JNIfTI support modular (cmake -DUSE_JNIFTI=OFF ..)

SuperBuild/SuperBuild.cmake

@@ -40,6 +40,7 @@ option(USE_TURBOJPEG "Use TurboJPEG to decode classic JPEG" OFF)
 option(USE_JASPER "Build with JPEG2000 support using Jasper" OFF)
 option(USE_OPENJPEG "Build with JPEG2000 support using OpenJPEG" OFF)
 option(USE_JPEGLS "Build with JPEG-LS support using CharLS" OFF)
+option(USE_JNIFTI "Build with JNIFTI support" ON)
 
 option(BATCH_VERSION "Build dcm2niibatch for multiple conversions" OFF)
 
@@ -139,6 +140,7 @@ ExternalProject_Add(console
         -DUSE_TURBOJPEG:BOOL=${USE_TURBOJPEG}
         -DUSE_JASPER:BOOL=${USE_JASPER}
         -DUSE_JPEGLS:BOOL=${USE_JPEGLS}
+        -DUSE_JNIFTI:BOOL=${USE_JNIFTI}
         -DZLIB_IMPLEMENTATION:STRING=${ZLIB_IMPLEMENTATION}
         -DZLIB_ROOT:PATH=${ZLIB_ROOT}
          # OpenJPEG

console/CMakeLists.txt

@@ -74,9 +74,14 @@ set(DCM2NIIX_SRCS
     nifti1_io_core.cpp
     nii_foreign.cpp
     nii_ortho.cpp
-    nii_dicom_batch.cpp
-    cJSON.c
-    base64.c)
+    nii_dicom_batch.cpp)
+
+
+option(USE_JNIfTI "Build with JNIfTI support" ON)
+if(USE_JNIFTI)
+    add_definitions(-DmyEnableJNIfTI)
+    set(DCM2NIIX_SRCS ${DCM2NIIX_SRCS} cJSON.cpp base64.cpp)
+endif()
 
 option(USE_JPEGLS "Build with JPEG-LS support using CharLS" OFF)
 if(USE_JPEGLS)

console/main_console.cpp

@@ -80,7 +80,11 @@ void showHelp(const char *argv[], struct TDCMopts opts) {
 	printf("   -ba : anonymize BIDS (y/n, default %c)\n", bool2Char(opts.isAnonymizeBIDS));
 	printf("  -c : comment stored in NIfTI aux_file (provide up to 24 characters e.g. '-c first_visit')\n");
 	printf("  -d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default %d)\n", opts.dirSearchDepth);
+#ifdef myEnableJNIfTI
 	printf("  -e : export as NRRD (y) or MGH (o) or JSON/JNIfTI (j) or BJNIfTI (b) instead of NIfTI (y/n/o/j/b, default n)\n");
+#else
+	printf("  -e : export as NRRD (y) or MGH (o) instead of NIfTI (y/n/o/j/b, default n)\n");
+#endif
 #ifdef mySegmentByAcq
 #define kQstr " %%q=sequence number,"
 #else
@@ -363,6 +367,12 @@ int main(int argc, const char *argv[]) {
 					opts.saveFormat = kSaveFormatJNII;
 				if ((argv[i][0] == 'b') || (argv[i][0] == 'B') || (argv[i][0] == '4'))
 					opts.saveFormat = kSaveFormatBNII;
+				#ifndef myEnableJNIfTI
+				if ((opts.saveFormat == kSaveFormatJNII) || (opts.saveFormat == kSaveFormatBNII)) {
+					printf("Recompile for JNIfTI support.\n");
+					return EXIT_SUCCESS;
+				}
+				#endif
 			} else if ((argv[i][1] == 'g') && ((i + 1) < argc)) {
 				i++;
 				if (invalidParam(i, argv))

console/makefile

@@ -13,7 +13,13 @@ CFLAGS=-s -O3
 #run "JPEGLS=1 make" for JPEGLS build
 JFLAGS=
 ifeq "$(JPEGLS)" "1"
-		JFLAGS=-std=c++14 -DmyEnableJPEGLS  charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp  charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp
+	JFLAGS=-std=c++14 -DmyEnableJPEGLS  charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp  charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp
+endif
+
+#run "JNIfTI=0 make" to disable JNIFTI build
+JSFLAGS=
+ifneq "$(JNIfTI)" "0"
+	JSFLAGS=-DmyEnableJNIfTI base64.cpp cJSON.cpp
 endif
 
 ifneq ($(OS),Windows_NT)
@@ -31,4 +37,4 @@ ifneq ($(OS),Windows_NT)
 	endif
 endif
 all:
-	g++ $(CFLAGS) -I. $(JFLAGS) 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 base64.c cJSON.c -o dcm2niix -DmyDisableOpenJPEG
+	g++ $(CFLAGS) -I. $(JSFLAGS) $(JFLAGS) 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

console/nii_dicom_batch.cpp

@@ -38,8 +38,10 @@
 #endif
 #include "nii_dicom.h"
 #include "nii_ortho.h"
-#include "base64.h"
-#include "cJSON.h"
+#ifdef myEnableJNIfTI
+ #include "base64.h"
+ #include "cJSON.h"
+#endif
 #include <ctype.h> //toupper
 #include <float.h>
 #include <math.h>
@@ -3298,10 +3300,12 @@ void nii_createDummyFilename(char *niiFilename, struct TDCMopts opts) {
 			strcat(niiFilename, ".nhdr'");
 		else
 			strcat(niiFilename, ".nrrd'");
+	#ifdef myEnableJNIfTI
 	} else if (opts.saveFormat == kSaveFormatJNII) {
 		strcat(niiFilename, ".jnii'");
 	} else if (opts.saveFormat == kSaveFormatBNII) {
 		strcat(niiFilename, ".bnii'");
+	#endif
 	} else {
 		if (opts.isGz)
 			strcat(niiFilename, ".nii.gz'");
@@ -4098,6 +4102,7 @@ int nii_saveNRRD(char *niiFilename, struct nifti_1_header hdr, unsigned char *im
 
 enum TZipMethod {zmZlib, zmGzip, zmBase64};
 
+#ifdef myEnableJNIfTI
 #ifdef Z_DEFLATED
 
 int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize, unsigned char **outputbuf, const int zipid, int *ret, const int iscompress){
@@ -4174,7 +4179,6 @@ int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize
 				count++;
 			}
 			*outputsize=zs.total_out;
-
 			if(*ret!=Z_STREAM_END && *ret!=Z_OK)
 				return -3;
 			inflateEnd(&zs);
@@ -4185,7 +4189,7 @@ int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize
 	return 0;
 }
 
-#endif
+#endif //Z_DEFLATED 
 
 int jnifti_lookup(int *keyid, int keylen, int val){
 	for(int i=0;i<keylen;i++){
@@ -4658,12 +4662,15 @@ int nii_savejnii(char *niiFilename, struct nifti_1_header hdr, unsigned char *im
 		cJSON_Delete(root);
 	return EXIT_SUCCESS;
 } // nii_savejnii()
+#endif //#ifdef myEnableJNIfTI
 
 int nii_saveForeign(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) {
 	if (opts.saveFormat == kSaveFormatMGH)
 		return nii_saveMGH(niiFilename, hdr, im, opts, d, dti4D, numDTI);
+	#ifdef myEnableJNIfTI
 	else if (opts.saveFormat == kSaveFormatJNII || opts.saveFormat == kSaveFormatBNII)
 		return nii_savejnii(niiFilename, hdr, im, opts, d, dti4D, numDTI);
+	#endif
 	return nii_saveNRRD(niiFilename, hdr, im, opts, d, dti4D, numDTI);
 }// nii_saveForeign()