int define_Computed_field_type_connected_threshold_image_filter(struct Parse_state *state,
void *field_modify_void, void *computed_field_simple_package_void)
/*******************************************************************************
LAST MODIFIED : 30 August 2006
DESCRIPTION :
Converts <field> into type COMPUTED_FIELD_CONNECTED_THRESHOLD_IMAGE_FILTER (if it is not
already) and allows its contents to be modified.
==============================================================================*/
{
double lower_threshold, upper_threshold, replace_value;
int num_seed_points;
int seed_dimension;
double *seed_points;
int return_code;
int seed_points_length;
int previous_state_index, expected_parameters;
struct Computed_field *source_field;
Computed_field_modify_data *field_modify;
struct Option_table *option_table;
struct Set_Computed_field_conditional_data set_source_field_data;
ENTER(define_Computed_field_type_connected_threshold_image_filter);
USE_PARAMETER(computed_field_simple_package_void);
if (state && (field_modify=(Computed_field_modify_data *)field_modify_void))
{
return_code = 1;
source_field = (struct Computed_field *)NULL;
lower_threshold = 0.0;
upper_threshold = 1.0;
replace_value = 1;
num_seed_points = 0;
seed_dimension = 2;
seed_points = (double *)NULL;
// should probably default to having 1 seed point
// seed_points[0] = 0.5; // pjb: is this ok?
// seed_points[1] = 0.5;
seed_points_length = 0;
/* get valid parameters for projection field */
if ((NULL != field_modify->get_field()) &&
(computed_field_connected_threshold_image_filter_type_string ==
Computed_field_get_type_string(field_modify->get_field())))
{
return_code =
Cmiss_field_get_type_connected_threshold_image_filter(field_modify->get_field(), &source_field,
&lower_threshold, &upper_threshold, &replace_value,
&num_seed_points, &seed_dimension, &seed_points);
}
if (return_code)
{
if (source_field)
{
ACCESS(Computed_field)(source_field);
}
if (state->current_token &&
(!(strcmp(PARSER_HELP_STRING, state->current_token)&&
strcmp(PARSER_RECURSIVE_HELP_STRING, state->current_token))))
{
/* Handle help separately */
option_table = CREATE(Option_table)();
Option_table_add_help(option_table,
"The connected_threshold_filter field uses the itk::ConnectedThresholdImageFilter code to segment a field. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The segmentation is based on a region growing algorithm which requires at least one seed point. To specify the seed points first set the <num_seed_points> and the <dimension> of the image. The <seed_points> are a list of the coordinates for the first and any subsequent seed points. Starting from the seed points any neighbouring pixels with an intensity between <lower_threshold> and the <upper_threshold> are added to the region. Pixels within the region have their pixel intensity set to <replace_value> while the remaining pixels are set to 0. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.");
/* field */
set_source_field_data.computed_field_manager =
field_modify->get_field_manager();
set_source_field_data.conditional_function = Computed_field_is_scalar;
set_source_field_data.conditional_function_user_data = (void *)NULL;
Option_table_add_entry(option_table, "field", &source_field,
&set_source_field_data, set_Computed_field_conditional);
/* lower_threshold */
Option_table_add_double_entry(option_table, "lower_threshold",
&lower_threshold);
/* upper_threshold */
Option_table_add_double_entry(option_table, "upper_threshold",
&upper_threshold);
/* replace_value */
Option_table_add_double_entry(option_table, "replace_value",
&replace_value);
/* num_seed_points */
Option_table_add_int_positive_entry(option_table, "num_seed_points",
&num_seed_points);
Option_table_add_int_positive_entry(option_table, "dimension",
&seed_dimension);
Option_table_add_double_vector_entry(option_table, "seed_points",
seed_points, &seed_points_length);
return_code = Option_table_multi_parse(option_table, state);
DESTROY(Option_table)(&option_table);
}
if (return_code)
{
// store previous state so that we can return to it
previous_state_index = state->current_index;
/* parse the two options which determine the number of seed values
and hence the size of the array that must be created to read in
the number of seed values. */
option_table = CREATE(Option_table)();
/* num_seed_points */
Option_table_add_int_positive_entry(option_table, "num_seed_points",
&num_seed_points);
/* dimension */
Option_table_add_int_positive_entry(option_table, "dimension",
&seed_dimension);
/* Ignore all the other entries */
Option_table_ignore_all_unmatched_entries(option_table);
return_code = Option_table_multi_parse(option_table, state);
DESTROY(Option_table)(&option_table);
/* Return back to where we were */
shift_Parse_state(state, previous_state_index - state->current_index);
}
/* parse the rest of the table */
if (return_code)
{
seed_points_length = num_seed_points * seed_dimension;
REALLOCATE(seed_points, seed_points, double, seed_points_length);
// pjb: should I populate array with dummy values?
option_table = CREATE(Option_table)();
/* field */
set_source_field_data.computed_field_manager =
field_modify->get_field_manager();
set_source_field_data.conditional_function = Computed_field_is_scalar;
set_source_field_data.conditional_function_user_data = (void *)NULL;
Option_table_add_entry(option_table, "field", &source_field,
&set_source_field_data, set_Computed_field_conditional);
/* lower_threshold */
Option_table_add_double_entry(option_table, "lower_threshold",
&lower_threshold);
/* upper_threshold */
Option_table_add_double_entry(option_table, "upper_threshold",
&upper_threshold);
/* replace_value */
Option_table_add_double_entry(option_table, "replace_value",
&replace_value);
expected_parameters = 1;
Option_table_add_ignore_token_entry(option_table, "num_seed_points",
&expected_parameters);
expected_parameters = 1;
Option_table_add_ignore_token_entry(option_table, "dimension",
&expected_parameters);
Option_table_add_double_vector_entry(option_table, "seed_points",
seed_points, &seed_points_length);
return_code=Option_table_multi_parse(option_table,state);
DESTROY(Option_table)(&option_table);
}
/* no errors,not asking for help */
if (return_code)
{
if (!source_field)
{
display_message(ERROR_MESSAGE,
"define_Computed_field_type_connected_threshold_image_filter. "
"Missing source field");
return_code = 0;
}
}
if (return_code)
{
return_code = field_modify->update_field_and_deaccess(
Cmiss_field_module_create_connected_threshold_image_filter(
field_modify->get_field_module(),
source_field, lower_threshold, upper_threshold, replace_value,
num_seed_points, seed_dimension, seed_points));
}
if (!return_code)
{
if ((!state->current_token) ||
(strcmp(PARSER_HELP_STRING, state->current_token)&&
strcmp(PARSER_RECURSIVE_HELP_STRING, state->current_token)))
{
/* error */
display_message(ERROR_MESSAGE,
"define_Computed_field_type_connected_threshold_image_filter. Failed");
}
}
if (source_field)
{
DEACCESS(Computed_field)(&source_field);
}
if (seed_points) {
DEALLOCATE(seed_points);
}
}
}
else
{
display_message(ERROR_MESSAGE,
"define_Computed_field_type_connected_threshold_image_filter. Invalid argument(s)");
return_code = 0;
}
LEAVE;
return (return_code);
} /* define_Computed_field_type_connected_threshold_image_filter */
int define_Computed_field_type_fast_marching_image_filter(struct Parse_state *state,
void *field_modify_void, void *computed_field_simple_package_void)
/*******************************************************************************
LAST MODIFIED : 30 August 2006
DESCRIPTION :
Converts <field> into type COMPUTED_FIELD_FAST_MARCHING_IMAGE_FILTER (if it is not
already) and allows its contents to be modified.
==============================================================================*/
{
double stopping_value;
int num_seed_points;
int dimension;
double *seed_points;
double *seed_values;
int *output_size;
int length_seed_points;
int return_code;
int previous_state_index;
int i;
struct Computed_field *source_field;
Computed_field_modify_data *field_modify;
struct Option_table *option_table;
struct Set_Computed_field_conditional_data set_source_field_data;
ENTER(define_Computed_field_type_fast_marching_image_filter);
USE_PARAMETER(computed_field_simple_package_void);
if (state && (field_modify=(Computed_field_modify_data *)field_modify_void))
{
return_code = 1;
source_field = (struct Computed_field *)NULL;
stopping_value = 100;
num_seed_points = 1;
dimension = 2;
length_seed_points = num_seed_points * dimension;
seed_points = (double *)NULL;
seed_values = (double *)NULL;
output_size = (int *)NULL;
ALLOCATE(seed_points, double, length_seed_points);
ALLOCATE(seed_values, double, num_seed_points);
ALLOCATE(output_size, int, dimension);
// should probably default to having 1 seed
seed_points[0] = 0.5; // pjb: is this ok?
seed_points[1] = 0.5;
seed_values[0] = 0.0;
output_size[0] = 128;
output_size[1] = 128;
/* get valid parameters for projection field */
if ((NULL != field_modify->get_field()) &&
(computed_field_fast_marching_image_filter_type_string ==
Computed_field_get_type_string(field_modify->get_field())))
{
return_code =
cmzn_field_get_type_fast_marching_image_filter(field_modify->get_field(), &source_field,
&stopping_value, &num_seed_points, &dimension, &seed_points, &seed_values, &output_size);
}
if (return_code)
{
if (source_field)
{
ACCESS(Computed_field)(source_field);
}
if (state->current_token &&
(!(strcmp(PARSER_HELP_STRING, state->current_token)&&
strcmp(PARSER_RECURSIVE_HELP_STRING, state->current_token))))
{
/* Handle help separately */
option_table = CREATE(Option_table)();
Option_table_add_help(option_table,
"The fast_marching_filter field uses the itk::FastMarchingImageFilter code to segment a field. The segmentation is based on a level set algorithm. The <field> it operates on is used as a speed term, to govern where the level set curve grows quickly. The speed term is usually some function (eg a sigmoid) of an image gradient field. The output field is a time crossing map, where the value at is each pixel is the time take to reach that location from the specified seed points. Values typically range from 0 through to extremely large (10 to the 38). To convert the time cross map into a segmented region use a binary threshold filter. To specify the seed points first set the <num_seed_points> and the <dimension> of the image. The <seed_points> are a list of the coordinates for the first and any subsequent seed points. It is also possible to specify non-zero initial <seed_values> if desired and to set the <output_size> of the time crossing map. See a/segmentation for an example of using this field. For more information see the itk software guide.");
/* field */
set_source_field_data.computed_field_manager =
field_modify->get_field_manager();
set_source_field_data.conditional_function = Computed_field_is_scalar;
set_source_field_data.conditional_function_user_data = (void *)NULL;
Option_table_add_entry(option_table, "field", &source_field,
&set_source_field_data, set_Computed_field_conditional);
/* stopping_value */
Option_table_add_double_entry(option_table, "stopping_value",
&stopping_value);
/* num_seed_points */
Option_table_add_int_positive_entry(option_table, "num_seed_points",
&num_seed_points);
/* dimension */
Option_table_add_int_positive_entry(option_table, "dimension",
&dimension);
/* seed_points */
Option_table_add_double_vector_entry(option_table, "seed_points",
seed_points, &length_seed_points);
/* seed_values */
Option_table_add_double_vector_entry(option_table, "seed_values",
seed_values, &num_seed_points);
/* output_size */
Option_table_add_int_vector_entry(option_table, "output_size",
output_size, &dimension);
return_code = Option_table_multi_parse(option_table, state);
DESTROY(Option_table)(&option_table);
}
if (return_code)
{
// store previous state so that we can return to it
previous_state_index = state->current_index;
/* parse the two options which determine the number of seed values
and hence the size of the array that must be created to read in
the number of seed values. */
option_table = CREATE(Option_table)();
/* num_seed_points */
Option_table_add_int_positive_entry(option_table, "num_seed_points",
&num_seed_points);
/* dimension */
Option_table_add_int_positive_entry(option_table, "dimension",
&dimension);
/* Ignore all the other entries */
Option_table_ignore_all_unmatched_entries(option_table);
return_code = Option_table_multi_parse(option_table, state);
DESTROY(Option_table)(&option_table);
/* Return back to where we were */
shift_Parse_state(state, previous_state_index - state->current_index);
}
/* parse the rest of the table */
if (return_code)
{
length_seed_points = num_seed_points * dimension;
/* reallocate memory for arrays */
REALLOCATE(seed_points, seed_points, double, length_seed_points);
REALLOCATE(seed_values, seed_values, double, num_seed_points);
REALLOCATE(output_size, output_size, int, dimension);
/* set default values, in case options are not specified in field definition. */
for (i=0; i < length_seed_points ;i++) {
seed_points[i] = 0;
}
for (i=0; i < num_seed_points ;i++) {
seed_values[i] = 0;
}
for (i=0; i < dimension ;i++) {
output_size[i] = 128;
}
option_table = CREATE(Option_table)();
/* field */
set_source_field_data.computed_field_manager =
field_modify->get_field_manager();
set_source_field_data.conditional_function = Computed_field_is_scalar;
set_source_field_data.conditional_function_user_data = (void *)NULL;
Option_table_add_entry(option_table, "field", &source_field,
&set_source_field_data, set_Computed_field_conditional);
/* stopping_value */
Option_table_add_double_entry(option_table, "stopping_value",
&stopping_value);
int num_seed_points_expected_parameters = 1;
Option_table_add_ignore_token_entry(option_table, "num_seed_points",
&num_seed_points_expected_parameters);
int dimension_expected_parameters = 1;
Option_table_add_ignore_token_entry(option_table, "dimension",
&dimension_expected_parameters);
Option_table_add_double_vector_entry(option_table, "seed_points",
seed_points, &length_seed_points);
Option_table_add_double_vector_entry(option_table, "seed_values",
seed_values, &num_seed_points);
Option_table_add_int_vector_entry(option_table, "output_size",
output_size, &dimension);
return_code=Option_table_multi_parse(option_table,state);
DESTROY(Option_table)(&option_table);
}
/* no errors,not asking for help */
if (return_code)
{
if (!source_field)
{
display_message(ERROR_MESSAGE,
"define_Computed_field_type_fast_marching_image_filter. "
"Missing source field");
return_code = 0;
}
}
if (return_code)
{
return_code = field_modify->update_field_and_deaccess(
cmzn_fieldmodule_create_field_imagefilter_fast_marching(
field_modify->get_field_module(),
source_field, stopping_value, num_seed_points, dimension,
seed_points, seed_values, output_size));
}
if (!return_code)
{
if ((!state->current_token) ||
(strcmp(PARSER_HELP_STRING, state->current_token)&&
strcmp(PARSER_RECURSIVE_HELP_STRING, state->current_token)))
{
/* error */
display_message(ERROR_MESSAGE,
"define_Computed_field_type_fast_marching_image_filter. Failed");
}
}
if (source_field)
{
DEACCESS(Computed_field)(&source_field);
}
if (seed_points) {
DEALLOCATE(seed_points);
}
if (seed_values) {
DEALLOCATE(seed_values);
}
if (output_size) {
DEALLOCATE(output_size);
}
}
}
else
{
display_message(ERROR_MESSAGE,
"define_Computed_field_type_fast_marching_image_filter. Invalid argument(s)");
return_code = 0;
}
LEAVE;
return (return_code);
} /* define_Computed_field_type_fast_marching_image_filter */
