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mharms suggestions for #130
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@neurolabusc
neurolabusc committed Sep 20, 2017
1 parent 2e42d38 commit f0220bf
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Showing 5 changed files with 92 additions and 81 deletions.
14 changes: 9 additions & 5 deletions console/jpg_0XC3.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -125,17 +125,21 @@ unsigned char * decode_JPEG_SOF_0XC3 (const char *fn, int skipBytes, bool verbo
unsigned char *lRawRA = (unsigned char*) malloc(lRawSz);
size_t lSz = fread(lRawRA, 1, lRawSz, reader);
fclose(reader);
if ((lSz < lRawSz) || (lRawRA[0] != 0xFF) || (lRawRA[1] != 0xD8) || (lRawRA[2] != 0xFF)) {
if ((lSz < (size_t)lRawSz) || (lRawRA[0] != 0xFF) || (lRawRA[1] != 0xD8) || (lRawRA[2] != 0xFF)) {
abortGoto("JPEG signature 0xFFD8FF not found at offset %d of %s\n", skipBytes, fn);//signature failure http://en.wikipedia.org/wiki/List_of_file_signatures
}
if (verbose)
printMessage("JPEG signature 0xFFD8FF found at offset %d of %s\n", skipBytes, fn);
//next: read header
long lRawPos = 2; //Skip initial 0xFFD8, begin with third byte
//long lRawPos = 0; //Skip initial 0xFFD8, begin with third byte
unsigned char btS1, btS2, SOSss, SOSse, SOSahal, SOSpttrans, btMarkerType, SOSns = 0x00; //tag
uint8_t SOFnf, SOFprecision;
uint16_t SOFydim, SOFxdim; //, lRestartSegmentSz;
unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; //tag
unsigned char SOSpttrans = 0;
unsigned char SOSss = 0;
uint8_t SOFnf = 0;
uint8_t SOFprecision = 0;
uint16_t SOFydim = 0;
uint16_t SOFxdim = 0;
// long SOSarrayPos; //SOFarrayPos
int lnHufTables = 0;
const int kmaxFrames = 4;
Expand Down Expand Up @@ -186,7 +190,7 @@ unsigned char * decode_JPEG_SOF_0XC3 (const char *fn, int skipBytes, bool verbo
DHTnLi = DHTnLi + l[lFrameCount].DHTliRA[lInc];
if (l[lFrameCount].DHTliRA[lInc] != 0) l[lFrameCount].MaxHufSi = lInc;
if (verbose) printMessage("DHT has %d combinations with %d bits\n", l[lFrameCount].DHTliRA[lInc], lInc);

}
if (DHTnLi > 17) {
abortGoto("Huffman table corrupted.\n");
Expand Down
6 changes: 3 additions & 3 deletions console/nifti1_io_core.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,19 +86,19 @@ int isSameFloat (float a, float b) {

ivec3 setiVec3(int x, int y, int z)
{
ivec3 v = {x, y, z};
ivec3 v = {{x, y, z}};
return v;
}

vec3 setVec3(float x, float y, float z)
{
vec3 v = {x, y, z};
vec3 v = {{x, y, z}};
return v;
}

vec4 setVec4(float x, float y, float z)
{
vec4 v= {x, y, z, 1};
vec4 v= {{x, y, z, 1}};
return v;
}

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30 changes: 14 additions & 16 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2085,8 +2085,7 @@ unsigned char * nii_XYTZ_XYZT(unsigned char* bImg, struct nifti_1_header *hdr, i
//memcpy(&tempImg[0], &bImg[0], imgSz);
uint64_t origPos = 0;
uint64_t Pos = 0; //

for (int t = 0; t < typeRepeats; t++) { //for each volume
for (int t = 0; t < (int)typeRepeats; t++) { //for each volume
for (int s = 0; s < seqRepeats; s++) {
origPos = (t*typeBytes) +s*sliceBytes;
for (int z = 0; z < hdr->dim[3]; z++) { //for each slice
Expand Down Expand Up @@ -2266,7 +2265,7 @@ TJPEG * decode_JPEG_SOF_0XC3_stack (const char *fn, int skipBytes, bool isVerbo
unsigned char *lRawRA = (unsigned char*) malloc(lRawSz);
size_t lSz = fread(lRawRA, 1, lRawSz, reader);
fclose(reader);
if (lSz < lRawSz) {
if (lSz < (size_t)lRawSz) {
printError("Unable to read %s\n", fn);
abortGoto(); //read failure
}
Expand Down Expand Up @@ -2471,7 +2470,7 @@ unsigned char * nii_loadImgRLE(char* imgname, struct nifti_1_header hdr, struct
}
fseek(file, 0, SEEK_END);
long fileLen=ftell(file);
if (fileLen < (dcm.imageBytes+dcm.imageStart)) {
if ((fileLen < 1) || (dcm.imageBytes < 1) || (fileLen < (dcm.imageBytes+dcm.imageStart))) {
printMessage("File not large enough to store image data: %s\n", imgname);
fclose(file);
return NULL;
Expand All @@ -2481,7 +2480,7 @@ unsigned char * nii_loadImgRLE(char* imgname, struct nifti_1_header hdr, struct
unsigned char *cImg = (unsigned char *)malloc(dcm.imageBytes); //compressed input
size_t sz = fread(cImg, 1, dcm.imageBytes, file);
fclose(file);
if (sz < dcm.imageBytes) {
if (sz < (size_t)dcm.imageBytes) {
printError("Only loaded %zu of %d bytes for %s\n", sz, dcm.imageBytes, imgname);
free(cImg);
return NULL;
Expand All @@ -2490,17 +2489,17 @@ unsigned char * nii_loadImgRLE(char* imgname, struct nifti_1_header hdr, struct
bool swap = (dcm.isLittleEndian != littleEndianPlatform());
int bytesPerSample = dcm.samplesPerPixel * (dcm.bitsAllocated / 8);
uint32_t bytesPerSampleRLE = rleInt(0, cImg, swap);
if (bytesPerSampleRLE != (bytesPerSample)) {
if ((bytesPerSample < 0) || (bytesPerSampleRLE != (uint32_t)bytesPerSample)) {
printError("RLE header corrupted %d != %d\n", bytesPerSampleRLE, bytesPerSample);
free(cImg);
return NULL;
}
unsigned char *bImg = (unsigned char *)malloc(imgsz); //binary output
for (int i = 0; i < imgsz; i++)
for (size_t i = 0; i < imgsz; i++)
bImg[i] = 0;
for (int i = 0; i < bytesPerSample; i++) {
uint32_t offset = rleInt(i+1, cImg, swap);
if (offset > dcm.imageBytes) {
if ((dcm.imageBytes < 0) || (offset > (uint32_t)dcm.imageBytes)) {
printError("RLE header error\n");
free(cImg);
free(bImg);
Expand Down Expand Up @@ -2685,7 +2684,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
#else
size_t MaxBufferSz = 1000000; //ideally size of DICOM header, but this varies from 2D to 4D files
#endif
if (MaxBufferSz > fileLen)
if (MaxBufferSz > (size_t)fileLen)
MaxBufferSz = fileLen;
//printf("%d -> %d\n", MaxBufferSz, fileLen);
long lFileOffset = 0;
Expand Down Expand Up @@ -2831,9 +2830,9 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
#define kImageStart 0x7FE0+(0x0010 << 16 )
#define kImageStartFloat 0x7FE0+(0x0008 << 16 )
#define kImageStartDouble 0x7FE0+(0x0009 << 16 )
#define kNest 0xFFFE +(0xE000 << 16 ) //Item follows SQ
#define kUnnest 0xFFFE +(0xE00D << 16 ) //ItemDelimitationItem [length defined] http://www.dabsoft.ch/dicom/5/7.5/
#define kUnnest2 0xFFFE +(0xE0DD << 16 )//SequenceDelimitationItem [length undefined]
uint32_t kNest = 0xFFFE +(0xE000 << 16 ); //#define kNest 0xFFFE +(0xE000 << 16 ) //Item follows SQ
uint32_t kUnnest = 0xFFFE +(0xE00D << 16 ); //#define kUnnest 0xFFFE +(0xE00D << 16 ) //ItemDelimitationItem [length defined] http://www.dabsoft.ch/dicom/5/7.5/
uint32_t kUnnest2 = 0xFFFE +(0xE0DD << 16 ); //#define kUnnest2 0xFFFE +(0xE0DD << 16 )//SequenceDelimitationItem [length undefined]
int nest = 0;
double zSpacing = -1.0l; //includes slice thickness plus gap
int locationsInAcquisitionGE = 0;
Expand Down Expand Up @@ -2871,10 +2870,9 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
float patientPositionStartPhilips[4] = {NAN, NAN, NAN, NAN};
while ((d.imageStart == 0) && ((lPos+8+lFileOffset) < fileLen)) {
#ifndef myLoadWholeFileToReadHeader //read one segment at a time
if ((lPos + 128) > MaxBufferSz) { //avoid overreading the file
if ((size_t)(lPos + 128) > MaxBufferSz) { //avoid overreading the file
lFileOffset = lFileOffset + lPos;
if ((lFileOffset+MaxBufferSz) > fileLen)
MaxBufferSz = fileLen - lFileOffset;
if ((lFileOffset+MaxBufferSz) > (size_t)fileLen) MaxBufferSz = fileLen - lFileOffset;
fseek(file, lFileOffset, SEEK_SET);
size_t sz = fread(buffer, 1, MaxBufferSz, file);
if (sz < MaxBufferSz) {
Expand Down Expand Up @@ -3596,7 +3594,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
tagStr[0] = 'X'; //avoid compiler warning: orientStr filled by dcmStr
dcmStr (lLength, &buffer[lPos], tagStr);
if (strlen(tagStr) > 1) {
for (int pos = 0; pos<strlen(tagStr); pos ++)
for (size_t pos = 0; pos<strlen(tagStr); pos ++)
if ((tagStr[pos] == '<') || (tagStr[pos] == '>') || (tagStr[pos] == ':')
|| (tagStr[pos] == '"') || (tagStr[pos] == '\\') || (tagStr[pos] == '/')
|| (tagStr[pos] == '^') || (tagStr[pos] < 33)
Expand Down
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