Fix for neurolabusc/dcm_qa#5

Update OpenJPEG seek to work with modern versions of OpenJPEG, see uclouvain/openjpeg#962

COMPILE.md

@@ -64,14 +64,19 @@ You should then be able to run then run:
 g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -lopenjp2
 ```
 
-But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these two options:
+But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these options:
 
 ```
+#for MacOS
 g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/include/openjpeg-2.1 /usr/local/lib/libopenjp2.a
 ```
-
 ```
-g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/lib /usr/local/lib/libopenjp2.a
+#For older Linux
+g++ -O3 -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/lib /usr/local/lib/libopenjp2.a
+```
+```
+#For modern Linux
+g++ -O3 -s -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -lpthread -o dcm2niix -I/usr/local/include/openjpeg-2.2 ~/openjpeg-master/build/bin/libopenjp2.a
 ```
 
  If you want to build this with JPEG2000 decompression support using Jasper: You will need to have the Jasper (http://www.ece.uvic.ca/~frodo/jasper/) and libjpeg (http://www.ijg.org) libraries installed which for Linux users may be as easy as running 'sudo apt-get install libjasper-dev' (otherwise, see http://www.ece.uvic.ca/~frodo/jasper/#doc). You can then run:

console/nii_dicom.cpp

@@ -169,15 +169,26 @@ static OPJ_SIZE_T opj_skip_from_buffer(OPJ_SIZE_T p_nb_bytes, BufInfo * p_file)
     return (OPJ_SIZE_T)-1;
 } //opj_skip_from_buffer()
 
+//fix for https://github.com/neurolabusc/dcm_qa/issues/5
 static OPJ_BOOL opj_seek_from_buffer(OPJ_SIZE_T p_nb_bytes, BufInfo * p_file) {
-    if(p_file->cur + p_nb_bytes < p_file->buf + p_file->len ) {
-        p_file->cur += p_nb_bytes;
+    //printf("opj_seek_from_buffer %d + %d -> %d + %d\n", p_file->cur , p_nb_bytes, p_file->buf, p_file->len);
+    if ((p_file->buf + p_nb_bytes < p_file->buf + p_file->len ) && (p_nb_bytes >= 0)){
+        p_file->cur = p_file->buf + p_nb_bytes;
         return OPJ_TRUE;
     }
     p_file->cur = p_file->buf + p_file->len;
     return OPJ_FALSE;
 } //opj_seek_from_buffer()
 
+/*static OPJ_BOOL opj_seek_from_buffer(OPJ_SIZE_T p_nb_bytes, BufInfo * p_file) {
+    if((p_file->cur + p_nb_bytes) < (p_file->buf + p_file->len) ) {
+        p_file->cur += p_nb_bytes;
+        return OPJ_TRUE;
+    }
+    p_file->cur = p_file->buf + p_file->len;
+    return OPJ_FALSE;
+} //opj_seek_from_buffer()*/
+
 opj_stream_t* opj_stream_create_buffer_stream(BufInfo* p_file, OPJ_UINT32 p_size, OPJ_BOOL p_is_read_stream) {
     opj_stream_t* l_stream;
     if(! p_file) return NULL;
@@ -214,13 +225,6 @@ unsigned char * nii_loadImgCoreOpenJPEG(char* imgname, struct nifti_1_header hdr
     //DICOM JPEG2k is SUPPOSED to start with codestream, but some vendors include a header
     if (data[0] == 0xFF && data[1] == 0x4F && data[2] == 0xFF && data[3] == 0x51) format = OPJ_CODEC_J2K;
     opj_set_default_decoder_parameters(&params);
-    #if OPJ_VERSION_MAJOR == 2
-     #if OPJ_VERSION_MINOR >= 1
-      #if OPJ_VERSION_BUILD > 0
-        #pragma message "\n\nYour OpenJPEG library version > 2.1.0, please make sure it's custom compiled with: -DOPJ_DISABLE_TPSOT_FIX=ON.\n"
-      #endif
-     #endif
-    #endif
     BufInfo dx;
     dx.buf = data;
     dx.cur = data;
@@ -518,7 +522,6 @@ mat44 set_nii_header_x(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1
         double nRowCol = ceil(sqrt((double) d.CSA.mosaicSlices));
         double lFactorX = (d.xyzDim[1] -(d.xyzDim[1]/nRowCol)   )/2.0;
         double lFactorY = (d.xyzDim[2] -(d.xyzDim[2]/nRowCol)   )/2.0;
-        //printf("%g %g\n", lFactorX, lFactorY);
         Q44.m[0][3] =(float)((Q44.m[0][0]*lFactorX)+(Q44.m[0][1]*lFactorY)+Q44.m[0][3]);
 		Q44.m[1][3] = (float)((Q44.m[1][0] * lFactorX) + (Q44.m[1][1] * lFactorY) + Q44.m[1][3]);
 		Q44.m[2][3] = (float)((Q44.m[2][0] * lFactorX) + (Q44.m[2][1] * lFactorY) + Q44.m[2][3]);
@@ -2256,7 +2259,7 @@ unsigned char * nii_loadImgJPEGC3(char* imgname, struct nifti_1_header hdr, stru
     // https://github.com/chafey/cornerstoneWADOImageLoader
     //I have never seen these segmented images in the wild, so we will simply warn the user if we encounter such a file
     //int Sz = JPEG_SOF_0XC3_sz (imgname, (dcm.imageStart - 4), dcm.isLittleEndian);
-    //printf("Sz %d %d\n", Sz, dcm.imageBytes );
+    //printMessage("Sz %d %d\n", Sz, dcm.imageBytes );
     //This behavior is legal but appears extremely rare
     //ftp://medical.nema.org/medical/dicom/final/cp900_ft.pdf
     if (65536 == dcm.imageBytes)
@@ -3136,7 +3139,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
                 break;
             /*case kStackSliceNumber: { //https://github.com/Kevin-Mattheus-Moerman/GIBBON/blob/master/dicomDict/PMS-R32-dict.txt
             	int stackSliceNumber = dcmInt(lLength,&buffer[lPos],d.isLittleEndian);
-            	printf("%d\n",stackSliceNumber);
+            	printMessage("StackSliceNumber %d\n",stackSliceNumber);
             	break;
 			}*/
             case 	kNumberOfDynamicScans: