int main_index(int argc, char* argv[])
{
mini_cmdline(&argc, argv, 3, usage_str, help_str);
num_init();
int N = atoi(argv[1]);
int s = atoi(argv[2]);
assert(N >= 0);
assert(s >= 0);
long dims[N + 1];
for (int i = 0; i < N; i++)
dims[i] = 1;
dims[N] = s;
complex float* x = create_cfl(argv[3], N + 1, dims);
for (int i = 0; i < s; i++)
x[i] = i;
unmap_cfl(N + 1, dims, x);
exit(0);
}
int main_conv(int argc, char* argv[])
{
cmdline(&argc, argv, 4, 4, usage_str, help_str, 0, NULL);
num_init();
unsigned int flags = atoi(argv[1]);
unsigned int N = DIMS;
long dims[N];
const complex float* in = load_cfl(argv[2], N, dims);
long krn_dims[N];
const complex float* krn = load_cfl(argv[3], N, krn_dims);
complex float* out = create_cfl(argv[4], N, dims);
struct conv_plan* plan = conv_plan(N, flags, CONV_CYCLIC, CONV_SYMMETRIC, dims, dims, krn_dims, krn);
conv_exec(plan, out, in);
conv_free(plan);
unmap_cfl(N, dims, out);
unmap_cfl(N, krn_dims, krn);
unmap_cfl(N, dims, in);
exit(0);
}
int main_transpose(int argc, char* argv[])
{
mini_cmdline(argc, argv, 4, usage_str, help_str);
int N = DIMS;
long idims[N];
int dim1 = atoi(argv[1]);
int dim2 = atoi(argv[2]);
assert((0 <= dim1) && (dim1 < N));
assert((0 <= dim2) && (dim2 < N));
complex float* idata = load_cfl(argv[3], N, idims);
long odims[N];
md_transpose_dims(N, dim1, dim2, odims, idims);
complex float* odata = create_cfl(argv[4], N, odims);
md_transpose(N, dim1, dim2, odims, odata, idims, idata, sizeof(complex float));
unmap_cfl(N, idims, idata);
unmap_cfl(N, odims, odata);
exit(0);
}
int main_repmat(int argc, char* argv[])
{
mini_cmdline(argc, argv, 4, usage_str, help_str);
long in_dims[DIMS];
long out_dims[DIMS];
complex float* in_data = load_cfl(argv[3], DIMS, in_dims);
int dim = atoi(argv[1]);
int rep = atoi(argv[2]);
assert(dim < DIMS);
assert(rep >= 0);
assert(1 == in_dims[dim]);
md_copy_dims(DIMS, out_dims, in_dims);
out_dims[dim] = rep;
complex float* out_data = create_cfl(argv[4], DIMS, out_dims);
long in_strs[DIMS];
long out_strs[DIMS];
md_calc_strides(DIMS, in_strs, in_dims, CFL_SIZE);
md_calc_strides(DIMS, out_strs, out_dims, CFL_SIZE);
md_copy2(DIMS, out_dims, out_strs, out_data, in_strs, in_data, CFL_SIZE);
unmap_cfl(DIMS, out_dims, out_data);
unmap_cfl(DIMS, in_dims, in_data);
exit(0);
}
int main_fft(int argc, char* argv[])
{
bool unitary = false;
bool inv = false;
const struct opt_s opts[] = {
OPT_SET('u', &unitary, "unitary"),
OPT_SET('i', &inv, "inverse"),
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
long dims[DIMS];
complex float* idata = load_cfl(argv[2], DIMS, dims);
complex float* data = create_cfl(argv[3], DIMS, dims);
unsigned long flags = labs(atol(argv[1]));
md_copy(DIMS, dims, data, idata, sizeof(complex float));
unmap_cfl(DIMS, dims, idata);
if (unitary)
fftscale(DIMS, dims, flags, data, data);
(inv ? ifftc : fftc)(DIMS, dims, flags, data, data);
unmap_cfl(DIMS, dims, data);
exit(0);
}
int main_slice(int argc, char* argv[])
{
mini_cmdline(&argc, argv, 4, usage_str, help_str);
num_init();
long in_dims[DIMS];
long out_dims[DIMS];
complex float* in_data = load_cfl(argv[3], DIMS, in_dims);
int dim = atoi(argv[1]);
int pos = atoi(argv[2]);
assert(dim < DIMS);
assert(pos >= 0);
assert(pos < in_dims[dim]);
for (int i = 0; i < DIMS; i++)
out_dims[i] = in_dims[i];
out_dims[dim] = 1;
complex float* out_data = create_cfl(argv[4], DIMS, out_dims);
long pos2[DIMS] = { [0 ... DIMS - 1] = 0 };
pos2[dim] = pos;
md_slice(DIMS, MD_BIT(dim), pos2, in_dims, out_data, in_data, CFL_SIZE);
unmap_cfl(DIMS, out_dims, out_data);
unmap_cfl(DIMS, in_dims, in_data);
return 0;
}
void dump_cfl(const char* name, int D, const long dimensions[D], const complex float* src)
{
complex float* out = create_cfl(name, D, dimensions);
md_copy(D, dimensions, out, src, sizeof(complex float));
unmap_cfl(D, dimensions, out);
}
int main_threshold(int argc, char* argv[])
{
unsigned int flags = 0;
enum th_type { NONE, WAV, LLR, DFW, MPDFW, HARD } th_type = NONE;
int llrblk = 8;
const struct opt_s opts[] = {
OPT_SELECT('H', enum th_type, &th_type, HARD, "hard thresholding"),
OPT_SELECT('W', enum th_type, &th_type, WAV, "daubechies wavelet soft-thresholding"),
OPT_SELECT('L', enum th_type, &th_type, LLR, "locally low rank soft-thresholding"),
OPT_SELECT('D', enum th_type, &th_type, DFW, "divergence-free wavelet soft-thresholding"),
OPT_UINT('j', &flags, "bitmask", "joint soft-thresholding"),
OPT_INT('b', &llrblk, "blocksize", "locally low rank block size"),
};
cmdline(&argc, argv, 3, 3, usage_str, help_str, ARRAY_SIZE(opts), opts);
num_init();
const int N = DIMS;
long dims[N];
complex float* idata = load_cfl(argv[2], N, dims);
complex float* odata = create_cfl(argv[3], N, dims);
float lambda = atof(argv[1]);
switch (th_type) {
case WAV:
wthresh(N, dims, lambda, flags, odata, idata);
break;
case LLR:
lrthresh(N, dims, llrblk, lambda, flags, odata, idata);
break;
case DFW:
dfthresh(N, dims, lambda, odata, idata);
break;
case HARD:
hard_thresh(N, dims, lambda, odata, idata);
break;
default:
md_zsoftthresh(N, dims, lambda, flags, odata, idata);
}
unmap_cfl(N, dims, idata);
unmap_cfl(N, dims, odata);
return 0;
}
int main_copy(int argc, char* argv[])
{
const struct opt_s opts[] = { };
cmdline(&argc, argv, 2, 1000, usage_str, help_str, ARRAY_SIZE(opts), opts);
num_init();
unsigned int N = DIMS;
int count = argc - 3;
assert((count >= 0) && (count % 2 == 0));
long in_dims[N];
long out_dims[N];
void* in_data = load_cfl(argv[argc - 2], N, in_dims);
if (count > 0) {
// get dimensions
void* out_data = load_cfl(argv[argc - 1], N, out_dims);
unmap_cfl(N, out_dims, out_data);
} else {
md_copy_dims(N, out_dims, in_dims);
}
void* out_data = create_cfl(argv[argc - 1], N, out_dims);
long position[N];
for (unsigned int i = 0; i < N; i++)
position[i] = 0;
for (int i = 0; i < count; i += 2) {
unsigned int dim = atoi(argv[i + 1]);
long pos = atol(argv[i + 2]);
assert(dim < N);
assert((0 <= pos) && (pos < out_dims[dim]));
position[dim] = pos;
}
md_copy_block(N, position, out_dims, out_data, in_dims, in_data, CFL_SIZE);
unmap_cfl(N, in_dims, in_data);
unmap_cfl(N, out_dims, out_data);
return 0;
}
int main_cdf97(int argc, char* argv[])
{
int c;
_Bool inv = false;
while (-1 != (c = getopt(argc, argv, "ih"))) {
switch (c) {
case 'i':
inv = 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);
}
unsigned int flags = atoi(argv[optind + 0]);
long dims[DIMS];
complex float* idata = load_cfl(argv[optind + 1], DIMS, dims);
complex float* odata = create_cfl(argv[optind + 2], DIMS, dims);
md_copy(DIMS, dims, odata, idata, CFL_SIZE);
unmap_cfl(DIMS, dims, idata);
if (inv) {
md_iresortz(DIMS, dims, flags, odata);
md_icdf97z(DIMS, dims, flags, odata);
} else {
md_cdf97z(DIMS, dims, flags, odata);
md_resortz(DIMS, dims, flags, odata);
}
unmap_cfl(DIMS, dims, odata);
exit(0);
}
int main_conj(int argc, char* argv[])
{
mini_cmdline(argc, argv, 2, usage_str, help_str);
const int N = 16;
long dims[N];
complex float* idata = load_cfl(argv[1], N, dims);
complex float* odata = create_cfl(argv[2], N, dims);
md_zconj(N, dims, odata, idata);
unmap_cfl(N, dims, idata);
unmap_cfl(N, dims, odata);
exit(0);
}
int main_carg(int argc, char* argv[])
{
mini_cmdline(argc, argv, 2, usage_str, help_str);
long dims[DIMS];
complex float* in_data = load_cfl(argv[1], DIMS, dims);
complex float* out_data = create_cfl(argv[2], DIMS, dims);
md_zarg(DIMS, dims, out_data, in_data);
unmap_cfl(DIMS, dims, out_data);
unmap_cfl(DIMS, dims, in_data);
exit(0);
}
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);
}
int main_reshape(int argc, char* argv[])
{
cmdline(&argc, argv, 3, 100, usage_str, help_str, 0, NULL);
num_init();
unsigned int flags = atoi(argv[1]);
unsigned int n = bitcount(flags);
assert((int)n + 3 == argc - 1);
long in_dims[DIMS];
long in_strs[DIMS];
long out_dims[DIMS];
long out_strs[DIMS];
complex float* in_data = load_cfl(argv[n + 2], DIMS, in_dims);
md_calc_strides(DIMS, in_strs, in_dims, CFL_SIZE);
md_copy_dims(DIMS, out_dims, in_dims);
unsigned int j = 0;
for (unsigned int i = 0; i < DIMS; i++)
if (MD_IS_SET(flags, i))
out_dims[i] = atoi(argv[j++ + 2]);
assert(j == n);
assert(md_calc_size(DIMS, in_dims) == md_calc_size(DIMS, out_dims));
md_calc_strides(DIMS, out_strs, out_dims, CFL_SIZE);
for (unsigned int i = 0; i < DIMS; i++)
if (!(MD_IS_SET(flags, i) || (in_strs[i] == out_strs[i])))
error("Dimensions are not consistent at index %d.\n");
complex float* out_data = create_cfl(argv[n + 3], DIMS, out_dims);
md_copy(DIMS, in_dims, out_data, in_data, CFL_SIZE);
unmap_cfl(DIMS, in_dims, in_data);
unmap_cfl(DIMS, out_dims, out_data);
exit(0);
}
int main_resize(int argc, char* argv[])
{
bool center = false;
const struct opt_s opts[] = {
OPT_SET('c', ¢er, "center"),
};
cmdline(&argc, argv, 4, 1000, usage_str, help_str, ARRAY_SIZE(opts), opts);
num_init();
unsigned int N = DIMS;
int count = argc - 3;
assert((count > 0) && (count % 2 == 0));
long in_dims[N];
long out_dims[N];
void* in_data = load_cfl(argv[argc - 2], N, in_dims);
md_copy_dims(N, out_dims, in_dims);
for (int i = 0; i < count; i += 2) {
unsigned int dim = atoi(argv[i + 1]);
unsigned int size = atoi(argv[i + 2]);
assert(dim < N);
assert(size >= 1);
out_dims[dim] = size;
}
void* out_data = create_cfl(argv[argc - 1], N, out_dims);
(center ? md_resize_center : md_resize)(N, out_dims, out_data, in_dims, in_data, CFL_SIZE);
unmap_cfl(N, in_dims, in_data);
unmap_cfl(N, out_dims, out_data);
return 0;
}
int main_flip(int argc, char* argv[])
{
mini_cmdline(argc, argv, 3, usage_str, help_str);
int N = DIMS;
long dims[N];
complex float* idata = load_cfl(argv[2], N, dims);
complex float* odata = create_cfl(argv[3], N, dims);
unsigned long flags = atoi(argv[1]);
md_flip(N, dims, flags, odata, idata, sizeof(complex float));
unmap_cfl(N, dims, idata);
unmap_cfl(N, dims, odata);
exit(0);
}
int main_conv(int argc, char* argv[])
{
int c;
while (-1 != (c = getopt(argc, argv, "ah"))) {
switch (c) {
case 'h':
usage(argv[0], stdout);
help();
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if (argc - optind != 4) {
usage(argv[0], stderr);
exit(1);
}
unsigned int flags = atoi(argv[optind + 0]);
unsigned int N = DIMS;
long dims[N];
const complex float* in = load_cfl(argv[optind + 1], N, dims);
long krn_dims[N];
const complex float* krn = load_cfl(argv[optind + 2], N, krn_dims);
complex float* out = create_cfl(argv[optind + 3], N, dims);
struct conv_plan* plan = conv_plan(N, flags, CONV_CYCLIC, CONV_SYMMETRIC, dims, dims, krn_dims, krn);
conv_exec(plan, out, in);
conv_free(plan);
unmap_cfl(N, dims, out);
unmap_cfl(N, krn_dims, krn);
unmap_cfl(N, dims, in);
exit(0);
}
int main_walsh(int argc, char* argv[])
{
long bsize[3] = { 20, 20, 20 };
long calsize[3] = { 24, 24, 24 };
const struct opt_s opts[] = {
{ 'r', true, opt_vec3, &calsize, " cal_size\tLimits the size of the calibration region." },
{ 'R', true, opt_vec3, &calsize, NULL },
{ 'b', true, opt_vec3, &bsize, " block_size\tBlock size." },
{ 'B', true, opt_vec3, &bsize, NULL },
};
cmdline(&argc, argv, 2, 2, usage_str, help_str, ARRAY_SIZE(opts), opts);
long dims[DIMS];
complex float* in_data = load_cfl(argv[1], DIMS, dims);
assert((dims[0] == 1) || (calsize[0] < dims[0]));
assert((dims[1] == 1) || (calsize[1] < dims[1]));
assert((dims[2] == 1) || (calsize[2] < dims[2]));
assert(1 == dims[MAPS_DIM]);
long caldims[DIMS];
complex float* cal_data = extract_calib(caldims, calsize, dims, in_data, false);
unmap_cfl(DIMS, dims, in_data);
debug_printf(DP_INFO, "Calibration region %ldx%ldx%ld\n", caldims[0], caldims[1], caldims[2]);
dims[COIL_DIM] = dims[COIL_DIM] * (dims[COIL_DIM] + 1) / 2;
complex float* out_data = create_cfl(argv[2], DIMS, dims);
walsh(bsize, dims, out_data, caldims, cal_data);
debug_printf(DP_INFO, "Done.\n");
md_free(cal_data);
unmap_cfl(DIMS, dims, out_data);
exit(0);
}
int main_invert(int argc, char* argv[])
{
mini_cmdline(&argc, argv, 2, usage_str, help_str);
num_init();
long dims[DIMS];
complex float* idata = load_cfl(argv[1], DIMS, dims);
complex float* odata = create_cfl(argv[2], DIMS, dims);
#pragma omp parallel for
for (long i = 0; i < md_calc_size(DIMS, dims); i++)
odata[i] = idata[i] == 0 ? 0. : 1. / idata[i];
unmap_cfl(DIMS, dims, idata);
unmap_cfl(DIMS, dims, odata);
return 0;
}
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);
}
int main_zeros(int argc, char* argv[])
{
mini_cmdline(argc, argv, -3, usage_str, help_str);
int N = atoi(argv[1]);
assert(N >= 0);
assert(argc == 3 + N);
long dims[N];
for (int i = 0; i < N; i++) {
dims[i] = atoi(argv[2 + i]);
assert(dims[i] >= 1);
}
complex float* x = create_cfl(argv[2 + N], N, dims);
md_clear(N, dims, x, sizeof(complex float));
unmap_cfl(N, dims, x);
exit(0);
}
int main_normalize(int argc, char* argv[])
{
bool l1 = false;
l1 = mini_cmdline_bool(argc, argv, 'b', 3, usage_str, help_str);
int N = DIMS;
long dims[N];
complex float* data = load_cfl(argv[2], N, dims);
int flags = atoi(argv[1]);
assert(flags >= 0);
complex float* out = create_cfl(argv[3], N, dims);
md_copy(N, dims, out, data, CFL_SIZE);
(l1 ? normalizel1 : normalize)(N, flags, dims, out);
unmap_cfl(N, dims, out);
exit(0);
}
int main_spow(int argc, char* argv[argc])
{
mini_cmdline(argc, argv, 3, usage_str, help_str);
complex float expo;
if (0 != parse_cfl(&expo, argv[1])) {
fprintf(stderr, "ERROR: exponent %s is not a number.\n", argv[1]);
exit(1);
}
const int N = DIMS;
long dims[N];
complex float* idata = load_cfl(argv[2], N, dims);
complex float* odata = create_cfl(argv[3], N, dims);
md_zspow(N, dims, odata, idata, expo);
unmap_cfl(N, dims, idata);
unmap_cfl(N, dims, odata);
exit(0);
}
int main_rss(int argc, char* argv[argc])
{
mini_cmdline(argc, argv, 3, usage_str, help_str);
long dims[DIMS];
complex float* data = load_cfl(argv[2], DIMS, dims);
int flags = atoi(argv[1]);
assert(0 <= flags);
long odims[DIMS];
md_select_dims(DIMS, ~flags, odims, dims);
complex float* out = create_cfl(argv[3], DIMS, odims);
md_zrss(DIMS, dims, flags, out, data);
unmap_cfl(DIMS, dims, data);
unmap_cfl(DIMS, odims, out);
exit(0);
}
int main_wavg(int argc, char* argv[argc])
{
cmdline(&argc, argv, 3, 3, usage_str, help_str, 0, NULL);
int N = DIMS;
unsigned int flags = atoi(argv[1]);
long idims[N];
complex float* data = load_cfl(argv[2], N, idims);
long odims[N];
md_select_dims(N, ~flags, odims, idims);
complex float* out = create_cfl(argv[3], N, odims);
md_zwavg(N, idims, flags, out, data);
unmap_cfl(N, idims, data);
unmap_cfl(N, odims, out);
exit(0);
}
int main_extract(int argc, char* argv[])
{
mini_cmdline(argc, argv, 5, usage_str, help_str);
num_init();
long in_dims[DIMS];
long out_dims[DIMS];
complex float* in_data = load_cfl(argv[4], DIMS, in_dims);
int dim = atoi(argv[1]);
int start = atoi(argv[2]);
int end = atoi(argv[3]);
assert((0 <= dim) && (dim < DIMS));
assert(start >= 0);
assert(start <= end);
assert(end < in_dims[dim]);
for (int i = 0; i < DIMS; i++)
out_dims[i] = in_dims[i];
out_dims[dim] = end - start + 1;
complex float* out_data = create_cfl(argv[5], DIMS, out_dims);
long pos2[DIMS] = { [0 ... DIMS - 1] = 0 };
pos2[dim] = start;
md_copy_block(DIMS, pos2, out_dims, out_data, in_dims, in_data, sizeof(complex float));
unmap_cfl(DIMS, in_dims, in_data);
unmap_cfl(DIMS, out_dims, out_data);
exit(0);
}
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_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_traj(int argc, char* argv[])
{
int X = 128;
int Y = 128;
int accel = 1;
bool radial = false;
bool golden = false;
bool dbl = false;
int c;
int turns = 1;
while (-1 != (c = getopt(argc, argv, "x:y:a:t:rDGh"))) {
switch (c) {
case 'x':
X = atoi(optarg);
break;
case 'y':
Y = atoi(optarg);
break;
case 'a':
accel = atoi(optarg);
break;
case 'G':
golden = true;
radial = true;
break;
case 'D':
dbl = true;
case 'r':
radial = true;
break;
case 't':
turns = atoi(optarg);
break;
case 'h':
usage(argv[0], stdout);
help();
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if (argc - optind != 1) {
usage(argv[0], stderr);
exit(1);
}
int N = X * Y / accel;
long dims[3] = { 3, X, Y / accel };
complex float* samples = create_cfl(argv[optind + 0], 3, dims);
int p = 0;
for (int j = 0; j < Y; j += accel) {
for (int i = 0; i < X; i++) {
if (radial) {
/* golden-ratio sampling
*
* Winkelmann S, Schaeffter T, Koehler T, Eggers H, Doessel O.
* An optimal radial profile order based on the Golden Ratio
* for time-resolved MRI. IEEE TMI 26:68--76 (2007)
*/
double golden_angle = 3. - sqrtf(5.);
double base = golden ? ((2. - golden_angle) / 2.) : (1. / (float)Y);
double angle = M_PI * (float)remap(Y, turns, j) * (dbl ? 2. : 1.) * base;
samples[p * 3 + 0] = ((float)i + 0.5 - (float)X / 2.) * sin(angle);
samples[p * 3 + 1] = ((float)i + 0.5 - (float)X / 2.) * cos(angle);
samples[p * 3 + 2] = 0.;
} else {
samples[p * 3 + 0] = (i - X / 2);
samples[p * 3 + 1] = (j - Y / 2);
samples[p * 3 + 2] = 0;
}
p++;
}
}
assert(p == N - 0);
unmap_cfl(3, dims, samples);
exit(0);
}
int main_poisson(int argc, char* argv[])
{
int yy = 128;
int zz = 128;
bool cutcorners = false;
float vardensity = 0.;
bool vd_def = false;
int T = 1;
int rnd = 0;
bool msk = true;
int points = -1;
float mindist = 1. / 1.275;
float yscale = 1.;
float zscale = 1.;
unsigned int calreg = 0;
const struct opt_s opts[] = {
OPT_INT('Y', &yy, "size", "size dimension 1"),
OPT_INT('Z', &zz, "size", "size dimension 2"),
OPT_FLOAT('y', &yscale, "acc", "acceleration dim 1"),
OPT_FLOAT('z', &zscale, "acc", "acceleration dim 2"),
OPT_UINT('C', &calreg, "size", "size of calibration region"),
OPT_SET('v', &vd_def, "variable density"),
OPT_FLOAT('V', &vardensity, "", "(variable density)"),
OPT_SET('e', &cutcorners, "elliptical scanning"),
OPT_FLOAT('D', &mindist, "", "()"),
OPT_INT('T', &T, "", "()"),
OPT_CLEAR('m', &msk, "()"),
OPT_INT('R', &points, "", "()"),
};
cmdline(&argc, argv, 1, 1, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (vd_def && (0. == vardensity))
vardensity = 20.;
if (-1 != points)
rnd = 1;
assert((yscale >= 1.) && (zscale >= 1.));
// compute mindest and scaling
float kspext = MAX(yy, zz);
int Pest = T * (int)(1.2 * powf(kspext, 2.) / (yscale * zscale));
mindist /= kspext;
yscale *= (float)kspext / (float)yy;
zscale *= (float)kspext / (float)zz;
if (vardensity != 0.) {
// TODO
}
long dims[5] = { 1, yy, zz, T, 1 };
complex float* mask = NULL;
if (msk) {
mask = create_cfl(argv[1], 5, dims);
md_clear(5, dims, mask, sizeof(complex float));
}
int M = rnd ? (points + 1) : Pest;
int P;
while (true) {
float (*points)[2] = xmalloc(M * sizeof(float[3]));
int* kind = xmalloc(M * sizeof(int));
kind[0] = 0;
if (!rnd) {
points[0][0] = 0.5;
points[0][1] = 0.5;
if (1 == T) {
P = poissondisc(2, M, 1, vardensity, mindist, points);
} else {
float (*delta)[T] = xmalloc(T * T * sizeof(complex float));
float dd[T];
for (int i = 0; i < T; i++)
dd[i] = mindist;
mc_poisson_rmatrix(2, T, delta, dd);
P = poissondisc_mc(2, T, M, 1, vardensity, (const float (*)[T])delta, points, kind);
}
} else { // random pattern
P = M - 1;
for (int i = 0; i < P; i++)
random_point(2, points[i]);
}
if (P < M) {
for (int i = 0; i < P; i++) {
points[i][0] = (points[i][0] - 0.5) * yscale + 0.5;
points[i][1] = (points[i][1] - 0.5) * zscale + 0.5;
}
// throw away points outside
float center[2] = { 0.5, 0.5 };
int j = 0;
for (int i = 0; i < P; i++) {
if ((cutcorners ? dist : maxn)(2, center, points[i]) <= 0.5) {
points[j][0] = points[i][0];
points[j][1] = points[i][1];
j++;
}
}
P = j;
if (msk) {
// rethink module here
for (int i = 0; i < P; i++) {
int yy = (int)floorf(points[i][0] * dims[1]);
int zz = (int)floorf(points[i][1] * dims[2]);
if ((yy < 0) || (yy >= dims[1]) || (zz < 0) || (zz >= dims[2]))
continue;
if (1 == T)
mask[zz * dims[1] + yy] = 1.;//cexpf(2.i * M_PI * (float)kind[i] / (float)T);
else
mask[(kind[i] * dims[2] + zz) * dims[1] + yy] = 1.;//cexpf(2.i * M_PI * (float)kind[i] / (float)T);
}
} else {
#if 1
long sdims[2] = { 3, P };
complex float* samples = create_cfl(argv[1], 2, sdims);
for (int i = 0; i < P; i++) {
samples[3 * i + 0] = 0.;
samples[3 * i + 1] = (points[i][0] - 0.5) * dims[1];
samples[3 * i + 2] = (points[i][1] - 0.5) * dims[2];
// printf("%f %f\n", creal(samples[3 * i + 0]), creal(samples[3 * i + 1]));
}
unmap_cfl(2, sdims, (void*)samples);
#endif
}
break;
}
// repeat with more points
M *= 2;
free(points);
free(kind);
}
// calibration region
assert((mask != NULL) || (0 == calreg));
assert((calreg <= dims[1]) && (calreg <= dims[2]));
for (unsigned int i = 0; i < calreg; i++) {
for (unsigned int j = 0; j < calreg; j++) {
int y = (dims[1] - calreg) / 2 + i;
int z = (dims[2] - calreg) / 2 + j;
for (int k = 0; k < T; k++) {
if (0. == mask[(k * dims[2] + z) * dims[1] + y]) {
mask[(k * dims[2] + z) * dims[1] + y] = 1.;
P++;
}
}
}
}
printf("points: %d", P);
if (1 != T)
printf(", classes: %d", T);
if (NULL != mask) {
float f = cutcorners ? (M_PI / 4.) : 1.;
printf(", grid size: %ldx%ld%s = %ld (R = %f)", dims[1], dims[2], cutcorners ? "x(pi/4)" : "",
(long)(f * dims[1] * dims[2]), f * T * dims[1] * dims[2] / (float)P);
unmap_cfl(5, dims, (void*)mask);
}
printf("\n");
exit(0);
}
