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Option to crop interest zone and filter min dbh trees #22

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Option to crop interest zone and filter min dbh trees #22

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3b0a861
Option to crop interest zone and filter min dbh trees
GabijaBern Nov 6, 2024
10fcc4a
Copying Tom's ideas
GabijaBern Nov 20, 2024
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65 changes: 45 additions & 20 deletions raycloudtools/rayextract/rayextract.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@
// Author: Thomas Lowe
#include "raylib/extraction/rayclusters.h"
#include "raylib/extraction/rayforest.h"
#include "raylib/extraction/rayleaves.h"
#include "raylib/extraction/rayterrain.h"
#include "raylib/extraction/raytrees.h"
#include "raylib/extraction/raytrunks.h"
#include "raylib/extraction/rayleaves.h"
#include "raylib/raycloud.h"
#include "raylib/rayforestgen.h"
#include "raylib/rayforeststructure.h"
Expand All @@ -25,7 +25,8 @@ static std::string extract_type;

void usage(int exit_code = 1)
{
const bool none = extract_type != "terrain" && extract_type != "trunks" && extract_type != "forest" && extract_type != "trees" && extract_type != "leaves";
const bool none = extract_type != "terrain" && extract_type != "trunks" && extract_type != "forest" &&
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extract_type != "trees" && extract_type != "leaves";
// clang-format off
std::cout << "Extract natural features into a text file or mesh file" << std::endl;
std::cout << "usage:" << std::endl;
Expand Down Expand Up @@ -54,19 +55,22 @@ void usage(int exit_code = 1)
std::cout << " --max_diameter 0.9 - (-m) maximum trunk diameter in segmenting trees" << std::endl;
std::cout << " --crop_length 1.0 - (-p) crops small branches to this distance from end" << std::endl;
std::cout << " --distance_limit 1 - (-d) maximum distance between neighbour points in a tree" << std::endl;
std::cout << " --height_min 2 - (-h) minimum height counted as a tree" << std::endl;
std::cout << " --height_min 2 - (-h) minimum height tree to reconstruct" << std::endl;
std::cout << " --radius_min 0 - (-r) minimum radius tree to reconstruct" << std::endl;
std::cout << " --girth_height_ratio 0.12 - (-i) the amount up tree's height to estimate trunk girth" << std::endl;
std::cout << " --global_taper 0.024 - (-a) force a taper value (diameter per length) for trees under global_taper_factor of max tree height. Use 0 to estimate global taper from the data" << std::endl;
std::cout << " --global_taper_factor 0.3- (-o) 1 estimates same taper for whole scan, 0 is per-tree tapering. Like a soft cutoff at this amount of max tree height" << std::endl;
std::cout << " --gravity_factor 0.3 - (-f) larger values preference vertical trees" << std::endl;
std::cout << " --branch_segmentation- (-b) _segmented.ply is per branch segment" << std::endl;
std::cout << " --grid_width 10 - (-w) crops results assuming cloud has been gridded with given width" << std::endl;
std::cout << " --use_rays - (-u) use rays to reduce trunk radius overestimation in noisy cloud data" << std::endl;
std::cout << " (for internal constants -c -g -s see source file rayextract)" << std::endl;
std::cout << " (for internal constants -c -g -s -d see source file rayextract)" << std::endl;
// These are the internal parameters that I don't expose as they are 'advanced' only, you shouldn't need to adjust them
// std::cout << " --cylinder_length_to_width 4- (-c) how slender the cylinders are" << std::endl;
// std::cout << " --gap_ratio 0.016 - (-g) will split for lateral gaps at this multiple of branch length" << std::endl;
// std::cout << " --span_ratio 4.5 - (-s) will split when branch width spans this multiple of radius" << std::endl;
// std::cout << " --grid_origin 0,0 - (-d) location of grid corner (any of them) when grid_width used, use 0,0 for grid with vertex at 0,0.
// Default is -grid_width/2,-grid_width/2 to match the grid in raysplit grid" << std::endl;
}
if (extract_type == "leaves" || none)
{
Expand Down Expand Up @@ -96,24 +100,29 @@ int rayExtract(int argc, char *argv[])
ray::OptionalKeyValueArgument trunks_option("trunks", 't', &trunks_file);
ray::DoubleArgument gradient(0.001, 1000.0, 1.0), global_taper(0.0, 1.0), global_taper_factor(0.0, 1.0);
ray::OptionalKeyValueArgument gradient_option("gradient", 'g', &gradient);
ray::OptionalFlagArgument exclude_rays("exclude_rays", 'e'), segment_branches("branch_segmentation", 'b'), stalks("stalks", 's'), use_rays("use_rays", 'u');
ray::OptionalFlagArgument exclude_rays("exclude_rays", 'e'), segment_branches("branch_segmentation", 'b'),
stalks("stalks", 's'), use_rays("use_rays", 'u');
ray::DoubleArgument width(0.01, 10.0, 0.25), drop(0.001, 1.0), max_gradient(0.01, 5.0), min_gradient(0.01, 5.0);

ray::DoubleArgument max_diameter(0.01, 100.0), distance_limit(0.01, 10.0), height_min(0.01, 1000.0),
min_diameter(0.01, 100.0), leaf_area(0.00001, 1.0, 0.002), leaf_droop(0.0, 10.0, 0.1), crop_length(0.01, 100.0);;
ray::DoubleArgument girth_height_ratio(0.001, 0.5), length_to_radius(0.01, 10000.0), cylinder_length_to_width(0.1, 20.0), gap_ratio(0.01, 10.0),
span_ratio(0.01, 10.0);
ray::DoubleArgument gravity_factor(0.0, 100.0), grid_width(1.0, 100000.0),
grid_overlap(0.0, 0.9);
radius_min(0.0, 1000.0), min_diameter(0.01, 100.0), leaf_area(0.00001, 1.0, 0.002), leaf_droop(0.0, 10.0, 0.1),
crop_length(0.01, 100.0);
;
ray::DoubleArgument girth_height_ratio(0.001, 0.5), length_to_radius(0.01, 10000.0),
cylinder_length_to_width(0.1, 20.0), gap_ratio(0.01, 10.0), span_ratio(0.01, 10.0);
ray::DoubleArgument gravity_factor(0.0, 100.0), grid_width(1.0, 100000.0), grid_overlap(0.0, 0.9);
ray::Vector2dArgument grid_origin(-1e10, 1e10);
ray::OptionalKeyValueArgument max_diameter_option("max_diameter", 'm', &max_diameter);
ray::OptionalKeyValueArgument crop_length_option("crop_length", 'n', &crop_length);
ray::OptionalKeyValueArgument distance_limit_option("distance_limit", 'd', &distance_limit);
ray::OptionalKeyValueArgument height_min_option("height_min", 'h', &height_min);
ray::OptionalKeyValueArgument radius_min_option("radius_min", 'r', &radius_min);
ray::OptionalKeyValueArgument girth_height_ratio_option("girth_height_ratio", 'i', &girth_height_ratio);
ray::OptionalKeyValueArgument cylinder_length_to_width_option("cylinder_length_to_width", 'c',
&cylinder_length_to_width);
ray::OptionalKeyValueArgument gap_ratio_option("gap_ratio", 'g', &gap_ratio);
ray::OptionalKeyValueArgument span_ratio_option("span_ratio", 's', &span_ratio);
ray::OptionalKeyValueArgument grid_origin_option("grid_origin", 'd', &grid_origin);
ray::OptionalKeyValueArgument gravity_factor_option("gravity_factor", 'f', &gravity_factor);
ray::OptionalKeyValueArgument grid_width_option("grid_width", 'w', &grid_width);
ray::OptionalKeyValueArgument global_taper_option("global_taper", 'a', &global_taper);
Expand All @@ -135,10 +144,12 @@ int rayExtract(int argc, char *argv[])
{ &groundmesh_option, &trunks_option, &width_option, &smooth_option, &drop_option, &verbose });
bool extract_trees = ray::parseCommandLine(
argc, argv, { &trees, &cloud_file, &mesh_file },
{ &max_diameter_option, &distance_limit_option, &height_min_option, &crop_length_option, &girth_height_ratio_option,
&cylinder_length_to_width_option, &gap_ratio_option, &span_ratio_option, &gravity_factor_option,
&segment_branches, &grid_width_option, &global_taper_option, &global_taper_factor_option, &use_rays, &verbose });
bool extract_leaves = ray::parseCommandLine(argc, argv, { &leaves, &cloud_file, &trees_file }, { &leaf_option, &leaf_area_option, &leaf_droop_option, &stalks });
{ &max_diameter_option, &distance_limit_option, &height_min_option, &radius_min_option, &crop_length_option,
&girth_height_ratio_option, &cylinder_length_to_width_option, &gap_ratio_option, &span_ratio_option,
&grid_origin_option, &gravity_factor_option, &segment_branches, &grid_width_option, &global_taper_option,
&global_taper_factor_option, &use_rays, &verbose });
bool extract_leaves = ray::parseCommandLine(argc, argv, { &leaves, &cloud_file, &trees_file },
{ &leaf_option, &leaf_area_option, &leaf_droop_option, &stalks });


if (!extract_trunks && !extract_forest && !extract_terrain && !extract_trees && !extract_leaves)
Expand Down Expand Up @@ -191,6 +202,10 @@ int rayExtract(int argc, char *argv[])
{
params.height_min = height_min.value();
}
if (radius_min_option.isSet())
{
params.radius_min = radius_min.value();
}
if (crop_length_option.isSet())
{
params.crop_length = crop_length.value();
Expand Down Expand Up @@ -218,6 +233,12 @@ int rayExtract(int argc, char *argv[])
if (grid_width_option.isSet())
{
params.grid_width = grid_width.value();
params.grid_origin =
-Eigen::Vector2d(grid_width.value(), grid_width.value()) / 2.0; // the centred grid used by raysplit grid
}
if (grid_origin_option.isSet())
{
params.grid_origin = grid_origin.value();
}
if (global_taper_option.isSet())
{
Expand All @@ -226,8 +247,8 @@ int rayExtract(int argc, char *argv[])
if (global_taper_factor_option.isSet())
{
params.global_taper_factor = global_taper_factor.value();
}
params.use_rays = use_rays.isSet();
}
params.use_rays = use_rays.isSet();
params.segment_branches = segment_branches.isSet();

ray::Trees trees(cloud, offset, mesh, params, verbose.isSet());
Expand All @@ -243,11 +264,15 @@ int rayExtract(int argc, char *argv[])
ray::ForestStructure forest;
if (!forest.load(cloud_file.nameStub() + "_trees.txt"))
{
usage();
std::cerr << "Unable to load "
<< cloud_file.nameStub() +
"_trees.txt to generate tree mesh file, this could mean that there were no trees output"
<< std::endl;
exit(true);
}
ray::Mesh tree_mesh;
forest.generateSmoothMesh(tree_mesh, -1, 1, 1, 1);
ray::writePlyMesh(cloud_file.nameStub() + "_trees_mesh.ply", tree_mesh, true);
ray::writePlyMesh(cloud_file.nameStub() + "_trees_mesh.ply", tree_mesh, true);
}
// extract the tree locations from a larger, aerial view of a forest
else if (extract_forest)
Expand Down Expand Up @@ -305,8 +330,8 @@ int rayExtract(int argc, char *argv[])
}
else if (extract_leaves)
{
ray::generateLeaves(cloud_file.nameStub(), trees_file.name(), leaf_file.name(),
leaf_area.value(), leaf_droop.value(), stalks.isSet());
ray::generateLeaves(cloud_file.nameStub(), trees_file.name(), leaf_file.name(), leaf_area.value(),
leaf_droop.value(), stalks.isSet());
}
else
{
Expand Down
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