BICPL: vol_prototypes.h Source File

00001 #ifndef DEF_vol_prototypes 00002 #define DEF_vol_prototypes 00003 00004 public Volume create_box_filtered_volume( 00005 Volume volume, 00006 nc_type nc_data_type, 00007 BOOLEAN sign_flag, 00008 Real real_min_value, 00009 Real real_max_value, 00010 Real x_width, 00011 Real y_width, 00012 Real z_width ); 00013 00014 public void modify_labels_in_range( 00015 Volume volume, 00016 Volume label_volume, 00017 int src_min, 00018 int src_max, 00019 int dest_label, 00020 Real min_threshold, 00021 Real max_threshold, 00022 int range_changed[2][N_DIMENSIONS] ); 00023 00024 public void initialize_colour_coding( 00025 colour_coding_struct *colour_coding, 00026 Colour_coding_types type, 00027 Colour under_colour, 00028 Colour over_colour, 00029 Real min_value, 00030 Real max_value ); 00031 00032 public void delete_colour_coding( 00033 colour_coding_struct *colour_coding ); 00034 00035 public void set_colour_coding_type( 00036 colour_coding_struct *colour_coding, 00037 Colour_coding_types type ); 00038 00039 public Colour_coding_types get_colour_coding_type( 00040 colour_coding_struct *colour_coding ); 00041 00042 public void set_colour_coding_min_max( 00043 colour_coding_struct *colour_coding, 00044 Real min_value, 00045 Real max_value ); 00046 00047 public void get_colour_coding_min_max( 00048 colour_coding_struct *colour_coding, 00049 Real *min_value, 00050 Real *max_value ); 00051 00052 public Colour get_colour_coding_under_colour( 00053 colour_coding_struct *colour_coding ); 00054 00055 public void set_colour_coding_under_colour( 00056 colour_coding_struct *colour_coding, 00057 Colour under_colour ); 00058 00059 public Colour get_colour_coding_over_colour( 00060 colour_coding_struct *colour_coding ); 00061 00062 public void set_colour_coding_over_colour( 00063 colour_coding_struct *colour_coding, 00064 Colour over_colour ); 00065 00066 public BOOLEAN define_colour_coding_user_defined( 00067 colour_coding_struct *colour_code, 00068 int n_colours, 00069 Colour colours[], 00070 Real positions[], 00071 Colour_spaces interpolation_space ); 00072 00073 public Colour get_colour_code( 00074 colour_coding_struct *colour_coding, 00075 Real value ); 00076 00077 public void colour_code_object( 00078 Volume volume, 00079 int continuity, 00080 colour_coding_struct *colour_coding, 00081 object_struct *object ); 00082 00083 public STRING get_default_user_def_colour_code_suffix( void ); 00084 00085 public Status input_user_defined_colour_coding( 00086 colour_coding_struct *colour_coding, 00087 STRING filename ); 00088 00089 public void create_volume_slice( 00090 Volume volume1, 00091 Filter_types filter_type1, 00092 Real filter_width1, 00093 Real slice_position1[], 00094 Real x_axis1[], 00095 Real y_axis1[], 00096 Real x_translation1, 00097 Real y_translation1, 00098 Real x_scale1, 00099 Real y_scale1, 00100 Volume volume2, 00101 Filter_types filter_type2, 00102 Real filter_width2, 00103 Real slice_position2[], 00104 Real x_axis2[], 00105 Real y_axis2[], 00106 Real x_translation2, 00107 Real y_translation2, 00108 Real x_scale2, 00109 Real y_scale2, 00110 int x_viewport_size, 00111 int y_viewport_size, 00112 int x_pixel_start, 00113 int x_pixel_end, 00114 int y_pixel_start, 00115 int y_pixel_end, 00116 Pixel_types pixel_type, 00117 int degrees_continuity, 00118 unsigned short **cmode_colour_map, 00119 Colour **rgb_colour_map, 00120 Colour empty_colour, 00121 void *render_storage, 00122 BOOLEAN clip_pixels_flag, 00123 int *n_pixels_alloced, 00124 pixels_struct *pixels ); 00125 00126 public void set_volume_slice_pixel_range( 00127 Volume volume1, 00128 Filter_types filter_type1, 00129 Real filter_width1, 00130 Real slice_position1[], 00131 Real x_axis1[], 00132 Real y_axis1[], 00133 Real x_translation1, 00134 Real y_translation1, 00135 Real x_scale1, 00136 Real y_scale1, 00137 Volume volume2, 00138 Filter_types filter_type2, 00139 Real filter_width2, 00140 Real slice_position2[], 00141 Real x_axis2[], 00142 Real y_axis2[], 00143 Real x_translation2, 00144 Real y_translation2, 00145 Real x_scale2, 00146 Real y_scale2, 00147 int x_viewport_size, 00148 int y_viewport_size, 00149 Pixel_types pixel_type, 00150 int *n_pixels_alloced, 00151 pixels_struct *pixels ); 00152 00153 public BOOLEAN find_volume_crop_bounds( 00154 Volume volume, 00155 Real min_crop_threshold, 00156 Real max_crop_threshold, 00157 int limits[2][MAX_DIMENSIONS] ); 00158 00159 public Volume create_cropped_volume( 00160 Volume volume, 00161 int limits[2][MAX_DIMENSIONS] ); 00162 00163 public Volume autocrop_volume( 00164 Volume volume ); 00165 00166 public int dilate_voxels_3d( 00167 Volume volume, 00168 Volume label_volume, 00169 Real min_inside_label, 00170 Real max_inside_label, 00171 Real min_inside_value, 00172 Real max_inside_value, 00173 Real min_outside_label, 00174 Real max_outside_label, 00175 Real min_outside_value, 00176 Real max_outside_value, 00177 Real new_label, 00178 Neighbour_types connectivity, 00179 int range_changed[2][N_DIMENSIONS] ); 00180 00181 public int get_slice_weights_for_filter( 00182 Volume volume, 00183 Real voxel_position[], 00184 Real voxel_direction[], /* if filter_type != NEAREST */ 00185 Filter_types filter_type, 00186 Real full_width_half_max, 00187 Real ***positions, 00188 Real *weights[] ); 00189 00190 public BOOLEAN fill_connected_voxels( 00191 Volume volume, 00192 Volume label_volume, 00193 Neighbour_types connectivity, 00194 int voxel[], 00195 int min_label_threshold, 00196 int max_label_threshold, 00197 int desired_label, 00198 Real min_threshold, 00199 Real max_threshold, 00200 int range_changed[2][N_DIMENSIONS] ); 00201 00202 public int get_neighbour_directions( 00203 Neighbour_types connectivity, 00204 int *dx[], 00205 int *dy[] ); 00206 00207 public int get_3D_neighbour_directions( 00208 Neighbour_types connectivity, 00209 int *dx[], 00210 int *dy[], 00211 int *dz[] ); 00212 00213 public BOOLEAN should_change_this_one( 00214 Volume volume, 00215 Volume label_volume, 00216 int voxel[], 00217 Real min_threshold, 00218 Real max_threshold, 00219 int label_min_threshold, 00220 int label_max_threshold, 00221 int desired_label ); 00222 00223 public void interpolate_volume_to_slice( 00224 Volume volume1, 00225 int n_dims1, 00226 Real origin1[], 00227 Real x_axis1[], 00228 Real y_axis1[], 00229 Volume volume2, 00230 int n_dims2, 00231 Real origin2[], 00232 Real x_axis2[], 00233 Real y_axis2[], 00234 int x_pixel_start, 00235 int x_pixel_end, 00236 int y_pixel_start, 00237 int y_pixel_end, 00238 int degrees_continuity, 00239 unsigned short **cmode_colour_map, 00240 Colour **rgb_colour_map, 00241 Colour empty_colour, 00242 pixels_struct *pixels ); 00243 00244 public Status input_volume_header_only( 00245 STRING filename, 00246 int n_dimensions, 00247 STRING dim_names[], 00248 Volume *volume, 00249 minc_input_options *options ); 00250 00251 public void set_label_volume_real_range( 00252 Volume volume ); 00253 00254 public Volume create_label_volume( 00255 Volume volume, 00256 nc_type type ); 00257 00258 public BOOLEAN is_label_volume_initialized( 00259 Volume volume ); 00260 00261 public void set_all_volume_label_data( 00262 Volume volume, 00263 int value ); 00264 00265 public void set_volume_label_data_5d( 00266 Volume volume, 00267 int v0, 00268 int v1, 00269 int v2, 00270 int v3, 00271 int v4, 00272 int value ); 00273 00274 public void set_volume_label_data( 00275 Volume volume, 00276 int voxel[], 00277 int value ); 00278 00279 public int get_volume_label_data( 00280 Volume volume, 00281 int voxel[] ); 00282 00283 public int get_volume_label_data_5d( 00284 Volume volume, 00285 int v0, 00286 int v1, 00287 int v2, 00288 int v3, 00289 int v4 ); 00290 00291 public int get_3D_volume_label_data( 00292 Volume volume, 00293 int x, 00294 int y, 00295 int z ); 00296 00297 public BOOLEAN get_voxel_label_bit( 00298 Volume volume, 00299 int voxel[], 00300 int bit ); 00301 00302 public void set_voxel_label_bit( 00303 Volume volume, 00304 int voxel[], 00305 int bit, 00306 BOOLEAN value ); 00307 00308 public void set_all_volume_label_data_bit( 00309 Volume volume, 00310 int bit, 00311 BOOLEAN value ); 00312 00313 public BOOLEAN get_volume_voxel_activity( 00314 Volume volume, 00315 Real voxel[], 00316 BOOLEAN activity_if_mixed ); 00317 00318 public Status load_label_volume( 00319 STRING filename, 00320 Volume label_volume ); 00321 00322 public Status save_label_volume( 00323 STRING filename, 00324 STRING original_filename, 00325 Volume label_volume, 00326 Real crop_threshold ); 00327 00328 public Status input_tags_as_labels( 00329 FILE *file, 00330 Volume volume, 00331 Volume label_volume ); 00332 00333 public Status create_label_volume_from_file( 00334 STRING filename, 00335 Volume volume, 00336 Volume *label_volume ); 00337 00338 public Status output_labels_as_tags( 00339 FILE *file, 00340 Volume volume, 00341 Volume label_volume, 00342 int desired_label, 00343 Real size, 00344 int patient_id ); 00345 00346 public Status input_landmarks_as_labels( 00347 FILE *file, 00348 Volume volume, 00349 Volume label_volume ); 00350 00351 public int get_volume_cross_section( 00352 Volume volume, 00353 Real origin[], 00354 Real x_axis[], 00355 Real y_axis[], 00356 Real clipped_voxels[][MAX_DIMENSIONS] ); 00357 00358 public void get_volume_mapping_range( 00359 Volume volume, 00360 Real origin[], 00361 Real x_axis[], 00362 Real y_axis[], 00363 Real x_trans, 00364 Real y_trans, 00365 Real x_scale, 00366 Real y_scale, 00367 Real *x_pixel_start, 00368 Real *x_pixel_end, 00369 Real *y_pixel_start, 00370 Real *y_pixel_end ); 00371 00372 public void clip_viewport_to_volume( 00373 Volume volume, 00374 Real origin[], 00375 Real x_axis[], 00376 Real y_axis[], 00377 int *x_pixel_start, 00378 int *x_pixel_end, 00379 int *y_pixel_start, 00380 int *y_pixel_end ); 00381 00382 public void get_mapping( 00383 Volume volume, 00384 Real origin[], 00385 Real x_axis[], 00386 Real y_axis[], 00387 Real x_translation, 00388 Real y_translation, 00389 Real x_scale, 00390 Real y_scale, 00391 Real pix_origin[], 00392 Real pix_x_axis[], 00393 Real pix_y_axis[] ); 00394 00395 public void map_voxel_to_pixel( 00396 int n, 00397 Real voxel[], 00398 Real origin[], 00399 Real x_axis[], 00400 Real y_axis[], 00401 Real *x_pixel, 00402 Real *y_pixel ); 00403 00404 public BOOLEAN convert_slice_pixel_to_voxel( 00405 Volume volume, 00406 Real x_pixel, 00407 Real y_pixel, 00408 Real origin[], 00409 Real x_axis[], 00410 Real y_axis[], 00411 Real x_translation, 00412 Real y_translation, 00413 Real x_scale, 00414 Real y_scale, 00415 Real voxel[] ); 00416 00417 public void convert_voxel_to_slice_pixel( 00418 Volume volume, 00419 Real voxel[], 00420 Real origin[], 00421 Real x_axis[], 00422 Real y_axis[], 00423 Real x_translation, 00424 Real y_translation, 00425 Real x_scale, 00426 Real y_scale, 00427 Real *x_pixel, 00428 Real *y_pixel ); 00429 00430 public void resize_volume_slice( 00431 int old_x_viewport_size, 00432 int old_y_viewport_size, 00433 int old_used_x_viewport_size, 00434 int old_used_y_viewport_size, 00435 int new_x_viewport_size, 00436 int new_y_viewport_size, 00437 Real *x_translation, 00438 Real *y_translation, 00439 Real *x_scale, 00440 Real *y_scale, 00441 int *used_x_viewport_size, 00442 int *used_y_viewport_size ); 00443 00444 public void fit_volume_slice_to_viewport( 00445 Volume volume, 00446 Real origin[], 00447 Real x_axis[], 00448 Real y_axis[], 00449 int x_viewport_size, 00450 int y_viewport_size, 00451 Real fraction_oversize, 00452 Real *x_translation, 00453 Real *y_translation, 00454 Real *x_scale, 00455 Real *y_scale, 00456 int *used_x_viewport_size, 00457 int *used_y_viewport_size ); 00458 00459 public void scale_slice_about_viewport_centre( 00460 Real scale_factor, 00461 int x_viewport_size, 00462 int y_viewport_size, 00463 Real *x_translation, 00464 Real *y_translation, 00465 Real *x_scale, 00466 Real *y_scale ); 00467 00468 public BOOLEAN voxel_is_within_volume( 00469 Volume volume, 00470 Real voxel_position[] ); 00471 00472 public BOOLEAN int_voxel_is_within_volume( 00473 Volume volume, 00474 int indices[] ); 00475 00476 public void convert_real_to_int_voxel( 00477 int n_dimensions, 00478 Real voxel[], 00479 int int_voxel[] ); 00480 00481 public void convert_int_to_real_voxel( 00482 int n_dimensions, 00483 int int_voxel[], 00484 Real voxel[] ); 00485 00486 public BOOLEAN voxel_contains_range( 00487 Volume volume, 00488 int int_voxel[], 00489 Real min_value, 00490 Real max_value ); 00491 00492 public BOOLEAN volumes_are_same_grid( 00493 Volume volume1, 00494 Volume volume2 ); 00495 00496 public Status output_volume_free_format( 00497 STRING prefix, 00498 Volume volume, 00499 int axis_ordering[] ); 00500 00501 public void *initialize_render_storage( void ); 00502 00503 public void delete_render_storage( 00504 void *ptr ); 00505 00506 public void render_volume_to_slice( 00507 int n_dims1, 00508 int sizes1[], 00509 void *volume_data1, 00510 Data_types volume1_type, 00511 int n_slices1, 00512 Real weights1[], 00513 int strides1[], 00514 Real **origins1, 00515 Real x_axis1[], 00516 Real y_axis1[], 00517 int n_dims2, 00518 int sizes2[], 00519 void *volume_data2, 00520 Data_types volume2_type, 00521 int n_slices2, 00522 Real weights2[], 00523 int strides2[], 00524 Real **origins2, 00525 Real x_axis2[], 00526 Real y_axis2[], 00527 int x_pixel_start, 00528 int x_pixel_end, 00529 int y_pixel_start, 00530 int y_pixel_end, 00531 unsigned short **cmode_colour_map, 00532 Colour **rgb_colour_map, 00533 Colour empty_colour, 00534 void *render_storage, 00535 pixels_struct *pixels ); 00536 00537 public void render_one_row ( 00538 void *volume_data1, 00539 Data_types volume1_type, 00540 int y, 00541 int start_x, 00542 int end_x, 00543 int **y_offsets1, 00544 int **row_offsets1, 00545 void **start_slices1, 00546 int n_slices1, 00547 Real weights1[], 00548 void *volume_data2, 00549 Data_types volume2_type, 00550 int **y_offsets2, 00551 int **row_offsets2, 00552 void **start_slices2, 00553 int n_slices2, 00554 Real weights2[], 00555 unsigned short **cmode_colour_map, 00556 Colour **rgb_colour_map, 00557 pixels_struct *pixels ); 00558 00559 public void initialize_resample_volume( 00560 resample_struct *resample, 00561 Volume src_volume, 00562 General_transform *dest_to_src_transform, 00563 Volume dest_volume ); 00564 00565 public BOOLEAN do_more_resampling( 00566 resample_struct *resample, 00567 Real max_seconds, 00568 Real *fraction_done ); 00569 00570 public void resample_volume( 00571 Volume src_volume, 00572 General_transform *dest_to_src_transform, 00573 Volume dest_volume ); 00574 00575 public void scan_lines_to_voxels( 00576 lines_struct *lines, 00577 Volume volume, 00578 Volume label_volume, 00579 int label ); 00580 00581 public void scan_marker_to_voxels( 00582 marker_struct *marker, 00583 Volume volume, 00584 Volume label_volume, 00585 int label ); 00586 00587 public void scan_object_to_volume( 00588 object_struct *object, 00589 Volume volume, 00590 Volume label_volume, 00591 int label, 00592 Real max_distance ); 00593 00594 public void scan_polygons_to_voxels( 00595 polygons_struct *polygons, 00596 Volume volume, 00597 Volume label_volume, 00598 int label, 00599 Real max_distance ); 00600 00601 public void scan_quadmesh_to_voxels( 00602 quadmesh_struct *quadmesh, 00603 Volume volume, 00604 Volume label_volume, 00605 int label, 00606 Real max_distance ); 00607 00608 public Volume smooth_resample_volume( 00609 Volume volume, 00610 int new_nx, 00611 int new_ny, 00612 int new_nz ); 00613 00614 public void convert_voxel_to_talairach( 00615 Real x_voxel, 00616 Real y_voxel, 00617 Real z_voxel, 00618 int nx_voxels, 00619 int ny_voxels, 00620 int nz_voxels, 00621 Real *x_tal, 00622 Real *y_tal, 00623 Real *z_tal ); 00624 00625 public void convert_talairach_to_voxel( 00626 Real x_tal, 00627 Real y_tal, 00628 Real z_tal, 00629 int nx_voxels, 00630 int ny_voxels, 00631 int nz_voxels, 00632 Real *x_voxel, 00633 Real *y_voxel, 00634 Real *z_voxel ); 00635 00636 public void convert_talairach_to_mm( 00637 Real x_tal, 00638 Real y_tal, 00639 Real z_tal, 00640 Real *x_mm, 00641 Real *y_mm, 00642 Real *z_mm ); 00643 00644 public void convert_mm_to_talairach( 00645 Real x_mm, 00646 Real y_mm, 00647 Real z_mm, 00648 Real *x_tal, 00649 Real *y_tal, 00650 Real *z_tal ); 00651 #endif