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Added fitting with lmfit (#128)

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- added stand alone fitting using:
https://jugit.fz-juelich.de/mlz/lmfit.git
- fit_gaus, fit_pol1 with and without errors
- multi threaded fitting

---------

Co-authored-by: JulianHeymes <julian.heymes@psi.ch>
This commit is contained in:
Erik Fröjdh
2025-02-12 16:35:48 +01:00
committed by GitHub
parent c0c5e07ad8
commit 7309cff47c
18 changed files with 893 additions and 160 deletions
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66
python/src/np_helper.hpp
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@ -39,65 +39,6 @@ template <typename T> py::array return_vector(std::vector<T> *vec) {
free_when_done); // numpy array references this parent
}
// template <typename Reader> py::array do_read(Reader &r, size_t n_frames) {
// py::array image;
// if (n_frames == 0)
// n_frames = r.total_frames();
// std::array<ssize_t, 3> shape{static_cast<ssize_t>(n_frames), r.rows(),
// r.cols()};
// const uint8_t item_size = r.bytes_per_pixel();
// if (item_size == 1) {
// image = py::array_t<uint8_t, py::array::c_style | py::array::forcecast>(
// shape);
// } else if (item_size == 2) {
// image =
// py::array_t<uint16_t, py::array::c_style | py::array::forcecast>(
// shape);
// } else if (item_size == 4) {
// image =
// py::array_t<uint32_t, py::array::c_style | py::array::forcecast>(
// shape);
// }
// r.read_into(reinterpret_cast<std::byte *>(image.mutable_data()), n_frames);
// return image;
// }
// py::array return_frame(pl::Frame *ptr) {
// py::capsule free_when_done(ptr, [](void *f) {
// pl::Frame *foo = reinterpret_cast<pl::Frame *>(f);
// delete foo;
// });
// const uint8_t item_size = ptr->bytes_per_pixel();
// std::vector<ssize_t> shape;
// for (auto val : ptr->shape())
// if (val > 1)
// shape.push_back(val);
// std::vector<ssize_t> strides;
// if (shape.size() == 1)
// strides.push_back(item_size);
// else if (shape.size() == 2) {
// strides.push_back(item_size * shape[1]);
// strides.push_back(item_size);
// }
// if (item_size == 1)
// return py::array_t<uint8_t>(
// shape, strides,
// reinterpret_cast<uint8_t *>(ptr->data()), free_when_done);
// else if (item_size == 2)
// return py::array_t<uint16_t>(shape, strides,
// reinterpret_cast<uint16_t *>(ptr->data()),
// free_when_done);
// else if (item_size == 4)
// return py::array_t<uint32_t>(shape, strides,
// reinterpret_cast<uint32_t *>(ptr->data()),
// free_when_done);
// return {};
// }
// todo rewrite generic
template <class T, int Flags> auto get_shape_3d(py::array_t<T, Flags> arr) {
return aare::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)};
@ -111,6 +52,13 @@ template <class T, int Flags> auto get_shape_2d(py::array_t<T, Flags> arr) {
return aare::Shape<2>{arr.shape(0), arr.shape(1)};
}
template <class T, int Flags> auto get_shape_1d(py::array_t<T, Flags> arr) {
return aare::Shape<1>{arr.shape(0)};
}
template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags> arr) {
return aare::NDView<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr));
}
template <class T, int Flags> auto make_view_1d(py::array_t<T, Flags> arr) {
return aare::NDView<T, 1>(arr.mutable_data(), get_shape_1d<T, Flags>(arr));
}