MH02 1-4 counters

include/aare/CtbRawFile.hpp

@@ -27,6 +27,8 @@ public:
 
     size_t image_size_in_bytes() const;
     size_t frames_in_file() const;
+
+    RawMasterFile master() const;
 private:
     void find_subfiles();
     size_t sub_file_index(size_t frame_index) const {

include/aare/PixelMap.hpp

@@ -5,7 +5,11 @@
 
 namespace aare {
 
-NDArray<size_t, 2> GenerateMoench03PixelMap();
-NDArray<size_t, 2> GenerateMoench05PixelMap();
+NDArray<ssize_t, 2> GenerateMoench03PixelMap();
+NDArray<ssize_t, 2> GenerateMoench05PixelMap();
+
+NDArray<ssize_t, 2>GenerateMH02SingleCounterPixelMap();
+NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap();
+
 
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -65,9 +65,11 @@ class RawMasterFile {
     //TODO! should these be bool?
     uint8_t m_analog_flag{};
     uint8_t m_digital_flag{};
+    uint8_t m_transceiver_flag{};
 
     std::optional<size_t> m_analog_samples;
     std::optional<size_t> m_digital_samples;
+    std::optional<size_t> m_transceiver_samples;
     std::optional<size_t> m_number_of_rows;
     std::optional<uint8_t> m_quad;
 
@@ -93,6 +95,7 @@ class RawMasterFile {
 
     std::optional<size_t> analog_samples() const;
     std::optional<size_t> digital_samples() const;
+    std::optional<size_t> transceiver_samples() const;
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> quad() const;
   private:

include/aare/SubFile.hpp

@@ -74,7 +74,7 @@ class SubFile {
     size_t n_frames{};
     int m_sub_file_index_{};
     DetectorType m_detector_type;
-    std::optional<NDArray<size_t, 2>> pixel_map;
+    std::optional<NDArray<ssize_t, 2>> pixel_map;
 };
 
 } // namespace aare

python/aare/CtbRawFile.py

@@ -36,6 +36,7 @@ class CtbRawFile(_aare.CtbRawFile):
         if frame_index is not None:
             self.seek(frame_index)
 
+
         header, data = super().read_frame()
         if header.shape == (1,):
             header = header[0]
@@ -47,6 +48,8 @@ class CtbRawFile(_aare.CtbRawFile):
                 return header, *res
             else:
                 return header, res
+        else:
+            return header, data
             
     def read_n(self, n_frames:int) -> tuple:
         """Read several frames from the file.
@@ -82,6 +85,13 @@ class CtbRawFile(_aare.CtbRawFile):
 
         return header, data
 
+    def read(self) -> tuple:
+        """Read the entire file.
+
+        Returns:
+            tuple: header, data
+        """
+        return self.read_n(self.frames_in_file)
 
     def seek(self, frame_index:int) -> None:
         """Seek to a specific frame in the file.

python/aare/transform.py

@@ -12,4 +12,17 @@ class Moench05Transform:
         return np.take(data.view(np.uint16), self.pixel_map)
 
 
+class Matterhorn02Transform:
+    def __init__(self):
+        self.pixel_map = _aare.GenerateMH02FourCounterPixelMap()
+
+    def __call__(self, data):
+        counters = int(data.size / 48**2 / 2)
+        if counters == 1:
+            return np.take(data.view(np.uint16), self.pixel_map[0])
+        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

@@ -9,6 +9,50 @@ from aare import transform
 print('transform imported')
 from pathlib import Path
 
+import json
+
+def decode(frames, rawdata):
+    # rawdata = np.fromfile(f, dtype = np.uint16)
+    counters = int((np.shape(rawdata)[0]/frames-56)/(48*48))
+    print('Counters:', counters)
+    rawdata = rawdata.reshape(frames,-1)[:,56:]
+    rawdata = rawdata.reshape(frames,576*counters,4) #Data come in "blocks" of 4 pixels/receiver
+    tr1 = rawdata[:,0:576*counters:2] #Transceiver1
+    tr1=tr1.reshape((frames,48*counters,24)) 
+
+    tr2 = rawdata[:,1:576*counters:2] #Transceiver2
+    tr2=tr2.reshape((frames,48*counters,24))     
+    
+    data = np.append(tr1,tr2,axis=2)
+    return data
+
+def get_Mh02_frames(fname):
+    # this function gives you the data from a file that is not a scan
+    # it returns a (frames,48*counters,48)
+
+    jsonf = open(fname)
+    jsonpar = json.load(jsonf)
+    jsonf.close()
+
+    frames=jsonpar["Frames in File"]
+    print('Frames:', frames)
+
+    rawf = fname.replace('master','d0_f0')	
+    rawf = rawf.replace('.json','.raw')	
+
+    with open(rawf, 'rb') as f:
+        rawdata = np.fromfile(f, dtype = np.uint16)
+        data = decode(frames, rawdata) 
+        print('Data:', np.shape(data))
+        
+        return data
+
+
+#target format
+# [frame, counter, row, col]
+# plt.imshow(data[0,0])
+
+
 # p = Path('/Users/erik/data/aare_test_data/jungfrau/jungfrau_single_master_0.json')
 
 # f = aare.File(p)
@@ -18,27 +62,75 @@ from pathlib import Path
 # im = ax.imshow(frame, cmap='viridis')
 
 
-fpath = Path('/Users/erik/data/Moench03old/test_034_irradiated_noise_g4_hg_exptime_2000us_master_0.json')
-# fpath = Path('/Users/erik/data/Moench05/moench05_multifile_master_0.json')
+# fpath = Path('/Users/erik/data/Moench03old/test_034_irradiated_noise_g4_hg_exptime_2000us_master_0.json')
+# # fpath = Path('/Users/erik/data/Moench05/moench05_multifile_master_0.json')
 
 
-# f = aare.CtbRawFile(fpath, transform = transform.moench05)
-# with CtbRawFile(fpath, transform = transform.moench05) as f:
-#     for header, image in f:
-#         print(f'Frame number: {header["frameNumber"]}')
+# # f = aare.CtbRawFile(fpath, transform = transform.moench05)
+# # with CtbRawFile(fpath, transform = transform.moench05) as f:
+# #     for header, image in f:
+# #         print(f'Frame number: {header["frameNumber"]}')
 
-# m = aare.RawMasterFile(fpath)
-f = aare.File(fpath)
+# # m = aare.RawMasterFile(fpath)
+# f = aare.File(fpath)
 
 
 
-cf = aare.ClusterFinder((400,400),(3,3))
+# cf = aare.ClusterFinder((400,400),(3,3))
 
-for i in range(100):
-    cf.push_pedestal_frame(f.read_frame())
+# for i in range(100):
+#     cf.push_pedestal_frame(f.read_frame())
 
 
-f.seek(0)
-pd = f.read_n(100).mean(axis=0)
+# f.seek(0)
+# pd = f.read_n(100).mean(axis=0)
+
+# clusters = cf.find_clusters_without_threshold(f.read_frame())
+
+
+
+base = Path('/Users/erik/data/matterhorn/raw')
+fpath = Path(base / 'scan_15keV_vrf700_vrsh700_th0_master_0.json')
+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')
+
+f = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
+f.seek(100)
+header4, image4 = f.read_frame()
+
+# n_counters = image.shape[1] / 48**2 / 2
+
+# for i in range(100):
+#     header, image = f.read_frame()
+#     print(header['frameNumber'])
+
+
+
+
+
+#Data come in "blocks" of 4 pixels/receiver
+data = get_Mh02_frames(fpath.as_posix())
+
+# rawi = np.zeros(48*48*4+56, dtype = np.uint16)
+# for i,v in enumerate(rawi[56:]):
+#     rawi[i+56] = i
+
+# raw = image.view(np.uint16)
+
+# pixel_map = decode(1, rawi)
+# # img = np.take(raw, pixel_map)
+
+# pm = np.zeros((4, 48,48), dtype = np.int64)
+# for counter in range(4):
+#     for row in range(48):
+#         for col in range(48):
+#             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])
 
-clusters = cf.find_clusters_without_threshold(f.read_frame())

python/src/file.hpp

@@ -48,6 +48,7 @@ void define_file_io_bindings(py::module &m) {
              })
         .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);
 
@@ -167,7 +168,8 @@ void define_file_io_bindings(py::module &m) {
         .def_property_readonly("bitdepth", &RawMasterFile::bitdepth)
         .def_property_readonly("analog_samples", &RawMasterFile::analog_samples)
         .def_property_readonly("digital_samples",
-                               &RawMasterFile::digital_samples);
+                               &RawMasterFile::digital_samples)
+        .def_property_readonly("transceiver_samples", &RawMasterFile::transceiver_samples);
 
     // py::class_<ClusterHeader>(m, "ClusterHeader")
     //     .def(py::init<>())

python/src/pixel_map.hpp

@@ -14,11 +14,19 @@ using namespace::aare;
 
 void define_pixel_map_bindings(py::module &m) {
     m.def("GenerateMoench03PixelMap", []() {
-        auto ptr = new NDArray<size_t,2>(GenerateMoench03PixelMap());
+        auto ptr = new NDArray<ssize_t,2>(GenerateMoench03PixelMap());
         return return_image_data(ptr);
     })
     .def("GenerateMoench05PixelMap", []() {
-        auto ptr = new NDArray<size_t,2>(GenerateMoench05PixelMap());
+        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap());
+        return return_image_data(ptr);
+    })
+    .def("GenerateMH02SingleCounterPixelMap", []() {
+        auto ptr = new NDArray<ssize_t,2>(GenerateMH02SingleCounterPixelMap());
+        return return_image_data(ptr);
+    })
+    .def("GenerateMH02FourCounterPixelMap", []() {
+        auto ptr = new NDArray<ssize_t,3>(GenerateMH02FourCounterPixelMap());
         return return_image_data(ptr);
     });
 

src/CtbRawFile.cpp

@@ -48,6 +48,8 @@ size_t CtbRawFile::image_size_in_bytes() const { return m_master.image_size_in_b
 
 size_t CtbRawFile::frames_in_file() const { return m_master.frames_in_file(); }
 
+RawMasterFile CtbRawFile::master() const { return m_master; }
+
 void CtbRawFile::find_subfiles() {
     // we can semi safely assume that there is only one module for CTB
     while (std::filesystem::exists(m_master.data_fname(0, m_num_subfiles)))

src/PixelMap.cpp

@@ -3,7 +3,7 @@
 #include <array>
 
 namespace aare {
-NDArray<size_t, 2> GenerateMoench03PixelMap() {
+NDArray<ssize_t, 2> GenerateMoench03PixelMap() {
     std::array<int, 32> const adc_nr = {300, 325, 350, 375, 300, 325, 350, 375,
                                         200, 225, 250, 275, 200, 225, 250, 275,
                                         100, 125, 150, 175, 100, 125, 150, 175,
@@ -11,7 +11,7 @@ NDArray<size_t, 2> GenerateMoench03PixelMap() {
     int const sc_width = 25;
     int const nadc = 32;
     int const pixels_per_sc = 5000;
-    NDArray<size_t, 2> order_map({400, 400});
+    NDArray<ssize_t, 2> order_map({400, 400});
 
     int pixel = 0;
     for (int i = 0; i != pixels_per_sc; ++i) {
@@ -30,9 +30,9 @@ NDArray<size_t, 2> GenerateMoench03PixelMap() {
     return order_map;
 }
 
-NDArray<size_t, 2> GenerateMoench05PixelMap() {
+NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
     std::array<int, 3> adc_numbers = {9, 13, 1};
-    NDArray<size_t, 2> order_map({160, 150});
+    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++) {
@@ -52,4 +52,26 @@ NDArray<size_t, 2> GenerateMoench05PixelMap() {
     return order_map;
 }
 
+NDArray<ssize_t, 2>GenerateMH02SingleCounterPixelMap(){
+    NDArray<ssize_t, 2> order_map({48, 48});
+    for(int row = 0; row < 48; row++){
+        for(int col = 0; col < 48; col++){
+            order_map(row, col) = row*48 + col;
+        }
+    }
+    return order_map;
+}
+
+NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap(){
+    NDArray<ssize_t, 3> order_map({4, 48, 48});
+    for (int counter=0; counter<4; counter++){
+        for(int row = 0; row < 48; row++){
+            for(int col = 0; col < 48; col++){
+                order_map(counter, row, col) = counter*48*48 + row*48 + col;
+            }
+        }
+    }
+    return order_map;
+}
+
 } // namespace aare

src/RawMasterFile.cpp

@@ -109,6 +109,10 @@ std::optional<size_t> RawMasterFile::digital_samples() const {
     return m_digital_samples;
 }
 
+std::optional<size_t> RawMasterFile::transceiver_samples() const {
+    return m_transceiver_samples;
+}
+
 void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     std::ifstream ifs(fpath);
     json j;
@@ -190,6 +194,15 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // keep the optional empty
     }
 
+    try{
+        m_transceiver_flag = j.at("Transceiver Flag");
+        if(m_transceiver_flag){
+            m_transceiver_samples = j.at("Transceiver Samples");
+        }
+    }catch (const json::out_of_range &e) {
+        // keep the optional empty
+    }
+
     // Update detector type for Moench
     // TODO! How does this work with old .raw master files?
     #ifdef AARE_VERBOSE