int main_ecalib(int argc, char* argv[])
{
long calsize[3] = { 24, 24, 24 };
int maps = 2;
bool one = false;
bool calcen = false;
bool print_svals = false;
struct ecalib_conf conf = ecalib_defaults;
const struct opt_s opts[] = {
OPT_FLOAT('t', &conf.threshold, "threshold", "This determined the size of the null-space."),
OPT_FLOAT('c', &conf.crop, "crop_value", "Crop the sensitivities if the eigenvalue is smaller than {crop_value}."),
OPT_VEC3('k', &conf.kdims, "ksize", "kernel size"),
OPT_VEC3('K', &conf.kdims, "", "()"),
OPT_VEC3('r', &calsize, "cal_size", "Limits the size of the calibration region."),
OPT_VEC3('R', &calsize, "", "()"),
OPT_INT('m', &maps, "maps", "Number of maps to compute."),
OPT_SET('S', &conf.softcrop, "create maps with smooth transitions (Soft-SENSE)."),
OPT_SET('W', &conf.weighting, "soft-weighting of the singular vectors."),
OPT_SET('I', &conf.intensity, "intensity correction"),
OPT_SET('1', &one, "perform only first part of the calibration"),
OPT_CLEAR('P', &conf.rotphase, "Do not rotate the phase with respect to the first principal component"),
OPT_CLEAR('O', &conf.orthiter, "()"),
OPT_FLOAT('b', &conf.perturb, "", "()"),
OPT_SET('V', &print_svals, "()"),
OPT_SET('C', &calcen, "()"),
OPT_SET('g', &conf.usegpu, "()"),
OPT_FLOAT('p', &conf.percentsv, "", "()"),
OPT_INT('n', &conf.numsv, "", "()"),
OPT_FLOAT('v', &conf.var, "variance", "Variance of noise in data."),
OPT_SET('a', &conf.automate, "Automatically pick thresholds."),
OPT_INT('d', &debug_level, "level", "Debug level"),
};
cmdline(&argc, argv, 2, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (-1. != conf.percentsv)
conf.threshold = -1.;
if (-1 != conf.numsv)
conf.threshold = -1.;
if (conf.automate) {
conf.crop = -1.;
conf.weighting = true;
}
if (conf.weighting) {
conf.numsv = -1.;
conf.threshold = 0;
conf.percentsv = -1.;
conf.orthiter = false;
}
int N = DIMS;
long ksp_dims[N];
complex float* in_data = load_cfl(argv[1], N, ksp_dims);
// assert((kdims[0] < calsize_ro) && (kdims[1] < calsize_ro) && (kdims[2] < calsize_ro));
// assert((ksp_dims[0] == 1) || (calsize_ro < ksp_dims[0]));
if (1 != ksp_dims[MAPS_DIM])
error("MAPS dimension is not of size one.\n");
long cal_dims[N];
complex float* cal_data = NULL;
if (!calcen) {
#ifdef USE_CC_EXTRACT_CALIB
cal_data = cc_extract_calib(cal_dims, calsize, ksp_dims, in_data);
#else
cal_data = extract_calib(cal_dims, calsize, ksp_dims, in_data, false);
#endif
} else {
for (int i = 0; i < 3; i++)
cal_dims[i] = (calsize[i] < ksp_dims[i]) ? calsize[i] : ksp_dims[i];
for (int i = 3; i < N; i++)
cal_dims[i] = ksp_dims[i];
cal_data = md_alloc(5, cal_dims, CFL_SIZE);
md_resize_center(5, cal_dims, cal_data, ksp_dims, in_data, CFL_SIZE);
}
for (int i = 0; i < 3; i++)
if (1 == ksp_dims[i])
conf.kdims[i] = 1;
long channels = cal_dims[3];
unsigned int K = conf.kdims[0] * conf.kdims[1] * conf.kdims[2] * channels;
float svals[K];
for (unsigned int i = 0; i < 3; i++)
if ((1 == cal_dims[i]) && (1 != ksp_dims[i]))
error("Calibration region not found!\n");
// To reproduce old results turn off rotation of phase.
// conf.rotphase = false;
// FIXME: we should scale the data
(conf.usegpu ? num_init_gpu : num_init)();
if ((conf.var < 0) && (conf.weighting || (conf.crop < 0)))
conf.var = estvar_calreg(conf.kdims, cal_dims, cal_data);
if (one) {
#if 0
long maps = out_dims[4];
assert(caldims[3] == out_dims[3]);
assert(maps <= channels);
#endif
long cov_dims[4];
calone_dims(&conf, cov_dims, channels);
complex float* imgcov = md_alloc(4, cov_dims, CFL_SIZE);
calone(&conf, cov_dims, imgcov, K, svals, cal_dims, cal_data);
complex float* out = create_cfl(argv[2], 4, cov_dims);
md_copy(4, cov_dims, out, imgcov, CFL_SIZE);
unmap_cfl(4, cov_dims, out);
// caltwo(crthr, out_dims, out_data, emaps, cov_dims, imgcov, NULL, NULL);
md_free(imgcov);
} else {
long out_dims[N];
long map_dims[N];
for (int i = 0; i < N; i++) {
out_dims[i] = 1;
map_dims[i] = 1;
if ((i < 3) && (1 < conf.kdims[i])) {
out_dims[i] = ksp_dims[i];
map_dims[i] = ksp_dims[i];
}
}
assert(maps <= ksp_dims[COIL_DIM]);
out_dims[COIL_DIM] = ksp_dims[COIL_DIM];
out_dims[MAPS_DIM] = maps;
map_dims[COIL_DIM] = 1;
map_dims[MAPS_DIM] = maps;
const char* emaps_file = NULL;
if (4 == argc)
emaps_file = argv[3];
complex float* out_data = create_cfl(argv[2], N, out_dims);
complex float* emaps = (emaps_file ? create_cfl : anon_cfl)(emaps_file, N, map_dims);
calib(&conf, out_dims, out_data, emaps, K, svals, cal_dims, cal_data);
unmap_cfl(N, out_dims, out_data);
unmap_cfl(N, map_dims, emaps);
}
if (print_svals) {
for (unsigned int i = 0; i < K; i++)
printf("SVALS %d %f\n", i, svals[i]);
}
printf("Done.\n");
unmap_cfl(N, ksp_dims, in_data);
md_free(cal_data);
return 0;
}
void calib2(const struct ecalib_conf* conf, const long out_dims[DIMS], complex float* out_data, complex float* eptr, unsigned int SN, float svals[SN], const long calreg_dims[DIMS], const complex float* data, const long msk_dims[3], const bool* msk)
{
long channels = calreg_dims[3];
long maps = out_dims[4];
assert(calreg_dims[3] == out_dims[3]);
assert(maps <= channels);
assert(1 == md_calc_size(DIMS - 5, out_dims + 5));
assert(1 == md_calc_size(DIMS - 5, calreg_dims + 5));
complex float rot[channels][channels];
if (conf->rotphase) {
long scc_dims[DIMS] = MD_INIT_ARRAY(DIMS, 1);
scc_dims[COIL_DIM] = channels;
scc_dims[MAPS_DIM] = channels;
scc(scc_dims, &rot[0][0], calreg_dims, data);
} else {
for (unsigned int i = 0; i < channels; i++)
for (unsigned int j = 0; j < channels; j++)
rot[i][j] = (i == j) ? 1. : 0.;
}
long cov_dims[4];
calone_dims(conf, cov_dims, channels);
complex float* imgcov = md_alloc(4, cov_dims, CFL_SIZE);
calone(conf, cov_dims, imgcov, SN, svals, calreg_dims, data);
caltwo(conf, out_dims, out_data, eptr, cov_dims, imgcov, msk_dims, msk);
/* Intensity and phase normalization similar as proposed
* for adaptive combine (Walsh's method) in
* Griswold et al., ISMRM 10:2410 (2002)
*/
if (conf->intensity) {
debug_printf(DP_DEBUG1, "Normalize...\n");
/* I think the reason this works is because inhomogeneity usually
* comes from only a few coil elements which are close. The l1-norm
* is more resilient against such outliers. -- Martin
*/
normalizel1(DIMS, COIL_FLAG, out_dims, out_data);
md_zsmul(DIMS, out_dims, out_data, out_data, sqrtf((float)channels));
}
debug_printf(DP_DEBUG1, "Crop maps... (%.2f)\n", conf->crop);
crop_sens(out_dims, out_data, conf->softcrop, conf->crop, eptr);
debug_printf(DP_DEBUG1, "Fix phase...\n");
// rotate the the phase with respect to the first principle component
fixphase2(DIMS, out_dims, COIL_DIM, rot[0], out_data, out_data);
md_free(imgcov);
}