Rewrote the multithreading to fix frame loss

RELEASE.md

@@ -1,22 +1,16 @@
 # Release notes
 
 
-### 2025.8.22
+### head
 
 Features:
 
 - Apply calibration works in G0 if passes a 2D calibration and pedestal
 - count pixels that switch
 - calculate pedestal (also g0 version)
-- NDArray::view() needs an lvalue to reduce issues with the view outliving the array
 
 
-Bugfixes:
-
-- Now using glibc 2.17 in conda builds (was using the host)
-- Fixed shifted pixels in clusters close to the edge of a frame
-
-### 2025.7.18
+### 2025.07.18
 
 Features:
 
@@ -30,7 +24,7 @@ Bugfixes:
 - Removed unused file: ClusterFile.cpp 
 
 
-### 2025.5.22
+### 2025.05.22
 
 Features:
 

VERSION

@@ -1 +1 @@
-2025.8.22
+2025.7.18

conda-recipe/conda_build_config.yaml

@@ -3,14 +3,3 @@ python:
     - 3.12
     - 3.13
 
-c_compiler:
-  - gcc                        # [linux]
-
-c_stdlib:
-  - sysroot                    # [linux]
-
-cxx_compiler:
-  - gxx                        # [linux]
-
-c_stdlib_version:              # [linux]
-  - 2.17                       # [linux]

conda-recipe/meta.yaml

@@ -16,8 +16,6 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
-    - {{ stdlib("c") }}
     - {{ compiler('cxx') }}
     - cmake
     - ninja

include/aare/BlockingQueue.hpp

@@ -0,0 +1,59 @@
+#pragma once
+#include <atomic>
+#include <cstdint>
+#include <memory>
+#include <thread>
+#include <vector>
+#include <condition_variable>
+#include <mutex>
+#include <deque>
+
+#include "aare/ClusterFinder.hpp"
+#include "aare/NDArray.hpp"
+#include "aare/logger.hpp"
+
+template <typename T>
+class BlockingQueue {
+    std::mutex mtx;
+    std::condition_variable cv_push, cv_pop;
+    std::deque<T> queue;
+    size_t max_size;
+    bool closed = false;
+
+public:
+    BlockingQueue(size_t capacity) : max_size(capacity) {}
+
+    void push(T item) {
+        std::unique_lock lock(mtx);
+        cv_push.wait(lock, [this] { return queue.size() < max_size; });
+        queue.push_back(std::move(item));
+        cv_pop.notify_one();
+    }
+
+    T pop() {
+        std::unique_lock lock(mtx);
+        cv_pop.wait(lock, [this] { return !queue.empty(); });
+        T item = std::move(queue.front());
+        queue.pop_front();
+        cv_push.notify_one();
+        return item;
+    }
+
+    void close() {
+        std::lock_guard lock(mtx);
+        closed = true;
+        cv_pop.notify_all();
+        cv_push.notify_all();
+    }
+
+    bool empty() {
+        std::lock_guard lock(mtx);
+        return queue.empty();
+    }
+
+
+    void write(T item) {push(item);}
+    bool isEmpty() {return empty();}
+    T frontPtr() {return pop();}
+    T popFront() {return pop();}
+};

include/aare/ClusterCollector.hpp

@@ -5,13 +5,15 @@
 #include "aare/ClusterFinderMT.hpp"
 #include "aare/ClusterVector.hpp"
 #include "aare/ProducerConsumerQueue.hpp"
+#include "aare/BlockingQueue.hpp"
 
 namespace aare {
 
 template <typename ClusterType,
           typename = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterCollector {
-    ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
+    // ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
+    BlockingQueue<ClusterVector<ClusterType>> *m_source;
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_stopped{true};
     std::chrono::milliseconds m_default_wait{1};
@@ -19,19 +21,47 @@ class ClusterCollector {
     std::vector<ClusterVector<ClusterType>> m_clusters;
 
     void process() {
+        // m_stopped = false;
+        // fmt::print("ClusterCollector started\n");
+        // // while (!m_stop_requested || !m_source->isEmpty()) {
+        // while (true) {
+        //     if (clusters.frame_number() == -1)
+        //         break;
+        
+        //     ClusterVector<ClusterType> clusters = m_source->pop();
+        //     m_clusters.push_back(std::move(clusters));
+        //     // if (ClusterVector<ClusterType> *clusters = m_source->frontPtr();
+        //     //     clusters != nullptr) {
+        //     //     m_clusters.push_back(std::move(*clusters));
+        //     //     m_source->popFront();
+        //     // } else {
+        //     //     std::this_thread::sleep_for(m_default_wait);
+        //     // }
+        // }
+        // fmt::print("ClusterCollector stopped\n");
+        // m_stopped = true;
+
+
         m_stopped = false;
         fmt::print("ClusterCollector started\n");
-        while (!m_stop_requested || !m_source->isEmpty()) {
-            if (ClusterVector<ClusterType> *clusters = m_source->frontPtr();
-                clusters != nullptr) {
-                m_clusters.push_back(std::move(*clusters));
-                m_source->popFront();
-            } else {
-                std::this_thread::sleep_for(m_default_wait);
+
+        while (true) {
+            // pop blocks until there is data
+            ClusterVector<ClusterType> clusters = m_source->pop();
+
+            // POISON DETECTION
+            if (clusters.frame_number() == -1) {
+                fmt::print("ClusterCollector received poison frame, stopping\n");
+                break;  // exit loop cleanly
             }
+
+            // NORMAL DATA: store or process
+            m_clusters.push_back(std::move(clusters));
         }
+
         fmt::print("ClusterCollector stopped\n");
         m_stopped = true;
+
     }
 
   public:

include/aare/ClusterFileSink.hpp

@@ -6,13 +6,15 @@
 #include "aare/ClusterFinderMT.hpp"
 #include "aare/ClusterVector.hpp"
 #include "aare/ProducerConsumerQueue.hpp"
+#include "aare/BlockingQueue.hpp"
 
 namespace aare {
 
 template <typename ClusterType,
           typename = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterFileSink {
-    ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
+    // ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
+    BlockingQueue<ClusterVector<ClusterType>> *m_source;
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_stopped{true};
     std::chrono::milliseconds m_default_wait{1};
@@ -20,29 +22,60 @@ class ClusterFileSink {
     std::ofstream m_file;
 
     void process() {
-        m_stopped = false;
+        // m_stopped = false;
+        // LOG(logDEBUG) << "ClusterFileSink started";
+        // while (!m_stop_requested || !m_source->isEmpty()) {
+        //     // if (ClusterVector<ClusterType> *clusters = m_source->pop(); m_source->frontPtr();
+        //     //     clusters != nullptr) {
+        //     {
+        //         ClusterVector<ClusterType> clusters = m_source->pop();
+        //         // Write clusters to file
+        //         int32_t frame_number =
+        //             clusters->frame_number(); // TODO! Should we store frame
+        //                                       // number already as int?
+        //         uint32_t num_clusters = clusters.size();
+                
+        //         if (frame_number >= 9910 && frame_number <= 9930)
+        //             std::cout << "prcoess: frame_number = " << frame_number << std::endl;
+
+        //         m_file.write(reinterpret_cast<const char *>(&frame_number),
+        //                      sizeof(frame_number));
+        //         m_file.write(reinterpret_cast<const char *>(&num_clusters),
+        //                      sizeof(num_clusters));
+        //         m_file.write(reinterpret_cast<const char *>(clusters.data()),
+        //                      clusters.size() * clusters.item_size());
+        //         m_source->popFront();
+        //     } 
+        //     // else {
+        //     //     std::this_thread::sleep_for(m_default_wait);
+        //     // }
+        // }
+        // LOG(logDEBUG) << "ClusterFileSink stopped";
+        // m_stopped = true;
+
         LOG(logDEBUG) << "ClusterFileSink started";
-        while (!m_stop_requested || !m_source->isEmpty()) {
-            if (ClusterVector<ClusterType> *clusters = m_source->frontPtr();
-                clusters != nullptr) {
-                // Write clusters to file
-                int32_t frame_number =
-                    clusters->frame_number(); // TODO! Should we store frame
-                                              // number already as int?
-                uint32_t num_clusters = clusters->size();
-                m_file.write(reinterpret_cast<const char *>(&frame_number),
-                             sizeof(frame_number));
-                m_file.write(reinterpret_cast<const char *>(&num_clusters),
-                             sizeof(num_clusters));
-                m_file.write(reinterpret_cast<const char *>(clusters->data()),
-                             clusters->size() * clusters->item_size());
-                m_source->popFront();
-            } else {
-                std::this_thread::sleep_for(m_default_wait);
+
+        while (true) {
+            ClusterVector<ClusterType> clusters = m_source->pop(); // blocks
+
+            // POISON PILL CHECK
+            if (clusters.frame_number() == -1) {
+                LOG(logDEBUG) << "ClusterFileSink received poison pill";
+                break;
             }
+
+            int32_t frame_number = clusters.frame_number();
+            uint32_t num_clusters = clusters.size();
+
+            m_file.write(reinterpret_cast<const char*>(&frame_number),
+                        sizeof(frame_number));
+            m_file.write(reinterpret_cast<const char*>(&num_clusters),
+                        sizeof(num_clusters));
+            m_file.write(reinterpret_cast<const char*>(clusters.data()),
+                        clusters.size() * clusters.item_size());
         }
+
         LOG(logDEBUG) << "ClusterFileSink stopped";
-        m_stopped = true;
     }
 
   public:

include/aare/ClusterFinder.hpp

@@ -19,9 +19,11 @@ class ClusterFinder {
     const PEDESTAL_TYPE c3;
     Pedestal<PEDESTAL_TYPE> m_pedestal;
     ClusterVector<ClusterType> m_clusters;
+    const uint32_t ClusterSizeX;
+    const uint32_t ClusterSizeY;
 
-    static const uint8_t ClusterSizeX = ClusterType::cluster_size_x;
-    static const uint8_t ClusterSizeY = ClusterType::cluster_size_y;
+    static const uint8_t SavedClusterSizeX = ClusterType::cluster_size_x;
+    static const uint8_t SavedClusterSizeY = ClusterType::cluster_size_y;
     using CT = typename ClusterType::value_type;
 
   public:
@@ -34,10 +36,12 @@ class ClusterFinder {
      *
      */
     ClusterFinder(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                  size_t capacity = 1000000)
+                  size_t capacity = 1000000,
+                  uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_image_size(image_size), m_nSigma(nSigma),
-          c2(sqrt((ClusterSizeY + 1) / 2 * (ClusterSizeX + 1) / 2)),
-          c3(sqrt(ClusterSizeX * ClusterSizeY)),
+          c2(sqrt((cluster_size_y + 1) / 2 * (cluster_size_x + 1) / 2)),
+          c3(sqrt(cluster_size_x * cluster_size_y)),
+          ClusterSizeX(cluster_size_x), ClusterSizeY(cluster_size_y),
           m_pedestal(image_size[0], image_size[1]), m_clusters(capacity) {
         LOG(logDEBUG) << "ClusterFinder: "
                       << "image_size: " << image_size[0] << "x" << image_size[1]
@@ -74,12 +78,20 @@ class ClusterFinder {
         // //  4,4 -> +/- 2
         int dy = ClusterSizeY / 2;
         int dx = ClusterSizeX / 2;
+        int dy2 = SavedClusterSizeY / 2;
+        int dx2 = SavedClusterSizeX / 2;
+
         int has_center_pixel_x =
             ClusterSizeX %
             2; // for even sized clusters there is no proper cluster center and
                // even amount of pixels around the center
         int has_center_pixel_y = ClusterSizeY % 2;
 
+        // if (frame_number >= 8000 && frame_number <= 9000)
+        //     // std::cout << "find_clusters: frame_number = " << frame_number << std::endl;
+        //     std::cout << frame_number << std::endl;
+
+
         m_clusters.set_frame_number(frame_number);
         for (int iy = 0; iy < frame.shape(0); iy++) {
             for (int ix = 0; ix < frame.shape(1); ix++) {
@@ -135,16 +147,14 @@ class ClusterFinder {
                     // It's worth redoing the look since most of the time we
                     // don't have a photon
                     int i = 0;
-                    for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                        for (int ic = -dx; ic < dx + has_center_pixel_y; ic++) {
+                    for (int ir = -dy2; ir < dy2 + has_center_pixel_y; ir++) {
+                        for (int ic = -dx2; ic < dx2 + has_center_pixel_y; ic++) {
                             if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                                 iy + ir >= 0 && iy + ir < frame.shape(0)) {
-                                CT tmp =
-                                    static_cast<CT>(frame(iy + ir, ix + ic)) -
-                                    static_cast<CT>(
-                                        m_pedestal.mean(iy + ir, ix + ic));
-                                cluster.data[i] =
-                                    tmp; // Watch for out of bounds access                                
+                                    
+                                CT tmp = static_cast<CT>(frame(iy + ir, ix + ic)) - static_cast<CT>(m_pedestal.mean(iy + ir, ix + ic));
+                                cluster.data[i] = tmp; // Watch for out of bounds access
+                                
                             }
                             i++;
                         }

include/aare/ClusterFinderMT.hpp

@@ -4,10 +4,14 @@
 #include <memory>
 #include <thread>
 #include <vector>
+#include <condition_variable>
+#include <mutex>
+#include <deque>
 
 #include "aare/ClusterFinder.hpp"
 #include "aare/NDArray.hpp"
 #include "aare/ProducerConsumerQueue.hpp"
+#include "aare/BlockingQueue.hpp"
 #include "aare/logger.hpp"
 
 namespace aare {
@@ -23,6 +27,14 @@ struct FrameWrapper {
     NDArray<uint16_t, 2> data;
 };
 
+static FrameWrapper make_poison_frame() {
+    return FrameWrapper{FrameType::DATA, UINT64_MAX, NDArray<uint16_t,2>()};
+}
+
+static bool is_poison(const FrameWrapper& f) {
+    return f.frame_number == UINT64_MAX;
+}
+
 /**
  * @brief ClusterFinderMT is a multi-threaded version of ClusterFinder. It uses
  * a producer-consumer queue to distribute the frames to the threads. The
@@ -37,11 +49,15 @@ class ClusterFinderMT {
 
   protected:
     using CT = typename ClusterType::value_type;
-    size_t m_current_thread{0};
+    // size_t m_current_thread{0};
+    std::atomic<size_t> m_current_thread{0};
+    
     size_t m_n_threads{0};
     using Finder = ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>;
-    using InputQueue = ProducerConsumerQueue<FrameWrapper>;
-    using OutputQueue = ProducerConsumerQueue<ClusterVector<ClusterType>>;
+    // using InputQueue = ProducerConsumerQueue<FrameWrapper>;
+    // using OutputQueue = ProducerConsumerQueue<ClusterVector<ClusterType>>;
+    using InputQueue = BlockingQueue<FrameWrapper>;
+    using OutputQueue = BlockingQueue<ClusterVector<ClusterType>>;
     std::vector<std::unique_ptr<InputQueue>> m_input_queues;
     std::vector<std::unique_ptr<OutputQueue>> m_output_queues;
 
@@ -50,41 +66,72 @@ class ClusterFinderMT {
     std::vector<std::unique_ptr<Finder>> m_cluster_finders;
     std::vector<std::thread> m_threads;
     std::thread m_collect_thread;
+    
+
     std::chrono::milliseconds m_default_wait{1};
 
   private:
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_processing_threads_stopped{true};
 
+    static ClusterVector<ClusterType> make_poison_cluster() {
+        ClusterVector<ClusterType> v;
+        v.set_frame_number(-1);
+        return v;
+    }
+
+    
+
     /**
      * @brief Function called by the processing threads. It reads the frames
      * from the input queue and processes them.
      */
     void process(int thread_id) {
+        // auto cf = m_cluster_finders[thread_id].get();
+        // auto q = m_input_queues[thread_id].get();
+        // bool realloc_same_capacity = true;
+
+        // while (!m_stop_requested || !q->isEmpty()) {
+        //     if (FrameWrapper *frame = q->frontPtr(); frame != nullptr) {
+
+        //         switch (frame->type) {
+        //         case FrameType::DATA:
+        //             cf->find_clusters(frame->data.view(), frame->frame_number);
+        //             m_output_queues[thread_id]->write(
+        //                 cf->steal_clusters(realloc_same_capacity));
+        //             break;
+
+        //         case FrameType::PEDESTAL:
+        //             m_cluster_finders[thread_id]->push_pedestal_frame(
+        //                 frame->data.view());
+        //             break;
+        //         }
+
+        //         // frame is processed now discard it
+        //         m_input_queues[thread_id]->popFront();
+        //     } else {
+        //         std::this_thread::sleep_for(m_default_wait);
+        //     }
+        // }
+
         auto cf = m_cluster_finders[thread_id].get();
-        auto q = m_input_queues[thread_id].get();
-        bool realloc_same_capacity = true;
+        auto q  = m_input_queues[thread_id].get();
 
-        while (!m_stop_requested || !q->isEmpty()) {
-            if (FrameWrapper *frame = q->frontPtr(); frame != nullptr) {
+        while (true) {
+            FrameWrapper frame = q->pop(); // blocks
 
-                switch (frame->type) {
+            if (is_poison(frame))
+                break;
+
+            switch (frame.type) {
                 case FrameType::DATA:
-                    cf->find_clusters(frame->data.view(), frame->frame_number);
-                    m_output_queues[thread_id]->write(
-                        cf->steal_clusters(realloc_same_capacity));
+                    cf->find_clusters(frame.data.view(), frame.frame_number);
+                    m_output_queues[thread_id]->push(cf->steal_clusters());
                     break;
 
                 case FrameType::PEDESTAL:
-                    m_cluster_finders[thread_id]->push_pedestal_frame(
-                        frame->data.view());
+                    cf->push_pedestal_frame(frame.data.view());
                     break;
-                }
-
-                // frame is processed now discard it
-                m_input_queues[thread_id]->popFront();
-            } else {
-                std::this_thread::sleep_for(m_default_wait);
             }
         }
     }
@@ -94,20 +141,66 @@ class ClusterFinderMT {
      * the sink
      */
     void collect() {
-        bool empty = true;
-        while (!m_stop_requested || !empty || !m_processing_threads_stopped) {
-            empty = true;
-            for (auto &queue : m_output_queues) {
-                if (!queue->isEmpty()) {
+        // std::ofstream frame_log("/mnt/datapool/JMulvey/Data_Analysis/aare_testing/Read_Frame_Bug/test2.txt");
 
-                    while (!m_sink.write(std::move(*queue->frontPtr()))) {
-                        std::this_thread::sleep_for(m_default_wait);
+        // bool empty = true;
+        // while (!m_stop_requested || !all_output_queues_empty() || !all_input_queues_empty()) {
+        // // while (!m_stop_requested || !empty || !m_processing_threads_stopped) {
+        //     empty = true;
+        //     for (auto &queue : m_output_queues) {
+        //         if (!queue->isEmpty()) {
+
+        //             // auto item = std::move(*queue->frontPtr()); //For Debug
+
+        //             // while (!m_sink.write(item)) {
+        //             //     std::this_thread::sleep_for(m_default_wait);
+        //             // }
+                    
+        //             // frame_log << item.frame_number() << '\n'; //For Debug
+
+        //             // queue->popFront();
+        //             // empty = false;
+
+
+        //             auto& item = *queue->frontPtr(); // use reference
+        //             while (!m_sink.write(std::move(item))) {
+        //                 std::this_thread::sleep_for(m_default_wait);
+        //             }
+        //             frame_log << item.frame_number() << '\n'; // log frame number
+        //             queue->popFront();
+        //             empty = false;
+
+        //         }
+        //     }
+        // }
+
+        // frame_log.close();
+
+
+        std::ofstream frame_log("/mnt/datapool/JMulvey/Data_Analysis/aare_testing/Read_Frame_Bug/test2.txt");
+
+        size_t poison_count = 0;
+
+        while (true) {
+            for (auto& queue : m_output_queues) {
+                auto item = queue->pop(); // BLOCKS
+
+                if (item.frame_number() == -1) {
+                    poison_count++;
+                    if (poison_count == m_n_threads) {
+                        // all workers finished
+                        m_sink.push(make_poison_cluster());
+                        return;
                     }
-                    queue->popFront();
-                    empty = false;
+                    continue;
                 }
+
+                m_sink.push(std::move(item));
+                frame_log << item.frame_number() << '\n';
             }
         }
+
+        frame_log.close();
     }
 
   public:
@@ -121,7 +214,8 @@ class ClusterFinderMT {
      * @param n_threads number of threads to use
      */
     ClusterFinderMT(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                    size_t capacity = 2000, size_t n_threads = 3)
+                    size_t capacity = 2000, size_t n_threads = 3,
+                    uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_n_threads(n_threads) {
 
         LOG(logDEBUG1) << "ClusterFinderMT: "
@@ -134,7 +228,7 @@ class ClusterFinderMT {
             m_cluster_finders.push_back(
                 std::make_unique<
                     ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>>(
-                    image_size, nSigma, capacity));
+                    image_size, nSigma, capacity, cluster_size_x, cluster_size_y));
         }
         for (size_t i = 0; i < n_threads; i++) {
             m_input_queues.emplace_back(std::make_unique<InputQueue>(200));
@@ -149,7 +243,8 @@ class ClusterFinderMT {
      * @warning You need to empty this queue otherwise the cluster finder will
      * wait forever
      */
-    ProducerConsumerQueue<ClusterVector<ClusterType>> *sink() {
+    BlockingQueue<ClusterVector<ClusterType>> *sink() {
+    //ProducerConsumerQueue<ClusterVector<ClusterType>> *sink() {
         return &m_sink;
     }
 
@@ -172,14 +267,31 @@ class ClusterFinderMT {
      * @brief Stop all processing threads
      */
     void stop() {
-        m_stop_requested = true;
+        // m_stop_requested = true;
 
-        for (auto &thread : m_threads) {
-            thread.join();
-        }
+        // for (auto &thread : m_threads) {
+        //     thread.join();
+        // }
+        // m_threads.clear();
+
+        // m_processing_threads_stopped = true;
+        // m_collect_thread.join();
+
+        
+        // 1. Send poison to ALL worker input queues
+        for (auto& q : m_input_queues)
+            q->push(make_poison_frame());
+
+        // 2. Wait for worker threads
+        for (auto& t : m_threads)
+            t.join();
         m_threads.clear();
 
-        m_processing_threads_stopped = true;
+        // 3. Send poison clusters from workers to collector
+        for (auto& q : m_output_queues)
+            q->push(make_poison_cluster());
+
+        // 4. Wait for collector
         m_collect_thread.join();
     }
 
@@ -211,9 +323,10 @@ class ClusterFinderMT {
                         NDArray(frame)}; // TODO! copies the data!
 
         for (auto &queue : m_input_queues) {
-            while (!queue->write(fw)) {
-                std::this_thread::sleep_for(m_default_wait);
-            }
+            queue->push(fw);
+            // while (!queue->write(fw)) {
+            //     std::this_thread::sleep_for(m_default_wait);
+            // }
         }
     }
 
@@ -223,12 +336,18 @@ class ClusterFinderMT {
      * @note Spin locks with a default wait if the queue is full.
      */
     void find_clusters(NDView<FRAME_TYPE, 2> frame, uint64_t frame_number = 0) {
-        FrameWrapper fw{FrameType::DATA, frame_number,
-                        NDArray(frame)}; // TODO! copies the data!
-        while (!m_input_queues[m_current_thread % m_n_threads]->write(fw)) {
-            std::this_thread::sleep_for(m_default_wait);
-        }
-        m_current_thread++;
+        // FrameWrapper fw{FrameType::DATA, frame_number,
+        //                 NDArray(frame)}; // TODO! copies the data!
+        // size_t thread_idx = m_current_thread.fetch_add(1) % m_n_threads;
+        // while (!m_input_queues[thread_idx]->write(fw)) {
+        // // while (!m_input_queues[m_current_thread % m_n_threads]->write(fw)) {
+        //     std::this_thread::sleep_for(m_default_wait);
+        // }
+        // // m_current_thread++;
+
+        FrameWrapper fw{FrameType::DATA, frame_number, NDArray(frame)};
+        size_t thread_idx = m_current_thread.fetch_add(1) % m_n_threads;
+        m_input_queues[thread_idx]->push(std::move(fw)); // blocks if full
     }
 
     void clear_pedestal() {

include/aare/Frame.hpp

@@ -105,7 +105,7 @@ class Frame {
      * @tparam T type of the pixels
      * @return NDView<T, 2>
      */
-    template <typename T> NDView<T, 2> view() & {
+    template <typename T> NDView<T, 2> view() {
         std::array<ssize_t, 2> shape = {static_cast<ssize_t>(m_rows),
                                         static_cast<ssize_t>(m_cols)};
         T *data = reinterpret_cast<T *>(m_data);

python/aare/ClusterFinder.py

@@ -26,24 +26,24 @@ def _get_class(name, cluster_size, dtype):
 
 
 
-def ClusterFinder(image_size, cluster_size, n_sigma=5, dtype = np.int32, capacity = 1024):
+def ClusterFinder(image_size, saved_cluster_size, checked_cluster_size, n_sigma=5, dtype = np.int32, capacity = 1024):
     """
     Factory function to create a ClusterFinder object. Provides a cleaner syntax for 
     the templated ClusterFinder in C++.
     """
-    cls = _get_class("ClusterFinder", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity)
+    cls = _get_class("ClusterFinder", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 
-def ClusterFinderMT(image_size, cluster_size = (3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3): 
+def ClusterFinderMT(image_size, saved_cluster_size = (3,3), checked_cluster_size = (3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3): 
     """ 
     Factory function to create a ClusterFinderMT object. Provides a cleaner syntax for 
     the templated ClusterFinderMT in C++.
     """
 
-    cls = _get_class("ClusterFinderMT", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads)
+    cls = _get_class("ClusterFinderMT", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads, cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 

python/src/bind_ClusterFinder.hpp

@@ -30,8 +30,9 @@ void define_ClusterFinder(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinder<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t>(), py::arg("image_size"),
-             py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000)
+        .def(py::init<Shape<2>, pd_type, size_t, uint32_t, uint32_t>(), py::arg("image_size"),
+             py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {

python/src/bind_ClusterFinderMT.hpp

@@ -30,9 +30,10 @@ void define_ClusterFinderMT(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinderMT<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t, size_t>(),
+        .def(py::init<Shape<2>, pd_type, size_t, size_t, uint32_t, uint32_t>(),
              py::arg("image_size"), py::arg("n_sigma") = 5.0,
-             py::arg("capacity") = 2048, py::arg("n_threads") = 3)
+             py::arg("capacity") = 2048, py::arg("n_threads") = 3,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {

python/src/module.cpp

@@ -84,4 +84,9 @@ PYBIND11_MODULE(_aare, m) {
     DEFINE_CLUSTER_BINDINGS(int, 9, 9, uint16_t, i);
     DEFINE_CLUSTER_BINDINGS(double, 9, 9, uint16_t, d);
     DEFINE_CLUSTER_BINDINGS(float, 9, 9, uint16_t, f);
+
+    DEFINE_CLUSTER_BINDINGS(int, 21, 21, uint16_t, i);
+    DEFINE_CLUSTER_BINDINGS(double, 21, 21, uint16_t, d);
+    DEFINE_CLUSTER_BINDINGS(float, 21, 21, uint16_t, f);
+    
 }

src/ClusterFinderMT.test.cpp

@@ -57,7 +57,6 @@ class ClusterFinderMTWrapper
     size_t m_sink_size() const { return this->m_sink.sizeGuess(); }
 };
 
-
 TEST_CASE("multithreaded cluster finder", "[.with-data]") {
     auto fpath =
         test_data_path() / "raw/moench03/cu_half_speed_master_4.json";
@@ -82,8 +81,7 @@ TEST_CASE("multithreaded cluster finder", "[.with-data]") {
     CHECK(cf.m_input_queues_are_empty() == true);
 
     for (size_t i = 0; i < n_frames_pd; ++i) {
-        auto frame = file.read_frame();
-        cf.find_clusters(frame.view<uint16_t>());
+        cf.find_clusters(file.read_frame().view<uint16_t>());
     }
 
     cf.stop();

update_version.py

@@ -7,7 +7,6 @@ Script to update VERSION file with semantic versioning if provided as an argumen
 import sys
 import os
 import re
-from datetime import datetime
 
 from packaging.version import Version, InvalidVersion
 
@@ -27,9 +26,9 @@ def get_version():
 
     # Check at least one argument is passed
     if len(sys.argv) < 2:
-        version =   datetime.today().strftime('%Y.%-m.%-d')
-    else: 
-        version = sys.argv[1]
+        return "0.0.0"
+
+    version = sys.argv[1]
 
     try:
         v = Version(version)  # normalize check if version follows PEP 440 specification
@@ -55,4 +54,4 @@ def write_version_to_file(version):
 if __name__ == "__main__":
 
     version = get_version()
-    write_version_to_file(version)
+    write_version_to_file(version)