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Faster conversion for systems with slow IO
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#104
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@neurolabusc
neurolabusc committed Jun 13, 2017
1 parent 1f456d8 commit eb127c4
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4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -11,11 +11,13 @@ This software is open source. The bulk of the code is covered by the BSD license

## Versions

13-June-2017
- Read DICOM header in 1Mb segments rather than loading whole file : reduces ram usage and [faster for systems with slow io](https://github.com/rordenlab/dcm2niix/issues/104).

9-June-2017
-Report [TotalReadoutTime](https://github.com/rordenlab/dcm2niix/issues/98).
-Fix JPEG2000 support in [Superbuild](https://github.com/rordenlab/dcm2niix/issues/105).


28-May-2017
- Remove all derived images from [Philips DTI series](http://www.nitrc.org/forum/message.php?msg_id=21025).
- Provide some [Siemens EPI sequence details](https://github.com/rordenlab/dcm2niix/issues).
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73 changes: 45 additions & 28 deletions console/nii_dicom.cpp
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Expand Up @@ -2467,14 +2467,12 @@ int isDICOMfile(const char * fname) { //0=NotDICOM, 1=DICOM, 2=Maybe(not Part 10
} //isDICOMfile()

struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, struct TDTI4D *dti4D) {
//struct TDICOMdata readDICOMv(char * fname, bool isVerbose, int compressFlag) {
struct TDICOMdata d = clear_dicom_data();
strcpy(d.protocolName, ""); //erase dummy with empty
strcpy(d.protocolName, ""); //erase dummy with empty
strcpy(d.seriesDescription, ""); //erase dummy with empty
strcpy(d.sequenceName, ""); //erase dummy with empty
//do not read folders - code specific to GCC (LLVM/Clang seems to recognize a small file size)

struct stat s;
if( stat(fname,&s) == 0 ) {
if( !(s.st_mode & S_IFREG) ){
Expand All @@ -2501,31 +2499,40 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
printMessage( "File too small to be a DICOM image %s\n", fname);
return d;
}
//Since size of DICOM header is unknown, we will load it in 1mb segments
//This uses less RAM and makes is faster for computers with slow disk access
//Benefit is largest for 4D images.
//To disable caching and load entire file to RAM, compile with "-dmyLoadWholeFileToReadHeader"
//To implement the segments, we define these variables:
// fileLen = size of file in bytes
// MaxBufferSz = maximum size of buffer in bytes
// Buffer = array with n elements, where n is smaller of fileLen or MaxBufferSz
// lPos = position in Buffer (indexed from 0), 0..(n-1)
// lFileOffset = offset of Buffer in file: true file position is lOffset+lPos (initially 0)
#ifdef myLoadWholeFileToReadHeader
int MaxBufferSz = fileLen;
#else
int MaxBufferSz = 1000000; //ideally size of DICOM header, but this varies from 2D to 4D files
#endif
long lFileOffset = 0;
fseek(file, 0, SEEK_SET);
//Allocate memory
unsigned char *buffer=(unsigned char *)malloc(fileLen+1);
unsigned char *buffer=(unsigned char *)malloc(MaxBufferSz+1);
if (!buffer) {
printError( "Memory exhausted!");
fclose(file);
return d;
}
//Read file contents into buffer
size_t sz = fread(buffer, 1, fileLen, file);
fclose(file);
if (sz < fileLen) {
printError("Only loaded %zu of %ld bytes for %s\n", sz, fileLen, fname);
size_t sz = fread(buffer, 1, MaxBufferSz, file);
if (sz < MaxBufferSz) {
printError("Only loaded %zu of %ld bytes for %s\n", sz, MaxBufferSz, fname);
fclose(file);
return d;
}
//bool isPart10prefix = true; //assume 132 byte header http://nipy.bic.berkeley.edu/nightly/nibabel/doc/dicom/dicom_intro.html
//if ((buffer[128] != 'D') || (buffer[129] != 'I') || (buffer[130] != 'C') || (buffer[131] != 'M')) {
// if ((buffer[0] != 8) || (buffer[1] != 0) || (buffer[2] != 5) || (buffer[3] != 0)){
// free (buffer);
// return d;
// }
// isPart10prefix = false; //no 132 byte header, not a valid part 10 file http://fileformats.archiveteam.org/wiki/DICOM
// d.isExplicitVR = false;
// //printWarning("Not a valid part 10 DICOM (missing 'DICM' signature): %s\n", fname);
//}
#ifdef myLoadWholeFileToReadHeader
fclose(file);
#endif
//DEFINE DICOM TAGS
#define kUnused 0x0001+(0x0001 << 16 )
#define kStart 0x0002+(0x0000 << 16 )
Expand Down Expand Up @@ -2674,7 +2681,17 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
float patientPosition[4] = {NAN, NAN, NAN, NAN}; //used to compute slice direction for Philips 4D
float patientPositionEndPhilips[4] = {NAN, NAN, NAN, NAN};
float patientPositionStartPhilips[4] = {NAN, NAN, NAN, NAN};
while ((d.imageStart == 0) && ((lPos+8) < fileLen)) {
while ((d.imageStart == 0) && ((lPos+8+lFileOffset) < fileLen)) {
#ifndef myLoadWholeFileToReadHeader //read one segment at a time
if ((lPos + 128) > MaxBufferSz) { //avoid overreading the file
lFileOffset = lFileOffset + lPos;
if ((lFileOffset+MaxBufferSz) > fileLen)
MaxBufferSz = fileLen - lFileOffset;
fseek(file, lFileOffset, SEEK_SET);
size_t sz = fread(buffer, 1, MaxBufferSz, file);
lPos = 0;
}
#endif
if (d.isLittleEndian)
groupElement = buffer[lPos] | (buffer[lPos+1] << 8) | (buffer[lPos+2] << 16) | (buffer[lPos+3] << 24);
else
Expand All @@ -2695,8 +2712,6 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
vr[0] = 'N';
vr[1] = 'A';
if (groupElement == kUnnest2) sqDepth--;
//if (groupElement == kUnnest2) printMessage("SQend %d\n", sqDepth);

//if (groupElement == kUnnest) geiisBug = false; //don't exit if there is a proprietary thumbnail
lLength = 4;
} else if (d.isExplicitVR) {
Expand Down Expand Up @@ -2754,7 +2769,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
d.imageBytes = dcmInt(4,&buffer[lPos-4],d.isLittleEndian);
//printMessage("compressed data %d-> %ld\n",d.imageBytes, lPos);
if (d.imageBytes > 128) {
d.imageStart = (int)lPos;
d.imageStart = (int)lPos + lFileOffset;
}
}
if ((isIconImageSequence) && ((groupElement & 0x0028) == 0x0028 )) groupElement = kUnused; //ignore icon dimensions
Expand Down Expand Up @@ -3300,7 +3315,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
case kImageStart:
//if ((!geiisBug) && (!isIconImageSequence)) //do not exit for proprietary thumbnails
if ((d.compressionScheme == kCompressNone ) && (!isIconImageSequence)) //do not exit for proprietary thumbnails
d.imageStart = (int)lPos;
d.imageStart = (int)lPos + lFileOffset;
//geiisBug = false;
//http://www.dclunie.com/medical-image-faq/html/part6.html
//unlike raw data, Encapsulated data is stored as Fragments contained in Items that are the Value field of Pixel Data
Expand All @@ -3313,14 +3328,14 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
case kImageStartFloat:
d.isFloat = true;
if (!isIconImageSequence) //do not exit for proprietary thumbnails
d.imageStart = (int)lPos;
d.imageStart = (int)lPos + lFileOffset;
isIconImageSequence = false;
break;
case kImageStartDouble:
printWarning("Double-precision DICOM conversion untested: please provide samples to developer\n");
d.isFloat = true;
if (!isIconImageSequence) //do not exit for proprietary thumbnails
d.imageStart = (int)lPos;
d.imageStart = (int)lPos + lFileOffset;
isIconImageSequence = false;
break;

Expand All @@ -3339,10 +3354,10 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
|| (tagStr[pos] == '*') || (tagStr[pos] == '|') || (tagStr[pos] == '?'))
tagStr[pos] = 'x';
}
printMessage(" Tag\t%04x,%04x\tSize=%u\tOffset=%ld\t%s\n", groupElement & 65535,groupElement>>16, lLength, lPos, tagStr);
printMessage(" Tag\t%04x,%04x\tSize=%u\tOffset=%ld\t%s\n", groupElement & 65535,groupElement>>16, lLength, lFileOffset+lPos, tagStr);
//printMessage(" Tag\t%04x,%04x\tSize=%u\tOffset=%ld\tnest=%d\t%s\n", groupElement & 65535,groupElement>>16, lLength, lPos, nest, tagStr);
} else
printMessage(" Tag\t%04x,%04x\tSize=%u\tOffset=%ld\tnest=%d\n", groupElement & 65535,groupElement>>16, lLength, lPos, nest);
printMessage(" Tag\t%04x,%04x\tSize=%u\tOffset=%ld\tnest=%d\n", groupElement & 65535,groupElement>>16, lLength, lFileOffset+lPos, nest);
} //printMessage(" tag=%04x,%04x length=%u pos=%ld %c%c nest=%d\n", groupElement & 65535,groupElement>>16, lLength, lPos,vr[0], vr[1], nest);
lPos = lPos + (lLength);
//printMessage("%d\n",d.imageStart);
Expand Down Expand Up @@ -3451,6 +3466,10 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
d.CSA.numDti = 0;
}
//d.isValid = false; //debug only - will not create output!
#ifndef myLoadWholeFileToReadHeader
fclose(file);
#endif
//printMessage("buffer usage %d %d %d\n",d.imageStart, lPos+lFileOffset, MaxBufferSz);
return d;
} // readDICOM()

Expand All @@ -3459,5 +3478,3 @@ struct TDICOMdata readDICOM(char * fname) {
return readDICOMv(fname, false, 0, &unused);
} // readDICOM()



2 changes: 1 addition & 1 deletion console/nii_dicom.h
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Expand Up @@ -38,7 +38,7 @@ extern "C" {
#define kCCsuf " CompilerNA" //unknown compiler!
#endif

#define kDCMvers "v1.0.20170609" kDCMsuf kCCsuf
#define kDCMvers "v1.0.20170613" kDCMsuf kCCsuf

static const int kMaxDTI4D = 4096; //maximum number of DTI directions for 4D (Philips) images, also maximum number of 3D slices for Philips 3D and 4D images
#define kDICOMStr 64
Expand Down

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