ported reading clusters (#95)

python/aare/__init__.py

@@ -5,6 +5,7 @@ from . import _aare
 from ._aare import File, RawFile, RawMasterFile, RawSubFile
 from ._aare import Pedestal, ClusterFinder, VarClusterFinder
 from ._aare import DetectorType
+from ._aare import ClusterFile
 
 from .CtbRawFile import CtbRawFile
 from .ScanParameters import ScanParameters

python/examples/play.py

@@ -1,95 +1,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 plt.ion()
-
-import aare
-from aare import CtbRawFile
-print('aare imported')
-from aare import transform
-print('transform imported')
 from pathlib import Path
+from aare import ClusterFile
 
-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
+base = Path('~/data/aare_test_data/clusters').expanduser()
+# f = ClusterFile(base / 'beam_En700eV_-40deg_300V_10us_d0_f0_100.clust')
+f = ClusterFile(base / 'single_frame_97_clustrers.clust')
 
 
-#target format
-# [frame, counter, row, col]
-# plt.imshow(data[0,0])
-
-
-base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/ci/aare_test_data')
-# p = Path(base / 'jungfrau/jungfrau_single_master_0.json')
-
-# f = aare.File(p)
-# for i in range(10):
-#     frame = f.read_frame()
-
-
-
-# # f2 = aare.CtbRawFile(fpath, transform=transform.matterhorn02)
-# # header, data = f2.read()
-# # plt.plot(data[:,0,20,20])
-# from aare import RawMasterFile, File, RawSubFile, DetectorType, RawFile
-# base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/SideBySide/')
-# fpath = Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
-# raw = Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_d0_f0_0.raw')
-
-
-
-# m = RawMasterFile(base / fpath)
-# # roi = m.roi
-# # rows = roi.ymax-roi.ymin+1
-# # cols = 1024-roi.xmin
-# # sf = RawSubFile(base / raw, DetectorType.Jungfrau, rows, cols, 16)
-
-from aare import RawFile
-
-
-
-from aare import RawFile, File
-
-base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/')
-fname = base / Path('SideBySide/241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
-# fname = Path(base / 'jungfrau/jungfrau_single_master_0.json')
-# fname = base / 'Stacked/241024_JF10_m450_m367_KnifeEdge_TestBesom_9keV_750umFilter_PedestalStart_ZPos_-6_master_0.json'
-
-
-f = RawFile(fname)
-h,img = f.read_frame()
-print(f'{h["frameNumber"]}')

python/src/cluster.hpp

@@ -33,20 +33,20 @@ void define_cluster_finder_bindings(py::module &m) {
                  return clusters;
              });
 
-    py::class_<Cluster>(m, "Cluster", py::buffer_protocol())
+    py::class_<DynamicCluster>(m, "DynamicCluster", py::buffer_protocol())
         .def(py::init<int, int, Dtype>())
-        .def("size", &Cluster::size)
-        .def("begin", &Cluster::begin)
-        .def("end", &Cluster::end)
-        .def_readwrite("x", &Cluster::x)
-        .def_readwrite("y", &Cluster::y)
-        .def_buffer([](Cluster &c) -> py::buffer_info {
+        .def("size", &DynamicCluster::size)
+        .def("begin", &DynamicCluster::begin)
+        .def("end", &DynamicCluster::end)
+        .def_readwrite("x", &DynamicCluster::x)
+        .def_readwrite("y", &DynamicCluster::y)
+        .def_buffer([](DynamicCluster &c) -> py::buffer_info {
             return py::buffer_info(c.data(), c.dt.bytes(), c.dt.format_descr(),
                                    1, {c.size()}, {c.dt.bytes()});
         })
 
-        .def("__repr__", [](const Cluster &a) {
-            return "<Cluster: x: " + std::to_string(a.x) +
+        .def("__repr__", [](const DynamicCluster &a) {
+            return "<DynamicCluster: x: " + std::to_string(a.x) +
                    ", y: " + std::to_string(a.y) + ">";
         });
 }

python/src/cluster_file.hpp

@@ -0,0 +1,34 @@
+#include "aare/ClusterFile.hpp"
+#include "aare/defs.hpp"
+
+
+#include <cstdint>
+#include <filesystem>
+#include <pybind11/iostream.h>
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/stl/filesystem.h>
+#include <string>
+
+namespace py = pybind11;
+using namespace ::aare;
+
+void define_cluster_file_io_bindings(py::module &m) {
+    PYBIND11_NUMPY_DTYPE(Cluster, x, y, data);
+
+    py::class_<ClusterFile>(m, "ClusterFile")
+        .def(py::init<const std::filesystem::path &>())
+        .def("read_clusters",
+             [](ClusterFile &self, size_t n_clusters) {
+                 auto* vec = new std::vector<Cluster>(self.read_clusters(n_clusters));
+                 return return_vector(vec);
+             })
+        .def("read_cluster_with_cut",
+             [](ClusterFile &self, size_t n_clusters, py::array_t<double> noise_map, int nx, int ny) {
+                 auto view = make_view_2d(noise_map);
+                 auto* vec = new std::vector<Cluster>(self.read_cluster_with_cut(n_clusters, view.data(), nx, ny));
+                 return return_vector(vec);
+             });
+
+}

python/src/file.hpp

@@ -264,7 +264,7 @@ void define_file_io_bindings(py::module &m) {
 
     //     .def("close", &ClusterFileV2::close);
 
-    // m.def("to_clustV2", [](std::vector<Cluster> &clusters, const int
+    // m.def("to_clustV2", [](std::vector<DynamicCluster> &clusters, const int
     // frame_number) {
     //     std::vector<ClusterV2> clusters_;
     //     for (auto &c : clusters) {

python/src/module.cpp

@@ -6,6 +6,7 @@
 #include "pixel_map.hpp"
 #include "pedestal.hpp"
 #include "cluster.hpp"
+#include "cluster_file.hpp"
 
 //Pybind stuff
 #include <pybind11/pybind11.h>
@@ -22,4 +23,5 @@ PYBIND11_MODULE(_aare, m) {
     define_pedestal_bindings<double>(m, "Pedestal");
     define_pedestal_bindings<float>(m, "Pedestal_float32");
     define_cluster_finder_bindings(m);
+    define_cluster_file_io_bindings(m);
 }