Support HTJ2K transfer syntax (#897)

console/makefile

@@ -1,8 +1,11 @@
 # Regular use
 CFLAGS=-s -O3
 
-# Universal files used for everything
-UFILES=main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG
+# Common files used for everything
+CFILES=main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix
+
+# Universal files used for almost everything
+UFILES=$(CFILES) -DmyDisableOpenJPEG
 # Debugging
 #CFLAGS=-g
 
@@ -55,10 +58,13 @@ sanitize:
 debug:
 	g++ -O0 $(LFLAGS) $(UFILES)
 
+jp2:
+	g++ -O0 $(LFLAGS) $(CFILES) -I/opt/homebrew/Cellar/openjpeg/2.5.3/include/openjpeg-2.5/ -L/opt/homebrew/Cellar/openjpeg/2.5.3/lib/ -lopenjp2
+
 noroi:
 	g++ $(CFLAGS) -I. $(JSFLAGS) $(JFLAGS) $(LFLAGS) $(UFILES) -DmyNoRois
 
 wasm:
-	emcc -O3 $(UFILES) -lz -s USE_ZLIB -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["callMain", "ccall", "cwrap", "FS", "FS_createDataFile", "FS_readFile", "FS_unlink", "allocateUTF8", "getValue", "stringToUTF8", "setValue"]' -s STACK_OVERFLOW_CHECK=2 -s STACK_SIZE=16MB -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORT_ES6=1 -s MODULARIZE=1 -s EXPORTED_FUNCTIONS='["_main", "_malloc", "_free"]' -s FORCE_FILESYSTEM=1 -s INVOKE_RUN=0 -o ../js/src/dcm2niix.js
+	emcc -O3 $(UFILES) -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["callMain", "ccall", "cwrap", "FS", "FS_createDataFile", "FS_readFile", "FS_unlink", "allocateUTF8", "getValue", "stringToUTF8", "setValue"]' -s STACK_OVERFLOW_CHECK=2 -s STACK_SIZE=16MB -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORT_ES6=1 -s MODULARIZE=1 -s EXPORTED_FUNCTIONS='["_main", "_malloc", "_free"]' -s FORCE_FILESYSTEM=1 -s INVOKE_RUN=0 -o ../js/src/dcm2niix.js
 	# STACK_SIZE=16MB is the minimum value found to work with the current codebase when targeting WASM
 

console/nii_dicom.cpp

@@ -5403,6 +5403,10 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 			} else if ((compressFlag != kCompressNone) && (strcmp(transferSyntax, "1.2.840.10008.1.2.4.90") == 0)) {
 				d.compressionScheme = kCompressYes;
 				// printMessage("JPEG2000 Lossless support is new: please validate conversion\n");
+			} else if ((compressFlag != kCompressNone) && (strcmp(transferSyntax, "1.2.840.10008.1.2.4.201") == 0)) {
+				d.compressionScheme = kCompressYes; //High-Throughput JPEG 2000 issue 897
+			} else if ((compressFlag != kCompressNone) && (strcmp(transferSyntax, "1.2.840.10008.1.2.4.203") == 0)) {
+				d.compressionScheme = kCompressYes; //High-Throughput JPEG 2000 issue 897
 			} else if ((strcmp(transferSyntax, "1.2.840.10008.1.2.1.99") == 0)) {
 				// n.b. Deflate compression applied applies to the encoding of the **entire** DICOM Data Set, not just image data
 				//  see https://www.medicalconnections.co.uk/kb/Transfer-Syntax/

console/nii_dicom.h

@@ -50,7 +50,7 @@ extern "C" {
 #define kCPUsuf " " // unknown CPU
 #endif
 
-#define kDCMdate "v1.0.20241208"
+#define kDCMdate "v1.0.20241211"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf
 
 static const int kMaxEPI3D = 1024; // maximum number of EPI images in Siemens Mosaic