Cluster finder improvements (#113)

.github/workflows/build_docs.yml

@@ -3,8 +3,7 @@ name: Build the package using cmake then documentation
 on:
   workflow_dispatch:
   push:
-    branches:
-     - main
+
 
 
 permissions:
@@ -58,6 +57,7 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     needs: build
+    if: github.ref == 'refs/heads/main'
     steps:
       - name: Deploy to GitHub Pages
         id: deployment

CMakeLists.txt

@@ -39,7 +39,8 @@ option(AARE_IN_GITHUB_ACTIONS "Running in Github Actions" OFF)
 option(AARE_DOCS "Build documentation" OFF)
 option(AARE_VERBOSE "Verbose output" OFF)
 option(AARE_CUSTOM_ASSERT "Use custom assert" OFF)
-
+option(AARE_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/aare/" OFF)
+option(AARE_ASAN "Enable AddressSanitizer" OFF)
 
 # Configure which of the dependencies to use FetchContent for
 option(AARE_FETCH_FMT "Use FetchContent to download fmt" ON)
@@ -224,13 +225,6 @@ if(CMAKE_BUILD_TYPE STREQUAL "Release")
     target_compile_options(aare_compiler_flags INTERFACE -O3)
 else()
     message(STATUS "Debug build")
-    target_compile_options(
-        aare_compiler_flags 
-        INTERFACE 
-            -Og 
-            -ggdb3 
-    )
-
 endif()
 
 # Common flags for GCC and Clang
@@ -255,7 +249,21 @@ target_compile_options(
 endif() #GCC/Clang specific
 
 
-
+if(AARE_ASAN)
+    message(STATUS "AddressSanitizer enabled")
+    target_compile_options(
+        aare_compiler_flags 
+        INTERFACE 
+            -fsanitize=address,undefined,pointer-compare 
+            -fno-omit-frame-pointer
+    )
+    target_link_libraries(
+        aare_compiler_flags 
+        INTERFACE 
+            -fsanitize=address,undefined,pointer-compare 
+            -fno-omit-frame-pointer
+    )
+endif()
 
 
 
@@ -274,6 +282,7 @@ set(PUBLICHEADERS
     include/aare/ClusterFinder.hpp
     include/aare/ClusterFile.hpp
     include/aare/CtbRawFile.hpp
+    include/aare/ClusterVector.hpp
     include/aare/defs.hpp
     include/aare/Dtype.hpp
     include/aare/File.hpp
@@ -315,6 +324,8 @@ target_include_directories(aare_core PUBLIC
     "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 )
 
+
+
 target_link_libraries(
     aare_core 
     PUBLIC 
@@ -343,6 +354,7 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterVector.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Pedestal.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.test.cpp

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: aare
-  version: 2024.11.28.dev0 #TODO! how to not duplicate this?
+  version: 2024.12.16.dev0 #TODO! how to not duplicate this?
 
 
 source:

docs/conf.py.in

@@ -29,7 +29,6 @@ version = '@PROJECT_VERSION@'
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['breathe',
-              'sphinx_rtd_theme',
               'sphinx.ext.autodoc',
               'sphinx.ext.napoleon',
              ]

docs/src/ClusterVector.rst

@@ -0,0 +1,6 @@
+ClusterVector
+=============
+
+.. doxygenclass:: aare::ClusterVector
+   :members:
+   :undoc-members:

docs/src/index.rst

@@ -46,6 +46,7 @@ AARE
     Dtype
     ClusterFinder
     ClusterFile
+    ClusterVector
     Pedestal
     RawFile
     RawSubFile

include/aare/ClusterFile.hpp

@@ -1,12 +1,14 @@
+#pragma once
 
-
+#include "aare/ClusterVector.hpp"
+#include "aare/NDArray.hpp"
 #include "aare/defs.hpp"
 #include <filesystem>
 #include <fstream>
 
 namespace aare {
 
-struct Cluster {
+struct Cluster3x3 {
     int16_t x;
     int16_t y;
     int32_t data[9];
@@ -38,30 +40,42 @@ struct ClusterAnalysis {
     double etay;
 };
 
-
-
+/*
+Binary cluster file. Expects data to be layed out as:
+int32_t frame_number
+uint32_t number_of_clusters
+int16_t x, int16_t y, int32_t data[9] x number_of_clusters
+int32_t frame_number
+uint32_t number_of_clusters
+....
+*/
 class ClusterFile {
     FILE *fp{};
     uint32_t m_num_left{};
     size_t m_chunk_size{};
+    const std::string m_mode;
 
   public:
-    ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000);
+    ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000,
+                const std::string &mode = "r");
     ~ClusterFile();
-    std::vector<Cluster> read_clusters(size_t n_clusters);
-    std::vector<Cluster> read_frame(int32_t &out_fnum);
-    std::vector<Cluster>
+    std::vector<Cluster3x3> read_clusters(size_t n_clusters);
+    std::vector<Cluster3x3> read_frame(int32_t &out_fnum);
+    void write_frame(int32_t frame_number,
+                     const ClusterVector<int32_t> &clusters);
+    std::vector<Cluster3x3>
     read_cluster_with_cut(size_t n_clusters, double *noise_map, int nx, int ny);
 
-    int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad,
-                 double *eta2x, double *eta2y, double *eta3x, double *eta3y);
-    int analyze_cluster(Cluster cl, int32_t *t2, int32_t *t3, char *quad,
-                    double *eta2x, double *eta2y, double *eta3x,
-                    double *eta3y);
-
     size_t chunk_size() const { return m_chunk_size; }
     void close();
-
 };
 
+int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad,
+                 double *eta2x, double *eta2y, double *eta3x, double *eta3y);
+int analyze_cluster(Cluster3x3& cl, int32_t *t2, int32_t *t3, char *quad,
+                    double *eta2x, double *eta2y, double *eta3x, double *eta3y);
+
+NDArray<double, 2> calculate_eta2( ClusterVector<int>& clusters);
+std::array<double,2> calculate_eta2( Cluster3x3& cl);
+
 } // namespace aare