void create_test_file(void)
{
int r;
double start_values[3]= {-6.96, -12.453, -9.48};
double separations[3]= {0.09,0.09,0.09};
midimhandle_t hdim[NDIMS];
mihandle_t hvol;
unsigned short *buf = ( unsigned short *) malloc(CX * CY * CZ * sizeof(unsigned short));
int i;
long count[NDIMS];
long start[NDIMS];
miboolean_t flag=1;
double min = -1.0;
double max = 1.0;
r = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[0]);
r = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[1]);
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[2]);
r = miset_dimension_starts(hdim, NDIMS, start_values);
r = miset_dimension_separations(hdim, NDIMS, separations);
r = micreate_volume("hyperslab-test2.mnc", NDIMS, hdim, MI_TYPE_USHORT,
MI_CLASS_REAL, NULL, &hvol);
/* set slice scaling flag to true */
r = miset_slice_scaling_flag(hvol, flag);
r = micreate_volume_image(hvol);
for (i = 0; i < CZ*CY*CX; i++) {
buf[i] = (unsigned short) i * 0.01;
}
start[0] = start[1] = start[2] = 0;
count[0] = CZ;
count[1] = CY;
count[2] = CX;
r = miset_voxel_value_hyperslab(hvol, MI_TYPE_USHORT, start, count, buf);
/* Set random values to slice min and max for slice scaling*/
start[0] =start[1]=start[2]=0;
for (i=0; i < CZ; i++) {
start[0] = i;
min += 0.1;
max += 0.1;
r = miset_slice_range(hvol,start, 3, max, min);
}
r = miclose_volume(hvol);
}
int create_4D_image(void)
{
int r;
double start_values[NDIMS+1]={-6.96, -12.453, -9.48, 20.002};
double separations[NDIMS+1]={0.09,0.09,0.09, 1};
midimhandle_t hdim[NDIMS+1];
mihandle_t hvol;
unsigned char *buf = (unsigned char *) malloc(CX * CU * CZ * CY * sizeof(unsigned char));
int i,j;
long count[NDIMS+1];
long start[NDIMS+1];
miboolean_t flag=1;
double min = -1.0;
double max = 1.0;
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[0]);
r = micreate_dimension("user", MI_DIMCLASS_USER,
MI_DIMATTR_REGULARLY_SAMPLED, CU, &hdim[1]);
r = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[2]);
r = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[3]);
r = miset_dimension_starts(hdim, NDIMS+1, start_values);
r = miset_dimension_separations(hdim, NDIMS+1, separations);
r = micreate_volume("4D_image.mnc", NDIMS+1, hdim, MI_TYPE_UBYTE,
MI_CLASS_REAL, NULL, &hvol);
/* set slice scaling flag to true */
r = miset_slice_scaling_flag(hvol, flag);
r = micreate_volume_image(hvol);
for (i = 0; i < CX*CU*CZ*CY; i++) {
buf[i] = (unsigned char) i;
}
start[0] = start[1] = start[2] = start[3] = 0;
count[0] = CX; count[1] = CU; count[2] = CZ; count[3] = CY;
r = miset_voxel_value_hyperslab(hvol, MI_TYPE_UBYTE, start, count, buf);
/* Set random values to slice min and max for slice scaling*/
start[0] =start[1]=start[2]=start[3]=0;
for (i=0; i < CX; i++) {
start[0] = i;
for ( j=0; j < CU; j++)
{
start[1] = j;
min += -0.1;
max += 0.1;
r = miset_slice_range(hvol,start,NDIMS+1 , max, min);
}
}
r = miclose_volume(hvol);
return r<0?1:0;
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Purpose:
*
*
*
*
*
*/
SEXP write_volume(SEXP filename, SEXP nDimensions,
SEXP dimLengths,
SEXP dimStarts,
SEXP dimSteps,
SEXP volumeDataType,
SEXP volumeRange,
SEXP hSlab) {
mihandle_t minc_volume;
midimhandle_t dim[MI2_MAX_VAR_DIMS];
mivolumeprops_t volume_properties;
int result;
int ndx;
int no_dimensions;
int dim_lengths[MI2_MAX_VAR_DIMS];
double dim_starts[MI2_MAX_VAR_DIMS];
double dim_steps[MI2_MAX_VAR_DIMS];
double volume_range_min, volume_range_max;
int volume_data_type;
// pointer to the volume data
double *hSlab_p;
misize_t hSlab_start[MI2_MAX_VAR_DIMS];
misize_t hSlab_count[MI2_MAX_VAR_DIMS];
// start ...
if ( R_DEBUG_mincIO ) Rprintf("write_volume: start ...\n");
/* init number of dimensions and their respective sizes
... yes, I could get this myself, but it's best set in the calling R code */
no_dimensions = INTEGER(nDimensions)[0];
volume_data_type = INTEGER(volumeDataType)[0];
volume_range_min = REAL(volumeRange)[0];
volume_range_max = REAL(volumeRange)[1];
// init volume data pointer
hSlab_p = REAL(hSlab);
// init lenghts, steps, and starts
for (ndx=0; ndx < no_dimensions; ++ndx) {
dim_lengths[ndx] = INTEGER(dimLengths)[ndx];
hSlab_count[ndx] = INTEGER(dimLengths)[ndx];
dim_starts[ndx] = REAL(dimStarts)[ndx];
dim_steps[ndx] = REAL(dimSteps)[ndx];
}
// set the properties for the new output volume
// ... no compression, no chunking, no multi-resolution, ... nothin fancy
result = minew_volume_props(&volume_properties);
if (result != MI_NOERROR) {
error("write_volume:minew_volume_props: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
result = miset_props_compression_type(volume_properties, MI_COMPRESS_NONE);
if (result != MI_NOERROR) {
error("write_volume:miset_props_compression_type: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
result = miset_props_multi_resolution(volume_properties, FALSE, 1);
if (result != MI_NOERROR) {
error("write_volume:miset_props_multi_resolution: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
/* create the 3 output dimensions in the order Z, Y, X, as the volume
is stored in this order */
// z-dim
result = micreate_dimension("zspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[0],
&dim[0]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "zspace");
}
// y-dim
result = micreate_dimension("yspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[1],
&dim[1]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "yspace");
}
// x-dim
result = micreate_dimension("xspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[2],
&dim[2]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "xspace");
}
// set the start values for each dimension
result = miset_dimension_starts(dim, no_dimensions, dim_starts);
if (result == MI_ERROR) {
error("write_volume: Error setting dimension start values.\n");
}
// set the step values for each dimension
result = miset_dimension_separations(dim, no_dimensions, dim_steps);
if (result == MI_ERROR) {
error("write_volume: Error setting dimension step values.\n");
}
// create the volume structure (no data yet, of course)
result = micreate_volume(CHAR(STRING_ELT(filename, 0)),
no_dimensions,
dim,
volume_data_type,
MI_CLASS_REAL,
volume_properties,
&minc_volume);
//
if (result != MI_NOERROR) {
error("write_volume: Error creating output volume structure: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// create the path to the image data
result = micreate_volume_image(minc_volume);
//
if (result != MI_NOERROR) {
error("write_volume: Error writing data to volume %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// set valid and real ranges
// ... 0xFFFF=65535=16-bits (unsigned)
miset_volume_valid_range(minc_volume, 0x7FFF, 0);
miset_volume_range(minc_volume, volume_range_max, volume_range_min);
// write hyperslab (entire volume)
hSlab_start[0] = hSlab_start[1] = hSlab_start[2] = 0;
if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..2] = %d, %d, %d\n",
hSlab_count[0], hSlab_count[1], hSlab_count[2]);
result = miset_real_value_hyperslab(minc_volume, MI_TYPE_DOUBLE,
hSlab_start,
hSlab_count,
hSlab_p);
if ( result != MI_NOERROR ) {
error("Error in miset_real_value_hyperslab: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// free resources
//
// in the current version of minc (libsrc2/volume.c), these volume properties
// as well as the dimension handles are already freed by the miclose_volume function.
//
//mifree_volume_props(volume_properties); // free the property list
//for ( ndx=0; ndx<no_dimensions; ++ndx) { // free the dimhandles
// mifree_dimension_handle(dim[ndx]);
//}
// close new volume
result = miclose_volume(minc_volume);
if (result != MI_NOERROR) {
error("write_volume: Error closing newly created volume %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// done, return NULL
if ( R_DEBUG_mincIO ) Rprintf("write_volume: returning ...\n");
return(R_NilValue);
}
