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Dev/multiple rois in aare (#263)
Reading multiple ROI's for aare - read_frame, read_n etc throws for multiple ROIs - new functions read_ROIs, read_n_ROIs - read_roi_into (used for python bindings - to not copy) all these functions use get_frame or get_frame_into where one passes the roi_index ## Refactoring: - each roi keeps track of its subfiles that one has to open e.g. subfiles can be opened several times - refactored class DetectorGeometry - keep track of the updated module geometries in new class ROIGeometry. - ModuleGeometry updates based on ROI ## ROIGeometry: - stores number of modules overlapping with ROI and its indices - size of ROI Note: only tested size of the resulting frames not the actual values --------- Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch> Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>
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// SPDX-License-Identifier: MPL-2.0
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#include "aare/CtbRawFile.hpp"
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#include "aare/File.hpp"
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#include "aare/Frame.hpp"
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#include "aare/RawFile.hpp"
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#include "aare/RawMasterFile.hpp"
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#include "aare/RawSubFile.hpp"
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#include "aare/defs.hpp"
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#include "np_helper.hpp"
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#include <cstdint>
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#include <filesystem>
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#include <pybind11/iostream.h>
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#include <pybind11/numpy.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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#include <pybind11/stl/filesystem.h>
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#include <string>
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namespace py = pybind11;
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using namespace ::aare;
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void define_raw_file_io_bindings(py::module &m) {
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py::class_<RawFile>(m, "RawFile")
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.def(py::init<const std::filesystem::path &>())
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.def("read_frame",
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[](RawFile &self) {
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if (self.n_modules_in_roi().size() > 1) {
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throw std::runtime_error(
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"File contains multiple ROIs - use read_ROIs()");
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}
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std::vector<size_t> shape;
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shape.reserve(2);
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shape.push_back(self.rows());
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shape.push_back(self.cols());
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// return headers from all subfiles
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py::array_t<DetectorHeader> header(self.n_modules());
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py::array image = allocate_image_data(self.bytes_per_pixel(), shape);
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self.read_into(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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header.mutable_data());
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return py::make_tuple(header, image);
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})
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.def(
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"read_n",
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[](RawFile &self, size_t n_frames) {
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if (self.n_modules_in_roi().size() > 1) {
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throw std::runtime_error(
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"File contains multiple ROIs - use read_n_ROIs() to "
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"read a specific ROI or use read_ROIs and "
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"read one frame at a time.");
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}
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// adjust for actual frames left in the file
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n_frames =
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std::min(n_frames, self.total_frames() - self.tell());
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if (n_frames == 0) {
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throw std::runtime_error("No frames left in file");
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}
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std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
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// return headers from all subfiles
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py::array_t<DetectorHeader> header;
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if (self.n_modules() == 1) {
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header = py::array_t<DetectorHeader>(n_frames);
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} else {
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header = py::array_t<DetectorHeader>(
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{self.n_modules_in_roi()[0], n_frames});
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}
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py::array images = allocate_image_data(self.bytes_per_pixel(), shape);
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self.read_into(
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reinterpret_cast<std::byte *>(images.mutable_data()),
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n_frames, header.mutable_data());
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return py::make_tuple(header, images);
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},
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R"(
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Read n frames from the file.
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)")
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.def(
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"read_roi",
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[](RawFile &self,
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const size_t roi_index) {
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if (self.num_rois() == 0) {
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throw std::runtime_error(LOCATION + "No ROIs defined.");
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}
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if ( roi_index >= self.num_rois()) {
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throw std::runtime_error(LOCATION +
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"ROI index out of range.");
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}
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// return headers from all subfiles
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py::array_t<DetectorHeader> header(self.n_modules_in_roi()[roi_index]);
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std::vector<size_t> shape;
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shape.reserve(2);
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shape.push_back(self.roi_geometries(roi_index).pixels_y());
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shape.push_back(self.roi_geometries(roi_index).pixels_x());
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py::array image = allocate_image_data(self.bytes_per_pixel(), shape);
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self.read_roi_into(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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roi_index, self.tell(), header.mutable_data());
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self.seek(self.tell() + 1); // advance frame number so the
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return py::make_tuple(header, image);
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},
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R"(
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Read one ROI from the current frame.
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Parameters
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----------
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roi_index : int
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Index of the ROI to read.
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Notes
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-----
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The method advances the frame number, so reading ROIs one after the other won't work.
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Returns
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-------
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tuple (header, image)
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)",
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py::arg("roi_index"))
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.def(
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"read_rois",
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[](RawFile &self) {
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if (self.num_rois() == 0) {
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throw std::runtime_error(LOCATION + "No ROIs defined.");
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}
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size_t number_of_ROIs = self.num_rois();
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// const uint8_t item_size = self.bytes_per_pixel();
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std::vector<py::array> images(number_of_ROIs);
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// return headers from all subfiles
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std::vector<py::array_t<DetectorHeader>> headers(number_of_ROIs);
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for (size_t r = 0; r < number_of_ROIs; r++) {
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headers[r] =
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py::array_t<DetectorHeader>(self.n_modules_in_roi()[r]);
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}
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for (size_t r = 0; r < number_of_ROIs; r++) {
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std::vector<size_t> shape;
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shape.reserve(2);
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shape.push_back(self.roi_geometries(r).pixels_y());
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shape.push_back(self.roi_geometries(r).pixels_x());
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images[r] = allocate_image_data(self.bytes_per_pixel(), shape);
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self.read_roi_into(
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reinterpret_cast<std::byte *>(images[r].mutable_data()),
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r, self.tell(),headers[r].mutable_data());
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}
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self.seek(self.tell() + 1); // advance frame number so the
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return py::make_tuple(headers, images);
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},
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R"(
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Read all ROIs for specific frame.
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Parameters
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----------
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frame_number : int
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Frame number to read.
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roi_index : Optional[int]
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Index of the ROI to read. If not provided, all ROIs are read.
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Returns
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-------
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list of numpy.ndarray
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One array per ROI.)")
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.def(
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"read_n_with_roi",
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[](RawFile &self, const size_t num_frames, const size_t roi_index) {
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if (self.num_rois() == 0) {
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throw std::runtime_error(LOCATION + "No ROIs defined.");
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}
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if (roi_index >= self.num_rois()) {
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throw std::runtime_error(LOCATION +
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"ROI index out of range.");
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}
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// adjust for actual frames left in the file
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size_t n_frames =
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std::min(num_frames, self.total_frames() - self.tell());
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if (n_frames == 0) {
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throw std::runtime_error("No frames left in file");
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}
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std::vector<size_t> shape{
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n_frames, self.roi_geometries(roi_index).pixels_y(),
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self.roi_geometries(roi_index).pixels_x()};
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// return headers from all subfiles
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auto n_mod = self.n_modules_in_roi()[roi_index];
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py::array_t<DetectorHeader> header({
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n_frames, n_mod}
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);
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py::array images = allocate_image_data(self.bytes_per_pixel(), shape);
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auto image_buffer =
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reinterpret_cast<std::byte *>(images.mutable_data());
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auto h = header.mutable_data();
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for (size_t i = 0; i < n_frames; i++) {
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self.read_roi_into(image_buffer, roi_index, self.tell(), h);
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self.seek(self.tell() + 1); // advance frame number
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image_buffer += self.bytes_per_frame(roi_index);
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h += n_mod;
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}
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return py::make_tuple(header, images);
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},
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R"(
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Read n frames for a specific ROI
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Parameters
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----------
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num_frames : int
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Number of frames to read.
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roi_index : int
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Index of the ROI to read.
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Returns
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-------
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three dimensional numpy.ndarray.)",
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py::arg("num_frames"), py::kw_only(), py::arg("roi_index"))
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.def("frame_number", &RawFile::frame_number)
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.def("bytes_per_frame",
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static_cast<size_t (RawFile::*)()>(&RawFile::bytes_per_frame))
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.def(
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"bytes_per_frame",
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[](RawFile &self, const size_t roi_index) {
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return self.bytes_per_frame(roi_index);
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},
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R"(
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Bytes per frame for the given ROI.
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)")
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.def("pixels_per_frame",
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static_cast<size_t (RawFile::*)()>(&RawFile::pixels_per_frame))
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.def(
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"pixels_per_frame",
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[](RawFile &self, const size_t roi_index) {
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return self.pixels_per_frame(roi_index);
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},
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R"(
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Pixels per frame for the given ROI.
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)")
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.def_property_readonly("bytes_per_pixel", &RawFile::bytes_per_pixel)
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.def("seek", &RawFile::seek, R"(
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Seek to a frame index in file.
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)")
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.def("tell", &RawFile::tell, R"(
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Return the current frame number.)")
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.def_property_readonly("total_frames", &RawFile::total_frames)
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.def("rows", static_cast<size_t (RawFile::*)() const>(&RawFile::rows))
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.def(
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"rows",
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[](RawFile &self, const size_t roi_index) {
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return self.rows(roi_index);
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},
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R"(
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Rows for the given ROI.
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)")
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.def("cols", static_cast<size_t (RawFile::*)() const>(&RawFile::cols))
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.def(
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"cols",
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[](RawFile &self, const size_t roi_index) {
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return self.cols(roi_index);
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},
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R"(
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Cols for the given ROI.
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)")
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.def_property_readonly("bitdepth", &RawFile::bitdepth)
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.def_property_readonly("geometry", &RawFile::geometry)
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.def_property_readonly("detector_type", &RawFile::detector_type)
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.def_property_readonly("master", &RawFile::master)
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.def_property_readonly("n_modules", &RawFile::n_modules)
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.def_property_readonly("n_modules_in_roi", &RawFile::n_modules_in_roi)
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.def_property_readonly("num_rois", &RawFile::num_rois);
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}
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