Force gzip (#35)

src/core.c

@@ -141,7 +141,7 @@ int nii_otsu(int* H, int nBin, int mode, int *dark, int *mid, int *bright) {
 	return thresh;
 }
 
-int nifti_save(nifti_image *nim, const char *postfix) {
+int nifti_save(nifti_image *nim, const char *postfix, gzModes gzMode) {
 	char extnii[5] = ".nii"; /* modifiable, for possible uppercase */
 	char exthdr[5] = ".hdr";
 	char extimg[5] = ".img";
@@ -200,6 +200,10 @@ int nifti_save(nifti_image *nim, const char *postfix) {
 #ifdef HAVE_ZLIB // if compression is requested, make sure of suffix
 	if ((value == NULL) || strstr(value, gzKey))
 		isGz = 1; //NIFTI2_GZ, NIFTI2_PAIR_GZ, NIFTI_GZ, NIFTI_PAIR_GZ
+	if (gzMode == GZ_FALSE)
+		isGz = 0;
+	if (gzMode == GZ_TRUE)
+		isGz = 1;
 #endif
 	if ((value != NULL) && strstr(value, pairKey)) {
 		strcat(hname, exthdr);

src/core.h

@@ -12,6 +12,11 @@ extern "C" {
 //#include <immintrin.h>
 #include <limits.h>
 
+typedef enum {
+    GZ_ENVIRONMENT, // Use the environment settings
+    GZ_FALSE,       // Uncompressed output
+    GZ_TRUE         // Gzipped output
+} gzModes;
 
 //CORE32 and CORE64 handle Float32 and Float64 operations, CORE handles shared code 
 
@@ -119,7 +124,7 @@ typedef struct {                   /** x4 vector struct **/
     float v[4] ;
 } vec4 ;
 
-int nifti_save(nifti_image * nim, const char *postfix);
+int nifti_save(nifti_image * nim, const char *postfix, gzModes gzMode);
 nifti_image *nifti_image_read2( const char *hname , int read_data );
 int * make_kernel_file(nifti_image * nim, int * nkernel,  char * fin);
 mat44 xform(nifti_image * nim);

src/coreFLT.c

@@ -2476,7 +2476,7 @@ staticx int nifti_tensor_2(nifti_image *nim, int lower2upper) {
 	return 0;
 } // nifti_tensor_2()
 
-staticx int nifti_tensor_decomp(nifti_image *nim, int isUpperTriangle) {
+staticx int nifti_tensor_decomp(nifti_image *nim, int isUpperTriangle, gzModes gzMode) {
 // MD= (Dxx+Dyy+Dzz)/3
 //https://github.com/ANTsX/ANTs/wiki/Importing-diffusion-tensor-data-from-other-software
 // dtifit produces upper-triangular order: xx xy xz yy yz zz
@@ -2561,17 +2561,17 @@ staticx int nifti_tensor_decomp(nifti_image *nim, int isUpperTriangle) {
 	//save V1
 	outv = out32 + (nvox3D * 3);
 	nim->data = (void *)outv;
-	nifti_save(nim, "_V1");
+	nifti_save(nim, "_V1", gzMode);
 	//save V2
 	outv = out32 + (nvox3D * 6);
 	//xmemcpy(fa32, outv, 3*nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
-	nifti_save(nim, "_V2");
+	nifti_save(nim, "_V2", gzMode);
 	//save V3
 	outv = out32 + (nvox3D * 9);
 	//xmemcpy(fa32, outv, 3*nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
-	nifti_save(nim, "_V3");
+	nifti_save(nim, "_V3", gzMode);
 	//release 4D memory
 	//free(dat);
 	//save 3D images
@@ -2587,26 +2587,26 @@ staticx int nifti_tensor_decomp(nifti_image *nim, int isUpperTriangle) {
 	//xmemcpy(fa32, outv, nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
 	nim->cal_max = calmax(nim);
-	nifti_save(nim, "_L1");
+	nifti_save(nim, "_L1", gzMode);
 	//save L2
 	outv = out32 + (nvox3D * 1);
 	//xmemcpy(fa32, outv, nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
 	nim->cal_max = calmax(nim);
-	nifti_save(nim, "_L2");
+	nifti_save(nim, "_L2", gzMode);
 	//save L3
 	outv = out32 + (nvox3D * 2);
 	//xmemcpy(fa32, outv, nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
 	nim->cal_max = calmax(nim);
-	nifti_save(nim, "_L3");
+	nifti_save(nim, "_L3", gzMode);
 	//save MD
 	outv = out32 + (nvox3D * 13);
 	//xmemcpy(fa32, outv, nvox3D*sizeof(flt));
 	nim->data = (void *)outv;
 	nim->cal_min = calmin(nim);
 	nim->cal_max = calmax(nim);
-	nifti_save(nim, "_MD");
+	nifti_save(nim, "_MD", gzMode);
 	//single volume data
 	//void *dat = (void *)calloc(1, nvox3D * sizeof(flt));
 	void *dat = (void *)aligned_calloc(nvox3D * sizeof(flt));
@@ -2644,13 +2644,13 @@ staticx int nifti_tensor_decomp(nifti_image *nim, int isUpperTriangle) {
 		d = MAX(d, -1.0);
 		fa32[i] = d;
 	}
-	nifti_save(nim, "_MO");
+	nifti_save(nim, "_MO", gzMode);
 	//save FA
 	outv = out32 + (nvox3D * 12);
 	xmemcpy(fa32, outv, nvox3D * sizeof(flt));
 	nim->cal_min = 0;
 	nim->cal_max = 1;
-	nifti_save(nim, "_FA");
+	nifti_save(nim, "_FA", gzMode);
 	//keep FA in memory
 	nim->cal_max = 0;
 	_mm_free(out32);
@@ -4995,6 +4995,7 @@ staticx void nifti_compare(nifti_image *nim, char *fin, double thresh) {
 		exit(1);
 		#endif
 	}
+	gzModes gzMode = GZ_ENVIRONMENT;
 	int dtCalc = DT_FLOAT32; //data type for calculation
 	int dtOut = DT_FLOAT32; //data type for calculation
 	int ac = 1;
@@ -5022,7 +5023,7 @@ staticx void nifti_compare(nifti_image *nim, char *fin, double thresh) {
 		ac++;
 		if (nifti_set_filenames(nim, fout, 0, 1))
 			return 1;
-		nifti_save(nim, ""); //nifti_image_write( nim );
+		nifti_save(nim, "", gzMode); //nifti_image_write( nim );
 		nifti_image_free(nim);
 		return 0;
 	} //end pass through
@@ -5402,6 +5403,15 @@ staticx void nifti_compare(nifti_image *nim, char *fin, double thresh) {
 			ok = EXIT_FAILURE;
 			#endif
 		#endif
+		} else if (!strcmp(argv[ac], "-gz")) {
+			ac ++;
+			int mode = atoi(argv[ac]);
+			if (mode == 0)
+				gzMode = GZ_FALSE;
+			else if (mode == 1)
+				gzMode = GZ_TRUE;
+			else
+				gzMode = GZ_ENVIRONMENT;
 		} else if (!strcmp(argv[ac], "-h2c"))
 			ok = nifti_h2c(nim, false); 
 		else if (!strcmp(argv[ac], "-c2h"))
@@ -5546,16 +5556,16 @@ staticx void nifti_compare(nifti_image *nim, char *fin, double thresh) {
 		} else if (!strcmp(argv[ac], "-tensor_2upper")) {
 			ok = nifti_tensor_2(nim, 1);
 		} else if (!strcmp(argv[ac], "-tensor_decomp")) {
-			ok = nifti_tensor_decomp(nim, 1);
+			ok = nifti_tensor_decomp(nim, 1, gzMode);
 		} else if (!strcmp(argv[ac], "-tensor_decomp_lower")) {
-			ok = nifti_tensor_decomp(nim, 0);
+			ok = nifti_tensor_decomp(nim, 0, gzMode);
 		} else if (!strcmp(argv[ac], "-save")) {
 			ac++;
 			char *fout2 = argv[ac];
 			if (nifti_set_filenames(nim, fout2, 1, 1))
 				ok = 1;
 			else {
-				nifti_save(nim, ""); //nifti_image_write( nim );
+				nifti_save(nim, "", gzMode); //nifti_image_write( nim );
 				nifti_set_filenames(nim, fout, 1, 1);
 			}
 		} 
@@ -5691,7 +5701,7 @@ staticx void nifti_compare(nifti_image *nim, char *fin, double thresh) {
 	if (nifti_image_change_datatype(nim, dtOut, &ihdr) != 0)
 		return 1;
 	// if we get here, write the output dataset
-	nifti_save(nim, ""); //nifti_image_write( nim );
+	nifti_save(nim, "", gzMode); //nifti_image_write( nim );
 	// and clean up memory
 	nifti_image_free(nim);
 	if (kernel != NULL)

src/niimath.c

@@ -290,6 +290,7 @@ int show_help( void ) {
 	printf(" -edt                     : estimate Euler Distance Transform (distance field). Assumes isotropic input\n");
 	printf(" -close <thr> <dx1> <dx2> : morphological close that binarizes with `thr`, dilates with `dx1` and erodes with `dx2` (fills bubbles with `thr`)\n");
 	printf(" -floor                   : round voxels downwards to the nearest integer\n");
+	printf(" -gz <mode>               : NIfTI gzip mode (0=uncompressed, 1=compressed, else FSL environment; default -1)\n");
 	printf(" -h2c                     : convert CT scans from 'Hounsfield' to 'Cormack' units to emphasize soft tissue contrast\n");
 #ifdef NII2MESH
 	printf("\n");