int main_twixread(int argc, char* argv[argc])
{
long adcs = 0;
bool autoc = false;
bool linectr = false;
bool partctr = false;
long dims[DIMS];
md_singleton_dims(DIMS, dims);
struct opt_s opts[] = {
OPT_LONG('x', &(dims[READ_DIM]), "X", "number of samples (read-out)"),
OPT_LONG('y', &(dims[PHS1_DIM]), "Y", "phase encoding steps"),
OPT_LONG('z', &(dims[PHS2_DIM]), "Z", "partition encoding steps"),
OPT_LONG('s', &(dims[SLICE_DIM]), "S", "number of slices"),
OPT_LONG('v', &(dims[AVG_DIM]), "V", "number of averages"),
OPT_LONG('c', &(dims[COIL_DIM]), "C", "number of channels"),
OPT_LONG('n', &(dims[TIME_DIM]), "N", "number of repetitions"),
OPT_LONG('a', &adcs, "A", "total number of ADCs"),
OPT_SET('A', &autoc, "automatic [guess dimensions]"),
OPT_SET('L', &linectr, "use linectr offset"),
OPT_SET('P', &partctr, "use partctr offset"),
};
cmdline(&argc, argv, 2, 2, usage_str, help_str, ARRAY_SIZE(opts), opts);
if (0 == adcs)
adcs = dims[PHS1_DIM] * dims[PHS2_DIM] * dims[SLICE_DIM] * dims[TIME_DIM];
debug_print_dims(DP_DEBUG1, DIMS, dims);
int ifd;
if (-1 == (ifd = open(argv[1], O_RDONLY)))
error("error opening file.");
struct hdr_s hdr;
bool vd = siemens_meas_setup(ifd, &hdr);
long off[DIMS] = { 0 };
if (autoc) {
long max[DIMS] = { [COIL_DIM] = 1000 };
long min[DIMS] = { 0 }; // min is always 0
adcs = 0;
while (true) {
if (-1 == siemens_bounds(vd, ifd, min, max))
break;
debug_print_dims(DP_DEBUG3, DIMS, max);
adcs++;
}
for (unsigned int i = 0; i < DIMS; i++) {
off[i] = -min[i];
dims[i] = max[i] + off[i];
}
debug_printf(DP_DEBUG2, "Dimensions: ");
debug_print_dims(DP_DEBUG2, DIMS, dims);
debug_printf(DP_DEBUG2, "Offset: ");
debug_print_dims(DP_DEBUG2, DIMS, off);
siemens_meas_setup(ifd, &hdr); // reset
}
complex float* out = create_cfl(argv[2], DIMS, dims);
md_clear(DIMS, dims, out, CFL_SIZE);
long adc_dims[DIMS];
md_select_dims(DIMS, READ_FLAG|COIL_FLAG, adc_dims, dims);
void* buf = md_alloc(DIMS, adc_dims, CFL_SIZE);
while (adcs--) {
long pos[DIMS] = { [0 ... DIMS - 1] = 0 };
if (-1 == siemens_adc_read(vd, ifd, linectr, partctr, dims, pos, buf)) {
debug_printf(DP_WARN, "Stopping.\n");
break;
}
for (unsigned int i = 0; i < DIMS; i++)
pos[i] += off[i];
debug_print_dims(DP_DEBUG1, DIMS, pos);
if (!md_is_index(DIMS, pos, dims)) {
debug_printf(DP_WARN, "Index out of bounds.\n");
continue;
}
md_copy_block(DIMS, pos, dims, out, adc_dims, buf, CFL_SIZE);
}
md_free(buf);
unmap_cfl(DIMS, dims, out);
exit(0);
}
int main_twixread(int argc, char* argv[argc])
{
int c;
long adcs = 0;
bool autoc = false;
bool linectr = false;
bool partctr = false;
long dims[DIMS];
md_singleton_dims(DIMS, dims);
while (-1 != (c = getopt(argc, argv, "x:y:z:s:c:a:n:PLAh"))) {
switch (c) {
case 'x':
dims[READ_DIM] = atoi(optarg);
break;
case 'y':
dims[PHS1_DIM] = atoi(optarg);
break;
case 'z':
dims[PHS2_DIM] = atoi(optarg);
break;
case 's':
dims[SLICE_DIM] = atoi(optarg);
break;
case 'v':
dims[AVG_DIM] = atoi(optarg);
break;
case 'n':
dims[TIME_DIM] = atoi(optarg);
break;
case 'a':
adcs = atoi(optarg);
break;
case 'A':
autoc = true;
break;
case 'c':
dims[COIL_DIM] = atoi(optarg);
break;
case 'P':
partctr = true;
break;
case 'L':
linectr = true;
break;
case 'h':
usage(argv[0], stdout);
help();
exit(0);
default:
usage(argv[0], stderr);
exit(1);
}
}
if (argc - optind != 2) {
usage(argv[0], stderr);
exit(1);
}
if (0 == adcs)
adcs = dims[PHS1_DIM] * dims[PHS2_DIM] * dims[SLICE_DIM] * dims[TIME_DIM];
debug_print_dims(DP_DEBUG1, DIMS, dims);
int ifd;
if (-1 == (ifd = open(argv[optind + 0], O_RDONLY)))
error("error opening file.");
struct hdr_s hdr;
bool vd = siemens_meas_setup(ifd, &hdr);
long off[DIMS] = { 0 };
if (autoc) {
long max[DIMS] = { [COIL_DIM] = 1000 };
long min[DIMS] = { 0 }; // min is always 0
adcs = 0;
while (true) {
if (-1 == siemens_bounds(vd, ifd, min, max))
break;
debug_print_dims(DP_DEBUG3, DIMS, max);
adcs++;
}
for (unsigned int i = 0; i < DIMS; i++) {
off[i] = -min[i];
dims[i] = max[i] + off[i];
}
debug_printf(DP_INFO, "Dimensions: ");
debug_print_dims(DP_INFO, DIMS, dims);
debug_printf(DP_INFO, "Offset: ");
debug_print_dims(DP_INFO, DIMS, off);
siemens_meas_setup(ifd, &hdr); // reset
}
complex float* out = create_cfl(argv[optind + 1], DIMS, dims);
md_clear(DIMS, dims, out, CFL_SIZE);
long adc_dims[DIMS];
md_select_dims(DIMS, READ_FLAG|COIL_FLAG, adc_dims, dims);
void* buf = md_alloc(DIMS, adc_dims, CFL_SIZE);
while (adcs--) {
long pos[DIMS] = { [0 ... DIMS - 1] = 0 };
if (-1 == siemens_adc_read(vd, ifd, linectr, partctr, dims, pos, buf)) {
debug_printf(DP_WARN, "Stopping.\n");
break;
}
for (unsigned int i = 0; i < DIMS; i++)
pos[i] += off[i];
debug_print_dims(DP_DEBUG1, DIMS, pos);
if (!md_is_index(DIMS, pos, dims)) {
debug_printf(DP_WARN, "Index out of bounds.\n");
continue;
}
md_copy_block(DIMS, pos, dims, out, adc_dims, buf, CFL_SIZE);
}
md_free(buf);
unmap_cfl(DIMS, dims, out);
exit(0);
}