added simple decoding of scan parameters

CMakeLists.txt

@@ -244,7 +244,6 @@ set(PUBLICHEADERS
     include/aare/FileInterface.hpp
     include/aare/RawMasterFile.hpp
     include/aare/Frame.hpp
-    include/aare/json.hpp
     include/aare/NDArray.hpp
     include/aare/NDView.hpp
     include/aare/NumpyFile.hpp

include/aare/RawMasterFile.hpp

@@ -23,7 +23,7 @@ class RawFileNameComponents {
     RawFileNameComponents(const std::filesystem::path &fname);
 
     /// @brief Get the filename including path of the master file.
-    /// (i.e. what was passed in to the constructor)) 
+    /// (i.e. what was passed in to the constructor))
     std::filesystem::path master_fname() const;
 
     /// @brief Get the filename including path of the data file.
@@ -31,16 +31,36 @@ class RawFileNameComponents {
     /// @param file_id file id run_d0_f[file_id]_0
     std::filesystem::path data_fname(size_t mod_id, size_t file_id) const;
 
-
     const std::filesystem::path &base_path() const;
     const std::string &base_name() const;
     const std::string &ext() const;
     int file_index() const;
 };
 
+class ScanParameters {
+    bool m_enabled = false;
+    std::string m_dac;
+    int m_start = 0;
+    int m_stop = 0;
+    int m_step = 0;
+    //TODO! add settleTime, requires string to time conversion
+
+  public:
+    ScanParameters(const std::string &par);
+    ScanParameters() = default;
+    ScanParameters(const ScanParameters &) = default;
+    ScanParameters &operator=(const ScanParameters &) = default;
+    ScanParameters(ScanParameters &&) = default;
+    int start() const;
+    int stop() const;
+    int step() const;
+    const std::string &dac() const;
+    bool enabled() const;
+};
 
 /**
- * @brief Class for parsing a master file either in our .json format or the old .raw format
+ * @brief Class for parsing a master file either in our .json format or the old
+ * .raw format
  */
 class RawMasterFile {
     RawFileNameComponents m_fnc;
@@ -62,11 +82,13 @@ class RawMasterFile {
     FrameDiscardPolicy m_frame_discard_policy{};
     size_t m_frame_padding{};
 
-    //TODO! should these be bool?
+    // TODO! should these be bool?
     uint8_t m_analog_flag{};
     uint8_t m_digital_flag{};
     uint8_t m_transceiver_flag{};
 
+    ScanParameters m_scan_parameters;
+
     std::optional<size_t> m_analog_samples;
     std::optional<size_t> m_digital_samples;
     std::optional<size_t> m_transceiver_samples;
@@ -78,7 +100,7 @@ class RawMasterFile {
 
     std::filesystem::path data_fname(size_t mod_id, size_t file_id) const;
 
-    const std::string &version() const; //!< For example "7.2" 
+    const std::string &version() const; //!< For example "7.2"
     const DetectorType &detector_type() const;
     const TimingMode &timing_mode() const;
     size_t image_size_in_bytes() const;
@@ -98,6 +120,9 @@ class RawMasterFile {
     std::optional<size_t> transceiver_samples() const;
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> quad() const;
+
+    ScanParameters scan_parameters() const;
+
   private:
     void parse_json(const std::filesystem::path &fpath);
     void parse_raw(const std::filesystem::path &fpath);

include/aare/json.hpp

@@ -1,68 +0,0 @@
-#pragma once
-#include <array>
-#include <map>
-#include <string>
-#include <vector>
-
-// helper functions to write json
-// append to string for better performance (not tested)
-
-namespace aare {
-
-/**
- * @brief write a digit to a string
- * takes key and value and outputs->"key": value,
- * @tparam T type of value (int, uint32_t, ...)
- * @param s string to append to
- * @param key key to write
- * @param value value to write
- * @return void
- * @note
- * - can't use concepts here because we are using c++17
- */
-template <typename T> inline void write_digit(std::string &s, const std::string &key, const T &value) {
-    s += "\"";
-    s += key;
-    s += "\": ";
-    s += std::to_string(value);
-    s += ", ";
-}
-inline void write_str(std::string &s, const std::string &key, const std::string &value) {
-    s += "\"";
-    s += key;
-    s += "\": \"";
-    s += value;
-    s += "\", ";
-}
-inline void write_map(std::string &s, const std::string &key, const std::map<std::string, std::string> &value) {
-    s += "\"";
-    s += key;
-    s += "\": {";
-    for (const auto &kv : value) {
-        write_str(s, kv.first, kv.second);
-    }
-    // remove last comma or trailing spaces
-    for (size_t i = s.size() - 1; i > 0; i--) {
-        if ((s[i] == ',') || (s[i] == ' ')) {
-            s.pop_back();
-        } else
-            break;
-    }
-    s += "}, ";
-}
-
-template <typename T, int N> void write_array(std::string &s, const std::string &key, const std::array<T, N> &value) {
-    s += "\"";
-    s += key;
-    s += "\": [";
-
-    for (size_t i = 0; i < N - 1; i++) {
-        s += std::to_string(value[i]);
-        s += ", ";
-    }
-    s += std::to_string(value[N - 1]);
-
-    s += "], ";
-}
-
-} // namespace aare

python/CMakeLists.txt

@@ -29,6 +29,7 @@ set( PYTHON_FILES
     aare/__init__.py
     aare/CtbRawFile.py
     aare/transform.py
+    aare/ScanParameters.py
 )
 
 # Copy the python files to the build directory

python/aare/CtbRawFile.py

@@ -1,7 +1,7 @@
 
 from . import _aare
 import numpy as np
-
+from .ScanParameters import ScanParameters
 class CtbRawFile(_aare.CtbRawFile):
     """File reader for the CTB raw file format.
     
@@ -108,7 +108,24 @@ class CtbRawFile(_aare.CtbRawFile):
             int: Frame position in file.
         """
         return super().tell()
+    
+    @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()
 
     @property
     def image_size_in_bytes(self) -> int:

python/aare/ScanParameters.py

@@ -0,0 +1,16 @@
+from . import _aare
+
+class ScanParameters(_aare.ScanParameters):
+    def __init__(self, s):
+        super().__init__(s)
+        
+    def __iter__(self):
+        return [getattr(self, a) for a in ['start', 'stop', 'step']].__iter__()
+    
+    def __str__(self):
+        return f'ScanParameters({self.dac}: {self.start}, {self.stop}, {self.step})'
+    
+    def __repr__(self):
+        return self.__str__()
+    
+    

python/aare/__init__.py

@@ -3,4 +3,5 @@ from . import _aare
 
 from ._aare import VarClusterFinder, File, RawMasterFile
 from ._aare import Pedestal, ClusterFinder
-from .CtbRawFile import CtbRawFile
+from .CtbRawFile import CtbRawFile
+from .ScanParameters import ScanParameters

python/aare/transform.py

@@ -5,7 +5,6 @@ from . import _aare
 class Moench05Transform:
     #Could be moved to C++ without changing the interface
     def __init__(self):
-        print('map created')
         self.pixel_map = _aare.GenerateMoench05PixelMap()
 
     def __call__(self, data):
@@ -23,6 +22,7 @@ class Matterhorn02Transform:
         else:
             return np.take(data.view(np.uint16), self.pixel_map[0:counters])
 
+
 #on import generate the pixel maps to avoid doing it every time
 moench05 = Moench05Transform()
 matterhorn02 = Matterhorn02Transform()

python/examples/play.py

@@ -95,11 +95,11 @@ f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
 f.seek(100)
 header1, image1 = f.read_frame()
 
-fpath = Path(base / 'scan_all15keV_vrf500_vrsh700_th0_master_0.json')
+# fpath = Path(base / 'scan_all15keV_vrf500_vrsh700_th0_master_0.json')
 
-f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
-f.seek(100)
-header4, image4 = f.read_frame()
+# f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
+# f.seek(100)
+# header4, image4 = f.read_frame()
 
 # n_counters = image.shape[1] / 48**2 / 2
 
@@ -112,7 +112,7 @@ header4, image4 = f.read_frame()
 
 
 #Data come in "blocks" of 4 pixels/receiver
-data = get_Mh02_frames(fpath.as_posix())
+# data = get_Mh02_frames(fpath.as_posix())
 
 # rawi = np.zeros(48*48*4+56, dtype = np.uint16)
 # for i,v in enumerate(rawi[56:]):
@@ -130,7 +130,7 @@ data = get_Mh02_frames(fpath.as_posix())
 #             pm[counter, row, col] = row*48 + col+counter*48*48
 
 
-f2 = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
-header, data = f2.read()
-plt.plot(data[:,0,20,20])
+# f2 = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
+# header, data = f2.read()
+# plt.plot(data[:,0,20,20])
 

python/src/file.hpp

@@ -166,11 +166,29 @@ void define_file_io_bindings(py::module &m) {
         .def_property_readonly("max_frames_per_file",
                                &RawMasterFile::max_frames_per_file)
         .def_property_readonly("bitdepth", &RawMasterFile::bitdepth)
+        .def_property_readonly("frame_padding", &RawMasterFile::frame_padding)
+        .def_property_readonly("frame_discard_policy",
+                               &RawMasterFile::frame_discard_policy)
+        .def_property_readonly("total_frames_expected", &RawMasterFile::total_frames_expected)
+        .def_property_readonly("geometry", &RawMasterFile::geometry)
         .def_property_readonly("analog_samples", &RawMasterFile::analog_samples)
         .def_property_readonly("digital_samples",
                                &RawMasterFile::digital_samples)
-        .def_property_readonly("transceiver_samples", &RawMasterFile::transceiver_samples);
+        .def_property_readonly("transceiver_samples", &RawMasterFile::transceiver_samples)
+        .def_property_readonly("number_of_rows", &RawMasterFile::number_of_rows)
+        .def_property_readonly("quad", &RawMasterFile::quad)
+        .def_property_readonly("scan_parameters", &RawMasterFile::scan_parameters);
 
+
+
+    py::class_<ScanParameters>(m, "ScanParameters")
+        .def(py::init<const std::string &>())
+        .def(py::init<const ScanParameters&>())
+        .def_property_readonly("enabled", &ScanParameters::enabled)
+        .def_property_readonly("dac", &ScanParameters::dac)
+        .def_property_readonly("start", &ScanParameters::start)
+        .def_property_readonly("stop", &ScanParameters::stop)
+        .def_property_readonly("step", &ScanParameters::step);
     // py::class_<ClusterHeader>(m, "ClusterHeader")
     //     .def(py::init<>())
     //     .def_readwrite("frame_number", &ClusterHeader::frame_number)

src/RawFile.cpp

@@ -1,7 +1,6 @@
 #include "aare/RawFile.hpp"
 #include "aare/PixelMap.hpp"
 #include "aare/defs.hpp"
-#include "aare/json.hpp"
 
 #include <fmt/format.h>
 #include <nlohmann/json.hpp>

src/RawMasterFile.cpp

@@ -1,5 +1,5 @@
 #include "aare/RawMasterFile.hpp"
-
+#include <sstream>  
 namespace aare {
 
 RawFileNameComponents::RawFileNameComponents(
@@ -51,6 +51,32 @@ const std::string &RawFileNameComponents::base_name() const {
 const std::string &RawFileNameComponents::ext() const { return m_ext; }
 int RawFileNameComponents::file_index() const { return m_file_index; }
 
+// "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
+ScanParameters::ScanParameters(const std::string& par){
+    std::istringstream iss(par.substr(1, par.size()-2));
+    std::string line;
+    while(std::getline(iss, line)){
+        if(line == "enabled"){
+            m_enabled = true;
+        }else if(line.find("dac") != std::string::npos){
+            m_dac = line.substr(4);
+        }else if(line.find("start") != std::string::npos){
+            m_start = std::stoi(line.substr(6));
+        }else if(line.find("stop") != std::string::npos){
+            m_stop = std::stoi(line.substr(5));
+        }else if(line.find("step") != std::string::npos){
+            m_step = std::stoi(line.substr(5));
+        }
+    }
+}
+
+int ScanParameters::start() const { return m_start; }
+int ScanParameters::stop() const { return m_stop; }
+int ScanParameters::step() const { return m_step; }
+const std::string &ScanParameters::dac() const { return m_dac; }
+bool ScanParameters::enabled() const { return m_enabled; }
+
+
 RawMasterFile::RawMasterFile(const std::filesystem::path &fpath)
     : m_fnc(fpath) {
     if (!std::filesystem::exists(fpath)) {
@@ -113,6 +139,10 @@ std::optional<size_t> RawMasterFile::transceiver_samples() const {
     return m_transceiver_samples;
 }
 
+ScanParameters RawMasterFile::scan_parameters() const {
+    return m_scan_parameters;
+}
+
 void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     std::ifstream ifs(fpath);
     json j;
@@ -203,6 +233,13 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // keep the optional empty
     }
 
+    try{
+        std::string scan_parameters = j.at("Scan Parameters");
+        m_scan_parameters = ScanParameters(scan_parameters);
+    }catch (const json::out_of_range &e) {
+        // not a scan
+    }
+
     // Update detector type for Moench
     // TODO! How does this work with old .raw master files?
     #ifdef AARE_VERBOSE

src/RawMasterFile.test.cpp

@@ -38,6 +38,26 @@ TEST_CASE("Master file name does not fit pattern"){
 }
 
 
+
+TEST_CASE("Parse scan parameters"){
+    ScanParameters s("[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]");
+    REQUIRE(s.enabled());
+    REQUIRE(s.dac() == "dac 4");
+    REQUIRE(s.start() == 500);
+    REQUIRE(s.stop() == 2200);
+    REQUIRE(s.step() == 5);
+}
+
+TEST_CASE("A disabled scan"){
+    ScanParameters s("[disabled]");
+    REQUIRE_FALSE(s.enabled());
+    REQUIRE(s.dac() == "");
+    REQUIRE(s.start() == 0);
+    REQUIRE(s.stop() == 0);
+    REQUIRE(s.step() == 0);
+}
+
+
 TEST_CASE("Parse a master file in .json format"){
     auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));