/* regrid a point in a file using the input co-ordinate and data */ void regrid_point(VIO_Volume * totals, VIO_Volume * weights, double x, double y, double z, int v_size, double *data_buf) { int sizes[MAX_VAR_DIMS]; VIO_Real steps[MAX_VAR_DIMS]; VIO_Real starts[MAX_VAR_DIMS]; int start_idx[3]; int stop_idx[3]; double value, weight; double euc_dist; double euc[3]; double c_pos[3]; int i, j, k, v; double coord[3]; /* target point in mm coordinates, in X, Y, Z order */ VIO_Transform dircos, invdircos; VIO_Vector vector; VIO_Real dir[3]; /* the coord used below has to be in mm coordinates in the dircos space of the target volume. Hence the manipulations with the vols direction_cosines */ make_identity_transform(&dircos); get_volume_direction_cosine(*totals, perm[0], dir); fill_Vector(vector, dir[0], dir[1], dir[2]); set_transform_x_axis(&dircos, &vector); get_volume_direction_cosine(*totals, perm[1], dir); fill_Vector(vector, dir[0], dir[1], dir[2]); set_transform_y_axis(&dircos, &vector); get_volume_direction_cosine(*totals, perm[2], dir); fill_Vector(vector, dir[0], dir[1], dir[2]); set_transform_z_axis(&dircos, &vector); for(i = 0; i < 4; i++){ for(j = 0; j < 4; j++){ Transform_elem(invdircos, i, j) = Transform_elem(dircos, j, i); } } transform_point(&invdircos, x, y, z, &coord[0], &coord[1], &coord[2]); get_volume_sizes(*totals, sizes); /* in volume voxel order, ie z,y,x with x fastest */ get_volume_separations(*totals, steps); get_volume_starts(*totals, starts); /* figure out the neighbouring voxels start and stop (in voxel co-ordinates) */ for(i = 0; i < 3; i++){ /* go through x, y and z */ start_idx[i] = (int)rint((coord[i] - starts[perm[i]] - regrid_radius[i]) / steps[perm[i]]); stop_idx[i] = start_idx[i] + rint((regrid_radius[i] * 2) / steps[perm[i]]); /* flip if required */ if(start_idx[i] > stop_idx[i]){ value = start_idx[i]; start_idx[i] = stop_idx[i]; stop_idx[i] = value; } /* check that we aren't off the edge */ if(start_idx[i] < 0){ start_idx[i] = 0; } if(stop_idx[i] >= sizes[perm[i]]){ stop_idx[i] = sizes[perm[i]] - 1; } } /* loop over the neighbours, getting euclidian distance */ c_pos[0] = starts[perm[0]] + (start_idx[0] * steps[perm[0]]); for(i = start_idx[0]; i <= stop_idx[0]; i++){ euc[0] = fabs(c_pos[0] - coord[0]); c_pos[1] = starts[perm[1]] + (start_idx[1] * steps[perm[1]]); for(j = start_idx[1]; j <= stop_idx[1]; j++){ euc[1] = fabs(c_pos[1] - coord[1]); c_pos[2] = starts[perm[2]] + (start_idx[2] * steps[perm[2]]); for(k = start_idx[2]; k <= stop_idx[2]; k++){ euc[2] = fabs(c_pos[2] - coord[2]); euc_dist = sqrt(SQR2(euc[0]) + SQR2(euc[1]) + SQR2(euc[2])); if((regrid_radius[0] == 0 || euc[0] <= regrid_radius[0]) && (regrid_radius[1] == 0 || euc[1] <= regrid_radius[1]) && (regrid_radius[2] == 0 || euc[2] <= regrid_radius[2])){ /* calculate the weighting factor */ switch (regrid_type){ default: fprintf(stderr, "Erk! unknown regrid_type. File: %s Line: %d\n", __FILE__, __LINE__); exit(EXIT_FAILURE); break; case NEAREST_FUNC: case LINEAR_FUNC: weight = euc_dist; break; case KAISERBESSEL_FUNC: weight = gsl_sf_bessel_I0(regrid_sigma[0] * sqrt(1 - SQR2(euc[0] / regrid_radius[0]))) * gsl_sf_bessel_I0(regrid_sigma[1] * sqrt(1 - SQR2(euc[1] / regrid_radius[1]))) * gsl_sf_bessel_I0(regrid_sigma[2] * sqrt(1 - SQR2(euc[2] / regrid_radius[2]))) / SQR3((regrid_radius[0] + regrid_radius[1] + regrid_radius[2]) / 3); break; case GAUSSIAN_FUNC: weight = exp(-SQR2(euc[0]) / SQR2(regrid_sigma[0])) * exp(-SQR2(euc[1]) / SQR2(regrid_sigma[1])) * exp(-SQR2(euc[2]) / SQR2(regrid_sigma[2])); break; } /* set data values */ if(regrid_type == NEAREST_FUNC){ value = get_volume_real_value(*weights, k, j, i, 0, 0); if(weight < value){ set_volume_real_value(*weights, k, j, i, 0, 0, weight); for(v = 0; v < v_size; v++){ set_volume_real_value(*totals, k, j, i, v, 0, data_buf[0 + v] * weight); } } } else{ for(v = 0; v < v_size; v++){ value = get_volume_real_value(*totals, k, j, i, v, 0); set_volume_real_value(*totals, k, j, i, v, 0, value + (data_buf[0 + v] * weight)); } /* increment count value */ value = get_volume_real_value(*weights, k, j, i, 0, 0); set_volume_real_value(*weights, k, j, i, 0, 0, value + weight); } } c_pos[2] += steps[perm[2]]; } c_pos[1] += steps[perm[1]]; } c_pos[0] += steps[perm[0]]; } }
static void append_new_default_deformation_field(Arg_Data *globals) { VIO_Volume new_field; VIO_Real zero, st[VIO_MAX_DIMENSIONS], wst[VIO_MAX_DIMENSIONS], step[VIO_MAX_DIMENSIONS], XYZstart[ VIO_MAX_DIMENSIONS ], XYZstep[ VIO_MAX_DIMENSIONS ], voxel[VIO_MAX_DIMENSIONS], point[VIO_N_DIMENSIONS], dir[3][3]; int index[VIO_MAX_DIMENSIONS], xyzv[VIO_MAX_DIMENSIONS], i, count[VIO_MAX_DIMENSIONS], XYZcount[VIO_MAX_DIMENSIONS], count_extended[VIO_MAX_DIMENSIONS]; VIO_General_transform *grid_trans; VectorR XYZdirections[ VIO_MAX_DIMENSIONS ]; /* build a vector volume to store the Grid VIO_Transform */ /* ALLOC(new_field,1); not needed since create volume allocs it internally and returns a pointer*/ if (globals->flags.debug) { print ("In append_new_default_deformation_field...\n"); } new_field = create_volume(4, dim_name_vector_vol, NC_DOUBLE, TRUE, 0.0, 0.0); get_volume_XYZV_indices(new_field, xyzv); /* get the global voxel count and voxel size */ for(i=0; i<VIO_N_DIMENSIONS; i++) { count[xyzv[i]] = globals->count[i]; count_extended[xyzv[i]] = count[xyzv[i]]; step[xyzv[i]] = globals->step[i]; } /* add info for the vector dimension */ count[xyzv[VIO_Z+1]] = 3; count_extended[xyzv[VIO_Z+1]] = 3; step[xyzv[VIO_Z+1]] = 0.0; set_volume_sizes( new_field, count); set_volume_separations( new_field, step); /* set_volume_voxel_range( new_field, -MY_MAX_VOX, MY_MAX_VOX); set_volume_real_range( new_field, -1.0*globals->trans_info.max_def_magnitude, globals->trans_info.max_def_magnitude); no longer needed, now using floats */ for(i=0; i<VIO_N_DIMENSIONS; i++) { dir[VIO_X][i]=globals->directions[VIO_X].coords[i]; dir[VIO_Y][i]=globals->directions[VIO_Y].coords[i]; dir[VIO_Z][i]=globals->directions[VIO_Z].coords[i]; } set_volume_direction_cosine(new_field,xyzv[VIO_X],dir[VIO_X]); set_volume_direction_cosine(new_field,xyzv[VIO_Y],dir[VIO_Y]); set_volume_direction_cosine(new_field,xyzv[VIO_Z],dir[VIO_Z]); for(i=0; i<VIO_MAX_DIMENSIONS; i++) /* set the voxel origin, used in the vol def */ voxel[i] = 0.0; set_volume_translation( new_field, voxel, globals->start); if (globals->flags.debug) { print("in append new def, the start is: %8.3f %8.3f %8.3f\n", globals->start[VIO_X], globals->start[VIO_Y], globals->start[VIO_Z]); } /* now pad the volume along the spatial axis to ensure good coverage of the data space with the deformation field */ for(i=0; i<VIO_N_DIMENSIONS; i++) { if (globals->count[i]>1) { voxel[xyzv[i]] = -2.5; count_extended[xyzv[i]] = globals->count[i]+5; } else { voxel[xyzv[i]] = 0.0; count_extended[xyzv[i]] = 1; } } if (globals->flags.debug) { print("in append_new_default_deformation_field:\n\tcount_extended= %d %d %d %d\n", count_extended[0],count_extended[1],count_extended[2],count_extended[3]); } set_volume_sizes(new_field, count_extended); for(i=0; i<VIO_MAX_DIMENSIONS; i++) count[i] = count_extended[i]; /* reset the first voxel position with the new origin */ convert_voxel_to_world(new_field, voxel, &(point[VIO_X]), &(point[VIO_Y]), &(point[VIO_Z])); for(i=0; i<VIO_MAX_DIMENSIONS; i++) voxel[i] = 0; set_volume_translation(new_field, voxel, point); if (globals->flags.debug) { print (" point: %8.3f %8.3f %8.3f \n", point[VIO_X], point[VIO_Y], point[VIO_Z]); get_volume_starts(new_field, st); print (" start: %8.3f %8.3f %8.3f \n", st[xyzv[VIO_X]], st[xyzv[VIO_Y]], st[xyzv[VIO_Z]]); voxel[0] = 0; voxel[1] = 0; voxel[2] = 0; get_volume_translation(new_field, voxel, wst); print (" wstrt: %8.3f %8.3f %8.3f \n", wst[VIO_X], wst[VIO_Y], wst[VIO_Z]); print (" voxel: %8.3f %8.3f %8.3f \n", voxel[xyzv[VIO_X]], voxel[xyzv[VIO_Y]], voxel[xyzv[VIO_Z]]); for(i=0; i<3; i++) { get_volume_direction_cosine(new_field,xyzv[i], wst); print (" dirs: %8.3f %8.3f %8.3f \n", wst[VIO_X], wst[VIO_Y], wst[VIO_Z]); } } /* allocate space for the deformation field data */ alloc_volume_data(new_field); /* Initilize the field to zero deformation */ /* zero = CONVERT_VALUE_TO_VOXEL(new_field, 0.0); not needed, defs are now doubles */ for(index[0]=0; index[0]<count[0]; index[0]++) for(index[1]=0; index[1]<count[1]; index[1]++) for(index[2]=0; index[2]<count[2]; index[2]++) for(index[3]=0; index[3]<count[3]; index[3]++) { SET_VOXEL(new_field, index[0],index[1],index[2],index[3],0, 0.0); /* was set to 'zero', but now as a double,can be set to 0.0 */ } /* build the new GRID_TRANSFORM */ ALLOC(grid_trans, 1); create_grid_transform(grid_trans, new_field, NULL); /* append the deforamation to the current transformation */ concat_general_transforms(globals->trans_info.transformation, grid_trans, globals->trans_info.transformation); delete_volume(new_field); delete_general_transform(grid_trans); }