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_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_relnorm(int argc, char* argv[])
{
if (0 == strcmp(basename(argv[0]), "relnorm"))
debug_printf(DP_WARN, "The \'relnorm\' command is deprecated. Use \'nrmse\' instead.\n");
int c;
while (-1 != (c = getopt(argc, argv, "h"))) {
switch (c) {
case 'h':
usage(argv[0], stdout);
printf( "Compute relative l2 norm of two images: norm(x1 - x2) / norm(x2) \n"
"\t-h\thelp\n" );
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if (argc - optind != 2) {
usage(argv[0], stderr);
exit(1);
}
int N = DIMS;
long in1_dims[N];
long in2_dims[N];
complex float* in1_data = load_cfl(argv[optind + 0], N, in1_dims);
complex float* in2_data = load_cfl(argv[optind + 1], N, in2_dims);
for (int i = 0; i < N; i++)
assert(in1_dims[i] == in2_dims[i]);
float value = md_zrnorme(DIMS, in1_dims, in1_data, in2_data);
printf("%+e\n", value);
unmap_cfl(N, in1_dims, in1_data);
unmap_cfl(N, in2_dims, in2_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;
}
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_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_estvar(int argc, char* argv[])
{
long calsize_dims[3] = { 24, 24, 24};
long kernel_dims[3] = { 6, 6, 6};
const struct opt_s opts[] = {
{ 'k', true, opt_vec3, &kernel_dims, " ksize\tkernel size" },
{ 'K', true, opt_vec3, &kernel_dims, NULL },
{ 'r', true, opt_vec3, &calsize_dims, " cal_size\tLimits the size of the calibration region." },
{ 'R', true, opt_vec3, &calsize_dims, NULL },
};
cmdline(&argc, argv, 1, 1, usage_str, help_str, ARRAY_SIZE(opts), opts);
int N = DIMS;
long kspace_dims[N];
complex float* kspace = load_cfl(argv[1], N, kspace_dims);
for (int idx = 0; idx < 3; idx++) {
kernel_dims[idx] = (kspace_dims[idx] == 1) ? 1 : kernel_dims[idx];
calsize_dims[idx] = (kspace_dims[idx] == 1) ? 1 : calsize_dims[idx];
}
float variance = estvar_kspace(N, kernel_dims, calsize_dims, kspace_dims, kspace);
unmap_cfl(N, kspace_dims, kspace);
printf("Estimated noise variance: %f\n", variance);
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_estdelay(int argc, char* argv[])
{
bool ring = false;
int pad_factor = 100;
unsigned int no_intersec_sp = 1;
float size = 1.5;
const struct opt_s opts[] = {
OPT_SET('R', &ring, "RING method"),
OPT_INT('p', &pad_factor, "p", "[RING] Padding"),
OPT_UINT('n', &no_intersec_sp, "n", "[RING] Number of intersecting spokes"),
OPT_FLOAT('r', &size, "r", "[RING] Central region size"),
};
cmdline(&argc, argv, 2, 2, usage_str, help_str, ARRAY_SIZE(opts), opts);
num_init();
if (pad_factor % 2 != 0)
error("Pad_factor -p should be even\n");
long tdims[DIMS];
const complex float* traj = load_cfl(argv[1], DIMS, tdims);
long tdims1[DIMS];
md_select_dims(DIMS, ~MD_BIT(1), tdims1, tdims);
complex float* traj1 = md_alloc(DIMS, tdims1, CFL_SIZE);
md_slice(DIMS, MD_BIT(1), (long[DIMS]){ 0 }, tdims, traj1, traj, CFL_SIZE);
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_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_estdelay(int argc, char* argv[])
{
mini_cmdline(&argc, argv, 2, usage_str, help_str);
long tdims[DIMS];
const complex float* traj = load_cfl(argv[1], DIMS, tdims);
long tdims1[DIMS];
md_select_dims(DIMS, ~MD_BIT(1), tdims1, tdims);
complex float* traj1 = md_alloc(DIMS, tdims1, CFL_SIZE);
md_slice(DIMS, MD_BIT(1), (long[DIMS]){ 0 }, tdims, traj1, traj, CFL_SIZE);
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_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_sdot(int argc, char* argv[])
{
cmdline(&argc, argv, 2, 2, usage_str, help_str, 0, NULL);
int N = DIMS;
long in1_dims[N];
long in2_dims[N];
complex float* in1_data = load_cfl(argv[1], N, in1_dims);
complex float* in2_data = load_cfl(argv[2], N, in2_dims);
for (int i = 0; i < N; i++)
assert(in1_dims[i] == in2_dims[i]);
// compute scalar product
complex float value = md_zscalar(N, in1_dims, in1_data, in2_data);
printf("%+e%+ei\n", crealf(value), cimagf(value));
unmap_cfl(N, in1_dims, in1_data);
unmap_cfl(N, in2_dims, in2_data);
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_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_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_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_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_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_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_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 {