enable tests

- Missing enums
- Matching values to slsDetectorPackage
- tests

.github/workflows/build_docs.yml

@@ -1,10 +1,9 @@
-name: Build the package using cmake then documentation
+name: Build package and docs, test, deploy if on main
 
 on:
   workflow_dispatch:
   push:
-    branches:
-     - main
+    
 
 
 permissions:
@@ -37,16 +36,22 @@ jobs:
           channels: conda-forge
 
       - name: Prepare
-        run: conda install doxygen sphinx=7.1.2 breathe pybind11 sphinx_rtd_theme furo nlohmann_json zeromq fmt numpy
+        run: conda install doxygen sphinx=7.1.2 breathe pybind11 sphinx_rtd_theme furo nlohmann_json zeromq fmt numpy catch2
 
-      - name: Build library 
+      - name: Build 
         run: |
             mkdir build 
             cd build 
-            cmake .. -DAARE_SYSTEM_LIBRARIES=ON -DAARE_DOCS=ON 
+            cmake .. -DAARE_SYSTEM_LIBRARIES=ON -DAARE_TESTS=ON -DAARE_DOCS=ON 
             make -j 2 
             make docs
 
+      - name: Test
+        working-directory: ${{github.workspace}}/build
+        # Execute tests defined by the CMake configuration.
+        # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+        run: ctest -C ${{env.BUILD_TYPE}} -j1
+
       - name: Upload static files as artifact
         id: deployment
         uses: actions/upload-pages-artifact@v3 
@@ -58,6 +63,7 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     needs: build
+    if: github.ref == 'refs/heads/main'
     steps:
       - name: Deploy to GitHub Pages
         id: deployment

.github/workflows/build_pkg.yml

@@ -1,43 +0,0 @@
-name: Build packages but don't deploy
-
-on:
-  workflow_dispatch:
-  push:
-    branches:
-     - main
-     - developer
-
-    #run on PRs as well?
-
-jobs:
-  build:
-    strategy:
-      fail-fast: false
-      matrix:
-        platform: [ubuntu-latest, ] # macos-12, windows-2019]
-        python-version: ["3.12",]
-
-    runs-on: ${{ matrix.platform }}
-
-    # The setup-miniconda action needs this to activate miniconda
-    defaults:
-      run:
-        shell: "bash -l {0}"
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Get conda
-        uses: conda-incubator/setup-miniconda@v3.0.4
-        with:
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-
-      - name: Prepare
-        run: conda install conda-build conda-verify pytest anaconda-client
-
-      - name: Build
-        env:
-          CONDA_TOKEN: ${{ secrets.CONDA_TOKEN }}
-        run: conda build conda-recipe
-

.github/workflows/deploy.yml

@@ -1,7 +1,10 @@
-name: Deploy to slsdetectorgroup conda channel
+name: Build pkgs and deploy if on main
 
 on:
-  workflow_dispatch
+  push:
+    branches:
+     - main
+     - developer
 
 jobs:
   build:
@@ -28,9 +31,10 @@ jobs:
           channels: conda-forge
 
       - name: Prepare
-        run: conda install conda-build conda-verify pytest anaconda-client
+        run: conda install conda-build=24.9 conda-verify pytest anaconda-client
 
       - name: Enable upload
+        if: github.ref == 'refs/heads/main'
         run: conda config --set anaconda_upload yes
 
       - name: Build

CMakeLists.txt

@@ -39,6 +39,7 @@ option(AARE_IN_GITHUB_ACTIONS "Running in Github Actions" OFF)
 option(AARE_DOCS "Build documentation" OFF)
 option(AARE_VERBOSE "Verbose output" OFF)
 option(AARE_CUSTOM_ASSERT "Use custom assert" OFF)
+option(AARE_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/aare/" OFF)
 
 
 # Configure which of the dependencies to use FetchContent for
@@ -241,6 +242,7 @@ target_compile_options(
         -Wextra 
         -pedantic 
         -Wshadow 
+        -Wold-style-cast
         -Wnon-virtual-dtor
         -Woverloaded-virtual
         -Wdouble-promotion
@@ -413,7 +415,7 @@ endif()
 
 add_custom_target(
     clang-tidy
-    COMMAND find \( -path "./src/*" -a -not -path "./src/python/*" -a \( -name "*.cpp"   -not -name "*.test.cpp"\)  \)    -not -name "CircularFifo.hpp" -not -name "ProducerConsumerQueue.hpp" -not -name "VariableSizeClusterFinder.hpp" | xargs -I {} -n 1 -P 10 bash -c "${CLANG_TIDY_COMMAND} --config-file=.clang-tidy -p build {}"
+    COMMAND find \( -path "./src/*" -a -not -path "./src/python/*" -a \( -name "*.cpp"   -not -name "*.test.cpp" \)  \)    -not -name "CircularFifo.hpp" -not -name "ProducerConsumerQueue.hpp" -not -name "VariableSizeClusterFinder.hpp" | xargs -I {} -n 1 -P 10 bash -c "${CLANG_TIDY_COMMAND} --config-file=.clang-tidy -p build {}"
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
     COMMENT "linting with clang-tidy"
     VERBATIM

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: aare
-  version: 2024.11.15.dev0 #TODO! how to not duplicate this?
+  version: 2024.11.28.dev0 #TODO! how to not duplicate this?
 
 
 source:

include/aare/ClusterFile.hpp

@@ -47,6 +47,7 @@ class ClusterFile {
 
   public:
     ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000);
+    ~ClusterFile();
     std::vector<Cluster> read_clusters(size_t n_clusters);
     std::vector<Cluster> read_frame(int32_t &out_fnum);
     std::vector<Cluster>
@@ -59,6 +60,7 @@ class ClusterFile {
                     double *eta3y);
 
     size_t chunk_size() const { return m_chunk_size; }
+    void close();
 
 };
 

include/aare/PixelMap.hpp

@@ -7,6 +7,8 @@ namespace aare {
 
 NDArray<ssize_t, 2> GenerateMoench03PixelMap();
 NDArray<ssize_t, 2> GenerateMoench05PixelMap();
+NDArray<ssize_t, 2> GenerateMoench05PixelMap1g();
+NDArray<ssize_t, 2> GenerateMoench05PixelMapOld();
 
 //Matterhorn02
 NDArray<ssize_t, 2>GenerateMH02SingleCounterPixelMap();

include/aare/RawMasterFile.hpp

@@ -14,6 +14,7 @@ namespace aare {
  * @brief Implementation used in RawMasterFile to parse the file name
  */
 class RawFileNameComponents {
+    bool m_old_scheme{false};
     std::filesystem::path m_base_path{};
     std::string m_base_name{};
     std::string m_ext{};
@@ -35,6 +36,7 @@ class RawFileNameComponents {
     const std::string &base_name() const;
     const std::string &ext() const;
     int file_index() const;
+    void set_old_scheme(bool old_scheme);
 };
 
 class ScanParameters {
@@ -61,14 +63,14 @@ class ScanParameters {
 
 
 struct ROI{
-  size_t xmin{};
-  size_t xmax{};
-  size_t ymin{};
-  size_t ymax{};
+  int64_t xmin{};
+  int64_t xmax{};
+  int64_t ymin{};
+  int64_t ymax{};
 
-  size_t height() const { return ymax - ymin; }
-  size_t width() const { return xmax - xmin; }
-}__attribute__((packed));
+  int64_t height() const { return ymax - ymin; }
+  int64_t width() const { return xmax - xmin; }
+};
 
 
 /**
@@ -88,10 +90,10 @@ class RawMasterFile {
     size_t m_pixels_x{};
     size_t m_bitdepth{};
 
-    xy m_geometry;
+    xy m_geometry{};
 
     size_t m_max_frames_per_file{};
-    uint32_t m_adc_mask{};
+    // uint32_t m_adc_mask{}; // TODO! implement reading
     FrameDiscardPolicy m_frame_discard_policy{};
     size_t m_frame_padding{};
 

include/aare/RawSubFile.hpp

@@ -16,6 +16,7 @@ namespace aare {
 class RawSubFile {
   protected:
     std::ifstream m_file;
+    DetectorType m_detector_type;
     size_t m_bitdepth;
     std::filesystem::path m_fname;
     size_t m_rows{};
@@ -25,7 +26,7 @@ class RawSubFile {
     uint32_t m_pos_row{};
     uint32_t m_pos_col{};
  
-    DetectorType m_detector_type;
+    
     std::optional<NDArray<ssize_t, 2>> m_pixel_map;
 
   public:

include/aare/VarClusterFinder.hpp

@@ -226,7 +226,7 @@ template <typename T> void VarClusterFinder<T>::single_pass(NDView<T, 2> img) {
 
 template <typename T> void VarClusterFinder<T>::first_pass() {
 
-    for (int i = 0; i < original_.size(); ++i) {
+    for (size_t i = 0; i < original_.size(); ++i) {
         if (use_noise_map)
             threshold_ = 5 * noiseMap(i);
         binary_(i) = (original_(i) > threshold_);
@@ -250,17 +250,17 @@ template <typename T> void VarClusterFinder<T>::first_pass() {
 
 template <typename T> void VarClusterFinder<T>::second_pass() {
 
-    for (int64_t i = 0; i != labeled_.size(); ++i) {
-        auto current_label = labeled_(i);
-        if (current_label != 0) {
-            auto it = child.find(current_label);
+    for (size_t i = 0; i != labeled_.size(); ++i) {
+        auto cl = labeled_(i);
+        if (cl != 0) {
+            auto it = child.find(cl);
             while (it != child.end()) {
-                current_label = it->second;
-                it = child.find(current_label);
+                cl = it->second;
+                it = child.find(cl);
                 // do this once before doing the second pass?
                 // all values point to the final one...
             }
-            labeled_(i) = current_label;
+            labeled_(i) = cl;
         }
     }
 }
@@ -271,7 +271,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
     // Do we always have monotonic increasing
     // labels? Then vector?
     // here the translation is label -> Hit
-    std::unordered_map<int, Hit> h_size;
+    std::unordered_map<int, Hit> h_map;
     for (int i = 0; i < shape_[0]; ++i) {
         for (int j = 0; j < shape_[1]; ++j) {
             if (labeled_(i, j) != 0 || false
@@ -280,7 +280,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
                 // (i+1 < shape_[0] and labeled_(i+1, j) != 0) or
                 // (j+1 < shape_[1] and labeled_(i, j+1) != 0)
             ) {
-                Hit &record = h_size[labeled_(i, j)];
+                Hit &record = h_map[labeled_(i, j)];
                 if (record.size < MAX_CLUSTER_SIZE) {
                     record.rows[record.size] = i;
                     record.cols[record.size] = j;
@@ -300,7 +300,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
         }
     }
 
-    for (const auto &h : h_size)
+    for (const auto &h : h_map)
         hits.push_back(h.second);
 }
 

include/aare/defs.hpp

@@ -93,7 +93,7 @@ class DynamicCluster {
         (sizeof(T) == dt.bytes())
             ? 0
             : throw std::invalid_argument("[ERROR] Type size mismatch");
-        return memcpy(m_data + idx * dt.bytes(), &val, (size_t)dt.bytes());
+        return memcpy(m_data + idx * dt.bytes(), &val, dt.bytes());
     }
 
     template <typename T> std::string to_string() const {
@@ -190,14 +190,27 @@ struct ModuleGeometry{
 using dynamic_shape = std::vector<int64_t>;
 
 //TODO! Can we uniform enums between the libraries?
+
+/**
+ * @brief Enum class to identify different detectors. 
+ * The values are the same as in slsDetectorPackage
+ * Different spelling to avoid confusion with the slsDetectorPackage
+ */
 enum class DetectorType {
-    Jungfrau,
+    //Standard detectors match the enum values from slsDetectorPackage
+    Generic,
     Eiger,
-    Mythen3,
-    Moench,
-    Moench03,
-    Moench03_old,
+    Gotthard,
+    Jungfrau,
     ChipTestBoard,
+    Moench,
+    Mythen3,
+    Gotthard2,
+    Xilinx_ChipTestBoard,
+
+    //Additional detectors used for defining processing. Variants of the standard ones.
+    Moench03=100,
+    Moench03_old,
     Unknown
 };
 

pyproject.toml

@@ -4,12 +4,12 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "aare"
-version = "2024.11.15.dev0"
-
+version = "2024.11.28.dev0"
 
 [tool.scikit-build]
 cmake.verbose = true
 
 [tool.scikit-build.cmake.define]
 AARE_PYTHON_BINDINGS = "ON"
-AARE_SYSTEM_LIBRARIES = "ON"
+AARE_SYSTEM_LIBRARIES = "ON"
+AARE_INSTALL_PYTHONEXT = "ON"

python/CMakeLists.txt

@@ -1,5 +1,5 @@
 
-find_package (Python 3.10 COMPONENTS Interpreter Development)
+find_package (Python 3.10 COMPONENTS Interpreter Development REQUIRED)
 
 # Download or find pybind11 depending on configuration
 if(AARE_FETCH_PYBIND11)
@@ -28,8 +28,10 @@ target_link_libraries(_aare PRIVATE aare_core aare_compiler_flags)
 set( PYTHON_FILES
     aare/__init__.py
     aare/CtbRawFile.py
+    aare/RawFile.py
     aare/transform.py
     aare/ScanParameters.py
+    aare/utils.py
 )
 
 # Copy the python files to the build directory
@@ -47,4 +49,11 @@ set_target_properties(_aare PROPERTIES
 configure_file(examples/play.py ${CMAKE_BINARY_DIR}/play.py)
 
 
-install(TARGETS _aare DESTINATION aare)
+if(AARE_INSTALL_PYTHONEXT)
+    install(TARGETS _aare
+        EXPORT "${TARGETS_EXPORT_NAME}"
+        LIBRARY DESTINATION aare
+    )
+
+    install(FILES ${PYTHON_FILES} DESTINATION aare)
+endif()

python/aare/CtbRawFile.py

@@ -2,18 +2,21 @@
 from . import _aare
 import numpy as np
 from .ScanParameters import ScanParameters
+
 class CtbRawFile(_aare.CtbRawFile):
     """File reader for the CTB raw file format.
     
     Args:  
             fname (pathlib.Path | str): Path to the file to be read.
+            chunk_size (int): Number of frames to read at a time. Default is 1.
             transform (function): Function to apply to the data after reading it. 
                 The function should take a numpy array of type uint8 and return one
                 or several numpy arrays.
     """
-    def __init__(self, fname, transform = None):
+    def __init__(self, fname, chunk_size = 1, transform = None):
         super().__init__(fname)
-        self.transform = transform
+        self._chunk_size = chunk_size
+        self._transform = transform
 
 
     def read_frame(self, frame_index: int | None = None ) -> tuple:
@@ -42,8 +45,8 @@ class CtbRawFile(_aare.CtbRawFile):
             header = header[0]
 
 
-        if self.transform:
-            res = self.transform(data)
+        if self._transform:
+            res = self._transform(data)
             if isinstance(res, tuple):
                 return header, *res
             else:
@@ -59,6 +62,10 @@ class CtbRawFile(_aare.CtbRawFile):
             Uses the position of the file pointer :py:meth:`~CtbRawFile.tell` to determine
             where to start reading from.
 
+        If the number of frames requested is larger than the number of frames left in the file,
+        the function will read the remaining frames. If no frames are left in the file
+        a RuntimeError is raised.
+
         Args:
             n_frames (int): Number of frames to read.
 
@@ -68,6 +75,12 @@ class CtbRawFile(_aare.CtbRawFile):
         Raises:
             RuntimeError: If EOF is reached.
         """
+        # Calculate the number of frames to actually read
+        n_frames = min(n_frames, self.frames_in_file - self.tell())
+        if n_frames == 0:
+            raise RuntimeError("No frames left in file.")
+
+
         # Do the first read to figure out what we have
         tmp_header, tmp_data = self.read_frame()
         
@@ -87,10 +100,12 @@ class CtbRawFile(_aare.CtbRawFile):
 
     def read(self) -> tuple:
         """Read the entire file.
+        Seeks to the beginning of the file before reading.
 
         Returns:
             tuple: header, data
         """
+        self.seek(0)
         return self.read_n(self.frames_in_file)
 
     def seek(self, frame_index:int) -> None:
@@ -101,7 +116,7 @@ class CtbRawFile(_aare.CtbRawFile):
         """
         super().seek(frame_index)
 
-    def tell() -> int:
+    def tell(self) -> int:
         """Return the current frame position in the file.
 
         Returns:
@@ -164,7 +179,12 @@ class CtbRawFile(_aare.CtbRawFile):
     
     def __next__(self):
         try:
-            return self.read_frame()
+            if self._chunk_size == 1:
+                return self.read_frame()
+            else:
+                return self.read_n(self._chunk_size)
+            
+                
         except RuntimeError:
             # TODO! find a good way to check that we actually have the right exception
             raise StopIteration

python/aare/RawFile.py

@@ -0,0 +1,66 @@
+from . import _aare
+import numpy as np
+from .ScanParameters import ScanParameters
+
+class RawFile(_aare.RawFile):
+    def __init__(self, fname, chunk_size = 1):
+        super().__init__(fname)
+        self._chunk_size = chunk_size
+
+
+    def read(self) -> tuple:
+        """Read the entire file.
+        Seeks to the beginning of the file before reading.
+
+        Returns:
+            tuple: header, data
+        """
+        self.seek(0)
+        return self.read_n(self.total_frames)
+
+    @property
+    def scan_parameters(self):
+        """Return the scan parameters.
+
+        Returns:
+            ScanParameters: Scan parameters.
+        """
+        return ScanParameters(self.master.scan_parameters)
+    
+    @property
+    def master(self):
+        """Return the master file.
+
+        Returns:
+            RawMasterFile: Master file.
+        """
+        return super().master
+    
+    def __len__(self) -> int:
+        """Return the number of frames in the file.
+
+        Returns:
+            int: Number of frames in file.
+        """
+        return super().frames_in_file
+
+    def __enter__(self):
+        return self
+    
+    def __exit__(self, exc_type, exc_value, traceback):
+        pass
+
+    def __iter__(self):
+        return self
+    
+    def __next__(self):
+        try:
+            if self._chunk_size == 1:
+                return self.read_frame()
+            else:
+                return self.read_n(self._chunk_size)
+            
+                
+        except RuntimeError:
+            # TODO! find a good way to check that we actually have the right exception
+            raise StopIteration

python/aare/__init__.py

@@ -2,10 +2,13 @@
 from . import _aare
 
 
-from ._aare import File, RawFile, RawMasterFile, RawSubFile
+from ._aare import File, RawMasterFile, RawSubFile
 from ._aare import Pedestal, ClusterFinder, VarClusterFinder
 from ._aare import DetectorType
 from ._aare import ClusterFile
 
 from .CtbRawFile import CtbRawFile
-from .ScanParameters import ScanParameters
+from .RawFile import RawFile
+from .ScanParameters import ScanParameters
+
+from .utils import random_pixels, random_pixel

python/aare/transform.py

@@ -9,6 +9,24 @@ class Moench05Transform:
 
     def __call__(self, data):
         return np.take(data.view(np.uint16), self.pixel_map)
+    
+
+class Moench05Transform1g:
+    #Could be moved to C++ without changing the interface
+    def __init__(self):
+        self.pixel_map = _aare.GenerateMoench05PixelMap1g()
+
+    def __call__(self, data):
+        return np.take(data.view(np.uint16), self.pixel_map)
+    
+
+class Moench05TransformOld:
+    #Could be moved to C++ without changing the interface
+    def __init__(self):
+        self.pixel_map = _aare.GenerateMoench05PixelMapOld()
+
+    def __call__(self, data):
+        return np.take(data.view(np.uint16), self.pixel_map)
 
 
 class Matterhorn02Transform:
@@ -25,4 +43,6 @@ class Matterhorn02Transform:
 
 #on import generate the pixel maps to avoid doing it every time
 moench05 = Moench05Transform()
+moench05_1g = Moench05Transform1g()
+moench05_old = Moench05TransformOld()
 matterhorn02 = Matterhorn02Transform()

python/aare/utils.py

@@ -0,0 +1,23 @@
+import numpy as np
+
+def random_pixels(n_pixels, xmin=0, xmax=512, ymin=0, ymax=1024):
+    """Return a list of random pixels.
+    
+    Args:
+        n_pixels (int): Number of pixels to return.
+        rows (int): Number of rows in the image.
+        cols (int): Number of columns in the image.
+        
+    Returns:
+        list: List of (row, col) tuples.
+    """
+    return [(np.random.randint(ymin, ymax), np.random.randint(xmin, xmax)) for _ in range(n_pixels)]
+
+
+def random_pixel(xmin=0, xmax=512, ymin=0, ymax=1024):
+    """Return a random pixel.
+    
+    Returns:
+        tuple: (row, col)
+    """
+    return random_pixels(1, xmin, xmax, ymin, ymax)[0]

python/src/cluster.hpp

@@ -21,9 +21,9 @@ void define_cluster_finder_bindings(py::module &m) {
              })
         .def("pedestal",
              [](ClusterFinder<uint16_t, double> &self) {
-                 auto m = new NDArray<double, 2>{};
-                 *m = self.pedestal();
-                 return return_image_data(m);
+                 auto pd = new NDArray<double, 2>{};
+                 *pd = self.pedestal();
+                 return return_image_data(pd);
              })
         .def("find_clusters_without_threshold",
              [](ClusterFinder<uint16_t, double> &self,

python/src/cluster_file.hpp

@@ -37,7 +37,7 @@ void define_cluster_file_io_bindings(py::module &m) {
                  return return_vector(vec);
              })
         .def("__enter__", [](ClusterFile &self) { return &self; })
-        .def("__exit__", [](ClusterFile &self, py::args args) { return; })
+        .def("__exit__", [](ClusterFile &self) {  self.close();})
         .def("__iter__", [](ClusterFile &self) { return &self; })
         .def("__next__", [](ClusterFile &self) {
             auto vec =  new std::vector<Cluster>(self.read_clusters(self.chunk_size()));

python/src/ctb_raw_file.hpp

@@ -0,0 +1,57 @@
+
+#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_ctb_raw_file_io_bindings(py::module &m) {
+
+ py::class_<CtbRawFile>(m, "CtbRawFile")
+        .def(py::init<const std::filesystem::path &>())
+        .def("read_frame",
+             [](CtbRawFile &self) {
+                 size_t image_size = self.image_size_in_bytes();
+                 py::array image;
+                 std::vector<ssize_t> shape;
+                 shape.reserve(2);
+                 shape.push_back(1);
+                 shape.push_back(image_size);
+
+                 py::array_t<DetectorHeader> header(1);
+
+                 // always read bytes
+                 image = py::array_t<uint8_t>(shape);
+
+                 self.read_into(
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
+                     header.mutable_data());
+
+                 return py::make_tuple(header, image);
+             })
+        .def("seek", &CtbRawFile::seek)
+        .def("tell", &CtbRawFile::tell)
+        .def("master", &CtbRawFile::master)
+
+        .def_property_readonly("image_size_in_bytes",
+                               &CtbRawFile::image_size_in_bytes)
+
+        .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
+
+}

python/src/file.hpp

@@ -38,36 +38,7 @@ void define_file_io_bindings(py::module &m) {
                          bunchId, timestamp, modId, row, column, reserved,
                          debug, roundRNumber, detType, version, packetMask);
 
-    py::class_<CtbRawFile>(m, "CtbRawFile")
-        .def(py::init<const std::filesystem::path &>())
-        .def("read_frame",
-             [](CtbRawFile &self) {
-                 size_t image_size = self.image_size_in_bytes();
-                 py::array image;
-                 std::vector<ssize_t> shape;
-                 shape.reserve(2);
-                 shape.push_back(1);
-                 shape.push_back(image_size);
-
-                 py::array_t<DetectorHeader> header(1);
-
-                 // always read bytes
-                 image = py::array_t<uint8_t>(shape);
-
-                 self.read_into(
-                     reinterpret_cast<std::byte *>(image.mutable_data()),
-                     header.mutable_data());
-
-                 return py::make_tuple(header, image);
-             })
-        .def("seek", &CtbRawFile::seek)
-        .def("tell", &CtbRawFile::tell)
-        .def("master", &CtbRawFile::master)
-
-        .def_property_readonly("image_size_in_bytes",
-                               &CtbRawFile::image_size_in_bytes)
-
-        .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
+   
 
     py::class_<File>(m, "File")
         .def(py::init([](const std::filesystem::path &fname) {
@@ -133,13 +104,15 @@ void define_file_io_bindings(py::module &m) {
                  return image;
              })
         .def("read_n", [](File &self, size_t n_frames) {
-            const uint8_t item_size = self.bytes_per_pixel();
+            //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()};
+            
             py::array image;
-            std::vector<ssize_t> shape;
-            shape.reserve(3);
-            shape.push_back(n_frames);
-            shape.push_back(self.rows());
-            shape.push_back(self.cols());
+            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) {
@@ -194,7 +167,7 @@ void define_file_io_bindings(py::module &m) {
             return fmt::format("<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin, self.xmax, self.ymin, self.ymax);
         })
         .def("__iter__", [](const ROI &self) {
-            return py::make_iterator(&self.xmin, &self.ymax+1);
+            return py::make_iterator(&self.xmin, &self.ymax+1); //NOLINT
         });
 
     

python/src/module.cpp

@@ -1,6 +1,7 @@
 //Files with bindings to the different classes
 #include "file.hpp"
 #include "raw_file.hpp"
+#include "ctb_raw_file.hpp"
 #include "raw_master_file.hpp"
 #include "var_cluster.hpp"
 #include "pixel_map.hpp"
@@ -17,6 +18,7 @@ namespace py = pybind11;
 PYBIND11_MODULE(_aare, m) {
     define_file_io_bindings(m);
     define_raw_file_io_bindings(m);
+    define_ctb_raw_file_io_bindings(m);
     define_raw_master_file_bindings(m);
     define_var_cluster_finder_bindings(m);
     define_pixel_map_bindings(m);

python/src/pedestal.hpp

@@ -15,19 +15,19 @@ template <typename SUM_TYPE> void define_pedestal_bindings(py::module &m, const
         .def(py::init<int, int>())
         .def("mean",
              [](Pedestal<SUM_TYPE> &self) {
-                 auto m = new NDArray<SUM_TYPE, 2>{};
-                 *m = self.mean();
-                 return return_image_data(m);
+                 auto mea = new NDArray<SUM_TYPE, 2>{};
+                 *mea = self.mean();
+                 return return_image_data(mea);
              })
         .def("variance", [](Pedestal<SUM_TYPE> &self) {
-            auto m = new NDArray<SUM_TYPE, 2>{};
-            *m = self.variance();
-            return return_image_data(m);
+            auto var = new NDArray<SUM_TYPE, 2>{};
+            *var = self.variance();
+            return return_image_data(var);
         })
         .def("std", [](Pedestal<SUM_TYPE> &self) {
-            auto m = new NDArray<SUM_TYPE, 2>{};
-            *m = self.std();
-            return return_image_data(m);
+            auto std = new NDArray<SUM_TYPE, 2>{};
+            *std = self.std();
+            return return_image_data(std);
         })
         .def("clear", py::overload_cast<>(&Pedestal<SUM_TYPE>::clear))
         .def_property_readonly("rows", &Pedestal<SUM_TYPE>::rows)

python/src/pixel_map.hpp

@@ -20,6 +20,14 @@ void define_pixel_map_bindings(py::module &m) {
     .def("GenerateMoench05PixelMap", []() {
         auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap());
         return return_image_data(ptr);
+    })
+        .def("GenerateMoench05PixelMap1g", []() {
+        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap1g());
+        return return_image_data(ptr);
+    })
+    .def("GenerateMoench05PixelMapOld", []() {
+        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMapOld());
+        return return_image_data(ptr);
     })
     .def("GenerateMH02SingleCounterPixelMap", []() {
         auto ptr = new NDArray<ssize_t,2>(GenerateMH02SingleCounterPixelMap());

python/src/raw_file.hpp

@@ -25,7 +25,6 @@ void define_raw_file_io_bindings(py::module &m) {
         .def(py::init<const std::filesystem::path &>())
         .def("read_frame",
              [](RawFile &self) {
-                 size_t image_size = self.bytes_per_frame();
                  py::array image;
                  std::vector<ssize_t> shape;
                  shape.reserve(2);
@@ -49,32 +48,44 @@ void define_raw_file_io_bindings(py::module &m) {
 
                  return py::make_tuple(header, image);
              })
-        .def("read_n",
-             [](RawFile &self, size_t n_frames) {
-                 py::array image;
-                 std::vector<ssize_t> shape;
-                 shape.reserve(3);
-                 shape.push_back(n_frames);
-                 shape.push_back(self.rows());
-                 shape.push_back(self.cols());
+        .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_mod() == 1) {
+                    header = py::array_t<DetectorHeader>(n_frames);
+                } else {
+                    header = py::array_t<DetectorHeader>({self.n_mod(), n_frames});
+                }
+                // py::array_t<DetectorHeader> header({self.n_mod(), n_frames});
 
-                 // return headers from all subfiles
-                 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());
 
-                 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);
-             })
+                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)

src/ClusterFile.cpp

@@ -9,6 +9,17 @@ ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size):
     }
 }
 
+ClusterFile::~ClusterFile() {
+    close();
+}
+
+void ClusterFile::close(){
+    if (fp){
+        fclose(fp);
+        fp = nullptr;
+    }  
+}
+
 std::vector<Cluster> ClusterFile::read_clusters(size_t n_clusters) {
     std::vector<Cluster> clusters(n_clusters);
 
@@ -27,7 +38,7 @@ std::vector<Cluster> ClusterFile::read_clusters(size_t n_clusters) {
         } else {
             nn = nph;
         }
-        nph_read += fread((void *)(buf + nph_read), sizeof(Cluster), nn, fp);
+        nph_read += fread(reinterpret_cast<void *>(buf + nph_read), sizeof(Cluster), nn, fp);
         m_num_left = nph - nn; // write back the number of photons left
     }
 
@@ -42,7 +53,7 @@ std::vector<Cluster> ClusterFile::read_clusters(size_t n_clusters) {
                     nn = nph;
 
                 nph_read +=
-                    fread((void *)(buf + nph_read), sizeof(Cluster), nn, fp);
+                    fread(reinterpret_cast<void *>(buf + nph_read), sizeof(Cluster), nn, fp);
                 m_num_left = nph - nn;
             }
             if (nph_read >= n_clusters)
@@ -65,13 +76,13 @@ std::vector<Cluster> ClusterFile::read_frame(int32_t &out_fnum) {
         throw std::runtime_error("Could not read frame number");
     }
 
-    int n_clusters;
+    int32_t n_clusters; // Saved as 32bit integer in the cluster file
     if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
         throw std::runtime_error("Could not read number of clusters");
     }
     std::vector<Cluster> clusters(n_clusters);
 
-    if (fread(clusters.data(), sizeof(Cluster), n_clusters, fp) != n_clusters) {
+    if (fread(clusters.data(), sizeof(Cluster), n_clusters, fp) != static_cast<size_t>(n_clusters)) {
         throw std::runtime_error("Could not read clusters");
     }
     return clusters;
@@ -113,7 +124,7 @@ std::vector<Cluster> ClusterFile::read_cluster_with_cut(size_t n_clusters,
         }
         for (size_t iph = 0; iph < nn; iph++) {
             // read photons 1 by 1
-            size_t n_read = fread((void *)(ptr), sizeof(Cluster), 1, fp);
+            size_t n_read = fread(reinterpret_cast<void *>(ptr), sizeof(Cluster), 1, fp);
             if (n_read != 1) {
                 clusters.resize(nph_read);
                 return clusters;
@@ -158,7 +169,7 @@ std::vector<Cluster> ClusterFile::read_cluster_with_cut(size_t n_clusters,
                     for (size_t iph = 0; iph < nph; iph++) {
     //                     // read photons 1 by 1
                         size_t n_read =
-                            fread((void *)(ptr), sizeof(Cluster), 1, fp);
+                            fread(reinterpret_cast<void *>(ptr), sizeof(Cluster), 1, fp);
                         if (n_read != 1) {
                             clusters.resize(nph_read);
                             return clusters;
@@ -269,27 +280,27 @@ int ClusterFile::analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *qua
         switch (c) {
         case cBottomLeft:
             if (eta2x && (data[3] + data[4]) != 0)
-                *eta2x = (double)(data[4]) / (data[3] + data[4]);
+                *eta2x = static_cast<double>(data[4]) / (data[3] + data[4]);
             if (eta2y && (data[1] + data[4]) != 0)
-                *eta2y = (double)(data[4]) / (data[1] + data[4]);
+                *eta2y = static_cast<double>(data[4]) / (data[1] + data[4]);
             break;
         case cBottomRight:
             if (eta2x && (data[2] + data[5]) != 0)
-                *eta2x = (double)(data[5]) / (data[4] + data[5]);
+                *eta2x = static_cast<double>(data[5]) / (data[4] + data[5]);
             if (eta2y && (data[1] + data[4]) != 0)
-                *eta2y = (double)(data[4]) / (data[1] + data[4]);
+                *eta2y = static_cast<double>(data[4]) / (data[1] + data[4]);
             break;
         case cTopLeft:
             if (eta2x && (data[7] + data[4]) != 0)
-                *eta2x = (double)(data[4]) / (data[3] + data[4]);
+                *eta2x = static_cast<double>(data[4]) / (data[3] + data[4]);
             if (eta2y && (data[7] + data[4]) != 0)
-                *eta2y = (double)(data[7]) / (data[7] + data[4]);
+                *eta2y = static_cast<double>(data[7]) / (data[7] + data[4]);
             break;
         case cTopRight:
             if (eta2x && t2max != 0)
-                *eta2x = (double)(data[5]) / (data[5] + data[4]);
+                *eta2x = static_cast<double>(data[5]) / (data[5] + data[4]);
             if (eta2y && t2max != 0)
-                *eta2y = (double)(data[7]) / (data[7] + data[4]);
+                *eta2y = static_cast<double>(data[7]) / (data[7] + data[4]);
             break;
         default:;
         }
@@ -297,10 +308,10 @@ int ClusterFile::analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *qua
 
     if (eta3x || eta3y) {
         if (eta3x && (data[3] + data[4] + data[5]) != 0)
-            *eta3x = (double)(-data[3] + data[3 + 2]) /
+            *eta3x = static_cast<double>(-data[3] + data[3 + 2]) /
                      (data[3] + data[4] + data[5]);
         if (eta3y && (data[1] + data[4] + data[7]) != 0)
-            *eta3y = (double)(-data[1] + data[2 * 3 + 1]) /
+            *eta3y = static_cast<double>(-data[1] + data[2 * 3 + 1]) /
                      (data[1] + data[4] + data[7]);
     }
 

src/CtbRawFile.cpp

@@ -16,7 +16,7 @@ CtbRawFile::CtbRawFile(const std::filesystem::path &fname) : m_master(fname) {
 
 void CtbRawFile::read_into(std::byte *image_buf, DetectorHeader* header) {
     if(m_current_frame >= m_master.frames_in_file()){
-        throw std::runtime_error(LOCATION + "End of file reached");
+        throw std::runtime_error(LOCATION + " End of file reached");
     }
 
     if(m_current_frame != 0 && m_current_frame % m_master.max_frames_per_file() == 0){

src/PixelMap.cpp

@@ -31,6 +31,49 @@ NDArray<ssize_t, 2> GenerateMoench03PixelMap() {
 }
 
 NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
+    std::array<int, 3> adc_numbers = {5, 9, 1};  
+    NDArray<ssize_t, 2> order_map({160, 150});
+    int n_pixel = 0;
+    for (int row = 0; row < 160; row++) {
+        for (int i_col = 0; i_col < 50; i_col++) {
+            n_pixel = row * 50 + i_col;
+            for (int i_sc = 0; i_sc < 3; i_sc++) {
+                int col = 50 * i_sc + i_col;
+                int adc_nr = adc_numbers[i_sc];
+                int i_analog = n_pixel * 12 + adc_nr;  
+
+                // analog_frame[row * 150 + col] = analog_data[i_analog] & 0x3FFF;
+                order_map(row, col) = i_analog;
+                
+            }
+        }
+    }
+    return order_map;
+}
+
+NDArray<ssize_t, 2> GenerateMoench05PixelMap1g() {
+    std::array<int, 3> adc_numbers = {1, 2, 0}; 
+    NDArray<ssize_t, 2> order_map({160, 150});
+    int n_pixel = 0;
+    for (int row = 0; row < 160; row++) {
+        for (int i_col = 0; i_col < 50; i_col++) {
+            n_pixel = row * 50 + i_col;
+            for (int i_sc = 0; i_sc < 3; i_sc++) {
+                int col = 50 * i_sc + i_col;
+                int adc_nr = adc_numbers[i_sc];
+                int i_analog = n_pixel * 3 + adc_nr;  
+
+
+                // analog_frame[row * 150 + col] = analog_data[i_analog] & 0x3FFF;
+                order_map(row, col) = i_analog;
+                
+            }
+        }
+    }
+    return order_map;
+}
+
+NDArray<ssize_t, 2> GenerateMoench05PixelMapOld() {
     std::array<int, 3> adc_numbers = {9, 13, 1};
     NDArray<ssize_t, 2> order_map({160, 150});
     int n_pixel = 0;

src/RawFile.cpp

@@ -17,6 +17,9 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
         n_subfiles = find_number_of_subfiles(); // f0,f1...fn
         n_subfile_parts =
             m_master.geometry().col * m_master.geometry().row; // d0,d1...dn
+
+        
+
         find_geometry();
         update_geometry_with_roi();
 
@@ -99,10 +102,7 @@ void RawFile::open_subfiles() {
         for (size_t i = 0; i != n_subfiles; ++i) {
             auto v = std::vector<RawSubFile *>(n_subfile_parts);
             for (size_t j = 0; j != n_subfile_parts; ++j) {
-                fmt::print("{} pos: {},{}\n", j,positions[j].row, positions[j].col);
-                
                 auto pos = m_module_pixel_0[j];
-                fmt::print("{} pos: {},{}\n", j,pos.y, pos.x);
                 v[j] = new RawSubFile(m_master.data_fname(j, i),
                                       m_master.detector_type(), pos.height,
                                       pos.width, m_master.bitdepth(),
@@ -266,8 +266,7 @@ size_t RawFile::bytes_per_pixel() const {
 }
 
 void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header) {
-
-    if (frame_index > total_frames()) {
+    if (frame_index >= total_frames()) {
         throw std::runtime_error(LOCATION + "Frame number out of range");
     }
     std::vector<size_t> frame_numbers(n_subfile_parts);
@@ -319,7 +318,8 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
 
             if (m_module_pixel_0[part_idx].x!=0)
                 throw std::runtime_error(LOCATION + "Implementation error. x pos not 0.");
-
+            
+            //TODO! Risk for out of range access
             subfiles[subfile_id][part_idx]->seek(corrected_idx % m_master.max_frames_per_file());
             subfiles[subfile_id][part_idx]->read_into(frame_buffer + offset, header);
             if (header)
@@ -349,7 +349,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
             if(header)
                 ++header;
 
-            for (size_t cur_row = 0; cur_row < (pos.height);
+            for (size_t cur_row = 0; cur_row < static_cast<size_t>(pos.height);
                  cur_row++) {
 
                 auto irow = (pos.y + cur_row);

src/RawMasterFile.cpp

@@ -37,11 +37,24 @@ std::filesystem::path RawFileNameComponents::master_fname() const {
 }
 
 std::filesystem::path RawFileNameComponents::data_fname(size_t mod_id,
-                                                        size_t file_id) const {
-    return m_base_path / fmt::format("{}_d{}_f{}_{}.raw", m_base_name, mod_id,
+                                                        size_t file_id
+                                                        ) const {
+    
+    
+    
+    std::string fmt = "{}_d{}_f{}_{}.raw";
+    //Before version X we used to name the data files f000000000000
+    if (m_old_scheme) {
+        fmt = "{}_d{}_f{:012}_{}.raw";
+    }
+    return m_base_path / fmt::format(fmt, m_base_name, mod_id,
                                      file_id, m_file_index);
 }
 
+void RawFileNameComponents::set_old_scheme(bool old_scheme) {
+    m_old_scheme = old_scheme;
+}
+
 const std::filesystem::path &RawFileNameComponents::base_path() const {
     return m_base_path;
 }
@@ -314,10 +327,22 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
             // do the actual parsing
             if (key == "Version") {
                 m_version = value;
+
+                //TODO!: How old versions can we handle?
+                auto v = std::stod(value);
+
+                //TODO! figure out exactly when we did the change
+                //This enables padding of f to 12 digits
+                if (v<4.0)
+                    m_fnc.set_old_scheme(true);
+
             } else if (key == "TimeStamp") {
 
             } else if (key == "Detector Type") {
                 m_type = StringTo<DetectorType>(value);
+                if(m_type==DetectorType::Moench){
+                    m_type = DetectorType::Moench03_old;
+                }
             } else if (key == "Timing Mode") {
                 m_timing_mode = StringTo<TimingMode>(value);
             } else if (key == "Image Size") {
@@ -352,6 +377,12 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
                 pos = value.find(',');
                 m_pixels_x = std::stoi(value.substr(1, pos));
                 m_pixels_y = std::stoi(value.substr(pos + 1));
+            }else if(key == "row"){
+                pos = value.find('p');
+                m_pixels_y = std::stoi(value.substr(0, pos));
+            }else if(key == "col"){
+                pos = value.find('p');
+                m_pixels_x = std::stoi(value.substr(0, pos));
             } else if (key == "Total Frames") {
                 m_total_frames_expected = std::stoi(value);
             } else if (key == "Dynamic Range") {
@@ -360,6 +391,9 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
                 m_quad = std::stoi(value);
             } else if (key == "Max Frames Per File") {
                 m_max_frames_per_file = std::stoi(value);
+            }else if(key == "Max. Frames Per File"){
+                //Version 3.0 way of writing it
+                m_max_frames_per_file = std::stoi(value);
             } else if (key == "Geometry") {
                 pos = value.find(',');
                 m_geometry = {
@@ -368,5 +402,19 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
             }
         }
     }
+    if (m_pixels_x == 400 && m_pixels_y == 400) {
+        m_type = DetectorType::Moench03_old;
+    }
+
+
+    //TODO! Look for d0, d1...dn and update geometry
+    if(m_geometry.col == 0 && m_geometry.row == 0){
+        m_geometry = {1,1};
+        fmt::print("Warning: No geometry found in master file. Assuming 1x1\n");
+    }
+
+    //TODO! Read files and find actual frames
+    if(m_frames_in_file==0)
+        m_frames_in_file = m_total_frames_expected;
 }
 } // namespace aare

src/RawMasterFile.test.cpp

@@ -31,6 +31,16 @@ TEST_CASE("Construction of master file name and data files"){
     REQUIRE(m.data_fname(1, 1) == "test_d1_f1_1.raw");
 }
 
+TEST_CASE("Construction of master file name and data files using old scheme"){
+    RawFileNameComponents m("test_master_1.raw");
+    m.set_old_scheme(true);
+    REQUIRE(m.master_fname() == "test_master_1.raw");
+    REQUIRE(m.data_fname(0, 0) == "test_d0_f000000000000_1.raw");
+    REQUIRE(m.data_fname(1, 0) == "test_d1_f000000000000_1.raw");
+    REQUIRE(m.data_fname(0, 1) == "test_d0_f000000000001_1.raw");
+    REQUIRE(m.data_fname(1, 1) == "test_d1_f000000000001_1.raw");
+}
+
 TEST_CASE("Master file name does not fit pattern"){
     REQUIRE_THROWS(RawFileNameComponents("somefile.json"));
     REQUIRE_THROWS(RawFileNameComponents("another_test_d0_f0_1.raw"));

src/RawSubFile.cpp

@@ -9,14 +9,12 @@ namespace aare {
 RawSubFile::RawSubFile(const std::filesystem::path &fname,
                        DetectorType detector, size_t rows, size_t cols,
                        size_t bitdepth, uint32_t pos_row, uint32_t pos_col)
-    : m_bitdepth(bitdepth), m_fname(fname), m_rows(rows), m_cols(cols),
-      m_detector_type(detector),
+    : m_detector_type(detector), m_bitdepth(bitdepth), m_fname(fname), m_rows(rows), m_cols(cols),
       m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols), m_pos_row(pos_row), m_pos_col(pos_col) {
     if (m_detector_type == DetectorType::Moench03_old) {
         m_pixel_map = GenerateMoench03PixelMap();
     }else if(m_detector_type == DetectorType::Eiger && m_pos_row % 2 == 0){
         m_pixel_map = GenerateEigerFlipRowsPixelMap();
-        fmt::print("Flipping rows\n");
     }
 
     if (std::filesystem::exists(fname)) {

src/defs.cpp

@@ -21,23 +21,37 @@ void assert_failed(const std::string &msg)
  */
 template <> std::string ToString(DetectorType arg) {
     switch (arg) {
-    case DetectorType::Jungfrau:
-        return "Jungfrau";
+    case DetectorType::Generic:
+        return "Generic";
     case DetectorType::Eiger:
         return "Eiger";
-    case DetectorType::Mythen3:
-        return "Mythen3";
+    case DetectorType::Gotthard:
+        return "Gotthard";
+    case DetectorType::Jungfrau:
+        return "Jungfrau";
+    case DetectorType::ChipTestBoard:
+        return "ChipTestBoard";
     case DetectorType::Moench:
         return "Moench";
+    case DetectorType::Mythen3:
+        return "Mythen3";
+    case DetectorType::Gotthard2:
+        return "Gotthard2";
+    case DetectorType::Xilinx_ChipTestBoard:
+        return "Xilinx_ChipTestBoard";
+
+    //Custom ones
     case DetectorType::Moench03:
         return "Moench03";
     case DetectorType::Moench03_old:
         return "Moench03_old";
-    case DetectorType::ChipTestBoard:
-        return "ChipTestBoard";
-    default:
+    case DetectorType::Unknown:
         return "Unknown";
+
+    //no default case to trigger compiler warning if not all 
+    //enum values are handled
     }
+    throw std::runtime_error("Could not decode detector to string");
 }
 
 /**
@@ -47,21 +61,34 @@ template <> std::string ToString(DetectorType arg) {
  * @throw runtime_error if the string does not match any DetectorType
  */
 template <> DetectorType StringTo(const std::string &arg) {
-    if (arg == "Jungfrau")
-        return DetectorType::Jungfrau;
+    if (arg == "Generic")
+        return DetectorType::Generic;
     if (arg == "Eiger")
         return DetectorType::Eiger;
-    if (arg == "Mythen3")
-        return DetectorType::Mythen3;
+    if (arg == "Gotthard")
+        return DetectorType::Gotthard;
+    if (arg == "Jungfrau")
+        return DetectorType::Jungfrau;
+    if (arg == "ChipTestBoard")
+        return DetectorType::ChipTestBoard;
     if (arg == "Moench")
         return DetectorType::Moench;
+    if (arg == "Mythen3")
+        return DetectorType::Mythen3;
+    if (arg == "Gotthard2")
+        return DetectorType::Gotthard2;
+    if (arg == "Xilinx_ChipTestBoard")
+        return DetectorType::Xilinx_ChipTestBoard;
+
+    //Custom ones
     if (arg == "Moench03")
         return DetectorType::Moench03;
     if (arg == "Moench03_old")
         return DetectorType::Moench03_old;
-    if (arg == "ChipTestBoard")
-        return DetectorType::ChipTestBoard;
-    throw std::runtime_error("Could not decode dector from: \"" + arg + "\"");
+    if (arg == "Unknown")
+        return DetectorType::Unknown;
+    
+    throw std::runtime_error("Could not decode detector from: \"" + arg + "\"");
 }
 
 /**

src/defs.test.cpp

@@ -1,12 +1,59 @@
 #include "aare/defs.hpp"
-// #include "aare/utils/floats.hpp"
 
 #include <catch2/catch_test_macros.hpp>
 #include <string>
+
+using aare::ToString;
+using aare::StringTo;
+
 TEST_CASE("Enum to string conversion") {
-    // By the way I don't think the enum string conversions should be in the defs.hpp file
+    // TODO! By the way I don't think the enum string conversions should be in the defs.hpp file
     // but let's use this to show a test
+    REQUIRE(ToString(aare::DetectorType::Generic) == "Generic");
+    REQUIRE(ToString(aare::DetectorType::Eiger) == "Eiger");
+    REQUIRE(ToString(aare::DetectorType::Gotthard) == "Gotthard");
     REQUIRE(ToString(aare::DetectorType::Jungfrau) == "Jungfrau");
+    REQUIRE(ToString(aare::DetectorType::ChipTestBoard) == "ChipTestBoard");
+    REQUIRE(ToString(aare::DetectorType::Moench) == "Moench");
+    REQUIRE(ToString(aare::DetectorType::Mythen3) == "Mythen3");
+    REQUIRE(ToString(aare::DetectorType::Gotthard2) == "Gotthard2");
+    REQUIRE(ToString(aare::DetectorType::Xilinx_ChipTestBoard) == "Xilinx_ChipTestBoard");
+    REQUIRE(ToString(aare::DetectorType::Moench03) == "Moench03");
+    REQUIRE(ToString(aare::DetectorType::Moench03_old) == "Moench03_old");
+    REQUIRE(ToString(aare::DetectorType::Unknown) == "Unknown");
+}
+
+TEST_CASE("String to enum"){
+    REQUIRE(StringTo<aare::DetectorType>("Generic") == aare::DetectorType::Generic);
+    REQUIRE(StringTo<aare::DetectorType>("Eiger") == aare::DetectorType::Eiger);
+    REQUIRE(StringTo<aare::DetectorType>("Gotthard") == aare::DetectorType::Gotthard);
+    REQUIRE(StringTo<aare::DetectorType>("Jungfrau") == aare::DetectorType::Jungfrau);
+    REQUIRE(StringTo<aare::DetectorType>("ChipTestBoard") == aare::DetectorType::ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Moench") == aare::DetectorType::Moench);
+    REQUIRE(StringTo<aare::DetectorType>("Mythen3") == aare::DetectorType::Mythen3);
+    REQUIRE(StringTo<aare::DetectorType>("Gotthard2") == aare::DetectorType::Gotthard2);
+    REQUIRE(StringTo<aare::DetectorType>("Xilinx_ChipTestBoard") == aare::DetectorType::Xilinx_ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Moench03") == aare::DetectorType::Moench03);
+    REQUIRE(StringTo<aare::DetectorType>("Moench03_old") == aare::DetectorType::Moench03_old);
+    REQUIRE(StringTo<aare::DetectorType>("Unknown") == aare::DetectorType::Unknown);
+}
+
+TEST_CASE("Enum values"){
+    //Since some of the enums are written to file we need to make sure 
+    //they match the value in the slsDetectorPackage
+
+    REQUIRE(static_cast<int>(aare::DetectorType::Generic) == 0);
+    REQUIRE(static_cast<int>(aare::DetectorType::Eiger) == 1);
+    REQUIRE(static_cast<int>(aare::DetectorType::Gotthard) == 2);
+    REQUIRE(static_cast<int>(aare::DetectorType::Jungfrau) == 3);
+    REQUIRE(static_cast<int>(aare::DetectorType::ChipTestBoard) == 4);
+    REQUIRE(static_cast<int>(aare::DetectorType::Moench) == 5);
+    REQUIRE(static_cast<int>(aare::DetectorType::Mythen3) == 6);
+    REQUIRE(static_cast<int>(aare::DetectorType::Gotthard2) == 7);
+    REQUIRE(static_cast<int>(aare::DetectorType::Xilinx_ChipTestBoard) == 8);
+
+    //Not included
+    REQUIRE(static_cast<int>(aare::DetectorType::Moench03) == 100);
 }
 
 TEST_CASE("DynamicCluster creation") {