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>

CMakeLists.txt

@@ -352,6 +352,7 @@ set(PUBLICHEADERS
     include/aare/FilePtr.hpp
     include/aare/Frame.hpp
     include/aare/GainMap.hpp
+    include/aare/ROIGeometry.hpp
     include/aare/DetectorGeometry.hpp
     include/aare/JungfrauDataFile.hpp
     include/aare/logger.hpp
@@ -374,6 +375,7 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/ROIGeometry.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp

RELEASE.md

@@ -12,6 +12,10 @@
 - Removed redundant arr.value(ix,iy...) on NDArray use arr(ix,iy...)
 - Removed Print/Print_some/Print_all form NDArray (operator << still works)
 - Added const* version of .data()
+- reading multiple ROI's supported for aare. 
+    - Use ``read_roi/rois`` to read multiple ROIs for one frame, the index of a specific ROI to only read that ROI
+    - Use ``read_n_with_roi`` to read multiple frames for a specific ROI. 
+    - Note ``read_frame`` and ``read_n`` is not supported for multiple ROI's. 
 
 ### Bugfixes: 
 

include/aare/DetectorGeometry.hpp

@@ -1,7 +1,10 @@
 // SPDX-License-Identifier: MPL-2.0
 #pragma once
+#include "aare/ROIGeometry.hpp"
 #include "aare/RawMasterFile.hpp" //ROI refactor away
 #include "aare/defs.hpp"
+#include <iostream>
+
 namespace aare {
 
 struct ModuleConfig {
@@ -18,16 +21,69 @@ struct ModuleConfig {
 };
 
 /**
- * @brief Class to hold the geometry of a module. Where pixel 0 is located and
+ * @brief Class to hold the geometry of a module. Where pixel 0 is located
- * the size of the module
+ * relative to full Detector/ROI and the size of the module e.g. size of ROI
+ * occupied by the module
  */
 struct ModuleGeometry {
+    /// @brief start x coordinate of the module in the full detector/ROI
     int origin_x{};
+    /// @brief start y coordinate of the module in the full detector/ROI
     int origin_y{};
+    /// @brief height of the module in pixels
     int height{};
+    /// @brief width of the module in pixels
     int width{};
+    /// @brief module index of the module in the detector
     int row_index{};
+    /// @brief module index of the module in the detector
     int col_index{};
+
+    /**
+     * @brief checks if module is in the region of interest
+     */
+    bool module_in_roi(const ROI &roi) {
+        // module is to the left of the roi
+        bool to_the_left = origin_x + width - 1 < roi.xmin;
+        bool to_the_right = origin_x >= roi.xmax;
+        bool above = origin_y + height - 1 < roi.ymin;
+        bool below = origin_y >= roi.ymax;
+
+        return !(to_the_left || to_the_right || below || above);
+    }
+
+    /**
+     * @brief Update the module geometry given a region of interest
+     */
+    void update_geometry_with_roi(const ROI &roi) {
+
+        if (!(module_in_roi(roi))) {
+            return; // do nothing
+        }
+
+        int new_width = std::min(origin_x + width, static_cast<int>(roi.xmax)) -
+                        std::max(origin_x, static_cast<int>(roi.xmin));
+
+        // ROI starts inside module
+        if (roi.xmin >= origin_x && roi.xmin < origin_x + width) {
+            origin_x = 0;
+        } else {
+            origin_x -= roi.xmin;
+        }
+
+        int new_height =
+            std::min(origin_y + height, static_cast<int>(roi.ymax)) -
+            std::max(origin_y, static_cast<int>(roi.ymin));
+
+        if (roi.ymin >= origin_y && roi.ymin < origin_y + height) {
+            origin_y = 0;
+        } else {
+            origin_y -= roi.ymin;
+        }
+
+        height = new_height;
+        width = new_width;
+    }
 };
 
 /**
@@ -49,34 +105,33 @@ class DetectorGeometry {
      * @param roi
      * @return DetectorGeometry
      */
-    void update_geometry_with_roi(ROI roi);
 
     size_t n_modules() const;
 
-    size_t n_modules_in_roi() const;
-
     size_t pixels_x() const;
     size_t pixels_y() const;
 
     size_t modules_x() const;
     size_t modules_y() const;
 
-    const std::vector<ssize_t> &get_modules_in_roi() const;
-
-    ssize_t get_modules_in_roi(const size_t index) const;
-
     const std::vector<ModuleGeometry> &get_module_geometries() const;
 
     const ModuleGeometry &get_module_geometries(const size_t index) const;
 
+    ModuleGeometry &get_module_geometries(const size_t index);
+
   private:
     size_t m_modules_x{};
     size_t m_modules_y{};
     size_t m_pixels_x{};
     size_t m_pixels_y{};
     static constexpr ModuleConfig cfg{0, 0};
-    std::vector<ModuleGeometry> module_geometries{};
+
-    std::vector<ssize_t> modules_in_roi{};
+    // TODO: maybe remove - should be a member in ROIGeometry - in particular
+    // only works as no overlap between ROIs allowed? maybe just have another
+    // additional vector of ModuleGeometry for each ROIGeometry - some
+    // duplication but nicer design?
+    std::vector<ModuleGeometry> module_geometries;
 };
 
 } // namespace aare

include/aare/ROIGeometry.hpp

@@ -0,0 +1,48 @@
+#pragma once
+#include "aare/DetectorGeometry.hpp"
+#include "aare/defs.hpp"
+
+namespace aare {
+
+class DetectorGeometry; // forward declaration to avoid circular dependency
+
+/**
+ * @brief Class to hold the geometry of a region of interest (ROI)
+ */
+class ROIGeometry {
+  public:
+    /** @brief Constructor
+     * @param roi
+     * @param geometry general detector geometry
+     */
+    ROIGeometry(const ROI &roi, DetectorGeometry &geometry);
+
+    /** @brief Constructor for ROI geometry expanding over full detector
+     * @param geometry general detector geometry
+     */
+    ROIGeometry(DetectorGeometry &geometry);
+
+    /// @brief Get number of modules in the ROI
+    size_t num_modules_in_roi() const;
+
+    /// @brief Get the indices of modules in the ROI
+    const std::vector<size_t> &module_indices_in_roi() const;
+
+    size_t module_indices_in_roi(const size_t module_index) const;
+
+    size_t pixels_x() const;
+    size_t pixels_y() const;
+
+  private:
+    /// @brief Size of the ROI in pixels in x direction
+    size_t m_pixels_x{};
+    /// @brief Size of the ROI in pixels in y direction
+    size_t m_pixels_y{};
+
+    DetectorGeometry &m_geometry;
+
+    /// @brief Indices of modules included in the ROI
+    std::vector<size_t> m_module_indices_in_roi;
+};
+
+} // namespace aare

include/aare/RawFile.hpp

@@ -4,6 +4,7 @@
 #include "aare/FileInterface.hpp"
 #include "aare/Frame.hpp"
 #include "aare/NDArray.hpp" //for pixel map
+#include "aare/ROIGeometry.hpp"
 #include "aare/RawMasterFile.hpp"
 #include "aare/RawSubFile.hpp"
 
@@ -23,13 +24,17 @@ namespace aare {
  */
 class RawFile : public FileInterface {
 
-    std::vector<std::unique_ptr<RawSubFile>> m_subfiles;
+    std::vector<std::vector<std::unique_ptr<RawSubFile>>>
+        m_subfiles; // [ROI][modules_per_ROI]
 
     RawMasterFile m_master;
     size_t m_current_frame{};
 
     DetectorGeometry m_geometry;
 
+    /// @brief Geometries e.g. number of modules, size etc. for each ROI
+    std::vector<ROIGeometry> m_ROI_geometries;
+
   public:
     /**
      * @brief RawFile constructor
@@ -43,26 +48,94 @@ class RawFile : public FileInterface {
     Frame read_frame() override;
     Frame read_frame(size_t frame_number) override;
     std::vector<Frame> read_n(size_t n_frames) override;
+
+
+    /**
+     * @brief Read one ROI defined in the master file
+     * @param roi_index index of the ROI to read
+     * @return Frame
+     * @note the frame index is incremented after calling this function so
+     * reading rois one after the other wont work.
+     */
+    Frame read_roi(const size_t roi_index);
+
+    /**
+     * @brief Read all ROIs defined in the master file
+     * @return vector of Frames (one Frame per ROI)
+     */
+    std::vector<Frame>read_rois();
+
+    /**
+     * @brief Read n frames for the given ROI index
+     * @param n_frames number of frames to read
+     * @param roi_index index of the ROI to read
+     * @return vector of Frames
+     */
+    std::vector<Frame> read_n_with_roi(const size_t n_frames,
+                                   const size_t roi_index);
+
     void read_into(std::byte *image_buf) override;
     void read_into(std::byte *image_buf, size_t n_frames) override;
 
     // TODO! do we need to adapt the API?
-    void read_into(std::byte *image_buf, DetectorHeader *header);
+    void read_into(std::byte *image_buf, DetectorHeader *header = nullptr);
     void read_into(std::byte *image_buf, size_t n_frames,
                    DetectorHeader *header);
 
+    void read_roi_into(std::byte *image_buf, const size_t roi_index,
+                       const size_t frame_number,
+                       DetectorHeader *header =
+                           nullptr); // maybe just make get_frame_into public
+
     size_t frame_number(size_t frame_index) override;
     size_t bytes_per_frame() override;
+    // TODO: mmh maybe also pass roi_index in Base class File. Leave it unused
+    // for NumpyFile and JungfrauDataFile
+    /**
+     * @brief bytes per frame for the given ROI
+     * @param roi_index index of the ROI
+     */
+    size_t bytes_per_frame(const size_t roi_index);
     size_t pixels_per_frame() override;
+    /**
+     * @brief pixels per frame for the given ROI
+     * @param roi_index index of the ROI
+     */
+    size_t pixels_per_frame(const size_t roi_index);
     size_t bytes_per_pixel() const;
     void seek(size_t frame_index) override;
     size_t tell() override;
     size_t total_frames() const override;
     size_t rows() const override;
+    /**
+     * @brief rows for the given ROI
+     * @param roi_index index of the ROI
+     */
+    size_t rows(const size_t roi_index) const;
     size_t cols() const override;
+    /**
+     * @brief cols for the given ROI
+     * @param roi_index index of the ROI
+     */
+    size_t cols(const size_t roi_index) const;
     size_t bitdepth() const override;
     size_t n_modules() const;
-    size_t n_modules_in_roi() const;
+
+    /**
+     * @brief number of ROIs defined
+     */
+    size_t num_rois() const;
+
+    /**
+     * @brief get the ROI geometry for the given ROI index
+     * @param roi_index index of the ROI
+     */
+    const ROIGeometry &roi_geometries(size_t roi_index) const;
+
+    /**
+     * @brief number of modules in each ROI
+     */
+    std::vector<size_t> n_modules_in_roi() const;
     xy geometry() const;
 
     RawMasterFile master() const;
@@ -79,21 +152,23 @@ class RawFile : public FileInterface {
   private:
     /**
      * @brief read the frame at the given frame index into the image buffer
-     * @param frame_number frame number to read
+     * @param frame_index frame number to read
-     * @param image_buf buffer to store the frame
+     * @param frame_buffer buffer to store the frame
+     * @param roi_index index of the ROI to read (default is 0 e.g. full frame)
      */
-
+    void get_frame_into(
-    void get_frame_into(size_t frame_index, std::byte *frame_buffer,
+        size_t frame_index, std::byte *frame_buffer, const size_t roi_index = 0,
-                        DetectorHeader *header = nullptr);
+        DetectorHeader *header = nullptr); // TODO read_into updates it!!!!
 
     /**
      * @brief get the frame at the given frame index
      * @param frame_number frame number to read
+     * @param roi_index index of the ROI to read (default is 0 e.g. full frame)
      * @return Frame
      */
-    Frame get_frame(size_t frame_index);
+    Frame get_frame(size_t frame_index, const size_t roi_index = 0);
 
-    void open_subfiles();
+    void open_subfiles(const size_t roi_index);
 };
 
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -2,11 +2,11 @@
 #pragma once
 #include "aare/defs.hpp"
 #include <algorithm>
+#include <chrono>
 #include <filesystem>
 #include <fmt/format.h>
 #include <fstream>
 #include <optional>
-#include <chrono>
 
 #include <nlohmann/json.hpp>
 using json = nlohmann::json;
@@ -109,7 +109,7 @@ class RawMasterFile {
     std::optional<size_t> m_number_of_rows;
     std::optional<uint8_t> m_counter_mask;
 
-    std::optional<ROI> m_roi;
+    std::optional<std::vector<ROI>> m_rois;
 
   public:
     RawMasterFile(const std::filesystem::path &fpath);
@@ -141,11 +141,15 @@ class RawMasterFile {
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> counter_mask() const;
 
+    std::optional<std::vector<ROI>> rois() const;
+
     std::optional<ROI> roi() const;
 
     ScanParameters scan_parameters() const;
 
-    std::optional<std::chrono::nanoseconds> exptime() const { return m_exptime; }
+    std::optional<std::chrono::nanoseconds> exptime() const {
+        return m_exptime;
+    }
     std::chrono::nanoseconds period() const { return m_period; }
 
   private:

python/src/bind_RawFile.hpp

@@ -0,0 +1,311 @@
+// SPDX-License-Identifier: MPL-2.0
+#include "aare/CtbRawFile.hpp"
+#include "aare/File.hpp"
+#include "aare/Frame.hpp"
+#include "aare/RawFile.hpp"
+#include "aare/RawMasterFile.hpp"
+#include "aare/RawSubFile.hpp"
+
+#include "aare/defs.hpp"
+#include "np_helper.hpp"
+
+#include <cstdint>
+#include <filesystem>
+#include <pybind11/iostream.h>
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/stl/filesystem.h>
+#include <string>
+
+namespace py = pybind11;
+using namespace ::aare;
+
+void define_raw_file_io_bindings(py::module &m) {
+    py::class_<RawFile>(m, "RawFile")
+        .def(py::init<const std::filesystem::path &>())
+        .def("read_frame",
+             [](RawFile &self) {
+                 if (self.n_modules_in_roi().size() > 1) {
+                     throw std::runtime_error(
+                         "File contains multiple ROIs - use read_ROIs()");
+                 }
+
+                 std::vector<size_t> shape;
+                 shape.reserve(2);
+                 shape.push_back(self.rows());
+                 shape.push_back(self.cols());
+
+                 // return headers from all subfiles
+                 py::array_t<DetectorHeader> header(self.n_modules());
+
+                py::array image = allocate_image_data(self.bytes_per_pixel(), shape);
+                 self.read_into(
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
+                     header.mutable_data());
+
+                 return py::make_tuple(header, image);
+             })
+        .def(
+            "read_n",
+            [](RawFile &self, size_t n_frames) {
+                if (self.n_modules_in_roi().size() > 1) {
+                    throw std::runtime_error(
+                        "File contains multiple ROIs - use read_n_ROIs() to "
+                        "read a specific ROI or use read_ROIs and "
+                        "read one frame at a time.");
+                }
+                // adjust for actual frames left in the file
+                n_frames =
+                    std::min(n_frames, self.total_frames() - self.tell());
+                if (n_frames == 0) {
+                    throw std::runtime_error("No frames left in file");
+                }
+                std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
+
+                // return headers from all subfiles
+                py::array_t<DetectorHeader> header;
+                if (self.n_modules() == 1) {
+                    header = py::array_t<DetectorHeader>(n_frames);
+                } else {
+                    header = py::array_t<DetectorHeader>(
+                        {self.n_modules_in_roi()[0], n_frames});
+                }
+
+                py::array images = allocate_image_data(self.bytes_per_pixel(), shape);
+                self.read_into(
+                    reinterpret_cast<std::byte *>(images.mutable_data()),
+                    n_frames, header.mutable_data());
+
+                return py::make_tuple(header, images);
+            },
+            R"(
+             Read n frames from the file.
+             )")
+
+        .def(
+            "read_roi",
+            [](RawFile &self,
+               const size_t roi_index) {
+                if (self.num_rois() == 0) {
+                    throw std::runtime_error(LOCATION + "No ROIs defined.");
+                }
+
+                if ( roi_index >= self.num_rois()) {
+                    throw std::runtime_error(LOCATION +
+                                             "ROI index out of range.");
+                }
+
+                // return headers from all subfiles
+                py::array_t<DetectorHeader> header(self.n_modules_in_roi()[roi_index]);
+
+                
+                std::vector<size_t> shape;
+                shape.reserve(2);
+                shape.push_back(self.roi_geometries(roi_index).pixels_y());
+                shape.push_back(self.roi_geometries(roi_index).pixels_x());
+
+                py::array image = allocate_image_data(self.bytes_per_pixel(), shape);
+
+
+                self.read_roi_into(
+                    reinterpret_cast<std::byte *>(image.mutable_data()),
+                    roi_index, self.tell(), header.mutable_data());
+                
+                self.seek(self.tell() + 1); // advance frame number so the
+                return py::make_tuple(header, image);
+            },
+            R"(
+            Read one ROI from the current frame.
+
+            Parameters
+            ----------
+
+            roi_index : int
+                Index of the ROI to read.
+
+            Notes
+            -----
+
+            The method advances the frame number, so reading ROIs one after the other won't work.
+
+            Returns
+            -------
+
+            tuple (header, image)
+            )",
+            py::arg("roi_index"))
+
+        .def(
+            "read_rois",
+            [](RawFile &self) {
+                if (self.num_rois() == 0) {
+                    throw std::runtime_error(LOCATION + "No ROIs defined.");
+                }
+
+
+
+                size_t number_of_ROIs = self.num_rois();
+
+                // const uint8_t item_size = self.bytes_per_pixel();
+
+                std::vector<py::array> images(number_of_ROIs);
+
+                // return headers from all subfiles
+                std::vector<py::array_t<DetectorHeader>> headers(number_of_ROIs);
+                for (size_t r = 0; r < number_of_ROIs; r++) {
+                    headers[r] =
+                        py::array_t<DetectorHeader>(self.n_modules_in_roi()[r]);
+                }
+
+
+
+                for (size_t r = 0; r < number_of_ROIs; r++) {
+                    std::vector<size_t> shape;
+                    shape.reserve(2);
+                    shape.push_back(self.roi_geometries(r).pixels_y());
+                    shape.push_back(self.roi_geometries(r).pixels_x());
+
+                    images[r] = allocate_image_data(self.bytes_per_pixel(), shape);
+
+                    self.read_roi_into(
+                        reinterpret_cast<std::byte *>(images[r].mutable_data()),
+                        r, self.tell(),headers[r].mutable_data());
+                }
+                self.seek(self.tell() + 1); // advance frame number so the
+                return py::make_tuple(headers, images);
+            },
+            R"(
+            Read all ROIs for specific frame.
+
+            Parameters
+            ----------
+
+            frame_number : int
+                Frame number to read.
+
+            roi_index : Optional[int]
+                Index of the ROI to read. If not provided, all ROIs are read.
+
+            Returns
+            -------
+
+            list of numpy.ndarray
+                One array per ROI.)")
+
+        .def(
+            "read_n_with_roi",
+            [](RawFile &self, const size_t num_frames, const size_t roi_index) {
+                if (self.num_rois() == 0) {
+                    throw std::runtime_error(LOCATION + "No ROIs defined.");
+                }
+
+                if (roi_index >= self.num_rois()) {
+                    throw std::runtime_error(LOCATION +
+                                             "ROI index out of range.");
+                }
+
+                // adjust for actual frames left in the file
+                size_t n_frames =
+                    std::min(num_frames, self.total_frames() - self.tell());
+                if (n_frames == 0) {
+                    throw std::runtime_error("No frames left in file");
+                }
+                std::vector<size_t> shape{
+                    n_frames, self.roi_geometries(roi_index).pixels_y(),
+                    self.roi_geometries(roi_index).pixels_x()};
+
+                // return headers from all subfiles
+                auto n_mod = self.n_modules_in_roi()[roi_index];
+                py::array_t<DetectorHeader> header({
+                    n_frames, n_mod}
+                );
+
+
+                py::array images = allocate_image_data(self.bytes_per_pixel(), shape);
+
+                auto image_buffer =
+                    reinterpret_cast<std::byte *>(images.mutable_data());
+                auto h = header.mutable_data();
+
+                for (size_t i = 0; i < n_frames; i++) {
+                    self.read_roi_into(image_buffer, roi_index, self.tell(), h);
+
+                    self.seek(self.tell() + 1); // advance frame number
+                    image_buffer += self.bytes_per_frame(roi_index);
+                    h += n_mod;
+                }
+
+                return py::make_tuple(header, images);
+            },
+            R"(
+            Read n frames for a specific ROI
+
+            Parameters
+            ----------
+
+            num_frames : int
+                Number of frames to read.
+            roi_index : int
+                Index of the ROI to read. 
+
+            Returns
+            -------
+
+            three dimensional numpy.ndarray.)",
+            py::arg("num_frames"), py::kw_only(), py::arg("roi_index"))
+
+        .def("frame_number", &RawFile::frame_number)
+        .def("bytes_per_frame",
+             static_cast<size_t (RawFile::*)()>(&RawFile::bytes_per_frame))
+        .def(
+            "bytes_per_frame",
+            [](RawFile &self, const size_t roi_index) {
+                return self.bytes_per_frame(roi_index);
+            },
+            R"(
+            Bytes per frame for the given ROI.
+            )")
+        .def("pixels_per_frame",
+             static_cast<size_t (RawFile::*)()>(&RawFile::pixels_per_frame))
+        .def(
+            "pixels_per_frame",
+            [](RawFile &self, const size_t roi_index) {
+                return self.pixels_per_frame(roi_index);
+            },
+            R"(
+            Pixels per frame for the given ROI.
+            )")
+        .def_property_readonly("bytes_per_pixel", &RawFile::bytes_per_pixel)
+        .def("seek", &RawFile::seek, R"(
+            Seek to a frame index in file.
+            )")
+        .def("tell", &RawFile::tell, R"(
+            Return the current frame number.)")
+        .def_property_readonly("total_frames", &RawFile::total_frames)
+        .def("rows", static_cast<size_t (RawFile::*)() const>(&RawFile::rows))
+        .def(
+            "rows",
+            [](RawFile &self, const size_t roi_index) {
+                return self.rows(roi_index);
+            },
+            R"(
+            Rows for the given ROI.
+            )")
+        .def("cols", static_cast<size_t (RawFile::*)() const>(&RawFile::cols))
+        .def(
+            "cols",
+            [](RawFile &self, const size_t roi_index) {
+                return self.cols(roi_index);
+            },
+            R"(
+            Cols for the given ROI.
+            )")
+        .def_property_readonly("bitdepth", &RawFile::bitdepth)
+        .def_property_readonly("geometry", &RawFile::geometry)
+        .def_property_readonly("detector_type", &RawFile::detector_type)
+        .def_property_readonly("master", &RawFile::master)
+        .def_property_readonly("n_modules", &RawFile::n_modules)
+        .def_property_readonly("n_modules_in_roi", &RawFile::n_modules_in_roi)
+        .def_property_readonly("num_rois", &RawFile::num_rois);
+}

python/src/module.cpp

@@ -11,6 +11,7 @@
 #include "bind_ClusterVector.hpp"
 #include "bind_Eta.hpp"
 #include "bind_Interpolator.hpp"
+#include "bind_RawFile.hpp"
 #include "bind_calibration.hpp"
 
 // TODO! migrate the other names
@@ -20,7 +21,6 @@
 #include "jungfrau_data_file.hpp"
 #include "pedestal.hpp"
 #include "pixel_map.hpp"
-#include "raw_file.hpp"
 #include "raw_master_file.hpp"
 #include "raw_sub_file.hpp"
 #include "var_cluster.hpp"

python/src/np_helper.hpp

@@ -85,3 +85,20 @@ struct fmt_format_trait<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
 
 template <typename ClusterType>
 auto fmt_format = fmt_format_trait<ClusterType>::value();
+
+/**  
+* Helper function to allocate image data given item size and shape 
+* used when we want to fill a numpy array and return to python
+*/
+py::array allocate_image_data(size_t item_size,
+                              const std::vector<size_t> &shape) {
+    py::array image_data;
+    if (item_size == 1) {
+        image_data = py::array_t<uint8_t>(shape);
+    } else if (item_size == 2) {
+        image_data  = py::array_t<uint16_t>(shape);
+    } else if (item_size == 4) {
+        image_data = py::array_t<uint32_t>(shape);
+    }
+    return image_data;
+}

python/src/raw_file.hpp

@@ -1,109 +0,0 @@
-// SPDX-License-Identifier: MPL-2.0
-#include "aare/CtbRawFile.hpp"
-#include "aare/File.hpp"
-#include "aare/Frame.hpp"
-#include "aare/RawFile.hpp"
-#include "aare/RawMasterFile.hpp"
-#include "aare/RawSubFile.hpp"
-
-#include "aare/defs.hpp"
-// #include "aare/fClusterFileV2.hpp"
-
-#include <cstdint>
-#include <filesystem>
-#include <pybind11/iostream.h>
-#include <pybind11/numpy.h>
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
-#include <pybind11/stl/filesystem.h>
-#include <string>
-
-namespace py = pybind11;
-using namespace ::aare;
-
-void define_raw_file_io_bindings(py::module &m) {
-    py::class_<RawFile>(m, "RawFile")
-        .def(py::init<const std::filesystem::path &>())
-        .def("read_frame",
-             [](RawFile &self) {
-                 py::array image;
-                 std::vector<ssize_t> shape;
-                 shape.reserve(2);
-                 shape.push_back(self.rows());
-                 shape.push_back(self.cols());
-
-                 // return headers from all subfiles
-                 py::array_t<DetectorHeader> header(self.n_modules());
-
-                 const uint8_t item_size = self.bytes_per_pixel();
-                 if (item_size == 1) {
-                     image = py::array_t<uint8_t>(shape);
-                 } else if (item_size == 2) {
-                     image = py::array_t<uint16_t>(shape);
-                 } else if (item_size == 4) {
-                     image = py::array_t<uint32_t>(shape);
-                 }
-                 self.read_into(
-                     reinterpret_cast<std::byte *>(image.mutable_data()),
-                     header.mutable_data());
-
-                 return py::make_tuple(header, image);
-             })
-        .def(
-            "read_n",
-            [](RawFile &self, size_t n_frames) {
-                // adjust for actual frames left in the file
-                n_frames =
-                    std::min(n_frames, self.total_frames() - self.tell());
-                if (n_frames == 0) {
-                    throw std::runtime_error("No frames left in file");
-                }
-                std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
-
-                // return headers from all subfiles
-                py::array_t<DetectorHeader> header;
-                if (self.n_modules() == 1) {
-                    header = py::array_t<DetectorHeader>(n_frames);
-                } else {
-                    header = py::array_t<DetectorHeader>(
-                        {self.n_modules_in_roi(), n_frames});
-                }
-                // py::array_t<DetectorHeader> header({self.n_mod(), n_frames});
-
-                py::array image;
-                const uint8_t item_size = self.bytes_per_pixel();
-                if (item_size == 1) {
-                    image = py::array_t<uint8_t>(shape);
-                } else if (item_size == 2) {
-                    image = py::array_t<uint16_t>(shape);
-                } else if (item_size == 4) {
-                    image = py::array_t<uint32_t>(shape);
-                }
-                self.read_into(
-                    reinterpret_cast<std::byte *>(image.mutable_data()),
-                    n_frames, header.mutable_data());
-
-                return py::make_tuple(header, image);
-            },
-            R"(
-             Read n frames from the file.
-             )")
-        .def("frame_number", &RawFile::frame_number)
-        .def_property_readonly("bytes_per_frame", &RawFile::bytes_per_frame)
-        .def_property_readonly("pixels_per_frame", &RawFile::pixels_per_frame)
-        .def_property_readonly("bytes_per_pixel", &RawFile::bytes_per_pixel)
-        .def("seek", &RawFile::seek, R"(
-            Seek to a frame index in file.
-            )")
-        .def("tell", &RawFile::tell, R"(
-            Return the current frame number.)")
-        .def_property_readonly("total_frames", &RawFile::total_frames)
-        .def_property_readonly("rows", &RawFile::rows)
-        .def_property_readonly("cols", &RawFile::cols)
-        .def_property_readonly("bitdepth", &RawFile::bitdepth)
-        .def_property_readonly("geometry", &RawFile::geometry)
-        .def_property_readonly("detector_type", &RawFile::detector_type)
-        .def_property_readonly("master", &RawFile::master)
-        .def_property_readonly("n_modules", &RawFile::n_modules)
-        .def_property_readonly("n_modules_in_roi", &RawFile::n_modules_in_roi);
-}

python/tests/test_RawFile.py

@@ -4,13 +4,45 @@ from aare import RawFile
 import numpy as np
 
 @pytest.mark.withdata
-def test_read_rawfile_with_roi(test_data_path):
+def test_read_rawfile_with_roi_spanning_over_one_module(test_data_path):
 
-   with RawFile(test_data_path / "raw/ROITestData/SingleChipROI/Data_master_0.json") as f:
+    with RawFile(test_data_path / "raw/ROITestData/SingleChipROI/Data_master_0.json") as f:
-    headers, frames = f.read()
+        headers, frames = f.read()
 
-    assert headers.size == 10100
+        num_rois = f.num_rois
-    assert frames.shape == (10100, 256, 256)
+        assert num_rois == 1
+        assert headers.size == 10100
+        assert frames.shape == (10100, 256, 256)
+
+@pytest.mark.withdata
+def test_read_rawfile_with_multiple_rois(test_data_path): 
+    with RawFile(test_data_path / "raw/ROITestData/MultipleROIs/run_master_0.json") as f:
+        num_rois = f.num_rois
+
+        #cannot read_frame for multiple ROIs
+        with pytest.raises(RuntimeError):
+            f.read_frame()
+
+        assert f.tell() == 0
+        frames = f.read_ROIs() 
+        assert num_rois == 2
+        assert len(frames) == 2
+        assert frames[0].shape == (301, 101)
+        assert frames[1].shape == (101, 101)
+
+        assert f.tell() == 1
+
+        # read multiple ROIs at once
+        frames = f.read_n_ROIs(2, 1) 
+        assert frames.shape == (2, 101, 101)
+
+        assert f.tell() == 3
+
+        # read specific ROI
+        frame = f.read_ROIs(1, 0)
+        assert len(frame) == 1
+        assert frame[0].shape == (301, 101)
+        assert f.tell() == 2
    
 @pytest.mark.withdata
 def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path): 

src/DetectorGeometry.cpp

@@ -41,31 +41,16 @@ DetectorGeometry::DetectorGeometry(const xy &geometry,
     m_modules_x = geometry.col;
     m_modules_y = geometry.row;
     m_pixels_y += static_cast<size_t>((geometry.row - 1) * cfg.module_gap_row);
-
-    modules_in_roi.resize(num_modules);
-    std::iota(modules_in_roi.begin(), modules_in_roi.end(), 0);
 }
 
 size_t DetectorGeometry::n_modules() const { return m_modules_x * m_modules_y; }
 
-size_t DetectorGeometry::n_modules_in_roi() const {
-    return modules_in_roi.size();
-};
-
 size_t DetectorGeometry::pixels_x() const { return m_pixels_x; }
 size_t DetectorGeometry::pixels_y() const { return m_pixels_y; }
 
 size_t DetectorGeometry::modules_x() const { return m_modules_x; };
 size_t DetectorGeometry::modules_y() const { return m_modules_y; };
 
-const std::vector<ssize_t> &DetectorGeometry::get_modules_in_roi() const {
-    return modules_in_roi;
-}
-
-ssize_t DetectorGeometry::get_modules_in_roi(const size_t index) const {
-    return modules_in_roi[index];
-}
-
 const std::vector<ModuleGeometry> &
 DetectorGeometry::get_module_geometries() const {
     return module_geometries;
@@ -76,77 +61,8 @@ DetectorGeometry::get_module_geometries(const size_t index) const {
     return module_geometries[index];
 }
 
-void DetectorGeometry::update_geometry_with_roi(ROI roi) {
+ModuleGeometry &DetectorGeometry::get_module_geometries(const size_t index) {
-#ifdef AARE_VERBOSE
+    return module_geometries[index];
-    fmt::println("update_geometry_with_roi() called with ROI: {} {} {} {}",
-                 roi.xmin, roi.xmax, roi.ymin, roi.ymax);
-    fmt::println("Geometry: {} {} {} {} {} {}", m_modules_x, m_modules_y,
-                 m_pixels_x, m_pixels_y, cfg.module_gap_row,
-                 cfg.module_gap_col);
-
-#endif
-
-    modules_in_roi.clear();
-    modules_in_roi.reserve(m_modules_x * m_modules_y);
-    int pos_y = 0;
-    int pos_y_increment = 0;
-    for (size_t row = 0; row < m_modules_y; row++) {
-        int pos_x = 0;
-        for (size_t col = 0; col < m_modules_x; col++) {
-            auto &m = module_geometries[row * m_modules_x + col];
-
-            auto original_height = m.height;
-            auto original_width = m.width;
-
-            // module is to the left of the roi
-            if (m.origin_x + m.width < roi.xmin) {
-                m.width = 0;
-
-                // roi is in module
-            } else {
-                // here we only arrive when the roi is in or to the left of
-                // the module
-                if (roi.xmin > m.origin_x) {
-                    m.width -= roi.xmin - m.origin_x;
-                }
-                if (roi.xmax < m.origin_x + original_width) {
-                    m.width -= m.origin_x + original_width - roi.xmax;
-                }
-                m.origin_x = pos_x;
-                pos_x += m.width;
-            }
-
-            if (m.origin_y + m.height < roi.ymin) {
-                m.height = 0;
-            } else {
-                if ((roi.ymin > m.origin_y) &&
-                    (roi.ymin < m.origin_y + m.height)) {
-                    m.height -= roi.ymin - m.origin_y;
-                }
-                if (roi.ymax < m.origin_y + original_height) {
-                    m.height -= m.origin_y + original_height - roi.ymax;
-                }
-                m.origin_y = pos_y;
-                pos_y_increment = m.height;
-            }
-
-            if (m.height != 0 && m.width != 0) {
-                modules_in_roi.push_back(row * m_modules_x + col);
-            }
-
-#ifdef AARE_VERBOSE
-            fmt::println("Module {} {} {} {}", m.origin_x, m.origin_y, m.width,
-                         m.height);
-#endif
-        }
-        // increment pos_y
-        pos_y += pos_y_increment;
-    }
-
-    // m_rows = roi.height();
-    // m_cols = roi.width();
-    m_pixels_x = roi.width();
-    m_pixels_y = roi.height();
 }
 
 } // namespace aare

src/DetectorGeometry.test.cpp

@@ -7,17 +7,20 @@
 #include <filesystem>
 
 #include "aare/DetectorGeometry.hpp"
+#include "aare/ROIGeometry.hpp"
 #include "test_config.hpp"
 
-TEST_CASE("Simple ROIs on one module") {
+TEST_CASE("Simple ROIs on one module", "[DetectorGeometry]") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
-    // roi)
     aare::DetectorGeometry geo(aare::xy{1, 1}, 1024, 512);
 
     REQUIRE(geo.get_module_geometries(0).origin_x == 0);
     REQUIRE(geo.get_module_geometries(0).origin_y == 0);
     REQUIRE(geo.get_module_geometries(0).width == 1024);
     REQUIRE(geo.get_module_geometries(0).height == 512);
+    REQUIRE(geo.modules_x() == 1);
+    REQUIRE(geo.modules_y() == 1);
+    REQUIRE(geo.pixels_x() == 1024);
+    REQUIRE(geo.pixels_y() == 512);
 
     SECTION("ROI is the whole module") {
         aare::ROI roi;
@@ -25,14 +28,18 @@ TEST_CASE("Simple ROIs on one module") {
         roi.xmax = 1024;
         roi.ymin = 0;
         roi.ymax = 512;
-        geo.update_geometry_with_roi(roi);
 
-        REQUIRE(geo.pixels_x() == 1024);
+        aare::ROIGeometry roi_geometry(roi, geo);
-        REQUIRE(geo.pixels_y() == 512);
+
-        REQUIRE(geo.modules_x() == 1);
+        REQUIRE(roi_geometry.pixels_x() == 1024);
-        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(roi_geometry.pixels_y() == 512);
-        REQUIRE(geo.get_module_geometries(0).height == 512);
+        REQUIRE(roi_geometry.num_modules_in_roi() == 1);
-        REQUIRE(geo.get_module_geometries(0).width == 1024);
+        auto module_geometry =
+            geo.get_module_geometries(roi_geometry.module_indices_in_roi(0));
+        REQUIRE(module_geometry.height == 512);
+        REQUIRE(module_geometry.width == 1024);
+        REQUIRE(module_geometry.origin_x == 0);
+        REQUIRE(module_geometry.origin_y == 0);
     }
     SECTION("ROI is the top left corner of the module") {
         aare::ROI roi;
@@ -40,51 +47,22 @@ TEST_CASE("Simple ROIs on one module") {
         roi.xmax = 200;
         roi.ymin = 150;
         roi.ymax = 200;
-        geo.update_geometry_with_roi(roi);
 
-        REQUIRE(geo.pixels_x() == 100);
+        aare::ROIGeometry roi_geometry(roi, geo);
-        REQUIRE(geo.pixels_y() == 50);
-        REQUIRE(geo.modules_x() == 1);
-        REQUIRE(geo.modules_y() == 1);
-        REQUIRE(geo.get_module_geometries(0).height == 50);
-        REQUIRE(geo.get_module_geometries(0).width == 100);
-    }
 
-    SECTION("ROI is a small square") {
+        REQUIRE(roi_geometry.pixels_x() == 100);
-        aare::ROI roi;
+        REQUIRE(roi_geometry.pixels_y() == 50);
-        roi.xmin = 1000;
+        REQUIRE(roi_geometry.num_modules_in_roi() == 1);
-        roi.xmax = 1010;
+        auto module_geometry =
-        roi.ymin = 500;
+            geo.get_module_geometries(roi_geometry.module_indices_in_roi(0));
-        roi.ymax = 510;
+        REQUIRE(module_geometry.height == 50);
-        geo.update_geometry_with_roi(roi);
+        REQUIRE(module_geometry.width == 100);
-
+        REQUIRE(module_geometry.origin_x == 0);
-        REQUIRE(geo.pixels_x() == 10);
+        REQUIRE(module_geometry.origin_y == 0);
-        REQUIRE(geo.pixels_y() == 10);
-        REQUIRE(geo.modules_x() == 1);
-        REQUIRE(geo.modules_y() == 1);
-        REQUIRE(geo.get_module_geometries(0).height == 10);
-        REQUIRE(geo.get_module_geometries(0).width == 10);
-    }
-    SECTION("ROI is a few columns") {
-        aare::ROI roi;
-        roi.xmin = 750;
-        roi.xmax = 800;
-        roi.ymin = 0;
-        roi.ymax = 512;
-        geo.update_geometry_with_roi(roi);
-
-        REQUIRE(geo.pixels_x() == 50);
-        REQUIRE(geo.pixels_y() == 512);
-        REQUIRE(geo.modules_x() == 1);
-        REQUIRE(geo.modules_y() == 1);
-        REQUIRE(geo.get_module_geometries(0).height == 512);
-        REQUIRE(geo.get_module_geometries(0).width == 50);
     }
 }
 
-TEST_CASE("Two modules side by side") {
+TEST_CASE("Two modules side by side", "[DetectorGeometry]") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
-    // roi)
     aare::DetectorGeometry geo(aare::xy{1, 2}, 1024, 512);
 
     REQUIRE(geo.get_module_geometries(0).origin_x == 0);
@@ -93,6 +71,10 @@ TEST_CASE("Two modules side by side") {
     REQUIRE(geo.get_module_geometries(0).height == 512);
     REQUIRE(geo.get_module_geometries(1).origin_x == 1024);
     REQUIRE(geo.get_module_geometries(1).origin_y == 0);
+    REQUIRE(geo.modules_x() == 2);
+    REQUIRE(geo.modules_y() == 1);
+    REQUIRE(geo.pixels_x() == 2048);
+    REQUIRE(geo.pixels_y() == 512);
 
     SECTION("ROI is the whole image") {
         aare::ROI roi;
@@ -100,12 +82,24 @@ TEST_CASE("Two modules side by side") {
         roi.xmax = 2048;
         roi.ymin = 0;
         roi.ymax = 512;
-        geo.update_geometry_with_roi(roi);
 
-        REQUIRE(geo.pixels_x() == 2048);
+        aare::ROIGeometry roi_geometry(roi, geo);
-        REQUIRE(geo.pixels_y() == 512);
+
-        REQUIRE(geo.modules_x() == 2);
+        REQUIRE(roi_geometry.pixels_x() == 2048);
-        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(roi_geometry.pixels_y() == 512);
+        REQUIRE(roi_geometry.num_modules_in_roi() == 2);
+
+        auto module_geometry_0 = geo.get_module_geometries(0);
+        auto module_geometry_1 = geo.get_module_geometries(1);
+
+        REQUIRE(module_geometry_0.height == 512);
+        REQUIRE(module_geometry_0.width == 1024);
+        REQUIRE(module_geometry_1.height == 512);
+        REQUIRE(module_geometry_1.width == 1024);
+        REQUIRE(module_geometry_0.origin_x == 0);
+        REQUIRE(module_geometry_1.origin_x == 1024);
+        REQUIRE(module_geometry_0.origin_y == 0);
+        REQUIRE(module_geometry_1.origin_y == 0);
     }
     SECTION("rectangle on both modules") {
         aare::ROI roi;
@@ -113,28 +107,30 @@ TEST_CASE("Two modules side by side") {
         roi.xmax = 1300;
         roi.ymin = 200;
         roi.ymax = 499;
-        geo.update_geometry_with_roi(roi);
 
-        REQUIRE(geo.pixels_x() == 500);
+        aare::ROIGeometry roi_geometry(roi, geo);
-        REQUIRE(geo.pixels_y() == 299);
+
-        REQUIRE(geo.modules_x() == 2);
+        REQUIRE(roi_geometry.pixels_x() == 500);
-        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(roi_geometry.pixels_y() == 299);
-        REQUIRE(geo.get_module_geometries(0).height == 299);
+        REQUIRE(roi_geometry.num_modules_in_roi() == 2);
-        REQUIRE(geo.get_module_geometries(0).width == 224);
+
-        REQUIRE(geo.get_module_geometries(1).height == 299);
+        auto module_geometry_0 = geo.get_module_geometries(0);
-        REQUIRE(geo.get_module_geometries(1).width == 276);
+        auto module_geometry_1 = geo.get_module_geometries(1);
+
+        REQUIRE(module_geometry_0.height == 299);
+        REQUIRE(module_geometry_0.width == 224);
+        REQUIRE(module_geometry_1.height == 299);
+        REQUIRE(module_geometry_1.width == 276);
+        REQUIRE(module_geometry_0.origin_x == 0);
+        REQUIRE(module_geometry_1.origin_x == 224);
+        REQUIRE(module_geometry_0.origin_y == 0);
+        REQUIRE(module_geometry_1.origin_y == 0);
     }
 }
 
-TEST_CASE("Three modules side by side") {
+TEST_CASE("Three modules side by side", "[DetectorGeometry]") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+
-    // roi)
     aare::DetectorGeometry geo(aare::xy{1, 3}, 1024, 512);
-    aare::ROI roi;
-    roi.xmin = 700;
-    roi.xmax = 2500;
-    roi.ymin = 0;
-    roi.ymax = 123;
 
     REQUIRE(geo.get_module_geometries(0).origin_x == 0);
     REQUIRE(geo.get_module_geometries(0).origin_y == 0);
@@ -142,24 +138,78 @@ TEST_CASE("Three modules side by side") {
     REQUIRE(geo.get_module_geometries(0).height == 512);
     REQUIRE(geo.get_module_geometries(1).origin_x == 1024);
     REQUIRE(geo.get_module_geometries(2).origin_x == 2048);
-
-    geo.update_geometry_with_roi(roi);
-
-    REQUIRE(geo.pixels_x() == 1800);
-    REQUIRE(geo.pixels_y() == 123);
     REQUIRE(geo.modules_x() == 3);
     REQUIRE(geo.modules_y() == 1);
-    REQUIRE(geo.get_module_geometries(0).height == 123);
+    REQUIRE(geo.pixels_x() == 3072);
-    REQUIRE(geo.get_module_geometries(0).width == 324);
+    REQUIRE(geo.pixels_y() == 512);
-    REQUIRE(geo.get_module_geometries(1).height == 123);
+
-    REQUIRE(geo.get_module_geometries(1).width == 1024);
+    SECTION("ROI overlapping all three modules") {
-    REQUIRE(geo.get_module_geometries(2).height == 123);
+        aare::ROI roi;
-    REQUIRE(geo.get_module_geometries(2).width == 452);
+        roi.xmin = 500;
+        roi.xmax = 2500;
+        roi.ymin = 0;
+        roi.ymax = 123;
+
+        aare::ROIGeometry roi_geometry(roi, geo);
+        REQUIRE(roi_geometry.pixels_x() == 2000);
+        REQUIRE(roi_geometry.pixels_y() == 123);
+        REQUIRE(roi_geometry.num_modules_in_roi() == 3);
+
+        auto module_geometry_0 = geo.get_module_geometries(0);
+        auto module_geometry_1 = geo.get_module_geometries(1);
+        auto module_geometry_2 = geo.get_module_geometries(2);
+
+        REQUIRE(module_geometry_0.height == 123);
+        REQUIRE(module_geometry_0.width == 524);
+        REQUIRE(module_geometry_0.origin_x == 0);
+        REQUIRE(module_geometry_0.origin_y == 0);
+
+        REQUIRE(module_geometry_1.height == 123);
+        REQUIRE(module_geometry_1.width == 1024);
+        REQUIRE(module_geometry_1.origin_x == 524);
+        REQUIRE(module_geometry_1.origin_y == 0);
+
+        REQUIRE(module_geometry_2.height == 123);
+        REQUIRE(module_geometry_2.width == 452);
+        REQUIRE(module_geometry_2.origin_x == 1548);
+        REQUIRE(module_geometry_2.origin_y == 0);
+    }
+
+    SECTION("ROI overlapping last two modules") {
+        aare::ROI roi;
+        roi.xmin = 1050;
+        roi.xmax = 2500;
+        roi.ymin = 0;
+        roi.ymax = 123;
+
+        aare::ROIGeometry roi_geometry(roi, geo);
+
+        REQUIRE(roi_geometry.pixels_x() == 1450);
+        REQUIRE(roi_geometry.pixels_y() == 123);
+        REQUIRE(roi_geometry.num_modules_in_roi() == 2);
+
+        auto module_geometry_0 = geo.get_module_geometries(0);
+        auto module_geometry_1 = geo.get_module_geometries(1);
+        auto module_geometry_2 = geo.get_module_geometries(2);
+
+        REQUIRE(module_geometry_0.height == 512);
+        REQUIRE(module_geometry_0.width == 1024);
+        REQUIRE(module_geometry_0.origin_x == 0);
+        REQUIRE(module_geometry_0.origin_y == 0);
+
+        REQUIRE(module_geometry_1.height == 123);
+        REQUIRE(module_geometry_1.width == 998);
+        REQUIRE(module_geometry_1.origin_x == 0);
+        REQUIRE(module_geometry_1.origin_y == 0);
+
+        REQUIRE(module_geometry_2.height == 123);
+        REQUIRE(module_geometry_2.width == 452);
+        REQUIRE(module_geometry_2.origin_x == 998);
+        REQUIRE(module_geometry_2.origin_y == 0);
+    }
 }
 
-TEST_CASE("Four modules as a square") {
+TEST_CASE("Four modules as a square", "[DetectorGeometry]") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
-    // roi)
     aare::DetectorGeometry geo(aare::xy{2, 2}, 1024, 512, aare::xy{1, 2});
     aare::ROI roi;
     roi.xmin = 500;
@@ -177,19 +227,99 @@ TEST_CASE("Four modules as a square") {
     REQUIRE(geo.get_module_geometries(2).origin_y == 512);
     REQUIRE(geo.get_module_geometries(3).origin_x == 1024);
     REQUIRE(geo.get_module_geometries(3).origin_y == 512);
-
-    geo.update_geometry_with_roi(roi);
-
-    REQUIRE(geo.pixels_x() == 1500);
-    REQUIRE(geo.pixels_y() == 100);
     REQUIRE(geo.modules_x() == 2);
     REQUIRE(geo.modules_y() == 2);
+    REQUIRE(geo.pixels_x() == 2048);
+    REQUIRE(geo.pixels_y() == 1024);
+
+    aare::ROIGeometry roi_geometry(roi, geo);
+
+    REQUIRE(roi_geometry.pixels_x() == 1500);
+    REQUIRE(roi_geometry.pixels_y() == 100);
+    REQUIRE(roi_geometry.num_modules_in_roi() == 4);
+
     REQUIRE(geo.get_module_geometries(0).height == 12);
     REQUIRE(geo.get_module_geometries(0).width == 524);
+    REQUIRE(geo.get_module_geometries(0).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(0).origin_y == 0);
+
     REQUIRE(geo.get_module_geometries(1).height == 12);
     REQUIRE(geo.get_module_geometries(1).width == 976);
+    REQUIRE(geo.get_module_geometries(1).origin_x == 524);
+    REQUIRE(geo.get_module_geometries(1).origin_y == 0);
+
     REQUIRE(geo.get_module_geometries(2).height == 88);
     REQUIRE(geo.get_module_geometries(2).width == 524);
+    REQUIRE(geo.get_module_geometries(2).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(2).origin_y == 12);
+
     REQUIRE(geo.get_module_geometries(3).height == 88);
     REQUIRE(geo.get_module_geometries(3).width == 976);
+    REQUIRE(geo.get_module_geometries(3).origin_x == 524);
+    REQUIRE(geo.get_module_geometries(3).origin_y == 12);
+}
+
+TEST_CASE("check if module in ROI", "[DetectorGeometry]") {
+    aare::DetectorGeometry geo(aare::xy{2, 2}, 1024, 512, aare::xy{1, 2});
+
+    SECTION("all modules in ROI") {
+        aare::ROI roi;
+        roi.xmin = 500;
+        roi.xmax = 2000;
+        roi.ymin = 500;
+        roi.ymax = 600;
+
+        REQUIRE(geo.get_module_geometries(0).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(1).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(2).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(3).module_in_roi(roi) == true);
+    }
+    SECTION("some modules on border of ROI") {
+        aare::ROI roi;
+        roi.xmin = 1024;
+        roi.xmax = 2000;
+        roi.ymin = 500;
+        roi.ymax = 600;
+
+        REQUIRE(geo.get_module_geometries(0).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(1).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(2).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(3).module_in_roi(roi) == true);
+    }
+    SECTION("one module on border of ROI") {
+        aare::ROI roi;
+        roi.xmin = 1025;
+        roi.xmax = 2000;
+        roi.ymin = 513;
+        roi.ymax = 600;
+
+        REQUIRE(geo.get_module_geometries(0).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(1).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(2).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(3).module_in_roi(roi) == true);
+    }
+    SECTION("some modules to the left of ROI") {
+        aare::ROI roi;
+        roi.xmin = 500;
+        roi.xmax = 1024;
+        roi.ymin = 500;
+        roi.ymax = 600;
+
+        REQUIRE(geo.get_module_geometries(0).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(1).module_in_roi(roi) == false);
+        REQUIRE(geo.get_module_geometries(2).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(3).module_in_roi(roi) == false);
+    }
+    SECTION("all modules in ROI") {
+        aare::ROI roi;
+        roi.xmin = 500;
+        roi.xmax = 2000;
+        roi.ymin = 10;
+        roi.ymax = 513;
+
+        REQUIRE(geo.get_module_geometries(0).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(1).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(2).module_in_roi(roi) == true);
+        REQUIRE(geo.get_module_geometries(3).module_in_roi(roi) == true);
+    }
 }

src/ROIGeometry.cpp

@@ -0,0 +1,42 @@
+#include "aare/ROIGeometry.hpp"
+#include <vector>
+
+namespace aare {
+
+ROIGeometry::ROIGeometry(const ROI &roi, DetectorGeometry &geometry)
+    : m_pixels_x(roi.width()), m_pixels_y(roi.height()), m_geometry(geometry) {
+    m_module_indices_in_roi.reserve(m_geometry.n_modules());
+    // determine which modules are in the roi
+    for (size_t i = 0; i < m_geometry.n_modules(); ++i) {
+        auto &module_geometry = m_geometry.get_module_geometries(i);
+        if (module_geometry.module_in_roi(roi)) {
+            module_geometry.update_geometry_with_roi(roi);
+            m_module_indices_in_roi.push_back(i);
+        }
+    }
+};
+
+ROIGeometry::ROIGeometry(DetectorGeometry &geometry)
+    : m_pixels_x(geometry.pixels_x()), m_pixels_y(geometry.pixels_y()),
+      m_geometry(geometry) {
+    m_module_indices_in_roi.resize(m_geometry.n_modules());
+    std::iota(m_module_indices_in_roi.begin(), m_module_indices_in_roi.end(),
+              0);
+};
+
+size_t ROIGeometry::num_modules_in_roi() const {
+    return m_module_indices_in_roi.size();
+}
+
+const std::vector<size_t> &ROIGeometry::module_indices_in_roi() const {
+    return m_module_indices_in_roi;
+}
+
+size_t ROIGeometry::module_indices_in_roi(const size_t module_index) const {
+    return m_module_indices_in_roi.at(module_index);
+}
+
+size_t ROIGeometry::pixels_x() const { return m_pixels_x; }
+size_t ROIGeometry::pixels_y() const { return m_pixels_y; }
+
+} // namespace aare

src/RawFile.cpp

@@ -2,6 +2,7 @@
 #include "aare/RawFile.hpp"
 #include "aare/DetectorGeometry.hpp"
 #include "aare/PixelMap.hpp"
+#include "aare/ROIGeometry.hpp"
 #include "aare/algorithm.hpp"
 #include "aare/defs.hpp"
 #include "aare/logger.hpp"
@@ -17,28 +18,98 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
     : m_master(fname),
       m_geometry(m_master.geometry(), m_master.pixels_x(), m_master.pixels_y(),
                  m_master.udp_interfaces_per_module(), m_master.quad()) {
+
     m_mode = mode;
 
+    m_subfiles.resize(m_master.rois().has_value() ? m_master.rois()->size()
+                                                  : 1);
+
     if (mode == "r") {
-        if (m_master.roi()) {
+        if (m_master.rois().has_value()) {
-            m_geometry.update_geometry_with_roi(m_master.roi().value());
+            m_ROI_geometries.reserve(m_master.rois()->size());
+
+            // iterate over all ROIS
+            size_t roi_index = 0;
+            const auto rois = m_master.rois().value();
+            for (const auto &roi : rois) {
+                m_ROI_geometries.push_back(ROIGeometry(roi, m_geometry));
+                // open subfiles
+                open_subfiles(roi_index);
+                ++roi_index;
+            }
+
+        } else {
+            // no ROI use full detector
+            m_ROI_geometries.reserve(1);
+            m_ROI_geometries.push_back(ROIGeometry(m_geometry));
+            open_subfiles(0);
         }
-        open_subfiles();
     } else {
         throw std::runtime_error(LOCATION +
                                  " Unsupported mode. Can only read RawFiles.");
     }
 }
 
-Frame RawFile::read_frame() { return get_frame(m_current_frame++); }
+Frame RawFile::read_roi(const size_t roi_index) {
+
+    if (!m_master.rois()) {
+        throw std::runtime_error(LOCATION +
+                                 "No ROIs defined in the master file.");
+    }
+    if (roi_index >= m_ROI_geometries.size()) {
+        throw std::runtime_error(LOCATION + "ROI index out of range.");
+    }
+    return get_frame(m_current_frame++, roi_index);
+}
+
+
+std::vector<Frame> RawFile::read_rois() {
+
+    if (!m_master.rois()) {
+        throw std::runtime_error(LOCATION +
+                                 "No ROIs defined in the master file.");
+    }
+
+    const size_t num_rois = m_ROI_geometries.size();
+
+    std::vector<Frame> frames;
+    frames.reserve(num_rois);
+
+    for (size_t roi_idx = 0; roi_idx < num_rois; ++roi_idx) {
+        frames.push_back(get_frame(m_current_frame, roi_idx));
+    }
+    ++m_current_frame;
+
+    return frames;
+}
+
+
+
+Frame RawFile::read_frame() {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Multiple ROIs defined in the master file. "
+                                 "Use read_ROIs() instead.");
+    }
+    return get_frame(m_current_frame++);
+}
 
 Frame RawFile::read_frame(size_t frame_number) {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(
+            LOCATION + "Multiple ROIs defined in the master file. "
+                       "Use read_ROIs(const size_t frame_number) instead.");
+    }
     seek(frame_number);
     return read_frame();
 }
 
 void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
     // TODO: implement this in a more efficient way
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Cannot use read_into for multiple ROIs.");
+    }
 
     for (size_t i = 0; i < n_frames; i++) {
         this->get_frame_into(m_current_frame++, image_buf);
@@ -47,33 +118,83 @@ void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
 }
 
 void RawFile::read_into(std::byte *image_buf) {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Cannot use read_into for multiple ROIs. Use "
+                                 "read_roi_into() for a single ROI instead.");
+    }
     return get_frame_into(m_current_frame++, image_buf);
 }
 
-void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
+void RawFile::read_roi_into(std::byte *image_buf, const size_t roi_index,
+                            const size_t frame_number, DetectorHeader *header) {
+    if (!m_master.rois().has_value()) {
+        throw std::runtime_error(LOCATION +
+                                 "No ROIs defined in the master file.");
+    }
+    if (roi_index >= num_rois()) {
+        throw std::runtime_error(LOCATION + "ROI index out of range.");
+    }
+    return get_frame_into(frame_number, image_buf, roi_index, header);
+}
 
-    return get_frame_into(m_current_frame++, image_buf, header);
+void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Cannot use read_into for multiple ROIs. Use "
+                                 "read_roi_into() for a single ROI instead.");
+    }
+    return get_frame_into(m_current_frame++, image_buf, 0, header);
 }
 
 void RawFile::read_into(std::byte *image_buf, size_t n_frames,
                         DetectorHeader *header) {
     // return get_frame_into(m_current_frame++, image_buf, header);
 
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(
+            LOCATION +
+            "Cannot use read_into for multiple ROIs."); // TODO: maybe pass
+                                                        // roi_index so one can
+                                                        // use read_into for a
+                                                        // specific ROI
+    }
+
     for (size_t i = 0; i < n_frames; i++) {
-        this->get_frame_into(m_current_frame++, image_buf, header);
+        this->get_frame_into(m_current_frame++, image_buf, 0, header);
         image_buf += bytes_per_frame();
         if (header)
-            header += m_geometry.n_modules_in_roi();
+            header += m_ROI_geometries[0].num_modules_in_roi();
     }
 }
 
 size_t RawFile::bytes_per_frame() {
-    return m_geometry.pixels_x() * m_geometry.pixels_y() * m_master.bitdepth() /
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(
+            LOCATION + "Pass the desired roi_index to bytes_per_frame to get "
+                       "bytes_per_frame for the specific ROI. ");
+    }
+    return bytes_per_frame(0);
+}
+
+size_t RawFile::bytes_per_frame(const size_t roi_index) {
+    return m_ROI_geometries.at(roi_index).pixels_x() *
+           m_ROI_geometries.at(roi_index).pixels_y() * m_master.bitdepth() /
            bits_per_byte;
 }
+
 size_t RawFile::pixels_per_frame() {
-    // return m_rows * m_cols;
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
-    return m_geometry.pixels_x() * m_geometry.pixels_y();
+        throw std::runtime_error(
+            LOCATION + "Pass the desired roi_index to pixels_per_frame to get "
+                       "pixels_per_frame for the specific ROI. ");
+    }
+    return pixels_per_frame(0);
+}
+
+size_t RawFile::pixels_per_frame(const size_t roi_index) {
+    return m_ROI_geometries.at(roi_index).pixels_x() *
+           m_ROI_geometries.at(roi_index).pixels_y();
 }
 
 DetectorType RawFile::detector_type() const { return m_master.detector_type(); }
@@ -93,8 +214,29 @@ void RawFile::seek(size_t frame_index) {
 size_t RawFile::tell() { return m_current_frame; }
 
 size_t RawFile::total_frames() const { return m_master.frames_in_file(); }
-size_t RawFile::rows() const { return m_geometry.pixels_y(); }
+
-size_t RawFile::cols() const { return m_geometry.pixels_x(); }
+size_t RawFile::rows() const {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Pass the desired roi_index to rows to get "
+                                 "rows for the specific ROI. ");
+    }
+    return rows(0);
+}
+size_t RawFile::rows(const size_t roi_index) const {
+    return m_ROI_geometries.at(roi_index).pixels_y();
+}
+size_t RawFile::cols() const {
+    if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Pass the desired roi_index to cols to get "
+                                 "cols for the specific ROI. ");
+    }
+    return cols(0);
+}
+size_t RawFile::cols(const size_t roi_index) const {
+    return m_ROI_geometries.at(roi_index).pixels_x();
+}
 size_t RawFile::bitdepth() const { return m_master.bitdepth(); }
 xy RawFile::geometry() const {
     return xy{static_cast<uint32_t>(m_geometry.modules_y()),
@@ -102,19 +244,46 @@ xy RawFile::geometry() const {
 }
 
 size_t RawFile::n_modules() const { return m_geometry.n_modules(); };
-size_t RawFile::n_modules_in_roi() const {
+
-    return m_geometry.n_modules_in_roi();
+size_t RawFile::num_rois() const {
+    if (m_master.rois().has_value()) {
+        return m_master.rois()->size();
+    } else {
+        return 0;
+    }
 };
 
-void RawFile::open_subfiles() {
+const ROIGeometry &RawFile::roi_geometries(size_t roi_index) const {
-    if (m_mode == "r")
+    return m_ROI_geometries[roi_index];
-        for (size_t i : m_geometry.get_modules_in_roi()) {
+}
-            auto pos = m_geometry.get_module_geometries(i);
+
-            m_subfiles.emplace_back(std::make_unique<RawSubFile>(
+std::vector<size_t> RawFile::n_modules_in_roi() const {
+
+    std::vector<size_t> results(m_ROI_geometries.size());
+    std::transform(
+        m_ROI_geometries.begin(), m_ROI_geometries.end(), results.begin(),
+        [](const ROIGeometry &roi) { return roi.num_modules_in_roi(); });
+    return results;
+};
+
+void RawFile::open_subfiles(const size_t roi_index) {
+
+    if (m_mode == "r") {
+
+        m_subfiles[roi_index].reserve(
+            m_ROI_geometries[roi_index].num_modules_in_roi());
+
+        auto module_indices =
+            m_ROI_geometries[roi_index].module_indices_in_roi();
+
+        for (const size_t i :
+             m_ROI_geometries[roi_index].module_indices_in_roi()) {
+            const auto pos = m_geometry.get_module_geometries(i);
+            m_subfiles[roi_index].emplace_back(std::make_unique<RawSubFile>(
                 m_master.data_fname(i, 0), m_master.detector_type(), pos.height,
                 pos.width, m_master.bitdepth(), pos.row_index, pos.col_index));
         }
-    else {
+    } else {
         throw std::runtime_error(LOCATION +
                                  "Unsupported mode. Can only read RawFiles.");
     }
@@ -139,33 +308,37 @@ DetectorHeader RawFile::read_header(const std::filesystem::path &fname) {
 
 RawMasterFile RawFile::master() const { return m_master; }
 
-Frame RawFile::get_frame(size_t frame_index) {
+Frame RawFile::get_frame(size_t frame_index, const size_t roi_index) {
-    auto f = Frame(m_geometry.pixels_y(), m_geometry.pixels_x(),
+    auto f = Frame(m_ROI_geometries[roi_index].pixels_y(),
+                   m_ROI_geometries[roi_index].pixels_x(),
                    Dtype::from_bitdepth(m_master.bitdepth()));
     std::byte *frame_buffer = f.data();
-    get_frame_into(frame_index, frame_buffer);
+    get_frame_into(frame_index, frame_buffer, roi_index);
     return f;
 }
 
 size_t RawFile::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
 
 void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
-                             DetectorHeader *header) {
+                             const size_t roi_index, DetectorHeader *header) {
     LOG(logDEBUG) << "RawFile::get_frame_into(" << frame_index << ")";
     if (frame_index >= total_frames()) {
         throw std::runtime_error(LOCATION + "Frame number out of range");
     }
-    std::vector<size_t> frame_numbers(m_geometry.n_modules_in_roi());
+    std::vector<size_t> frame_numbers(
-    std::vector<size_t> frame_indices(m_geometry.n_modules_in_roi(),
+        m_ROI_geometries[roi_index].num_modules_in_roi());
-                                      frame_index);
+    std::vector<size_t> frame_indices(
+        m_ROI_geometries[roi_index].num_modules_in_roi(), frame_index);
 
     // sync the frame numbers
 
-    if (m_geometry.n_modules() != 1) { // if we have more than one module
+    if (m_ROI_geometries[roi_index].num_modules_in_roi() !=
-        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+        1) { // if we have more than one module
+        for (size_t part_idx = 0;
+             part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
              ++part_idx) {
             frame_numbers[part_idx] =
-                m_subfiles[part_idx]->frame_number(frame_index);
+                m_subfiles[roi_index][part_idx]->frame_number(frame_index);
         }
 
         // 1. if frame number vector is the same break
@@ -176,7 +349,8 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
                 frame_numbers.begin(),
                 std::min_element(frame_numbers.begin(), frame_numbers.end()));
 
-            // 3. increase its index and update its respective frame number
+            // 3. increase its index and update its respective frame
+            // number
             frame_indices[min_frame_idx]++;
 
             // 4. if we can't increase its index => throw error
@@ -186,42 +360,50 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
             }
 
             frame_numbers[min_frame_idx] =
-                m_subfiles[min_frame_idx]->frame_number(
+                m_subfiles[roi_index][min_frame_idx]->frame_number(
                     frame_indices[min_frame_idx]);
         }
     }
 
     if (m_master.geometry().col == 1) {
         // get the part from each subfile and copy it to the frame
-        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+        for (size_t part_idx = 0;
+             part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
              ++part_idx) {
             auto corrected_idx = frame_indices[part_idx];
 
             // This is where we start writing
-            auto offset = (m_geometry
+            auto offset =
-                                   .get_module_geometries(
+                (m_geometry
-                                       m_geometry.get_modules_in_roi(part_idx))
+                         .get_module_geometries(
-                                   .origin_y *
+                             m_ROI_geometries[roi_index].module_indices_in_roi(
-                               m_geometry.pixels_x() +
+                                 part_idx))
-                           m_geometry
+                         .origin_y *
-                               .get_module_geometries(
+                     m_ROI_geometries[roi_index].pixels_x() +
-                                   m_geometry.get_modules_in_roi(part_idx))
+                 m_geometry
-                               .origin_x) *
+                     .get_module_geometries(
-                          m_master.bitdepth() / 8;
+                         m_ROI_geometries[roi_index].module_indices_in_roi(
+                             part_idx))
+                     .origin_x) *
+                m_master.bitdepth() / 8;
 
             if (m_geometry
                     .get_module_geometries(
-                        m_geometry.get_modules_in_roi(part_idx))
+                        m_ROI_geometries[roi_index].module_indices_in_roi(
+                            part_idx))
                     .origin_x != 0)
                 throw std::runtime_error(
                     LOCATION +
-                    " Implementation error. x pos not 0."); // TODO: origin
+                    " Implementation error. x pos not 0."); // TODO:
+                                                            // origin
                                                             // can still
-                                                            // change if roi
+                                                            // change if
+                                                            // roi
                                                             // changes
             // TODO! What if the files don't match?
-            m_subfiles[part_idx]->seek(corrected_idx);
+            m_subfiles[roi_index][part_idx]->seek(corrected_idx);
-            m_subfiles[part_idx]->read_into(frame_buffer + offset, header);
+            m_subfiles[roi_index][part_idx]->read_into(frame_buffer + offset,
+                                                       header);
             if (header)
                 ++header;
         }
@@ -230,23 +412,25 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
         // TODO! should we read row by row?
 
         // create a buffer large enough to hold a full module
-        auto bytes_per_part = m_master.pixels_y() * m_master.pixels_x() *
+        auto bytes_per_part =
-                              m_master.bitdepth() /
+            m_master.pixels_y() * m_master.pixels_x() * m_master.bitdepth() /
-                              8; // TODO! replace with image_size_in_bytes
+            8; // TODO! replace with image_size_in_bytes // TODO
+               // shouldnt it only be the module size? - check
 
         auto *part_buffer = new std::byte[bytes_per_part];
 
-        // TODO! if we have many submodules we should reorder them on the
+        // TODO! if we have many submodules we should reorder them on
-        // module level
+        // the module level
 
-        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+        for (size_t part_idx = 0;
+             part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
              ++part_idx) {
             auto pos = m_geometry.get_module_geometries(
-                m_geometry.get_modules_in_roi(part_idx));
+                m_ROI_geometries[roi_index].module_indices_in_roi(part_idx));
             auto corrected_idx = frame_indices[part_idx];
 
-            m_subfiles[part_idx]->seek(corrected_idx);
+            m_subfiles[roi_index][part_idx]->seek(corrected_idx);
-            m_subfiles[part_idx]->read_into(part_buffer, header);
+            m_subfiles[roi_index][part_idx]->read_into(part_buffer, header);
             if (header)
                 ++header;
 
@@ -255,7 +439,8 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
 
                 auto irow = (pos.origin_y + cur_row);
                 auto icol = pos.origin_x;
-                auto dest = (irow * this->m_geometry.pixels_x() + icol);
+                auto dest =
+                    (irow * m_ROI_geometries[roi_index].pixels_x() + icol);
                 dest = dest * m_master.bitdepth() / 8;
                 memcpy(frame_buffer + dest,
                        part_buffer +
@@ -269,7 +454,17 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
 
 std::vector<Frame> RawFile::read_n(size_t n_frames) {
     // TODO: implement this in a more efficient way
+    if (num_rois() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Multiple ROIs defined in the master "
+                                 "file. Use "
+                                 "read_num_rois for a specific ROI or use "
+                                 "read_ROIs to read one frame after "
+                                 "the other.");
+    }
+
     std::vector<Frame> frames;
+    frames.reserve(n_frames);
     for (size_t i = 0; i < n_frames; i++) {
         frames.push_back(this->get_frame(m_current_frame));
         m_current_frame++;
@@ -277,11 +472,26 @@ std::vector<Frame> RawFile::read_n(size_t n_frames) {
     return frames;
 }
 
+std::vector<Frame> RawFile::read_n_with_roi(const size_t n_frames,
+                                        const size_t roi_index) {
+    if (roi_index >= num_rois()) {
+        throw std::runtime_error(LOCATION + "ROI index out of range.");
+    }
+
+    std::vector<Frame> frames;
+    frames.reserve(n_frames);
+    for (size_t i = 0; i < n_frames; i++) {
+        frames.push_back(this->get_frame(m_current_frame, roi_index));
+        m_current_frame++;
+    }
+    return frames;
+}
+
 size_t RawFile::frame_number(size_t frame_index) {
     if (frame_index >= m_master.frames_in_file()) {
         throw std::runtime_error(LOCATION + " Frame number out of range");
     }
-    return m_subfiles[0]->frame_number(frame_index);
+    return m_subfiles[0][0]->frame_number(frame_index);
 }
 
 } // namespace aare

src/RawFile.test.cpp

@@ -14,7 +14,8 @@ using aare::File;
 using aare::RawFile;
 using namespace aare;
 
-TEST_CASE("Read number of frames from a jungfrau raw file", "[.with-data]") {
+TEST_CASE("Read number of frames from a jungfrau raw file",
+          "[.with-data][RawFile]") {
 
     auto fpath =
         test_data_path() / "raw/jungfrau/jungfrau_single_master_0.json";
@@ -24,7 +25,8 @@ TEST_CASE("Read number of frames from a jungfrau raw file", "[.with-data]") {
     REQUIRE(f.total_frames() == 10);
 }
 
-TEST_CASE("Read frame numbers from a jungfrau raw file", "[.with-data]") {
+TEST_CASE("Read frame numbers from a jungfrau raw file",
+          "[.with-data][RawFile]") {
     auto fpath =
         test_data_path() / "raw/jungfrau/jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -41,7 +43,7 @@ TEST_CASE("Read frame numbers from a jungfrau raw file", "[.with-data]") {
     }
 }
 
-TEST_CASE("Read a frame number too high throws", "[.with-data]") {
+TEST_CASE("Read a frame number too high throws", "[.with-data][RawFile]") {
     auto fpath =
         test_data_path() / "raw/jungfrau/jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -57,7 +59,7 @@ TEST_CASE("Read a frame number too high throws", "[.with-data]") {
 }
 
 TEST_CASE("Read a frame numbers where the subfile is missing throws",
-          "[.with-data]") {
+          "[.with-data][RawFile]") {
     auto fpath = test_data_path() / "raw/jungfrau" /
                  "jungfrau_missing_subfile_master_0.json";
 
@@ -80,7 +82,7 @@ TEST_CASE("Read a frame numbers where the subfile is missing throws",
 }
 
 TEST_CASE("Read data from a jungfrau 500k single port raw file",
-          "[.with-data]") {
+          "[.with-data][RawFile]") {
     auto fpath =
         test_data_path() / "raw/jungfrau/jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -99,7 +101,7 @@ TEST_CASE("Read data from a jungfrau 500k single port raw file",
     }
 }
 
-TEST_CASE("Read frame numbers from a raw file", "[.with-data]") {
+TEST_CASE("Read frame numbers from a raw file", "[.with-data][RawFile]") {
     auto fpath =
         test_data_path() / "raw/eiger" / "eiger_500k_16bit_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -113,7 +115,8 @@ TEST_CASE("Read frame numbers from a raw file", "[.with-data]") {
     }
 }
 
-TEST_CASE("Compare reading from a numpy file with a raw file", "[.with-data]") {
+TEST_CASE("Compare reading from a numpy file with a raw file",
+          "[.with-data][RawFile]") {
 
     SECTION("jungfrau data") {
         auto fpath_raw =
@@ -155,6 +158,11 @@ TEST_CASE("Compare reading from a numpy file with a raw file", "[.with-data]") {
         auto raw_frame = raw.read_frame();
 
         auto npy_frame = npy.read_frame();
+        CHECK(raw_frame.rows() == 512);
+        CHECK(raw_frame.cols() == 512);
+        CHECK(npy_frame.rows() == 512);
+        CHECK(npy_frame.cols() == 512);
+
         CHECK((raw_frame.view<uint32_t>() == npy_frame.view<uint32_t>()));
     }
     SECTION("eiger data") {
@@ -176,7 +184,7 @@ TEST_CASE("Compare reading from a numpy file with a raw file", "[.with-data]") {
     }
 }
 
-TEST_CASE("Read multipart files", "[.with-data]") {
+TEST_CASE("Read multipart files", "[.with-data][RawFile]") {
     auto fpath =
         test_data_path() / "raw/jungfrau" / "jungfrau_double_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -217,7 +225,7 @@ struct TestParameters {
     std::vector<ModuleGeometry> module_geometries{};
 };
 
-TEST_CASE("check find_geometry", "[.with-data]") {
+TEST_CASE("check find_geometry", "[.with-data][RawFile]") {
 
     auto test_parameters = GENERATE(
         TestParameters{"raw/jungfrau_2modules_version6.1.2/run_master_0.raw", 2,
@@ -290,7 +298,8 @@ TEST_CASE("check find_geometry", "[.with-data]") {
     }
 }
 
-TEST_CASE("Open multi module file with ROI", "[.with-data]") {
+TEST_CASE("Open multi module file with ROI",
+          "[.with-data][read_rois][RawFile]") {
 
     auto fpath =
         test_data_path() / "raw/ROITestData/SingleChipROI/Data_master_0.json";
@@ -304,7 +313,8 @@ TEST_CASE("Open multi module file with ROI", "[.with-data]") {
 
         CHECK(f.n_modules() == 2);
 
-        CHECK(f.n_modules_in_roi() == 1);
+        REQUIRE(f.n_modules_in_roi().size() == 1);
+        CHECK(f.n_modules_in_roi()[0] == 1);
 
         auto frames = f.read_n(2);
 
@@ -315,7 +325,70 @@ TEST_CASE("Open multi module file with ROI", "[.with-data]") {
     }
 }
 
-TEST_CASE("Read file with unordered frames", "[.with-data]") {
+TEST_CASE("Open multi module file with ROI spanning over multiple modules",
+          "[.width-data][read_rois][RawFile]") {
+
+    auto fpath =
+        test_data_path() / "raw/ROITestData/MultipleChipROI/run_master_2.json";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    RawFile f(fpath, "r");
+
+    CHECK(f.n_modules() == 2);
+    CHECK(f.n_modules_in_roi().size() == 1);
+    CHECK(f.n_modules_in_roi()[0] == 2);
+
+    auto frame = f.read_frame();
+
+    CHECK(frame.rows() == 301);
+    CHECK(frame.cols() == 101);
+
+    CHECK(f.rows() == 301);
+    CHECK(f.cols() == 101);
+}
+
+TEST_CASE("Open multi module file with two ROIs",
+          "[.width-data][read_rois][RawFile]") {
+
+    auto fpath =
+        test_data_path() / "raw/ROITestData/MultipleROIs/run_master_0.json";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    RawFile f(fpath, "r");
+
+    CHECK(f.n_modules() == 2);
+    REQUIRE(f.n_modules_in_roi().size() == 2);
+    CHECK(f.n_modules_in_roi()[0] == 1);
+    CHECK(f.n_modules_in_roi()[1] == 1);
+
+    CHECK_THROWS(f.read_frame());
+
+    CHECK(f.tell() == 0);
+
+    auto frame = f.read_rois();
+
+    CHECK(f.tell() == 1);
+
+    REQUIRE(frame.size() == 2);
+
+    CHECK(frame[0].rows() == 301);
+    CHECK(frame[0].cols() == 101);
+    CHECK(frame[1].rows() == 101);
+    CHECK(frame[1].cols() == 101);
+
+    CHECK_THROWS(f.rows());
+    CHECK(f.rows(0) == 301);
+
+    auto frames = f.read_n_with_roi(2, 1);
+    REQUIRE(frames.size() == 2);
+    CHECK(f.tell() == 3);
+    for (const auto &frm : frames) {
+        CHECK(frm.rows() == 101);
+        CHECK(frm.cols() == 101);
+    }
+}
+
+TEST_CASE("Read file with unordered frames", "[.with-data][RawFile]") {
     // TODO! Better explanation and error message
     auto fpath = test_data_path() / "raw/mythen/scan242_master_3.raw";
     REQUIRE(std::filesystem::exists(fpath));
@@ -323,7 +396,7 @@ TEST_CASE("Read file with unordered frames", "[.with-data]") {
     REQUIRE_THROWS((f.read_frame()));
 }
 
-TEST_CASE("Read Mythenframe", "[.with-data]") {
+TEST_CASE("Read Mythenframe", "[.with-data][RawFile]") {
     auto fpath = test_data_path() / "raw/newmythen03/run_2_master_1.json";
     REQUIRE(std::filesystem::exists(fpath));
     RawFile f(fpath);

src/RawMasterFile.cpp

@@ -71,7 +71,7 @@ ScanParameters::ScanParameters(const bool enabled, const DACIndex dac,
                                const int start, const int stop, const int step,
                                const int64_t settleTime)
     : m_enabled(enabled), m_dac(dac), m_start(start), m_stop(stop),
-      m_step(step), m_settleTime(settleTime) {};
+      m_step(step), m_settleTime(settleTime){};
 
 // "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
 ScanParameters::ScanParameters(const std::string &par) {
@@ -193,7 +193,18 @@ ScanParameters RawMasterFile::scan_parameters() const {
     return m_scan_parameters;
 }
 
-std::optional<ROI> RawMasterFile::roi() const { return m_roi; }
+std::optional<ROI> RawMasterFile::roi() const {
+    if (m_rois.value().size() > 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Multiple ROIs present, use rois() method.");
+    } else {
+        return m_rois.has_value()
+                   ? std::optional<ROI>(m_rois.value().at(0))
+                   : std::nullopt; // TODO: maybe throw if no roi exists
+    }
+}
+
+std::optional<std::vector<ROI>> RawMasterFile::rois() const { return m_rois; }
 
 void RawMasterFile::parse_json(std::istream &is) {
     json j;
@@ -255,7 +266,7 @@ void RawMasterFile::parse_json(std::istream &is) {
     m_frame_discard_policy = string_to<FrameDiscardPolicy>(
         j["Frame Discard Policy"].get<std::string>());
 
-    if(j.contains("Number of rows") && j["Number of rows"].is_number()){ 
+    if (j.contains("Number of rows") && j["Number of rows"].is_number()) {
         m_number_of_rows = j["Number of rows"];
     }
 
@@ -338,34 +349,35 @@ void RawMasterFile::parse_json(std::istream &is) {
         }
     }
     try {
-        ROI tmp_roi;
         if (v < 8.0) {
             auto obj = j.at("Receiver Roi");
-            tmp_roi.xmin = obj.at("xmin");
+            if (obj.at("xmin") != 4294967295 || obj.at("xmax") != 4294967295 ||
-            tmp_roi.xmax = obj.at("xmax");
+                obj.at("ymin") != 4294967295 || obj.at("ymax") != 4294967295) {
-            tmp_roi.ymin = obj.at("ymin");
+                // Handle Mythen
-            tmp_roi.ymax = obj.at("ymax");
+                if (obj.at("ymin") == -1 && obj.at("ymax") == -1) {
-        } else {
+                    obj.at("ymin") = 0;
-            // TODO: for now only handle single ROI
+                    obj.at("ymax") = 0;
-            auto obj = j.at("Receiver Rois");
+                }
-            tmp_roi.xmin = obj[0].at("xmin");
+                m_rois.emplace();
-            tmp_roi.xmax = obj[0].at("xmax");
+                m_rois.value().push_back(ROI{
-            tmp_roi.ymin = obj[0].at("ymin");
+                    obj.at("xmin"), static_cast<ssize_t>(obj.at("xmax")) + 1,
-            tmp_roi.ymax = obj[0].at("ymax");
+                    obj.at("ymin"), static_cast<ssize_t>(obj.at("ymax")) + 1});
-        }
+            }
-
+        } else {
-        // if any of the values are set update the roi
+            auto obj = j.at("Receiver Rois");
-        // TODO: doesnt it write garbage if one of them is not set
+            m_rois.emplace();
-        if (tmp_roi.xmin != 4294967295 || tmp_roi.xmax != 4294967295 ||
+            for (auto &elem : obj) {
-            tmp_roi.ymin != 4294967295 || tmp_roi.ymax != 4294967295) {
+                // handle Mythen
-            tmp_roi.xmax++;
+                if (elem.at("ymin") == -1 && elem.at("ymax") == -1) {
-            // Handle Mythen
+                    elem.at("ymin") = 0;
-            if (tmp_roi.ymin == -1 && tmp_roi.ymax == -1) {
+                    elem.at("ymax") = 0;
-                tmp_roi.ymin = 0;
+                }
-                tmp_roi.ymax = 0;
+
+                m_rois.value().push_back(ROI{
+                    elem.at("xmin"), static_cast<ssize_t>(elem.at("xmax")) + 1,
+                    elem.at("ymin"),
+                    static_cast<ssize_t>(elem.at("ymax")) + 1});
             }
-            tmp_roi.ymax++;
-            m_roi = tmp_roi;
         }
 
     } catch (const json::out_of_range &e) {
@@ -380,7 +392,6 @@ void RawMasterFile::parse_json(std::istream &is) {
                 std::stoi(j["Counter Mask"].get<std::string>(), nullptr, 16);
     }
 
-
     // Update detector type for Moench
     // TODO! How does this work with old .raw master files?
     if (m_type == DetectorType::Moench && !m_analog_samples &&