added cluster finder

src/CMakeLists.txt

@@ -23,6 +23,8 @@ if(AARE_TESTS)
             # ${CMAKE_CURRENT_SOURCE_DIR}/test/ProducerConsumerQueue.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/NDArray.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/NDView.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/ClusterFinder.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/Pedestal.test.cpp
             # ${CMAKE_CURRENT_SOURCE_DIR}/test/CircularFifo.test.cpp
             # ${CMAKE_CURRENT_SOURCE_DIR}/test/wrappers.test.cpp
             # ${CMAKE_CURRENT_SOURCE_DIR}/test/Transforms.test.cpp

src/ClusterFinder.test.cpp

@@ -0,0 +1,59 @@
+#include "aare/ClusterFinder.hpp"
+#include "aare/Pedestal.hpp"
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <chrono>
+#include <random>
+
+using namespace aare;
+
+class ClusterFinderUnitTest : public ClusterFinder {
+  public:
+    ClusterFinderUnitTest(int cluster_sizeX, int cluster_sizeY, double nSigma = 5.0, double threshold = 0.0)
+        : ClusterFinder(cluster_sizeX, cluster_sizeY, nSigma, threshold) {}
+    double get_c2() { return c2; }
+    double get_c3() { return c3; }
+    auto get_threshold() { return m_threshold; }
+    auto get_nSigma() { return m_nSigma; }
+    auto get_cluster_sizeX() { return m_cluster_sizeX; }
+    auto get_cluster_sizeY() { return m_cluster_sizeY; }
+};
+
+TEST_CASE("test ClusterFinder constructor") {
+    ClusterFinderUnitTest cf(55, 100);
+    REQUIRE(cf.get_cluster_sizeX() == 55);
+    REQUIRE(cf.get_cluster_sizeY() == 100);
+    REQUIRE(cf.get_threshold() == 0.0);
+    REQUIRE(cf.get_nSigma() == 5.0);
+    double c2 = sqrt((100 + 1) / 2 * (55 + 1) / 2);
+    double c3 = sqrt(55 * 100);
+    // REQUIRE(compare_floats<double>(cf.get_c2(), c2));
+    // REQUIRE(compare_floats<double>(cf.get_c3(), c3));
+    REQUIRE_THAT(cf.get_c2(), Catch::Matchers::WithinRel(c2, 1e-9));
+    REQUIRE_THAT(cf.get_c3(), Catch::Matchers::WithinRel(c3, 1e-9));
+}
+
+TEST_CASE("test cluster finder") {
+    aare::Pedestal pedestal(10, 10, 5);
+    NDArray<double, 2> frame({10, 10});
+    frame = 0;
+    ClusterFinder clusterFinder(3, 3, 1, 1); // 3x3 cluster, 1 nSigma, 1 threshold
+
+    auto clusters = clusterFinder.find_clusters_without_threshold(frame.span(), pedestal);
+
+    REQUIRE(clusters.size() == 0);
+
+    frame(5, 5) = 10;
+    clusters = clusterFinder.find_clusters_without_threshold(frame.span(), pedestal);
+    REQUIRE(clusters.size() == 1);
+    REQUIRE(clusters[0].x == 5);
+    REQUIRE(clusters[0].y == 5);
+    for (int i = 0; i < 3; i++) {
+        for (int j = 0; j < 3; j++) {
+            if (i == 1 && j == 1)
+                REQUIRE(clusters[0].get<double>(i * 3 + j) == 10);
+            else
+                REQUIRE(clusters[0].get<double>(i * 3 + j) == 0);
+        }
+    }
+}

src/Pedestal.test.cpp

@@ -0,0 +1,103 @@
+#include "aare/Pedestal.hpp"
+
+
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <chrono>
+#include <random>
+
+using namespace aare;
+TEST_CASE("test pedestal constructor") {
+    aare::Pedestal pedestal(10, 10, 5);
+    REQUIRE(pedestal.rows() == 10);
+    REQUIRE(pedestal.cols() == 10);
+    REQUIRE(pedestal.n_samples() == 5);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < 10; j++) {
+            REQUIRE(pedestal.get_sum()(i, j) == 0);
+            REQUIRE(pedestal.get_sum2()(i, j) == 0);
+            REQUIRE(pedestal.cur_samples()(i, j) == 0);
+        }
+    }
+}
+
+TEST_CASE("test pedestal push") {
+    aare::Pedestal pedestal(10, 10, 5);
+    aare::Frame frame(10, 10, Dtype::UINT16);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < 10; j++) {
+            frame.set<uint16_t>(i, j, i + j);
+        }
+    }
+
+    // test single push
+    pedestal.push<uint16_t>(frame);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < 10; j++) {
+            REQUIRE(pedestal.get_sum()(i, j) == i + j);
+            REQUIRE(pedestal.get_sum2()(i, j) == (i + j) * (i + j));
+            REQUIRE(pedestal.cur_samples()(i, j) == 1);
+        }
+    }
+
+    // test clear
+    pedestal.clear();
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < 10; j++) {
+            REQUIRE(pedestal.get_sum()(i, j) == 0);
+            REQUIRE(pedestal.get_sum2()(i, j) == 0);
+            REQUIRE(pedestal.cur_samples()(i, j) == 0);
+        }
+    }
+
+    // test number of samples after multiple push
+    for (uint32_t k = 0; k < 50; k++) {
+        pedestal.push<uint16_t>(frame);
+        for (uint32_t i = 0; i < 10; i++) {
+            for (uint32_t j = 0; j < 10; j++) {
+                if (k < 5) {
+                    REQUIRE(pedestal.cur_samples()(i, j) == k + 1);
+                    REQUIRE(pedestal.get_sum()(i, j) == (k + 1) * (i + j));
+                    REQUIRE(pedestal.get_sum2()(i, j) == (k + 1) * (i + j) * (i + j));
+                } else {
+                    REQUIRE(pedestal.cur_samples()(i, j) == 5);
+                    REQUIRE(pedestal.get_sum()(i, j) == 5 * (i + j));
+                    REQUIRE(pedestal.get_sum2()(i, j) == 5 * (i + j) * (i + j));
+                }
+                REQUIRE(pedestal.mean(i, j) == (i + j));
+                REQUIRE(pedestal.variance(i, j) == 0);
+                REQUIRE(pedestal.standard_deviation(i, j) == 0);
+            }
+        }
+    }
+}
+
+TEST_CASE("test pedestal with normal distribution") {
+    const double MEAN = 5.0, STD = 2.0, VAR = STD * STD, TOLERANCE = 0.1;
+
+    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
+    std::default_random_engine generator(seed);
+    std::normal_distribution<double> distribution(MEAN, STD);
+
+    aare::Pedestal pedestal(3, 5, 10000);
+    for (int i = 0; i < 10000; i++) {
+        aare::Frame frame(3, 5, Dtype::DOUBLE);
+        for (int j = 0; j < 3; j++) {
+            for (int k = 0; k < 5; k++) {
+                frame.set<double>(j, k, distribution(generator));
+            }
+        }
+        pedestal.push<double>(frame);
+    }
+    auto mean = pedestal.mean();
+    auto variance = pedestal.variance();
+    auto standard_deviation = pedestal.standard_deviation();
+
+    for (int i = 0; i < 3; i++) {
+        for (int j = 0; j < 5; j++) {
+            REQUIRE_THAT(mean(i, j), Catch::Matchers::WithinAbs(MEAN, MEAN * TOLERANCE));
+            REQUIRE_THAT(variance(i, j), Catch::Matchers::WithinAbs(VAR, VAR * TOLERANCE));
+            REQUIRE_THAT(standard_deviation(i, j), Catch::Matchers::WithinAbs(STD, STD * TOLERANCE));
+        }
+    }
+}