int main(int argc, char *argv[])
{
struct Option *vector_opt, *seed_opt, *flowlines_opt, *flowacc_opt, *sampled_opt,
*scalar_opt, *unit_opt, *step_opt, *limit_opt, *skip_opt, *dir_opt,
*error_opt;
struct Flag *table_fl;
struct GModule *module;
RASTER3D_Region region;
RASTER3D_Map *flowacc, *sampled;
struct Integration integration;
struct Seed seed;
struct Gradient_info gradient_info;
struct Map_info seed_Map;
struct line_pnts *seed_points;
struct line_cats *seed_cats;
struct Map_info fl_map;
struct line_cats *fl_cats; /* for flowlines */
struct line_pnts *fl_points; /* for flowlines */
struct field_info *finfo;
dbDriver *driver;
int cat; /* cat of flowlines */
int if_table;
int i, r, c, d;
char *desc;
int n_seeds, seed_count, ltype;
int skip[3];
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("raster3d"));
G_add_keyword(_("hydrology"));
G_add_keyword(_("voxel"));
module->description =
_("Computes 3D flow lines and 3D flow accumulation.");
scalar_opt = G_define_standard_option(G_OPT_R3_INPUT);
scalar_opt->required = NO;
scalar_opt->guisection = _("Input");
vector_opt = G_define_standard_option(G_OPT_R3_INPUTS);
vector_opt->key = "vector_field";
vector_opt->required = NO;
vector_opt->description = _("Names of three 3D raster maps describing "
"x, y, z components of vector field");
vector_opt->guisection = _("Input");
seed_opt = G_define_standard_option(G_OPT_V_INPUT);
seed_opt->required = NO;
seed_opt->key = "seed_points";
seed_opt->description = _("If no map is provided, "
"flow lines are generated "
"from each cell of the input 3D raster");
seed_opt->label = _("Name of vector map with points "
"from which flow lines are generated");
seed_opt->guisection = _("Input");
flowlines_opt = G_define_standard_option(G_OPT_V_OUTPUT);
flowlines_opt->key = "flowline";
flowlines_opt->required = NO;
flowlines_opt->description = _("Name for vector map of flow lines");
flowlines_opt->guisection = _("Output");
flowacc_opt = G_define_standard_option(G_OPT_R3_OUTPUT);
flowacc_opt->key = "flowaccumulation";
flowacc_opt->required = NO;
flowacc_opt->description =
_("Name for output flowaccumulation 3D raster");
flowacc_opt->guisection = _("Output");
sampled_opt = G_define_standard_option(G_OPT_R3_INPUT);
sampled_opt->key = "sampled";
sampled_opt->required = NO;
sampled_opt->label =
_("Name for 3D raster sampled by flowlines");
sampled_opt->description =
_("Values of this 3D raster will be stored "
"as attributes of flowlines segments");
unit_opt = G_define_option();
unit_opt->key = "unit";
unit_opt->type = TYPE_STRING;
unit_opt->required = NO;
unit_opt->answer = "cell";
unit_opt->options = "time,length,cell";
desc = NULL;
G_asprintf(&desc,
"time;%s;"
"length;%s;"
"cell;%s",
_("elapsed time"),
_("length in map units"), _("length in cells (voxels)"));
unit_opt->descriptions = desc;
unit_opt->label = _("Unit of integration step");
unit_opt->description = _("Default unit is cell");
unit_opt->guisection = _("Integration");
step_opt = G_define_option();
step_opt->key = "step";
step_opt->type = TYPE_DOUBLE;
step_opt->required = NO;
step_opt->answer = "0.25";
step_opt->label = _("Integration step in selected unit");
step_opt->description = _("Default step is 0.25 cell");
step_opt->guisection = _("Integration");
limit_opt = G_define_option();
limit_opt->key = "limit";
limit_opt->type = TYPE_INTEGER;
limit_opt->required = NO;
limit_opt->answer = "2000";
limit_opt->description = _("Maximum number of steps");
limit_opt->guisection = _("Integration");
error_opt = G_define_option();
error_opt->key = "max_error";
error_opt->type = TYPE_DOUBLE;
error_opt->required = NO;
error_opt->answer = "1e-5";
error_opt->label = _("Maximum error of integration");
error_opt->description = _("Influences step, increase maximum error "
"to allow bigger steps");
error_opt->guisection = _("Integration");
skip_opt = G_define_option();
skip_opt->key = "skip";
skip_opt->type = TYPE_INTEGER;
skip_opt->required = NO;
skip_opt->multiple = YES;
skip_opt->description =
_("Number of cells between flow lines in x, y and z direction");
dir_opt = G_define_option();
dir_opt->key = "direction";
dir_opt->type = TYPE_STRING;
dir_opt->required = NO;
dir_opt->multiple = NO;
dir_opt->options = "up,down,both";
dir_opt->answer = "down";
dir_opt->description = _("Compute flowlines upstream, "
"downstream or in both direction.");
table_fl = G_define_flag();
table_fl->key = 'a';
table_fl->description = _("Create and fill attribute table");
G_option_required(scalar_opt, vector_opt, NULL);
G_option_exclusive(scalar_opt, vector_opt, NULL);
G_option_required(flowlines_opt, flowacc_opt, NULL);
G_option_requires(seed_opt, flowlines_opt, NULL);
G_option_requires(table_fl, flowlines_opt, NULL);
G_option_requires(sampled_opt, table_fl, NULL);
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
driver = NULL;
finfo = NULL;
if_table = table_fl->answer ? TRUE : FALSE;
check_vector_input_maps(vector_opt, seed_opt);
Rast3d_init_defaults();
Rast3d_get_window(®ion);
/* set up integration variables */
if (step_opt->answer) {
integration.step = atof(step_opt->answer);
integration.unit = unit_opt->answer;
}
else {
integration.unit = "cell";
integration.step = 0.25;
}
integration.max_error = atof(error_opt->answer);
integration.max_step = 5 * integration.step;
integration.min_step = integration.step / 5;
integration.limit = atof(limit_opt->answer);
if (strcmp(dir_opt->answer, "up") == 0)
integration.direction_type = FLOWDIR_UP;
else if (strcmp(dir_opt->answer, "down") == 0)
integration.direction_type = FLOWDIR_DOWN;
else
integration.direction_type = FLOWDIR_BOTH;
/* cell size is the diagonal */
integration.cell_size = sqrt(region.ns_res * region.ns_res +
region.ew_res * region.ew_res +
region.tb_res * region.tb_res);
/* set default skip if needed */
if (skip_opt->answers) {
for (i = 0; i < 3; i++) {
if (skip_opt->answers[i] != NULL) {
skip[i] = atoi(skip_opt->answers[i]);
}
else {
G_fatal_error(_("Please provide 3 integer values for skip option."));
}
}
}
else {
skip[0] = fmax(1, region.cols / 10);
skip[1] = fmax(1, region.rows / 10);
skip[2] = fmax(1, region.depths / 10);
}
/* open raster 3D maps of velocity components */
gradient_info.initialized = FALSE;
load_input_raster3d_maps(scalar_opt, vector_opt, &gradient_info, ®ion);
/* open new 3D raster map of flowacumulation */
if (flowacc_opt->answer) {
flowacc = Rast3d_open_new_opt_tile_size(flowacc_opt->answer,
RASTER3D_USE_CACHE_DEFAULT,
®ion, FCELL_TYPE, 32);
if (!flowacc)
Rast3d_fatal_error(_("Unable to open 3D raster map <%s>"),
flowacc_opt->answer);
init_flowaccum(®ion, flowacc);
}
/* open 3D raster map used for sampling */
if (sampled_opt->answer) {
sampled = Rast3d_open_cell_old(sampled_opt->answer,
G_find_raster3d(sampled_opt->answer, ""),
®ion, RASTER3D_TILE_SAME_AS_FILE,
RASTER3D_USE_CACHE_DEFAULT);
if (!sampled)
Rast3d_fatal_error(_("Unable to open 3D raster map <%s>"),
sampled_opt->answer);
}
else
sampled = NULL;
/* open new vector map of flowlines */
if (flowlines_opt->answer) {
fl_cats = Vect_new_cats_struct();
fl_points = Vect_new_line_struct();
if (Vect_open_new(&fl_map, flowlines_opt->answer, TRUE) < 0)
G_fatal_error(_("Unable to create vector map <%s>"),
flowlines_opt->answer);
Vect_hist_command(&fl_map);
if (if_table) {
create_table(&fl_map, &finfo, &driver,
gradient_info.compute_gradient, sampled ? 1 : 0);
}
}
n_seeds = 0;
/* open vector map of seeds */
if (seed_opt->answer) {
if (Vect_open_old2(&seed_Map, seed_opt->answer, "", "1") < 0)
G_fatal_error(_("Unable to open vector map <%s>"),
seed_opt->answer);
if (!Vect_is_3d(&seed_Map))
G_fatal_error(_("Vector map <%s> is not 3D"), seed_opt->answer);
n_seeds = Vect_get_num_primitives(&seed_Map, GV_POINT);
}
if (flowacc_opt->answer || (!seed_opt->answer && flowlines_opt->answer)) {
if (flowacc_opt->answer)
n_seeds += region.cols * region.rows * region.depths;
else {
n_seeds += ceil(region.cols / (double)skip[0]) *
ceil(region.rows / (double)skip[1]) *
ceil(region.depths / (double)skip[2]);
}
}
G_debug(1, "Number of seeds is %d", n_seeds);
seed_count = 0;
cat = 1;
if (seed_opt->answer) {
seed_points = Vect_new_line_struct();
seed_cats = Vect_new_cats_struct();
/* compute flowlines from vector seed map */
while (TRUE) {
ltype = Vect_read_next_line(&seed_Map, seed_points, seed_cats);
if (ltype == -1) {
Vect_close(&seed_Map);
G_fatal_error(_("Error during reading seed vector map"));
}
else if (ltype == -2) {
break;
}
else if (ltype == GV_POINT) {
seed.x = seed_points->x[0];
seed.y = seed_points->y[0];
seed.z = seed_points->z[0];
seed.flowline = TRUE;
seed.flowaccum = FALSE;
}
G_percent(seed_count, n_seeds, 1);
if (integration.direction_type == FLOWDIR_UP ||
integration.direction_type == FLOWDIR_BOTH) {
integration.actual_direction = FLOWDIR_UP;
compute_flowline(®ion, &seed, &gradient_info, flowacc, sampled,
&integration, &fl_map, fl_cats, fl_points,
&cat, if_table, finfo, driver);
}
if (integration.direction_type == FLOWDIR_DOWN ||
integration.direction_type == FLOWDIR_BOTH) {
integration.actual_direction = FLOWDIR_DOWN;
compute_flowline(®ion, &seed, &gradient_info, flowacc, sampled,
&integration, &fl_map, fl_cats, fl_points,
&cat, if_table, finfo, driver);
}
seed_count++;
}
Vect_destroy_line_struct(seed_points);
Vect_destroy_cats_struct(seed_cats);
Vect_close(&seed_Map);
}
if (flowacc_opt->answer || (!seed_opt->answer && flowlines_opt->answer)) {
/* compute flowlines from points on grid */
for (r = region.rows; r > 0; r--) {
for (c = 0; c < region.cols; c++) {
for (d = 0; d < region.depths; d++) {
seed.x =
region.west + c * region.ew_res + region.ew_res / 2;
seed.y =
region.south + r * region.ns_res - region.ns_res / 2;
seed.z =
region.bottom + d * region.tb_res + region.tb_res / 2;
seed.flowline = FALSE;
seed.flowaccum = FALSE;
if (flowacc_opt->answer)
seed.flowaccum = TRUE;
if (flowlines_opt->answer && !seed_opt->answer &&
(c % skip[0] == 0) && (r % skip[1] == 0) && (d % skip[2] == 0))
seed.flowline = TRUE;
if (seed.flowaccum || seed.flowline) {
G_percent(seed_count, n_seeds, 1);
if (integration.direction_type == FLOWDIR_UP ||
integration.direction_type == FLOWDIR_BOTH) {
integration.actual_direction = FLOWDIR_UP;
compute_flowline(®ion, &seed, &gradient_info,
flowacc, sampled, &integration, &fl_map,
fl_cats, fl_points, &cat,
if_table, finfo, driver);
}
if (integration.direction_type == FLOWDIR_DOWN ||
integration.direction_type == FLOWDIR_BOTH) {
integration.actual_direction = FLOWDIR_DOWN;
compute_flowline(®ion, &seed, &gradient_info,
flowacc, sampled, &integration, &fl_map,
fl_cats, fl_points, &cat,
if_table, finfo, driver);
}
seed_count++;
}
}
}
}
}
G_percent(1, 1, 1);
if (flowlines_opt->answer) {
if (if_table) {
db_commit_transaction(driver);
db_close_database_shutdown_driver(driver);
}
Vect_destroy_line_struct(fl_points);
Vect_destroy_cats_struct(fl_cats);
Vect_build(&fl_map);
Vect_close(&fl_map);
}
if (flowacc_opt->answer)
Rast3d_close(flowacc);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
int out_fd, base_raster;
char *infile, *outmap;
int percent;
double zrange_min, zrange_max, d_tmp;
double irange_min, irange_max;
unsigned long estimated_lines;
RASTER_MAP_TYPE rtype, base_raster_data_type;
struct History history;
char title[64];
SEGMENT base_segment;
struct PointBinning point_binning;
void *base_array;
void *raster_row;
struct Cell_head region;
struct Cell_head input_region;
int rows, last_rows, row0, cols; /* scan box size */
int row; /* counters */
int pass, npasses;
unsigned long line, line_total;
unsigned int counter;
unsigned long n_invalid;
char buff[BUFFSIZE];
double x, y, z;
double intensity;
int arr_row, arr_col;
unsigned long count, count_total;
int point_class;
double zscale = 1.0;
double iscale = 1.0;
double res = 0.0;
struct BinIndex bin_index_nodes;
bin_index_nodes.num_nodes = 0;
bin_index_nodes.max_nodes = 0;
bin_index_nodes.nodes = 0;
struct GModule *module;
struct Option *input_opt, *output_opt, *percent_opt, *type_opt, *filter_opt, *class_opt;
struct Option *method_opt, *base_raster_opt;
struct Option *zrange_opt, *zscale_opt;
struct Option *irange_opt, *iscale_opt;
struct Option *trim_opt, *pth_opt, *res_opt;
struct Option *file_list_opt;
struct Flag *print_flag, *scan_flag, *shell_style, *over_flag, *extents_flag;
struct Flag *intens_flag, *intens_import_flag;
struct Flag *set_region_flag;
struct Flag *base_rast_res_flag;
struct Flag *only_valid_flag;
/* LAS */
LASReaderH LAS_reader;
LASHeaderH LAS_header;
LASSRSH LAS_srs;
LASPointH LAS_point;
int return_filter;
const char *projstr;
struct Cell_head cellhd, loc_wind;
unsigned int n_filtered;
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("raster"));
G_add_keyword(_("import"));
G_add_keyword(_("LIDAR"));
G_add_keyword(_("statistics"));
G_add_keyword(_("conversion"));
G_add_keyword(_("aggregation"));
G_add_keyword(_("binning"));
module->description =
_("Creates a raster map from LAS LiDAR points using univariate statistics.");
input_opt = G_define_standard_option(G_OPT_F_BIN_INPUT);
input_opt->required = NO;
input_opt->label = _("LAS input file");
input_opt->description = _("LiDAR input files in LAS format (*.las or *.laz)");
input_opt->guisection = _("Input");
output_opt = G_define_standard_option(G_OPT_R_OUTPUT);
output_opt->required = NO;
output_opt->guisection = _("Output");
file_list_opt = G_define_standard_option(G_OPT_F_INPUT);
file_list_opt->key = "file";
file_list_opt->label = _("File containing names of LAS input files");
file_list_opt->description = _("LiDAR input files in LAS format (*.las or *.laz)");
file_list_opt->required = NO;
file_list_opt->guisection = _("Input");
method_opt = G_define_option();
method_opt->key = "method";
method_opt->type = TYPE_STRING;
method_opt->required = NO;
method_opt->description = _("Statistic to use for raster values");
method_opt->options =
"n,min,max,range,sum,mean,stddev,variance,coeff_var,median,percentile,skewness,trimmean";
method_opt->answer = "mean";
method_opt->guisection = _("Statistic");
G_asprintf((char **)&(method_opt->descriptions),
"n;%s;"
"min;%s;"
"max;%s;"
"range;%s;"
"sum;%s;"
"mean;%s;"
"stddev;%s;"
"variance;%s;"
"coeff_var;%s;"
"median;%s;"
"percentile;%s;"
"skewness;%s;"
"trimmean;%s",
_("Number of points in cell"),
_("Minimum value of point values in cell"),
_("Maximum value of point values in cell"),
_("Range of point values in cell"),
_("Sum of point values in cell"),
_("Mean (average) value of point values in cell"),
_("Standard deviation of point values in cell"),
_("Variance of point values in cell"),
_("Coefficient of variance of point values in cell"),
_("Median value of point values in cell"),
_("pth (nth) percentile of point values in cell"),
_("Skewness of point values in cell"),
_("Trimmed mean of point values in cell"));
type_opt = G_define_standard_option(G_OPT_R_TYPE);
type_opt->required = NO;
type_opt->answer = "FCELL";
base_raster_opt = G_define_standard_option(G_OPT_R_INPUT);
base_raster_opt->key = "base_raster";
base_raster_opt->required = NO;
base_raster_opt->label =
_("Subtract raster values from the Z coordinates");
base_raster_opt->description =
_("The scale for Z is applied beforehand, the range filter for"
" Z afterwards");
base_raster_opt->guisection = _("Transform");
zrange_opt = G_define_option();
zrange_opt->key = "zrange";
zrange_opt->type = TYPE_DOUBLE;
zrange_opt->required = NO;
zrange_opt->key_desc = "min,max";
zrange_opt->description = _("Filter range for Z data (min,max)");
zrange_opt->guisection = _("Selection");
zscale_opt = G_define_option();
zscale_opt->key = "zscale";
zscale_opt->type = TYPE_DOUBLE;
zscale_opt->required = NO;
zscale_opt->answer = "1.0";
zscale_opt->description = _("Scale to apply to Z data");
zscale_opt->guisection = _("Transform");
irange_opt = G_define_option();
irange_opt->key = "intensity_range";
irange_opt->type = TYPE_DOUBLE;
irange_opt->required = NO;
irange_opt->key_desc = "min,max";
irange_opt->description = _("Filter range for intensity values (min,max)");
irange_opt->guisection = _("Selection");
iscale_opt = G_define_option();
iscale_opt->key = "intensity_scale";
iscale_opt->type = TYPE_DOUBLE;
iscale_opt->required = NO;
iscale_opt->answer = "1.0";
iscale_opt->description = _("Scale to apply to intensity values");
iscale_opt->guisection = _("Transform");
percent_opt = G_define_option();
percent_opt->key = "percent";
percent_opt->type = TYPE_INTEGER;
percent_opt->required = NO;
percent_opt->answer = "100";
percent_opt->options = "1-100";
percent_opt->description = _("Percent of map to keep in memory");
/* I would prefer to call the following "percentile", but that has too
* much namespace overlap with the "percent" option above */
pth_opt = G_define_option();
pth_opt->key = "pth";
pth_opt->type = TYPE_INTEGER;
pth_opt->required = NO;
pth_opt->options = "1-100";
pth_opt->description = _("pth percentile of the values");
pth_opt->guisection = _("Statistic");
trim_opt = G_define_option();
trim_opt->key = "trim";
trim_opt->type = TYPE_DOUBLE;
trim_opt->required = NO;
trim_opt->options = "0-50";
trim_opt->label = _("Discard given percentage of the smallest and largest values");
trim_opt->description =
_("Discard <trim> percent of the smallest and <trim> percent of the largest observations");
trim_opt->guisection = _("Statistic");
res_opt = G_define_option();
res_opt->key = "resolution";
res_opt->type = TYPE_DOUBLE;
res_opt->required = NO;
res_opt->description =
_("Output raster resolution");
res_opt->guisection = _("Output");
filter_opt = G_define_option();
filter_opt->key = "return_filter";
filter_opt->type = TYPE_STRING;
filter_opt->required = NO;
filter_opt->label = _("Only import points of selected return type");
filter_opt->description = _("If not specified, all points are imported");
filter_opt->options = "first,last,mid";
filter_opt->guisection = _("Selection");
class_opt = G_define_option();
class_opt->key = "class_filter";
class_opt->type = TYPE_INTEGER;
class_opt->multiple = YES;
class_opt->required = NO;
class_opt->label = _("Only import points of selected class(es)");
class_opt->description = _("Input is comma separated integers. "
"If not specified, all points are imported.");
class_opt->guisection = _("Selection");
print_flag = G_define_flag();
print_flag->key = 'p';
print_flag->description =
_("Print LAS file info and exit");
extents_flag = G_define_flag();
extents_flag->key = 'e';
extents_flag->label =
_("Use the extent of the input for the raster extent");
extents_flag->description =
_("Set internally computational region extents based on the"
" point cloud");
extents_flag->guisection = _("Output");
set_region_flag = G_define_flag();
set_region_flag->key = 'n';
set_region_flag->label =
_("Set computation region to match the new raster map");
set_region_flag->description =
_("Set computation region to match the 2D extent and resolution"
" of the newly created new raster map");
set_region_flag->guisection = _("Output");
over_flag = G_define_flag();
over_flag->key = 'o';
over_flag->label =
_("Override projection check (use current location's projection)");
over_flag->description =
_("Assume that the dataset has same projection as the current location");
scan_flag = G_define_flag();
scan_flag->key = 's';
scan_flag->description = _("Scan data file for extent then exit");
shell_style = G_define_flag();
shell_style->key = 'g';
shell_style->description =
_("In scan mode, print using shell script style");
intens_flag = G_define_flag();
intens_flag->key = 'i';
intens_flag->label =
_("Use intensity values rather than Z values");
intens_flag->description =
_("Uses intensity values everywhere as if they would be Z"
" coordinates");
intens_import_flag = G_define_flag();
intens_import_flag->key = 'j';
intens_import_flag->description =
_("Use Z values for filtering, but intensity values for statistics");
base_rast_res_flag = G_define_flag();
base_rast_res_flag->key = 'd';
base_rast_res_flag->label =
_("Use base raster resolution instead of computational region");
base_rast_res_flag->description =
_("For getting values from base raster, use its actual"
" resolution instead of computational region resolution");
only_valid_flag = G_define_flag();
only_valid_flag->key = 'v';
only_valid_flag->label = _("Use only valid points");
only_valid_flag->description =
_("Points invalid according to APSRS LAS specification will be"
" filtered out");
only_valid_flag->guisection = _("Selection");
G_option_required(input_opt, file_list_opt, NULL);
G_option_exclusive(input_opt, file_list_opt, NULL);
G_option_required(output_opt, print_flag, scan_flag, shell_style, NULL);
G_option_exclusive(intens_flag, intens_import_flag, NULL);
G_option_requires(base_rast_res_flag, base_raster_opt, NULL);
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
int only_valid = FALSE;
n_invalid = 0;
if (only_valid_flag->answer)
only_valid = TRUE;
/* we could use rules but this gives more info and allows continuing */
if (set_region_flag->answer && !(extents_flag->answer || res_opt->answer)) {
G_warning(_("Flag %c makes sense only with %s option or -%c flag"),
set_region_flag->key, res_opt->key, extents_flag->key);
/* avoid the call later on */
set_region_flag->answer = '\0';
}
struct StringList infiles;
if (file_list_opt->answer) {
if (access(file_list_opt->answer, F_OK) != 0)
G_fatal_error(_("File <%s> does not exist"), file_list_opt->answer);
string_list_from_file(&infiles, file_list_opt->answer);
}
else {
string_list_from_one_item(&infiles, input_opt->answer);
}
/* parse input values */
outmap = output_opt->answer;
if (shell_style->answer && !scan_flag->answer) {
scan_flag->answer = 1; /* pointer not int, so set = shell_style->answer ? */
}
/* check zrange and extent relation */
if (scan_flag->answer || extents_flag->answer) {
if (zrange_opt->answer)
G_warning(_("zrange will not be taken into account during scan"));
}
Rast_get_window(®ion);
/* G_get_window seems to be unreliable if the location has been changed */
G_get_set_window(&loc_wind); /* TODO: v.in.lidar uses G_get_default_window() */
estimated_lines = 0;
int i;
for (i = 0; i < infiles.num_items; i++) {
infile = infiles.items[i];
/* don't if file not found */
if (access(infile, F_OK) != 0)
G_fatal_error(_("Input file <%s> does not exist"), infile);
/* Open LAS file*/
LAS_reader = LASReader_Create(infile);
if (LAS_reader == NULL)
G_fatal_error(_("Unable to open file <%s> as a LiDAR point cloud"),
infile);
LAS_header = LASReader_GetHeader(LAS_reader);
if (LAS_header == NULL) {
G_fatal_error(_("Unable to read LAS header of <%s>"), infile);
}
LAS_srs = LASHeader_GetSRS(LAS_header);
/* print info or check projection if we are actually importing */
if (print_flag->answer) {
/* print filename when there is more than one file */
if (infiles.num_items > 1)
fprintf(stdout, "File: %s\n", infile);
/* Print LAS header */
print_lasinfo(LAS_header, LAS_srs);
}
else {
/* report that we are checking more files */
if (i == 1)
G_message(_("First file's projection checked,"
" checking projection of the other files..."));
/* Fetch input map projection in GRASS form. */
projstr = LASSRS_GetWKT_CompoundOK(LAS_srs);
/* we are printing the non-warning messages only for first file */
projection_check_wkt(cellhd, loc_wind, projstr, over_flag->answer,
shell_style->answer || i);
/* if there is a problem in some other file, first OK message
* is printed but than a warning, this is not ideal but hopefully
* not so confusing when importing multiple files */
}
if (scan_flag->answer || extents_flag->answer) {
/* we assign to the first one (i==0) but update for the rest */
scan_bounds(LAS_reader, shell_style->answer, extents_flag->answer, i,
zscale, ®ion);
}
/* number of estimated point across all files */
/* TODO: this should be ull which won't work with percent report */
estimated_lines += LASHeader_GetPointRecordsCount(LAS_header);
/* We are closing all again and we will be opening them later,
* so we don't have to worry about limit for open files. */
LASSRS_Destroy(LAS_srs);
LASHeader_Destroy(LAS_header);
LASReader_Destroy(LAS_reader);
}
/* if we are not importing, end */
if (print_flag->answer || scan_flag->answer)
exit(EXIT_SUCCESS);
return_filter = LAS_ALL;
if (filter_opt->answer) {
if (strcmp(filter_opt->answer, "first") == 0)
return_filter = LAS_FIRST;
else if (strcmp(filter_opt->answer, "last") == 0)
return_filter = LAS_LAST;
else if (strcmp(filter_opt->answer, "mid") == 0)
return_filter = LAS_MID;
else
G_fatal_error(_("Unknown filter option <%s>"), filter_opt->answer);
}
struct ReturnFilter return_filter_struct;
return_filter_struct.filter = return_filter;
struct ClassFilter class_filter;
class_filter_create_from_strings(&class_filter, class_opt->answers);
percent = atoi(percent_opt->answer);
/* TODO: we already used zscale */
/* TODO: we don't report intensity range */
if (zscale_opt->answer)
zscale = atof(zscale_opt->answer);
if (iscale_opt->answer)
iscale = atof(iscale_opt->answer);
/* parse zrange */
if (zrange_opt->answer != NULL) {
if (zrange_opt->answers[0] == NULL)
G_fatal_error(_("Invalid zrange"));
sscanf(zrange_opt->answers[0], "%lf", &zrange_min);
sscanf(zrange_opt->answers[1], "%lf", &zrange_max);
if (zrange_min > zrange_max) {
d_tmp = zrange_max;
zrange_max = zrange_min;
zrange_min = d_tmp;
}
}
/* parse irange */
if (irange_opt->answer != NULL) {
if (irange_opt->answers[0] == NULL)
G_fatal_error(_("Invalid %s"), irange_opt->key);
sscanf(irange_opt->answers[0], "%lf", &irange_min);
sscanf(irange_opt->answers[1], "%lf", &irange_max);
if (irange_min > irange_max) {
d_tmp = irange_max;
irange_max = irange_min;
irange_min = d_tmp;
}
}
point_binning_set(&point_binning, method_opt->answer, pth_opt->answer,
trim_opt->answer, FALSE);
base_array = NULL;
if (strcmp("CELL", type_opt->answer) == 0)
rtype = CELL_TYPE;
else if (strcmp("DCELL", type_opt->answer) == 0)
rtype = DCELL_TYPE;
else
rtype = FCELL_TYPE;
if (point_binning.method == METHOD_N)
rtype = CELL_TYPE;
if (res_opt->answer) {
/* align to resolution */
res = atof(res_opt->answer);
if (!G_scan_resolution(res_opt->answer, &res, region.proj))
G_fatal_error(_("Invalid input <%s=%s>"), res_opt->key, res_opt->answer);
if (res <= 0)
G_fatal_error(_("Option '%s' must be > 0.0"), res_opt->key);
region.ns_res = region.ew_res = res;
region.north = ceil(region.north / res) * res;
region.south = floor(region.south / res) * res;
region.east = ceil(region.east / res) * res;
region.west = floor(region.west / res) * res;
G_adjust_Cell_head(®ion, 0, 0);
}
else if (extents_flag->answer) {
/* align to current region */
Rast_align_window(®ion, &loc_wind);
}
Rast_set_output_window(®ion);
rows = last_rows = region.rows;
npasses = 1;
if (percent < 100) {
rows = (int)(region.rows * (percent / 100.0));
npasses = region.rows / rows;
last_rows = region.rows - npasses * rows;
if (last_rows)
npasses++;
else
last_rows = rows;
}
cols = region.cols;
G_debug(2, "region.n=%f region.s=%f region.ns_res=%f", region.north,
region.south, region.ns_res);
G_debug(2, "region.rows=%d [box_rows=%d] region.cols=%d", region.rows,
rows, region.cols);
/* using row-based chunks (used for output) when input and output
* region matches and using segment library when they don't */
int use_segment = 0;
int use_base_raster_res = 0;
/* TODO: see if the input region extent is smaller than the raster
* if yes, the we need to load the whole base raster if the -e
* flag was defined (alternatively clip the regions) */
if (base_rast_res_flag->answer)
use_base_raster_res = 1;
if (base_raster_opt->answer && (res_opt->answer || use_base_raster_res
|| extents_flag->answer))
use_segment = 1;
if (base_raster_opt->answer && !use_segment) {
/* TODO: do we need to test existence first? mapset? */
base_raster = Rast_open_old(base_raster_opt->answer, "");
base_raster_data_type = Rast_get_map_type(base_raster);
base_array = G_calloc((size_t)rows * (cols + 1), Rast_cell_size(base_raster_data_type));
}
if (base_raster_opt->answer && use_segment) {
if (use_base_raster_res) {
/* read raster actual extent and resolution */
Rast_get_cellhd(base_raster_opt->answer, "", &input_region);
/* TODO: make it only as small as the output is or points are */
Rast_set_input_window(&input_region); /* we have split window */
} else {
Rast_get_input_window(&input_region);
}
rast_segment_open(&base_segment, base_raster_opt->answer, &base_raster_data_type);
}
if (!scan_flag->answer) {
if (!check_rows_cols_fit_to_size_t(rows, cols))
G_fatal_error(_("Unable to process the hole map at once. "
"Please set the '%s' option to some value lower than 100."),
percent_opt->key);
point_binning_memory_test(&point_binning, rows, cols, rtype);
}
/* open output map */
out_fd = Rast_open_new(outmap, rtype);
/* allocate memory for a single row of output data */
raster_row = Rast_allocate_output_buf(rtype);
G_message(_("Reading data ..."));
count_total = line_total = 0;
/* main binning loop(s) */
for (pass = 1; pass <= npasses; pass++) {
if (npasses > 1)
G_message(_("Pass #%d (of %d) ..."), pass, npasses);
/* figure out segmentation */
row0 = (pass - 1) * rows;
if (pass == npasses) {
rows = last_rows;
}
if (base_array) {
G_debug(2, "filling base raster array");
for (row = 0; row < rows; row++) {
Rast_get_row(base_raster, base_array + ((size_t) row * cols * Rast_cell_size(base_raster_data_type)), row, base_raster_data_type);
}
}
G_debug(2, "pass=%d/%d rows=%d", pass, npasses, rows);
point_binning_allocate(&point_binning, rows, cols, rtype);
line = 0;
count = 0;
counter = 0;
G_percent_reset();
/* loop of input files */
for (i = 0; i < infiles.num_items; i++) {
infile = infiles.items[i];
/* we already know file is there, so just do basic checks */
LAS_reader = LASReader_Create(infile);
if (LAS_reader == NULL)
G_fatal_error(_("Unable to open file <%s>"), infile);
while ((LAS_point = LASReader_GetNextPoint(LAS_reader)) != NULL) {
line++;
counter++;
if (counter == 100000) { /* speed */
if (line < estimated_lines)
G_percent(line, estimated_lines, 3);
counter = 0;
}
/* We always count them and report because behavior
* changed in between 7.0 and 7.2 from undefined (but skipping
* invalid points) to filtering them out only when requested. */
if (!LASPoint_IsValid(LAS_point)) {
n_invalid++;
if (only_valid)
continue;
}
x = LASPoint_GetX(LAS_point);
y = LASPoint_GetY(LAS_point);
if (intens_flag->answer)
/* use intensity as z here to allow all filters (and
* modifications) below to be applied for intensity */
z = LASPoint_GetIntensity(LAS_point);
else
z = LASPoint_GetZ(LAS_point);
int return_n = LASPoint_GetReturnNumber(LAS_point);
int n_returns = LASPoint_GetNumberOfReturns(LAS_point);
if (return_filter_is_out(&return_filter_struct, return_n, n_returns)) {
n_filtered++;
continue;
}
point_class = (int) LASPoint_GetClassification(LAS_point);
if (class_filter_is_out(&class_filter, point_class))
continue;
if (y <= region.south || y > region.north) {
continue;
}
if (x < region.west || x >= region.east) {
continue;
}
/* find the bin in the current array box */
arr_row = (int)((region.north - y) / region.ns_res) - row0;
if (arr_row < 0 || arr_row >= rows)
continue;
arr_col = (int)((x - region.west) / region.ew_res);
z = z * zscale;
if (base_array) {
double base_z;
if (row_array_get_value_row_col(base_array, arr_row, arr_col,
cols, base_raster_data_type,
&base_z))
z -= base_z;
else
continue;
}
else if (use_segment) {
double base_z;
if (rast_segment_get_value_xy(&base_segment, &input_region,
base_raster_data_type, x, y,
&base_z))
z -= base_z;
else
continue;
}
if (zrange_opt->answer) {
if (z < zrange_min || z > zrange_max) {
continue;
}
}
if (intens_import_flag->answer || irange_opt->answer) {
intensity = LASPoint_GetIntensity(LAS_point);
intensity *= iscale;
if (irange_opt->answer) {
if (intensity < irange_min || intensity > irange_max) {
continue;
}
}
/* use intensity for statistics */
if (intens_import_flag->answer)
z = intensity;
}
count++;
/* G_debug(5, "x: %f, y: %f, z: %f", x, y, z); */
update_value(&point_binning, &bin_index_nodes, cols,
arr_row, arr_col, rtype, x, y, z);
} /* while !EOF of one input file */
/* close input LAS file */
LASReader_Destroy(LAS_reader);
} /* end of loop for all input files files */
G_percent(1, 1, 1); /* flush */
G_debug(2, "pass %d finished, %lu coordinates in box", pass, count);
count_total += count;
line_total += line;
/* calc stats and output */
G_message(_("Writing to map ..."));
for (row = 0; row < rows; row++) {
/* potentially vector writing can be independent on the binning */
write_values(&point_binning, &bin_index_nodes, raster_row, row,
cols, rtype, NULL);
/* write out line of raster data */
Rast_put_row(out_fd, raster_row, rtype);
}
/* free memory */
point_binning_free(&point_binning, &bin_index_nodes);
} /* passes loop */
if (base_array)
Rast_close(base_raster);
if (use_segment)
Segment_close(&base_segment);
G_percent(1, 1, 1); /* flush */
G_free(raster_row);
/* close raster file & write history */
Rast_close(out_fd);
sprintf(title, "Raw X,Y,Z data binned into a raster grid by cell %s",
method_opt->answer);
Rast_put_cell_title(outmap, title);
Rast_short_history(outmap, "raster", &history);
Rast_command_history(&history);
Rast_set_history(&history, HIST_DATSRC_1, infile);
Rast_write_history(outmap, &history);
/* set computation region to the new raster map */
/* TODO: should be in the done message */
if (set_region_flag->answer)
G_put_window(®ion);
if (n_invalid && only_valid)
G_message(_("%lu input points were invalid and filtered out"),
n_invalid);
if (n_invalid && !only_valid)
G_message(_("%lu input points were invalid, use -%c flag to filter"
" them out"), n_invalid, only_valid_flag->key);
if (infiles.num_items > 1) {
sprintf(buff, _("Raster map <%s> created."
" %lu points from %d files found in region."),
outmap, count_total, infiles.num_items);
}
else {
sprintf(buff, _("Raster map <%s> created."
" %lu points found in region."),
outmap, count_total);
}
G_done_msg("%s", buff);
G_debug(1, "Processed %lu points.", line_total);
string_list_free(&infiles);
exit(EXIT_SUCCESS);
}
/*--------------------------------------------------------------------*/
int main(int argc, char *argv[])
{
/* Variables declarations */
int nsplx_adj, nsply_adj;
int nsubregion_col, nsubregion_row;
int subregion = 0, nsubregions = 0;
double N_extension, E_extension, edgeE, edgeN;
int dim_vect, nparameters, BW, npoints;
double mean, lambda;
const char *dvr, *db, *mapset;
char table_name[GNAME_MAX];
char xname[GNAME_MAX], xmapset[GMAPSET_MAX];
int last_row, last_column, flag_auxiliar = FALSE;
int filter_mode;
int *lineVect;
double *TN, *Q, *parVect; /* Interpolating and least-square vectors */
double **N, **obsVect; /* Interpolation and least-square matrix */
/* Structs declarations */
struct Map_info In, Out, Outlier, Qgis;
struct Option *in_opt, *out_opt, *outlier_opt, *qgis_opt, *stepE_opt,
*stepN_opt, *lambda_f_opt, *Thres_O_opt, *filter_opt;
struct Flag *spline_step_flag;
struct GModule *module;
struct Reg_dimens dims;
struct Cell_head elaboration_reg, original_reg;
struct bound_box general_box, overlap_box;
struct Point *observ;
dbDriver *driver;
/*----------------------------------------------------------------*/
/* Options declaration */
module = G_define_module();
G_add_keyword(_("vector"));
G_add_keyword(_("statistics"));
G_add_keyword(_("extract"));
G_add_keyword(_("select"));
G_add_keyword(_("filter"));
G_add_keyword(_("LIDAR"));
module->description = _("Removes outliers from vector point data.");
spline_step_flag = G_define_flag();
spline_step_flag->key = 'e';
spline_step_flag->label = _("Estimate point density and distance");
spline_step_flag->description =
_("Estimate point density and distance for the input vector points within the current region extends and quit");
spline_step_flag->suppress_required = YES;
in_opt = G_define_standard_option(G_OPT_V_INPUT);
out_opt = G_define_standard_option(G_OPT_V_OUTPUT);
outlier_opt = G_define_standard_option(G_OPT_V_OUTPUT);
outlier_opt->key = "outlier";
outlier_opt->description = _("Name for output outlier vector map");
qgis_opt = G_define_standard_option(G_OPT_V_OUTPUT);
qgis_opt->key = "qgis";
qgis_opt->required = NO;
qgis_opt->description = _("Name for vector map for visualization in QGIS");
stepE_opt = G_define_option();
stepE_opt->key = "ew_step";
stepE_opt->type = TYPE_DOUBLE;
stepE_opt->required = NO;
stepE_opt->answer = "10";
stepE_opt->description =
_("Length of each spline step in the east-west direction");
stepE_opt->guisection = _("Settings");
stepN_opt = G_define_option();
stepN_opt->key = "ns_step";
stepN_opt->type = TYPE_DOUBLE;
stepN_opt->required = NO;
stepN_opt->answer = "10";
stepN_opt->description =
_("Length of each spline step in the north-south direction");
stepN_opt->guisection = _("Settings");
lambda_f_opt = G_define_option();
lambda_f_opt->key = "lambda";
lambda_f_opt->type = TYPE_DOUBLE;
lambda_f_opt->required = NO;
lambda_f_opt->description = _("Tykhonov regularization weight");
lambda_f_opt->answer = "0.1";
lambda_f_opt->guisection = _("Settings");
Thres_O_opt = G_define_option();
Thres_O_opt->key = "threshold";
Thres_O_opt->type = TYPE_DOUBLE;
Thres_O_opt->required = NO;
Thres_O_opt->description = _("Threshold for the outliers");
Thres_O_opt->answer = "50";
filter_opt = G_define_option();
filter_opt->key = "filter";
filter_opt->type = TYPE_STRING;
filter_opt->required = NO;
filter_opt->description = _("Filtering option");
filter_opt->options = "both,positive,negative";
filter_opt->answer = "both";
G_gisinit(argv[0]);
G_option_requires(spline_step_flag, in_opt, NULL);
/* Parsing */
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
if (!(db = G_getenv_nofatal2("DB_DATABASE", G_VAR_MAPSET)))
G_fatal_error(_("Unable to read name of database"));
if (!(dvr = G_getenv_nofatal2("DB_DRIVER", G_VAR_MAPSET)))
G_fatal_error(_("Unable to read name of driver"));
stepN = atof(stepN_opt->answer);
stepE = atof(stepE_opt->answer);
lambda = atof(lambda_f_opt->answer);
Thres_Outlier = atof(Thres_O_opt->answer);
filter_mode = 0;
if (strcmp(filter_opt->answer, "positive") == 0)
filter_mode = 1;
else if (strcmp(filter_opt->answer, "negative") == 0)
filter_mode = -1;
P_set_outlier_fn(filter_mode);
flag_auxiliar = FALSE;
/* Checking vector names */
if (out_opt->answer)
Vect_check_input_output_name(in_opt->answer, out_opt->answer,
G_FATAL_EXIT);
if ((mapset = G_find_vector2(in_opt->answer, "")) == NULL) {
G_fatal_error(_("Vector map <%s> not found"), in_opt->answer);
}
/* Setting auxiliary table's name */
if (out_opt->answer) {
if (G_name_is_fully_qualified(out_opt->answer, xname, xmapset)) {
sprintf(table_name, "%s_aux", xname);
}
else
sprintf(table_name, "%s_aux", out_opt->answer);
}
/* Something went wrong in a previous v.outlier execution */
if (db_table_exists(dvr, db, table_name)) {
/* Start driver and open db */
driver = db_start_driver_open_database(dvr, db);
if (driver == NULL)
G_fatal_error(_("No database connection for driver <%s> is defined. Run db.connect."),
dvr);
db_set_error_handler_driver(driver);
if (P_Drop_Aux_Table(driver, table_name) != DB_OK)
G_fatal_error(_("Old auxiliary table could not be dropped"));
db_close_database_shutdown_driver(driver);
}
/* Open input vector */
Vect_set_open_level(1); /* WITHOUT TOPOLOGY */
if (1 > Vect_open_old(&In, in_opt->answer, mapset))
G_fatal_error(_("Unable to open vector map <%s> at the topological level"),
in_opt->answer);
/* Input vector must be 3D */
if (!Vect_is_3d(&In))
G_fatal_error(_("Input vector map <%s> is not 3D!"), in_opt->answer);
/* Estimate point density and mean distance for current region */
if (spline_step_flag->answer) {
double dens, dist;
if (P_estimate_splinestep(&In, &dens, &dist) == 0) {
G_message("Estimated point density: %.4g", dens);
G_message("Estimated mean distance between points: %.4g", dist);
}
else
G_warning(_("No points in current region!"));
Vect_close(&In);
exit(EXIT_SUCCESS);
}
/* Open output vector */
if (qgis_opt->answer)
if (0 > Vect_open_new(&Qgis, qgis_opt->answer, WITHOUT_Z))
G_fatal_error(_("Unable to create vector map <%s>"),
qgis_opt->answer);
if (0 > Vect_open_new(&Out, out_opt->answer, WITH_Z)) {
Vect_close(&Qgis);
G_fatal_error(_("Unable to create vector map <%s>"), out_opt->answer);
}
if (0 > Vect_open_new(&Outlier, outlier_opt->answer, WITH_Z)) {
Vect_close(&Out);
Vect_close(&Qgis);
G_fatal_error(_("Unable to create vector map <%s>"), out_opt->answer);
}
/* Copy vector Head File */
Vect_copy_head_data(&In, &Out);
Vect_hist_copy(&In, &Out);
Vect_hist_command(&Out);
Vect_copy_head_data(&In, &Outlier);
Vect_hist_copy(&In, &Outlier);
Vect_hist_command(&Outlier);
if (qgis_opt->answer) {
Vect_copy_head_data(&In, &Qgis);
Vect_hist_copy(&In, &Qgis);
Vect_hist_command(&Qgis);
}
/* Open driver and database */
driver = db_start_driver_open_database(dvr, db);
if (driver == NULL)
G_fatal_error(_("No database connection for driver <%s> is defined. Run db.connect."),
dvr);
db_set_error_handler_driver(driver);
/* Create auxiliary table */
if ((flag_auxiliar =
P_Create_Aux2_Table(driver, table_name)) == FALSE)
G_fatal_error(_("It was impossible to create <%s> table."), table_name);
db_create_index2(driver, table_name, "ID");
/* sqlite likes that ??? */
db_close_database_shutdown_driver(driver);
driver = db_start_driver_open_database(dvr, db);
/* Setting regions and boxes */
G_get_set_window(&original_reg);
G_get_set_window(&elaboration_reg);
Vect_region_box(&elaboration_reg, &overlap_box);
Vect_region_box(&elaboration_reg, &general_box);
/*------------------------------------------------------------------
| Subdividing and working with tiles:
| Each original region will be divided into several subregions.
| Each one will be overlapped by its neighbouring subregions.
| The overlapping is calculated as a fixed OVERLAP_SIZE times
| the largest spline step plus 2 * edge
----------------------------------------------------------------*/
/* Fixing parameters of the elaboration region */
P_zero_dim(&dims); /* Set dim struct to zero */
nsplx_adj = NSPLX_MAX;
nsply_adj = NSPLY_MAX;
if (stepN > stepE)
dims.overlap = OVERLAP_SIZE * stepN;
else
dims.overlap = OVERLAP_SIZE * stepE;
P_get_edge(P_BILINEAR, &dims, stepE, stepN);
P_set_dim(&dims, stepE, stepN, &nsplx_adj, &nsply_adj);
G_verbose_message(_("Adjusted EW splines %d"), nsplx_adj);
G_verbose_message(_("Adjusted NS splines %d"), nsply_adj);
/* calculate number of subregions */
edgeE = dims.ew_size - dims.overlap - 2 * dims.edge_v;
edgeN = dims.sn_size - dims.overlap - 2 * dims.edge_h;
N_extension = original_reg.north - original_reg.south;
E_extension = original_reg.east - original_reg.west;
nsubregion_col = ceil(E_extension / edgeE) + 0.5;
nsubregion_row = ceil(N_extension / edgeN) + 0.5;
if (nsubregion_col < 0)
nsubregion_col = 0;
if (nsubregion_row < 0)
nsubregion_row = 0;
nsubregions = nsubregion_row * nsubregion_col;
elaboration_reg.south = original_reg.north;
last_row = FALSE;
while (last_row == FALSE) { /* For each row */
P_set_regions(&elaboration_reg, &general_box, &overlap_box, dims,
GENERAL_ROW);
if (elaboration_reg.north > original_reg.north) { /* First row */
P_set_regions(&elaboration_reg, &general_box, &overlap_box, dims,
FIRST_ROW);
}
if (elaboration_reg.south <= original_reg.south) { /* Last row */
P_set_regions(&elaboration_reg, &general_box, &overlap_box, dims,
LAST_ROW);
last_row = TRUE;
}
nsply =
ceil((elaboration_reg.north -
elaboration_reg.south) / stepN) + 0.5;
/*
if (nsply > NSPLY_MAX)
nsply = NSPLY_MAX;
*/
G_debug(1, "nsply = %d", nsply);
elaboration_reg.east = original_reg.west;
last_column = FALSE;
while (last_column == FALSE) { /* For each column */
subregion++;
if (nsubregions > 1)
G_message(_("Processing subregion %d of %d..."), subregion, nsubregions);
else /* v.outlier -e will report mean point distance: */
G_warning(_("No subregions found! Check values for 'ew_step' and 'ns_step' parameters"));
P_set_regions(&elaboration_reg, &general_box, &overlap_box, dims,
GENERAL_COLUMN);
if (elaboration_reg.west < original_reg.west) { /* First column */
P_set_regions(&elaboration_reg, &general_box, &overlap_box,
dims, FIRST_COLUMN);
}
if (elaboration_reg.east >= original_reg.east) { /* Last column */
P_set_regions(&elaboration_reg, &general_box, &overlap_box,
dims, LAST_COLUMN);
last_column = TRUE;
}
nsplx =
ceil((elaboration_reg.east -
elaboration_reg.west) / stepE) + 0.5;
/*
if (nsplx > NSPLX_MAX)
nsplx = NSPLX_MAX;
*/
G_debug(1, "nsplx = %d", nsplx);
/*Setting the active region */
dim_vect = nsplx * nsply;
observ =
P_Read_Vector_Region_Map(&In, &elaboration_reg, &npoints,
dim_vect, 1);
if (npoints > 0) { /* If there is any point falling into elaboration_reg... */
int i;
nparameters = nsplx * nsply;
/* Mean calculation */
mean = P_Mean_Calc(&elaboration_reg, observ, npoints);
/* Least Squares system */
G_debug(1, "Allocation memory for bilinear interpolation");
BW = P_get_BandWidth(P_BILINEAR, nsply); /* Bilinear interpolation */
N = G_alloc_matrix(nparameters, BW); /* Normal matrix */
TN = G_alloc_vector(nparameters); /* vector */
parVect = G_alloc_vector(nparameters); /* Bicubic parameters vector */
obsVect = G_alloc_matrix(npoints, 3); /* Observation vector */
Q = G_alloc_vector(npoints); /* "a priori" var-cov matrix */
lineVect = G_alloc_ivector(npoints);
/* Setting obsVect vector & Q matrix */
for (i = 0; i < npoints; i++) {
obsVect[i][0] = observ[i].coordX;
obsVect[i][1] = observ[i].coordY;
obsVect[i][2] = observ[i].coordZ - mean;
lineVect[i] = observ[i].lineID;
Q[i] = 1; /* Q=I */
}
G_free(observ);
G_verbose_message(_("Bilinear interpolation"));
normalDefBilin(N, TN, Q, obsVect, stepE, stepN, nsplx,
nsply, elaboration_reg.west,
elaboration_reg.south, npoints, nparameters,
BW);
nCorrectGrad(N, lambda, nsplx, nsply, stepE, stepN);
G_math_solver_cholesky_sband(N, parVect, TN, nparameters, BW);
G_free_matrix(N);
G_free_vector(TN);
G_free_vector(Q);
G_verbose_message(_("Outlier detection"));
if (qgis_opt->answer)
P_Outlier(&Out, &Outlier, &Qgis, elaboration_reg,
general_box, overlap_box, obsVect, parVect,
mean, dims.overlap, lineVect, npoints,
driver, table_name);
else
P_Outlier(&Out, &Outlier, NULL, elaboration_reg,
general_box, overlap_box, obsVect, parVect,
mean, dims.overlap, lineVect, npoints,
driver, table_name);
G_free_vector(parVect);
G_free_matrix(obsVect);
G_free_ivector(lineVect);
} /*! END IF; npoints > 0 */
else {
G_free(observ);
G_warning(_("No data within this subregion. "
"Consider increasing spline step values."));
}
} /*! END WHILE; last_column = TRUE */
} /*! END WHILE; last_row = TRUE */
/* Drop auxiliary table */
if (npoints > 0) {
G_debug(1, "%s: Dropping <%s>", argv[0], table_name);
if (P_Drop_Aux_Table(driver, table_name) != DB_OK)
G_fatal_error(_("Auxiliary table could not be dropped"));
}
db_close_database_shutdown_driver(driver);
Vect_close(&In);
Vect_close(&Out);
Vect_close(&Outlier);
if (qgis_opt->answer) {
Vect_build(&Qgis);
Vect_close(&Qgis);
}
G_done_msg(" ");
exit(EXIT_SUCCESS);
} /*END MAIN */
int main(int argc, char **argv)
{
struct GModule *module;
struct Option *voutput_opt, *routput_opt, *color_output_opt, *ply_opt, *zrange_opt, *trim_opt, *rotate_Z_opt,
*smooth_radius_opt, *region_opt, *raster_opt, *zexag_opt, *resolution_opt,
*method_opt, *calib_matrix_opt, *numscan_opt, *trim_tolerance_opt,
*contours_map, *contours_step_opt, *draw_opt, *draw_vector_opt, *draw_threshold_opt;
struct Flag *loop_flag, *calib_flag, *equalize_flag;
struct Map_info Map;
struct line_pnts *Points;
struct line_cats *Cats;
int cat = 1;
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("vector"));
G_add_keyword(_("scan"));
G_add_keyword(_("points"));
module->label = _("Imports a point cloud from Kinect v2");
module->description = _("Imports a point cloud from Kinect v2");
routput_opt = G_define_standard_option(G_OPT_R_OUTPUT);
routput_opt->guisection = _("Output");
routput_opt->required = NO;
resolution_opt = G_define_option();
resolution_opt->key = "resolution";
resolution_opt->type = TYPE_DOUBLE;
resolution_opt->required = NO;
resolution_opt->answer = "0.002";
resolution_opt->label = _("Raster resolution");
resolution_opt->description = _("Recommended values between 0.001-0.003");
resolution_opt->guisection = _("Output");
color_output_opt = G_define_standard_option(G_OPT_R_BASENAME_OUTPUT);
color_output_opt->key = "color_output";
color_output_opt->description = _("Basename for color output");
color_output_opt->guisection = _("Output");
color_output_opt->required = NO;
voutput_opt = G_define_standard_option(G_OPT_V_OUTPUT);
voutput_opt->required = NO;
voutput_opt->key = "vector";
voutput_opt->guisection = _("Output");
ply_opt = G_define_standard_option(G_OPT_F_OUTPUT);
ply_opt->required = NO;
ply_opt->key = "ply";
ply_opt->description = _("Name of output binary PLY file");
ply_opt->guisection = _("Output");
zrange_opt = G_define_option();
zrange_opt->key = "zrange";
zrange_opt->type = TYPE_DOUBLE;
zrange_opt->required = NO;
zrange_opt->key_desc = "min,max";
zrange_opt->label = _("Filter range for z data (min,max)");
zrange_opt->description = _("Z is distance from scanner in cm");
zrange_opt->guisection = _("Filter");
trim_opt = G_define_option();
trim_opt->key = "trim";
trim_opt->type = TYPE_DOUBLE;
trim_opt->required = NO;
trim_opt->key_desc = "N,S,E,W";
trim_opt->description = _("Clip box from center in cm");
trim_opt->guisection = _("Filter");
trim_tolerance_opt = G_define_option();
trim_tolerance_opt->key = "trim_tolerance";
trim_tolerance_opt->type = TYPE_DOUBLE;
trim_tolerance_opt->required = NO;
trim_tolerance_opt->description = _("Influences how much are model sides trimmed automatically, "
" should be higher for rectangular models");
trim_tolerance_opt->label = _("Trim tolerance between 0 and 1");
trim_tolerance_opt->options = "0-1";
trim_tolerance_opt->guisection = _("Filter");
rotate_Z_opt = G_define_option();
rotate_Z_opt->key = "rotate";
rotate_Z_opt->type = TYPE_DOUBLE;
rotate_Z_opt->required = NO;
rotate_Z_opt->answer = "0";
rotate_Z_opt->description = _("Rotate along Z axis");
rotate_Z_opt->guisection = _("Georeferencing");
smooth_radius_opt = G_define_option();
smooth_radius_opt->key = "smooth_radius";
smooth_radius_opt->type = TYPE_DOUBLE;
smooth_radius_opt->required = NO;
smooth_radius_opt->label = _("Smooth radius");
smooth_radius_opt->description = _("Recommended values between 0.006-0.009");
region_opt = G_define_option();
region_opt->key = "region";
region_opt->key_desc = "name";
region_opt->required = NO;
region_opt->multiple = NO;
region_opt->type = TYPE_STRING;
region_opt->description = _("Region of the resulting raster");
region_opt->gisprompt = "old,windows,region";
region_opt->guisection = _("Georeferencing");
raster_opt = G_define_standard_option(G_OPT_R_MAP);
raster_opt->key = "raster";
raster_opt->required = NO;
raster_opt->multiple = NO;
raster_opt->description = _("Match resulting raster to this raster map");
raster_opt->guisection = _("Georeferencing");
zexag_opt = G_define_option();
zexag_opt->key = "zexag";
zexag_opt->type = TYPE_DOUBLE;
zexag_opt->required = NO;
zexag_opt->required = NO;
zexag_opt->answer = "1";
zexag_opt->description = _("Vertical exaggeration");
zexag_opt->guisection = _("Georeferencing");
method_opt = G_define_option();
method_opt->key = "method";
method_opt->multiple = NO;
method_opt->required = NO;
method_opt->type = TYPE_STRING;
method_opt->options = "interpolation,mean,min,max";
method_opt->answer = "mean";
method_opt->description = _("Surface reconstruction method");
calib_matrix_opt = G_define_option();
calib_matrix_opt->key = "calib_matrix";
calib_matrix_opt->multiple = YES;
calib_matrix_opt->type = TYPE_DOUBLE;
calib_matrix_opt->required = NO;
calib_matrix_opt->description = _("Calibration matrix");
calib_matrix_opt->guisection = _("Calibration");
numscan_opt = G_define_option();
numscan_opt->answer = "1";
numscan_opt->key = "numscan";
numscan_opt->type = TYPE_INTEGER;
numscan_opt->description = _("Number of scans to intergrate");
numscan_opt->required = NO;
contours_map = G_define_standard_option(G_OPT_V_MAP);
contours_map->key = "contours";
contours_map->required = NO;
contours_map->description = _("Name of contour vector map");
contours_step_opt = G_define_option();
contours_step_opt->key = "contours_step";
contours_step_opt->description = _("Increment between contour levels");
contours_step_opt->type = TYPE_DOUBLE;
contours_step_opt->required = NO;
equalize_flag = G_define_flag();
equalize_flag->key = 'e';
equalize_flag->description = _("Histogram equalized color table");
loop_flag = G_define_flag();
loop_flag->key = 'l';
loop_flag->description = _("Keep scanning in a loop");
calib_flag = G_define_flag();
calib_flag->key = 'c';
calib_flag->description = _("Calibrate");
calib_flag->guisection = _("Calibration");
draw_opt = G_define_option();
draw_opt->key = "draw";
draw_opt->description = _("Draw with laser pointer");
draw_opt->type = TYPE_STRING;
draw_opt->required = NO;
draw_opt->options = "point,line,area";
draw_opt->answer = "point";
draw_opt->guisection = _("Drawing");
draw_threshold_opt = G_define_option();
draw_threshold_opt->key = "draw_threshold";
draw_threshold_opt->description = _("Brightness threshold for detecting laser pointer");
draw_threshold_opt->type = TYPE_INTEGER;
draw_threshold_opt->required = YES;
draw_threshold_opt->answer = "760";
draw_threshold_opt->guisection = _("Drawing");
draw_vector_opt = G_define_standard_option(G_OPT_V_OUTPUT);
draw_vector_opt->key = "draw_output";
draw_vector_opt->guisection = _("Drawing");
draw_vector_opt->required = NO;
G_option_required(calib_flag, routput_opt, voutput_opt, ply_opt, draw_vector_opt, NULL);
G_option_requires(routput_opt, resolution_opt, NULL);
G_option_requires(color_output_opt, resolution_opt, NULL);
G_option_requires(contours_map, contours_step_opt, routput_opt, NULL);
G_option_requires(equalize_flag, routput_opt, NULL);
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
// initailization of variables
double resolution = 0.002;
if (resolution_opt->answer)
resolution = atof(resolution_opt->answer);
double smooth_radius = 0.008;
if (smooth_radius_opt->answer)
smooth_radius = atof(smooth_radius_opt->answer);
char* routput = NULL;
if (routput_opt->answer)
routput = routput_opt->answer;
/* parse zrange */
double zrange_min, zrange_max;
if (zrange_opt->answer != NULL) {
zrange_min = atof(zrange_opt->answers[0])/100;
zrange_max = atof(zrange_opt->answers[1])/100;
}
/* parse trim */
double clip_N, clip_S, clip_E, clip_W;
if (trim_opt->answer != NULL) {
clip_N = atof(trim_opt->answers[0])/100;
clip_S = atof(trim_opt->answers[1])/100;
clip_E = atof(trim_opt->answers[2])/100;
clip_W = atof(trim_opt->answers[3])/100;
}
double trim_tolerance;
if (trim_tolerance_opt->answer)
trim_tolerance = atof(trim_tolerance_opt->answer);
double angle = pcl::deg2rad(atof(rotate_Z_opt->answer) + 180);
double zexag = atof(zexag_opt->answer);
Eigen::Matrix4f transform_matrix;
if (calib_matrix_opt->answer) {
transform_matrix = read_matrix(calib_matrix_opt);
}
char *method = method_opt->answer;
int numscan = atoi(numscan_opt->answer);
char *color_output = color_output_opt->answer;
char *voutput = voutput_opt->answer;
char *ply = ply_opt->answer;
char *contours_output = contours_map->answer;
double contours_step;
if (contours_output)
contours_step = atof(contours_step_opt->answer);
bool use_equalized = false;
if (equalize_flag->answer)
use_equalized = true;
// drawing
int vect_type;
get_draw_type(draw_opt->answer, vect_type);
int draw_threshold = atoi(draw_threshold_opt->answer);
char* draw_output = NULL;
if (draw_vector_opt->answer)
draw_output = draw_vector_opt->answer;
std::vector<double> draw_x;
std::vector<double> draw_y;
std::vector<double> draw_z;
bool drawing = false;
unsigned int last_detected_loop_count = 1e6;
struct Map_info Map_draw;
struct line_pnts *Points_draw;
struct line_cats *Cats_draw;
Points_draw = Vect_new_line_struct();
Cats_draw = Vect_new_cats_struct();
Points = Vect_new_line_struct();
Cats = Vect_new_cats_struct();
pcl::PointCloud<pcl::PointXYZRGB>::Ptr cloud(new pcl::PointCloud<pcl::PointXYZRGB>(512, 424));
pcl::PointCloud<pcl::PointXYZRGB>::Ptr cloud_filtered_pass (new pcl::PointCloud<pcl::PointXYZRGB>(512, 424));
struct bound_box bbox;
struct Cell_head cellhd, window;
double offset, scale;
bool region3D = false;
bool paused = false;
update_input_region(raster_opt->answer, region_opt->answer, window, offset, region3D);
K2G k2g(OPENGL);
k2g.getCloud();
cloud->sensor_orientation_.w() = 0.0;
cloud->sensor_orientation_.x() = 1.0;
cloud->sensor_orientation_.y() = 0.0;
cloud->sensor_orientation_.z() = 0.0;
int j = 0;
// get terminating signals
signal(SIGTERM, terminate);
signal(SIGINT, terminate);
signal(SIGUSR1, signal_read_new_input);
while (j < 1) {
if (signaled == 1) {
break;
}
if (signal_new_input == 1) {
signal_new_input = 0;
read_new_input(routput, zrange_min, zrange_max, clip_N, clip_S, clip_E, clip_W,
trim_tolerance, angle, zexag, method, numscan, smooth_radius, resolution, use_equalized,
window, offset, region3D,
color_output, voutput, ply,
contours_output, contours_step,
vect_type, draw_threshold, draw_output, paused);
}
cloud = k2g.getCloud();
if (paused) {
continue;
}
if (!drawing) {
for (int s = 0; s < numscan - 1; s++)
*(cloud) += *(k2g.getCloud());
}
// remove invalid points
std::vector<int> index_nans;
pcl::removeNaNFromPointCloud(*cloud, *cloud, index_nans);
// calibration
if(calib_flag->answer) {
calibrate(cloud);
j++;
continue;
}
// rotation of the point cloud based on calibration
if (calib_matrix_opt->answer) {
rotate_with_matrix(cloud, transform_matrix);
}
// trim Z
if (zrange_opt->answer != NULL) {
trim_Z(cloud, zrange_min, zrange_max);
}
// rotation Z
rotate_Z(cloud, angle);
// specify bounding box from center
if (trim_opt->answer != NULL) {
clipNSEW(cloud, clip_N, clip_S, clip_E, clip_W);
}
// drawing
if (draw_output) {
int maxbright = 0;
int maxbright_idx = 0;
for (int i=0; i < cloud->points.size(); i++) {
Eigen::Vector3i rgbv = cloud->points[i].getRGBVector3i();
int sum = rgbv[0] + rgbv[1] + rgbv[2];
if (sum > maxbright) {
maxbright = sum;
maxbright_idx = i;
}
}
if (maxbright >= draw_threshold) {
drawing = true;
draw_x.push_back(cloud->points[maxbright_idx].x);
draw_y.push_back(cloud->points[maxbright_idx].y);
draw_z.push_back(cloud->points[maxbright_idx].z);
last_detected_loop_count = 0;
continue;
}
else {
last_detected_loop_count++;
if (last_detected_loop_count <= 2) {
continue;
}
}
}
pcl::StatisticalOutlierRemoval<pcl::PointXYZRGB> sor;
sor.setInputCloud(cloud);
sor.setMeanK(20);
sor.setStddevMulThresh(0.5);
sor.filter(*cloud_filtered_pass);
cloud_filtered_pass.swap (cloud);
if (trim_tolerance_opt->answer != NULL) {
double autoclip_N, autoclip_S, autoclip_E, autoclip_W;
autotrim(cloud, autoclip_N, autoclip_S, autoclip_E, autoclip_W, trim_tolerance);
if (autoclip_E > 0 || autoclip_N > 0 || autoclip_S > 0 || autoclip_W > 0)
trimNSEW(cloud, autoclip_N, autoclip_S, autoclip_E, autoclip_W);
}
if (drawing) {
// get Z scaling
getMinMax(*cloud, bbox);
if ((vect_type == GV_AREA && draw_x.size() > 2) ||
(vect_type == GV_LINE && draw_x.size() > 1) ||
(vect_type == GV_POINT && draw_x.size() > 0)) {
save_vector(draw_output, Map_draw, Points_draw, Cats_draw,
bbox, window, draw_x, draw_y, draw_z, vect_type, offset, zexag);
}
else
G_warning(_("Tolopogically incorrect vector feature"));
drawing = false;
draw_x.clear();
draw_y.clear();
draw_z.clear();
last_detected_loop_count = 1e6;
}
if (voutput|| routput || ply || color_output) {
if (smooth_radius_opt->answer)
smooth(cloud, smooth_radius);
// get Z scaling
getMinMax(*cloud, bbox);
scale = ((window.north - window.south) / (bbox.N - bbox.S) +
(window.east - window.west) / (bbox.E - bbox.W)) / 2;
}
// write to vector
if (voutput|| (routput && strcmp(method, "interpolation") == 0)) {
double z;
if (voutput) {
if (Vect_open_new(&Map, voutput, WITH_Z) < 0)
G_fatal_error(_("Unable to create temporary vector map <%s>"), voutput);
}
else {
if (Vect_open_tmp_new(&Map, routput, WITH_Z) < 0)
G_fatal_error(_("Unable to create temporary vector map <%s>"), routput);
}
for (int i=0; i < cloud->points.size(); i++) {
Vect_reset_line(Points);
Vect_reset_cats(Cats);
if (region3D)
z = (cloud->points[i].z + zrange_max) * scale / zexag + offset;
else
z = (cloud->points[i].z - bbox.B) * scale / zexag + offset;
Vect_append_point(Points, cloud->points[i].x,
cloud->points[i].y,
z);
Vect_cat_set(Cats, 1, cat);
Vect_write_line(&Map, GV_POINT, Points, Cats);
}
if (strcmp(method, "interpolation") == 0) {
// interpolate
Vect_rewind(&Map);
interpolate(&Map, routput, 20, 2, 50, 40, -1,
&bbox, resolution);
}
Vect_close(&Map);
}
if (routput || color_output) {
if (routput) {
if (strcmp(method, "interpolation") != 0) {
binning(cloud, routput, &bbox, resolution,
scale, zexag, region3D ? -zrange_max : bbox.B, offset, method);
}
Rast_get_cellhd(routput, "", &cellhd);
}
if (color_output) {
binning_color(cloud, color_output, &bbox, resolution);
Rast_get_cellhd(get_color_name(color_output, "r"), "", &cellhd);
}
// georeference horizontally
window.rows = cellhd.rows;
window.cols = cellhd.cols;
G_adjust_Cell_head(&window, 1, 1);
cellhd.north = window.north;
cellhd.south = window.south;
cellhd.east = window.east;
cellhd.west = window.west;
if (routput)
Rast_put_cellhd(routput, &cellhd);
if (color_output) {
char* output_r = get_color_name(color_output, "r");
char* output_g = get_color_name(color_output, "g");
char* output_b = get_color_name(color_output, "b");
Rast_put_cellhd(output_r, &cellhd);
Rast_put_cellhd(output_g, &cellhd);
Rast_put_cellhd(output_b, &cellhd);
}
set_default_color(routput);
if (contours_output) {
contours(routput, contours_output, atof(contours_step_opt->answer));
}
if (use_equalized) {
equalized(routput);
}
}
// write to PLY
if (ply) {
pcl::PLYWriter writer;
for (int i=0; i < cloud->points.size(); i++) {
if (region3D)
cloud->points[i].z = (cloud->points[i].z + zrange_max) * scale / zexag + offset;
else
cloud->points[i].z = (cloud->points[i].z - bbox.B) * scale / zexag + offset;
cloud->points[i].x = (cloud->points[i].x - bbox.W) * scale + window.west;
cloud->points[i].y = (cloud->points[i].y - bbox.S) * scale + window.south;
}
writer.write<pcl::PointXYZRGB>(ply, *cloud, true, true);
}
if (!loop_flag->answer)
j++;
}
k2g.shutDown();
return EXIT_SUCCESS;
}
