From 7550a2cb9749750a5bc39caaa9267e3eb4708e06 Mon Sep 17 00:00:00 2001
From: froejdh_e <erik.frojdh@psi.ch>
Date: Fri, 10 Jan 2025 15:33:56 +0100
Subject: [PATCH] fixing read bug

---
 python/src/cluster.hpp      | 34 +++++++++++++++++-----------------
 python/src/cluster_file.hpp |  2 +-
 src/ClusterFile.cpp         |  4 ++--
 3 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/python/src/cluster.hpp b/python/src/cluster.hpp
index 5b7d20e..768593a 100644
--- a/python/src/cluster.hpp
+++ b/python/src/cluster.hpp
@@ -39,14 +39,14 @@ void define_cluster_vector(py::module &m, const std::string &typestr) {
                       &ClusterVector<T>::set_frame_number)
         .def_buffer([typestr](ClusterVector<T> &self) -> py::buffer_info {
             return py::buffer_info(
-                self.data(),           /* Pointer to buffer */
+                self.data(),      /* Pointer to buffer */
                 self.item_size(), /* Size of one scalar */
                 fmt::format(self.fmt_base(), self.cluster_size_x(),
                             self.cluster_size_y(),
-                            typestr),   /* Format descriptor */
-                1,                      /* Number of dimensions */
-                {self.size()},          /* Buffer dimensions */
-                {self.item_size()} /* Strides (in bytes) for each index */
+                            typestr), /* Format descriptor */
+                1,                    /* Number of dimensions */
+                {self.size()},        /* Buffer dimensions */
+                {self.item_size()}    /* Strides (in bytes) for each index */
             );
         });
 }
@@ -75,18 +75,18 @@ void define_cluster_finder_mt_bindings(py::module &m) {
         .def("sync", &ClusterFinderMT<uint16_t, pd_type>::sync)
         .def("stop", &ClusterFinderMT<uint16_t, pd_type>::stop)
         .def("start", &ClusterFinderMT<uint16_t, pd_type>::start)
-        .def_property_readonly("pedestal",
-                               [](ClusterFinderMT<uint16_t, pd_type> &self) {
-                                   auto pd = new NDArray<pd_type, 2>{};
-                                   *pd = self.pedestal();
-                                   return return_image_data(pd);
-                               })
-        .def_property_readonly("noise",
-                               [](ClusterFinderMT<uint16_t, pd_type> &self) {
-                                   auto arr = new NDArray<pd_type, 2>{};
-                                   *arr = self.noise();
-                                   return return_image_data(arr);
-                               });
+        .def("pedestal",
+             [](ClusterFinderMT<uint16_t, pd_type> &self, size_t thread_index) {
+                 auto pd = new NDArray<pd_type, 2>{};
+                 *pd = self.pedestal(thread_index);
+                 return return_image_data(pd);
+             },py::arg("thread_index") = 0)
+        .def("noise",
+             [](ClusterFinderMT<uint16_t, pd_type> &self, size_t thread_index) {
+                 auto arr = new NDArray<pd_type, 2>{};
+                 *arr = self.noise(thread_index);
+                 return return_image_data(arr);
+             },py::arg("thread_index") = 0);
 }
 
 void define_cluster_collector_bindings(py::module &m) {
diff --git a/python/src/cluster_file.hpp b/python/src/cluster_file.hpp
index 82d4453..baae7a1 100644
--- a/python/src/cluster_file.hpp
+++ b/python/src/cluster_file.hpp
@@ -35,7 +35,7 @@ void define_cluster_file_io_bindings(py::module &m) {
              [](ClusterFile &self) {
                 auto v = new ClusterVector<int32_t>(self.read_frame());
                 return v;
-             },py::return_value_policy::take_ownership)
+             })
         .def("write_frame", &ClusterFile::write_frame)
         .def("read_cluster_with_cut",
              [](ClusterFile &self, size_t n_clusters,
diff --git a/src/ClusterFile.cpp b/src/ClusterFile.cpp
index dab4552..4d0d6df 100644
--- a/src/ClusterFile.cpp
+++ b/src/ClusterFile.cpp
@@ -72,7 +72,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters) {
         } else {
             nn = nph;
         }
-        nph_read += fread(reinterpret_cast<void *>(buf + nph_read),
+        nph_read += fread((buf + nph_read*clusters.item_size()),
                           clusters.item_size(), nn, fp);
         m_num_left = nph - nn; // write back the number of photons left
     }
@@ -87,7 +87,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters) {
                 else
                     nn = nph;
 
-                nph_read += fread(reinterpret_cast<void *>(buf + nph_read),
+                nph_read += fread((buf + nph_read*clusters.item_size()),
                                   clusters.item_size(), nn, fp);
                 m_num_left = nph - nn;
             }