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cmbtodcm.sh
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cmbtodcm.sh
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#!/bin/sh
#
# Usage: ./cmbtodcm.sh folder/filename.svs [outdir]
infile="$1"
outdir="$2"
#JAVATMPDIRARG="-Djava.io.tmpdir=/Volumes/Elements5TBNonEncD/tmp"
TMPJSONFILE="/tmp/`basename $0`.$$"
#CSVFILENAMEFORMETADATA="draft-cmb-path-slides-idc-20231010.csv"
#CSVFILENAMEFORMETADATA="cmb-path-slides-query-20240501_plus_MSB-04591-13-02.csv"
CSVFILENAMEFORMETADATA="cmb-path-slides-20241025_plus_MSB-04591-13-02.csv"
if [ ! -f "${CSVFILENAMEFORMETADATA}" ]
then
echo 1>&2 "Error: no metadata CSV file called ${CSVFILENAMEFORMETADATA}"
exit 1
fi
# these persist across invocations ...
FILEMAPPINGSPECIMENIDTOUID="CMBspecimenIDToUIDMap.csv"
FILEMAPPINGSTUDYIDTOUID="CMBstudyIDToUIDMap.csv"
FILEMAPPINGSTUDYIDTODATETIME="CMBstudyIDToDateTimeMap.csv"
UIDMAPPINGFILE="idc-conversion-outputs-cmb-old_tabulateduids.csv"
TMPSLIDEUIDFILE="slideuid.csv"
#JHOVE="${HOME}/work/jhove/jhove"
if [ -f "${HOME}/work/pixelmed/imgbook/pixelmed.jar" ]
then
PIXELMEDDIR="${HOME}/work/pixelmed/imgbook"
PATHTOADDITIONAL="${PIXELMEDDIR}/lib/additional"
elif [ -f "${HOME}/pixelmed.jar" ]
then
PIXELMEDDIR="${HOME}"
PATHTOADDITIONAL="${HOME}"
fi
# will get collection from metadata and populate other clinical trial attributes later ...
dicomclinicaltrialcoordinatingcentername=""
dicomclinicaltrialsponsorname="National Cancer Institute (NCI)"
issuerofdicomclinicaltrialprotocolid="NCI"
dicomclinicaltrialsiteid=""
# "source-data-cmb/CMB-PCA/MSB-02472-03-01.svs"
# do not remove suffix '.svs' from filename since need to match what is in CSVFILENAMEFORIMAGING
filename=`basename "${infile}"`
foldername=`dirname "${infile}"`
slide_id=`echo ${filename} | sed -e 's/^\([A-Z0-9-]*\).*$/\1/'`
# slide_id = MSB-02472-03-01
if [ -z "${outdir}" ]
then
outdir="Converted/${slide_id}"
fi
slidefilenameforuid="${filename}"
echo "slidefilenameforuid = ${slidefilenameforuid}"
echo "TMPSLIDEUIDFILE = ${TMPSLIDEUIDFILE}"
rm -f "${TMPSLIDEUIDFILE}"
uidarg=""
if [ -f "${UIDMAPPINGFILE}" ]
then
egrep "(Filename|${slidefilenameforuid})" "${UIDMAPPINGFILE}" > "${TMPSLIDEUIDFILE}"
uidarg="UIDFILE ${TMPSLIDEUIDFILE}"
fi
echo "uidarg = ${uidarg}"
sample_id="${slide_id}"
specimen_id="${sample_id}"
echo "infile = ${infile}"
echo "filename = ${filename}"
echo "slide_id = ${slide_id}"
echo "sample_id = ${sample_id}"
echo "specimen_id = ${specimen_id}"
if [ -f "${CSVFILENAMEFORMETADATA}" ]
then
# ,participant_id,gender,race,ethnicity,dbGaP_subject_id,primary_diagnosis,participant_ID,file_name,file_format,image_modality,imaging_equipment_manufacturer,imaging_equipment_model,organ_or_tissue,sample_id,sample_type,tumor_tissue_type,tissue_fixative,embedding_medium,staining_method,collection,material_type,collection_event
# ,MSB-02472,M,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,MSB-02472,Prostate Carcinoma,MSB-02472,189568.svs,SVS,SM,Aperio,AT2,Prostate,MSB-02472-03-01,NA,Metastatic,Formalin,Paraffin wax,Hematoxylin and Eosin Staining Method,CMB-PCA,Glass H&E Slide,Archival
# participant_id,sample_id,gender,race,ethnicity,primary_diagnosis,file_name,file_format,image_modality,imaging_equipment_manufacturer,imaging_equipment_model,organ_or_tissue,sample_type,tumor_tissue_type,tissue_fixative,embedding_medium,staining_method,collection,material_type,collection_event
# MSB-00089,MSB-00089-01-02,Female,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,Plasma Cell Myeloma,MSB-00089-01-02.svs,SVS,SM,Aperio,AT2,Bone Marrow,Iliac Crest,PRIMARY,Formalin,Paraffin wax,Hematoxylin and Eosin Staining Method,CMB-MML,Glass H&E Slide,ARCHIVAL
# participant_id,sample_id,gender,race,ethnicity,primary_diagnosis,file_name,file_format,image_modality,imaging_equipment_manufacturer,imaging_equipment_model,organ_or_tissue,sample_type,tumor_tissue_type,tissue_fixative,embedding_medium,staining_method,collection,material_type,collection_event
# MSB-00043,MSB-00043-01-02,Male,WHITE,NOT HISPANIC OR LATINO,Prostate Carcinoma,MSB-00043-01-02.svs,SVS,SM,Aperio,AT2,Prostate,Prostate Gland,PRIMARY,Formalin,Paraffin Wax,Hematoxylin and Eosin Staining Method,CMB-PCA,Glass H&E Slide,ARCHIVAL
# note that despite the "file_name" column, which has entries like "189568.svs", the image files we have from TCIA via Aspera are of the form "MSB-02472-03-01.svs", which matches the "sample_id" column, so the following grep works ...
csvlineformetadata=`grep ",${sample_id}," "${CSVFILENAMEFORMETADATA}" | head -1 | sed 's/\r$//'`
echo "csvlineformetadata = ${csvlineformetadata}"
fi
if [ -z "${csvlineformetadata}" ]
then
echo 1>&2 "Warning: cannot find metadata CSV file entry for slide_id ${slide_id}"
#slide_id = MSB-07656-07-04
#patient_id = MSB-07656
patient_id=`echo "${slide_id}" | sed -e 's/^\(MSB-[0-9]*\)-[0-9-]*$/\1/'`
#infile = idc-source-data-cmb/CMB-AML/MSB-07656-07-04.svs
#collection = CMB-AML
collection=`echo "${infile}" | sed -e 's/^.*\(CMB-[A-Z]*\).*$/\1/'`
else
collection=`echo "${csvlineformetadata}" | awk -F, '{print $18}'`
patient_id=`echo "${csvlineformetadata}" | awk -F, '{print $1}'`
gender=`echo "${csvlineformetadata}" | awk -F, '{print $3}'`
race=`echo "${csvlineformetadata}" | awk -F, '{print $4}'`
#ethnicity=`echo "${csvlineformetadata}" | awk -F, '{print $5}'`
organ_or_tissue=`echo "${csvlineformetadata}" | awk -F, '{print $12}'`
primary_diagnosis=`echo "${csvlineformetadata}" | awk -F, '{print $6}'`
tumor_tissue_type=`echo "${csvlineformetadata}" | awk -F, '{print $14}'`
tissue_fixative=`echo "${csvlineformetadata}" | awk -F, '{print $15}'`
embedding_medium=`echo "${csvlineformetadata}" | awk -F, '{print $16}'`
staining_method=`echo "${csvlineformetadata}" | awk -F, '{print $17}'`
material_type=`echo "${csvlineformetadata}" | awk -F, '{print $19}'`
#collection_event is sometimes quoted, specifically, '"Post Treatment, No Progression"' ...
csvlineformetadata_cleaned=`echo "${csvlineformetadata}" | sed -e 's/"Post Treatment, No Progression"/Post Treatment No Progression/'`
collection_event=`echo "${csvlineformetadata_cleaned}" | awk -F, '{print $20}'`
fi
echo "collection = ${collection}"
echo "patient_id = ${patient_id}"
dicomclinicaltrialsubjectid="${patient_id}"
echo "dicomclinicaltrialsubjectid = ${dicomclinicaltrialsubjectid}"
if [ ! -z "${collection_event}" -a "${collection_event}" != "NA" ]
then
dicomclinicaltrialtimepointid=`echo "${collection_event}" | tr 'A-Z' 'a-z'`
fi
echo "dicomclinicaltrialtimepointid = ${dicomclinicaltrialtimepointid}"
echo "gender = ${gender}"
echo "race = ${race}"
#echo "ethnicity = ${ethnicity}"
echo "organ_or_tissue = ${organ_or_tissue}"
echo "primary_diagnosis = ${primary_diagnosis}"
echo "tumor_tissue_type = ${tumor_tissue_type}"
echo "tissue_fixative = ${tissue_fixative}"
echo "embedding_medium = ${embedding_medium}"
echo "staining_method = ${staining_method}"
echo "material_type = ${material_type}"
# from https://www.cancerimagingarchive.net/research/cmb/
# decision is not to use TCIA collection-specific DOI, but IDC-specific Zenodo doi (vide supra)
dicomclinicaltrialprotocolid="${collection}"
if [ "${collection}" = "CMB-AML" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/PCTE-6M66" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993760" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Acute Myeloid Leukemia (${collection})"
elif [ "${collection}" = "CMB-BRCA" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/dx22-8j71" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993762" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Invasive Breast Carcinoma (${collection})"
elif [ "${collection}" = "CMB-CRC" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/DJG7-GZ87" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993770" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Colorectal Cancer (${collection})"
elif [ "${collection}" = "CMB-GEC" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/E7KH-R486" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993774" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Gastroesophageal Cancer (${collection})"
elif [ "${collection}" = "CMB-LCA" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/3CX3-S132" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993777" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Lung Cancer (${collection})"
elif [ "${collection}" = "CMB-MEL" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/GWSP-WH72" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993787" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Melanoma (${collection})"
elif [ "${collection}" = "CMB-MML" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/SZKB-SW39" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993793" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Multiple Myeloma (${collection})"
elif [ "${collection}" = "CMB-OV" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/4nx6-e061" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993797" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Ovarian Carcinoma (${collection})"
elif [ "${collection}" = "CMB-PCA" ]
then
#doiclinicaltrialprotocolid="doi:10.7937/25T7-6Y12" # not using the TCIA DOI
doiclinicaltrialprotocolid="doi:10.5281/zenodo.13993799" # use IDC-specific, collection-specific DOI
dicomclinicaltrialprotocolname="Cancer Moonshot Biobank - Prostate Cancer (${collection})"
else
echo 1>&2 "Warning: unrecognized collection \"${collection}\""
doiclinicaltrialprotocolid="doi:10.5281/zenodo.11099112" # use generic IDC-specific Zenodo DOI rather than collection-specific DOI
fi
echo "outdir = ${outdir}"
dicompatientid="${patient_id}"
# DO NOT match TCIA radiology collection pattern with collection included ... the TCIA radiology was updated
#dicompatientid="${collection}-${patient_id}"
dicompatientname="${dicompatientid}"
dicomspecimenidentifier="${specimen_id}"
dicomstudyid="${patient_id}"
dicomaccessionnumber="${patient_id}"
# container is the slide
dicomcontaineridentifier="${slide_id}"
dicomspecimenuid=""
if [ ! -f "${FILEMAPPINGSPECIMENIDTOUID}" ]
then
touch "${FILEMAPPINGSPECIMENIDTOUID}"
fi
if [ ! -z "${dicomspecimenidentifier}" ]
then
# dicomspecimenidentifier may be prefix for other identifiers, so assure bounded by delimiters, and use first if duplicates else fails later
dicomspecimenuid=`egrep "^${dicomspecimenidentifier}," "${FILEMAPPINGSPECIMENIDTOUID}" | awk -F, '{print $2}' | head -1`
if [ -z "${dicomspecimenuid}" ]
then
dicomspecimenuid=`java -cp ${PIXELMEDDIR}/pixelmed.jar -Djava.awt.headless=true com.pixelmed.utils.UUIDBasedOID 2>&1`
echo "${dicomspecimenidentifier},${dicomspecimenuid}" >>"${FILEMAPPINGSPECIMENIDTOUID}"
echo "Created Specimen UID ${dicomspecimenuid} for Specimen ID ${dicomspecimenidentifier}"
else
echo "Reusing Specimen UID ${dicomspecimenuid} for Specimen ID ${dicomspecimenidentifier}"
fi
fi
# dicomspecimenuid may still be unassigned if there is no dicomspecimenidentifier - let Java code fill in new one
dicomstudyuid=""
if [ ! -f "${FILEMAPPINGSTUDYIDTOUID}" ]
then
touch "${FILEMAPPINGSTUDYIDTOUID}"
fi
if [ ! -z "${dicomstudyid}" ]
then
# dicomstudyid may be prefix for other identifiers, so assure bounded by delimiters, and use first if duplicates else fails later
dicomstudyuid=`egrep "^${dicomstudyid}," "${FILEMAPPINGSTUDYIDTOUID}" | awk -F, '{print $2}' | head -1`
if [ -z "${dicomstudyuid}" ]
then
dicomstudyuid=`java -cp ${PIXELMEDDIR}/pixelmed.jar -Djava.awt.headless=true com.pixelmed.utils.UUIDBasedOID 2>&1`
echo "${dicomstudyid},${dicomstudyuid}" >>"${FILEMAPPINGSTUDYIDTOUID}"
echo "Created Study UID ${dicomstudyuid} for Study ID ${dicomstudyid}"
else
echo "Reusing Study UID ${dicomstudyuid} for Study ID ${dicomstudyid}"
fi
fi
# dicomstudyuid may still be unassigned if there is no dicomstudyid - let Java code fill in new one
# Aperio "...ScanScope ID = SS1302|Filename = 11952||Date = 04/07/14|Time = 12:30:08|Time Zone = GMT-04:00|..."
# Aperio "...AppMag = 40|Date = 07/24/2023|Exposure Scale = 0.000001|Exposure Time = 8|Filtered = 3|Focus Offset = 0.500000|Gamma = 2.2|Left = 19.347723007202|MPP = 0.263447|Rack = 10|ScanScope ID = SS12035|Slide = 27|StripeWidth = 4096|Time = 15:22:42|Time Zone = GMT-0400|Top = 44.411762237549..."
# Hamamatsu "...|Date=12/12/2013|Time=03:21:44 PM|Copyright=Hamamatsu Photonics KK|"
# ignore timezone
# ignore Hamamatsu since would need us to add 12 to PM times
# try 4 digit year "|Date = 07/24/2023|"
svsdatetime=`tiffinfo "${infile}" | grep -v Hamamatsu | grep ScanScope | grep Date | grep Time | head -1 | egrep 'Date = [0-9][0-9][/][0-9][0-9][/]20[0-9][0-9][|]' | sed -e 's/^.*Date = \([0-9][0-9]\)[/]\([0-9][0-9]\)[/]\([0-9][0-9][0-9][0-9]\).*Time = \([0-9][0-9]\)[:]\([0-9][0-9]\)[:]\([0-9][0-9]\).*$/\3\1\2\4\5\6/'`
if [ -z "${svsdatetime}" ]
then
# try 2 digit year "|Date = 04/07/14|"
svsdatetime=`tiffinfo "${infile}" | grep -v Hamamatsu | grep ScanScope | grep Date | grep Time | head -1 | egrep 'Date = [0-9][0-9][/][0-9][0-9][/][0-9][0-9][|]' | sed -e 's/^.*Date = \([0-9][0-9]\)[/]\([0-9][0-9]\)[/]\([0-9][0-9]\).*Time = \([0-9][0-9]\)[:]\([0-9][0-9]\)[:]\([0-9][0-9]\).*$/20\3\1\2\4\5\6/'`
fi
if [ -z "${svsdatetime}" ]
then
# SCN "...|Date = 2014-07-23T16:33:58.37Z|..."
# ignore fraction, ignore that it is Zulu time
svsdatetime=`tiffinfo "${infile}" | grep -v Hamamatsu | grep SCN | grep Date | head -1 | sed -e 's/^.*Date = \([0-9][0-9][0-9][0-9]\)-\([0-9][0-9]\)-\([0-9][0-9]\)T\([0-9][0-9]\)[:]\([0-9][0-9]\)[:]\([0-9][0-9]\).*$/\1\2\3\4\5\6/'`
if [ -z "${svsdatetime}" ]
then
echo "Cannot extract an svsdatetime"
else
echo "SCN-style svsdatetime"
fi
else
echo "Aperio-style svsdatetime"
fi
echo "svsdatetime = ${svsdatetime}"
# ideally we would pick the earliest study date time, but that would require multiple passes, so just record the 1st encountered and make all the same to satisfy information model (dcentvfy)
dicomstudydatetime=""
if [ ! -f "${FILEMAPPINGSTUDYIDTODATETIME}" ]
then
touch "${FILEMAPPINGSTUDYIDTODATETIME}"
fi
if [ ! -z "${dicomstudyid}" ]
then
# should only be zero or one, but head -1 just in case
dicomstudydatetime=`grep "${dicomstudyid}" "${FILEMAPPINGSTUDYIDTODATETIME}" | head -1 | awk -F, '{print $2}'`
if [ -z "${dicomstudydatetime}" ]
then
if [ -z "${svsdatetime}" ]
then
# use current datetime, just as TIFFToDicom would, so that this is set now and reused for all future series for the same StudyID
dicomstudydatetime=`date '+%Y%m%d%H%M%S'`
echo "No SVS datetime, so using current datetime ${dicomstudydatetime}"
else
dicomstudydatetime="${svsdatetime}"
fi
echo "${dicomstudyid},${dicomstudydatetime}" >>"${FILEMAPPINGSTUDYIDTODATETIME}"
echo "Created Study Date Time ${dicomstudydatetime} for Study ID ${dicomstudyid}"
else
echo "Reusing Study Date Time ${dicomstudydatetime} for Study ID ${dicomstudyid}"
fi
fi
# dicomstudydatetime may still be unassigned if there is no dicomstudyid, or if not found in SVS header - let Java code fill in one based on SVS files ImageDescription
dicomstudydate=""
dicomstudytime=""
if [ ! -z "${dicomstudydatetime}" ]
then
dicomstudydate=`echo "${dicomstudydatetime}" | sed -e 's/^\([0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]\).*$/\1/'`
dicomstudytime=`echo "${dicomstudydatetime}" | sed -e 's/^.*\([0-9][0-9][0-9][0-9][0-9][0-9]\)$/\1/'`
fi
dicomstudydescription="Histopathology"
dicomsex=""
lcgender=`echo "${gender}" | tr 'A-Z' 'a-z'`
if [ "${lcgender}" = "male" -o "${lcgender}" = "m" ]
then
dicomsex="M"
elif [ "${lcgender}" = "female" -o "${lcgender}" = "f" ]
then
dicomsex="F"
else
echo 1>&2 "Warning: ignoring unrecognized gender ${gender}"
fi
echo "dicomsex = ${dicomsex}"
dicomage=""
echo "dicomage = ${dicomage}"
dicomethnicgroup=""
# SH, so limited to 16 characters
if [ "${race}" = "AMERICAN INDIAN OR ALASKA NATIVE" ]
then
dicomethnicgroup="American Indian"
elif [ "${race}" = "ASIAN" ]
then
dicomethnicgroup="Asian"
elif [ "${race}" = "BLACK OR AFRICAN AMERICAN" ]
then
dicomethnicgroup="Black"
elif [ "${race}" = "BLACK OR AFRICAN AMERICAN+AMERICAN INDIAN OR ALASKA NATIVE" ]
then
dicomethnicgroup="Black+AmerIndian"
elif [ "${race}" = "NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER" ]
then
dicomethnicgroup="Pacific Islander"
elif [ "${race}" = "WHITE" ]
then
dicomethnicgroup="White"
elif [ "${race}" = "WHITE+AMERICAN INDIAN OR ALASKA NATIVE" ]
then
dicomethnicgroup="White+AmerIndian"
elif [ "${race}" != "UNKNOWN" -a "${race}" != "NOT REPORTED" -a ! -z "${race}" ]
then
echo 1>&2 "Warning: ignoring unrecognized race ${race}"
fi
echo "dicomethnicgroup = ${dicomethnicgroup}"
anatomycodevalue=""
anatomycsd=""
anatomycodemeaning=""
lateralitycodevalue=""
lateralitycsd=""
lateralitycodemeaning=""
anatomymodifiercodevalue=""
anatomymodifiercsd=""
anatomymodifiercodemeaning=""
echo "extracted organ_or_tissue = ${organ_or_tissue}"
if [ ! -z "${organ_or_tissue}" ]
then
organ_or_tissue=`echo "${organ_or_tissue}" | tr 'A-Z' 'a-z' | sed -e 's/[^a-z]/ /g' | sed -e 's/[ ][ ]*/ /g'`
echo "normalized organ_or_tissue = ${organ_or_tissue}"
if [ "${organ_or_tissue}" = "bone" ]
then
anatomycodevalue="272673000"
anatomycsd="SCT"
anatomycodemeaning="Bone"
elif [ "${organ_or_tissue}" = "bone marrow" ]
then
anatomycodevalue="14016003"
anatomycsd="SCT"
anatomycodemeaning="Bone marrow"
elif [ "${organ_or_tissue}" = "colon" ]
then
anatomycodevalue="71854001"
anatomycsd="SCT"
anatomycodemeaning="Colon"
elif [ "${organ_or_tissue}" = "esophagus" ]
then
anatomycodevalue="32849002"
anatomycsd="SCT"
anatomycodemeaning="Esophagus"
elif [ "${organ_or_tissue}" = "intestines" ]
then
anatomycodevalue="113276009"
anatomycsd="SCT"
anatomycodemeaning="Intestine"
elif [ "${organ_or_tissue}" = "liver" ]
then
anatomycodevalue="10200004"
anatomycsd="SCT"
anatomycodemeaning="Liver"
elif [ "${organ_or_tissue}" = "lung" ]
then
anatomycodevalue="39607008"
anatomycsd="SCT"
anatomycodemeaning="Lung"
elif [ "${organ_or_tissue}" = "prostate" ]
then
anatomycodevalue="41216001"
anatomycsd="SCT"
anatomycodemeaning="Prostate"
elif [ "${organ_or_tissue}" = "rectum" ]
then
anatomycodevalue="34402009"
anatomycsd="SCT"
anatomycodemeaning="Rectum"
elif [ "${organ_or_tissue}" = "skin" ]
then
anatomycodevalue="39937001"
anatomycsd="SCT"
anatomycodemeaning="Skin"
elif [ "${organ_or_tissue}" = "stomach" ]
then
anatomycodevalue="69695003"
anatomycsd="SCT"
anatomycodemeaning="Stomach"
elif [ "${organ_or_tissue}" = "breast" ]
then
anatomycodevalue="76752008"
anatomycsd="SCT"
anatomycodemeaning="Breast"
elif [ "${organ_or_tissue}" = "ovary" ]
then
anatomycodevalue="15497006"
anatomycsd="SCT"
anatomycodemeaning="Ovary"
elif [ "${organ_or_tissue}" = "fallopian tube" ]
then
anatomycodevalue="31435000"
anatomycsd="SCT"
anatomycodemeaning="Fallopian tube"
elif [ "${organ_or_tissue}" = "omentum" ]
then
anatomycodevalue="27398004"
anatomycsd="SCT"
anatomycodemeaning="Omentum"
elif [ "${organ_or_tissue}" = "whole blood" ]
then
# is substance not structure
anatomycodevalue="420135007"
anatomycsd="SCT"
anatomycodemeaning="Whole Blood"
else
echo 1>&2 "Warning: unrecognized body site \"${organ_or_tissue}\" for sample_id ${sample_id}"
fi
fi
echo "anatomycodemeaning = ${anatomycodemeaning}"
echo "lateralitycodemeaning = ${lateralitycodemeaning}"
echo "anatomymodifiercodemeaning = ${anatomymodifiercodemeaning}"
if [ ! -z "${tumor_tissue_type}" ]
then
if [ "${tumor_tissue_type}" = "Adjacent Non-Tumor" ]
then
tissuetypecodevalue="17621005"
tissuetypecsd="SCT"
tissuetypecodemeaning="Normal"
tissuetypeshortdescription="N"
elif [ "${tumor_tissue_type}" = "Primary" ]
then
tissuetypecodevalue="372087000"
tissuetypecsd="SCT"
tissuetypecodemeaning="Primary malignant neoplasm"
tissuetypeshortdescription="P"
elif [ "${tumor_tissue_type}" = "Metastatic" ]
then
tissuetypecodevalue="14799000"
tissuetypecsd="SCT"
tissuetypecodemeaning="Metastatic neoplasm"
tissuetypeshortdescription="M"
elif [ "${tumor_tissue_type}" != "NA" -a ]
then
echo 1>&2 "Warning: ignoring unrecognized tumor_tissue_type ${tumor_tissue_type}"
fi
fi
echo "tissuetypecodemeaning = ${tissuetypecodemeaning}"
dicomdiagnosisdescription=""
dicomdiagnosiscodevalue=""
dicomdiagnosiscsd=""
dicomdiagnosiscodemeaning=""
if [ ! -z "${primary_diagnosis}" ]
then
diagnosislc=`echo "${primary_diagnosis}" | tr 'A-Z' 'a-z'`
if [ ! -z "${diagnosislc}" ]
then
dicomdiagnosisdescription="${primary_diagnosis}"
# use SCT disorder rather than morphologic abnormality codes when both; none of these are in DICOM subset (yet) :(
if [ "${diagnosislc}" = "acute myeloid leukemia not otherwise specified" ]
then
dicomdiagnosiscodevalue="91861009"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Acute myeloid leukemia"
elif [ "${diagnosislc}" = "adenocarcinoma of the gastroesophageal junction" ]
then
dicomdiagnosiscodevalue="721628002"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Primary adenocarcinoma of esophagogastric junction"
elif [ "${diagnosislc}" = "colorectal carcinoma" ]
then
dicomdiagnosiscodevalue="1286877004"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Colorectal cancer"
elif [ "${diagnosislc}" = "melanoma" ]
then
dicomdiagnosiscodevalue="372244006"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Malignant melanoma"
elif [ "${diagnosislc}" = "non-small cell lung carcinoma" ]
then
dicomdiagnosiscodevalue="254637007"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Non-small cell lung cancer"
elif [ "${diagnosislc}" = "plasma cell myeloma" ]
then
dicomdiagnosiscodevalue="1162576007"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Plasma cell myeloma"
elif [ "${diagnosislc}" = "prostate carcinoma" ]
then
dicomdiagnosiscodevalue="254900004"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Carcinoma of prostate"
elif [ "${diagnosislc}" = "small cell lung carcinoma" ]
then
dicomdiagnosiscodevalue="254632001"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Small cell carcinoma of lung"
elif [ "${diagnosislc}" = "invasive breast carcinoma" ]
then
dicomdiagnosiscodevalue="713609000"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Invasive carcinoma of breast"
elif [ "${diagnosislc}" = "ovarian carcinoma" ]
then
dicomdiagnosiscodevalue="254849005"
dicomdiagnosiscsd="SCT"
dicomdiagnosiscodemeaning="Carcinoma of ovary"
else
echo 1>&2 "Warning: ignoring unrecognized diagnosis ${diagnosislc}"
fi
fi
fi
echo "dicompatientname = ${dicompatientname}"
echo "dicompatientid = ${dicompatientid}"
echo "dicomstudyid = ${dicomstudyid}"
echo "dicomstudyuid = ${dicomstudyuid}"
echo "dicomstudydatetime = ${dicomstudydatetime}"
echo "dicomstudydate = ${dicomstudydate}"
echo "dicomstudytime = ${dicomstudytime}"
echo "dicomstudydescription = ${dicomstudydescription}"
echo "dicomaccessionnumber = ${dicomaccessionnumber}"
echo "dicomspecimenidentifier = ${dicomspecimenidentifier}"
echo "dicomspecimenuid = ${dicomspecimenuid}"
echo "dicomcontaineridentifier = ${dicomcontaineridentifier}"
echo "anatomycodevalue = ${anatomycodevalue}"
echo "anatomycsd = ${anatomycsd}"
echo "anatomycodemeaning = ${anatomycodemeaning}"
echo "lateralitycodevalue = ${lateralitycodevalue}"
echo "lateralitycsd = ${lateralitycsd}"
echo "lateralitycodemeaning = ${lateralitycodemeaning}"
echo "anatomymodifiercodevalue = ${anatomymodifiercodevalue}"
echo "anatomymodifiercsd = ${anatomymodifiercsd}"
echo "anatomymodifiercodemeaning = ${anatomymodifiercodemeaning}"
echo "tissuetypecodevalue = ${tissuetypecodevalue}"
echo "tissuetypecsd = ${tissuetypecsd}"
echo "tissuetypecodemeaning = ${tissuetypecodemeaning}"
echo "tissuetypeshortdescription = ${tissuetypeshortdescription}"
tissue_fixative_forshortdescription="${tissue_fixative}"
if [ "${tissue_fixative}" = "Formalin" ]
then
tissue_fixative_forshortdescription="FF"
fi
if [ "${material_type}" = "Glass W-G Slide Smear" ]
then
# incorrectly specified as "Paraffin wax" in supplied metadata
echo 1>&2 "Warning: suppressing embedding_medium ${embedding_medium} for material_type ${material_type}"
embedding_medium=""
fi
embedding_medium_forshortdescription="${embedding_medium}"
if [ "${embedding_medium}" = "Paraffin wax" -o "${embedding_medium}" = "Paraffin Wax" ]
then
embedding_medium_forshortdescription="PE"
fi
staining_method_forshortdescription="${staining_method}"
if [ "${staining_method}" = "Hematoxylin and Eosin Staining Method" ]
then
staining_method_forshortdescription="HE"
elif [ "${staining_method}" = "Wright-Giemsa Staining Method" ]
then
staining_method_forshortdescription="WG"
fi
dicomspecimenshortdescription="${tissue_fixative_forshortdescription} ${embedding_medium_forshortdescription} ${staining_method_forshortdescription} ${tissuetypeshortdescription}"
echo "dicomspecimenshortdescription = ${dicomspecimenshortdescription}"
dicomspecimendetaileddescription="${tissue_fixative} ${embedding_medium} ${staining_method} ${tumor_tissue_type}"
echo "dicomspecimendetaileddescription = ${dicomspecimendetaileddescription}"
dicomseriesdescription="${dicomspecimenshortdescription}"
echo "dicomseriesdescription = ${dicomseriesdescription}"
echo "dicomdiagnosisdescription = ${dicomdiagnosisdescription}"
echo "dicomdiagnosiscodevalue = ${dicomdiagnosiscodevalue}"
echo "dicomdiagnosiscsd = ${dicomdiagnosiscsd}"
echo "dicomdiagnosiscodemeaning = ${dicomdiagnosiscodemeaning}"
echo >"${TMPJSONFILE}" "{"
echo >>"${TMPJSONFILE}" " \"options\" : {"
echo >>"${TMPJSONFILE}" " \"AppendToContributingEquipmentSequence\" : false"
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " \"top\" : {"
echo >>"${TMPJSONFILE}" " \"PatientName\" : \"${dicompatientname}\","
echo >>"${TMPJSONFILE}" " \"PatientID\" : \"${dicompatientid}\","
if [ ! -z "${dicomsex}" ]
then
echo >>"${TMPJSONFILE}" " \"PatientSex\" : \"${dicomsex}\","
fi
if [ ! -z "${dicomdiagnosisdescription}" ]
then
echo >>"${TMPJSONFILE}" " \"AdmittingDiagnosesDescription\" : \"${dicomdiagnosisdescription}\","
fi
if [ ! -z "${dicomdiagnosiscodevalue}" ]
then
echo >>"${TMPJSONFILE}" " \"AdmittingDiagnosesCodeSequence\" : { \"cv\" : \"${dicomdiagnosiscodevalue}\", \"csd\" : \"${dicomdiagnosiscsd}\", \"cm\" : \"${dicomdiagnosiscodemeaning}\" },"
fi
if [ ! -z "${dicomage}" ]
then
echo >>"${TMPJSONFILE}" " \"PatientAge\" : \"${dicomage}\","
fi
if [ ! -z "${dicomsize}" ]
then
echo >>"${TMPJSONFILE}" " \"PatientSize\" : \"${dicomsize}\","
fi
if [ ! -z "${dicomweight}" ]
then
echo >>"${TMPJSONFILE}" " \"PatientWeight\" : \"${dicomweight}\","
fi
if [ ! -z "${dicomethnicgroup}" ]
then
echo >>"${TMPJSONFILE}" " \"EthnicGroup\" : \"${dicomethnicgroup}\","
fi
echo >>"${TMPJSONFILE}" " \"StudyID\" : \"${dicomstudyid}\","
echo >>"${TMPJSONFILE}" " \"StudyInstanceUID\" : \"${dicomstudyuid}\","
if [ ! -z "${dicomstudydate}" ]
then
echo >>"${TMPJSONFILE}" " \"StudyDate\" : \"${dicomstudydate}\","
fi
if [ ! -z "${dicomstudytime}" ]
then
echo >>"${TMPJSONFILE}" " \"StudyTime\" : \"${dicomstudytime}\","
fi
echo >>"${TMPJSONFILE}" " \"StudyDescription\" : \"${dicomstudydescription}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialSponsorName\" : \"${dicomclinicaltrialsponsorname}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialProtocolID\" : \"${dicomclinicaltrialprotocolid}\","
if [ ! -z "${issuerofdicomclinicaltrialprotocolid}" ]
then
echo >>"${TMPJSONFILE}" " \"IssuerOfClinicalTrialProtocolID\" : \"${issuerofdicomclinicaltrialprotocolid}\","
fi
if [ ! -z "${doiclinicaltrialprotocolid}" ]
then
echo >>"${TMPJSONFILE}" " \"OtherClinicalTrialProtocolIDsSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ClinicalTrialProtocolID\" : \"${doiclinicaltrialprotocolid}\","
echo >>"${TMPJSONFILE}" " \"IssuerOfClinicalTrialProtocolID\" : \"DOI\""
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ],"
fi
echo >>"${TMPJSONFILE}" " \"00130010\" : \"CTP\","
echo >>"${TMPJSONFILE}" " \"00131010\" : \"${dicomclinicaltrialprotocolid}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialProtocolName\" : \"${dicomclinicaltrialprotocolname}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialSiteID\" : \"${dicomclinicaltrialsiteid}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialSiteName\" : \"${dicomclinicaltrialsitename}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialSubjectID\" : \"${dicomclinicaltrialsubjectid}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialCoordinatingCenterName\" : \"${dicomclinicaltrialcoordinatingcentername}\","
echo >>"${TMPJSONFILE}" " \"ClinicalTrialTimePointID\" : \"${dicomclinicaltrialtimepointid}\","
if [ ! -z "${dicominstitutionname}" ]
then
echo >>"${TMPJSONFILE}" " \"InstitutionName\" : \"${dicominstitutionname}\","
fi
echo >>"${TMPJSONFILE}" " \"AcquisitionContextSequence\" : ["
echo >>"${TMPJSONFILE}" " ],"
echo >>"${TMPJSONFILE}" " \"SeriesNumber\" : \"1\","
echo >>"${TMPJSONFILE}" " \"SeriesDescription\" : \"${dicomseriesdescription}\","
echo >>"${TMPJSONFILE}" " \"AccessionNumber\" : \"${dicomaccessionnumber}\","
echo >>"${TMPJSONFILE}" " \"ContainerIdentifier\" : \"${dicomcontaineridentifier}\","
echo >>"${TMPJSONFILE}" " \"IssuerOfTheContainerIdentifierSequence\" : [],"
echo >>"${TMPJSONFILE}" " \"ContainerTypeCodeSequence\" : { \"cv\" : \"433466003\", \"csd\" : \"SCT\", \"cm\" : \"Microscope slide\" },"
echo >>"${TMPJSONFILE}" " \"SpecimenDescriptionSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"SpecimenIdentifier\" : \"${dicomspecimenidentifier}\","
echo >>"${TMPJSONFILE}" " \"IssuerOfTheSpecimenIdentifierSequence\" : [],"
echo >>"${TMPJSONFILE}" " \"SpecimenUID\" : \"${dicomspecimenuid}\","
if [ ! -z "${dicomspecimenshortdescription}" ]
then
echo >>"${TMPJSONFILE}" " \"SpecimenShortDescription\" : \"${dicomspecimenshortdescription}\","
fi
if [ ! -z "${dicomspecimendetaileddescription}" ]
then
echo >>"${TMPJSONFILE}" " \"SpecimenDetailedDescription\" : \"${dicomspecimendetaileddescription}\","
fi
echo >>"${TMPJSONFILE}" " \"SpecimenPreparationSequence\" : ["
if [ "${tissue_fixative}" = "Formalin" -o "${tissue_fixative}" = "EDTA" ]
then
populated_tissue_fixative="true"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"SpecimenPreparationStepContentItemSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"TEXT\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"121041\", \"csd\" : \"DCM\", \"cm\" : \"Specimen Identifier\" },"
echo >>"${TMPJSONFILE}" " \"TextValue\" : \"${dicomspecimenidentifier}\""
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"111701\", \"csd\" : \"DCM\", \"cm\" : \"Processing type\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"9265001\", \"csd\" : \"SCT\", \"cm\" : \"Specimen processing\" }"
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"430864009\", \"csd\" : \"SCT\", \"cm\" : \"Tissue Fixative\" },"
if [ "${tissue_fixative}" = "Formalin" ]
then
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"431510009\", \"csd\" : \"SCT\", \"cm\" : \"Formalin\" }"
elif [ "${tissue_fixative}" = "EDTA" ]
then
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"69519002\", \"csd\" : \"SCT\", \"cm\" : \"EDTA\" }"
fi
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ]"
echo >>"${TMPJSONFILE}" " }"
elif [ ! -z "${tissue_fixative}" ]
then
echo 1>&2 "Warning: ignoring unrecognized tissue_fixative ${tissue_fixative}"
fi
if [ "${embedding_medium}" = "Paraffin wax" -o "${embedding_medium}" = "Paraffin Wax" ]
then
populated_embedding_medium="true"
if [ ! -z "${populated_tissue_fixative}" ]
then
echo >>"${TMPJSONFILE}" " ,"
fi
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"SpecimenPreparationStepContentItemSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"TEXT\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"121041\", \"csd\" : \"DCM\", \"cm\" : \"Specimen Identifier\" },"
echo >>"${TMPJSONFILE}" " \"TextValue\" : \"${dicomspecimenidentifier}\""
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"111701\", \"csd\" : \"DCM\", \"cm\" : \"Processing type\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"9265001\", \"csd\" : \"SCT\", \"cm\" : \"Specimen processing\" }"
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"430863003\", \"csd\" : \"SCT\", \"cm\" : \"Embedding medium\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"311731000\", \"csd\" : \"SCT\", \"cm\" : \"Paraffin wax\" }"
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ]"
echo >>"${TMPJSONFILE}" " }"
elif [ ! -z "${embedding_medium}" ]
then
echo 1>&2 "Warning: ignoring unrecognized embedding_medium ${embedding_medium}"
fi
if [ "${staining_method}" = "Hematoxylin and Eosin Staining Method" -o "${staining_method}" = "Wright-Giemsa Staining Method" ]
then
populated_staining_method="true"
if [ ! -z "${populated_tissue_fixative}" -o ! -z "${populated_embedding_medium}" ]
then
echo >>"${TMPJSONFILE}" " ,"
fi
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"SpecimenPreparationStepContentItemSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"TEXT\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"121041\", \"csd\" : \"DCM\", \"cm\" : \"Specimen Identifier\" },"
echo >>"${TMPJSONFILE}" " \"TextValue\" : \"${dicomspecimenidentifier}\""
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"111701\", \"csd\" : \"DCM\", \"cm\" : \"Processing type\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"127790008\", \"csd\" : \"SCT\", \"cm\" : \"Staining\" }"
echo >>"${TMPJSONFILE}" " }"
if [ "${staining_method}" = "Hematoxylin and Eosin Staining Method" ]
then
echo >>"${TMPJSONFILE}" " ,"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"424361007\", \"csd\" : \"SCT\", \"cm\" : \"Using substance\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"12710003\", \"csd\" : \"SCT\", \"cm\" : \"hematoxylin stain\" }"
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"424361007\", \"csd\" : \"SCT\", \"cm\" : \"Using substance\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"36879007\", \"csd\" : \"SCT\", \"cm\" : \"water soluble eosin stain\" }"
echo >>"${TMPJSONFILE}" " }"
elif [ "${staining_method}" = "Wright-Giemsa Staining Method" ]
then
echo >>"${TMPJSONFILE}" " ,"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"424361007\", \"csd\" : \"SCT\", \"cm\" : \"Using substance\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"373682001\", \"csd\" : \"SCT\", \"cm\" : \"wright stain\" }"
echo >>"${TMPJSONFILE}" " },"
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"ValueType\" : \"CODE\","
echo >>"${TMPJSONFILE}" " \"ConceptNameCodeSequence\" : { \"cv\" : \"424361007\", \"csd\" : \"SCT\", \"cm\" : \"Using substance\" },"
echo >>"${TMPJSONFILE}" " \"ConceptCodeSequence\" : { \"cv\" : \"373646006\", \"csd\" : \"SCT\", \"cm\" : \"giemsa stain\" }"
echo >>"${TMPJSONFILE}" " }"
fi
echo >>"${TMPJSONFILE}" " ]"
echo >>"${TMPJSONFILE}" " }"
elif [ ! -z "${staining_method}" ]
then
echo 1>&2 "Warning: ignoring unrecognized staining_method ${staining_method}"
fi
if [ ! -z "${anatomycodevalue}" ]
then
echo >>"${TMPJSONFILE}" " ],"
if [ -z "${lateralitycodevalue}" -a -z "${anatomymodifiercodevalue}" -a -z "${tissuetypecodevalue}" ]
then
echo >>"${TMPJSONFILE}" " \"PrimaryAnatomicStructureSequence\" : { \"cv\" : \"${anatomycodevalue}\", \"csd\" : \"${anatomycsd}\", \"cm\" : \"${anatomycodemeaning}\" }"
else
echo >>"${TMPJSONFILE}" " \"PrimaryAnatomicStructureSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"CodeValue\" : \"${anatomycodevalue}\","
echo >>"${TMPJSONFILE}" " \"CodingSchemeDesignator\" : \"${anatomycsd}\","
echo >>"${TMPJSONFILE}" " \"CodeMeaning\" : \"${anatomycodemeaning}\","
echo >>"${TMPJSONFILE}" " \"PrimaryAnatomicStructureModifierSequence\" : ["
if [ ! -z "${lateralitycodevalue}" ]
then
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"CodeValue\" : \"${lateralitycodevalue}\","
echo >>"${TMPJSONFILE}" " \"CodingSchemeDesignator\" : \"${lateralitycsd}\","
echo >>"${TMPJSONFILE}" " \"CodeMeaning\" : \"${lateralitycodemeaning}\""
echo >>"${TMPJSONFILE}" " }"
fi
if [ ! -z "${anatomymodifiercodevalue}" ]
then
if [ ! -z "${lateralitycodevalue}" ]
then
echo >>"${TMPJSONFILE}" " ,"
fi
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"CodeValue\" : \"${anatomymodifiercodevalue}\","
echo >>"${TMPJSONFILE}" " \"CodingSchemeDesignator\" : \"${anatomymodifiercsd}\","
echo >>"${TMPJSONFILE}" " \"CodeMeaning\" : \"${anatomymodifiercodemeaning}\""
echo >>"${TMPJSONFILE}" " }"
fi
if [ ! -z "${tissuetypecodevalue}" ]
then
if [ ! -z "${lateralitycodevalue}" -o ! -z "${anatomymodifiercodevalue}" ]
then
echo >>"${TMPJSONFILE}" " ,"
fi
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"CodeValue\" : \"${tissuetypecodevalue}\","
echo >>"${TMPJSONFILE}" " \"CodingSchemeDesignator\" : \"${tissuetypecsd}\","
echo >>"${TMPJSONFILE}" " \"CodeMeaning\" : \"${tissuetypecodemeaning}\""
echo >>"${TMPJSONFILE}" " }"
fi
echo >>"${TMPJSONFILE}" " ]"
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ]"
fi
else
echo >>"${TMPJSONFILE}" " ]"
fi
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ],"
echo >>"${TMPJSONFILE}" " \"OpticalPathSequence\" : ["
echo >>"${TMPJSONFILE}" " {"
echo >>"${TMPJSONFILE}" " \"OpticalPathIdentifier\" : \"1\","
echo >>"${TMPJSONFILE}" " \"IlluminationColorCodeSequence\" : { \"cv\" : \"414298005\", \"csd\" : \"SCT\", \"cm\" : \"Full Spectrum\" },"
echo >>"${TMPJSONFILE}" " \"IlluminationTypeCodeSequence\" : { \"cv\" : \"111744\", \"csd\" : \"DCM\", \"cm\" : \"Brightfield illumination\" }"
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" " ]"
echo >>"${TMPJSONFILE}" " }"
echo >>"${TMPJSONFILE}" "}"
cat "${TMPJSONFILE}"
tiffinfo "${infile}"
# transfersyntaxargs derivation copied from htantodcm.sh (as of 2022/06/20) (which is why the unused 16-bit if grayscale stuff is present) ...
firstifdcompression=`tiffinfo "${infile}" | grep 'Compression Scheme' | sed -e 's/ Compression Scheme: //' | head -1`
echo "firstifdcompression=${firstifdcompression}"
if [ "${firstifdcompression}" = "None" -o "${firstifdcompression}" = "LZW" ]
then
# do J2k reversible if 8-bit whether RGB or grayscale, 16-bit if grayscale, but only if too large for GHC to cope (bytes in Pixeldata > 2GB)
firstifdbitspersample=`tiffinfo "${infile}" | grep 'Bits/Sample' | sed -e 's/ Bits.Sample: //' | head -1`
echo "firstifdbitspersample=${firstifdbitspersample}"
firstifdsamplesperpixel=`tiffinfo "${infile}" | grep 'Samples/Pixel' | sed -e 's/ Samples.Pixel: //' | head -1`
echo "firstifdsamplesperpixel=${firstifdsamplesperpixel}"
#firstifdphotometric=`tiffinfo "${infile}" | grep 'Photometric Interpretation' | sed -e 's/ Photometric Interpretation: //' | head -1`
#echo "firstifdphotometric=${firstifdphotometric}"
#Image Width: 29879 Image Length: 22448
firstifdimagewidth=`tiffinfo "${infile}" | grep 'Image Width:' | sed -e 's/^.*Image Width: \([0-9][0-9]*\).*$/\1/' | head -1`
echo "firstifdimagewidth=${firstifdimagewidth}"
firstifdimagelength=`tiffinfo "${infile}" | grep 'Image Length:' | sed -e 's/^.*Image Length: \([0-9][0-9]*\).*$/\1/' | head -1`
echo "firstifdimagelength=${firstifdimagelength}"
#pixeldatasizeinbytesrel2gb=`echo "scale=0; ${firstifdbitspersample} / 8 * ${firstifdsamplesperpixel} * ${firstifdimagewidth} * ${firstifdimagelength} / 2147483648" | bc -l`
# Google limit is 2GiB not 2GB
pixeldatasizeinbytesrel2gb=`echo "scale=0; ${firstifdbitspersample} / 8 * ${firstifdsamplesperpixel} * ${firstifdimagewidth} * ${firstifdimagelength} / 2000000000" | bc -l`
echo "pixeldatasizeinbytesrel2gb=${pixeldatasizeinbytesrel2gb}"
if [ ${pixeldatasizeinbytesrel2gb} -gt 0 ]
then
echo "Uncompressed or LZW compressed and when decompressed is greater than or equal to 2GB"
if [ "${firstifdbitspersample}" = "8" ]
then
echo "Uncompressed or LZW compressed 8 bit so requesting J2K Reversible compression"
transfersyntaxargs="1.2.840.10008.1.2.4.90"
# cannot guarantee compressed bitstream will fit in BOT so use EOT
offsettableargs="ADDEXTENDEDOFFSETTABLE DONOTADDBASICOFFSETTABLE"
elif [ "${firstifdsamplesperpixel}" = "1" -a "${firstifdbitspersample}" = "16" ]
then
echo "Uncompressed or LZW compressed single channel 16 bit so requesting J2K Reversible compression"
transfersyntaxargs="1.2.840.10008.1.2.4.90"
# cannot guarantee compressed bitstream will fit in BOT so use EOT
offsettableargs="ADDEXTENDEDOFFSETTABLE DONOTADDBASICOFFSETTABLE"
fi
else
echo "Uncompressed or LZW compressed and when decompressed is less than 2GB"
# do not set offsettableargs
fi
else
# can assume compressed
totalfilesizeinbytes=`ls -l "${infile}" | awk '{print $5}'`
echo "totalfilesizeinbytes=${totalfilesizeinbytes}"
totalfilesizeinbytesrel4gb=`echo "scale=0; ${totalfilesizeinbytes} / 4294967296" | bc -l`
echo "totalfilesizeinbytesrel4gb=${totalfilesizeinbytesrel4gb}"
if [ ${totalfilesizeinbytesrel4gb} -gt 0 ]
then
echo "Likely greater than 4GB so use EOT"
offsettableargs="ADDEXTENDEDOFFSETTABLE DONOTADDBASICOFFSETTABLE"
else
echo "Less than 4GB so use BOT"
offsettableargs="ADDBASICOFFSETTABLE DONOTADDEXTENDEDOFFSETTABLE"
fi
fi
echo "transfersyntaxargs=${transfersyntaxargs}"
echo "offsettableargs=${offsettableargs}"
#rm "${TMPJSONFILE}"; exit 1
rm -rf "${outdir}"
mkdir -p "${outdir}"
date
# ${PATHTOADDITIONAL}/jai_imageio.jar:${PATHTOADDITIONAL}/jai_imageio-1_1/lib/clibwrapper_jiio.jar not needed if installed in JRE
java -cp ${PIXELMEDDIR}/pixelmed.jar:${PATHTOADDITIONAL}/javax.json-1.0.4.jar:${PATHTOADDITIONAL}/opencsv-2.4.jar \
-Djava.awt.headless=true \
-XX:-UseGCOverheadLimit \
-Xmx8g \
${JAVATMPDIRARG} \
-Dorg.slf4j.simpleLogger.log.com.pixelmed.convert.TIFFToDicom=debug \
-Dorg.slf4j.simpleLogger.log.com.pixelmed.convert.AddTIFFOrOffsetTables=info \
com.pixelmed.convert.TIFFToDicom \
"${TMPJSONFILE}" \
"${infile}" \
"${outdir}/DCM" \
SM 1.2.840.10008.5.1.4.1.1.77.1.6 \