Over zealous XA enhanced DICOM warnings (#949)

Author: neurolabusc

console/makefile

@@ -26,9 +26,30 @@ endif
 
 #run "make" for default build
 #run "JPEGLS=1 make" for JPEGLS build
-JFLAGS=
-ifeq "$(JPEGLS)" "1"
-	JFLAGS=-std=c++14 -DmyEnableJPEGLS  charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp  charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp
+#run "JPEGLS=2 make" for JPEGLS build with system CharLS
+# JPEGLS=0 : disable JPEG-LS
+# JPEGLS=1 : use local ./charls source files
+# JPEGLS=2 : use system-installed CharLS via pkg-config
+
+ifeq ($(JPEGLS),1)
+	CFLAGS += -DmyEnableJPEGLS
+	CHARLS_SRCS = charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp \
+								charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp
+	CFILES := $(CHARLS_SRCS) $(CFILES)
+endif
+
+ifeq ($(JPEGLS),2)
+	CFLAGS += -DmyEnableJPEGLS
+	CHARLS_CFLAGS := $(shell pkg-config --cflags charls 2>/dev/null)
+	CHARLS_LIBS := $(shell pkg-config --libs charls 2>/dev/null)
+	ifeq ($(CHARLS_CFLAGS),)
+		CHARLS_CFLAGS := -I/usr/include -I/opt/homebrew/include
+	endif
+	ifeq ($(CHARLS_LIBS),)
+		CHARLS_LIBS := -lcharls -L/usr/lib -L/opt/homebrew/lib
+	endif
+	CFLAGS += $(CHARLS_CFLAGS)
+	CFILES += $(CHARLS_LIBS)
 endif
 
 #run "JNIfTI=0 make" to disable JNIFTI build

console/nii_dicom.cpp

@@ -5313,7 +5313,9 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 			lPos = lPos + 4;
 			// https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_8.2.html
 			// detect and skip  Basic Offset Table
-			bool  isBasicOffsetTable = (d.imageBytes < 1) && ((lLength == 4 * numberOfFrames) || (lLength <= 0));
+			bool isBasicOffsetTable = (d.imageBytes < 1) && ((lLength == 4 * numberOfFrames) || (lLength <= 0));
+			if ((numberOfFrames < 2) && (lLength == 4))
+				isBasicOffsetTable = true;
 			if (lLength == 0xFFFFFFFF) {
 				// printf("Fragment has undefined length\n");
 				// to do: see pixelmed microscopy https://www.aliza-dicom-viewer.com/download/datasets

console/nii_dicom_batch.cpp

@@ -6881,8 +6881,9 @@ void sliceTimingXA(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct
 	if (hdr->dim[3] > kMaxEPI3D) {
 		printWarning("Unable to set Siemens XA sliceTiming due to excessive slices per volume (%d).\n", hdr->dim[3]);
 		return;
-	} else {
-		printWarning("4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate.\n");
+	} else if (nConvert > hdr->dim[4]) {
+		// XA enhanced DICOM saves 1 file per 3D volume, classic DICOM saves multiple volumes
+		printWarning("4D Siemens XA images should be exported as enhanced not classic DICOM. Slice times and other properties may be inaccurate %d.\n");
 	}
 	if ((nConvert == (hdr->dim[3] * hdr->dim[4])) && (hdr->dim[3] < (kMaxEPI3D - 1)) && (hdr->dim[3] > 1)) {
 		// issue875 use 2nd volume