Dev/stuff from pyctbgui (#273)

Matterhorn10 Transform 
some other Transformations from pyctbGUI 
added method get_reading_mode for easier error handling in decoders 


## TODO: 

- proper error handling for all other decoders 
- proper documentation for all other decoders 
- refactoring all other decoders to store hard coded values in a Struct
ChipSpecification

include/aare/PixelMap.hpp

@@ -10,11 +10,21 @@ NDArray<ssize_t, 2> GenerateMoench03PixelMap();
 NDArray<ssize_t, 2> GenerateMoench05PixelMap();
 NDArray<ssize_t, 2> GenerateMoench05PixelMap1g();
 NDArray<ssize_t, 2> GenerateMoench05PixelMapOld();
+NDArray<ssize_t, 2> GenerateMoench04AnalogPixelMap();
 
 // Matterhorn02
 NDArray<ssize_t, 2> GenerateMH02SingleCounterPixelMap();
 NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap();
 
+/**
+ * @brief Generate pixel map for Matterhorn10 detector
+ * @param dynamic_range Dynamic range of the detector (16, 8, or 4)
+ * @param n_counters Number of counters (1 to 4)
+ */
+NDArray<ssize_t, 2>
+GenerateMatterhorn10PixelMap(const size_t dynamic_range = 16,
+                             const size_t n_counters = 1);
+
 // Eiger
 NDArray<ssize_t, 2> GenerateEigerFlipRowsPixelMap();
 

include/aare/RawMasterFile.hpp

@@ -97,9 +97,9 @@ class RawMasterFile {
     size_t m_frame_padding{};
 
     // TODO! should these be bool?
-    uint8_t m_analog_flag{};
+    bool m_analog_flag{};
-    uint8_t m_digital_flag{};
+    bool m_digital_flag{};
-    uint8_t m_transceiver_flag{};
+    bool m_transceiver_flag{};
 
     ScanParameters m_scan_parameters;
 
@@ -135,6 +135,8 @@ class RawMasterFile {
     size_t n_modules() const;
     uint8_t quad() const;
 
+    ReadoutMode get_reading_mode() const;
+
     std::optional<size_t> analog_samples() const;
     std::optional<size_t> digital_samples() const;
     std::optional<size_t> transceiver_samples() const;

include/aare/decode.hpp

@@ -38,6 +38,13 @@ uint32_t mask32to24bits(uint32_t input, BitOffset offset = {});
 void expand24to32bit(NDView<uint8_t, 1> input, NDView<uint32_t, 1> output,
                      BitOffset offset = {});
 
+/**
+ * @brief expands the two 4 bit values of an 8 bit buffer into two 8 bit values
+ * @param input input buffer with 4 bit values packed into 8 bit
+ * @param output output buffer with 8 bit values
+ */
+void expand4to8bit(NDView<uint8_t, 1> input, NDView<uint8_t, 1> output);
+
 /**
  * @brief Apply custom weights to a 16-bit input value. Will sum up
  * weights[i]**i for each bit i that is set in the input value.

include/aare/defs.hpp

@@ -188,6 +188,46 @@ struct ROI {
     }
 };
 
+/// @brief  Chip specifications for Matterhorn1
+struct Matterhorn10 {
+    constexpr static size_t nRows = 256;
+    constexpr static size_t nCols = 256;
+};
+
+/// @brief  Chip specifications for Matterhorn2
+struct Matterhorn02 {
+    constexpr static size_t nRows = 48;
+    constexpr static size_t nCols = 48;
+    constexpr static size_t nHalfCols = 24;
+};
+
+/// @brief  Chip specifications for Moench04
+struct Moench04 {
+    constexpr static size_t nRows = 400;
+    constexpr static size_t nCols = 400;
+    constexpr static std::array<int, 32>
+        adcNumbers =
+            {
+                9,  8,  11, 10, 13, 12, 15, 14, 1,  0,  3,
+                2,  5,  4,  7,  6,  23, 22, 21, 20, 19, 18,
+                17, 16, 31, 30, 29, 28, 27, 26, 25, 24}; // TODO : should we
+                                                         // only have chip
+                                                         // specifications or
+                                                         // also wiring in
+                                                         // chiptestboard?
+    constexpr static size_t nPixelsPerSuperColumn = 5000;
+    constexpr static size_t superColumnWidth = 25;
+};
+
+enum ReadoutMode : uint8_t {
+    ANALOG_ONLY = 0,
+    DIGITAL_ONLY = 1,
+    ANALOG_AND_DIGITAL = 2,
+    TRANSCEIVER_ONLY = 3,
+    DIGITAL_AND_TRANSCEIVER = 4,
+    UNKNOWN = 5
+};
+
 using dynamic_shape = std::vector<ssize_t>;
 
 // TODO! Can we uniform enums between the libraries?

python/aare/CtbRawFile.py

@@ -18,6 +18,9 @@ class CtbRawFile(_aare.CtbRawFile):
         super().__init__(fname)
         self._chunk_size = chunk_size
         self._transform = transform
+        if self._transform:
+            if hasattr(self._transform, "compatibility") and callable(getattr(self._transform, "compatibility")):
+                self._transform.compatibility(self.master.reading_mode)
 
 
     def read_frame(self, frame_index: int | None = None ) -> tuple:
@@ -45,7 +48,6 @@ class CtbRawFile(_aare.CtbRawFile):
         if header.shape == (1,):
             header = header[0]
 
-
         if self._transform:
             res = self._transform(data)
             if isinstance(res, tuple):

python/aare/__init__.py

@@ -5,7 +5,7 @@ from . import _aare
 
 from ._aare import File, RawMasterFile, RawSubFile, JungfrauDataFile
 from ._aare import Pedestal_d, Pedestal_f, ClusterFinder_Cluster3x3i, VarClusterFinder
-from ._aare import DetectorType
+from ._aare import DetectorType, ReadoutMode 
 from ._aare import hitmap
 from ._aare import ROI
 from ._aare import corner 

python/aare/transform.py

@@ -1,7 +1,8 @@
 # SPDX-License-Identifier: MPL-2.0
 import numpy as np
 from . import _aare
-
+from aare import ReadoutMode 
+from aare._aare import Matterhorn10 
 
 class AdcSar04Transform64to16:
     def __call__(self, data):
@@ -24,6 +25,14 @@ class Moench05Transform:
         return np.take(data.view(np.uint16), self.pixel_map)
     
 
+class Moench03Transform: 
+    def __init__(self): 
+        self.pixel_map = _aare.GenerateMoench03PixelMap()
+
+    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):
@@ -41,17 +50,79 @@ class Moench05TransformOld:
     def __call__(self, data):
         return np.take(data.view(np.uint16), self.pixel_map)
     
-
+class Moench04AnalogTransform:
-class Matterhorn02Transform:
+    #Could be moved to C++ without changing the interface
     def __init__(self):
-        self.pixel_map = _aare.GenerateMH02FourCounterPixelMap()
+        self.pixel_map = _aare.GenerateMoench04AnalogPixelMap()
 
     def __call__(self, data):
-        counters = int(data.size / 48**2 / 2)
+        return np.take(data.view(np.uint16), self.pixel_map)
-        if counters == 1:
+    
-            return np.take(data.view(np.uint16), self.pixel_map[0])
+class Matterhorn02TransceiverTransform: 
-        else:
+    #Could be moved to C++ without changing the interface
-            return np.take(data.view(np.uint16), self.pixel_map[0:counters])
+    def __init__(self):
+        self.pixel_map = _aare.GenerateMH02SingleCounterPixelMap()
+
+    def __call__(self, data):
+        return np.take(data.view(np.uint16), self.pixel_map)
+
+class Matterhorn10Transform:
+    """
+    Transforms Matterhorn10 chip data from a buffer of bytes (uint8_t)
+    to a numpy array of uint8, uint16 depending on dynamic range.
+    Assumes data taken with transceiver samples only.
+
+    :param dynamic_range: How many bits a pixel is encoded dynamic range (4, 8, or 16)
+    :type dynamic_range: int
+    :param num_counters: num counters used (1 to 4)
+    :type num_counters: int
+
+    .. note::
+        A matterhorn chip has 256 columns and 256 rows.
+        A matterhornchip with dynamic range 16 and 2 counters thus requires 
+        256*256*16*2/(2*64) = 1024 transceiver samples. (Per default 2 channels are enabled per transceiver sample, each channel storing 64 bits)
+    """
+    def __init__(self, dynamic_range : int, num_counters : int):
+        self.pixel_map = _aare.GenerateMatterhorn10PixelMap(dynamic_range, num_counters)
+        self.dynamic_range = dynamic_range
+        self.num_counters = num_counters 
+
+    def compatibility(self, readingmode : ReadoutMode):
+        """
+        checks if Matterhorn10Transform is compatible with given parameters
+
+        :param readingmode: Reading mode set
+        :type readingmode: ReadoutMode
+        :raises ValueError: if not compatible
+        """
+        if(readingmode != ReadoutMode.TRANSCEIVER_ONLY): 
+            raise ValueError(f"Incompatible Transformation. Matterhorn10Transform only requires transceiver samples. However reading mode is  {readingmode}.")
+        
+        pass
+
+    def data_compatibility(self, data):
+        """
+        checks if data is compatible for transformation 
+        
+        :param data: data to be transformed, expected to be a 1D numpy array of uint8
+        :type data: np.ndarray
+        :raises ValueError: if not compatible
+        """
+        expected_size = (Matterhorn10.nRows*Matterhorn10.nCols*self.num_counters*self.dynamic_range)//8 # read_frame returns data in uint8_t 
+
+        if(data.size != expected_size): 
+            raise ValueError(f"Data size {data.size} does not match expected size {expected_size} for Matterhorn10 with dynamic range {self.dynamic_range} and num_counters {self.num_counters}.")
+        
+        pass
+        
+    def __call__(self, data):
+        self.data_compatibility(data)
+        if self.dynamic_range == 16:
+            return np.take(data.view(np.uint16), self.pixel_map)
+        elif self.dynamic_range == 8: 
+            return np.take(data.view(np.uint8), self.pixel_map)
+        else: #dynamic range 4
+            return np.take(_aare.expand4to8bit(data.view(np.uint8)), self.pixel_map)
             
 class Mythen302Transform:
     """
@@ -95,7 +166,7 @@ class Mythen302Transform:
 moench05 = Moench05Transform()
 moench05_1g = Moench05Transform1g()
 moench05_old = Moench05TransformOld()
-matterhorn02 = Matterhorn02Transform()
+matterhorn02 = Matterhorn02TransceiverTransform()
 adc_sar_04_64to16 = AdcSar04Transform64to16()
 adc_sar_05_64to16 = AdcSar05Transform64to16()
 adc_sar_05_06_07_08_64to16 = AdcSar05060708Transform64to16()

python/src/bind_Defs.hpp

@@ -0,0 +1,25 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "aare/defs.hpp"
+
+namespace py = pybind11;
+using namespace aare;
+
+void define_defs_bindings(py::module &m) {
+    auto matterhorn10 = py::class_<Matterhorn10>(m, "Matterhorn10");
+    matterhorn10.attr("nRows") = Matterhorn10::nRows;
+    matterhorn10.attr("nCols") = Matterhorn10::nCols;
+
+    auto matterhorn02 = py::class_<Matterhorn02>(m, "Matterhorn02");
+    matterhorn02.attr("nRows") = Matterhorn02::nRows;
+    matterhorn02.attr("nCols") = Matterhorn02::nCols;
+    matterhorn02.attr("nHalfCols") = Matterhorn02::nHalfCols;
+
+    auto moench04 = py::class_<Moench04>(m, "Moench04");
+    moench04.attr("nRows") = Moench04::nRows;
+    moench04.attr("nCols") = Moench04::nCols;
+    moench04.attr("nPixelsPerSuperColumn") = Moench04::nPixelsPerSuperColumn;
+    moench04.attr("superColumnWidth") = Moench04::superColumnWidth;
+    moench04.attr("adcNumbers") = Moench04::adcNumbers;
+}

python/src/bind_PixelMap.hpp

@@ -33,15 +33,35 @@ void define_pixel_map_bindings(py::module &m) {
                      new NDArray<ssize_t, 2>(GenerateMoench05PixelMapOld());
                  return return_image_data(ptr);
              })
+
+        .def("GenerateMoench04AnalogPixelMap",
+             []() {
+                 auto ptr =
+                     new NDArray<ssize_t, 2>(GenerateMoench04AnalogPixelMap());
+                 return return_image_data(ptr);
+             })
+
         .def("GenerateMH02SingleCounterPixelMap",
              []() {
                  auto ptr = new NDArray<ssize_t, 2>(
                      GenerateMH02SingleCounterPixelMap());
                  return return_image_data(ptr);
              })
-        .def("GenerateMH02FourCounterPixelMap", []() {
+        .def("GenerateMH02FourCounterPixelMap",
-            auto ptr =
+             []() {
-                new NDArray<ssize_t, 3>(GenerateMH02FourCounterPixelMap());
+                 auto ptr =
-            return return_image_data(ptr);
+                     new NDArray<ssize_t, 3>(GenerateMH02FourCounterPixelMap());
-        });
+                 return return_image_data(ptr);
+             })
+
+        .def(
+            "GenerateMatterhorn10PixelMap",
+            [](const size_t dynamic_range, const size_t n_counters) {
+                auto ptr = new NDArray<ssize_t, 2>(
+                    GenerateMatterhorn10PixelMap(dynamic_range, n_counters));
+                return return_image_data(ptr);
+            },
+            py::arg("dynamic_range") = 16, py::arg("n_counters") = 1,
+            R"(
+        Generate pixel map for Matterhorn02 detector)");
 }

python/src/ctb_raw_file.hpp

@@ -139,6 +139,22 @@ void define_ctb_raw_file_io_bindings(py::module &m) {
               return output;
           });
 
+    m.def("expand4to8bit",
+          [](py::array_t<uint8_t, py::array::c_style | py::array::forcecast>
+                 &input) {
+              py::buffer_info buf = input.request();
+
+              py::array_t<uint8_t> output(buf.size * 2);
+
+              NDView<uint8_t, 1> input_view(input.mutable_data(),
+                                            {input.size()});
+              NDView<uint8_t, 1> output_view(output.mutable_data(),
+                                             {output.size()});
+
+              aare::expand4to8bit(input_view, output_view);
+              return output;
+          });
+
     m.def("decode_my302",
           [](py::array_t<uint8_t, py::array::c_style | py::array::forcecast>
                  &input,

python/src/module.cpp

@@ -9,8 +9,10 @@
 #include "bind_ClusterFinder.hpp"
 #include "bind_ClusterFinderMT.hpp"
 #include "bind_ClusterVector.hpp"
+#include "bind_Defs.hpp"
 #include "bind_Eta.hpp"
 #include "bind_Interpolator.hpp"
+#include "bind_PixelMap.hpp"
 #include "bind_RawFile.hpp"
 #include "bind_calibration.hpp"
 
@@ -20,7 +22,6 @@
 #include "fit.hpp"
 #include "jungfrau_data_file.hpp"
 #include "pedestal.hpp"
-#include "pixel_map.hpp"
 #include "raw_master_file.hpp"
 #include "raw_sub_file.hpp"
 #include "var_cluster.hpp"
@@ -140,6 +141,8 @@ PYBIND11_MODULE(_aare, m) {
     register_calculate_3x3eta<float, 3, 3, uint16_t>(m);
     register_calculate_3x3eta<int16_t, 3, 3, uint16_t>(m);
 
+    define_defs_bindings(m);
+
     using Sum_index_pair_d = Sum_index_pair<double, corner>;
     PYBIND11_NUMPY_DTYPE(Sum_index_pair_d, sum, index);
     using Sum_index_pair_f = Sum_index_pair<float, corner>;

python/src/raw_master_file.hpp

@@ -23,6 +23,16 @@ namespace py = pybind11;
 using namespace ::aare;
 
 void define_raw_master_file_bindings(py::module &m) {
+
+    py::enum_<ReadoutMode>(m, "ReadoutMode")
+        .value("ANALOG_ONLY", ReadoutMode::ANALOG_ONLY)
+        .value("DIGITAL_ONLY", ReadoutMode::DIGITAL_ONLY)
+        .value("ANALOG_AND_DIGITAL", ReadoutMode::ANALOG_AND_DIGITAL)
+        .value("TRANSCEIVER_ONLY", ReadoutMode::TRANSCEIVER_ONLY)
+        .value("DIGITAL_AND_TRANSCEIVER", ReadoutMode::DIGITAL_AND_TRANSCEIVER)
+        .value("UNKNOWN", ReadoutMode::UNKNOWN)
+        .export_values();
+
     py::class_<RawMasterFile>(m, "RawMasterFile")
         .def(py::init<const std::filesystem::path &>())
         .def("data_fname", &RawMasterFile::data_fname, R"(
@@ -81,6 +91,7 @@ void define_raw_master_file_bindings(py::module &m) {
 
         .def_property_readonly("transceiver_samples",
                                &RawMasterFile::transceiver_samples)
+        .def_property_readonly("reading_mode", &RawMasterFile::get_reading_mode)
         .def_property_readonly("number_of_rows", &RawMasterFile::number_of_rows)
         .def_property_readonly("quad", &RawMasterFile::quad)
         .def_property_readonly("scan_parameters",

python/tests/test_RawFile.py

@@ -14,6 +14,9 @@ def test_read_rawfile_with_roi_spanning_over_one_module(test_data_path):
         assert headers.size == 10100
         assert frames.shape == (10100, 256, 256)
 
+        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:
@@ -44,6 +47,8 @@ def test_read_rawfile_with_multiple_rois(test_data_path):
         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): 
     
@@ -68,7 +73,6 @@ def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path):
     
     assert (image == image1).all()
 
-
 @pytest.mark.withdata
 def test_read_rawfile_eiger_and_compare_to_numpy(test_data_path): 
     d0 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d0_f0_7.raw'

python/tests/test_RawMasterFile.py

@@ -0,0 +1,14 @@
+
+
+import pytest
+from aare import RawMasterFile, ReadoutMode, DetectorType
+
+
+@pytest.mark.withdata
+def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path): 
+    
+    file_name = test_data_path/'raw/jungfrau/jungfrau_single_master_0.json'
+   
+    f = RawMasterFile(file_name)
+    assert(f.reading_mode == ReadoutMode.UNKNOWN)
+    assert(f.detector_type == DetectorType.Jungfrau)

src/PixelMap.cpp

@@ -1,5 +1,6 @@
 // SPDX-License-Identifier: MPL-2.0
 #include "aare/PixelMap.hpp"
+#include "aare/defs.hpp"
 
 #include <array>
 
@@ -31,6 +32,29 @@ NDArray<ssize_t, 2> GenerateMoench03PixelMap() {
     return order_map;
 }
 
+NDArray<ssize_t, 2> GenerateMoench04AnalogPixelMap() {
+    std::array<int, 32> const adc_nr = Moench04::adcNumbers;
+    int const nadc = adc_nr.size();
+    NDArray<ssize_t, 2> order_map({Moench04::nRows, Moench04::nCols});
+
+    int pixel = 0;
+    for (size_t i = 0; i != Moench04::nPixelsPerSuperColumn; ++i) {
+        for (size_t i_adc = 0; i_adc != nadc; ++i_adc) {
+            int const col =
+                (adc_nr[i_adc] % 16) * 25 + (i % Moench04::superColumnWidth);
+            int row = 0;
+            if (i_adc < 16)
+                row = 199 - (i / Moench04::superColumnWidth);
+            else
+                row = 200 + (i / Moench04::superColumnWidth);
+
+            order_map(row, col) = pixel;
+            pixel++;
+        }
+    }
+    return order_map;
+}
+
 NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
     std::array<int, 3> adc_numbers = {5, 9, 1};
     NDArray<ssize_t, 2> order_map({160, 150});
@@ -104,16 +128,18 @@ NDArray<ssize_t, 2> GenerateEigerFlipRowsPixelMap() {
     return order_map;
 }
 
+// transceiver pixel map for Matterhorn02
 NDArray<ssize_t, 2> GenerateMH02SingleCounterPixelMap() {
     // This is the pixel map for a single counter Matterhorn02, i.e. 48x48
     // pixels. Data is read from two transceivers in blocks of 4 pixels.
-    NDArray<ssize_t, 2> order_map({48, 48});
+    NDArray<ssize_t, 2> order_map({Matterhorn02::nRows, Matterhorn02::nCols});
     size_t offset = 0;
     size_t nSamples = 4;
-    for (int row = 0; row < 48; row++) {
+    for (size_t row = 0; row < Matterhorn02::nRows; row++) {
-        for (int col = 0; col < 24; col++) {
+        for (size_t col = 0; col < Matterhorn02::nHalfCols; col++) {
-            for (int iTrans = 0; iTrans < 2; iTrans++) {
+            for (size_t iTrans = 0; iTrans < 2; iTrans++) {
-                order_map(row, iTrans * 24 + col) = offset + nSamples * iTrans;
+                order_map(row, iTrans * Matterhorn02::nHalfCols + col) =
+                    offset + nSamples * iTrans;
             }
             offset += 1;
             if ((col + 1) % nSamples == 0) {
@@ -126,16 +152,64 @@ NDArray<ssize_t, 2> GenerateMH02SingleCounterPixelMap() {
 
 NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap() {
     auto single_counter_map = GenerateMH02SingleCounterPixelMap();
-    NDArray<ssize_t, 3> order_map({4, 48, 48});
+    NDArray<ssize_t, 3> order_map(
-    for (int counter = 0; counter < 4; counter++) {
+        {4, Matterhorn02::nRows, Matterhorn02::nCols});
-        for (int row = 0; row < 48; row++) {
+    for (size_t counter = 0; counter < 4; counter++) {
-            for (int col = 0; col < 48; col++) {
+        for (size_t row = 0; row < Matterhorn02::nRows; row++) {
+            for (size_t col = 0; col < Matterhorn02::nCols; col++) {
                 order_map(counter, row, col) =
-                    single_counter_map(row, col) + counter * 48 * 48;
+                    single_counter_map(row, col) +
+                    counter * Matterhorn02::nRows * Matterhorn02::nCols;
             }
         }
     }
     return order_map;
 }
 
+NDArray<ssize_t, 2> GenerateMatterhorn10PixelMap(const size_t dynamic_range,
+                                                 const size_t n_counters) {
+
+    // Matterhorn10 uses transceiver samples (each transceiver sample has 1-4
+    // channels storing 8 bytes each)
+    constexpr size_t n_cols = Matterhorn10::nCols;
+    constexpr size_t n_rows = Matterhorn10::nRows;
+    NDArray<ssize_t, 2> pixel_map(
+        {static_cast<ssize_t>(n_rows * n_counters), n_cols});
+
+    size_t num_consecutive_pixels{};
+    switch (dynamic_range) {
+    case 16:
+        num_consecutive_pixels = 4;
+        break;
+    case 8:
+        num_consecutive_pixels = 8;
+        break;
+    case 4:
+        num_consecutive_pixels = 16;
+        break;
+    default:
+        throw std::runtime_error("Unsupported dynamic range for Matterhorn02");
+    }
+
+    for (size_t row = 0; row < n_rows; ++row) {
+        for (size_t counter = 0; counter < n_counters; ++counter) {
+            size_t col = 0;
+            for (size_t offset = 0; offset < 64;
+                 offset += num_consecutive_pixels) {
+                for (size_t pkg = offset; pkg < Matterhorn10::nCols;
+                     pkg += 64) {
+                    for (size_t pixel = 0; pixel < num_consecutive_pixels;
+                         ++pixel) {
+                        pixel_map(row + counter * n_rows, col) =
+                            pkg + pixel + row * n_cols * n_counters +
+                            n_cols * counter;
+                        ++col;
+                    }
+                }
+            }
+        }
+    }
+    return pixel_map;
+}
+
 } // namespace aare

src/RawMasterFile.cpp

@@ -206,6 +206,30 @@ std::optional<ROI> RawMasterFile::roi() const {
 
 std::optional<std::vector<ROI>> RawMasterFile::rois() const { return m_rois; }
 
+ReadoutMode RawMasterFile::get_reading_mode() const {
+
+    if (m_type != DetectorType::ChipTestBoard &&
+        m_type != DetectorType::Xilinx_ChipTestBoard) {
+        LOG(TLogLevel::logINFO)
+            << "reading mode is only available for CTB detectors.";
+        return ReadoutMode::UNKNOWN;
+    }
+
+    if (m_analog_flag && m_digital_flag) {
+        return ReadoutMode::ANALOG_AND_DIGITAL;
+    } else if (m_analog_flag) {
+        return ReadoutMode::ANALOG_ONLY;
+    } else if (m_digital_flag && m_transceiver_flag) {
+        return ReadoutMode::DIGITAL_AND_TRANSCEIVER;
+    } else if (m_digital_flag) {
+        return ReadoutMode::DIGITAL_ONLY;
+    } else if (m_transceiver_flag) {
+        return ReadoutMode::TRANSCEIVER_ONLY;
+    } else {
+        return ReadoutMode::UNKNOWN;
+    }
+}
+
 void RawMasterFile::parse_json(std::istream &is) {
     json j;
     is >> j;
@@ -216,10 +240,10 @@ void RawMasterFile::parse_json(std::istream &is) {
     m_type = string_to<DetectorType>(j["Detector Type"].get<std::string>());
     m_timing_mode = string_to<TimingMode>(j["Timing Mode"].get<std::string>());
 
-    m_geometry = {
+    m_geometry = {j["Geometry"]["y"],
-        j["Geometry"]["y"],
+                  j["Geometry"]["x"]}; // TODO: isnt it only available for
-        j["Geometry"]["x"]}; // TODO: isnt it only available for version > 7.1?
+                                       // version > 7.1?
-                             // - try block default should be 1x1
+                                       // - try block default should be 1x1
 
     m_image_size_in_bytes =
         v < 8.0 ? j["Image Size in bytes"] : j["Image Size"];
@@ -272,22 +296,15 @@ void RawMasterFile::parse_json(std::istream &is) {
 
     // ----------------------------------------------------------------
     // Special treatment of analog flag because of Moench03
+    m_analog_flag = v < 8.0 && (m_type == DetectorType::Moench);
+
     try {
-        m_analog_flag = j.at("Analog Flag");
+        m_analog_flag = static_cast<bool>(j.at("Analog Flag").get<int>());
-    } catch (const json::out_of_range &e) {
-        // if it doesn't work still set it to one
-        // to try to decode analog samples (Old Moench03)
-        m_analog_flag = 1;
-    }
-    try {
         if (m_analog_flag) {
             m_analog_samples = j.at("Analog Samples");
         }
-
     } catch (const json::out_of_range &e) {
         // keep the optional empty
-        // and set analog flag to 0
-        m_analog_flag = 0;
     }
     //-----------------------------------------------------------------
     try {
@@ -302,7 +319,7 @@ void RawMasterFile::parse_json(std::istream &is) {
     //     m_adc_mask = 0;
     // }
     try {
-        int digital_flag = j.at("Digital Flag");
+        bool digital_flag = static_cast<bool>(j.at("Digital Flag").get<int>());
         if (digital_flag) {
             m_digital_samples = j.at("Digital Samples");
         }
@@ -310,7 +327,8 @@ void RawMasterFile::parse_json(std::istream &is) {
         // keep the optional empty
     }
     try {
-        m_transceiver_flag = j.at("Transceiver Flag");
+        m_transceiver_flag =
+            static_cast<bool>(j.at("Transceiver Flag").get<int>());
         if (m_transceiver_flag) {
             m_transceiver_samples = j.at("Transceiver Samples");
         }
@@ -444,9 +462,9 @@ void RawMasterFile::parse_raw(std::istream &is) {
                 // } else if (key == "Number of rows"){
                 //     m_number_of_rows = std::stoi(value);
             } else if (key == "Analog Flag") {
-                m_analog_flag = std::stoi(value);
+                m_analog_flag = static_cast<bool>(std::stoi(value));
             } else if (key == "Digital Flag") {
-                m_digital_flag = std::stoi(value);
+                m_digital_flag = static_cast<bool>(std::stoi(value));
 
             } else if (key == "Analog Samples") {
                 if (m_analog_flag == 1) {

src/RawMasterFile.test.cpp

@@ -146,6 +146,8 @@ TEST_CASE("Parse a master file in .json format", "[.integration]") {
 
     REQUIRE_FALSE(f.analog_samples());
     REQUIRE_FALSE(f.digital_samples());
+
+    REQUIRE(f.get_reading_mode() == ReadoutMode::UNKNOWN);
 }
 
 TEST_CASE("Parse a master file in old .raw format",
@@ -211,6 +213,8 @@ TEST_CASE("Parse a master file in .raw format", "[.integration]") {
     // Frames in File             : 100
     REQUIRE(f.frames_in_file() == 100);
 
+    REQUIRE(f.get_reading_mode() == ReadoutMode::ANALOG_AND_DIGITAL);
+
     // #Frame Header
     // Frame Number               : 8 bytes
     // SubFrame Number/ExpLength  : 4 bytes
@@ -560,6 +564,7 @@ TEST_CASE("Parse a CTB file from stream") {
     REQUIRE(f.digital_samples() == std::nullopt); // Digital Flag is 0
     REQUIRE(f.transceiver_samples() == 1152);
     REQUIRE(f.frames_in_file() == 40);
+    REQUIRE(f.get_reading_mode() == ReadoutMode::TRANSCEIVER_ONLY);
 }
 
 TEST_CASE("Parse v8.0 MYTHEN3 from stream") {

src/decode.cpp

@@ -144,6 +144,24 @@ uint32_t mask32to24bits(uint32_t input, BitOffset offset) {
     return (input >> offset.value()) & mask24bits;
 }
 
+void expand4to8bit(NDView<uint8_t, 1> input, NDView<uint8_t, 1> output) {
+
+    if (2 * input.size() != output.size())
+        throw std::runtime_error(
+            fmt::format("Mismatch between input and output size. Input "
+                        "size of {} requires an output of at least {} "
+                        "bytes. Called with input size: {} output size: {}",
+                        LOCATION, input.size(), 2 * input.size(), input.size(),
+                        output.size()));
+
+    // assumes little-endian
+    for (ssize_t i = 0; i < input.size(); ++i) {
+        uint8_t val = input(i);
+        output[2 * i] = (val & 0x0F);
+        output[2 * i + 1] = (val & 0xF0) >> 4;
+    }
+}
+
 void expand24to32bit(NDView<uint8_t, 1> input, NDView<uint32_t, 1> output,
                      BitOffset bit_offset) {
 

src/decode.test.cpp

@@ -153,3 +153,23 @@ TEST_CASE("Expand container with 24 bit data to 32") {
         CHECK(out(2) == 0xFF0);
     }
 }
+
+TEST_CASE("Expand 4 bit values packed into 8 bit to 8 bit values") {
+    {
+        uint8_t buffer[] = {
+            0x00, 0xF0, 0xFF, 0x00, 0xF0, 0xFF,
+        };
+
+        aare::NDView<uint8_t, 1> input(&buffer[0], {6});
+        aare::NDArray<uint8_t, 1> out({12});
+        aare::expand4to8bit(input, out.view());
+
+        uint8_t expected_output[] = {
+            0x0, 0x0, 0x0, 0xF, 0xF, 0xF,
+            0x0, 0x0, 0x0, 0xF, 0xF, 0xF}; // assuming little endian
+
+        for (size_t i = 0; i < 12; ++i) {
+            CHECK(out(i) == expected_output[i]);
+        }
+    }
+}