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added variable cluster finder

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This commit is contained in:
Erik Fröjdh 2024-10-30 17:22:57 +01:00
parent dde92b993f
commit a466887064
5 changed files with 109 additions and 62 deletions
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2
include/aare/VarClusterFinder.hpp
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@ -49,7 +49,7 @@ template <typename T> class VarClusterFinder {
int check_neighbours(int i, int j); int check_neighbours(int i, int j);
public: public:
VarClusterFinder(image_shape shape, T threshold) VarClusterFinder(Shape<2> shape, T threshold)
: shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0), binary_(shape), threshold_(threshold) { : shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0), binary_(shape), threshold_(threshold) {
hits.reserve(2000); hits.reserve(2000);
} }

1
python/aare/__init__.py
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@ -1,2 +1,3 @@
# Make the compiled classes that live in _aare available from aare. # Make the compiled classes that live in _aare available from aare.
from ._aare import File from ._aare import File
from ._aare import VarClusterFinder

2
python/src/module.cpp
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@ -1,5 +1,6 @@
#include "file.hpp" #include "file.hpp"
#include "var_cluster.hpp"
#include <pybind11/pybind11.h> #include <pybind11/pybind11.h>
#include <pybind11/stl.h> #include <pybind11/stl.h>
@ -11,4 +12,5 @@ PYBIND11_MODULE(_aare, m) {
define_file_io_bindings(m); define_file_io_bindings(m);
define_var_cluster_finder_bindings(m);
} }

121
python/src/np_helper.hpp
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@ -7,36 +7,37 @@
#include "aare/Frame.hpp" #include "aare/Frame.hpp"
#include "aare/NDArray.hpp" #include "aare/NDArray.hpp"
#include "aare/NDView.hpp"
namespace py = pybind11; namespace py = pybind11;
// Pass image data back to python as a numpy array // Pass image data back to python as a numpy array
// template <typename T, ssize_t Ndim> template <typename T, int64_t Ndim>
// py::array return_image_data(pl::ImageData<T, Ndim> *image) { py::array return_image_data(aare::NDArray<T, Ndim> *image) {
// py::capsule free_when_done(image, [](void *f) { py::capsule free_when_done(image, [](void *f) {
// pl::ImageData<T, Ndim> *foo = aare::NDArray<T, Ndim> *foo =
// reinterpret_cast<pl::ImageData<T, Ndim> *>(f); reinterpret_cast<aare::NDArray<T, Ndim> *>(f);
// delete foo; delete foo;
// }); });
// return py::array_t<T>( return py::array_t<T>(
// image->shape(), // shape image->shape(), // shape
// image->byte_strides(), // C-style contiguous strides for double image->byte_strides(), // C-style contiguous strides for double
// image->data(), // the data pointer image->data(), // the data pointer
// free_when_done); // numpy array references this parent free_when_done); // numpy array references this parent
// } }
// template <typename T> py::array return_vector(std::vector<T> *vec) { template <typename T> py::array return_vector(std::vector<T> *vec) {
// py::capsule free_when_done(vec, [](void *f) { py::capsule free_when_done(vec, [](void *f) {
// std::vector<T> *foo = reinterpret_cast<std::vector<T> *>(f); std::vector<T> *foo = reinterpret_cast<std::vector<T> *>(f);
// delete foo; delete foo;
// }); });
// return py::array_t<T>({vec->size()}, // shape return py::array_t<T>({vec->size()}, // shape
// {sizeof(T)}, // C-style contiguous strides for double {sizeof(T)}, // C-style contiguous strides for double
// vec->data(), // the data pointer vec->data(), // the data pointer
// free_when_done); // numpy array references this parent free_when_done); // numpy array references this parent
// } }
// template <typename Reader> py::array do_read(Reader &r, size_t n_frames) { // template <typename Reader> py::array do_read(Reader &r, size_t n_frames) {
// py::array image; // py::array image;
@ -62,54 +63,54 @@ namespace py = pybind11;
// return image; // return image;
// } // }
py::array return_frame(pl::Frame *ptr) { // py::array return_frame(pl::Frame *ptr) {
py::capsule free_when_done(ptr, [](void *f) { // py::capsule free_when_done(ptr, [](void *f) {
pl::Frame *foo = reinterpret_cast<pl::Frame *>(f); // pl::Frame *foo = reinterpret_cast<pl::Frame *>(f);
delete foo; // delete foo;
}); // });
const uint8_t item_size = ptr->bytes_per_pixel(); // const uint8_t item_size = ptr->bytes_per_pixel();
std::vector<ssize_t> shape; // std::vector<ssize_t> shape;
for (auto val : ptr->shape()) // for (auto val : ptr->shape())
if (val > 1) // if (val > 1)
shape.push_back(val); // shape.push_back(val);
std::vector<ssize_t> strides; // std::vector<ssize_t> strides;
if (shape.size() == 1) // if (shape.size() == 1)
strides.push_back(item_size); // strides.push_back(item_size);
else if (shape.size() == 2) { // else if (shape.size() == 2) {
strides.push_back(item_size * shape[1]); // strides.push_back(item_size * shape[1]);
strides.push_back(item_size); // strides.push_back(item_size);
} // }
if (item_size == 1) // if (item_size == 1)
return py::array_t<uint8_t>( // return py::array_t<uint8_t>(
shape, strides, // shape, strides,
reinterpret_cast<uint8_t *>(ptr->data()), free_when_done); // reinterpret_cast<uint8_t *>(ptr->data()), free_when_done);
else if (item_size == 2) // else if (item_size == 2)
return py::array_t<uint16_t>(shape, strides, // return py::array_t<uint16_t>(shape, strides,
reinterpret_cast<uint16_t *>(ptr->data()), // reinterpret_cast<uint16_t *>(ptr->data()),
free_when_done); // free_when_done);
else if (item_size == 4) // else if (item_size == 4)
return py::array_t<uint32_t>(shape, strides, // return py::array_t<uint32_t>(shape, strides,
reinterpret_cast<uint32_t *>(ptr->data()), // reinterpret_cast<uint32_t *>(ptr->data()),
free_when_done); // free_when_done);
return {}; // return {};
} // }
// todo rewrite generic // todo rewrite generic
template <class T, int Flags> auto get_shape_3d(py::array_t<T, Flags> arr) { template <class T, int Flags> auto get_shape_3d(py::array_t<T, Flags> arr) {
return pl::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)}; return aare::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)};
} }
template <class T, int Flags> auto make_span_3d(py::array_t<T, Flags> arr) { template <class T, int Flags> auto make_view_3d(py::array_t<T, Flags> arr) {
return pl::DataSpan<T, 3>(arr.mutable_data(), get_shape_3d<T, Flags>(arr)); return aare::NDView<T, 3>(arr.mutable_data(), get_shape_3d<T, Flags>(arr));
} }
template <class T, int Flags> auto get_shape_2d(py::array_t<T, Flags> arr) { template <class T, int Flags> auto get_shape_2d(py::array_t<T, Flags> arr) {
return pl::Shape<2>{arr.shape(0), arr.shape(1)}; return aare::Shape<2>{arr.shape(0), arr.shape(1)};
} }
template <class T, int Flags> auto make_span_2d(py::array_t<T, Flags> arr) { template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags> arr) {
return pl::DataSpan<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr)); return aare::NDView<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr));
} }

43
python/src/var_cluster.hpp Normal file
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@ -0,0 +1,43 @@
#include "aare/VarClusterFinder.hpp"
#include "np_helper.hpp"
// #include "aare/defs.hpp"
// #include "aare/fClusterFileV2.hpp"
#include <cstdint>
// #include <filesystem>
#include <pybind11/numpy.h>
// #include <pybind11/iostream.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
// #include <pybind11/stl/filesystem.h>
// #include <string>
namespace py = pybind11;
using namespace::aare;
void define_var_cluster_finder_bindings(py::module &m) {
py::class_<VarClusterFinder<double>>(m, "VarClusterFinder")
.def(py::init<Shape<2>, double>())
.def("labeled",
[](VarClusterFinder<double> &self) {
auto ptr = new NDArray<int, 2>(self.labeled());
return return_image_data(ptr);
})
.def("find_clusters",
[](VarClusterFinder<double> &self,
py::array_t<double, py::array::c_style | py::array::forcecast>
img) {
auto view = make_view_2d(img);
self.find_clusters(view);
})
.def("steal_hits",
[](VarClusterFinder<double> &self) {
auto ptr = new std::vector<VarClusterFinder<double>::Hit>(
self.steal_hits());
return return_vector(ptr);
})
.def("total_clusters", &VarClusterFinder<double>::total_clusters);
}