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nii_dicom.cpp
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nii_dicom.cpp
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//#define MY_DEBUG
#if defined(_WIN64) || defined(_WIN32)
#define NOMINMAX
#include <windows.h> //write to registry
#endif
#ifdef _MSC_VER
#include <direct.h>
#define getcwd _getcwd
#define chdir _chrdir
#include "io.h"
#include <math.h>
//#define snprintf _snprintf
//#define vsnprintf _vsnprintf
#define strcasecmp _stricmp
#define strncasecmp _strnicmp
#ifdef _WIN32
#pragma comment(lib, "advapi32")
#endif
#else
#include <unistd.h>
#endif
//#include <time.h> //clock()
#ifndef USING_R
#include "nifti1.h"
#endif
#include "jpg_0XC3.h"
#include "nifti1_io_core.h"
#include "nii_dicom.h"
#include "print.h"
#include <ctype.h> //toupper
#include <float.h>
#include <math.h>
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h> // discriminate files from folders
#include <sys/types.h>
#ifndef USING_DCM2NIIXFSWRAPPER
#include <algorithm>
#endif
#ifdef USING_R
#undef isnan
#define isnan ISNAN
#endif
#ifndef myDisableClassicJPEG
#ifdef myTurboJPEG
#include <turbojpeg.h>
#else
#include "ujpeg.h"
#endif
#endif
#ifdef myEnableJasper
#include <jasper/jasper.h>
#endif
#ifndef myDisableOpenJPEG
#include "openjpeg.h"
#ifdef myEnableJasper
ERROR : YOU CAN NOT COMPILE WITH myEnableJasper AND NOT myDisableOpenJPEG OPTIONS SET SIMULTANEOUSLY
#endif
unsigned char * imagetoimg(opj_image_t *image) {
int numcmpts = image->numcomps;
int sgnd = image->comps[0].sgnd;
int width = image->comps[0].w;
int height = image->comps[0].h;
int bpp = (image->comps[0].prec + 7) >> 3; //e.g. 12 bits requires 2 bytes
int imgbytes = bpp * width * height * numcmpts;
bool isOK = true;
if (numcmpts > 1) {
for (int comp = 1; comp < numcmpts; comp++) { //check RGB data
if (image->comps[0].w != image->comps[comp].w)
isOK = false;
if (image->comps[0].h != image->comps[comp].h)
isOK = false;
if (image->comps[0].dx != image->comps[comp].dx)
isOK = false;
if (image->comps[0].dy != image->comps[comp].dy)
isOK = false;
if (image->comps[0].prec != image->comps[comp].prec)
isOK = false;
if (image->comps[0].sgnd != image->comps[comp].sgnd)
isOK = false;
}
if (numcmpts != 3)
isOK = false; //we only handle Gray and RedGreenBlue, not GrayAlpha or RedGreenBlueAlpha
if (image->comps[0].prec != 8)
isOK = false; //only 8-bit for RGB data
}
if ((image->comps[0].prec < 1) || (image->comps[0].prec > 16))
isOK = false; //currently we only handle 1 and 2 byte data
if (!isOK) {
printMessage("jpeg decode failure w*h %d*%d bpp %d sgnd %d components %d OpenJPEG=%s\n", width, height, bpp, sgnd, numcmpts, opj_version());
return NULL;
}
#ifdef MY_DEBUG
printMessage("w*h %d*%d bpp %d sgnd %d components %d OpenJPEG=%s\n", width, height, bpp, sgnd, numcmpts, opj_version());
#endif
//extract the data
if ((bpp < 1) || (bpp > 2) || (width < 1) || (height < 1) || (imgbytes < 1)) {
printError("Catastrophic decompression error\n");
return NULL;
}
unsigned char *img = (unsigned char *)malloc(imgbytes);
uint16_t *img16ui = (uint16_t *)img; //unsigned 16-bit
int16_t *img16i = (int16_t *)img; //signed 16-bit
if (sgnd)
bpp = -bpp;
if (bpp == -1) {
free(img);
printError("Signed 8-bit DICOM?\n");
return NULL;
}
//n.b. Analyze rgb-24 are PLANAR e.g. RRR..RGGG..GBBB..B not RGBRGBRGB...RGB
int pix = 0; //output pixel
for (int cmptno = 0; cmptno < numcmpts; ++cmptno) {
int cpix = 0; //component pixel
int *v = image->comps[cmptno].data;
for (int y = 0; y < height; ++y) {
for (int x = 0; x < width; ++x) {
switch (bpp) {
case 1:
img[pix] = (unsigned char)v[cpix];
break;
case 2:
img16ui[pix] = (uint16_t)v[cpix];
break;
case -2:
img16i[pix] = (int16_t)v[cpix];
break;
}
pix++;
cpix++;
} //for x
} //for y
} //for each component
return img;
} // imagetoimg()
typedef struct bufinfo {
unsigned char *buf;
unsigned char *cur;
size_t len;
} BufInfo;
static void my_stream_free(void *p_user_data) { //do nothing
//BufInfo d = (BufInfo) p_user_data;
//free(d.buf);
} // my_stream_free()
static OPJ_UINT32 opj_read_from_buffer(void *p_buffer, OPJ_UINT32 p_nb_bytes, BufInfo *p_file) {
OPJ_UINT32 l_nb_read;
if (p_file->cur + p_nb_bytes < p_file->buf + p_file->len) {
l_nb_read = p_nb_bytes;
} else {
l_nb_read = (OPJ_UINT32)(p_file->buf + p_file->len - p_file->cur);
}
memcpy(p_buffer, p_file->cur, l_nb_read);
p_file->cur += l_nb_read;
return l_nb_read ? l_nb_read : ((OPJ_UINT32)-1);
} //opj_read_from_buffer()
static OPJ_UINT32 opj_write_from_buffer(void *p_buffer, OPJ_UINT32 p_nb_bytes, BufInfo *p_file) {
memcpy(p_file->cur, p_buffer, p_nb_bytes);
p_file->cur += p_nb_bytes;
p_file->len += p_nb_bytes;
return p_nb_bytes;
} // opj_write_from_buffer()
static OPJ_SIZE_T opj_skip_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 p_nb_bytes;
}
p_file->cur = p_file->buf + p_file->len;
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) {
//printf("opj_seek_from_buffer %d + %d -> %d + %d\n", p_file->cur , p_nb_bytes, p_file->buf, p_file->len);
if (p_nb_bytes < p_file->len) {
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()
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;
l_stream = opj_stream_create(p_size, p_is_read_stream);
if (!l_stream)
return NULL;
opj_stream_set_user_data(l_stream, p_file, my_stream_free);
opj_stream_set_user_data_length(l_stream, p_file->len);
opj_stream_set_read_function(l_stream, (opj_stream_read_fn)opj_read_from_buffer);
opj_stream_set_write_function(l_stream, (opj_stream_write_fn)opj_write_from_buffer);
opj_stream_set_skip_function(l_stream, (opj_stream_skip_fn)opj_skip_from_buffer);
opj_stream_set_seek_function(l_stream, (opj_stream_seek_fn)opj_seek_from_buffer);
return l_stream;
} //opj_stream_create_buffer_stream()
unsigned char *nii_loadImgCoreOpenJPEG(char *imgname, struct nifti_1_header hdr, struct TDICOMdata dcm, int compressFlag) {
//OpenJPEG library is not well documented and has changed between versions
//Since the JPEG is embedded in a DICOM we need to skip bytes at the start of the file
// In theory we might also want to strip data that exists AFTER the image, see gdcmJPEG2000Codec.c
unsigned char *ret = NULL;
opj_dparameters_t params;
opj_codec_t *codec;
opj_image_t *jpx;
opj_stream_t *stream;
FILE *reader = fopen(imgname, "rb");
fseek(reader, 0, SEEK_END);
long size = ftell(reader) - dcm.imageStart;
if (size <= 8)
return NULL;
fseek(reader, dcm.imageStart, SEEK_SET);
unsigned char *data = (unsigned char *)malloc(size);
size_t sz = fread(data, 1, size, reader);
fclose(reader);
if (sz < size)
return NULL;
OPJ_CODEC_FORMAT format = OPJ_CODEC_JP2;
//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(¶ms);
BufInfo dx;
dx.buf = data;
dx.cur = data;
dx.len = size;
stream = opj_stream_create_buffer_stream(&dx, (OPJ_UINT32)size, true);
if (stream == NULL)
return NULL;
codec = opj_create_decompress(format);
// setup the decoder decoding parameters using user parameters
if (!opj_setup_decoder(codec, ¶ms))
goto cleanup2;
// Read the main header of the codestream and if necessary the JP2 boxes
if (!opj_read_header(stream, codec, &jpx)) {
printError("OpenJPEG failed to read the header %s (offset %d)\n", imgname, dcm.imageStart);
//comment these next lines to abort: include these to create zero-padded slice
#ifdef MY_ZEROFILLBROKENJPGS
//fix broken slices https://github.com/scitran-apps/dcm2niix/issues/4
printError("Zero-filled slice created\n");
int imgbytes = (hdr.bitpix / 8) * hdr.dim[1] * hdr.dim[2];
ret = (unsigned char *)calloc(imgbytes, 1);
#endif
goto cleanup2;
}
// Get the decoded image
if (!(opj_decode(codec, stream, jpx) && opj_end_decompress(codec, stream))) {
printError("OpenJPEG j2k_to_image failed to decode %s\n", imgname);
goto cleanup1;
}
ret = imagetoimg(jpx);
cleanup1:
opj_image_destroy(jpx);
cleanup2:
free(dx.buf);
opj_stream_destroy(stream);
opj_destroy_codec(codec);
return ret;
}
#endif //myDisableOpenJPEG
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
float deFuzz(float v) {
if (fabs(v) < 0.00001)
return 0;
else
return v;
}
#ifdef MY_DEBUG
void reportMat33(char *str, mat33 A) {
printMessage("%s = [%g %g %g ; %g %g %g; %g %g %g ]\n", str,
deFuzz(A.m[0][0]), deFuzz(A.m[0][1]), deFuzz(A.m[0][2]),
deFuzz(A.m[1][0]), deFuzz(A.m[1][1]), deFuzz(A.m[1][2]),
deFuzz(A.m[2][0]), deFuzz(A.m[2][1]), deFuzz(A.m[2][2]));
}
void reportMat44(char *str, mat44 A) {
//example: reportMat44((char*)"out",*R);
printMessage("%s = [%g %g %g %g; %g %g %g %g; %g %g %g %g; 0 0 0 1]\n", str,
deFuzz(A.m[0][0]), deFuzz(A.m[0][1]), deFuzz(A.m[0][2]), deFuzz(A.m[0][3]),
deFuzz(A.m[1][0]), deFuzz(A.m[1][1]), deFuzz(A.m[1][2]), deFuzz(A.m[1][3]),
deFuzz(A.m[2][0]), deFuzz(A.m[2][1]), deFuzz(A.m[2][2]), deFuzz(A.m[2][3]));
}
#endif
int verify_slice_dir(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, mat44 *R, int isVerbose) {
//returns slice direction: 1=sag,2=coronal,3=axial, -= flipped
if (h->dim[3] < 2)
return 0; //don't care direction for single slice
int iSL = 1; //find Z-slice direction: row with highest magnitude of 3rd column
if ((fabs(R->m[1][2]) >= fabs(R->m[0][2])) && (fabs(R->m[1][2]) >= fabs(R->m[2][2])))
iSL = 2; //
if ((fabs(R->m[2][2]) >= fabs(R->m[0][2])) && (fabs(R->m[2][2]) >= fabs(R->m[1][2])))
iSL = 3; //axial acquisition
float pos = NAN;
if (!isnan(d2.patientPosition[iSL])) { //patient position fields exist
pos = d2.patientPosition[iSL];
if (isSameFloat(pos, d.patientPosition[iSL]))
pos = NAN;
#ifdef MY_DEBUG
if (!isnan(pos))
printMessage("position determined using lastFile %f\n", pos);
#endif
}
if (isnan(pos) && (!isnan(d.patientPositionLast[iSL]))) { //patient position fields exist
pos = d.patientPositionLast[iSL];
if (isSameFloat(pos, d.patientPosition[iSL]))
pos = NAN;
#ifdef MY_DEBUG
if (!isnan(pos))
printMessage("position determined using last (4d) %f\n", pos);
#endif
}
if (isnan(pos) && (!isnan(d.stackOffcentre[iSL])))
pos = d.stackOffcentre[iSL];
if (isnan(pos) && (!isnan(d.lastScanLoc)))
pos = d.lastScanLoc;
vec4 x;
x.v[0] = 0.0;
x.v[1] = 0.0;
x.v[2] = (float)(h->dim[3] - 1.0);
x.v[3] = 1.0;
vec4 pos1v = nifti_vect44mat44_mul(x, *R);
float pos1 = pos1v.v[iSL - 1]; //-1 as C indexed from 0
bool flip = false;
if (!isnan(pos)) // we have real SliceLocation for last slice or volume center
flip = (pos > R->m[iSL - 1][3]) != (pos1 > R->m[iSL - 1][3]); // same direction?, note C indices from 0
else { // we do some guess work and warn user
vec3 readV = setVec3(d.orient[1], d.orient[2], d.orient[3]);
vec3 phaseV = setVec3(d.orient[4], d.orient[5], d.orient[6]);
//printMessage("rd %g %g %g\n",readV.v[0],readV.v[1],readV.v[2]);
//printMessage("ph %g %g %g\n",phaseV.v[0],phaseV.v[1],phaseV.v[2]);
vec3 sliceV = crossProduct(readV, phaseV); //order important: this is our hail mary
flip = ((sliceV.v[0] + sliceV.v[1] + sliceV.v[2]) < 0);
//printMessage("verify slice dir %g %g %g\n",sliceV.v[0],sliceV.v[1],sliceV.v[2]);
if (isVerbose) { //1st pass only
if (!d.isDerived) { //do not warn user if image is derived
printWarning("Unable to determine slice direction: please check whether slices are flipped\n");
} else {
printWarning("Unable to determine slice direction: please check whether slices are flipped (derived image)\n");
}
}
}
if (flip) {
for (int i = 0; i < 4; i++)
R->m[i][2] = -R->m[i][2];
}
if (flip)
iSL = -iSL;
#ifdef MY_DEBUG
printMessage("verify slice dir %d %d %d\n", h->dim[1], h->dim[2], h->dim[3]);
//reportMat44((char*)"Rout",*R);
printMessage("flip = %d\n", flip);
printMessage("sliceDir = %d\n", iSL);
printMessage(" pos1 = %f\n", pos1);
#endif
return iSL;
} //verify_slice_dir()
mat44 noNaN(mat44 Q44, bool isVerbose, bool *isBogus) //simplify any headers that have NaN values
{
mat44 ret = Q44;
bool isNaN44 = false;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 4; j++)
if (isnan(ret.m[i][j]))
isNaN44 = true;
if (isNaN44) {
*isBogus = true;
if (isVerbose)
printWarning("Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation\n");
for (int i = 0; i < 4; i++)
for (int j = 0; j < 4; j++)
if (i == j)
ret.m[i][j] = 1;
else
ret.m[i][j] = 0;
ret.m[1][1] = -1;
} //if isNaN detected
return ret;
}
#define kYYYYMMDDlen 8 //how many characters to encode year,month,day in "YYYYDDMM" format
/*double dicomTimeToSecX(double dicomTime) {
//convert HHMMSS to seconds, 135300.024 -> 135259.731 are 0.293 sec apart
char acqTimeBuf[64];
snprintf(acqTimeBuf, sizeof acqTimeBuf, "%+013.5f", (double)dicomTime);
int ahour, amin;
double asec;
int count = 0;
sscanf(acqTimeBuf, "%3d%2d%lf%n", &ahour, &amin, &asec, &count);
if (!count)
return -1;
return (ahour * 3600) + (amin * 60) + asec;
}
double DateTimeToTime(char *dstr) {
if (strlen(dstr) > (kYYYYMMDDlen + 5)) {
// 20161117131643.80000 -> date 20161117 time 131643.80000
//printMessage("acquisitionDateTime %s\n",acquisitionDateTimeTxt);
//char acquisitionDateTxt[kDICOMStr];
//memcpy(acquisitionDateTxt, dstr, kYYYYMMDDlen);
//acquisitionDateTxt[kYYYYMMDDlen] = '\0'; // IMPORTANT!
//d.acquisitionDate = atof(acquisitionDateTxt);
char acquisitionTimeTxt[kDICOMStr];
int timeLen = (int)strlen(dstr) - kYYYYMMDDlen;
strncpy(acquisitionTimeTxt, &dstr[kYYYYMMDDlen], timeLen);
acquisitionTimeTxt[timeLen] = '\0'; // IMPORTANT!
printf(">>>%s\n", acquisitionTimeTxt);
return atof(acquisitionTimeTxt);
}
return 0.0;
}*/
#define kSessionOK 0
#define kSessionBadMatrix 1
void setQSForm(struct nifti_1_header *h, mat44 Q44i, bool isVerbose) {
bool isBogus = false;
mat44 Q44 = noNaN(Q44i, isVerbose, &isBogus);
if ((h->session_error == kSessionBadMatrix) || (isBogus)) {
h->session_error = kSessionBadMatrix;
h->sform_code = NIFTI_XFORM_UNKNOWN;
} else
h->sform_code = NIFTI_XFORM_SCANNER_ANAT;
h->srow_x[0] = Q44.m[0][0];
h->srow_x[1] = Q44.m[0][1];
h->srow_x[2] = Q44.m[0][2];
h->srow_x[3] = Q44.m[0][3];
h->srow_y[0] = Q44.m[1][0];
h->srow_y[1] = Q44.m[1][1];
h->srow_y[2] = Q44.m[1][2];
h->srow_y[3] = Q44.m[1][3];
h->srow_z[0] = Q44.m[2][0];
h->srow_z[1] = Q44.m[2][1];
h->srow_z[2] = Q44.m[2][2];
h->srow_z[3] = Q44.m[2][3];
float dumdx, dumdy, dumdz;
nifti_mat44_to_quatern(Q44, &h->quatern_b, &h->quatern_c, &h->quatern_d, &h->qoffset_x, &h->qoffset_y, &h->qoffset_z, &dumdx, &dumdy, &dumdz, &h->pixdim[0]);
h->qform_code = h->sform_code;
} //setQSForm()
#ifdef my_unused
ivec3 maxCol(mat33 R) {
//return index of maximum column in 3x3 matrix, e.g. [1 0 0; 0 1 0; 0 0 1] -> 1,2,3
ivec3 ixyz;
mat33 foo;
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
foo.m[i][j] = fabs(R.m[i][j]);
//ixyz.v[0] : row with largest value in column 1
ixyz.v[0] = 1;
if ((foo.m[1][0] > foo.m[0][0]) && (foo.m[1][0] >= foo.m[2][0]))
ixyz.v[0] = 2; //2nd column largest column
else if ((foo.m[2][0] > foo.m[0][0]) && (foo.m[2][0] > foo.m[1][0]))
ixyz.v[0] = 3; //3rd column largest column
//ixyz.v[1] : row with largest value in column 2, but not the same row as ixyz.v[1]
if (ixyz.v[0] == 1) {
ixyz.v[1] = 2;
if (foo.m[2][1] > foo.m[1][1])
ixyz.v[1] = 3;
} else if (ixyz.v[0] == 2) {
ixyz.v[1] = 1;
if (foo.m[2][1] > foo.m[0][1])
ixyz.v[1] = 3;
} else { //ixyz.v[0] == 3
ixyz.v[1] = 1;
if (foo.m[1][1] > foo.m[0][1])
ixyz.v[1] = 2;
}
//ixyz.v[2] : 3rd row, constrained by previous rows
ixyz.v[2] = 6 - ixyz.v[1] - ixyz.v[0]; //sum of 1+2+3
return ixyz;
}
int sign(float x) {
//returns -1,0,1 depending on if X is less than, equal to or greater than zero
if (x < 0)
return -1;
else if (x > 0)
return 1;
return 0;
}
// Subfunction: get dicom xform matrix and related info
// This is a direct port of Xiangrui Li's dicm2nii function
mat44 xform_mat(struct TDICOMdata d) {
vec3 readV = setVec3(d.orient[1], d.orient[2], d.orient[3]);
vec3 phaseV = setVec3(d.orient[4], d.orient[5], d.orient[6]);
vec3 sliceV = crossProduct(readV, phaseV);
mat33 R;
LOAD_MAT33(R, readV.v[0], readV.v[1], readV.v[2],
phaseV.v[0], phaseV.v[1], phaseV.v[2],
sliceV.v[0], sliceV.v[1], sliceV.v[2]);
R = nifti_mat33_transpose(R);
//reportMat33((char*)"R",R);
ivec3 ixyz = maxCol(R);
//printMessage("%d %d %d\n", ixyz.v[0], ixyz.v[1], ixyz.v[2]);
int iSL = ixyz.v[2]; // 1/2/3 for Sag/Cor/Tra slice
float cosSL = R.m[iSL - 1][2];
//printMessage("cosSL\t%g\n", cosSL);
//vec3 pixdim = setVec3(d.xyzMM[1], d.xyzMM[2], d.xyzMM[3]);
//printMessage("%g %g %g\n", pixdim.v[0], pixdim.v[1], pixdim.v[2]);
mat33 pixdim;
LOAD_MAT33(pixdim, d.xyzMM[1], 0.0, 0.0,
0.0, d.xyzMM[2], 0.0,
0.0, 0.0, d.xyzMM[3]);
R = nifti_mat33_mul(R, pixdim);
//reportMat33((char*)"R",R);
mat44 R44;
LOAD_MAT44(R44, R.m[0][0], R.m[0][1], R.m[0][2], d.patientPosition[1],
R.m[1][0], R.m[1][1], R.m[1][2], d.patientPosition[2],
R.m[2][0], R.m[2][1], R.m[2][2], d.patientPosition[3]);
//reportMat44((char*)"R",R44);
//rest are former: R = verify_slice_dir(R, s, dim, iSL)
if ((d.xyzDim[3] < 2) && (d.CSA.mosaicSlices < 2))
return R44; //don't care direction for single slice
vec3 dim = setVec3(d.xyzDim[1], d.xyzDim[2], d.xyzDim[3]);
if (d.CSA.mosaicSlices > 1) { //Siemens mosaic: use dim(1) since no transpose to img
float nRowCol = ceil(sqrt((double)d.CSA.mosaicSlices));
dim.v[0] = dim.v[0] / nRowCol;
dim.v[1] = dim.v[1] / nRowCol;
dim.v[2] = d.CSA.mosaicSlices;
vec4 dim4 = setVec4((nRowCol - 1) * dim.v[0] / 2.0f, (nRowCol - 1) * dim.v[1] / 2.0f, 0);
vec4 offset = nifti_vect44mat44_mul(dim4, R44);
//printMessage("%g %g %g\n", dim.v[0], dim.v[1], dim.v[2]);
//printMessage("%g %g %g\n", dim4.v[0], dim4.v[1], dim4.v[2]);
//printMessage("%g %g %g %g\n", offset.v[0], offset.v[1], offset.v[2], offset.v[3]);
//printMessage("nRowCol\t%g\n", nRowCol);
R44.m[0][3] = offset.v[0];
R44.m[1][3] = offset.v[1];
R44.m[2][3] = offset.v[2];
//R44.m[3][3] = offset.v[3];
if (sign(d.CSA.sliceNormV[iSL]) != sign(cosSL)) {
R44.m[0][2] = -R44.m[0][2];
R44.m[1][2] = -R44.m[1][2];
R44.m[2][2] = -R44.m[2][2];
R44.m[3][2] = -R44.m[3][2];
}
//reportMat44((char*)"iR44",R44);
return R44;
} else if (true) {
//SliceNormalVector TO DO
printMessage("Not completed");
#ifndef USING_R
exit(2);
#endif
return R44;
}
printMessage("Unable to determine spatial transform\n");
#ifndef USING_R
exit(1);
#else
return R44;
#endif
}
mat44 set_nii_header(struct TDICOMdata d) {
mat44 R = xform_mat(d);
//R(1:2,:) = -R(1:2,:); % dicom LPS to nifti RAS, xform matrix before reorient
for (int i = 0; i < 2; i++)
for (int j = 0; j < 4; j++)
R.m[i][j] = -R.m[i][j];
#ifdef MY_DEBUG
reportMat44((char *)"R44", R);
#endif
}
#endif
// This code predates Xiangrui Li's set_nii_header function
mat44 set_nii_header_x(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, int *sliceDir, int isVerbose) {
*sliceDir = 0;
mat44 Q44 = nifti_dicom2mat(d.orient, d.patientPosition, d.xyzMM);
//Q44 = doQuadruped(Q44);
if (d.isSegamiOasis == true) {
//Segami reconstructions appear to disregard DICOM spatial parameters: assume center of volume is isocenter and no table tilt
// Consider sample image with d.orient (0020,0037) = -1 0 0; 0 1 0: this suggests image RAI (L->R, P->A, S->I) but the vendors viewing software suggests LPS
//Perhaps we should ignore 0020,0037 and 0020,0032 as they are hidden in sequence 0054,0022, but in this case no positioning is provided
// http://www.cs.ucl.ac.uk/fileadmin/cmic/Documents/DavidAtkinson/DICOM.pdf
// https://www.slicer.org/wiki/Coordinate_systems
LOAD_MAT44(Q44, -h->pixdim[1], 0, 0, 0, 0, -h->pixdim[2], 0, 0, 0, 0, h->pixdim[3], 0); //X and Y dimensions flipped in NIfTI (RAS) vs DICOM (LPS)
vec4 originVx = setVec4((h->dim[1] + 1.0f) / 2.0f, (h->dim[2] + 1.0f) / 2.0f, (h->dim[3] + 1.0f) / 2.0f);
vec4 originMm = nifti_vect44mat44_mul(originVx, Q44);
for (int i = 0; i < 3; i++)
Q44.m[i][3] = -originMm.v[i]; //set origin to center voxel
if (isVerbose) {
//printMessage("origin (vx) %g %g %g\n",originVx.v[0],originVx.v[1],originVx.v[2]);
//printMessage("origin (mm) %g %g %g\n",originMm.v[0],originMm.v[1],originMm.v[2]);
printWarning("Segami coordinates defy DICOM convention, please check orientation\n");
}
return Q44;
}
//next line only for Siemens mosaic: ignore for UIH grid
// https://github.com/xiangruili/dicm2nii/commit/47ad9e6d9bc8a999344cbd487d602d420fb1509f
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.mosaicSlices > 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;
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]);
for (int c = 0; c < 2; c++)
for (int r = 0; r < 4; r++)
Q44.m[c][r] = -Q44.m[c][r];
mat33 Q;
LOAD_MAT33(Q, d.orient[1], d.orient[4], d.CSA.sliceNormV[1],
d.orient[2], d.orient[5], d.CSA.sliceNormV[2],
d.orient[3], d.orient[6], d.CSA.sliceNormV[3]);
if (nifti_mat33_determ(Q) < 0) { //Siemens sagittal are R>>L, whereas NIfTI is L>>R, we retain Siemens order on disk so ascending is still ascending, but we need to have the spatial transform reflect this.
mat44 det;
*sliceDir = kSliceOrientMosaicNegativeDeterminant; //we need to handle DTI vectors accordingly
LOAD_MAT44(det, 1.0l, 0.0l, 0.0l, 0.0l, 0.0l, 1.0l, 0.0l, 0.0l, 0.0l, 0.0l, -1.0l, 0.0l);
//patient_to_tal.m[2][3] = 1-d.CSA.MosaicSlices;
Q44 = nifti_mat44_mul(Q44, det);
}
} else { //not a mosaic
*sliceDir = verify_slice_dir(d, d2, h, &Q44, isVerbose);
for (int c = 0; c < 4; c++) // LPS to nifti RAS, xform matrix before reorient
for (int r = 0; r < 2; r++) //swap rows 1 & 2
Q44.m[r][c] = -Q44.m[r][c];
}
#ifdef MY_DEBUG
reportMat44((char *)"Q44", Q44);
#endif
return Q44;
}
int headerDcm2NiiSForm(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, int isVerbose) { //fill header s and q form
//see http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1_io.c
//returns sliceDir: 0=unknown,1=sag,2=coro,3=axial,-=reversed slices
int sliceDir = 0;
if (h->dim[3] < 2) {
mat44 Q44 = set_nii_header_x(d, d2, h, &sliceDir, isVerbose);
setQSForm(h, Q44, isVerbose);
return sliceDir; //don't care direction for single slice
}
h->sform_code = NIFTI_XFORM_UNKNOWN;
h->qform_code = NIFTI_XFORM_UNKNOWN;
bool isOK = false;
for (int i = 1; i <= 6; i++)
if (d.orient[i] != 0.0)
isOK = true;
if (!isOK) {
//we will have to guess, assume axial acquisition saved in standard Siemens style?
d.orient[1] = 1.0f;
d.orient[2] = 0.0f;
d.orient[3] = 0.0f;
d.orient[4] = 0.0f;
d.orient[5] = 1.0f;
d.orient[6] = 0.0f;
if ((d.isDerived) || ((d.bitsAllocated == 8) && (d.samplesPerPixel == 3) && (d.manufacturer == kMANUFACTURER_SIEMENS))) {
printMessage("Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)\n");
} else {
printMessage("Unable to determine spatial orientation: 0020,0037 missing (Type 1 attribute: not a valid DICOM) Series %ld\n", d.seriesNum);
}
}
mat44 Q44 = set_nii_header_x(d, d2, h, &sliceDir, isVerbose);
setQSForm(h, Q44, isVerbose);
return sliceDir;
} //headerDcm2NiiSForm()
int headerDcm2Nii2(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, int isVerbose) { //final pass after de-mosaic
char txt[1024] = {""};
if (h->slice_code == NIFTI_SLICE_UNKNOWN)
h->slice_code = d.CSA.sliceOrder;
if (h->slice_code == NIFTI_SLICE_UNKNOWN)
h->slice_code = d2.CSA.sliceOrder; //sometimes the first slice order is screwed up https://github.com/eauerbach/CMRR-MB/issues/29
if (d.modality == kMODALITY_MR)
snprintf(txt, 1024, "TE=%.2g;Time=%.3f", d.TE, d.acquisitionTime);
else
snprintf(txt, 1024, "Time=%.3f", d.acquisitionTime);
if (d.CSA.phaseEncodingDirectionPositive >= 0) {
char dtxt[1024] = {""};
snprintf(dtxt, 1024, ";phase=%d", d.CSA.phaseEncodingDirectionPositive);
strcat(txt, dtxt);
}
//from dicm2nii 20151117 InPlanePhaseEncodingDirection
if (d.phaseEncodingRC == 'R')
h->dim_info = (3 << 4) + (1 << 2) + 2;
if (d.phaseEncodingRC == 'C')
h->dim_info = (3 << 4) + (2 << 2) + 1;
if (d.CSA.multiBandFactor > 1) {
char dtxt[1024] = {""};
snprintf(dtxt, 1024, ";mb=%d", d.CSA.multiBandFactor);
strcat(txt, dtxt);
}
// GCC 8 warns about truncation using snprintf
// snprintf(h->descrip,80, "%s",txt);
memcpy(h->descrip, txt, 79);
h->descrip[79] = '\0';
if ((strlen(d.imageComments) > 0) && (h->aux_file[0] == 0)) //issue691
snprintf(h->aux_file, 24, "%.23s", d.imageComments);
if ((h->aux_file[0] == '\t') && (h->aux_file[1] == 0))
h->aux_file[0] = 0; //issue691
return headerDcm2NiiSForm(d, d2, h, isVerbose);
} //headerDcm2Nii2()
int dcmStrLen(int len, int kMaxLen) {
if (len < kMaxLen)
return len + 1;
else
return kMaxLen;
} //dcmStrLen()
struct TDICOMdata clear_dicom_data() {
struct TDICOMdata d;
//d.dti4D = NULL;
d.locationsInAcquisition = 0;
d.locationsInAcquisitionConflict = 0; //for GE discrepancy between tags 0020,1002; 0021,104F; 0054,0081
d.modality = kMODALITY_UNKNOWN;
d.effectiveEchoSpacingGE = 0;
for (int i = 0; i < 4; i++) {
d.CSA.dtiV[i] = 0;
d.patientPosition[i] = NAN;
//d.patientPosition2nd[i] = NAN; //used to distinguish XYZT vs XYTZ for Philips 4D
d.patientPositionLast[i] = NAN; //used to compute slice direction for Philips 4D
d.stackOffcentre[i] = NAN;
d.angulation[i] = 0.0f;
d.xyzMM[i] = 1;
}
for (int i = 0; i < MAX_NUMBER_OF_DIMENSIONS; ++i)
d.dimensionIndexValues[i] = 0;
//d.CSA.sliceTiming[0] = -1.0f; //impossible value denotes not known
for (int z = 0; z < kMaxEPI3D; z++)
d.CSA.sliceTiming[z] = -1.0;
d.CSA.numDti = 0;
for (int i = 0; i < 5; i++)
d.xyzDim[i] = 1;
for (int i = 0; i < 7; i++)
d.orient[i] = 0.0f;
strcpy(d.patientName, "");
strcpy(d.patientID, "");
strcpy(d.accessionNumber, "");
strcpy(d.imageType, "");
strcpy(d.imageTypeText, "");
strcpy(d.imageComments, "");
strcpy(d.imageBaseName, "");
strcpy(d.phaseEncodingDirectionDisplayedUIH, "");
strcpy(d.studyDate, "");
strcpy(d.studyTime, "");
strcpy(d.protocolName, "");
strcpy(d.patientOrient, "");
strcpy(d.seriesDescription, "");
strcpy(d.sequenceName, "");
strcpy(d.scanningSequence, "");
strcpy(d.sequenceVariant, "");
strcpy(d.manufacturersModelName, "");
strcpy(d.institutionalDepartmentName, "");
strcpy(d.procedureStepDescription, "");
strcpy(d.institutionName, "");
strcpy(d.referringPhysicianName, "");
strcpy(d.institutionAddress, "");
strcpy(d.deviceSerialNumber, "");
strcpy(d.softwareVersions, "");
strcpy(d.stationName, "");
strcpy(d.scanOptions, "");
//strcpy(d.mrAcquisitionType, "");
strcpy(d.seriesInstanceUID, "");
strcpy(d.instanceUID, "");
strcpy(d.studyID, "");
strcpy(d.studyInstanceUID, "");
strcpy(d.bodyPartExamined, "");
strcpy(d.coilName, "");
strcpy(d.coilElements, "");
strcpy(d.pulseSequenceName, "");
strcpy(d.radiopharmaceutical, "");
strcpy(d.convolutionKernel, "");
strcpy(d.parallelAcquisitionTechnique, "");
strcpy(d.imageOrientationText, "");
strcpy(d.unitsPT, "");
strcpy(d.decayCorrection, "");
strcpy(d.attenuationCorrectionMethod, "");
strcpy(d.reconstructionMethod, "");
d.phaseEncodingLines = 0;
//~ d.patientPositionSequentialRepeats = 0;
//~ d.patientPositionRepeats = 0;
d.isHasPhase = false;
d.isHasReal = false;
d.isHasImaginary = false;
d.isHasMagnitude = false;
//d.maxGradDynVol = -1; //PAR/REC only
d.sliceOrient = kSliceOrientUnknown;
d.dateTime = (double)19770703150928.0;
d.acquisitionTime = 0.0f;
d.acquisitionDate = 0.0f;
d.manufacturer = kMANUFACTURER_UNKNOWN;
d.isPlanarRGB = false;
d.lastScanLoc = NAN;
d.TR = 0.0;
d.TE = 0.0;
#ifdef USING_DCM2NIIXFSWRAPPER
d.TI = -1.0; // default when there is no TI in dicom file
#else
d.TI = 0.0;
#endif
d.flipAngle = 0.0;
d.bandwidthPerPixelPhaseEncode = 0.0;
d.acquisitionDuration = 0.0;
d.imagingFrequency = 0.0;
d.numberOfAverages = 0.0;
d.fieldStrength = 0.0;
d.SAR = 0.0;
d.pixelBandwidth = 0.0;
d.zSpacing = 0.0;
d.zThick = 0.0;
//~ d.numberOfDynamicScans = 0;
d.echoNum = 0;
d.echoTrainLength = 0;
d.waterFatShift = 0.0;
d.groupDelay = 0.0;
d.postLabelDelay = 0;
d.shimGradientX = -33333;//impossible value for UINT16
d.shimGradientY = -33333;//impossible value for UINT16
d.shimGradientZ = -33333;//impossible value for UINT16
strcpy(d.prescanReuseString, "");
d.decayFactor = 0.0;
d.percentSampling = 0.0;
d.phaseFieldofView = 0.0;
d.dwellTime = 0;
d.protocolBlockStartGE = 0;
d.protocolBlockLengthGE = 0;
d.phaseEncodingSteps = 0;
d.frequencyEncodingSteps = 0;
d.phaseEncodingStepsOutOfPlane = 0;
d.coilCrc = 0;
d.seriesUidCrc = 0;
d.instanceUidCrc = 0;
d.accelFactPE = 0.0;
d.accelFactOOP = 0.0;
d.compressedSensingFactor = 0.0;
d.isDeepLearning = false;
strcpy(d.deepLearningText, "");
//d.patientPositionNumPhilips = 0;
d.imageBytes = 0;
d.intenScale = 1;
d.intenScalePhilips = 0;
d.intenIntercept = 0;
d.gantryTilt = 0.0;
d.exposureTimeMs = 0.0;
d.xRayTubeCurrent = 0.0;
d.radionuclidePositronFraction = 0.0;
d.radionuclideHalfLife = 0.0;
d.doseCalibrationFactor = 0.0;
d.ecat_isotope_halflife = 0.0;
d.frameDuration = -1.0;
d.frameReferenceTime = -1.0;
d.ecat_dosage = 0.0;
d.radionuclideTotalDose = 0.0;
d.seriesNum = 1;
d.acquNum = 0;
d.imageNum = 1;
d.imageStart = 0;
d.is3DAcq = false; //e.g. MP-RAGE, SPACE, TFE
d.is2DAcq = false; //
d.isDerived = false; //0008,0008 = DERIVED,CSAPARALLEL,POSDISP
d.isSegamiOasis = false; //these images do not store spatial coordinates
d.isBVecWorldCoordinates = false; //bvecs can be in image space (GE) or world coordinates (Siemens)
d.isGrayscaleSoftcopyPresentationState = false;
d.isRawDataStorage = false;
d.isPartialFourier = false;
d.isIR = false;
d.isEPI = false;
d.isDiffusion = false;
d.isVectorFromBMatrix = false;
d.isStackableSeries = false; //combine DCE series https://github.com/rordenlab/dcm2niix/issues/252
d.isXA10A = false; //https://github.com/rordenlab/dcm2niix/issues/236
d.triggerDelayTime = 0.0;
d.RWVScale = 0.0;
d.RWVIntercept = 0.0;
d.isScaleOrTEVaries = false;
d.isScaleVariesEnh = false; //issue363
d.bitsAllocated = 16; //bits
d.bitsStored = 0;
d.samplesPerPixel = 1;
d.pixelPaddingValue = NAN;
d.isValid = false;
d.isXRay = false;
d.isMultiEcho = false;
d.numberOfTR = 1;
d.isSigned = false; //default is unsigned!
d.isFloat = false; //default is for integers, not single or double precision
d.isResampled = false; //assume data not resliced to remove gantry tilt problems
d.isLocalizer = false;
d.isNonParallelSlices = false;
d.isCoilVaries = false;
d.compressionScheme = 0; //none
d.isExplicitVR = true;
d.isLittleEndian = true; //DICOM initially always little endian
d.converted2NII = 0;
d.numberOfDiffusionDirectionGE = -1;
d.velocityEncodeScaleGE = 1.0;
d.phaseEncodingGE = kGE_PHASE_ENCODING_POLARITY_UNKNOWN;
d.rtia_timerGE = -1.0;
d.rawDataRunNumber = -1;
d.maxEchoNumGE = -1;
d.epiVersionGE = -1;
d.internalepiVersionGE = -1;
d.diffCyclingModeGE = kGE_DIFF_CYCLING_UNKNOWN;
d.tensorFileGE = 0;
d.durationLabelPulseGE = -1;
d.aslFlags = kASL_FLAG_NONE;
d.partialFourierDirection = kPARTIAL_FOURIER_DIRECTION_UNKNOWN;
d.mtState = -1;
d.numberOfExcitations = -1;
d.numberOfArms = -1;
d.numberOfPointsPerArm = -1;
d.phaseNumber = - 1; //Philips Multi-Phase ASL
d.spoiling = kSPOILING_UNKOWN;
d.interp3D = -1;
for (int i = 0; i < kMaxOverlay; i++)
d.overlayStart[i] = 0;
d.isHasOverlay = false;
d.isPrivateCreatorRemap = false;
d.isRealIsPhaseMapHz = false;
d.isVariableFlipAngle = false;
d.isQuadruped = false;
d.numberOfImagesInGridUIH = 0;
d.phaseEncodingRC = '?';
d.patientSex = '?';
d.patientWeight = 0.0;
strcpy(d.patientBirthDate, "");
strcpy(d.patientAge, "");
d.CSA.bandwidthPerPixelPhaseEncode = 0.0;
d.CSA.mosaicSlices = 0;
d.CSA.sliceNormV[1] = 0.0;
d.CSA.sliceNormV[2] = 0.0;
d.CSA.sliceNormV[3] = 1.0; //default Siemens Image Numbering is F>>H https://www.mccauslandcenter.sc.edu/crnl/tools/stc
d.CSA.sliceOrder = NIFTI_SLICE_UNKNOWN;
d.CSA.slice_start = 0;
d.CSA.slice_end = 0;
d.CSA.protocolSliceNumber1 = 0;
d.CSA.phaseEncodingDirectionPositive = -1; //unknown
d.CSA.isPhaseMap = false;
d.CSA.multiBandFactor = 1;
d.CSA.SeriesHeader_offset = 0;
d.CSA.SeriesHeader_length = 0;
d.CSA.coilNumber = -1;
strcpy(d.CSA.bidsDataType, "");
strcpy(d.CSA.bidsEntitySuffix, "");
strcpy(d.CSA.bidsTask, "");
return d;
} //clear_dicom_data()
int isdigitdot(int c) { //returns true if digit or '.'
if (c == '.')
return 1;
return isdigit(c);
}
void dcmStrDigitsDotOnlyKey(char key, char *lStr) {
//e.g. string "F:2.50" returns 2.50 if key==":"
size_t len = strlen(lStr);
if (len < 1)
return;
bool isKey = false;
for (int i = 0; i < (int)len; i++) {
if (!isdigitdot(lStr[i])) {
isKey = (lStr[i] == key);
lStr[i] = ' ';
} else if (!isKey)
lStr[i] = ' ';
}
} //dcmStrDigitsDotOnlyKey()
void dcmStrDigitsOnlyKey(char key, char *lStr) {
//e.g. string "p2s3" returns 2 if key=="p" and 3 if key=="s"
size_t len = strlen(lStr);
if (len < 1)
return;
bool isKey = false;
for (int i = 0; i < (int)len; i++) {
if (!isdigitdot(lStr[i])) {
isKey = (lStr[i] == key);
lStr[i] = ' ';
} else if (!isKey)
lStr[i] = ' ';
}
} //dcmStrDigitsOnlyKey()
void dcmStrDigitsOnly(char *lStr) {
//e.g. change "H11" to " 11"