vol_prototypes.h File Reference

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Functions
public Volume	create_box_filtered_volume (Volume volume, nc_type nc_data_type, BOOLEAN sign_flag, Real real_min_value, Real real_max_value, Real x_width, Real y_width, Real z_width)
public void	modify_labels_in_range (Volume volume, Volume label_volume, int src_min, int src_max, int dest_label, Real min_threshold, Real max_threshold, int range_changed[2][N_DIMENSIONS])
public void	initialize_colour_coding (colour_coding_struct *colour_coding, Colour_coding_types type, Colour under_colour, Colour over_colour, Real min_value, Real max_value)
public void	delete_colour_coding (colour_coding_struct *colour_coding)
public void	set_colour_coding_type (colour_coding_struct *colour_coding, Colour_coding_types type)
public Colour_coding_types	get_colour_coding_type (colour_coding_struct *colour_coding)
public void	set_colour_coding_min_max (colour_coding_struct *colour_coding, Real min_value, Real max_value)
public void	get_colour_coding_min_max (colour_coding_struct *colour_coding, Real *min_value, Real *max_value)
public Colour	get_colour_coding_under_colour (colour_coding_struct *colour_coding)
public void	set_colour_coding_under_colour (colour_coding_struct *colour_coding, Colour under_colour)
public Colour	get_colour_coding_over_colour (colour_coding_struct *colour_coding)
public void	set_colour_coding_over_colour (colour_coding_struct *colour_coding, Colour over_colour)
public BOOLEAN	define_colour_coding_user_defined (colour_coding_struct *colour_code, int n_colours, Colour colours[], Real positions[], Colour_spaces interpolation_space)
public Colour	get_colour_code (colour_coding_struct *colour_coding, Real value)
public void	colour_code_object (Volume volume, int continuity, colour_coding_struct *colour_coding, object_struct *object)
public STRING	get_default_user_def_colour_code_suffix (void)
public Status	input_user_defined_colour_coding (colour_coding_struct *colour_coding, STRING filename)
public void	create_volume_slice (Volume volume1, Filter_types filter_type1, Real filter_width1, Real slice_position1[], Real x_axis1[], Real y_axis1[], Real x_translation1, Real y_translation1, Real x_scale1, Real y_scale1, Volume volume2, Filter_types filter_type2, Real filter_width2, Real slice_position2[], Real x_axis2[], Real y_axis2[], Real x_translation2, Real y_translation2, Real x_scale2, Real y_scale2, int x_viewport_size, int y_viewport_size, int x_pixel_start, int x_pixel_end, int y_pixel_start, int y_pixel_end, Pixel_types pixel_type, int degrees_continuity, unsigned short **cmode_colour_map, Colour **rgb_colour_map, Colour empty_colour, void *render_storage, BOOLEAN clip_pixels_flag, int *n_pixels_alloced, pixels_struct *pixels)
public void	set_volume_slice_pixel_range (Volume volume1, Filter_types filter_type1, Real filter_width1, Real slice_position1[], Real x_axis1[], Real y_axis1[], Real x_translation1, Real y_translation1, Real x_scale1, Real y_scale1, Volume volume2, Filter_types filter_type2, Real filter_width2, Real slice_position2[], Real x_axis2[], Real y_axis2[], Real x_translation2, Real y_translation2, Real x_scale2, Real y_scale2, int x_viewport_size, int y_viewport_size, Pixel_types pixel_type, int *n_pixels_alloced, pixels_struct *pixels)
public BOOLEAN	find_volume_crop_bounds (Volume volume, Real min_crop_threshold, Real max_crop_threshold, int limits[2][MAX_DIMENSIONS])
public Volume	create_cropped_volume (Volume volume, int limits[2][MAX_DIMENSIONS])
public Volume	autocrop_volume (Volume volume)
public int	dilate_voxels_3d (Volume volume, Volume label_volume, Real min_inside_label, Real max_inside_label, Real min_inside_value, Real max_inside_value, Real min_outside_label, Real max_outside_label, Real min_outside_value, Real max_outside_value, Real new_label, Neighbour_types connectivity, int range_changed[2][N_DIMENSIONS])
public int	get_slice_weights_for_filter (Volume volume, Real voxel_position[], Real voxel_direction[], Filter_types filter_type, Real full_width_half_max, Real ***positions, Real *weights[])
public BOOLEAN	fill_connected_voxels (Volume volume, Volume label_volume, Neighbour_types connectivity, int voxel[], int min_label_threshold, int max_label_threshold, int desired_label, Real min_threshold, Real max_threshold, int range_changed[2][N_DIMENSIONS])
public int	get_neighbour_directions (Neighbour_types connectivity, int *dx[], int *dy[])
public int	get_3D_neighbour_directions (Neighbour_types connectivity, int *dx[], int *dy[], int *dz[])
public BOOLEAN	should_change_this_one (Volume volume, Volume label_volume, int voxel[], Real min_threshold, Real max_threshold, int label_min_threshold, int label_max_threshold, int desired_label)
public void	interpolate_volume_to_slice (Volume volume1, int n_dims1, Real origin1[], Real x_axis1[], Real y_axis1[], Volume volume2, int n_dims2, Real origin2[], Real x_axis2[], Real y_axis2[], int x_pixel_start, int x_pixel_end, int y_pixel_start, int y_pixel_end, int degrees_continuity, unsigned short **cmode_colour_map, Colour **rgb_colour_map, Colour empty_colour, pixels_struct *pixels)
public Status	input_volume_header_only (STRING filename, int n_dimensions, STRING dim_names[], Volume *volume, minc_input_options *options)
public void	set_label_volume_real_range (Volume volume)
public Volume	create_label_volume (Volume volume, nc_type type)
public BOOLEAN	is_label_volume_initialized (Volume volume)
public void	set_all_volume_label_data (Volume volume, int value)
public void	set_volume_label_data_5d (Volume volume, int v0, int v1, int v2, int v3, int v4, int value)
public void	set_volume_label_data (Volume volume, int voxel[], int value)
public int	get_volume_label_data (Volume volume, int voxel[])
public int	get_volume_label_data_5d (Volume volume, int v0, int v1, int v2, int v3, int v4)
public int	get_3D_volume_label_data (Volume volume, int x, int y, int z)
public BOOLEAN	get_voxel_label_bit (Volume volume, int voxel[], int bit)
public void	set_voxel_label_bit (Volume volume, int voxel[], int bit, BOOLEAN value)
public void	set_all_volume_label_data_bit (Volume volume, int bit, BOOLEAN value)
public BOOLEAN	get_volume_voxel_activity (Volume volume, Real voxel[], BOOLEAN activity_if_mixed)
public Status	load_label_volume (STRING filename, Volume label_volume)
public Status	save_label_volume (STRING filename, STRING original_filename, Volume label_volume, Real crop_threshold)
public Status	input_tags_as_labels (FILE *file, Volume volume, Volume label_volume)
public Status	create_label_volume_from_file (STRING filename, Volume volume, Volume *label_volume)
public Status	output_labels_as_tags (FILE *file, Volume volume, Volume label_volume, int desired_label, Real size, int patient_id)
public Status	input_landmarks_as_labels (FILE *file, Volume volume, Volume label_volume)
public int	get_volume_cross_section (Volume volume, Real origin[], Real x_axis[], Real y_axis[], Real clipped_voxels[][MAX_DIMENSIONS])
public void	get_volume_mapping_range (Volume volume, Real origin[], Real x_axis[], Real y_axis[], Real x_trans, Real y_trans, Real x_scale, Real y_scale, Real *x_pixel_start, Real *x_pixel_end, Real *y_pixel_start, Real *y_pixel_end)
public void	clip_viewport_to_volume (Volume volume, Real origin[], Real x_axis[], Real y_axis[], int *x_pixel_start, int *x_pixel_end, int *y_pixel_start, int *y_pixel_end)
public void	get_mapping (Volume volume, Real origin[], Real x_axis[], Real y_axis[], Real x_translation, Real y_translation, Real x_scale, Real y_scale, Real pix_origin[], Real pix_x_axis[], Real pix_y_axis[])
public void	map_voxel_to_pixel (int n, Real voxel[], Real origin[], Real x_axis[], Real y_axis[], Real *x_pixel, Real *y_pixel)
public BOOLEAN	convert_slice_pixel_to_voxel (Volume volume, Real x_pixel, Real y_pixel, Real origin[], Real x_axis[], Real y_axis[], Real x_translation, Real y_translation, Real x_scale, Real y_scale, Real voxel[])
public void	convert_voxel_to_slice_pixel (Volume volume, Real voxel[], Real origin[], Real x_axis[], Real y_axis[], Real x_translation, Real y_translation, Real x_scale, Real y_scale, Real *x_pixel, Real *y_pixel)
public void	resize_volume_slice (int old_x_viewport_size, int old_y_viewport_size, int old_used_x_viewport_size, int old_used_y_viewport_size, int new_x_viewport_size, int new_y_viewport_size, Real *x_translation, Real *y_translation, Real *x_scale, Real *y_scale, int *used_x_viewport_size, int *used_y_viewport_size)
public void	fit_volume_slice_to_viewport (Volume volume, Real origin[], Real x_axis[], Real y_axis[], int x_viewport_size, int y_viewport_size, Real fraction_oversize, Real *x_translation, Real *y_translation, Real *x_scale, Real *y_scale, int *used_x_viewport_size, int *used_y_viewport_size)
public void	scale_slice_about_viewport_centre (Real scale_factor, int x_viewport_size, int y_viewport_size, Real *x_translation, Real *y_translation, Real *x_scale, Real *y_scale)
public BOOLEAN	voxel_is_within_volume (Volume volume, Real voxel_position[])
public BOOLEAN	int_voxel_is_within_volume (Volume volume, int indices[])
public void	convert_real_to_int_voxel (int n_dimensions, Real voxel[], int int_voxel[])
public void	convert_int_to_real_voxel (int n_dimensions, int int_voxel[], Real voxel[])
public BOOLEAN	voxel_contains_range (Volume volume, int int_voxel[], Real min_value, Real max_value)
public BOOLEAN	volumes_are_same_grid (Volume volume1, Volume volume2)
public Status	output_volume_free_format (STRING prefix, Volume volume, int axis_ordering[])
public void *	initialize_render_storage (void)
public void	delete_render_storage (void *ptr)
public void	render_volume_to_slice (int n_dims1, int sizes1[], void *volume_data1, Data_types volume1_type, int n_slices1, Real weights1[], int strides1[], Real **origins1, Real x_axis1[], Real y_axis1[], int n_dims2, int sizes2[], void *volume_data2, Data_types volume2_type, int n_slices2, Real weights2[], int strides2[], Real **origins2, Real x_axis2[], Real y_axis2[], int x_pixel_start, int x_pixel_end, int y_pixel_start, int y_pixel_end, unsigned short **cmode_colour_map, Colour **rgb_colour_map, Colour empty_colour, void *render_storage, pixels_struct *pixels)
public void	render_one_row (void *volume_data1, Data_types volume1_type, int y, int start_x, int end_x, int **y_offsets1, int **row_offsets1, void **start_slices1, int n_slices1, Real weights1[], void *volume_data2, Data_types volume2_type, int **y_offsets2, int **row_offsets2, void **start_slices2, int n_slices2, Real weights2[], unsigned short **cmode_colour_map, Colour **rgb_colour_map, pixels_struct *pixels)
public void	initialize_resample_volume (resample_struct *resample, Volume src_volume, General_transform *dest_to_src_transform, Volume dest_volume)
public BOOLEAN	do_more_resampling (resample_struct *resample, Real max_seconds, Real *fraction_done)
public void	resample_volume (Volume src_volume, General_transform *dest_to_src_transform, Volume dest_volume)
public void	scan_lines_to_voxels (lines_struct *lines, Volume volume, Volume label_volume, int label)
public void	scan_marker_to_voxels (marker_struct *marker, Volume volume, Volume label_volume, int label)
public void	scan_object_to_volume (object_struct *object, Volume volume, Volume label_volume, int label, Real max_distance)
public void	scan_polygons_to_voxels (polygons_struct *polygons, Volume volume, Volume label_volume, int label, Real max_distance)
	Add label to all voxels that intersect polygons.
public void	scan_quadmesh_to_voxels (quadmesh_struct *quadmesh, Volume volume, Volume label_volume, int label, Real max_distance)
	Add label to all voxels that intersect a quadmesh.
public Volume	smooth_resample_volume (Volume volume, int new_nx, int new_ny, int new_nz)
public void	convert_voxel_to_talairach (Real x_voxel, Real y_voxel, Real z_voxel, int nx_voxels, int ny_voxels, int nz_voxels, Real *x_tal, Real *y_tal, Real *z_tal)
public void	convert_talairach_to_voxel (Real x_tal, Real y_tal, Real z_tal, int nx_voxels, int ny_voxels, int nz_voxels, Real *x_voxel, Real *y_voxel, Real *z_voxel)
public void	convert_talairach_to_mm (Real x_tal, Real y_tal, Real z_tal, Real *x_mm, Real *y_mm, Real *z_mm)
public void	convert_mm_to_talairach (Real x_mm, Real y_mm, Real z_mm, Real *x_tal, Real *y_tal, Real *z_tal)

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Function Documentation

public Volume autocrop_volume (  Volume  volume  )

Definition at line 285 of file crop_volume.c. References create_cropped_volume(), and find_volume_crop_bounds().

public void clip_viewport_to_volume (  Volume  volume, Real  origin[], Real  x_axis[], Real  y_axis[], int *  x_pixel_start, int *  x_pixel_end, int *  y_pixel_start, int *  y_pixel_end )

Definition at line 447 of file mapping.c. References get_volume_slice_range(). Referenced by set_pixel_range().

public void colour_code_object (  Volume  volume, int  continuity, colour_coding_struct *  colour_coding, object_struct *  object )

Definition at line 99 of file col_code_points.c. References colour_code_points(), polygons_struct::colour_flag, quadmesh_struct::colour_flag, lines_struct::colour_flag, polygons_struct::colours, quadmesh_struct::colours, lines_struct::colours, get_lines_ptr(), get_polygons_ptr(), get_quadmesh_ptr(), LINES, quadmesh_struct::m, quadmesh_struct::n, polygons_struct::n_points, lines_struct::n_points, object_struct::object_type, polygons_struct::points, quadmesh_struct::points, lines_struct::points, POLYGONS, and QUADMESH.

public void convert_int_to_real_voxel (  int  n_dimensions, int  int_voxel[], Real  voxel[] )

Definition at line 1099 of file mapping.c. Referenced by scan_marker_to_voxels().

public void convert_mm_to_talairach (  Real  x_mm, Real  y_mm, Real  z_mm, Real *  x_tal, Real *  y_tal, Real *  z_tal )

Definition at line 397 of file talairach.c. References check_initialized(), convert_from_mm(), nx, ny, nz, TALAIRACH_OFFSET, x_dist_1, x_dist_minus_1, x_high, x_low, y_dist_1, y_dist_minus_1, y_high, y_low, z_dist_0, z_dist_1, z_high, and z_low.

public void convert_real_to_int_voxel (  int  n_dimensions, Real  voxel[], int  int_voxel[] )

Definition at line 1074 of file mapping.c.

public BOOLEAN convert_slice_pixel_to_voxel (  Volume  volume, Real  x_pixel, Real  y_pixel, Real  origin[], Real  x_axis[], Real  y_axis[], Real  x_translation, Real  y_translation, Real  x_scale, Real  y_scale, Real  voxel[] )

Definition at line 717 of file mapping.c. References get_mapping(), map_pixel_to_voxel(), and voxel_is_within_volume().

public void convert_talairach_to_mm (  Real  x_tal, Real  y_tal, Real  z_tal, Real *  x_mm, Real *  y_mm, Real *  z_mm )

Definition at line 320 of file talairach.c. References check_initialized(), convert_to_mm(), nx, ny, nz, TALAIRACH_OFFSET, x_dist_1, x_dist_minus_1, x_high, x_low, y_dist_1, y_dist_minus_1, y_high, y_low, z_dist_0, z_dist_1, z_high, and z_low.

public void convert_talairach_to_voxel (  Real  x_tal, Real  y_tal, Real  z_tal, int  nx_voxels, int  ny_voxels, int  nz_voxels, Real *  x_voxel, Real *  y_voxel, Real *  z_voxel )

Definition at line 244 of file talairach.c. References check_initialized(), nx, ny, and nz. Referenced by io_tag_point().

public void convert_voxel_to_slice_pixel (  Volume  volume, Real  voxel[], Real  origin[], Real  x_axis[], Real  y_axis[], Real  x_translation, Real  y_translation, Real  x_scale, Real  y_scale, Real *  x_pixel, Real *  y_pixel )

Definition at line 769 of file mapping.c. References get_mapping(), and map_voxel_to_pixel().

public void convert_voxel_to_talairach (  Real  x_voxel, Real  y_voxel, Real  z_voxel, int  nx_voxels, int  ny_voxels, int  nz_voxels, Real *  x_tal, Real *  y_tal, Real *  z_tal )

Definition at line 206 of file talairach.c. References check_initialized(), nx, ny, and nz. Referenced by io_tag_point().

public Volume create_box_filtered_volume (  Volume  volume, nc_type  nc_data_type, BOOLEAN  sign_flag, Real  real_min_value, Real  real_max_value, Real  x_width, Real  y_width, Real  z_width )

Definition at line 113 of file box_filter.c. References FALSE, GET_FIRST_SAMPLE, GET_NEXT_SAMPLE, INITIALIZE_SAMPLE, numerically_close(), and y.

public Volume create_cropped_volume (  Volume  volume, int  limits[2][MAX_DIMENSIONS] )

Definition at line 165 of file crop_volume.c. References FALSE, make_translation_transform(), and TRUE. Referenced by autocrop_volume(), and save_label_volume().

public Volume create_label_volume (  Volume  volume, nc_type  type )

Definition at line 63 of file labels.c. References FALSE, and set_label_volume_real_range(). Referenced by create_label_volume_from_file().

public Status create_label_volume_from_file (  STRING  filename, Volume  volume, Volume *  label_volume )

Definition at line 929 of file labels.c. References create_label_volume(), FALSE, input_tags_as_labels(), input_volume_header_only(), load_label_volume(), TRUE, and volumes_are_same_grid().

public void create_volume_slice (  Volume  volume1, Filter_types  filter_type1, Real  filter_width1, Real  slice_position1[], Real  x_axis1[], Real  y_axis1[], Real  x_translation1, Real  y_translation1, Real  x_scale1, Real  y_scale1, Volume  volume2, Filter_types  filter_type2, Real  filter_width2, Real  slice_position2[], Real  x_axis2[], Real  y_axis2[], Real  x_translation2, Real  y_translation2, Real  x_scale2, Real  y_scale2, int  x_viewport_size, int  y_viewport_size, int  x_pixel_start, int  x_pixel_end, int  y_pixel_start, int  y_pixel_end, Pixel_types  pixel_type, int  degrees_continuity, unsigned short **  cmode_colour_map, Colour **  rgb_colour_map, Colour  empty_colour, void *  render_storage, BOOLEAN  clip_pixels_flag, int *  n_pixels_alloced, pixels_struct *  pixels )

Definition at line 420 of file create_slice.c. References create_pixel_mapping(), create_weighted_volume_slices(), get_filter_slices(), modify_pixels_size(), n_slices1, rgb_colour_map, set_pixel_range(), and weights1.

public BOOLEAN define_colour_coding_user_defined (  colour_coding_struct *  colour_code, int  n_colours, Colour  colours[], Real  positions[], Colour_spaces  interpolation_space )

Definition at line 454 of file colour_coding.c. References colour_point::a, colour_point::b, FALSE, colour_point::g, get_colour_coding_type(), colour_point::interpolation_space, colour_point::position, colour_point::r, recreate_piecewise_function(), TRUE, USER_DEFINED_COLOUR_MAP, colour_coding_struct::user_defined_colour_points, and colour_coding_struct::user_defined_n_colour_points. Referenced by input_user_defined_colour_coding().

public void delete_colour_coding (  colour_coding_struct *  colour_coding  )

Definition at line 85 of file colour_coding.c. References colour_coding_struct::colour_points, colour_coding_struct::n_colour_points, colour_coding_struct::user_defined_colour_points, and colour_coding_struct::user_defined_n_colour_points.

public void delete_render_storage (  void *  ptr  )

Definition at line 157 of file render.c. References render_storage_struct::end_x, render_storage_struct::n_slices1_alloced, render_storage_struct::n_slices2_alloced, render_storage_struct::row_offsets1, render_storage_struct::row_offsets2, render_storage_struct::start_slices1, render_storage_struct::start_slices2, render_storage_struct::start_x, render_storage_struct::total_cases1_alloced, render_storage_struct::total_cases2_alloced, render_storage_struct::which_x_offsets1, render_storage_struct::which_x_offsets2, render_storage_struct::x_offsets1, render_storage_struct::x_offsets2, render_storage_struct::x_size1_alloced, render_storage_struct::x_size2_alloced, render_storage_struct::y_offsets1, render_storage_struct::y_offsets2, render_storage_struct::y_size1_alloced, and render_storage_struct::y_size2_alloced. Referenced by render_volume_to_slice().

public int dilate_voxels_3d (  Volume  volume, Volume  label_volume, Real  min_inside_label, Real  max_inside_label, Real  min_inside_value, Real  max_inside_value, Real  min_outside_label, Real  max_outside_label, Real  min_outside_value, Real  max_outside_value, Real  new_label, Neighbour_types  connectivity, int  range_changed[2][N_DIMENSIONS] )

Definition at line 49 of file dilate.c. References CANDIDATE, FALSE, get_3D_neighbour_directions(), INSIDE_REGION, n_dirs, NOT_INVOLVED, TRUE, Voxel_classes, and y.

public BOOLEAN do_more_resampling (  resample_struct *  resample, Real  max_seconds, Real *  fraction_done )

Definition at line 37 of file resample.c. References resample_struct::dest_volume, FALSE, resample_struct::src_volume, resample_struct::transform, resample_struct::x, and resample_struct::y. Referenced by resample_volume().

public BOOLEAN fill_connected_voxels (  Volume  volume, Volume  label_volume, Neighbour_types  connectivity, int  voxel[], int  min_label_threshold, int  max_label_threshold, int  desired_label, Real  min_threshold, Real  max_threshold, int  range_changed[2][N_DIMENSIONS] )

Definition at line 48 of file fill_volume.c. References create_bitlist_3d(), delete_bitlist_3d(), DELETE_QUEUE, FALSE, get_3D_neighbour_directions(), get_bitlist_bit_3d(), INITIALIZE_QUEUE, INSERT_IN_QUEUE, IS_QUEUE_EMPTY, n_dirs, QUEUE_STRUCT, REMOVE_FROM_QUEUE, set_bitlist_bit_3d(), set_volume_label_data(), should_change_this_one(), TRUE, xyz_struct::x, y, xyz_struct::y, and xyz_struct::z.

public BOOLEAN find_volume_crop_bounds (  Volume  volume, Real  min_crop_threshold, Real  max_crop_threshold, int  limits[2][MAX_DIMENSIONS] )

Definition at line 40 of file crop_volume.c. References FALSE, and TRUE. Referenced by autocrop_volume(), and save_label_volume().

public void fit_volume_slice_to_viewport (  Volume  volume, Real  origin[], Real  x_axis[], Real  y_axis[], int  x_viewport_size, int  y_viewport_size, Real  fraction_oversize, Real *  x_translation, Real *  y_translation, Real *  x_scale, Real *  y_scale, int *  used_x_viewport_size, int *  used_y_viewport_size )

Definition at line 892 of file mapping.c. References get_volume_mapping_range().

public int get_3D_neighbour_directions (  Neighbour_types  connectivity, int *  dx[], int *  dy[], int *  dz[] )

Definition at line 267 of file fill_volume.c. References create_3D_neighbours(), Dx26, Dx6, Dy26, Dy6, Dz26, Dz6, EIGHT_NEIGHBOURS, FALSE, FOUR_NEIGHBOURS, n_dirs, and TRUE. Referenced by dilate_voxels_3d(), and fill_connected_voxels().

public int get_3D_volume_label_data (  Volume  volume, int  x, int  y, int  z )

Definition at line 249 of file labels.c. References y.

public Colour get_colour_code (  colour_coding_struct *  colour_coding, Real  value )

Definition at line 540 of file colour_coding.c. References colour_coding_struct::colour_points, interpolate_colours(), colour_coding_struct::max_value, colour_coding_struct::min_value, colour_coding_struct::n_colour_points, colour_coding_struct::over_colour, colour_point::position, and colour_coding_struct::under_colour. Referenced by colour_code_points().

public void get_colour_coding_min_max (  colour_coding_struct *  colour_coding, Real *  min_value, Real *  max_value )

Definition at line 174 of file colour_coding.c. References colour_coding_struct::max_value, and colour_coding_struct::min_value.

public Colour get_colour_coding_over_colour (  colour_coding_struct *  colour_coding  )

Definition at line 236 of file colour_coding.c. References colour_coding_struct::over_colour.

public Colour_coding_types get_colour_coding_type (  colour_coding_struct *  colour_coding  )

Definition at line 130 of file colour_coding.c. References Colour_coding_types, and colour_coding_struct::type. Referenced by define_colour_coding_user_defined(), and set_colour_coding_over_colour().

public Colour get_colour_coding_under_colour (  colour_coding_struct *  colour_coding  )

Definition at line 196 of file colour_coding.c. References colour_coding_struct::under_colour.

public STRING get_default_user_def_colour_code_suffix (  void   )

Definition at line 24 of file col_code_io.c. References DEFAULT_USER_DEFINED_COLOUR_CODE_SUFFIX. Referenced by input_user_defined_colour_coding().

public void get_mapping (  Volume  volume, Real  origin[], Real  x_axis[], Real  y_axis[], Real  x_translation, Real  y_translation, Real  x_scale, Real  y_scale, Real  pix_origin[], Real  pix_x_axis[], Real  pix_y_axis[] )

Definition at line 502 of file mapping.c. Referenced by convert_slice_pixel_to_voxel(), convert_voxel_to_slice_pixel(), create_pixel_mapping(), get_volume_cross_section(), and get_volume_mapping_range().

public int get_neighbour_directions (  Neighbour_types  connectivity, int *  dx[], int *  dy[] )

Definition at line 182 of file fill_volume.c. References Dx4, Dx8, Dy4, Dy8, EIGHT_NEIGHBOURS, FOUR_NEIGHBOURS, and n_dirs.

public int get_slice_weights_for_filter (  Volume  volume, Real  voxel_position[], Real  voxel_direction[], Filter_types  filter_type, Real  full_width_half_max, Real ***  positions, Real *  weights[] )

Definition at line 43 of file filters.c. References N_SAMPLES, and N_STD_DEVIATIONS. Referenced by get_filter_slices().

public int get_volume_cross_section (  Volume  volume, Real  origin[], Real  x_axis[], Real  y_axis[], Real  clipped_voxels[][MAX_DIMENSIONS] )

Definition at line 281 of file mapping.c. References get_cross_section(), and get_mapping(). Referenced by create_slice_3d().

public int get_volume_label_data (  Volume  volume, int  voxel[] )

Definition at line 206 of file labels.c. References get_volume_label_data_5d(). Referenced by get_volume_voxel_activity(), get_voxel_label_bit(), modify_labels_in_range(), output_labels_as_tags(), and should_change_this_one().

public int get_volume_label_data_5d (  Volume  volume, int  v0, int  v1, int  v2, int  v3, int  v4 )

Definition at line 214 of file labels.c. Referenced by get_volume_label_data().

public void get_volume_mapping_range (  Volume  volume, Real  origin[], Real  x_axis[], Real  y_axis[], Real  x_trans, Real  y_trans, Real  x_scale, Real  y_scale, Real *  x_pixel_start, Real *  x_pixel_end, Real *  y_pixel_start, Real *  y_pixel_end )

Definition at line 402 of file mapping.c. References get_mapping(), and get_volume_slice_range(). Referenced by fit_volume_slice_to_viewport().

public BOOLEAN get_volume_voxel_activity (  Volume  volume, Real  voxel[], BOOLEAN  activity_if_mixed )

Definition at line 386 of file labels.c. References FALSE, get_volume_label_data(), and TRUE. Referenced by check_voxel_for_isovalue(), and is_point_inside_surface().

public BOOLEAN get_voxel_label_bit (  Volume  volume, int  voxel[], int  bit )

Definition at line 281 of file labels.c. References get_volume_label_data().

public void initialize_colour_coding (  colour_coding_struct *  colour_coding, Colour_coding_types  type, Colour  under_colour, Colour  over_colour, Real  min_value, Real  max_value )

Definition at line 53 of file colour_coding.c. References GRAY_SCALE, colour_coding_struct::n_colour_points, recreate_piecewise_function(), set_colour_coding_min_max(), set_colour_coding_over_colour(), set_colour_coding_type(), set_colour_coding_under_colour(), TRUE, and colour_coding_struct::user_defined_n_colour_points.

public void* initialize_render_storage (  void   )

Definition at line 122 of file render.c. References render_storage_struct::n_slices1_alloced, render_storage_struct::n_slices2_alloced, render_storage_struct::total_cases1_alloced, render_storage_struct::total_cases2_alloced, render_storage_struct::x_size1_alloced, render_storage_struct::x_size2_alloced, render_storage_struct::y_size1_alloced, and render_storage_struct::y_size2_alloced. Referenced by render_volume_to_slice().

public void initialize_resample_volume (  resample_struct *  resample, Volume  src_volume, General_transform *  dest_to_src_transform, Volume  dest_volume )

Definition at line 4 of file resample.c. References resample_struct::dest_volume, resample_struct::src_volume, resample_struct::transform, resample_struct::x, and resample_struct::y. Referenced by resample_volume().

public Status input_landmarks_as_labels (  FILE *  file, Volume  volume, Volume  label_volume )

Definition at line 1083 of file labels.c. References check_alloc_label_data(), int_voxel_is_within_volume(), io_tag_point(), marker_struct::position, set_volume_label_data(), and marker_struct::structure_id.

public Status input_tags_as_labels (  FILE *  file, Volume  volume, Volume  label_volume )

Definition at line 872 of file labels.c. References check_alloc_label_data(), int_voxel_is_within_volume(), and set_volume_label_data(). Referenced by create_label_volume_from_file().

public Status input_user_defined_colour_coding (  colour_coding_struct *  colour_coding, STRING  filename )

Definition at line 29 of file col_code_io.c. References convert_string_to_colour(), define_colour_coding_user_defined(), get_default_user_def_colour_code_suffix(), and RGB_SPACE.

public Status input_volume_header_only (  STRING  filename, int  n_dimensions, STRING  dim_names[], Volume *  volume, minc_input_options *  options )

Definition at line 4 of file input.c. References FALSE, and TRUE. Referenced by create_label_volume_from_file(), and load_label_volume().

public BOOLEAN int_voxel_is_within_volume (  Volume  volume, int  indices[] )

Definition at line 1036 of file mapping.c. References FALSE, and TRUE. Referenced by input_landmarks_as_labels(), and input_tags_as_labels().

public void interpolate_volume_to_slice (  Volume  volume1, int  n_dims1, Real  origin1[], Real  x_axis1[], Real  y_axis1[], Volume  volume2, int  n_dims2, Real  origin2[], Real  x_axis2[], Real  y_axis2[], int  x_pixel_start, int  x_pixel_end, int  y_pixel_start, int  y_pixel_end, int  degrees_continuity, unsigned short **  cmode_colour_map, Colour **  rgb_colour_map, Colour  empty_colour, pixels_struct *  pixels )

Definition at line 51 of file interpolate.c. References FALSE, PIXEL_COLOUR_INDEX_16, PIXEL_RGB_COLOUR, pixels_struct::pixel_type, Pixel_types, rgb_colour_map, RGB_PIXEL, voxel_is_within_volume(), and y. Referenced by create_weighted_volume_slices().

public BOOLEAN is_label_volume_initialized (  Volume  volume  )

Definition at line 103 of file labels.c.

public Status load_label_volume (  STRING  filename, Volume  label_volume )

Definition at line 542 of file labels.c. References check_alloc_label_data(), FALSE, get_input_volume_label_limits(), input_volume_header_only(), set_volume_label_data(), and TRUE. Referenced by create_label_volume_from_file().

public void map_voxel_to_pixel (  int  n, Real  voxel[], Real  origin[], Real  x_axis[], Real  y_axis[], Real *  x_pixel, Real *  y_pixel )

Definition at line 675 of file mapping.c. References get_two_axes_coordinates(). Referenced by convert_voxel_to_slice_pixel(), and get_cross_section().

public void modify_labels_in_range (  Volume  volume, Volume  label_volume, int  src_min, int  src_max, int  dest_label, Real  min_threshold, Real  max_threshold, int  range_changed[2][N_DIMENSIONS] )

Definition at line 42 of file change_labels.c. References FALSE, get_volume_label_data(), set_volume_label_data(), and TRUE.

public Status output_labels_as_tags (  FILE *  file, Volume  volume, Volume  label_volume, int  desired_label, Real  size, int  patient_id )

Definition at line 1007 of file labels.c. References check_alloc_label_data(), and get_volume_label_data().

public Status output_volume_free_format (  STRING  prefix, Volume  volume, int  axis_ordering[] )

Definition at line 38 of file output_free.c. References FALSE.

public void render_one_row (  void *  volume_data1, Data_types  volume1_type, int  y, int  start_x, int  end_x, int **  y_offsets1, int **  row_offsets1, void **  start_slices1, int  n_slices1, Real  weights1[], void *  volume_data2, Data_types  volume2_type, int **  y_offsets2, int **  row_offsets2, void **  start_slices2, int  n_slices2, Real  weights2[], unsigned short **  cmode_colour_map, Colour **  rgb_colour_map, pixels_struct *  pixels )

Definition at line 38 of file rend_f.c. References pixels_struct::data, pixels_struct::pixel_type, RGB_PIXEL, start_x, pixels_struct::x_size, and y. Referenced by render_volume_to_slice().

public void render_volume_to_slice (  int  n_dims1, int  sizes1[], void *  volume_data1, Data_types  volume1_type, int  n_slices1, Real  weights1[], int  strides1[], Real **  origins1, Real  x_axis1[], Real  y_axis1[], int  n_dims2, int  sizes2[], void *  volume_data2, Data_types  volume2_type, int  n_slices2, Real  weights2[], int  strides2[], Real **  origins2, Real  x_axis2[], Real  y_axis2[], int  x_pixel_start, int  x_pixel_end, int  y_pixel_start, int  y_pixel_end, unsigned short **  cmode_colour_map, Colour **  rgb_colour_map, Colour  empty_colour, void *  render_storage, pixels_struct *  pixels )

Definition at line 216 of file render.c. References clip(), pixels_struct::data, delete_render_storage(), end_x, render_storage_struct::end_x, initialize_render_storage(), n_slices1, render_storage_struct::n_slices1_alloced, render_storage_struct::n_slices2_alloced, pixels_struct::pixel_type, render_one_row(), rgb_colour_map, RGB_PIXEL, row_offsets1, render_storage_struct::row_offsets1, render_storage_struct::row_offsets2, start_slices1, render_storage_struct::start_slices1, render_storage_struct::start_slices2, start_x, render_storage_struct::start_x, render_storage_struct::total_cases1_alloced, render_storage_struct::total_cases2_alloced, volume_data1, weights1, render_storage_struct::which_x_offsets1, render_storage_struct::which_x_offsets2, render_storage_struct::x_offsets1, render_storage_struct::x_offsets2, pixels_struct::x_size, render_storage_struct::x_size1_alloced, render_storage_struct::x_size2_alloced, y, y_offsets1, render_storage_struct::y_offsets1, render_storage_struct::y_offsets2, pixels_struct::y_size, render_storage_struct::y_size1_alloced, and render_storage_struct::y_size2_alloced. Referenced by create_weighted_volume_slices().

public void resample_volume (  Volume  src_volume, General_transform *  dest_to_src_transform, Volume  dest_volume )

Definition at line 109 of file resample.c. References do_more_resampling(), FACTOR, FALSE, and initialize_resample_volume().

public void resize_volume_slice (  int  old_x_viewport_size, int  old_y_viewport_size, int  old_used_x_viewport_size, int  old_used_y_viewport_size, int  new_x_viewport_size, int  new_y_viewport_size, Real *  x_translation, Real *  y_translation, Real *  x_scale, Real *  y_scale, int *  used_x_viewport_size, int *  used_y_viewport_size )

Definition at line 820 of file mapping.c. References scale_slice_about_viewport_centre().

public Status save_label_volume (  STRING  filename, STRING  original_filename, Volume  label_volume, Real  crop_threshold )

Definition at line 791 of file labels.c. References check_alloc_label_data(), create_cropped_volume(), FALSE, find_volume_crop_bounds(), and TRUE.

public void scale_slice_about_viewport_centre (  Real  scale_factor, int  x_viewport_size, int  y_viewport_size, Real *  x_translation, Real *  y_translation, Real *  x_scale, Real *  y_scale )

Definition at line 969 of file mapping.c. Referenced by resize_volume_slice().

public void scan_lines_to_voxels (  lines_struct *  lines, Volume  volume, Volume  label_volume, int  label )

Definition at line 47 of file scan_lines.c. References lines_struct::end_indices, GET_OBJECT_SIZE, lines_struct::indices, lines_struct::line_thickness, lines_struct::n_items, POINT_INDEX, lines_struct::points, and scan_line_segment_to_voxels(). Referenced by scan_object_to_volume().

public void scan_marker_to_voxels (  marker_struct *  marker, Volume  volume, Volume  label_volume, int  label )

Definition at line 39 of file scan_markers.c. References convert_int_to_real_voxel(), marker_struct::position, set_volume_label_data(), marker_struct::size, and voxel_is_within_volume(). Referenced by scan_object_to_volume().

public void scan_object_to_volume (  object_struct *  object, Volume  volume, Volume  label_volume, int  label, Real  max_distance )

Definition at line 39 of file scan_objects.c. References FALSE, get_lines_ptr(), get_marker_ptr(), get_next_object_traverse(), get_object_type(), get_polygons_ptr(), get_quadmesh_ptr(), initialize_object_traverse(), LINES, MARKER, POLYGONS, QUADMESH, scan_lines_to_voxels(), scan_marker_to_voxels(), scan_polygons_to_voxels(), and scan_quadmesh_to_voxels().

public void scan_polygons_to_voxels (  polygons_struct *  polygons, Volume  volume, Volume  label_volume, int  label, Real  max_distance )

Add label to all voxels that intersect polygons. Parameters: polygons  list of polygons to scan volume  specifies world-to-volume transformation label_volume  output volume label  value to store in label_volume max_distance  ignored Definition at line 240 of file scan_polygons.c. References polygons_struct::end_indices, GET_OBJECT_SIZE, polygons_struct::indices, polygons_struct::n_items, POINT_INDEX, polygons_struct::points, and scan_a_polygon(). Referenced by scan_object_to_volume().

public void scan_quadmesh_to_voxels (  quadmesh_struct *  quadmesh, Volume  volume, Volume  label_volume, int  label, Real  max_distance )

Add label to all voxels that intersect a quadmesh. Parameters: quadmesh  the mesh to scan volume  specifies world-to-volume transformation label_volume  output volume label  value to store in label_volume max_distance  ignored Definition at line 314 of file scan_polygons.c. References get_quadmesh_n_objects(), get_quadmesh_patch(), and scan_a_polygon(). Referenced by scan_object_to_volume().

public void set_all_volume_label_data (  Volume  volume, int  value )

Definition at line 124 of file labels.c. References check_alloc_label_data(). Referenced by check_alloc_label_data().

public void set_all_volume_label_data_bit (  Volume  volume, int  bit, BOOLEAN  value )

Definition at line 354 of file labels.c. References check_alloc_label_data(), and set_voxel_label_bit().

public void set_colour_coding_min_max (  colour_coding_struct *  colour_coding, Real  min_value, Real  max_value )

Definition at line 151 of file colour_coding.c. References colour_coding_struct::max_value, and colour_coding_struct::min_value. Referenced by initialize_colour_coding().

public void set_colour_coding_over_colour (  colour_coding_struct *  colour_coding, Colour  over_colour )

Definition at line 256 of file colour_coding.c. References FALSE, get_colour_coding_type(), colour_coding_struct::over_colour, recreate_piecewise_function(), and SINGLE_COLOUR_SCALE. Referenced by initialize_colour_coding().

public void set_colour_coding_type (  colour_coding_struct *  colour_coding, Colour_coding_types  type )

Definition at line 108 of file colour_coding.c. References FALSE, recreate_piecewise_function(), and colour_coding_struct::type. Referenced by initialize_colour_coding().

public void set_colour_coding_under_colour (  colour_coding_struct *  colour_coding, Colour  under_colour )

Definition at line 216 of file colour_coding.c. References colour_coding_struct::under_colour. Referenced by initialize_colour_coding().

public void set_label_volume_real_range (  Volume  volume  )

Definition at line 35 of file labels.c. References FALSE. Referenced by create_label_volume().

public void set_volume_label_data (  Volume  volume, int  voxel[], int  value )

Definition at line 183 of file labels.c. References set_volume_label_data_5d(). Referenced by fill_connected_voxels(), input_landmarks_as_labels(), input_tags_as_labels(), load_label_volume(), modify_labels_in_range(), recursive_scan_polygon_to_voxels(), scan_line_segment_to_voxels(), and scan_marker_to_voxels().

public void set_volume_label_data_5d (  Volume  volume, int  v0, int  v1, int  v2, int  v3, int  v4, int  value )

Definition at line 169 of file labels.c. References check_alloc_label_data(). Referenced by set_volume_label_data().

public void set_volume_slice_pixel_range (  Volume  volume1, Filter_types  filter_type1, Real  filter_width1, Real  slice_position1[], Real  x_axis1[], Real  y_axis1[], Real  x_translation1, Real  y_translation1, Real  x_scale1, Real  y_scale1, Volume  volume2, Filter_types  filter_type2, Real  filter_width2, Real  slice_position2[], Real  x_axis2[], Real  y_axis2[], Real  x_translation2, Real  y_translation2, Real  x_scale2, Real  y_scale2, int  x_viewport_size, int  y_viewport_size, Pixel_types  pixel_type, int *  n_pixels_alloced, pixels_struct *  pixels )

Definition at line 524 of file create_slice.c. References create_pixel_mapping(), get_filter_slices(), modify_pixels_size(), n_slices1, set_pixel_range(), and weights1.

public void set_voxel_label_bit (  Volume  volume, int  voxel[], int  bit, BOOLEAN  value )

Definition at line 305 of file labels.c. References check_alloc_label_data(). Referenced by set_all_volume_label_data_bit().

public BOOLEAN should_change_this_one (  Volume  volume, Volume  label_volume, int  voxel[], Real  min_threshold, Real  max_threshold, int  label_min_threshold, int  label_max_threshold, int  desired_label )

Definition at line 322 of file fill_volume.c. References FALSE, get_volume_label_data(), and TRUE. Referenced by fill_connected_voxels().

public Volume smooth_resample_volume (  Volume  volume, int  new_nx, int  new_ny, int  new_nz )

Definition at line 47 of file smooth.c. References calculate_weight(), FALSE, make_scale_transform(), and make_translation_transform().

public BOOLEAN volumes_are_same_grid (  Volume  volume1, Volume  volume2 )

Definition at line 1185 of file mapping.c. References FALSE, and TRUE. Referenced by create_label_volume_from_file().

public BOOLEAN voxel_contains_range (  Volume  volume, int  int_voxel[], Real  min_value, Real  max_value )

Definition at line 1124 of file mapping.c. References FALSE, and TRUE.

public BOOLEAN voxel_is_within_volume (  Volume  volume, Real  voxel_position[] )

Definition at line 1000 of file mapping.c. References FALSE, and TRUE. Referenced by convert_slice_pixel_to_voxel(), interpolate_volume_to_slice(), and scan_marker_to_voxels().

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