update branch to latest

.github/workflows/build-test.yml

@@ -42,7 +42,7 @@ jobs:
     steps:
 
       - name: Setup Python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: 3.8
 
@@ -53,7 +53,7 @@ jobs:
         shell: bash
 
       - name: Get specific version of CMake, Ninja
-        uses: lukka/[email protected].0
+        uses: lukka/[email protected].1
 
       - name: Install ocl-icd-loader - windows
         if: matrix.os == 'windows-latest'

.github/workflows/pages.yml

@@ -32,12 +32,12 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: 3.11
 
       - name: Get specific version of CMake, Ninja
-        uses: lukka/[email protected].0
+        uses: lukka/[email protected].1
 
       - name: Install doxygen
         run: |

clic/include/array.hpp

@@ -103,7 +103,7 @@ class Array
    * @param host_data pointer to the host data
    */
   auto
-  write(const void * host_data) -> void;
+  writeFrom(const void * host_data) -> void;
 
   /**
    * @brief Write host data into the Array region
@@ -112,9 +112,9 @@ class Array
    * @param buffer_origin origin of the buffer to write
    */
   auto
-  write(const void *                  host_data,
-        const std::array<size_t, 3> & region,
-        const std::array<size_t, 3> & buffer_origin) -> void;
+  writeFrom(const void *                  host_data,
+            const std::array<size_t, 3> & region,
+            const std::array<size_t, 3> & buffer_origin) -> void;
 
   /**
    * @brief Write host data into the Array at a specific position (x, y, z)
@@ -124,14 +124,14 @@ class Array
    * @param z_coord z coordinate
    */
   auto
-  write(const void * host_data, size_t x_coord, size_t y_coord, size_t z_coord) -> void;
+  writeFrom(const void * host_data, size_t x_coord, size_t y_coord, size_t z_coord) -> void;
 
   /**
    * @brief Read the Array data into host memory
    * @param host_data pointer to the host data
    */
   auto
-  read(void * host_data) const -> void;
+  readTo(void * host_data) const -> void;
 
   /**
    * @brief Read the Array region data into host memory
@@ -140,9 +140,9 @@ class Array
    * @param buffer_origin origin of the buffer to read
    */
   auto
-  read(void *                        host_data,
-       const std::array<size_t, 3> & region,
-       const std::array<size_t, 3> & buffer_origin) const -> void;
+  readTo(void *                        host_data,
+         const std::array<size_t, 3> & region,
+         const std::array<size_t, 3> & buffer_origin) const -> void;
 
   /**
    * @brief Read the Array data at a specific position (x, y, z) into host memory
@@ -152,14 +152,14 @@ class Array
    * @param z_coord z coordinate
    */
   auto
-  read(void * host_data, size_t x_coord, size_t y_coord, size_t z_coord) const -> void;
+  readTo(void * host_data, size_t x_coord, size_t y_coord, size_t z_coord) const -> void;
 
   /**
    * @brief Copy the Array data into another Array
    * @param dst destination Array::Pointer
    */
   auto
-  copy(const Array::Pointer & dst) const -> void;
+  copyTo(const Array::Pointer & dst) const -> void;
 
   /**
    * @brief Copy the Array region data into another Array
@@ -169,10 +169,10 @@ class Array
    * @param dst_origin origin of the destination buffer
    */
   auto
-  copy(const Array::Pointer &        dst,
-       const std::array<size_t, 3> & region,
-       const std::array<size_t, 3> & src_origin,
-       const std::array<size_t, 3> & dst_origin) const -> void;
+  copyTo(const Array::Pointer &        dst,
+         const std::array<size_t, 3> & region,
+         const std::array<size_t, 3> & src_origin,
+         const std::array<size_t, 3> & dst_origin) const -> void;
 
   /**
    * @brief Fill the Array with a specific value
@@ -337,7 +337,7 @@ print(const Array::Pointer & array, const char * name = "Array::Pointer") -> voi
     return;
   }
   std::vector<T> host_data(array->size());
-  array->read(host_data.data());
+  array->readTo(host_data.data());
   std::ostringstream oss;
   oss << name << ":\n";
   for (auto i = 0; i < array->depth(); ++i)

clic/src/array.cpp

@@ -55,7 +55,7 @@ Array::create(const size_t            width,
               const Device::Pointer & device_ptr) -> Array::Pointer
 {
   auto ptr = create(width, height, depth, dimension, data_type, mem_type, device_ptr);
-  ptr->write(host_data);
+  ptr->writeFrom(host_data);
   return ptr;
 }
 
@@ -97,7 +97,7 @@ Array::allocate() -> void
 }
 
 auto
-Array::write(const void * host_data) -> void
+Array::writeFrom(const void * host_data) -> void
 {
   if (host_data == nullptr)
   {
@@ -110,9 +110,9 @@ Array::write(const void * host_data) -> void
 }
 
 auto
-Array::write(const void *                  host_data,
-             const std::array<size_t, 3> & region,
-             const std::array<size_t, 3> & buffer_origin) -> void
+Array::writeFrom(const void *                  host_data,
+                 const std::array<size_t, 3> & region,
+                 const std::array<size_t, 3> & buffer_origin) -> void
 {
   if (host_data == nullptr)
   {
@@ -125,13 +125,13 @@ Array::write(const void *                  host_data,
 }
 
 auto
-Array::write(const void * host_data, const size_t x_coord, const size_t y_coord, const size_t z_coord) -> void
+Array::writeFrom(const void * host_data, const size_t x_coord, const size_t y_coord, const size_t z_coord) -> void
 {
-  write(host_data, { 1, 1, 1 }, { x_coord, y_coord, z_coord });
+  writeFrom(host_data, { 1, 1, 1 }, { x_coord, y_coord, z_coord });
 }
 
 auto
-Array::read(void * host_data) const -> void
+Array::readTo(void * host_data) const -> void
 {
   if (host_data == nullptr)
   {
@@ -144,9 +144,9 @@ Array::read(void * host_data) const -> void
 }
 
 auto
-Array::read(void *                        host_data,
-            const std::array<size_t, 3> & region,
-            const std::array<size_t, 3> & buffer_origin) const -> void
+Array::readTo(void *                        host_data,
+              const std::array<size_t, 3> & region,
+              const std::array<size_t, 3> & buffer_origin) const -> void
 {
   if (host_data == nullptr)
   {
@@ -159,13 +159,13 @@ Array::read(void *                        host_data,
 }
 
 auto
-Array::read(void * host_data, const size_t x_coord, const size_t y_coord, const size_t z_coord) const -> void
+Array::readTo(void * host_data, const size_t x_coord, const size_t y_coord, const size_t z_coord) const -> void
 {
-  read(host_data, { 1, 1, 1 }, { x_coord, y_coord, z_coord });
+  readTo(host_data, { 1, 1, 1 }, { x_coord, y_coord, z_coord });
 }
 
 auto
-Array::copy(const Array::Pointer & dst) const -> void
+Array::copyTo(const Array::Pointer & dst) const -> void
 {
   check_ptr(dst, "Error: Destination Array is null");
   if (device() != dst->device())
@@ -208,10 +208,10 @@ Array::copy(const Array::Pointer & dst) const -> void
 }
 
 auto
-Array::copy(const Array::Pointer &        dst,
-            const std::array<size_t, 3> & region,
-            const std::array<size_t, 3> & src_origin,
-            const std::array<size_t, 3> & dst_origin) const -> void
+Array::copyTo(const Array::Pointer &        dst,
+              const std::array<size_t, 3> & region,
+              const std::array<size_t, 3> & src_origin,
+              const std::array<size_t, 3> & dst_origin) const -> void
 {
   check_ptr(dst, "Error: Destination Array is null");
   if (device() != dst->device())
@@ -259,37 +259,37 @@ Array::fill(const float value) -> void
   {
     case dType::FLOAT: {
       std::vector<float> data(this->size(), value);
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::INT8: {
       std::vector<int8_t> data(this->size(), static_cast<int8_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::INT16: {
       std::vector<int16_t> data(this->size(), static_cast<int16_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::INT32: {
       std::vector<int32_t> data(this->size(), static_cast<int32_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::UINT8: {
       std::vector<uint8_t> data(this->size(), static_cast<uint8_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::UINT16: {
       std::vector<uint16_t> data(this->size(), static_cast<uint16_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     case dType::UINT32: {
       std::vector<uint32_t> data(this->size(), static_cast<uint32_t>(value));
-      write(data.data());
+      writeFrom(data.data());
       return;
     }
     default: {

clic/src/execution.cpp

@@ -294,7 +294,7 @@ execute_separable(const Device::Pointer &      device,
     }
     else
     {
-      input->copy(output);
+      input->copyTo(output);
     }
   };
 

clic/src/tier1/write_values_to_positions.cpp

@@ -26,7 +26,7 @@ write_values_to_positions_func(const Device::Pointer & device,
     auto temp = Array::create(1, list->height(), 1, 2, dType::INT32, list->mtype(), list->device());
     maximum_x_projection_func(device, list, temp);
     std::vector<int> max_position(temp->size());
-    temp->read(max_position.data());
+    temp->readTo(max_position.data());
     size_t max_pos_x = max_position[0] + 1;
     size_t max_pos_y = (list->height() > 2) ? max_position[1] + 1 : 1;
     size_t max_pos_z = (list->height() > 3) ? max_position[2] + 1 : 1;

clic/src/tier2/extend_labeling_via_voronoi.cpp

@@ -31,17 +31,17 @@ extend_labeling_via_voronoi_func(const Device::Pointer & device,
     {
       tier1::onlyzero_overwrite_maximum_func(device, flop, flag, flip, "box");
     }
-    flag->read(&flag_value);
+    flag->readTo(&flag_value);
     flag->fill(0);
     iteration_count++;
   }
   if (iteration_count % 2 == 0)
   {
-    flip->copy(dst);
+    flip->copyTo(dst);
   }
   else
   {
-    flop->copy(dst);
+    flop->copyTo(dst);
   }
   return dst;
 }

clic/src/tier2/maximum_of_all_pixels.cpp

@@ -26,7 +26,7 @@ maximum_of_all_pixels_func(const Device::Pointer & device, const Array::Pointer
   tier1::maximum_x_projection_func(device, tmp, dst);
 
   float res;
-  dst->read(&res);
+  dst->readTo(&res);
   return res;
 }
 

clic/src/tier2/minimum_of_all_pixels.cpp

@@ -26,7 +26,7 @@ minimum_of_all_pixels_func(const Device::Pointer & device, const Array::Pointer
   tier1::minimum_x_projection_func(device, tmp, dst);
 
   float res;
-  dst->read(&res);
+  dst->readTo(&res);
   return res;
 }
 

clic/src/tier2/minimum_of_masked_pixels.cpp

@@ -48,7 +48,7 @@ minimum_of_masked_pixels_func(const Device::Pointer & device,
   tier1::minimum_of_masked_pixels_reduction_func(device, tmp_src, tmp_mask, dst_src, dst_mask);
 
   float res;
-  dst_src->read(&res);
+  dst_src->readTo(&res);
   return res;
 }
 

clic/src/tier2/sum_of_all_pixels.cpp

@@ -26,7 +26,7 @@ sum_of_all_pixels_func(const Device::Pointer & device, const Array::Pointer & sr
   tier1::sum_x_projection_func(device, tmp, dst);
 
   float res;
-  dst->read(&res);
+  dst->readTo(&res);
   return res;
 }
 

clic/src/tier3/exclude_labels.cpp

@@ -20,7 +20,7 @@ exclude_labels_func(const Device::Pointer & device,
     throw std::runtime_error("exclude_labels: label list must be of type uint32");
   }
   std::vector<uint32_t> labels_list(list->size());
-  list->read(labels_list.data());
+  list->readTo(labels_list.data());
 
   labels_list.front() = 0;
   uint32_t count = 1;
@@ -38,7 +38,7 @@ exclude_labels_func(const Device::Pointer & device,
   }
 
   auto index_list = Array::create(list->size(), 1, 1, 1, dType::LABEL, mType::BUFFER, src->device());
-  index_list->write(labels_list.data());
+  index_list->writeFrom(labels_list.data());
   tier1::replace_values_func(device, src, index_list, dst);
   return dst;
 }

clic/src/tier3/exclude_labels_on_edges.cpp

@@ -41,7 +41,7 @@ exclude_labels_on_edges_func(const Device::Pointer & device,
   execute_if_needed(exclude_z, src->depth(), "exclude_on_edges_z");
 
   std::vector<uint32_t> label_map_vector(label_map->size());
-  label_map->read(label_map_vector.data());
+  label_map->readTo(label_map_vector.data());
   int32_t count = 1;
   for (auto & i : label_map_vector)
   {
@@ -51,7 +51,7 @@ exclude_labels_on_edges_func(const Device::Pointer & device,
       count++;
     }
   }
-  label_map->write(label_map_vector.data());
+  label_map->writeFrom(label_map_vector.data());
   return tier1::replace_values_func(device, src, label_map, dst);
 }
 

clic/src/tier3/maximum_position.cpp

@@ -37,17 +37,17 @@ maximum_position_func(const Device::Pointer & device, const Array::Pointer & src
 
   if (pos_x != nullptr)
   {
-    pos_x->read(&x_coord, { 1, 1, 1 }, { 0, 0, 0 });
+    pos_x->readTo(&x_coord, { 1, 1, 1 }, { 0, 0, 0 });
     coord[0] = x_coord;
   }
   if (pos_y != nullptr)
   {
-    pos_y->read(&y_coord, { 1, 1, 1 }, { x_coord, 0, 0 });
+    pos_y->readTo(&y_coord, { 1, 1, 1 }, { x_coord, 0, 0 });
     coord[1] = y_coord;
   }
   if (pos_z != nullptr)
   {
-    pos_z->read(&z_coord, { 1, 1, 1 }, { x_coord, y_coord, 0 });
+    pos_z->readTo(&z_coord, { 1, 1, 1 }, { x_coord, y_coord, 0 });
     coord[2] = z_coord;
   }
   return coord;