Merge pull request #902 from rordenlab/development

Development

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
 
@@ -55,6 +58,9 @@ 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
 

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/

js/index.html

@@ -114,7 +114,7 @@ <h1>dcm2niix WASM Demo</h1>
         const t0 = performance.now();
 
         const inputFileList = selectedFiles
-        const resultFileList = await dcm2niix.input(inputFileList).run()
+        const resultFileList = await dcm2niix.input(inputFileList).z('y').run()
         console.log(resultFileList);
 
         const t1 = performance.now();

js/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@niivue/dcm2niix",
-  "version": "0.1.1-dev.2",
+  "version": "1.0.0",
   "main": "dist/index.js",
   "module": "dist/index.js",
   "exports": {