read write cluster file (#60)

* Read and write cluster files (save work)

* add reading test

* use define for examples env variable and fix ci

* read and write cluster files (working)

* fix cluster CI

examples/CMakeLists.txt

@@ -1,8 +1,10 @@
 
 set(EXAMPLE_LIST "json_example;logger_example;numpy_read_example;multiport_example;raw_example;zmq_restream_example")
 set(EXAMPLE_LIST "${EXAMPLE_LIST};mythen_example;numpy_write_example;zmq_receiver_example;zmq_sender_example;")    
+set(EXAMPLE_LIST "${EXAMPLE_LIST};cluster_example")
 foreach(example ${EXAMPLE_LIST})
     add_executable(${example} ${example}.cpp)
+    target_include_directories(${example} PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
     target_link_libraries(${example} PUBLIC aare PRIVATE aare_compiler_flags)
 endforeach()
 

examples/cluster_example.cpp

@@ -0,0 +1,53 @@
+#include "aare/core/defs.hpp"
+#include "aare/file_io/ClusterFile.hpp"
+#include <cassert>
+#include <iostream>
+
+using namespace aare;
+int main() {
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv("AARE_ROOT_DIR"));
+    std::filesystem::path const fpath(PROJECT_ROOT_DIR / "data" / "clusters" / "single_frame_97_clustrers.clust");
+
+    // reading a file
+    aare::ClusterFile cf(fpath, "r");
+    std::cout << "file opened " << '\n';
+    std::cout << "n_clusters " << cf.count() << '\n';
+    std::cout << "frame_number " << cf.frame() << '\n';
+    std::cout << "file size: " << cf.count() << '\n';
+    cf.seek(0); // seek to the beginning of the file (this is the default behavior of the constructor)
+
+    auto cluster = cf.read(97);
+
+    std::cout << "read 10 clusters" << '\n';
+    int offset = 0;
+    int data_offset = 0;
+    for (auto c : cluster) {
+        assert(c.y == offset + 200);
+        for (int i = 0; i < 9; i++) {
+            assert(c.data[i] == data_offset + i);
+        }
+
+        offset++;
+        data_offset += 9;
+    }
+
+    // writing a file
+    std::filesystem::path const fpath_out("/tmp/cluster_example_file.clust");
+    aare::ClusterFile cf_out(fpath_out, "w", ClusterFileConfig(1, 44));
+    std::cout << "file opened for writing" << '\n';
+    std::vector<Cluster> clusters;
+    for (int i = 0; i < 1084; i++) {
+        Cluster c;
+        c.x = i;
+        c.y = i + 200;
+        for (int j = 0; j < 9; j++) {
+            c.data[j] = j;
+        }
+        clusters.push_back(c);
+    }
+    cf_out.write(clusters);
+    std::cout << "wrote 10 clusters" << '\n';
+    cf_out.update_header();
+
+    return 0;
+}

examples/include/aare/examples/defs.hpp

@@ -0,0 +1,2 @@
+#pragma once
+#define AARE_ROOT_DIR "AARE_ROOT_DIR"

examples/json_example.cpp

@@ -1,10 +1,9 @@
 // Your First C++ Program
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
 #include "aare/utils/logger.hpp"
 #include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
-
 using aare::File;
 using aare::Frame;
 
@@ -18,7 +17,7 @@ void test(File &f, int frame_number) {
 }
 
 int main() {
-    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR));
     std::filesystem::path const fpath(PROJECT_ROOT_DIR / "data" / "jungfrau" / "jungfrau_single_master_0.json");
     std::cout << fpath << '\n';
 

examples/logger_example.cpp

@@ -1,4 +1,6 @@
+#include "aare/examples/defs.hpp"
 #include "aare/utils/logger.hpp"
+
 #include <fstream>
 #include <iostream>
 
@@ -11,7 +13,7 @@ int main() {
 
     // writing to file
     std::ofstream textfile;
-    textfile.open("Test.txt");
+    textfile.open("/tmp/Test.txt");
     aare::logger::set_streams(textfile.rdbuf());
     aare::logger::info(LOCATION, "info printed to file");
 
@@ -26,7 +28,7 @@ int main() {
 
     // setting file output by path
     // user doesn't have to close file
-    aare::logger::set_output_file("Test2.txt");
+    aare::logger::set_output_file("/tmp/Test2.txt");
     aare::logger::info(LOCATION, "info printed to Test2.txt");
     return 0;
 }

examples/multiport_example.cpp

@@ -1,9 +1,9 @@
 // Your First C++ Program
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
 #include "aare/utils/logger.hpp"
-#include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
+#include <iostream>
 
 using aare::File;
 using aare::Frame;
@@ -19,7 +19,7 @@ void test(File &f, int frame_number) {
 }
 
 int main() {
-    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR));
     std::filesystem::path const fpath(PROJECT_ROOT_DIR / "data" / "jungfrau" / "jungfrau_double_master_0.json");
     std::cout << fpath << '\n';
 

examples/mythen_example.cpp

@@ -1,9 +1,9 @@
 // Your First C++ Program
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
 #include "aare/utils/logger.hpp"
-#include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
+#include <iostream>
 
 using aare::File;
 using aare::Frame;
@@ -32,7 +32,7 @@ void test2(File &f, int frame_number) {
 }
 
 int main() {
-    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR));
     if (PROJECT_ROOT_DIR.empty()) {
         throw std::runtime_error("environment variable PROJECT_ROOT_DIR is not set");
     }

examples/numpy_read_example.cpp

@@ -1,8 +1,8 @@
 // Your First C++ Program
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
-#include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
+#include <iostream>
 
 using aare::File;
 using aare::Frame;
@@ -18,7 +18,7 @@ void test(File &f, int frame_number) {
 
 int main() {
 
-    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR));
     std::filesystem::path const fpath(PROJECT_ROOT_DIR / "data" / "numpy" / "test_numpy_file.npy");
     std::cout << fpath << '\n';
 

examples/numpy_write_example.cpp

@@ -1,9 +1,9 @@
 // Your First C++ Program
 #include "aare/core/Frame.hpp"
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
-#include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
+#include <iostream>
 
 using aare::File;
 using aare::FileConfig;

examples/raw_example.cpp

@@ -1,10 +1,9 @@
 // Your First C++ Program
+#include "aare/examples/defs.hpp"
 #include "aare/file_io/File.hpp"
 #include "aare/utils/logger.hpp"
 #include <iostream>
 
-#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
-
 using aare::File;
 using aare::Frame;
 
@@ -17,7 +16,7 @@ void test(File &f, int frame_number) {
 }
 
 int main() {
-    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    auto PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR));
     if (PROJECT_ROOT_DIR.empty()) {
         throw std::runtime_error("environment variable PROJECT_ROOT_DIR is not set");
     }

examples/zmq_receiver_example.cpp

@@ -1,3 +1,4 @@
+#include "aare/examples/defs.hpp"
 #include "aare/network_io/ZmqSocketReceiver.hpp"
 #include "aare/network_io/defs.hpp"
 

examples/zmq_restream_example.cpp

@@ -1,3 +1,4 @@
+#include "aare/examples/defs.hpp"
 #include <chrono>
 #include <thread>
 

examples/zmq_sender_example.cpp

@@ -1,4 +1,5 @@
 #include "aare/core/Frame.hpp"
+#include "aare/examples/defs.hpp"
 #include "aare/network_io/ZmqHeader.hpp"
 #include "aare/network_io/ZmqSocketSender.hpp"
 #include "aare/network_io/defs.hpp"