Merge branch 'master' into rename_parameters

Signed-off-by: Stephane Rigaud <[email protected]>

clic/include/tier1.hpp

@@ -1030,7 +1030,7 @@ maximum_images_func(const Device::Pointer & device,
  *
  * @note 'filter', 'in assistant'
  * @see https://clij.github.io/clij2-docs/reference_maximum3DBox
- * @deprecated This function is deprecated. Consider using maximum() instead.
+ * @deprecated This function is deprecated. Consider using maximum_filter() instead.
  */
 auto
 maximum_box_func(const Device::Pointer & device,
@@ -1041,7 +1041,7 @@ maximum_box_func(const Device::Pointer & device,
                  int                     radius_z) -> Array::Pointer;
 
 /**
- * @name maximum
+ * @name maximum_filter
  * @brief Computes the local maximum of a pixels neighborhood (box or sphere). The neighborhood size is specified by its
  * halfwidth, halfheight and halfdepth (radius).
  *
@@ -1059,13 +1059,13 @@ maximum_box_func(const Device::Pointer & device,
  * @see https://clij.github.io/clij2-docs/reference_maximum3DSphere
  */
 auto
-maximum_func(const Device::Pointer & device,
-             const Array::Pointer &  src,
-             Array::Pointer          dst,
-             float                   radius_x,
-             float                   radius_y,
-             float                   radius_z,
-             std::string             connectivity) -> Array::Pointer;
+maximum_filter_func(const Device::Pointer & device,
+                    const Array::Pointer &  src,
+                    Array::Pointer          dst,
+                    float                   radius_x,
+                    float                   radius_y,
+                    float                   radius_z,
+                    std::string             connectivity) -> Array::Pointer;
 
 
 /**
@@ -1342,7 +1342,7 @@ median_func(const Device::Pointer & device,
  *
  * @note 'filter', 'in assistant'
  * @see https://clij.github.io/clij2-docs/reference_minimum3DBox
- * @deprecated This function is deprecated. Consider using minimum() instead.
+ * @deprecated This function is deprecated. Consider using minimum_filter() instead.
  */
 auto
 minimum_box_func(const Device::Pointer & device,
@@ -1354,7 +1354,7 @@ minimum_box_func(const Device::Pointer & device,
 
 
 /**
- * @name minimum
+ * @name minimum_filter
  * @brief Computes the local minimum of a pixels cube neighborhood. The cubes size is specified by its halfwidth,
  * halfheight and halfdepth (radius).
  *
@@ -1372,13 +1372,13 @@ minimum_box_func(const Device::Pointer & device,
  * @see https://clij.github.io/clij2-docs/reference_minimum3DSphere
  */
 auto
-minimum_func(const Device::Pointer & device,
-             const Array::Pointer &  src,
-             Array::Pointer          dst,
-             float                   radius_x,
-             float                   radius_y,
-             float                   radius_z,
-             std::string             connectivity) -> Array::Pointer;
+minimum_filter_func(const Device::Pointer & device,
+                    const Array::Pointer &  src,
+                    Array::Pointer          dst,
+                    float                   radius_x,
+                    float                   radius_y,
+                    float                   radius_z,
+                    std::string             connectivity) -> Array::Pointer;
 
 
 /**

clic/include/tier3.hpp

@@ -360,39 +360,40 @@ morphological_chan_vese_func(const Device::Pointer & device,
  * standard deviation of the intensity, and some shape descriptors of labelled objects in a label image and its
  * corresponding intensity image.
  *
- * The intensity image is optional and set to 0 if not provided.
+ * The intensity image is equal to the label image if not provided.
+ * The label image is set to the entire image if not provided.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param label Label image to compute the statistics. [const Array::Pointer &]]
  * @param intensity Intensity image. [Array::Pointer ( = None )]
+ * @param label Label image to compute the statistics. [Array::Pointer ( = None )]]
  * @return StatisticsMap
  *
  * @see https://clij.github.io/clij2-docs/reference_statisticsOfLabelledPixels
  */
 auto
-statistics_of_labelled_pixels_func(const Device::Pointer & device,
-                                   const Array::Pointer &  label,
-                                   Array::Pointer          intensity) -> StatisticsMap;
+statistics_of_labelled_pixels_func(const Device::Pointer & device, Array::Pointer intensity, Array::Pointer label)
+  -> StatisticsMap;
 
 /**
  * @name statistics_of_background_and_labelled_pixels
  * @brief Compute, for the background and labels, the bounding box, area (in pixels/voxels), minimum intensity,
  * maximum intensity, average intensity, standard deviation of the intensity, and some shape descriptors of
  * labelled objects in a label image and its corresponding intensity image.
  *
- * The intensity image is optional and set to 0 if not provided.
+ * The intensity image is equal to the label image if not provided.
+ * The label image is set to the entire image if not provided.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param label Label image to compute the statistics. [const Array::Pointer &]]
  * @param intensity Intensity image. [Array::Pointer ( = None )]
+ * @param label Label image to compute the statistics. [Array::Pointer ( = None )]]
  * @return StatisticsMap
  *
  * @see https://clij.github.io/clij2-docs/reference_statisticsOfBackgroundAndLabelledPixels
  */
 auto
 statistics_of_background_and_labelled_pixels_func(const Device::Pointer & device,
-                                                  const Array::Pointer &  label,
-                                                  const Array::Pointer &  intensity) -> StatisticsMap;
+                                                  Array::Pointer          intensity,
+                                                  Array::Pointer          label) -> StatisticsMap;
 
 } // namespace cle::tier3
 

clic/include/tier4.hpp

@@ -212,8 +212,8 @@ remove_labels_with_map_values_within_range_func(const Device::Pointer & device,
  * associated with the labels.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input image where labels will be filtered. [const Array::Pointer &]
- * @param values Vector of values associated with the labels. [const Array::Pointer &]
+ * @param values_map Vector of values associated with the labels. [const Array::Pointer &]
+ * @param label_map_input Input image where labels will be filtered. [const Array::Pointer &]
  * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
  * @param minimum_value_range Minimum value to keep. [float ( = 0 )]
  * @param maximum_value_range Maximum value to keep. [float ( = 100 )]
@@ -225,8 +225,8 @@ remove_labels_with_map_values_within_range_func(const Device::Pointer & device,
  */
 auto
 exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
-                                                 const Array::Pointer &  src,
-                                                 const Array::Pointer &  values,
+                                                 const Array::Pointer &  values_map,
+                                                 const Array::Pointer &  label_map_input,
                                                  Array::Pointer          dst,
                                                  float                   minimum_value_range,
                                                  float                   maximum_value_range) -> Array::Pointer;
@@ -237,8 +237,8 @@ exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
  * associated with the labels.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input image where labels will be filtered. [const Array::Pointer &]
- * @param values Vector of values associated with the labels. [const Array::Pointer &]
+ * @param values_map Vector of values associated with the labels. [const Array::Pointer &]
+ * @param label_map_input Input image where labels will be filtered. [const Array::Pointer &]
  * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
  * @param minimum_value_range Minimum value to keep. [float ( = 0 )]
  * @param maximum_value_range Maximum value to keep. [float ( = 100 )]
@@ -250,8 +250,8 @@ exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
  */
 auto
 exclude_labels_with_map_values_within_range_func(const Device::Pointer & device,
-                                                 const Array::Pointer &  src,
-                                                 const Array::Pointer &  values,
+                                                 const Array::Pointer &  values_map,
+                                                 const Array::Pointer &  label_map_input,
                                                  Array::Pointer          dst,
                                                  float                   minimum_value_range,
                                                  float                   maximum_value_range) -> Array::Pointer;

clic/src/tier1/maximum.cpp

@@ -22,13 +22,13 @@ namespace cle::tier1
 {
 
 auto
-maximum_func(const Device::Pointer & device,
-             const Array::Pointer &  src,
-             Array::Pointer          dst,
-             float                   radius_x,
-             float                   radius_y,
-             float                   radius_z,
-             std::string             connectivity) -> Array::Pointer
+maximum_filter_func(const Device::Pointer & device,
+                    const Array::Pointer &  src,
+                    Array::Pointer          dst,
+                    float                   radius_x,
+                    float                   radius_y,
+                    float                   radius_z,
+                    std::string             connectivity) -> Array::Pointer
 {
   tier0::create_like(src, dst);
   auto r_x = radius2kernelsize(radius_x);

clic/src/tier1/minimum.cpp

@@ -21,13 +21,13 @@ namespace cle::tier1
 {
 
 auto
-minimum_func(const Device::Pointer & device,
-             const Array::Pointer &  src,
-             Array::Pointer          dst,
-             float                   radius_x,
-             float                   radius_y,
-             float                   radius_z,
-             std::string             connectivity) -> Array::Pointer
+minimum_filter_func(const Device::Pointer & device,
+                    const Array::Pointer &  src,
+                    Array::Pointer          dst,
+                    float                   radius_x,
+                    float                   radius_y,
+                    float                   radius_z,
+                    std::string             connectivity) -> Array::Pointer
 {
   tier0::create_like(src, dst);
   auto r_x = radius2kernelsize(radius_x);

clic/src/tier2/bottom_hat.cpp

@@ -16,8 +16,8 @@ bottom_hat_func(const Device::Pointer & device,
                 float                   radius_z,
                 std::string             connectivity) -> Array::Pointer
 {
-  auto temp1 = tier1::maximum_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
-  auto temp2 = tier1::minimum_func(device, temp1, nullptr, radius_x, radius_y, radius_z, connectivity);
+  auto temp1 = tier1::maximum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
+  auto temp2 = tier1::minimum_filter_func(device, temp1, nullptr, radius_x, radius_y, radius_z, connectivity);
   return tier1::add_images_weighted_func(device, temp2, src, dst, 1, -1);
 }
 

clic/src/tier2/bottom_hat_box.cpp

@@ -16,8 +16,8 @@ bottom_hat_box_func(const Device::Pointer & device,
                     int                     radius_z) -> Array::Pointer
 {
   std::cerr << "Deprecated: this function is deprecated, use bottom_hat instead\n";
-  auto temp1 = tier1::maximum_box_func(device, src, nullptr, radius_x, radius_y, radius_z);
-  auto temp2 = tier1::minimum_box_func(device, temp1, nullptr, radius_x, radius_y, radius_z);
+  auto temp1 = tier1::maximum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, "box");
+  auto temp2 = tier1::minimum_filter_func(device, temp1, nullptr, radius_x, radius_y, radius_z, "box");
   return tier1::add_images_weighted_func(device, temp2, src, dst, 1, -1);
 }
 

clic/src/tier2/closing.cpp

@@ -16,8 +16,8 @@ closing_func(const Device::Pointer & device,
              float                   radius_z,
              std::string             connectivity) -> Array::Pointer
 {
-  auto temp = tier1::maximum_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
-  return tier1::minimum_func(device, temp, dst, radius_x, radius_y, radius_z, connectivity);
+  auto temp = tier1::maximum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
+  return tier1::minimum_filter_func(device, temp, dst, radius_x, radius_y, radius_z, connectivity);
 }
 
 } // namespace cle::tier2

clic/src/tier2/closing_box.cpp

@@ -16,8 +16,8 @@ closing_box_func(const Device::Pointer & device,
                  int                     radius_z) -> Array::Pointer
 {
   std::cerr << "Deprecated: this function is deprecated, use closing instead\n";
-  auto temp = tier1::maximum_box_func(device, src, nullptr, radius_x, radius_y, radius_z);
-  return tier1::minimum_box_func(device, temp, dst, radius_x, radius_y, radius_z);
+  auto temp = tier1::maximum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, "box");
+  return tier1::minimum_filter_func(device, temp, dst, radius_x, radius_y, radius_z, "box");
 }
 
 } // namespace cle::tier2

clic/src/tier2/opening.cpp

@@ -16,8 +16,8 @@ opening_func(const Device::Pointer & device,
              float                   radius_z,
              std::string             connectivity) -> Array::Pointer
 {
-  auto temp = tier1::minimum_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
-  return tier1::maximum_func(device, temp, dst, radius_x, radius_y, radius_z, connectivity);
+  auto temp = tier1::minimum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
+  return tier1::maximum_filter_func(device, temp, dst, radius_x, radius_y, radius_z, connectivity);
 }
 
 } // namespace cle::tier2

clic/src/tier2/opening_box.cpp

@@ -16,8 +16,8 @@ opening_box_func(const Device::Pointer & device,
                  int                     radius_z) -> Array::Pointer
 {
   std::cerr << "Deprecated: this function is deprecated, use opening instead\n";
-  auto temp = tier1::minimum_box_func(device, src, nullptr, radius_x, radius_y, radius_z);
-  return tier1::maximum_box_func(device, temp, dst, radius_x, radius_y, radius_z);
+  auto temp = tier1::minimum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, "box");
+  return tier1::maximum_filter_func(device, temp, dst, radius_x, radius_y, radius_z, "box");
 }
 
 } // namespace cle::tier2

clic/src/tier2/top_hat.cpp

@@ -16,8 +16,8 @@ top_hat_func(const Device::Pointer & device,
              float                   radius_z,
              std::string             connectivity) -> Array::Pointer
 {
-  auto temp1 = tier1::minimum_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
-  auto temp2 = tier1::maximum_func(device, temp1, nullptr, radius_x, radius_y, radius_z, connectivity);
+  auto temp1 = tier1::minimum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, connectivity);
+  auto temp2 = tier1::maximum_filter_func(device, temp1, nullptr, radius_x, radius_y, radius_z, connectivity);
   return tier1::add_images_weighted_func(device, src, temp2, dst, 1, -1);
 }
 

clic/src/tier2/top_hat_box.cpp

@@ -16,8 +16,8 @@ top_hat_box_func(const Device::Pointer & device,
                  int                     radius_z) -> Array::Pointer
 {
   std::cerr << "Deprecated: this function is deprecated, use top_hat instead\n";
-  auto temp1 = tier1::minimum_box_func(device, src, nullptr, radius_x, radius_y, radius_z);
-  auto temp2 = tier1::maximum_box_func(device, temp1, nullptr, radius_x, radius_y, radius_z);
+  auto temp1 = tier1::minimum_filter_func(device, src, nullptr, radius_x, radius_y, radius_z, "box");
+  auto temp2 = tier1::maximum_filter_func(device, temp1, nullptr, radius_x, radius_y, radius_z, "box");
   return tier1::add_images_weighted_func(device, src, temp2, dst, 1, -1);
 }
 

clic/src/tier3/statistics_of_labelled_pixels.cpp

@@ -6,16 +6,25 @@ namespace cle::tier3
 {
 
 auto
-statistics_of_labelled_pixels_func(const Device::Pointer & device,
-                                   const Array::Pointer &  label,
-                                   Array::Pointer          intensity) -> StatisticsMap
+statistics_of_labelled_pixels_func(const Device::Pointer & device, Array::Pointer intensity, Array::Pointer label)
+  -> StatisticsMap
 {
+  if (intensity == nullptr && label == nullptr)
+  {
+    throw std::runtime_error(
+      "Error: no intensity nor label was provided to the 'statistics_of_labelled_pixels' function.");
+  }
+  if (label == nullptr)
+  {
+    std::cerr << "Warning: no label was provided. Label will be the entire image." << std::endl;
+    tier0::create_like(intensity, label, dType::LABEL);
+    label->fill(1);
+  }
   if (intensity == nullptr)
   {
-    // std::cerr << "Warning: no intensity was provided. Pixels intensity will be set to their label value." <<
-    // std::endl;
+    std::cerr << "Warning: no intensity was provided. Pixels intensity will be set to their label value." << std::endl;
     tier0::create_like(label, intensity, dType::FLOAT);
-    intensity->fill(0);
+    tier1::copy_func(device, label, intensity);
   }
 
   return compute_statistics_per_labels(device, label, intensity);
@@ -24,11 +33,28 @@ statistics_of_labelled_pixels_func(const Device::Pointer & device,
 
 auto
 statistics_of_background_and_labelled_pixels_func(const Device::Pointer & device,
-                                                  const Array::Pointer &  label,
-                                                  const Array::Pointer &  intensity) -> StatisticsMap
+                                                  Array::Pointer          intensity,
+                                                  Array::Pointer          label) -> StatisticsMap
 {
+  if (intensity == nullptr && label == nullptr)
+  {
+    throw std::runtime_error(
+      "Error: no intensity nor label was provided to the 'statistics_of_labelled_pixels' function.");
+  }
+  if (label == nullptr)
+  {
+    std::cerr << "Warning: no label was provided. Label will be the entire image." << std::endl;
+    tier0::create_like(intensity, label, dType::LABEL);
+    label->fill(1);
+  }
+  if (intensity == nullptr)
+  {
+    std::cerr << "Warning: no intensity was provided. Pixels intensity will be set to their label value." << std::endl;
+    tier0::create_like(label, intensity, dType::FLOAT);
+    tier1::copy_func(device, label, intensity);
+  }
   auto               temp = tier1::add_image_and_scalar_func(device, label, nullptr, 1);
-  auto               props = tier3::statistics_of_labelled_pixels_func(device, temp, intensity);
+  auto               props = tier3::statistics_of_labelled_pixels_func(device, intensity, temp);
   std::vector<float> labels = props["label"];
   std::transform(labels.begin(), labels.end(), labels.begin(), [](float label) { return label - 1; });
   props["label"] = labels;

clic/src/tier4/centroids_of_labels.cpp

@@ -20,11 +20,11 @@ centroids_of_labels_func(const Device::Pointer & device,
   cle::StatisticsMap props;
   if (include_background)
   {
-    props = tier3::statistics_of_background_and_labelled_pixels_func(device, src, nullptr);
+    props = tier3::statistics_of_background_and_labelled_pixels_func(device, nullptr, src);
   }
   else
   {
-    props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
+    props = tier3::statistics_of_labelled_pixels_func(device, nullptr, src);
   }
   auto centroid_x = props["centroid_x"];
   auto centroid_y = props["centroid_y"];