wip at fixing hdf5 master file

include/aare/Hdf5File.hpp

@@ -8,7 +8,7 @@
 
 namespace aare {
 
-struct H5Handles {
+class H5Handles {
   std::string file_name;
   std::string dataset_name;
   H5::H5File file;
@@ -20,6 +20,7 @@ struct H5Handles {
   std::vector<hsize_t> count;
   std::vector<hsize_t> offset;
 
+  public:
   H5Handles(const std::string& fname, const std::string& dname):
     file_name(fname),
     dataset_name(dname),
@@ -31,6 +32,10 @@ struct H5Handles {
       initialize_memspace();
     }
 
+  std::vector<hsize_t> get_dims() const {
+    return dims;
+  }
+
   void seek(size_t frame_index) {
     if (frame_index >= dims[0]) {
         throw std::runtime_error(LOCATION + "Invalid frame number");

include/aare/Hdf5MasterFile.hpp

@@ -6,18 +6,6 @@
 #include <fstream>
 #include <optional>
 
-namespace fmt {
-template <typename T> struct formatter<std::optional<T>> : formatter<T> {
-    template <typename FormatContext>
-    auto format(const std::optional<T> &opt, FormatContext &ctx) {
-        if (opt) {
-            return formatter<T>::format(*opt, ctx);
-        } else {
-            return format_to(ctx.out(), "nullopt");
-        }
-    }
-};
-} // namespace fmt
 
 namespace aare {
 
@@ -29,7 +17,7 @@ class Hdf5FileNameComponents {
     std::filesystem::path m_base_path{};
     std::string m_base_name{};
     std::string m_ext{};
-    int m_file_index{}; // TODO! is this measurement_index?
+    int m_file_index{}; 
 
   public:
     Hdf5FileNameComponents(const std::filesystem::path &fname);
@@ -50,39 +38,6 @@ class Hdf5FileNameComponents {
     void set_old_scheme(bool old_scheme);
 };
 
-/*
-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;
-    void increment_stop();
-};
-
-struct ROI {
-    int64_t xmin{};
-    int64_t xmax{};
-    int64_t ymin{};
-    int64_t ymax{};
-
-    int64_t height() const { return ymax - ymin; }
-    int64_t width() const { return xmax - xmin; }
-};
-*/
 
 /**
  * @brief Class for parsing a master file either in our .json format or the old
@@ -104,7 +59,7 @@ class Hdf5MasterFile {
     xy m_geometry{};
 
     size_t m_max_frames_per_file{};
-    // uint32_t m_adc_mask{}; // TODO! implement reading
+    uint32_t m_adc_mask{}; // TODO! implement reading
     FrameDiscardPolicy m_frame_discard_policy{};
     size_t m_frame_padding{};
 
@@ -113,7 +68,7 @@ class Hdf5MasterFile {
     uint8_t m_digital_flag{};
     uint8_t m_transceiver_flag{};
 
-    // ScanParameters m_scan_parameters;
+    ScanParameters m_scan_parameters;
 
     std::optional<size_t> m_analog_samples;
     std::optional<size_t> m_digital_samples;
@@ -121,7 +76,7 @@ class Hdf5MasterFile {
     std::optional<size_t> m_number_of_rows;
     std::optional<uint8_t> m_quad;
 
-    // std::optional<ROI> m_roi;
+    std::optional<ROI> m_roi;
 
   public:
     Hdf5MasterFile(const std::filesystem::path &fpath);
@@ -151,9 +106,9 @@ class Hdf5MasterFile {
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> quad() const;
 
-    // std::optional<ROI> roi() const;
+    std::optional<ROI> roi() const;
 
-    // ScanParameters scan_parameters() const;
+    ScanParameters scan_parameters() const;
 
   private:
     static const std::string metadata_group_name;

include/aare/RawMasterFile.hpp

@@ -39,28 +39,6 @@ class RawFileNameComponents {
     void set_old_scheme(bool old_scheme);
 };
 
-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;
-    void increment_stop();
-};
-
 
 /**
  * @brief Class for parsing a master file either in our .json format or the old
@@ -132,7 +110,6 @@ class RawMasterFile {
 
     std::optional<ROI> roi() const;
 
-
     ScanParameters scan_parameters() const;
 
   private:

include/aare/defs.hpp

@@ -12,7 +12,8 @@
 #include <variant>
 #include <vector>
 #include <iostream>
-
+#include <sstream>  
+#include <optional>
 
 /**
  * @brief LOCATION macro to get the current location in the code
@@ -225,6 +226,46 @@ struct ROI{
 
 using dynamic_shape = std::vector<ssize_t>;
 
+
+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:
+    // "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
+    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));
+            }
+        }   
+    };
+    ScanParameters() = default;
+    ScanParameters(const ScanParameters &) = default;
+    ScanParameters &operator=(const ScanParameters &) = default;
+    ScanParameters(ScanParameters &&) = default;
+    int start() const { return m_start; };
+    int stop() const { return m_stop; };
+    int step() const { return m_step; };
+    const std::string &dac() const { return m_dac; };
+    bool enabled() const { return m_enabled; };
+    void increment_stop() { m_stop += 1; };
+};
+
 //TODO! Can we uniform enums between the libraries?
 
 /**
@@ -266,6 +307,8 @@ template <> std::string ToString(TimingMode arg);
 template <> FrameDiscardPolicy StringTo(const std::string & /*mode*/);
 template <> std::string ToString(FrameDiscardPolicy arg);
 
+template <> std::string ToString(ScanParameters arg);
+
 using DataTypeVariants = std::variant<uint16_t, uint32_t>;
 
 template <typename T>
@@ -280,5 +323,14 @@ std::ostream &operator<<(std::ostream &os, const std::vector<T> &vec) {
     return os;
 }
 
+template <typename T>
+std::ostream &operator<<(std::ostream &os, const std::optional<T> &opt) {
+    if (opt)
+        os << *opt;
+    else
+        os << "nullopt";
+    return os;
+}
+
 
 } // namespace aare