void direct_calib(const long dims[5], complex float* sens, const long caldims[5], const complex float* data)
{
complex float* tmp = md_alloc(5, caldims, CFL_SIZE);
assert(1 == caldims[4]);
assert(1 == dims[4]);
md_copy(5, caldims, tmp, data, CFL_SIZE);
// apply Kaiser-Bessel Window beta=4
for (int z = 0; z < caldims[2]; z++)
for (int y = 0; y < caldims[1]; y++)
for (int x = 0; x < caldims[0]; x++)
for (int c = 0; c < caldims[3]; c++)
tmp[((c * caldims[2] + z) * caldims[1] + y) * caldims[0] + x]
*= kaiser(4., caldims[2], z)
* kaiser(4., caldims[1], y)
* kaiser(4., caldims[0], x);
md_resize_center(5, dims, sens, caldims, tmp, CFL_SIZE);
ifftc(5, dims, 7, sens, sens);
long dims1[5];
md_select_dims(5, ~MD_BIT(COIL_DIM), dims1, dims);
complex float* img = md_alloc(5, dims1, CFL_SIZE);
md_zrss(5, dims, COIL_FLAG, img, sens);
#if 1
long T = md_calc_size(5, dims1);
for (int i = 0; i < T; i++)
for (int j = 0; j < dims[COIL_DIM]; j++)
sens[j * T + i] *= (cabs(img[i]) == 0.) ? 0. : (1. / cabs(img[i]));
#endif
md_free(img);
}
static void sense_reco(struct sense_data* data, complex float* imgs, const complex float* kspace)
{
complex float* adj = md_alloc(DIMS, data->imgs_dims, CFL_SIZE);
md_clear(DIMS, data->imgs_dims, imgs, CFL_SIZE);
sense_adjoint(data, adj, kspace);
long size = md_calc_size(DIMS, data->imgs_dims);
conjgrad(100, data->alpha, 1.E-3, 2 * size, data, &cpu_iter_ops, sense_normal,
(float*)imgs, (const float*)adj, NULL, NULL, NULL);
md_free(adj);
}
int main_mip(int argc, char* argv[argc])
{
bool mIP = false;
const struct opt_s opts[] = {
OPT_SET('m', &mIP, "minimum" ),
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
unsigned int flags = atoi(argv[1]);
long idims[DIMS];
complex float* in = load_cfl(argv[2], DIMS, idims);
long odims[DIMS];
md_select_dims(DIMS, ~flags, odims, idims);
complex float* out = create_cfl(argv[3], DIMS, odims);
complex float* tmp = md_alloc(DIMS, idims, CFL_SIZE);
md_zabs(DIMS, idims, tmp, in);
long istr[DIMS];
long ostr[DIMS];
md_calc_strides(DIMS, istr, idims, CFL_SIZE);
md_calc_strides(DIMS, ostr, odims, CFL_SIZE);
md_clear(DIMS, odims, out, CFL_SIZE);
md_max2(DIMS, idims, ostr, (float*)out, ostr, (const float*)out, istr, (const float*)tmp);
if (mIP) {
// need result of max in output
md_min2(DIMS, idims, ostr, (float*)out, ostr, (const float*)out, istr, (const float*)tmp);
}
md_free(tmp);
unmap_cfl(DIMS, idims, in);
unmap_cfl(DIMS, odims, out);
exit(0);
}
void md_gaussian_rand(unsigned int D, const long dims[D], complex float* dst)
{
#ifdef USE_CUDA
if (cuda_ondevice(dst)) {
complex float* tmp = md_alloc(D, dims, sizeof(complex float));
md_gaussian_rand(D, dims, tmp);
md_copy(D, dims, dst, tmp, sizeof(complex float));
md_free(tmp);
return;
}
#endif
//#pragma omp parallel for
for (long i = 0; i < md_calc_size(D, dims); i++)
dst[i] = (float)gaussian_rand();
}
static void nufft_apply_normal(const void* _data, complex float* dst, const complex float* src)
{
const struct nufft_data* data = _data;
if (data->conf.toeplitz) {
toeplitz_mult(data, dst, src);
} else {
complex float* tmp_ksp = md_alloc(data->N + 3, data->ksp_dims, CFL_SIZE);
nufft_apply((const void*)data, tmp_ksp, src);
nufft_apply_adjoint((const void*)data, dst, tmp_ksp);
md_free(tmp_ksp);
}
}
static complex float* compute_linphases(unsigned int N, long lph_dims[N + 3], const long img_dims[N + 3])
{
float shifts[8][3];
int s = 0;
for(int i = 0; i < 8; i++) {
bool skip = false;
for(int j = 0; j < 3; j++) {
shifts[s][j] = 0.;
if (MD_IS_SET(i, j)) {
skip = skip || (1 == img_dims[j]);
shifts[s][j] = -0.5;
}
}
if (!skip)
s++;
}
unsigned int ND = N + 3;
md_select_dims(ND, FFT_FLAGS, lph_dims, img_dims);
lph_dims[N + 0] = s;
complex float* linphase = md_alloc(ND, lph_dims, CFL_SIZE);
for(int i = 0; i < s; i++) {
float shifts2[ND];
for (unsigned int j = 0; j < ND; j++)
shifts2[j] = 0.;
shifts2[0] = shifts[i][0];
shifts2[1] = shifts[i][1];
shifts2[2] = shifts[i][2];
linear_phase(ND, img_dims, shifts2,
linphase + i * md_calc_size(ND, img_dims));
}
return linphase;
}
void sum_apply_normal(const void* _data, complex float* dst, const complex float* src)
{
struct sum_data* data = (struct sum_data*)_data;
if (NULL == data->tmp) {
#ifdef USE_CUDA
data->tmp = (data->use_gpu ? md_alloc_gpu : md_alloc)(DIMS, data->img_dims, CFL_SIZE);
#else
data->tmp = md_alloc(DIMS, data->img_dims, CFL_SIZE);
#endif
}
sum_apply(_data, data->tmp, src);
sum_apply_adjoint( _data, dst, data->tmp);
}
static bool test_md_zavg_flags(unsigned int D, const long idims[D], unsigned int flags, const complex float* in, const complex float* out_ref, bool wavg)
{
long odims[D];
md_select_dims(D, ~flags, odims, idims);
complex float* out = md_alloc(D, odims, CFL_SIZE);
(wavg ? md_zwavg : md_zavg)(D, idims, flags, out, in);
float err = md_znrmse(D, odims, out_ref, out);
md_free(out);
UT_ASSERT(err < UT_TOL);
return true;
}
void overlapandadd(int N, const long dims[N], const long blk[N], complex float* dst, complex float* src1, const long dim2[N], complex float* src2)
{
long ndims[2 * N];
long L[2 * N];
long ndim2[2 * N];
long ndim3[2 * N];
for (int i = 0; i < N; i++) {
assert(0 == dims[i] % blk[i]);
assert(dim2[i] <= blk[i]);
ndims[i * 2 + 1] = dims[i] / blk[i];
ndims[i * 2 + 0] = blk[i];
L[i * 2 + 1] = dims[i] / blk[i];
L[i * 2 + 0] = blk[i] + dim2[i] - 1;
ndim2[i * 2 + 1] = 1;
ndim2[i * 2 + 0] = dim2[i];
ndim3[i * 2 + 1] = dims[i] / blk[i] + 1;
ndim3[i * 2 + 0] = blk[i];
}
complex float* tmp = md_alloc(2 * N, L, CFL_SIZE);
// conv_causal_extend(2 * N, L, tmp, ndims, src1, ndim2, src2);
conv(2 * N, ~0, CONV_EXTENDED, CONV_CAUSAL, L, tmp, ndims, src1, ndim2, src2);
// [------++++||||||||
//long str1[2 * N];
long str2[2 * N];
long str3[2 * N];
//md_calc_strides(2 * N, str1, ndims, 8);
md_calc_strides(2 * N, str2, L, 8);
md_calc_strides(2 * N, str3, ndim3, 8);
md_clear(2 * N, ndim3, dst, CFL_SIZE);
md_zadd2(2 * N, L, str3, dst, str3, dst, str2, tmp);
md_free(tmp);
}
void overlapandsave(int N, const long dims[N], const long blk[N], complex float* dst, complex float* src1, const long dim2[N], complex float* src2)
{
// [------++++
// [------
long ndims[2 * N];
long L[2 * N];
long ndim2[2 * N];
long ndim3[2 * N];
for (int i = 0; i < N; i++) {
assert(0 == dims[i] % blk[i]);
assert(dim2[i] <= blk[i]);
ndims[i * 2 + 1] = dims[i] / blk[i];
ndims[i * 2 + 0] = blk[i];
L[i * 2 + 1] = dims[i] / blk[i];
L[i * 2 + 0] = blk[i] + dim2[i] - 1;
ndim2[i * 2 + 1] = 1;
ndim2[i * 2 + 0] = dim2[i];
ndim3[i * 2 + 1] = dims[i] / blk[i] - 0;
ndim3[i * 2 + 0] = blk[i];
}
complex float* tmp = md_alloc(2 * N, L, CFL_SIZE);
long str1[2 * N];
long str2[2 * N];
long str3[2 * N];
md_calc_strides(2 * N, str1, ndims, 8);
md_calc_strides(2 * N, str2, L, 8);
md_calc_strides(2 * N, str3, ndim3, 8);
md_clear(2 * N, L, tmp, 8);
md_copy2(2 * N, ndim3, str2, tmp, str1, src1, 8);
conv(2 * N, ~0, CONV_VALID, CONV_CAUSAL, ndims, dst, L, tmp, ndim2, src2);
md_free(tmp);
}
void caltwo(const struct ecalib_conf* conf, const long out_dims[DIMS], complex float* out_data, complex float* emaps, const long in_dims[4], complex float* in_data, const long msk_dims[3], const bool* msk)
{
long xx = out_dims[0];
long yy = out_dims[1];
long zz = out_dims[2];
long xh = in_dims[0];
long yh = in_dims[1];
long zh = in_dims[2];
long channels = out_dims[3];
long cosize = channels * (channels + 1) / 2;
assert(DIMS >= 5);
assert(1 == md_calc_size(DIMS - 5, out_dims + 5));
assert(in_dims[3] == cosize);
long cov_dims[4] = { xh, yh, zh, cosize };
long covbig_dims[4] = { xx, yy, zz, cosize };
assert(((xx == 1) && (xh == 1)) || (xx >= xh));
assert(((yy == 1) && (yh == 1)) || (yy >= yh));
assert(((zz == 1) && (zh == 1)) || (zz >= zh));
assert((1 == xh) || (0 == xh % 2));
assert((1 == yh) || (0 == yh % 2));
assert((1 == zh) || (0 == zh % 2));
complex float* imgcov2 = md_alloc(4, covbig_dims, CFL_SIZE);
debug_printf(DP_DEBUG1, "Resize...\n");
sinc_zeropad(4, covbig_dims, imgcov2, cov_dims, in_data);
debug_printf(DP_DEBUG1, "Point-wise eigen-decomposition...\n");
eigenmaps(out_dims, out_data, emaps, imgcov2, msk_dims, msk, conf->orthiter, conf->usegpu);
md_free(imgcov2);
}
int main_itsense(int argc, char* argv[])
{
mini_cmdline(argc, argv, 5, usage_str, help_str);
struct sense_data data;
data.alpha = atof(argv[1]);
complex float* kspace = load_cfl(argv[3], DIMS, data.data_dims);
data.sens = load_cfl(argv[2], DIMS, data.sens_dims);
data.pattern = load_cfl(argv[4], DIMS, data.mask_dims);
// 1 2 4 8
md_select_dims(DIMS, ~COIL_FLAG, data.imgs_dims, data.sens_dims);
assert(check_dimensions(&data));
complex float* image = create_cfl(argv[5], DIMS, data.imgs_dims);
md_calc_strides(DIMS, data.sens_strs, data.sens_dims, CFL_SIZE);
md_calc_strides(DIMS, data.imgs_strs, data.imgs_dims, CFL_SIZE);
md_calc_strides(DIMS, data.data_strs, data.data_dims, CFL_SIZE);
md_calc_strides(DIMS, data.mask_strs, data.mask_dims, CFL_SIZE);
data.tmp = md_alloc(DIMS, data.data_dims, CFL_SIZE);
num_init();
sense_reco(&data, image, kspace);
unmap_cfl(DIMS, data.imgs_dims, image);
unmap_cfl(DIMS, data.mask_dims, data.pattern);
unmap_cfl(DIMS, data.sens_dims, data.sens);
unmap_cfl(DIMS, data.data_dims, data.sens);
md_free(data.tmp);
exit(0);
}
static void perturb(const long dims[2], complex float* vecs, float amt)
{
complex float* noise = md_alloc(2, dims, CFL_SIZE);
md_gaussian_rand(2, dims, noise);
for (long j = 0; j < dims[1]; j++) {
float nrm = md_znorm(1, dims, noise + j * dims[0]);
complex float val = amt / nrm;
md_zsmul(1, dims, noise + j * dims[0], noise + j * dims[0], val);
}
md_zadd(2, dims, vecs, vecs, noise);
for (long j = 0; j < dims[1]; j++) {
float nrm = md_znorm(1, dims, vecs + j * dims[0]);
complex float val = 1 / nrm;
md_zsmul(1, dims, vecs + j * dims[0], vecs + j * dims[0], val);
}
md_free(noise);
}
static struct ufft_data* ufft_create_data(const long ksp_dims[DIMS], const long pat_dims[DIMS], const complex float* pat, unsigned int flags, bool use_gpu)
{
PTR_ALLOC(struct ufft_data, data);
data->flags = flags;
data->use_gpu = use_gpu;
md_copy_dims(DIMS, data->pat_dims, pat_dims);
md_copy_dims(DIMS, data->ksp_dims, ksp_dims);
md_calc_strides(DIMS, data->pat_strs, pat_dims, CFL_SIZE);
md_calc_strides(DIMS, data->ksp_strs, ksp_dims, CFL_SIZE);
#ifdef USE_CUDA
data->pat = (use_gpu ? md_alloc_gpu : md_alloc)(DIMS, data->pat_dims, CFL_SIZE);
#else
data->pat = md_alloc(DIMS, data->pat_dims, CFL_SIZE);
#endif
md_copy(DIMS, data->pat_dims, data->pat, pat, CFL_SIZE);
data->fft_op = linop_fftc_create(DIMS, ksp_dims, flags, use_gpu);
return data;
}
static bool test_md_swap(void)
{
enum { N = 4 };
long dims[N] = { 10, 10, 10, 10 };
complex float* a = md_alloc(N, dims, sizeof(complex float));
complex float* b = md_alloc(N, dims, sizeof(complex float));
complex float* c = md_alloc(N, dims, sizeof(complex float));
md_gaussian_rand(N, dims, a);
md_gaussian_rand(N, dims, b);
md_gaussian_rand(N, dims, c);
complex float* d = md_alloc(N, dims, sizeof(complex float));
complex float* e = md_alloc(N, dims, sizeof(complex float));
complex float* f = md_alloc(N, dims, sizeof(complex float));
md_copy(N, dims, d, a, sizeof(complex float));
md_copy(N, dims, e, b, sizeof(complex float));
md_copy(N, dims, f, c, sizeof(complex float));
md_circular_swap(3, N, dims, (void*[]){ a, b, c }, sizeof(complex float));
void walsh(const long bsize[3], const long dims[DIMS], complex float* sens, const long caldims[DIMS], const complex float* data)
{
assert(1 == caldims[MAPS_DIM]);
assert(1 == dims[MAPS_DIM]);
int channels = caldims[COIL_DIM];
int cosize = channels * (channels + 1) / 2;
assert(dims[COIL_DIM] == cosize);
long dims1[DIMS];
md_copy_dims(DIMS, dims1, dims);
dims1[COIL_DIM] = channels;
long kdims[4];
kdims[0] = MIN(bsize[0], dims[0]);
kdims[1] = MIN(bsize[1], dims[1]);
kdims[2] = MIN(bsize[2], dims[2]);
md_resize_center(DIMS, dims1, sens, caldims, data, CFL_SIZE);
ifftc(DIMS, dims1, FFT_FLAGS, sens, sens);
long odims[DIMS];
md_copy_dims(DIMS, odims, dims1);
for (int i = 0; i < 3; i++)
odims[i] = dims[i] + kdims[i] - 1;
complex float* tmp = md_alloc(DIMS, odims, CFL_SIZE);
#if 0
md_resizec(DIMS, odims, tmp, dims1, sens, CFL_SIZE);
#else
long cen[DIMS] = { 0 };
for (int i = 0; i < 3; i++)
cen[i] = (odims[i] - dims[i] + 1) / 2;
complex float* tmp1 = md_alloc(DIMS, odims, CFL_SIZE);
md_circ_ext(DIMS, odims, tmp1, dims1, sens, CFL_SIZE);
// md_resize(DIMS, odims, tmp1, dims1, sens, CFL_SIZE);
md_circ_shift(DIMS, odims, cen, tmp, tmp1, CFL_SIZE);
md_free(tmp1);
#endif
long calmat_dims[2];
complex float* cm = calibration_matrix(calmat_dims, kdims, odims, tmp);
md_free(tmp);
int xh = dims[0];
int yh = dims[1];
int zh = dims[2];
int pixels = calmat_dims[1] / channels;
#pragma omp parallel for
for (int k = 0; k < zh; k++) {
complex float in[channels][pixels];
complex float cov[cosize];
for (int j = 0; j < yh; j++) {
for (int i = 0; i < xh; i++) {
for (int c = 0; c < channels; c++)
for (int p = 0; p < pixels; p++)
in[c][p] = cm[((((c * pixels + p) * zh) + k) * yh + j) * xh + i];
gram_matrix2(channels, cov, pixels, in);
for (int l = 0; l < cosize; l++)
sens[(((l * zh) + k) * yh + j) * xh + i] = cov[l];
}
}
}
}
int main_nlinv(int argc, char* argv[])
{
int iter = 8;
float l1 = -1.;
bool waterfat = false;
bool rvc = false;
bool normalize = true;
float restrict_fov = -1.;
float csh[3] = { 0., 0., 0. };
bool usegpu = false;
const char* psf = NULL;
const struct opt_s opts[] = {
{ 'l', true, opt_float, &l1, NULL },
{ 'i', true, opt_int, &iter, NULL },
{ 'c', false, opt_set, &rvc, NULL },
{ 'N', false, opt_clear, &normalize, NULL },
{ 'f', true, opt_float, &restrict_fov, NULL },
{ 'p', true, opt_string, &psf, NULL },
{ 'g', false, opt_set, &usegpu, NULL },
};
cmdline(&argc, argv, 2, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
num_init();
assert(iter > 0);
long ksp_dims[DIMS];
complex float* kspace_data = load_cfl(argv[1], DIMS, ksp_dims);
long dims[DIMS];
md_copy_dims(DIMS, dims, ksp_dims);
if (waterfat)
dims[CSHIFT_DIM] = 2;
long img_dims[DIMS];
md_select_dims(DIMS, FFT_FLAGS|CSHIFT_FLAG, img_dims, dims);
long img_strs[DIMS];
md_calc_strides(DIMS, img_strs, img_dims, CFL_SIZE);
complex float* image = create_cfl(argv[2], DIMS, img_dims);
long msk_dims[DIMS];
md_select_dims(DIMS, FFT_FLAGS, msk_dims, dims);
long msk_strs[DIMS];
md_calc_strides(DIMS, msk_strs, msk_dims, CFL_SIZE);
complex float* mask;
complex float* norm = md_alloc(DIMS, msk_dims, CFL_SIZE);
complex float* sens;
if (4 == argc) {
sens = create_cfl(argv[3], DIMS, ksp_dims);
} else {
sens = md_alloc(DIMS, ksp_dims, CFL_SIZE);
}
complex float* pattern = NULL;
long pat_dims[DIMS];
if (NULL != psf) {
pattern = load_cfl(psf, DIMS, pat_dims);
// FIXME: check compatibility
} else {
pattern = md_alloc(DIMS, img_dims, CFL_SIZE);
estimate_pattern(DIMS, ksp_dims, COIL_DIM, pattern, kspace_data);
}
if (waterfat) {
size_t size = md_calc_size(DIMS, msk_dims);
md_copy(DIMS, msk_dims, pattern + size, pattern, CFL_SIZE);
long shift_dims[DIMS];
md_select_dims(DIMS, FFT_FLAGS, shift_dims, msk_dims);
long shift_strs[DIMS];
md_calc_strides(DIMS, shift_strs, shift_dims, CFL_SIZE);
complex float* shift = md_alloc(DIMS, shift_dims, CFL_SIZE);
unsigned int X = shift_dims[READ_DIM];
unsigned int Y = shift_dims[PHS1_DIM];
unsigned int Z = shift_dims[PHS2_DIM];
for (unsigned int x = 0; x < X; x++)
for (unsigned int y = 0; y < Y; y++)
for (unsigned int z = 0; z < Z; z++)
shift[(z * Z + y) * Y + x] = cexp(2.i * M_PI * ((csh[0] * x) / X + (csh[1] * y) / Y + (csh[2] * z) / Z));
md_zmul2(DIMS, msk_dims, msk_strs, pattern + size, msk_strs, pattern + size, shift_strs, shift);
md_free(shift);
}
#if 0
float scaling = 1. / estimate_scaling(ksp_dims, NULL, kspace_data);
#else
float scaling = 100. / md_znorm(DIMS, ksp_dims, kspace_data);
#endif
debug_printf(DP_INFO, "Scaling: %f\n", scaling);
md_zsmul(DIMS, ksp_dims, kspace_data, kspace_data, scaling);
if (-1. == restrict_fov) {
mask = md_alloc(DIMS, msk_dims, CFL_SIZE);
md_zfill(DIMS, msk_dims, mask, 1.);
} else {
float restrict_dims[DIMS] = { [0 ... DIMS - 1] = 1. };
restrict_dims[0] = restrict_fov;
restrict_dims[1] = restrict_fov;
restrict_dims[2] = restrict_fov;
mask = compute_mask(DIMS, msk_dims, restrict_dims);
}
#ifdef USE_CUDA
if (usegpu) {
complex float* kspace_gpu = md_alloc_gpu(DIMS, ksp_dims, CFL_SIZE);
md_copy(DIMS, ksp_dims, kspace_gpu, kspace_data, CFL_SIZE);
noir_recon(dims, iter, l1, image, NULL, pattern, mask, kspace_gpu, rvc, usegpu);
md_free(kspace_gpu);
md_zfill(DIMS, ksp_dims, sens, 1.);
} else
#endif
noir_recon(dims, iter, l1, image, sens, pattern, mask, kspace_data, rvc, usegpu);
if (normalize) {
md_zrss(DIMS, ksp_dims, COIL_FLAG, norm, sens);
md_zmul2(DIMS, img_dims, img_strs, image, img_strs, image, msk_strs, norm);
}
if (4 == argc) {
long strs[DIMS];
md_calc_strides(DIMS, strs, ksp_dims, CFL_SIZE);
if (norm)
md_zdiv2(DIMS, ksp_dims, strs, sens, strs, sens, img_strs, norm);
fftmod(DIMS, ksp_dims, FFT_FLAGS, sens, sens);
unmap_cfl(DIMS, ksp_dims, sens);
} else {
md_free(sens);
}
md_free(norm);
md_free(mask);
if (NULL != psf)
unmap_cfl(DIMS, pat_dims, pattern);
else
md_free(pattern);
unmap_cfl(DIMS, img_dims, image);
unmap_cfl(DIMS, ksp_dims, kspace_data);
exit(0);
}
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;
}
int main_nufft(int argc, char* argv[])
{
int c;
bool adjoint = false;
bool inverse = false;
bool toeplitz = false;
bool precond = false;
bool use_gpu = false;
bool two = false;
bool calib = false;
bool sizeinit = false;
bool stoch = false;
long coilim_dims[DIMS];
md_singleton_dims(DIMS, coilim_dims);
int maxiter = 50;
float lambda = 0.00;
const char* pat_str = NULL;
while (-1 != (c = getopt(argc, argv, "d:m:l:p:aihCto:w:2:c:S"))) {
switch (c) {
case '2':
two = true;
break;
case 'i':
inverse = true;
break;
case 'a':
adjoint = true;
break;
case 'C':
precond = true;
break;
case 'S':
stoch = true;
break;
case 'c':
calib = true;
inverse = true;
case 'd':
sscanf(optarg, "%ld:%ld:%ld", &coilim_dims[0], &coilim_dims[1], &coilim_dims[2]);
sizeinit = true;
break;
case 'm':
maxiter = atoi(optarg);
break;
case 'p':
pat_str = strdup(optarg);
break;
case 'l':
lambda = atof(optarg);
break;
case 't':
toeplitz = true;
break;
case 'h':
usage(argv[0], stdout);
help();
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if (argc - optind != 3) {
usage(argv[0], stderr);
exit(1);
}
// Read trajectory
long traj_dims[2];
complex float* traj = load_cfl(argv[optind + 0], 2, traj_dims);
assert(3 == traj_dims[0]);
if (!sizeinit)
estimate_im_dims(coilim_dims, traj_dims, traj);
num_init();
// Load pattern / density compensation (if any)
complex float* pat = NULL;
long pat_dims[2];
if (pat_str) {
pat = load_cfl(pat_str, 2, pat_dims);
assert(pat_dims[0] == 1);
assert(pat_dims[1] == traj_dims[1]);
}
if (inverse || adjoint) {
long ksp_dims[DIMS];
const complex float* ksp = load_cfl(argv[optind + 1], DIMS, ksp_dims);
coilim_dims[COIL_DIM] = ksp_dims[COIL_DIM];
long out_dims[DIMS];
if (calib) {
md_singleton_dims(DIMS, out_dims);
estimate_im_dims(out_dims, traj_dims, traj);
out_dims[COIL_DIM] = ksp_dims[COIL_DIM];
} else {
md_copy_dims(DIMS, out_dims, coilim_dims);
}
complex float* out = create_cfl(argv[optind + 2], DIMS, out_dims);
complex float* img = out;
if (calib)
img = md_alloc(DIMS, coilim_dims, CFL_SIZE);
md_clear(DIMS, coilim_dims, img, CFL_SIZE);
struct iter_conjgrad_conf cgconf = iter_conjgrad_defaults;
cgconf.maxiter = maxiter;
cgconf.l2lambda = 0.;
cgconf.tol = 0;
const struct linop_s* nufft_op;
// Get nufft_op
if (two)
#ifdef BERKELEY_SVN
nufft_op = nufft2_create(ksp_dims, coilim_dims, traj, pat, toeplitz, precond, &cgconf, use_gpu);
#else
assert(!two);
#endif
else
int
g_process_math_string(__g_handle hdl, char *string, pmda mdm, pmda chain,
int *ret, void **p_ret, uint32_t flags, uint32_t int_flags)
{
g_setjmp(0, "g_process_math_string", NULL, NULL);
char *ptr = string, *left, oper = 0x0;
size_t i;
size_t sin_len = strlen(string);
if (sin_len == 0)
{
return 0;
}
//g_del_char(string, string_p, 0x20);
int f_ret = 0;
while (ptr[0])
{
if (ptr[0] == 0x0 || ptr[0] == 0x23 || ptr[0] == 0x7D || ptr[0] == 0x29
|| ptr[0] == 0x3A)
{
if (ptr[0] == 0x29)
{
if (!(int_flags & F_PROC_MATH_STR_INB))
{
f_ret = 0;
goto f_end;
}
else
{
*p_ret = ptr;
}
}
else
{
/*if ((int_flags & F_PROC_MATH_STR_INB))
{
return 12;
}*/
}
break;
}
while (ptr[0] == 0x20)
{
ptr++;
}
if (ptr[0] == 0x28)
{
if (ptr[1] == 0x29)
{
break;
}
pmda object = (pmda) md_alloc(chain, sizeof(mda));
if (NULL == object)
{
f_ret = -1;
goto f_end;
}
md_init(object, 8);
char *pms_ret = "";
ptr++;
int r = g_process_math_string(hdl, ptr, object, chain, ret,
(void*) &pms_ret, flags, int_flags | F_PROC_MATH_STR_INB);
if (0 != r)
{
ERROR(
"g_process_math_string (F_PROC_MATH_STR_INB): FAILED: [%d]: %s\n",
r, pms_ret);
md_free(object);
f_ret = r;
goto f_end;
}
else
{
__g_math math_c = (__g_math ) m_find_last_dtype(chain,
chain->pos);
__g_math math = (__g_math ) md_alloc(mdm, sizeof(_g_math));
if (NULL == math)
{
f_ret = 16;
goto f_end;
}
if (NULL == math_c)
{
f_ret = 17;
goto f_end;
}
math->next = object;
math->flags |= F_MATH_NITEM;
pms_ret++;
ptr = pms_ret;
math->flags |= (math_c->flags & F_MATH_TYPES);
__g_math math_p = (__g_math ) m_find_prev_dtype(mdm,
(p_md_obj) mdm->pos);
math->_m_p = g_get_math_m_p(math, math_p);
if (!(is_ascii_arith_bin_oper(ptr[0])))
{
if (NULL == math_c->_m_p)
{
f_ret = 21;
goto f_end;
}
math->op_t = m_get_op_proc(ptr[0], math_c);
if ( NULL == math->op_t)
{
f_ret = 22;
goto f_end;
}
//math->_m_p = math_c->_m_p;
}
math->vb = math_c->vb;
math->l_off = math_c->l_off;
if (ptr[0] == 0x0 || ptr[0] == 0x23 || ptr[0] == 0x7D
|| ptr[0] == 0x3A || ptr[0] == 0x29)
{
continue;
}
ptr++;
continue;
}
}
i = 0;
left = ptr;
uint32_t add_flags = 0;
char in_dummy[8192];
if (ptr[0] == 0x5B)
{
void *l_next_ref;
char *s_ptr = l_mppd_shell_ex(ptr, in_dummy, sizeof(in_dummy),
&l_next_ref,
0x5B,
0x5D, F_MPPD_SHX_TZERO);
if (NULL == s_ptr)
{
f_ret = 130;
goto f_end;
}
if (NULL == l_next_ref || ((char*) l_next_ref)[0] == 0x0)
{
f_ret = 131;
goto f_end;
}
left = s_ptr;
ptr = l_next_ref;
add_flags |= F_MATH_STRCONV;
}
else
{
if (ptr[0] == 0x2B || ptr[0] == 0x2D)
{
ptr++;
}
while (is_ascii_arith_bin_oper(ptr[0]) && ptr[0] && ptr[0] != 0x23
&& ptr[0] != 0x7D && ptr[0] != 0x29 && ptr[0] != 0x3A
&& ptr[0] != 0x29 && ptr[0] != 0x20)
{
i++;
ptr++;
}
if (!i)
{
f_ret = 1;
goto f_end;
}
}
if (ptr[0] && ptr[0] != 0x23 && ptr[0] != 0x7D && ptr[0] != 0x29
&& ptr[0] != 0x3A && ptr[0] != 0x29)
{
if (is_ascii_arith_bin_oper(ptr[0]))
{
f_ret = 23;
goto f_end;
}
if (ptr[0] == 0x3C || ptr[0] == 0x3E)
{
if (ptr[0] != ptr[1])
{
f_ret = 2;
goto f_end;
}
ptr++;
}
oper = ptr[0];
ptr++;
}
else
{
oper = 0x0;
}
__g_math mm;
*ret = g_build_math_packet(hdl, left, oper, mdm, &mm, flags | add_flags);
if (*ret)
{
f_ret = 6;
goto f_end;
}
if (oper == 0x7E && (ptr[0] == 0x7D || ptr[0] == 0x29))
{
*ret = g_build_math_packet(hdl, left, oper, mdm, NULL,
flags | add_flags);
if (*ret)
{
f_ret = 7;
goto f_end;
}
}
}
f_end: ;
//free(string_p);
return f_ret;
}
void overlapandsave2NE(int N, unsigned int flags, const long blk[N], const long odims[N], complex float* dst, const long dims1[N], complex float* src1, const long dims2[N], complex float* src2, const long mdims[N], complex float* msk)
{
long dims1B[N];
long tdims[2 * N];
long nodims[2 * N];
long ndims1[2 * N];
long ndims2[2 * N];
long shift[2 * N];
unsigned int nflags = 0;
for (int i = 0; i < N; i++) {
if (MD_IS_SET(flags, i)) {
nflags = MD_SET(nflags, 2 * i);
assert(1 == dims2[i] % 2);
assert(0 == blk[i] % 2);
assert(0 == dims1[i] % 2);
assert(0 == odims[i] % blk[i]);
assert(0 == dims1[i] % blk[i]);
assert(dims1[i] == odims[i]);
assert(dims2[i] <= blk[i]);
assert(dims1[i] >= dims2[i]);
// blocked output
nodims[i * 2 + 1] = odims[i] / blk[i];
nodims[i * 2 + 0] = blk[i];
// expanded temporary storage
tdims[i * 2 + 1] = dims1[i] / blk[i];
tdims[i * 2 + 0] = blk[i] + dims2[i] - 1;
// blocked input
// ---|---,---,---|---
// + +++ +
// + +++ +
// resized input
dims1B[i] = dims1[i] + 2 * blk[i];
ndims1[i * 2 + 1] = dims1[i] / blk[i] + 2; // do we need two full blocks?
ndims1[i * 2 + 0] = blk[i];
shift[i * 2 + 1] = 0;
shift[i * 2 + 0] = blk[i] - (dims2[i] - 1) / 2;
// kernel
ndims2[i * 2 + 1] = 1;
ndims2[i * 2 + 0] = dims2[i];
} else {
nodims[i * 2 + 1] = 1;
nodims[i * 2 + 0] = odims[i];
tdims[i * 2 + 1] = 1;
tdims[i * 2 + 0] = dims1[i];
ndims1[i * 2 + 1] = 1;
ndims1[i * 2 + 0] = dims1[i];
shift[i * 2 + 1] = 0;
shift[i * 2 + 0] = 0;
dims1B[i] = dims1[i];
ndims2[i * 2 + 1] = 1;
ndims2[i * 2 + 0] = dims2[i];
}
}
complex float* src1B = md_alloc(N, dims1B, CFL_SIZE);
complex float* tmp = md_alloc(2 * N, tdims, CFL_SIZE);
complex float* tmpX = md_alloc(N, odims, CFL_SIZE);
long str1[2 * N];
long str2[2 * N];
md_calc_strides(2 * N, str1, ndims1, sizeof(complex float));
md_calc_strides(2 * N, str2, tdims, sizeof(complex float));
long off = md_calc_offset(2 * N, str1, shift);
md_resize_center(N, dims1B, src1B, dims1, src1, sizeof(complex float));
// we can loop here
md_copy2(2 * N, tdims, str2, tmp, str1, ((void*)src1B) + off, sizeof(complex float));
conv(2 * N, nflags, CONV_VALID, CONV_SYMMETRIC, nodims, tmpX, tdims, tmp, ndims2, src2);
long ostr[N];
long mstr[N];
md_calc_strides(N, ostr, odims, sizeof(complex float));
md_calc_strides(N, mstr, mdims, sizeof(complex float));
md_zmul2(N, odims, ostr, tmpX, ostr, tmpX, mstr, msk);
convH(2 * N, nflags, CONV_VALID, CONV_SYMMETRIC, tdims, tmp, nodims, tmpX, ndims2, src2);
md_clear(N, dims1B, src1B, sizeof(complex float));
md_zadd2(2 * N, tdims, str1, ((void*)src1B) + off, str1, ((void*)src1B) + off, str2, tmp);
//
md_resize_center(N, dims1, dst, dims1B, src1B, sizeof(complex float));
md_free(src1B);
md_free(tmpX);
md_free(tmp);
}
int
g_build_math_packet(__g_handle hdl, char *field, char oper, pmda mdm,
__g_math *ret, uint32_t flags)
{
g_setjmp(0, "g_build_math_packet", NULL, NULL);
int rt = 0;
md_init(mdm, 16);
__g_math p_math = (__g_math ) mdm->pos->ptr;
__g_math math = (__g_math ) md_alloc(mdm, sizeof(_g_math));
if (!math)
{
rt = 1;
goto end;
}
math->flags |= flags;
if ((rt = g_get_math_g_t_ptr(hdl, field, math, 0, p_math)))
{
goto end;
}
if (!(math->flags & F_MATH_TYPES))
{
rt = 6;
goto end;
}
if (math->_m_p)
{
math->op_t = m_get_op_proc(oper, math);
if ( NULL == math->op_t)
{
rt = 7;
goto end;
}
/*if (oper == 0x7E)
{
math->flags |= F_MATH_IS_SQRT;
}*/
}
if (ret)
{
*ret = math;
}
end:
if (rt)
{
md_unlink(mdm, mdm->pos);
}
return rt;
}
int main_pics(int argc, char* argv[])
{
// Initialize default parameters
struct sense_conf conf = sense_defaults;
bool use_gpu = false;
bool randshift = true;
unsigned int maxiter = 30;
float step = -1.;
// Start time count
double start_time = timestamp();
// Read input options
struct nufft_conf_s nuconf = nufft_conf_defaults;
nuconf.toeplitz = false;
float restrict_fov = -1.;
const char* pat_file = NULL;
const char* traj_file = NULL;
bool scale_im = false;
bool eigen = false;
float scaling = 0.;
unsigned int llr_blk = 8;
const char* image_truth_file = NULL;
bool im_truth = false;
const char* image_start_file = NULL;
bool warm_start = false;
bool hogwild = false;
bool fast = false;
float admm_rho = iter_admm_defaults.rho;
unsigned int admm_maxitercg = iter_admm_defaults.maxitercg;
struct opt_reg_s ropts;
ropts.r = 0;
ropts.algo = CG;
ropts.lambda = -1.;
const struct opt_s opts[] = {
{ 'l', true, opt_reg, &ropts, "1/-l2\t\ttoggle l1-wavelet or l2 regularization." },
OPT_FLOAT('r', &ropts.lambda, "lambda", "regularization parameter"),
{ 'R', true, opt_reg, &ropts, " <T>:A:B:C\tgeneralized regularization options (-Rh for help)" },
OPT_SET('c', &conf.rvc, "real-value constraint"),
OPT_FLOAT('s', &step, "step", "iteration stepsize"),
OPT_UINT('i', &maxiter, "iter", "max. number of iterations"),
OPT_STRING('t', &traj_file, "file", "k-space trajectory"),
OPT_CLEAR('n', &randshift, "disable random wavelet cycle spinning"),
OPT_SET('g', &use_gpu, "use GPU"),
OPT_STRING('p', &pat_file, "file", "pattern or weights"),
OPT_SELECT('I', enum algo_t, &ropts.algo, IST, "(select IST)"),
OPT_UINT('b', &llr_blk, "blk", "Lowrank block size"),
OPT_SET('e', &eigen, "Scale stepsize based on max. eigenvalue"),
OPT_SET('H', &hogwild, "(hogwild)"),
OPT_SET('F', &fast, "(fast)"),
OPT_STRING('T', &image_truth_file, "file", "(truth file)"),
OPT_STRING('W', &image_start_file, "<img>", "Warm start with <img>"),
OPT_INT('d', &debug_level, "level", "Debug level"),
OPT_INT('O', &conf.rwiter, "rwiter", "(reweighting)"),
OPT_FLOAT('o', &conf.gamma, "gamma", "(reweighting)"),
OPT_FLOAT('u', &admm_rho, "rho", "ADMM rho"),
OPT_UINT('C', &admm_maxitercg, "iter", "ADMM max. CG iterations"),
OPT_FLOAT('q', &conf.cclambda, "cclambda", "(cclambda)"),
OPT_FLOAT('f', &restrict_fov, "rfov", "restrict FOV"),
OPT_SELECT('m', enum algo_t, &ropts.algo, ADMM, "Select ADMM"),
OPT_FLOAT('w', &scaling, "val", "scaling"),
OPT_SET('S', &scale_im, "Re-scale the image after reconstruction"),
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (NULL != image_truth_file)
im_truth = true;
if (NULL != image_start_file)
warm_start = true;
long max_dims[DIMS];
long map_dims[DIMS];
long pat_dims[DIMS];
long img_dims[DIMS];
long coilim_dims[DIMS];
long ksp_dims[DIMS];
long traj_dims[DIMS];
// load kspace and maps and get dimensions
complex float* kspace = load_cfl(argv[1], DIMS, ksp_dims);
complex float* maps = load_cfl(argv[2], DIMS, map_dims);
complex float* traj = NULL;
if (NULL != traj_file)
traj = load_cfl(traj_file, DIMS, traj_dims);
md_copy_dims(DIMS, max_dims, ksp_dims);
md_copy_dims(5, max_dims, map_dims);
md_select_dims(DIMS, ~COIL_FLAG, img_dims, max_dims);
md_select_dims(DIMS, ~MAPS_FLAG, coilim_dims, max_dims);
if (!md_check_compat(DIMS, ~(MD_BIT(MAPS_DIM)|FFT_FLAGS), img_dims, map_dims))
error("Dimensions of image and sensitivities do not match!\n");
assert(1 == ksp_dims[MAPS_DIM]);
(use_gpu ? num_init_gpu : num_init)();
// print options
if (use_gpu)
debug_printf(DP_INFO, "GPU reconstruction\n");
if (map_dims[MAPS_DIM] > 1)
debug_printf(DP_INFO, "%ld maps.\nESPIRiT reconstruction.\n", map_dims[MAPS_DIM]);
if (hogwild)
debug_printf(DP_INFO, "Hogwild stepsize\n");
if (im_truth)
debug_printf(DP_INFO, "Compare to truth\n");
// initialize sampling pattern
complex float* pattern = NULL;
if (NULL != pat_file) {
pattern = load_cfl(pat_file, DIMS, pat_dims);
assert(md_check_compat(DIMS, COIL_FLAG, ksp_dims, pat_dims));
} else {
md_select_dims(DIMS, ~COIL_FLAG, pat_dims, ksp_dims);
pattern = md_alloc(DIMS, pat_dims, CFL_SIZE);
estimate_pattern(DIMS, ksp_dims, COIL_DIM, pattern, kspace);
}
if ((NULL != traj_file) && (NULL == pat_file)) {
md_free(pattern);
pattern = NULL;
nuconf.toeplitz = true;
} else {
// print some statistics
long T = md_calc_size(DIMS, pat_dims);
long samples = (long)pow(md_znorm(DIMS, pat_dims, pattern), 2.);
debug_printf(DP_INFO, "Size: %ld Samples: %ld Acc: %.2f\n", T, samples, (float)T / (float)samples);
}
if (NULL == traj_file) {
fftmod(DIMS, ksp_dims, FFT_FLAGS, kspace, kspace);
fftmod(DIMS, map_dims, FFT_FLAGS, maps, maps);
}
// apply fov mask to sensitivities
if (-1. != restrict_fov) {
float restrict_dims[DIMS] = { [0 ... DIMS - 1] = 1. };
restrict_dims[0] = restrict_fov;
restrict_dims[1] = restrict_fov;
restrict_dims[2] = restrict_fov;
apply_mask(DIMS, map_dims, maps, restrict_dims);
}
/**
*
* NUFFT operator initialization
*
* @param N - number of dimensions
* @param ksp_dims - kspace dimension
* @param cim_dims - coil images dimension
* @param traj - trajectory
* @param conf - configuration options
* @param use_gpu - use gpu boolean
*
*/
struct linop_s* nufft_create(unsigned int N, const long ksp_dims[N], const long cim_dims[N], const long traj_dims[N], const complex float* traj, const complex float* weights, struct nufft_conf_s conf, bool use_gpu)
{
struct nufft_data* data = (struct nufft_data*)xmalloc(sizeof(struct nufft_data));
data->N = N;
data->use_gpu = use_gpu;
data->traj = traj;
data->conf = conf;
data->width = 3.;
data->beta = calc_beta(2., data->width);
// get dims
assert(md_check_compat(N - 3, 0, ksp_dims + 3, cim_dims + 3));
unsigned int ND = N + 3;
data->ksp_dims = xmalloc(ND * sizeof(long));
data->cim_dims = xmalloc(ND * sizeof(long));
data->cml_dims = xmalloc(ND * sizeof(long));
data->img_dims = xmalloc(ND * sizeof(long));
data->trj_dims = xmalloc(ND * sizeof(long));
data->lph_dims = xmalloc(ND * sizeof(long));
data->psf_dims = xmalloc(ND * sizeof(long));
data->wgh_dims = xmalloc(ND * sizeof(long));
data->ksp_strs = xmalloc(ND * sizeof(long));
data->cim_strs = xmalloc(ND * sizeof(long));
data->cml_strs = xmalloc(ND * sizeof(long));
data->img_strs = xmalloc(ND * sizeof(long));
data->trj_strs = xmalloc(ND * sizeof(long));
data->lph_strs = xmalloc(ND * sizeof(long));
data->psf_strs = xmalloc(ND * sizeof(long));
data->wgh_strs = xmalloc(ND * sizeof(long));
md_singleton_dims(ND, data->cim_dims);
md_singleton_dims(ND, data->ksp_dims);
md_copy_dims(N, data->cim_dims, cim_dims);
md_copy_dims(N, data->ksp_dims, ksp_dims);
md_select_dims(ND, FFT_FLAGS, data->img_dims, data->cim_dims);
assert(3 == traj_dims[0]);
assert(traj_dims[1] == ksp_dims[1]);
assert(traj_dims[2] == ksp_dims[2]);
assert(md_check_compat(N - 3, ~0, traj_dims + 3, ksp_dims + 3));
assert(md_check_bounds(N - 3, ~0, traj_dims + 3, ksp_dims + 3));
md_singleton_dims(ND, data->trj_dims);
md_copy_dims(N, data->trj_dims, traj_dims);
// get strides
md_calc_strides(ND, data->cim_strs, data->cim_dims, CFL_SIZE);
md_calc_strides(ND, data->img_strs, data->img_dims, CFL_SIZE);
md_calc_strides(ND, data->trj_strs, data->trj_dims, CFL_SIZE);
md_calc_strides(ND, data->ksp_strs, data->ksp_dims, CFL_SIZE);
data->weights = NULL;
if (NULL != weights) {
md_singleton_dims(ND, data->wgh_dims);
md_select_dims(N, ~MD_BIT(0), data->wgh_dims, data->trj_dims);
md_calc_strides(ND, data->wgh_strs, data->wgh_dims, CFL_SIZE);
complex float* tmp = md_alloc(ND, data->wgh_dims, CFL_SIZE);
md_copy(ND, data->wgh_dims, tmp, weights, CFL_SIZE);
data->weights = tmp;
}
complex float* roll = md_alloc(ND, data->img_dims, CFL_SIZE);
rolloff_correction(2., data->width, data->beta, data->img_dims, roll);
data->roll = roll;
complex float* linphase = compute_linphases(N, data->lph_dims, data->img_dims);
md_calc_strides(ND, data->lph_strs, data->lph_dims, CFL_SIZE);
if (!conf.toeplitz)
md_zmul2(ND, data->lph_dims, data->lph_strs, linphase, data->lph_strs, linphase, data->img_strs, data->roll);
fftmod(ND, data->lph_dims, FFT_FLAGS, linphase, linphase);
fftscale(ND, data->lph_dims, FFT_FLAGS, linphase, linphase);
// md_zsmul(ND, data->lph_dims, linphase, linphase, 1. / (float)(data->trj_dims[1] * data->trj_dims[2]));
complex float* fftm = md_alloc(ND, data->img_dims, CFL_SIZE);
md_zfill(ND, data->img_dims, fftm, 1.);
fftmod(ND, data->img_dims, FFT_FLAGS, fftm, fftm);
data->fftmod = fftm;
data->linphase = linphase;
data->psf = NULL;
if (conf.toeplitz) {
#if 0
md_copy_dims(ND, data->psf_dims, data->lph_dims);
#else
md_copy_dims(3, data->psf_dims, data->lph_dims);
md_copy_dims(ND - 3, data->psf_dims + 3, data->trj_dims + 3);
data->psf_dims[N] = data->lph_dims[N];
#endif
md_calc_strides(ND, data->psf_strs, data->psf_dims, CFL_SIZE);
data->psf = compute_psf2(N, data->psf_dims, data->trj_dims, data->traj, data->weights);
}
md_copy_dims(ND, data->cml_dims, data->cim_dims);
data->cml_dims[N + 0] = data->lph_dims[N + 0];
md_calc_strides(ND, data->cml_strs, data->cml_dims, CFL_SIZE);
data->cm2_dims = xmalloc(ND * sizeof(long));
// !
md_copy_dims(ND, data->cm2_dims, data->cim_dims);
for (int i = 0; i < 3; i++)
data->cm2_dims[i] = (1 == cim_dims[i]) ? 1 : (2 * cim_dims[i]);
data->grid = md_alloc(ND, data->cml_dims, CFL_SIZE);
data->fft_op = linop_fft_create(ND, data->cml_dims, FFT_FLAGS, use_gpu);
return linop_create(N, ksp_dims, N, cim_dims,
data, nufft_apply, nufft_apply_adjoint, nufft_apply_normal, NULL, nufft_free_data);
}
// [RING] Caclucate intersection points
static void calc_intersections(unsigned int Nint, unsigned int N, unsigned int no_intersec_sp, float dist[2][Nint], long idx[2][Nint], const float angles[N], const long kc_dims[DIMS], const complex float* kc, const int ROI)
{
long spoke_dims[DIMS];
md_copy_dims(DIMS, spoke_dims, kc_dims);
spoke_dims[PHS2_DIM] = 1;
complex float* spoke_i = md_alloc(DIMS, spoke_dims, CFL_SIZE);
complex float* spoke_j = md_alloc(DIMS, spoke_dims, CFL_SIZE);
long pos_i[DIMS] = { 0 };
long pos_j[DIMS] = { 0 };
long coilPixel_dims[DIMS];
md_copy_dims(DIMS, coilPixel_dims, spoke_dims);
coilPixel_dims[PHS1_DIM] = 1;
complex float* coilPixel_l = md_alloc(DIMS, coilPixel_dims, CFL_SIZE);
complex float* coilPixel_m = md_alloc(DIMS, coilPixel_dims, CFL_SIZE);
complex float* diff = md_alloc(DIMS, coilPixel_dims, CFL_SIZE);
long diff_rss_dims[DIMS];
md_copy_dims(DIMS, diff_rss_dims, coilPixel_dims);
diff_rss_dims[COIL_DIM] = 1;
diff_rss_dims[PHS1_DIM] = 1;
complex float* diff_rss = md_alloc(DIMS, diff_rss_dims, CFL_SIZE);
long pos_l[DIMS] = { 0 };
long pos_m[DIMS] = { 0 };
// Array to store indices of spokes that build an angle close to pi/2 with the current spoke
long intersec_sp[no_intersec_sp];
for (unsigned int i = 0; i < no_intersec_sp; i++)
intersec_sp[i] = -1;
// Boundaries for spoke comparison
int myROI = ROI;
myROI += (ROI % 2 == 0) ? 1 : 0; // make odd
int low = 0;
int high = myROI - 1;
int count = 0;
// Intersection determination
for (unsigned int i = 0; i < N; i++) {
pos_i[PHS2_DIM] = i;
md_slice(DIMS, PHS2_FLAG, pos_i, kc_dims, spoke_i, kc, CFL_SIZE);
find_intersec_sp(no_intersec_sp, intersec_sp, i, N, angles);
for (unsigned int j = 0; j < no_intersec_sp; j++) {
pos_j[PHS2_DIM] = intersec_sp[j];
md_slice(DIMS, PHS2_FLAG, pos_j, kc_dims, spoke_j, kc, CFL_SIZE);
idx[0][i * no_intersec_sp + j] = i;
idx[1][i * no_intersec_sp + j] = intersec_sp[j];
// Elementwise rss comparisson
float rss = FLT_MAX;
for (int l = low; l <= high; l++) {
pos_l[PHS1_DIM] = l;
md_copy_block(DIMS, pos_l, coilPixel_dims, coilPixel_l, spoke_dims, spoke_i, CFL_SIZE);
for (int m = low; m <= high; m++) {
pos_m[PHS1_DIM] = m;
md_copy_block(DIMS, pos_m, coilPixel_dims, coilPixel_m, spoke_dims, spoke_j, CFL_SIZE);
md_zsub(DIMS, coilPixel_dims, diff, coilPixel_l, coilPixel_m);
md_zrss(DIMS, coilPixel_dims, PHS1_FLAG|COIL_FLAG, diff_rss, diff);
if (cabsf(diff_rss[0]) < rss) { // New minimum found
rss = cabsf(diff_rss[0]);
dist[0][i * no_intersec_sp + j] = (l + 1/2 - ROI/2);
dist[1][i * no_intersec_sp + j] = (m + 1/2 - ROI/2);
}
}
}
count++;
}
}
#ifdef RING_PAPER
// Print projection angles and corresponding offsets to files
const char* idx_out = "projangle.txt";
FILE* fp = fopen(idx_out, "w");
const char* d_out = "offset.txt";
FILE* fp1 = fopen(d_out, "w");
for (unsigned int i = 0; i < N; i++) {
for (unsigned int j = 0; j < no_intersec_sp; j++) {
fprintf(fp, "%f \t %f\n", angles[idx[0][i * no_intersec_sp + j]], angles[idx[1][i * no_intersec_sp + j]]);
fprintf(fp1, "%f \t %f\n", dist[0][i * no_intersec_sp + j], dist[1][i * no_intersec_sp + j]);
}
}
fclose(fp);
fclose(fp1);
#endif
md_free(spoke_i);
md_free(spoke_j);
md_free(coilPixel_l);
md_free(coilPixel_m);
md_free(diff);
md_free(diff_rss);
}
int main_pocsense(int argc, char* argv[])
{
float alpha = 0.;
int maxiter = 50;
bool l1wav = false;
float lambda = -1.;
bool use_gpu = false;
bool use_admm = false;
float admm_rho = -1.;
int l1type = 2;
const struct opt_s opts[] = {
{ 'i', true, opt_int, &maxiter, NULL },
{ 'r', true, opt_float, &alpha, " alpha\tregularization parameter" },
{ 'l', true, opt_int, &l1type, "1/-l2\t\ttoggle l1-wavelet or l2 regularization" },
{ 'g', false, opt_set, &use_gpu, NULL },
{ 'o', true, opt_float, &lambda, NULL },
{ 'm', true, opt_float, &admm_rho, NULL },
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (1 == l1type)
l1wav = true;
else
if (2 == l1type)
l1wav = false;
else
error("Unknown regularization type.");
unsigned int N = DIMS;
long dims[N];
long ksp_dims[N];
complex float* kspace_data = load_cfl(argv[1], N, ksp_dims);
complex float* sens_maps = load_cfl(argv[2], N, dims);
for (int i = 0; i < 4; i++) // sizes2[4] may be > 1
if (ksp_dims[i] != dims[i])
error("Dimensions of kspace and sensitivities do not match!\n");
assert(1 == ksp_dims[MAPS_DIM]);
num_init();
long dims1[N];
md_select_dims(N, ~(COIL_FLAG|MAPS_FLAG), dims1, dims);
// -----------------------------------------------------------
// memory allocation
complex float* result = create_cfl(argv[3], N, ksp_dims);
complex float* pattern = md_alloc(N, dims1, CFL_SIZE);
// -----------------------------------------------------------
// pre-process data
float scaling = estimate_scaling(ksp_dims, NULL, kspace_data);
md_zsmul(N, ksp_dims, kspace_data, kspace_data, 1. / scaling);
estimate_pattern(N, ksp_dims, COIL_DIM, pattern, kspace_data);
// -----------------------------------------------------------
// l1-norm threshold operator
const struct operator_p_s* thresh_op = NULL;
const struct linop_s* wave_op = NULL;
if (l1wav) {
long minsize[DIMS] = { [0 ... DIMS - 1] = 1 };
minsize[0] = MIN(ksp_dims[0], 16);
minsize[1] = MIN(ksp_dims[1], 16);
minsize[2] = MIN(ksp_dims[2], 16);
wave_op = wavelet_create(DIMS, ksp_dims, FFT_FLAGS, minsize, true, use_gpu);
thresh_op = prox_unithresh_create(DIMS, wave_op, alpha, COIL_FLAG, use_gpu);
}
#if 0
else {
int main_homodyne(int argc, char* argv[])
{
bool clear = false;
bool image = false;
const char* phase_ref = NULL;
float alpha = 0.;
num_init();
const struct opt_s opts[] = {
{ 'r', true, opt_float, &alpha, " <alpha>\tOffset of ramp filter, between 0 and 1. alpha=0 is a full ramp, alpha=1 is a horizontal line" },
{ 'I', false, opt_set, &image, "\tInput is in image domain" },
{ 'C', false, opt_set, &clear, "\tClear unacquired portion of kspace" },
{ 'P', true, opt_string, &phase_ref, " <phase_ref>\tUse <phase_ref> as phase reference" },
};
cmdline(&argc, argv, 4, 4, usage_str, help_str, ARRAY_SIZE(opts), opts);
const int N = DIMS;
long dims[N];
complex float* idata = load_cfl(argv[3], N, dims);
complex float* data = create_cfl(argv[4], N, dims);
int pfdim = atoi(argv[1]);
float frac = atof(argv[2]);
assert((0 <= pfdim) && (pfdim < N));
assert(frac > 0.);
if (image) {
complex float* ksp_in = md_alloc(N, dims, CFL_SIZE);
fftuc(N, dims, FFT_FLAGS, ksp_in, idata);
md_copy(N, dims, idata, ksp_in, CFL_SIZE);
md_free(ksp_in);
}
long strs[N];
md_calc_strides(N, strs, dims, CFL_SIZE);
struct wdata wdata;
wdata.frac = frac;
wdata.pfdim = pfdim;
md_select_dims(N, MD_BIT(pfdim), wdata.wdims, dims);
md_calc_strides(N, wdata.wstrs, wdata.wdims, CFL_SIZE);
wdata.weights = md_alloc(N, wdata.wdims, CFL_SIZE);
wdata.alpha = alpha;
wdata.clear = clear;
md_loop(N, wdata.wdims, &wdata, comp_weights);
long pstrs[N];
long pdims[N];
complex float* phase = NULL;
if (NULL == phase_ref) {
phase = estimate_phase(wdata, FFT_FLAGS, N, dims, idata);
md_copy_dims(N, pdims, dims);
}
else
phase = load_cfl(phase_ref, N, pdims);
md_calc_strides(N, pstrs, pdims, CFL_SIZE);
homodyne(wdata, FFT_FLAGS, N, dims, strs, data, idata, pstrs, phase);
md_free(wdata.weights);
if (NULL == phase_ref)
md_free(phase);
else {
unmap_cfl(N, pdims, phase);
free((void*)phase_ref);
}
unmap_cfl(N, dims, idata);
unmap_cfl(N, dims, data);
exit(0);
}
struct noir_data* noir_init(const long dims[DIMS], const complex float* mask, const complex float* psf, bool rvc, bool use_gpu)
{
#ifdef USE_CUDA
md_alloc_fun_t my_alloc = use_gpu ? md_alloc_gpu : md_alloc;
#else
assert(!use_gpu);
md_alloc_fun_t my_alloc = md_alloc;
#endif
PTR_ALLOC(struct noir_data, data);
data->rvc = rvc;
md_copy_dims(DIMS, data->dims, dims);
md_select_dims(DIMS, FFT_FLAGS|COIL_FLAG|CSHIFT_FLAG, data->sign_dims, dims);
md_calc_strides(DIMS, data->sign_strs, data->sign_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS|COIL_FLAG|MAPS_FLAG, data->coil_dims, dims);
md_calc_strides(DIMS, data->coil_strs, data->coil_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS|MAPS_FLAG|CSHIFT_FLAG, data->imgs_dims, dims);
md_calc_strides(DIMS, data->imgs_strs, data->imgs_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS|COIL_FLAG, data->data_dims, dims);
md_calc_strides(DIMS, data->data_strs, data->data_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS, data->mask_dims, dims);
md_calc_strides(DIMS, data->mask_strs, data->mask_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS, data->wght_dims, dims);
md_calc_strides(DIMS, data->wght_strs, data->wght_dims, CFL_SIZE);
md_select_dims(DIMS, FFT_FLAGS|CSHIFT_FLAG, data->ptrn_dims, dims);
md_calc_strides(DIMS, data->ptrn_strs, data->ptrn_dims, CFL_SIZE);
complex float* weights = md_alloc(DIMS, data->wght_dims, CFL_SIZE);
noir_calc_weights(dims, weights);
fftmod(DIMS, data->wght_dims, FFT_FLAGS, weights, weights);
fftscale(DIMS, data->wght_dims, FFT_FLAGS, weights, weights);
data->weights = weights;
#ifdef USE_CUDA
if (use_gpu) {
data->weights = md_gpu_move(DIMS, data->wght_dims, weights, CFL_SIZE);
}
#endif
complex float* ptr = my_alloc(DIMS, data->ptrn_dims, CFL_SIZE);
md_copy(DIMS, data->ptrn_dims, ptr, psf, CFL_SIZE);
fftmod(DIMS, data->ptrn_dims, FFT_FLAGS, ptr, ptr);
data->pattern = ptr;
complex float* msk = my_alloc(DIMS, data->mask_dims, CFL_SIZE);
if (NULL == mask) {
assert(!use_gpu);
md_zfill(DIMS, data->mask_dims, msk, 1.);
} else {
md_copy(DIMS, data->mask_dims, msk, mask, CFL_SIZE);
}
// fftmod(DIMS, data->mask_dims, 7, msk, msk);
fftscale(DIMS, data->mask_dims, FFT_FLAGS, msk, msk);
data->mask = msk;
data->sens = my_alloc(DIMS, data->coil_dims, CFL_SIZE);
data->xn = my_alloc(DIMS, data->imgs_dims, CFL_SIZE);
data->tmp = my_alloc(DIMS, data->sign_dims, CFL_SIZE);
return data;
}
int main_bpsense(int argc, char* argv[])
{
// -----------------------------------------------------------
// set up conf and option parser
struct bpsense_conf conf = bpsense_defaults;
struct iter_admm_conf iconf = iter_admm_defaults;
conf.iconf = &iconf;
conf.iconf->rho = 10; // more sensibile default
bool usegpu = false;
const char* psf = NULL;
const char* image_truth_fname = NULL;
bool im_truth = false;
bool use_tvnorm = false;
double start_time = timestamp();
const struct opt_s opts[] = {
OPT_FLOAT('e', &conf.eps, "eps", "data consistency error"),
OPT_FLOAT('r', &conf.lambda, "lambda", "l2 regularization parameter"),
OPT_FLOAT('u', &conf.iconf->rho, "rho", "ADMM penalty parameter"),
OPT_SET('c', &conf.rvc, "real-value constraint"),
OPT_SET('t', &use_tvnorm, "use TV norm"),
OPT_STRING('T', &image_truth_fname, "file", "compare to truth image"),
OPT_UINT('i', &conf.iconf->maxiter, "iter", "max. iterations"),
OPT_SET('g', &usegpu, "(use gpu)"),
OPT_STRING('p', &psf, "file", "point-spread function"),
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (NULL != image_truth_fname)
im_truth = true;
// -----------------------------------------------------------
// load data and print some info about the recon
int N = DIMS;
long dims[N];
long dims1[N];
long img_dims[N];
long ksp_dims[N];
complex float* kspace_data = load_cfl(argv[1], N, ksp_dims);
complex float* sens_maps = load_cfl(argv[2], N, dims);
for (int i = 0; i < 4; i++) // sizes2[4] may be > 1
if (ksp_dims[i] != dims[i])
error("Dimensions of kspace and sensitivities do not match!\n");
assert(1 == ksp_dims[MAPS_DIM]);
(usegpu ? num_init_gpu : num_init)();
if (dims[MAPS_DIM] > 1)
debug_printf(DP_INFO, "%ld maps.\nESPIRiT reconstruction.\n", dims[4]);
if (conf.lambda > 0.)
debug_printf(DP_INFO, "l2 regularization: %f\n", conf.lambda);
if (use_tvnorm)
debug_printf(DP_INFO, "use Total Variation\n");
else
debug_printf(DP_INFO, "use Wavelets\n");
if (im_truth)
debug_printf(DP_INFO, "Compare to truth\n");
md_select_dims(N, ~(COIL_FLAG | MAPS_FLAG), dims1, dims);
md_select_dims(N, ~COIL_FLAG, img_dims, dims);
// -----------------------------------------------------------
// initialize sampling pattern
complex float* pattern = NULL;
long pat_dims[N];
if (NULL != psf) {
pattern = load_cfl(psf, N, pat_dims);
// FIXME: check compatibility
} else {
pattern = md_alloc(N, dims1, CFL_SIZE);
estimate_pattern(N, ksp_dims, COIL_DIM, pattern, kspace_data);
}
// -----------------------------------------------------------
// print some statistics
size_t T = md_calc_size(N, dims1);
long samples = (long)pow(md_znorm(N, dims1, pattern), 2.);
debug_printf(DP_INFO, "Size: %ld Samples: %ld Acc: %.2f\n", T, samples, (float)T/(float)samples);
// -----------------------------------------------------------
// fftmod to un-center data
fftmod(N, ksp_dims, FFT_FLAGS, kspace_data, kspace_data);
fftmod(N, dims, FFT_FLAGS, sens_maps, sens_maps);
// -----------------------------------------------------------
// apply scaling
float scaling = estimate_scaling(ksp_dims, NULL, kspace_data);
debug_printf(DP_INFO, "Scaling: %f\n", scaling);
if (scaling != 0.)
md_zsmul(N, ksp_dims, kspace_data, kspace_data, 1. / scaling);
// -----------------------------------------------------------
// create l1 prox operator and transform
long minsize[DIMS] = { [0 ... DIMS - 1] = 1 };
minsize[0] = MIN(img_dims[0], 16);
minsize[1] = MIN(img_dims[1], 16);
minsize[2] = MIN(img_dims[2], 16);
const struct linop_s* l1op = NULL;
const struct operator_p_s* l1prox = NULL;
if (use_tvnorm) {
l1op = grad_init(DIMS, img_dims, FFT_FLAGS);
l1prox = prox_thresh_create(DIMS + 1, linop_codomain(l1op)->dims, 1., 0u, usegpu);
conf.l1op_obj = l1op;
} else {
bool randshift = true;
l1op = linop_identity_create(DIMS, img_dims);
conf.l1op_obj = wavelet_create(DIMS, img_dims, FFT_FLAGS, minsize, false, usegpu);
l1prox = prox_wavethresh_create(DIMS, img_dims, FFT_FLAGS, minsize, 1., randshift, usegpu);
}
// -----------------------------------------------------------
// create image and load truth image
complex float* image = create_cfl(argv[3], N, img_dims);
md_clear(N, img_dims, image, CFL_SIZE);
long img_truth_dims[DIMS];
complex float* image_truth = NULL;
if (im_truth)
image_truth = load_cfl(image_truth_fname, DIMS, img_truth_dims);
// -----------------------------------------------------------
// call recon
if (usegpu)
#ifdef USE_CUDA
bpsense_recon_gpu(&conf, dims, image, sens_maps, dims1, pattern, l1op, l1prox, ksp_dims, kspace_data, image_truth);
#else
assert(0);
#endif
else
int main_ecaltwo(int argc, char* argv[])
{
long maps = 2; // channels;
struct ecalib_conf conf = ecalib_defaults;
int c;
while (-1 != (c = getopt(argc, argv, "OSc:m:gh"))) {
switch (c) {
case 'S':
conf.softcrop = true;
break;
case 'O':
conf.orthiter = false;
break;
case 'c':
conf.crop = atof(optarg);
break;
case 'm':
maps = atoi(optarg);
break;
case 'g':
conf.usegpu = true;
break;
case 'h':
usage(argv[0], stdout);
help();
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if ((argc - optind != 5) && (argc - optind != 6)) {
usage(argv[0], stderr);
exit(1);
}
long in_dims[DIMS];
complex float* in_data = load_cfl(argv[optind + 3], DIMS, in_dims);
int channels = 0;
while (in_dims[3] != (channels * (channels + 1) / 2))
channels++;
printf("Channels: %d\n", channels);
assert(maps <= channels);
long out_dims[DIMS] = { [0 ... DIMS - 1] = 1 };
long map_dims[DIMS] = { [0 ... DIMS - 1] = 1 };
out_dims[0] = atoi(argv[optind + 0]);
out_dims[1] = atoi(argv[optind + 1]);
out_dims[2] = atoi(argv[optind + 2]);
out_dims[3] = channels;
out_dims[4] = maps;
assert((out_dims[0] >= in_dims[0]));
assert((out_dims[1] >= in_dims[1]));
assert((out_dims[2] >= in_dims[2]));
for (int i = 0; i < 3; i++)
map_dims[i] = out_dims[i];
map_dims[3] = 1;
map_dims[4] = maps;
complex float* out_data = create_cfl(argv[optind + 4], DIMS, out_dims);
complex float* emaps;
if (6 == argc - optind)
emaps = create_cfl(argv[optind + 5], DIMS, map_dims);
else
emaps = md_alloc(DIMS, map_dims, CFL_SIZE);
caltwo(&conf, out_dims, out_data, emaps, in_dims, in_data, NULL, NULL);
if (conf.intensity) {
debug_printf(DP_DEBUG1, "Normalize...\n");
normalizel1(DIMS, COIL_FLAG, out_dims, out_data);
}
debug_printf(DP_DEBUG1, "Crop maps... (%.2f)\n", conf.crop);
crop_sens(out_dims, out_data, conf.softcrop, conf.crop, emaps);
debug_printf(DP_DEBUG1, "Fix phase...\n");
fixphase(DIMS, out_dims, COIL_DIM, out_data, out_data);
printf("Done.\n");
unmap_cfl(DIMS, in_dims, in_data);
unmap_cfl(DIMS, out_dims, out_data);
if (6 == argc - optind)
unmap_cfl(DIMS, map_dims, emaps);
else
md_free(emaps);
exit(0);
}