Feature/reactivate python bindings (#74)

major changes:
- add python bindings for all c++ features except network_io
- changes to cross compile on windows,linux and macos
- fix bugs with cluster_finder
- use Dtype in Frame instead of bitdepth
- remove boost::program_options and replace with our implementation 
- add Transforms class that applies a sequence of functions (c++ or
python functions) on a Frame.
- remove frame reorder and flip from SubFile.cpp. use Transforms instead
- Test clusterFinder and Pedestal results in comparison with
slsDetectorCalibration

---------

Co-authored-by: Bechir <bechir.brahem420@gmail.com>
Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>

examples/cluster_example.cpp

@@ -7,33 +7,26 @@
 using namespace aare;
 int main() {
     auto PROJECT_ROOT_DIR = std::filesystem::path(getenv("AARE_ROOT_DIR"));
-    std::filesystem::path const fpath("/mnt/sls_det_storage/moench_data/testNewFW20230714/cu_half_speed_master_4.json");
-
-    NDArray<double, 2> frame({10, 10});
-    frame = 0;
-
-    for (int i = 5; i < 8; i++) {
-        for (int j = 5; j < 8; j++) {
-            frame(i, j) = (i + j) % 10;
-        }
+    std::filesystem::path const fpath("/home/l_bechir/tmp/testNewFW20230714/cu_half_speed_master_4.json");
+    auto f = File(fpath, "r");
+    // calculate pedestal
+    Pedestal pedestal(400,400,1000);
+    for (int i = 0; i < 1000; i++) {
+        auto frame = f.read();
+        pedestal.push<uint16_t>(frame);
     }
-
-    for (int i = 0; i < frame.shape(0); i++) {
-        for (int j = 0; j < frame.shape(1); j++) {
-            std::cout << frame(i, j) << " ";
-        }
-        std::cout << std::endl;
+    // find clusters
+    ClusterFinder clusterFinder(3, 3, 5, 0);
+    f.seek(0);
+    std::vector<std::vector<Cluster>> clusters_vector;
+    auto start = std::chrono::high_resolution_clock::now();
+    for (int i = 0; i < 1000; i++) {
+        auto frame = f.iread(i);
+        auto clusters = clusterFinder.find_clusters_without_threshold(frame.view<uint16_t>(), pedestal,false);
+        clusters_vector.emplace_back(clusters);
     }
+    auto end = std::chrono::high_resolution_clock::now();
+    std::chrono::duration<double> elapsed_seconds = end-start;
+    std::cout << "elapsed time: " << elapsed_seconds.count() << "s\n";
 
-    ClusterFinder clusterFinder(3, 3, 1, 1); // 3x3 cluster, 1 nSigma, 1 threshold
-
-    Pedestal p(10, 10);
-
-    auto clusters = clusterFinder.find_clusters(frame.span(), p);
-
-    aare::logger::info("nclusters:", clusters.size());
-
-    for (auto &cluster : clusters) {
-        aare::logger::info("cluster center:", cluster.to_string<double>());
-    }
 }