROOT}/Makefile.common.mk

testamicas:	ConvertAmicasJPEG2000FilesetToDicom.class
	mkdir -p /tmp/todicomMR1
	java -cp ${PATHTOROOT}:${PATHTOADDITIONAL}/jai_imageio.jar com.pixelmed.convert.ConvertAmicasJPEG2000FilesetToDicom "${PATHTOHOME}/Pictures/Medical/AmicasJ2K/ELMR20030206" /tmp/todicomMR1
	mkdir -p /tmp/todicomCT1
	java -cp ${PATHTOROOT}:${PATHTOADDITIONAL}/jai_imageio.jar com.pixelmed.convert.ConvertAmicasJPEG2000FilesetToDicom "${PATHTOHOME}/Pictures/Medical/AmicasJ2K/CD0105153529" /tmp/todicomCT1
	mkdir -p /tmp/todicomCT2
	java -cp ${PATHTOROOT}:${PATHTOADDITIONAL}/jai_imageio.jar com.pixelmed.convert.ConvertAmicasJPEG2000FilesetToDicom "${PATHTOHOME}/Pictures/Medical/AmicasJ2K/CD0114154520" /tmp/todicomCT2

testamicasdialog:	ConvertAmicasJPEG2000FilesetToDicom.class
	java -cp ${PATHTOROOT}:${PATHTOADDITIONAL}/jai_imageio.jar com.pixelmed.convert.ConvertAmicasJPEG2000FilesetToDicom


testnifti1header:	NIfTI1Header.class NIfTI1Exception.class
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NIfTI1Header \
		"$${HOME}/Pictures/Medical/ParametricMaps/DICOM_FP/GE_Normalized_Boxerman_rBFMap_LeakageCorrected.nii"
		#"$${HOME}/Pictures/Medical/ParametricMaps/DICOM_FP/dti_adc.nii"

testnifti1convert:	NIfTI1ToDicom.class NIfTI1Header.class NIfTI1Exception.class
	rm -rf /tmp/crap
	rm -rf /tmp/crap2
	java -Xmx512m -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NIfTI1ToDicom \
		"$${HOME}/Pictures/Medical/ParametricMaps/DICOM_FP/GE_Normalized_Boxerman_rBFMap_LeakageCorrected.nii" \
		/tmp/crap \
		"Doe^Jane" 1234 5678 100 1
	java -Xmx512m -cp .:${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.apps.IntegerScalingOfFloatingPointPixelData \
		/tmp/crap /tmp/crap2
	andump /tmp/crap
	dciodvfy /tmp/crap
	andump /tmp/crap2
	dciodvfy /tmp/crap2
	#dchist -h /tmp/crap2


testnifti1talairach:	NIfTI1ToDicom.class NIfTI1Header.class NIfTI1Exception.class
	java -Xmx512m -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NIfTI1ToDicom \
		"$${HOME}/Documents/Medical/stuff/Atlases/Talairach/talairach.nii" \
		"$${HOME}/Documents/Medical/stuff/Atlases/Talairach/talairach.dcmm" \
		"Talairach" 1234 5678 100 1

testnrrdheaderseparate:	NRRDHeader.class NRRDException.class
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NRRDHeader \
		"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/MRMLMultiVolume.nhdr"

testnrrdheadercombined:	NRRDHeader.class NRRDException.class
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NRRDHeader \
		"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/MRMLMultiVolume frame 21.nrrd"

testnrrdconvertseparate:	NRRDToDicom.class NRRDHeader.class NRRDException.class
	rm -rf /tmp/crap
	rm -rf /tmp/crap2
	java -Xmx1g -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NRRDToDicom \
		"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/MRMLMultiVolume.nhdr" \
		/tmp/crap \
		"Doe^Jane" 1234 5678 100 1
	java -Xmx1g -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.apps.IntegerScalingOfFloatingPointPixelData \
		/tmp/crap /tmp/crap2
	#andump /tmp/crap
	#dciodvfy /tmp/crap
	andump /tmp/crap2
	dciodvfy /tmp/crap2
	#dchist -h /tmp/crap2

testnrrdconvertcombined:	NRRDToDicom.class NRRDHeader.class NRRDException.class
	rm -rf /tmp/crap
	rm -rf /tmp/crap2
	java -Xmx1g -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NRRDToDicom \
		"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/OncoQuant-AutoAIF-Results/PCAMPMRI-0241_GE-Ktrans.nrrd" \
		/tmp/crap \
		"Doe^Jane" 1234 5678 100 1
	#"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/MRMLMultiVolume frame 21.nrrd"
	java -Xmx1g -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.apps.IntegerScalingOfFloatingPointPixelData \
		/tmp/crap /tmp/crap2
	#andump /tmp/crap
	#dciodvfy /tmp/crap
	andump /tmp/crap2
	dciodvfy /tmp/crap2
	#dchist -h /tmp/crap2

testnrrdheaderseparate:	NRRDHeader.class NRRDException.class
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.NRRDHeader \
		"$${HOME}/Pictures/Medical/ParametricMaps/PkModeling_verification/PCAMPMRI-0241/SlicerScene/MRMLMultiVolume.nhdr"

testrawrgbheader:	RawRGBInformation.class
	if [ ! -f "$${HOME}/work/vhm/testfiles/README" ]; \
	then \
		mkdir -p "$${HOME}/work/vhm/testfiles"; \
		cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/README" "$${HOME}/work/vhm/testfiles/README"; \
	fi
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.RawRGBInformation \
		"$${HOME}/work/vhm/testfiles/README"

testrawrgbvhmuncompressed:	RawRGBToDicomMultiFrame.class RawRGBInformation.class
	mkdir -p "$${HOME}/work/vhm/testfiles"
	mkdir -p "$${HOME}/work/vhm/testfiles/srcimages/uncompressed"
	mkdir -p "$${HOME}/work/vhm/testfiles/dstimages/testrawrgbvhm"
	cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/README" "$${HOME}/work/vhm/testfiles/"
	gzcat <"$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2000.rgb.gz" >"$${HOME}/work/vhm/testfiles/srcimages/uncompressed/2000.rgb"
	gzcat <"$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2001.rgb.gz" >"$${HOME}/work/vhm/testfiles/srcimages/uncompressed/2001.rgb"
	gzcat <"$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2002.rgb.gz" >"$${HOME}/work/vhm/testfiles/srcimages/uncompressed/2002.rgb"
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.RawRGBToDicomMultiFrame \
		"$${HOME}/work/vhm/testfiles/README" \
		"$${HOME}/work/vhm/testfiles/srcimages/uncompressed" \
		".rgb" \
		"$${HOME}/work/vhm/testfiles/dstimages/testrawrgbvhm" \
		"Doe^Jane" 1234 5678 100

testrawrgbvhmcompressed:	RawRGBToDicomMultiFrame.class RawRGBInformation.class
	mkdir -p "$${HOME}/work/vhm/testfiles"
	mkdir -p "$${HOME}/work/vhm/testfiles/srcimages/compressed"
	mkdir -p "$${HOME}/work/vhm/testfiles/dstimages/testrawrgbvhm"
	cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/README" "$${HOME}/work/vhm/testfiles/"
	cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2000.rgb.gz" "$${HOME}/work/vhm/testfiles/srcimages/compressed/"
	cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2001.rgb.gz" "$${HOME}/work/vhm/testfiles/srcimages/compressed/"
	cp "$${HOME}/work/vhm/srcimages/vhnet.nlm.nih.gov/Male/70mm/fullbody/2002.rgb.gz" "$${HOME}/work/vhm/testfiles/srcimages/compressed/"
	java -cp ${PATHTOROOT} -Djava.awt.headless=true \
		com.pixelmed.convert.RawRGBToDicomMultiFrame \
		"$${HOME}/work/vhm/testfiles/README" \
		"$${HOME}/work/vhm/testfiles/srcimages/compressed" \
		".rgb.gz" \
		"$${HOME}/work/vhm/testfiles/dstimages/testrawrgbvhm" \
		"Doe^Jane" 1234 5678 100

