conversion warnings

include/aare/ClusterFile.hpp

@@ -47,6 +47,7 @@ class ClusterFile {
 
   public:
     ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000);
+    ~ClusterFile();
     std::vector<Cluster> read_clusters(size_t n_clusters);
     std::vector<Cluster> read_frame(int32_t &out_fnum);
     std::vector<Cluster>
@@ -59,6 +60,7 @@ class ClusterFile {
                     double *eta3y);
 
     size_t chunk_size() const { return m_chunk_size; }
+    void close();
 
 };
 

include/aare/RawMasterFile.hpp

@@ -61,14 +61,14 @@ class ScanParameters {
 
 
 struct ROI{
-  size_t xmin{};
-  size_t xmax{};
-  size_t ymin{};
-  size_t ymax{};
+  int64_t xmin{};
+  int64_t xmax{};
+  int64_t ymin{};
+  int64_t ymax{};
 
-  size_t height() const { return ymax - ymin; }
-  size_t width() const { return xmax - xmin; }
-}__attribute__((packed));
+  int64_t height() const { return ymax - ymin; }
+  int64_t width() const { return xmax - xmin; }
+};
 
 
 /**
@@ -91,7 +91,7 @@ class RawMasterFile {
     xy m_geometry;
 
     size_t m_max_frames_per_file{};
-    uint32_t m_adc_mask{};
+    // uint32_t m_adc_mask{}; // TODO! implement reading
     FrameDiscardPolicy m_frame_discard_policy{};
     size_t m_frame_padding{};
 

include/aare/RawSubFile.hpp

@@ -16,6 +16,7 @@ namespace aare {
 class RawSubFile {
   protected:
     std::ifstream m_file;
+    DetectorType m_detector_type;
     size_t m_bitdepth;
     std::filesystem::path m_fname;
     size_t m_rows{};
@@ -25,7 +26,7 @@ class RawSubFile {
     uint32_t m_pos_row{};
     uint32_t m_pos_col{};
  
-    DetectorType m_detector_type;
+    
     std::optional<NDArray<ssize_t, 2>> m_pixel_map;
 
   public:

include/aare/VarClusterFinder.hpp

@@ -226,7 +226,7 @@ template <typename T> void VarClusterFinder<T>::single_pass(NDView<T, 2> img) {
 
 template <typename T> void VarClusterFinder<T>::first_pass() {
 
-    for (int i = 0; i < original_.size(); ++i) {
+    for (size_t i = 0; i < original_.size(); ++i) {
         if (use_noise_map)
             threshold_ = 5 * noiseMap(i);
         binary_(i) = (original_(i) > threshold_);
@@ -250,17 +250,17 @@ template <typename T> void VarClusterFinder<T>::first_pass() {
 
 template <typename T> void VarClusterFinder<T>::second_pass() {
 
-    for (int64_t i = 0; i != labeled_.size(); ++i) {
-        auto current_label = labeled_(i);
-        if (current_label != 0) {
-            auto it = child.find(current_label);
+    for (size_t i = 0; i != labeled_.size(); ++i) {
+        auto cl = labeled_(i);
+        if (cl != 0) {
+            auto it = child.find(cl);
             while (it != child.end()) {
-                current_label = it->second;
-                it = child.find(current_label);
+                cl = it->second;
+                it = child.find(cl);
                 // do this once before doing the second pass?
                 // all values point to the final one...
             }
-            labeled_(i) = current_label;
+            labeled_(i) = cl;
         }
     }
 }
@@ -271,7 +271,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
     // Do we always have monotonic increasing
     // labels? Then vector?
     // here the translation is label -> Hit
-    std::unordered_map<int, Hit> h_size;
+    std::unordered_map<int, Hit> h_map;
     for (int i = 0; i < shape_[0]; ++i) {
         for (int j = 0; j < shape_[1]; ++j) {
             if (labeled_(i, j) != 0 || false
@@ -280,7 +280,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
                 // (i+1 < shape_[0] and labeled_(i+1, j) != 0) or
                 // (j+1 < shape_[1] and labeled_(i, j+1) != 0)
             ) {
-                Hit &record = h_size[labeled_(i, j)];
+                Hit &record = h_map[labeled_(i, j)];
                 if (record.size < MAX_CLUSTER_SIZE) {
                     record.rows[record.size] = i;
                     record.cols[record.size] = j;
@@ -300,7 +300,7 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
         }
     }
 
-    for (const auto &h : h_size)
+    for (const auto &h : h_map)
         hits.push_back(h.second);
 }
 

include/aare/defs.hpp

@@ -93,7 +93,7 @@ class DynamicCluster {
         (sizeof(T) == dt.bytes())
             ? 0
             : throw std::invalid_argument("[ERROR] Type size mismatch");
-        return memcpy(m_data + idx * dt.bytes(), &val, (size_t)dt.bytes());
+        return memcpy(m_data + idx * dt.bytes(), &val, dt.bytes());
     }
 
     template <typename T> std::string to_string() const {