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Memory optimizations
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@jonasteuwen
jonasteuwen committed Aug 13, 2024
1 parent 19d644d commit 4943171
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Showing 2 changed files with 22 additions and 60 deletions.
21 changes: 14 additions & 7 deletions meson.build
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
project('dlup', 'cpp', 'cython',
version : '0.7.0',
default_options : ['warning_level=3', 'cpp_std=c++17'])
default_options : ['buildtype=release', 'warning_level=3', 'cpp_std=c++17'])

cpp_args = ['-O3', '-march=native', '-ffast-math', '-funroll-loops', '-flto', '-pipe', '-fomit-frame-pointer']
link_args = ['-flto']

b_unity = true


### Includes ####
Expand Down Expand Up @@ -62,29 +67,31 @@ _background = py.extension_module('_background',
include_directories : [incdir_numpy],
install : true,
subdir : '',
cpp_args : ['-O3', '-march=native', '-ffast-math'])
link_args : link_args,
cpp_args : cpp_args)

# Define the base dependencies and compiler arguments
base_deps = [libtiff_dep]
base_cpp_args = ['-std=c++17', '-O3', '-march=native', '-ffast-math']

# Add ZSTD support if available
base_deps = [libtiff_dep]
if have_zstd
base_deps += [zstd_dep]
base_cpp_args += ['-DHAVE_ZSTD']
cpp_args += ['-DHAVE_ZSTD']
endif

# tiff writer extension
_libtiff_tiff_writer = py.extension_module('_libtiff_tiff_writer',
'src/libtiff_tiff_writer.cpp',
include_directories : [incdir_pybind11],
install : true,
cpp_args : base_cpp_args,
cpp_args : cpp_args,
link_args : link_args,
dependencies : base_deps)

_geometry = py.extension_module('_geometry',
'src/geometry.cpp',
include_directories : [incdir_pybind11],
install : true,
cpp_args : base_cpp_args,
cpp_args : cpp_args,
link_args : link_args,
dependencies : base_deps + boost_dep + opencv_dep)
61 changes: 8 additions & 53 deletions src/geometry.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,8 @@ class Polygon : public BaseGeometry {

Polygon() : polygon(std::make_shared<BoostPolygon>()) {}
Polygon(const BoostPolygon &p) : polygon(std::make_shared<BoostPolygon>(p)) {}
// This doesn't work, but is probably
// Polygon(BoostPolygon &&p) : polygon(std::make_shared<BoostPolygon>(std::move(p))) {}
Polygon(std::shared_ptr<BoostPolygon> p) : polygon(p) {}

Polygon(const std::vector<std::pair<double, double>> &exterior,
Expand All @@ -154,6 +156,7 @@ class Polygon : public BaseGeometry {

std::vector<std::pair<double, double>> Polygon::getExterior() const {
std::vector<std::pair<double, double>> result;
result.reserve(bg::exterior_ring(*polygon).size());
for (const auto &point : bg::exterior_ring(*polygon)) {
result.emplace_back(bg::get<0>(point), bg::get<1>(point));
}
Expand All @@ -162,6 +165,7 @@ std::vector<std::pair<double, double>> Polygon::getExterior() const {

std::vector<std::vector<std::pair<double, double>>> Polygon::getInteriors() const {
std::vector<std::vector<std::pair<double, double>>> result;
result.reserve(polygon->inners().size());
for (const auto &inner : polygon->inners()) {
std::vector<std::pair<double, double>> inner_result;
for (const auto &point : inner) {
Expand All @@ -174,6 +178,7 @@ std::vector<std::vector<std::pair<double, double>>> Polygon::getInteriors() cons

void Polygon::setExterior(const std::vector<std::pair<double, double>> &coordinates) {
bg::exterior_ring(*polygon).clear();
bg::exterior_ring(*polygon).reserve(coordinates.size());
for (const auto &coord : coordinates) {
bg::append(*polygon, BoostPoint(coord.first, coord.second));
}
Expand All @@ -185,6 +190,7 @@ void Polygon::setExterior(const std::vector<std::pair<double, double>> &coordina

void Polygon::setInteriors(const std::vector<std::vector<std::pair<double, double>>> &interiors) {
bg::interior_rings(*polygon).clear();
bg::exterior_ring(*polygon).reserve(interiors.size());
polygon->inners().resize(interiors.size());
for (size_t i = 0; i < interiors.size(); ++i) {
const auto &interior_coords = interiors[i];
Expand Down Expand Up @@ -249,8 +255,8 @@ class Point : public BaseGeometry {
bg::set<1>(*point, y);
}
std::pair<double, double> getCoordinates() const { return std::make_pair(bg::get<0>(*point), bg::get<1>(*point)); }
double getX() const { return bg::get<0>(*point); }
double getY() const { return bg::get<1>(*point); }
inline double getX() const { return bg::get<0>(*point); }
inline double getY() const { return bg::get<1>(*point); }
double distanceTo(const Point &other) const { return bg::distance(*point, *(other.point)); }
bool equals(const Point &other) const { return bg::equals(*point, *(other.point)); }
bool within(const Polygon &polygon) const { return bg::within(*point, *(polygon.polygon)); }
Expand Down Expand Up @@ -346,57 +352,6 @@ cv::Mat generateMaskFromAnnotations(const std::vector<std::shared_ptr<Polygon>>
return mask;
}

// cv::Mat generateMaskFromAnnotations(const std::vector<std::shared_ptr<Polygon>> &annotations, cv::Size region_size,
// const std::unordered_map<std::string, int> &index_map, int default_value) {
// // Create the mask and initialize with the default value
// cv::Mat mask(region_size, CV_32S, cv::Scalar(default_value));

// for (const auto &annotation : annotations) {
// // Extract the label and map it to an index value
// int index_value = index_map.at(annotation->getField("label")->cast<std::string>());

// // Convert the exterior and interiors to OpenCV points
// std::vector<cv::Point> exterior_cv_points;
// for (const auto &[x, y] : annotation->getExterior()) {
// exterior_cv_points.emplace_back(static_cast<int>(std::round(x)), static_cast<int>(std::round(y)));
// }

// std::vector<std::vector<cv::Point>> interiors_cv_points;
// for (const auto &interior : annotation->getInteriors()) {
// std::vector<cv::Point> interior_cv;
// for (const auto &[x, y] : interior) {
// interior_cv.emplace_back(static_cast<int>(std::round(x)), static_cast<int>(std::round(y)));
// }
// interiors_cv_points.push_back(std::move(interior_cv));
// }

// // Backup original mask values where holes will be drawn
// cv::Mat original_values = mask.clone();
// cv::Mat holes_mask = cv::Mat::zeros(region_size, CV_8U);
// if (!interiors_cv_points.empty()) {
// cv::fillPoly(holes_mask, interiors_cv_points, cv::Scalar(1));
// }

// #ifdef DLUPDEBUG
// // Debug: Check matrix types and sizes before the setTo operation
// std::cout << "mask type: " << mask.type() << ", size: " << mask.size << std::endl;
// std::cout << "original_values type: " << original_values.type() << ", size: " << original_values.size <<
// std::endl; std::cout << "holes_mask type: " << holes_mask.type() << ", size: " << holes_mask.size <<
// std::endl;
// #endif

// // Fill the exterior polygon in the mask
// cv::fillPoly(mask, std::vector<std::vector<cv::Point>>{exterior_cv_points}, cv::Scalar(index_value));

// // If interiors exist, reset the holes in the mask using the backup
// if (!interiors_cv_points.empty()) {
// original_values.copyTo(mask, holes_mask);

// }
// }

// return mask;
// }

py::array_t<int> maskToPyArray(const cv::Mat &mask) {
// Ensure the mask is of type CV_32S (int type)
Expand Down

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