Fixing ROI read of RawFile (#125)

- Bugfixes
- New abstraction for detector geometry
- Tests for updating geo with ROI

include/aare/RawFile.hpp

@@ -34,15 +34,19 @@ class RawFile : public FileInterface {
     size_t n_subfile_parts{}; // d0,d1...dn
     //TODO! move to vector of SubFile instead of pointers
     std::vector<std::vector<RawSubFile *>> subfiles; //subfiles[f0,f1...fn][d0,d1...dn]
-    std::vector<xy> positions;
-    std::vector<ModuleGeometry> m_module_pixel_0;
+    // std::vector<xy> positions;
+    
     ModuleConfig cfg{0, 0};
 
     RawMasterFile m_master;
 
     size_t m_current_frame{};
-    size_t m_rows{};
-    size_t m_cols{};
+
+    // std::vector<ModuleGeometry> m_module_pixel_0;
+    // size_t m_rows{};
+    // size_t m_cols{};
+
+    DetectorGeometry m_geometry;
 
   public:
     /**
@@ -111,11 +115,12 @@ class RawFile : public FileInterface {
      */
     static DetectorHeader read_header(const std::filesystem::path &fname);
 
-    void update_geometry_with_roi();
+    // void update_geometry_with_roi();
     int find_number_of_subfiles();
 
     void open_subfiles();
     void find_geometry();
 };
 
+
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -62,17 +62,6 @@ class ScanParameters {
 };
 
 
-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
  * .raw format

include/aare/defs.hpp

@@ -179,13 +179,42 @@ template <typename T> struct t_xy {
 using xy = t_xy<uint32_t>;
 
 
+/**
+ * @brief Class to hold the geometry of a module. Where pixel 0 is located and the size of the module
+ */
 struct ModuleGeometry{
-    int x{};
-    int y{};
+    int origin_x{};
+    int origin_y{};
     int height{};
     int width{};
+    int row_index{};
+    int col_index{}; 
 };
 
+/**
+ * @brief Class to hold the geometry of a detector. Number of modules, their size and where pixel 0 
+ * for each module is located
+ */
+struct DetectorGeometry{
+    int modules_x{};
+    int modules_y{};
+    int pixels_x{};
+    int pixels_y{};
+    int module_gap_row{};
+    int module_gap_col{};
+    std::vector<ModuleGeometry> module_pixel_0;
+};
+
+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; }
+  };
+
 
 using dynamic_shape = std::vector<int64_t>;
 

include/aare/geo_helpers.hpp

@@ -0,0 +1,16 @@
+#pragma once
+#include "aare/defs.hpp"
+#include "aare/RawMasterFile.hpp" //ROI refactor away
+namespace aare{
+
+/**
+ * @brief Update the detector geometry given a region of interest
+ * 
+ * @param geo 
+ * @param roi 
+ * @return DetectorGeometry 
+ */
+DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, ROI roi);
+
+
+} // namespace aare