From 639c52655473029f72ab3bdd1c2ab56ba041d5fd Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 10:35:20 +0200
Subject: [PATCH 01/16] rename parameters in convolve

---
 clic/include/tier1.hpp      | 8 ++++----
 clic/src/tier1/convolve.cpp | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
index 8cb735612..b54e898ee 100644
--- a/clic/include/tier1.hpp
+++ b/clic/include/tier1.hpp
@@ -250,8 +250,8 @@ block_enumerate_func(const Device::Pointer & device,
  * and Z.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 First input image to process. [const Array::Pointer &]
- * @param src1 Second input image to process. [const Array::Pointer &]
+ * @param src First input image to process. [const Array::Pointer &]
+ * @param kernel Second input image to process. [const Array::Pointer &]
  * @param dst Output result image. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
@@ -260,8 +260,8 @@ block_enumerate_func(const Device::Pointer & device,
  */
 auto
 convolve_func(const Device::Pointer & device,
-              const Array::Pointer &  src0,
-              const Array::Pointer &  src1,
+              const Array::Pointer &  src,
+              const Array::Pointer &  kernel,
               Array::Pointer          dst) -> Array::Pointer;
 
 
diff --git a/clic/src/tier1/convolve.cpp b/clic/src/tier1/convolve.cpp
index 68ca9dcd9..67bdb2201 100644
--- a/clic/src/tier1/convolve.cpp
+++ b/clic/src/tier1/convolve.cpp
@@ -10,13 +10,13 @@ namespace cle::tier1
 
 auto
 convolve_func(const Device::Pointer & device,
-              const Array::Pointer &  src0,
-              const Array::Pointer &  src1,
+              const Array::Pointer &  src,
+              const Array::Pointer &  kernel,
               Array::Pointer          dst) -> Array::Pointer
 {
-  tier0::create_like(src0, dst, dType::FLOAT);
+  tier0::create_like(src, dst, dType::FLOAT);
   const KernelInfo    kernel = { "convolve", kernel::convolve };
-  const ParameterList params = { { "src0", src0 }, { "src1", src1 }, { "dst", dst } };
+  const ParameterList params = { { "src0", src }, { "src1", kernel }, { "dst", dst } };
   const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
   execute(device, kernel, params, range);
   return dst;

From 263210548c0c7bb97f704dc5d0398bf1944ee42c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 17 Oct 2024 08:37:01 +0000
Subject: [PATCH 02/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 clic/include/tier4.hpp                    | 6 ++++--
 clic/src/tier4/centroids_of_labels.cpp    | 6 ++++--
 clic/src/tier4/filter_label_by_values.cpp | 6 ++++--
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index ad6992da0..67b175e2b 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -152,8 +152,10 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_centroidsOfLabels
  */
 auto
-centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, bool include_background)
-  -> Array::Pointer;
+centroids_of_labels_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst,
+                         bool                    include_background) -> Array::Pointer;
 
 
 /**
diff --git a/clic/src/tier4/centroids_of_labels.cpp b/clic/src/tier4/centroids_of_labels.cpp
index 471bc9e39..a04efdd09 100644
--- a/clic/src/tier4/centroids_of_labels.cpp
+++ b/clic/src/tier4/centroids_of_labels.cpp
@@ -12,8 +12,10 @@ namespace cle::tier4
 {
 
 auto
-centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, bool include_background)
-  -> Array::Pointer
+centroids_of_labels_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst,
+                         bool                    include_background) -> Array::Pointer
 {
   cle::StatisticsMap props;
   if (include_background)
diff --git a/clic/src/tier4/filter_label_by_values.cpp b/clic/src/tier4/filter_label_by_values.cpp
index b4d657f75..5dcd3a72b 100644
--- a/clic/src/tier4/filter_label_by_values.cpp
+++ b/clic/src/tier4/filter_label_by_values.cpp
@@ -53,7 +53,8 @@ exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
                                                  float                   minimum_value_range,
                                                  float                   maximum_value_range) -> Array::Pointer
 {
-  return remove_labels_with_map_values_out_of_range_func(device, src, values, dst, minimum_value_range, maximum_value_range);
+  return remove_labels_with_map_values_out_of_range_func(
+    device, src, values, dst, minimum_value_range, maximum_value_range);
 }
 
 
@@ -65,7 +66,8 @@ exclude_labels_with_map_values_within_range_func(const Device::Pointer & device,
                                                  float                   minimum_value_range,
                                                  float                   maximum_value_range) -> Array::Pointer
 {
-  return remove_labels_with_map_values_within_range_func(device, src, values, dst, minimum_value_range, maximum_value_range);
+  return remove_labels_with_map_values_within_range_func(
+    device, src, values, dst, minimum_value_range, maximum_value_range);
 }
 
 } // namespace cle::tier4

From 08369e90bf23344b4a83efc0477559f97c332ca1 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 10:40:15 +0200
Subject: [PATCH 03/16] renamed parameter names in generate_distance_matrix

---
 clic/include/tier1.hpp                      | 10 +++++-----
 clic/src/tier1/generate_distance_matrix.cpp | 16 ++++++++--------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
index b54e898ee..681f12818 100644
--- a/clic/include/tier1.hpp
+++ b/clic/include/tier1.hpp
@@ -675,8 +675,8 @@ gaussian_blur_func(const Device::Pointer & device,
  * meshes.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 First input image to process. [const Array::Pointer &]
- * @param src1 Second input image to process. [const Array::Pointer &]
+ * @param coordinate_list1 First coordinate list to process. [const Array::Pointer &]
+ * @param coordinate_list2 Second coordinate list to process. [const Array::Pointer &]
  * @param dst Output result image. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
@@ -684,9 +684,9 @@ gaussian_blur_func(const Device::Pointer & device,
  */
 auto
 generate_distance_matrix_func(const Device::Pointer & device,
-                              const Array::Pointer &  src0,
-                              const Array::Pointer &  src1,
-                              Array::Pointer          dst) -> Array::Pointer;
+                              const Array::Pointer &  coordinate_list1,
+                              const Array::Pointer &  coordinate_list2,
+                              Array::Pointer          distance_matrix_destination) -> Array::Pointer;
 
 
 /**
diff --git a/clic/src/tier1/generate_distance_matrix.cpp b/clic/src/tier1/generate_distance_matrix.cpp
index 6bc745e0b..f9b63ea3c 100644
--- a/clic/src/tier1/generate_distance_matrix.cpp
+++ b/clic/src/tier1/generate_distance_matrix.cpp
@@ -10,17 +10,17 @@ namespace cle::tier1
 
 auto
 generate_distance_matrix_func(const Device::Pointer & device,
-                              const Array::Pointer &  src0,
-                              const Array::Pointer &  src1,
-                              Array::Pointer          dst) -> Array::Pointer
+                              const Array::Pointer &  coordinate_list1,
+                              const Array::Pointer &  coordinate_list2,
+                              Array::Pointer          distance_matrix_destination) -> Array::Pointer
 {
-  tier0::create_dst(src0, dst, src0->width() + 1, src0->width() + 1, 1, dType::FLOAT);
-  dst->fill(0);
+  tier0::create_dst(coordinate_list1, distance_matrix_destination, coordinate_list1->width() + 1, coordinate_list1->width() + 1, 1, dType::FLOAT);
+  distance_matrix_destination->fill(0);
   const KernelInfo    kernel = { "generate_distance_matrix", kernel::generate_distance_matrix };
-  const ParameterList params = { { "src0", src0 }, { "src1", src1 }, { "dst", dst } };
-  const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
+  const ParameterList params = { { "src0", coordinate_list1 }, { "src1", coordinate_list2 }, { "dst", distance_matrix_destination } };
+  const RangeArray    range = { distance_matrix_destination->width(), distance_matrix_destination->height(), distance_matrix_destination->depth() };
   execute(device, kernel, params, range);
-  return dst;
+  return distance_matrix_destination;
 }
 
 } // namespace cle::tier1

From 37f2d901afa6b2cc8391d147da39b6bea4347713 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 10:45:10 +0200
Subject: [PATCH 04/16] rename parameters of multiply_matrix

---
 clic/include/tier1.hpp             | 12 ++++++------
 clic/src/tier1/multiply_matrix.cpp | 14 +++++++-------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
index 681f12818..c7c79d9c3 100644
--- a/clic/include/tier1.hpp
+++ b/clic/include/tier1.hpp
@@ -2145,18 +2145,18 @@ minimum_sphere_func(const Device::Pointer & device,
  * @brief Multiplies two matrices with each other. Shape of matrix1 should be equal to shape of matrix2 transposed.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 First input image to process. [const Array::Pointer &]
- * @param src1 Second input image to process. [const Array::Pointer &]
- * @param dst Output result image. [Array::Pointer ( = None )]
+ * @param matrix1 First matrix to process. [const Array::Pointer &]
+ * @param matrix2 Second matrix to process. [const Array::Pointer &]
+ * @param matrix_destination Output result matrix. [Array::Pointer ( = None )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_multiplyMatrix
  *
  */
 auto
 multiply_matrix_func(const Device::Pointer & device,
-                     const Array::Pointer &  src0,
-                     const Array::Pointer &  src1,
-                     Array::Pointer          dst) -> Array::Pointer;
+                     const Array::Pointer &  matrix1,
+                     const Array::Pointer &  matrix2,
+                     Array::Pointer          matrix_destination) -> Array::Pointer;
 
 
 /**
diff --git a/clic/src/tier1/multiply_matrix.cpp b/clic/src/tier1/multiply_matrix.cpp
index 189a36fb2..93e37128c 100644
--- a/clic/src/tier1/multiply_matrix.cpp
+++ b/clic/src/tier1/multiply_matrix.cpp
@@ -10,16 +10,16 @@ namespace cle::tier1
 
 auto
 multiply_matrix_func(const Device::Pointer & device,
-                     const Array::Pointer &  src0,
-                     const Array::Pointer &  src1,
-                     Array::Pointer          dst) -> Array::Pointer
+                     const Array::Pointer &  matrix1,
+                     const Array::Pointer &  matrix2,
+                     Array::Pointer          matrix_destination) -> Array::Pointer
 {
-  tier0::create_dst(src0, dst, src1->width(), src0->height(), src0->depth(), dType::FLOAT);
+  tier0::create_dst(matrix1, matrix_destination, matrix2->width(), matrix1->height(), matrix1->depth(), dType::FLOAT);
   const KernelInfo    kernel = { "multiply_matrix", kernel::multiply_matrix };
-  const ParameterList params = { { "src0", src0 }, { "src1", src1 }, { "dst", dst } };
-  const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
+  const ParameterList params = { { "src0", matrix1 }, { "src1", matrix2 }, { "dst", matrix_destination } };
+  const RangeArray    range = { matrix_destination->width(), matrix_destination->height(), matrix_destination->depth() };
   execute(device, kernel, params, range);
-  return dst;
+  return matrix_destination;
 }
 
 } // namespace cle::tier1

From 78091e259ad0986f57a22a4b3f2dc8cd13c1cd67 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 10:50:59 +0200
Subject: [PATCH 05/16] renamed parameters of count_touching_neighbors

---
 clic/include/tier2.hpp                      |  8 ++++----
 clic/src/tier2/count_touching_neighbors.cpp | 10 +++++-----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/clic/include/tier2.hpp b/clic/include/tier2.hpp
index f5528808e..75a55fd44 100644
--- a/clic/include/tier2.hpp
+++ b/clic/include/tier2.hpp
@@ -283,8 +283,8 @@ concatenate_along_z_func(const Device::Pointer & device,
  * matrix where the first column (index = 0) has been set to 0. Use set_column for that.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input image to process. [const Array::Pointer &]
- * @param dst Output result image. [Array::Pointer ( = None )]
+ * @param touch_matrix Input touch matrix to process. [const Array::Pointer &]
+ * @param touching_neighbors_count_destination Output vector of touch count. [Array::Pointer ( = None )]
  * @param ignore_background [bool ( = True )]
  * @return Array::Pointer
  *
@@ -292,8 +292,8 @@ concatenate_along_z_func(const Device::Pointer & device,
  */
 auto
 count_touching_neighbors_func(const Device::Pointer & device,
-                              const Array::Pointer &  src,
-                              Array::Pointer          dst,
+                              const Array::Pointer &  touch_matrix,
+                              Array::Pointer          touching_neighbors_count_destination,
                               bool                    ignore_background) -> Array::Pointer;
 
 
diff --git a/clic/src/tier2/count_touching_neighbors.cpp b/clic/src/tier2/count_touching_neighbors.cpp
index 107f71dc8..6332234e3 100644
--- a/clic/src/tier2/count_touching_neighbors.cpp
+++ b/clic/src/tier2/count_touching_neighbors.cpp
@@ -9,19 +9,19 @@ namespace cle::tier2
 
 auto
 count_touching_neighbors_func(const Device::Pointer & device,
-                              const Array::Pointer &  src,
-                              Array::Pointer          dst,
+                              const Array::Pointer &  touch_matrix,
+                              Array::Pointer          touching_neighbors_count_destination,
                               bool                    ignore_background) -> Array::Pointer
 {
-  tier0::create_vector(src, dst, src->width(), dType::UINT32);
-  auto bin_matrix = tier1::greater_constant_func(device, src, nullptr, 0);
+  tier0::create_vector(touch_matrix, touching_neighbors_count_destination, touch_matrix->width(), dType::UINT32);
+  auto bin_matrix = tier1::greater_constant_func(device, touch_matrix, nullptr, 0);
   if (ignore_background)
   {
     tier1::set_row_func(device, bin_matrix, 0, 0);
     tier1::set_column_func(device, bin_matrix, 0, 0);
     tier1::set_where_x_equals_y_func(device, bin_matrix, 0);
   }
-  return tier1::sum_y_projection_func(device, bin_matrix, dst);
+  return tier1::sum_y_projection_func(device, bin_matrix, touching_neighbors_count_destination);
 }
 
 } // namespace cle::tier2

From cc179e44c423ffc058d99100a74ef8d3d00a720a Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 10:53:38 +0200
Subject: [PATCH 06/16] Revert "rename parameters in convolve"

This reverts commit 639c52655473029f72ab3bdd1c2ab56ba041d5fd.
---
 clic/include/tier1.hpp      | 8 ++++----
 clic/src/tier1/convolve.cpp | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
index c7c79d9c3..7d5c3b91d 100644
--- a/clic/include/tier1.hpp
+++ b/clic/include/tier1.hpp
@@ -250,8 +250,8 @@ block_enumerate_func(const Device::Pointer & device,
  * and Z.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src First input image to process. [const Array::Pointer &]
- * @param kernel Second input image to process. [const Array::Pointer &]
+ * @param src0 First input image to process. [const Array::Pointer &]
+ * @param src1 Second input image to process. [const Array::Pointer &]
  * @param dst Output result image. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
@@ -260,8 +260,8 @@ block_enumerate_func(const Device::Pointer & device,
  */
 auto
 convolve_func(const Device::Pointer & device,
-              const Array::Pointer &  src,
-              const Array::Pointer &  kernel,
+              const Array::Pointer &  src0,
+              const Array::Pointer &  src1,
               Array::Pointer          dst) -> Array::Pointer;
 
 
diff --git a/clic/src/tier1/convolve.cpp b/clic/src/tier1/convolve.cpp
index 67bdb2201..68ca9dcd9 100644
--- a/clic/src/tier1/convolve.cpp
+++ b/clic/src/tier1/convolve.cpp
@@ -10,13 +10,13 @@ namespace cle::tier1
 
 auto
 convolve_func(const Device::Pointer & device,
-              const Array::Pointer &  src,
-              const Array::Pointer &  kernel,
+              const Array::Pointer &  src0,
+              const Array::Pointer &  src1,
               Array::Pointer          dst) -> Array::Pointer
 {
-  tier0::create_like(src, dst, dType::FLOAT);
+  tier0::create_like(src0, dst, dType::FLOAT);
   const KernelInfo    kernel = { "convolve", kernel::convolve };
-  const ParameterList params = { { "src0", src }, { "src1", kernel }, { "dst", dst } };
+  const ParameterList params = { { "src0", src0 }, { "src1", src1 }, { "dst", dst } };
   const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
   execute(device, kernel, params, range);
   return dst;

From e421e0c6f8deff7945f8da0968d3a80858475a2e Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:09:58 +0200
Subject: [PATCH 07/16] renamed parameters of centroids_of_labels

---
 clic/include/tier4.hpp                 | 8 ++++----
 clic/src/tier4/centroids_of_labels.cpp | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 67b175e2b..cf34f942e 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -144,8 +144,8 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  * where n is the number of labels and d=3 the dimensionality (x,y,z) of the original image.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image where the centroids will be determined from. [const Array::Pointer &]
- * @param dst Output image where the centroids will be written to. [Array::Pointer ( = None )]
+ * @param label_image Label image where the centroids will be determined from. [const Array::Pointer &]
+ * @param coorindate_list_destination Output list of coordinates where the centroids will be written to. [Array::Pointer ( = None )]
  * @param include_background Determines if the background label should be included. [bool ( = False )]
  * @return Array::Pointer
  *
@@ -153,8 +153,8 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  */
 auto
 centroids_of_labels_func(const Device::Pointer & device,
-                         const Array::Pointer &  src,
-                         Array::Pointer          dst,
+                         const Array::Pointer &  label_image,
+                         Array::Pointer          coorindate_list_destination,
                          bool                    include_background) -> Array::Pointer;
 
 
diff --git a/clic/src/tier4/centroids_of_labels.cpp b/clic/src/tier4/centroids_of_labels.cpp
index a04efdd09..0a5439399 100644
--- a/clic/src/tier4/centroids_of_labels.cpp
+++ b/clic/src/tier4/centroids_of_labels.cpp
@@ -13,18 +13,18 @@ namespace cle::tier4
 
 auto
 centroids_of_labels_func(const Device::Pointer & device,
-                         const Array::Pointer &  src,
-                         Array::Pointer          dst,
+                         const Array::Pointer &  label_image,
+                         Array::Pointer          coorindate_list_destination,
                          bool                    include_background) -> Array::Pointer
 {
   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, label_image, nullptr);
   }
   else
   {
-    props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
+    props = tier3::statistics_of_labelled_pixels_func(device, label_image, nullptr);
   }
   auto centroid_x = props["centroid_x"];
   auto centroid_y = props["centroid_y"];

From 739d4e3b99ab0051842495bf0bfcfc8b84c8df5d Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:17:14 +0200
Subject: [PATCH 08/16] renamed parameters of voronoi_labeling

---
 clic/include/tier6.hpp              | 6 +++---
 clic/src/tier6/voronoi_labeling.cpp | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/clic/include/tier6.hpp b/clic/include/tier6.hpp
index 2b5d76848..522f98912 100644
--- a/clic/include/tier6.hpp
+++ b/clic/include/tier6.hpp
@@ -103,15 +103,15 @@ masked_voronoi_labeling_func(const Device::Pointer & device,
  * touch. The resulting label map is written to the output.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param input_binary [const Array::Pointer &]
+ * @param output_labels [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label', 'in assistant', 'bia-bob-suggestion'
  * @see https://clij.github.io/clij2-docs/reference_voronoiLabeling
  */
 auto
-voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst) -> Array::Pointer;
+voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels) -> Array::Pointer;
 
 
 /**
diff --git a/clic/src/tier6/voronoi_labeling.cpp b/clic/src/tier6/voronoi_labeling.cpp
index 1b720f5b9..3cec4ae33 100644
--- a/clic/src/tier6/voronoi_labeling.cpp
+++ b/clic/src/tier6/voronoi_labeling.cpp
@@ -12,11 +12,11 @@ namespace cle::tier6
 {
 
 auto
-voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst) -> Array::Pointer
+voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels) -> Array::Pointer
 {
-  tier0::create_like(src, dst, dType::LABEL);
-  auto flip = tier5::connected_component_labeling_func(device, src, nullptr, "box");
-  return tier2::extend_labeling_via_voronoi_func(device, flip, dst);
+  tier0::create_like(input_binary, output_labels, dType::LABEL);
+  auto flip = tier5::connected_component_labeling_func(device, input_binary, nullptr, "box");
+  return tier2::extend_labeling_via_voronoi_func(device, flip, output_labels);
 }
 
 } // namespace cle::tier6

From 691a5ae013c8cd5b7a737e3ecb83c1fb55246caa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 17 Oct 2024 11:19:35 +0000
Subject: [PATCH 09/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 clic/include/tier4.hpp                      |  3 ++-
 clic/include/tier6.hpp                      |  3 ++-
 clic/src/tier1/generate_distance_matrix.cpp | 15 ++++++++++++---
 clic/src/tier1/multiply_matrix.cpp          |  2 +-
 clic/src/tier6/voronoi_labeling.cpp         |  3 ++-
 5 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 0df81fa9f..86a51b63d 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -145,7 +145,8 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param label_image Label image where the centroids will be determined from. [const Array::Pointer &]
- * @param coorindate_list_destination Output list of coordinates where the centroids will be written to. [Array::Pointer ( = None )]
+ * @param coorindate_list_destination Output list of coordinates where the centroids will be written to. [Array::Pointer
+ * ( = None )]
  * @param include_background Determines if the background label should be included. [bool ( = False )]
  * @return Array::Pointer
  *
diff --git a/clic/include/tier6.hpp b/clic/include/tier6.hpp
index 522f98912..1ecccc5f8 100644
--- a/clic/include/tier6.hpp
+++ b/clic/include/tier6.hpp
@@ -111,7 +111,8 @@ masked_voronoi_labeling_func(const Device::Pointer & device,
  * @see https://clij.github.io/clij2-docs/reference_voronoiLabeling
  */
 auto
-voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels) -> Array::Pointer;
+voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels)
+  -> Array::Pointer;
 
 
 /**
diff --git a/clic/src/tier1/generate_distance_matrix.cpp b/clic/src/tier1/generate_distance_matrix.cpp
index f9b63ea3c..bb82884e0 100644
--- a/clic/src/tier1/generate_distance_matrix.cpp
+++ b/clic/src/tier1/generate_distance_matrix.cpp
@@ -14,11 +14,20 @@ generate_distance_matrix_func(const Device::Pointer & device,
                               const Array::Pointer &  coordinate_list2,
                               Array::Pointer          distance_matrix_destination) -> Array::Pointer
 {
-  tier0::create_dst(coordinate_list1, distance_matrix_destination, coordinate_list1->width() + 1, coordinate_list1->width() + 1, 1, dType::FLOAT);
+  tier0::create_dst(coordinate_list1,
+                    distance_matrix_destination,
+                    coordinate_list1->width() + 1,
+                    coordinate_list1->width() + 1,
+                    1,
+                    dType::FLOAT);
   distance_matrix_destination->fill(0);
   const KernelInfo    kernel = { "generate_distance_matrix", kernel::generate_distance_matrix };
-  const ParameterList params = { { "src0", coordinate_list1 }, { "src1", coordinate_list2 }, { "dst", distance_matrix_destination } };
-  const RangeArray    range = { distance_matrix_destination->width(), distance_matrix_destination->height(), distance_matrix_destination->depth() };
+  const ParameterList params = { { "src0", coordinate_list1 },
+                                 { "src1", coordinate_list2 },
+                                 { "dst", distance_matrix_destination } };
+  const RangeArray    range = { distance_matrix_destination->width(),
+                                distance_matrix_destination->height(),
+                                distance_matrix_destination->depth() };
   execute(device, kernel, params, range);
   return distance_matrix_destination;
 }
diff --git a/clic/src/tier1/multiply_matrix.cpp b/clic/src/tier1/multiply_matrix.cpp
index 93e37128c..de09c6eba 100644
--- a/clic/src/tier1/multiply_matrix.cpp
+++ b/clic/src/tier1/multiply_matrix.cpp
@@ -17,7 +17,7 @@ multiply_matrix_func(const Device::Pointer & device,
   tier0::create_dst(matrix1, matrix_destination, matrix2->width(), matrix1->height(), matrix1->depth(), dType::FLOAT);
   const KernelInfo    kernel = { "multiply_matrix", kernel::multiply_matrix };
   const ParameterList params = { { "src0", matrix1 }, { "src1", matrix2 }, { "dst", matrix_destination } };
-  const RangeArray    range = { matrix_destination->width(), matrix_destination->height(), matrix_destination->depth() };
+  const RangeArray range = { matrix_destination->width(), matrix_destination->height(), matrix_destination->depth() };
   execute(device, kernel, params, range);
   return matrix_destination;
 }
diff --git a/clic/src/tier6/voronoi_labeling.cpp b/clic/src/tier6/voronoi_labeling.cpp
index 3cec4ae33..be5051ba7 100644
--- a/clic/src/tier6/voronoi_labeling.cpp
+++ b/clic/src/tier6/voronoi_labeling.cpp
@@ -12,7 +12,8 @@ namespace cle::tier6
 {
 
 auto
-voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels) -> Array::Pointer
+voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels)
+  -> Array::Pointer
 {
   tier0::create_like(input_binary, output_labels, dType::LABEL);
   auto flip = tier5::connected_component_labeling_func(device, input_binary, nullptr, "box");

From 2cc1a087a320d1e688783b07422e114a3c152470 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:22:52 +0200
Subject: [PATCH 10/16] documentation update tier7

---
 clic/include/tier7.hpp | 40 ++++++++++++++++++++--------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/clic/include/tier7.hpp b/clic/include/tier7.hpp
index 98f7a5297..aa974f064 100644
--- a/clic/include/tier7.hpp
+++ b/clic/include/tier7.hpp
@@ -19,8 +19,8 @@ namespace cle::tier7
  *  If no matrix is given, the identity matrix will be used.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be transformed. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be transformed. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
  * @param transform_matrix Affine transformation matrix (3x3 or 4x4). [std::vector<float> * ( = None )]
  * @param interpolate If true, bi/trilinear interpolation will be applied, if hardware allows. [bool ( = False )]
  * @param resize Automatically determines the size of the output depending on the rotation angles. [bool ( = False )]
@@ -51,8 +51,8 @@ affine_transform_func(const Device::Pointer & device,
  *  This function is inspired by a similar implementation in Java by Jan Brocher (Biovoxxel) [0] [1]
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be transformed. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be transformed. [const Array::Pointer &]
+ * @param dst Output label image. [Array::Pointer ( = None )]
  * @param number_of_erosions Number of iteration of erosion. [int ( = 5 )]
  * @param outline_sigma Gaussian blur sigma applied before Otsu thresholding. [float ( = 2 )]
  * @return Array::Pointer
@@ -75,8 +75,8 @@ eroded_otsu_labeling_func(const Device::Pointer & device,
  * radians to degrees, use this formula: angle_in_degrees = angle_in_radians / numpy.pi * 180.0
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be transformed. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be transformed. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
  * @param translate_x Translation along x axis in pixels. [float ( = 0 )]
  * @param translate_y Translation along y axis in pixels. [float ( = 0 )]
  * @param translate_z Translation along z axis in pixels. [float ( = 0 )]
@@ -111,8 +111,8 @@ rigid_transform_func(const Device::Pointer & device,
  * formula: angle_in_degrees = angle_in_radians / numpy.pi * 180.0
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be rotated. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be rotated. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
  * @param angle_x Rotation around x axis in degrees. [float ( = 0 )]
  * @param angle_y Rotation around y axis in degrees. [float ( = 0 )]
  * @param angle_z Rotation around z axis in degrees. [float ( = 0 )]
@@ -140,8 +140,8 @@ rotate_func(const Device::Pointer & device,
  * @brief Scale the image by given factors.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be scaleded. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be scaled. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
  * @param factor_x Scaling along x axis. [float ( = 1 )]
  * @param factor_y Scaling along y axis. [float ( = 1 )]
  * @param factor_z Scaling along z axis. [float ( = 1 )]
@@ -169,8 +169,8 @@ scale_func(const Device::Pointer & device,
  * @brief Translate the image by a given vector.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input Array to be translated. [const Array::Pointer &]
- * @param dst Output Array. [Array::Pointer ( = None )]
+ * @param src Input image to be translated. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
  * @param translate_x Translation along x axis in pixels. [float ( = 0 )]
  * @param translate_y Translation along y axis in pixels. [float ( = 0 )]
  * @param translate_z Translation along z axis in pixels. [float ( = 0 )]
@@ -196,8 +196,8 @@ translate_func(const Device::Pointer & device,
  * operation has an octagon as structuring element. Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input label Array. [const Array::Pointer &]
- * @param dst Output label Array. [Array::Pointer ( = None )]
+ * @param src Input label image. [const Array::Pointer &]
+ * @param dst Output label image. [Array::Pointer ( = None )]
  * @param radius Radius size for the closing. [int ( = 0 )]
  * @return Array::Pointer
  *
@@ -215,8 +215,8 @@ closing_labels_func(const Device::Pointer & device, const Array::Pointer & src,
  *  not have the same identifier.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src result [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input image to process [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param radius [int ( = 1 )]
  * @return Array::Pointer
  *
@@ -233,8 +233,8 @@ erode_connected_labels_func(const Device::Pointer & device, const Array::Pointer
  * operation has an octagon as structuring element. Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input label Array. [const Array::Pointer &]
- * @param dst Output label Array. [Array::Pointer ( = None )]
+ * @param src Input label image. [const Array::Pointer &]
+ * @param dst Output label image. [Array::Pointer ( = None )]
  * @param radius Radius size for the opening. [int ( = 0 )]
  * @return Array::Pointer
  *
@@ -253,8 +253,8 @@ opening_labels_func(const Device::Pointer & device, const Array::Pointer & src,
  * Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input intensity Array. [const Array::Pointer &]
- * @param dst Output label Array. [Array::Pointer ( = None )]
+ * @param src Input intensity image. [const Array::Pointer &]
+ * @param dst Output label image. [Array::Pointer ( = None )]
  * @param spot_sigma Controls how close detected cells can be. [float ( = 2 )]
  * @param outline_sigma Controls how precise segmented objects are outlined. [float ( = 2 )]
  * @return Array::Pointer

From 624db19c409d1a1c891b39a12f8c08c63c8ade19 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:26:32 +0200
Subject: [PATCH 11/16] Documentation upgrade tier6

---
 clic/include/tier6.hpp | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/clic/include/tier6.hpp b/clic/include/tier6.hpp
index 522f98912..eab8ef013 100644
--- a/clic/include/tier6.hpp
+++ b/clic/include/tier6.hpp
@@ -16,8 +16,8 @@ namespace cle::tier6
  * scikitimage [2] and MorpholibJ[3] Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src label image to erode [const Array::Pointer &]
- * @param dst result [Array::Pointer ( = None )]
+ * @param src Input label image to erode [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param radius [int ( = 2 )]
  * @return Array::Pointer
  *
@@ -35,10 +35,10 @@ dilate_labels_func(const Device::Pointer & device, const Array::Pointer & src, A
  * identifier. Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src result [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param radius [int ( = 1 )]
- * @param relabel and all label indices exist. [bool ( = False )]
+ * @param relabel Relabel the image, e.g. if object disappear or split. [bool ( = False )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'in assistant'
@@ -60,7 +60,7 @@ erode_labels_func(const Device::Pointer & device,
  *  thresholded binary image is flooded using the Voronoi tesselation approach starting from the found local maxima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 intensity image to add labels [const Array::Pointer &]
+ * @param src0 Intensity image to segment [const Array::Pointer &]
  * @param dst Output label image. [Array::Pointer ( = None )]
  * @param outline_sigma Gaussian blur sigma along all axes [float ( = 0 )]
  * @return Array::Pointer
@@ -82,9 +82,9 @@ gauss_otsu_labeling_func(const Device::Pointer & device,
  * touch. The region growing is limited to a masked area. The resulting label map is written to the output.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param mask [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input binary image [const Array::Pointer &]
+ * @param mask Input mask [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label'
@@ -103,8 +103,8 @@ masked_voronoi_labeling_func(const Device::Pointer & device,
  * touch. The resulting label map is written to the output.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param input_binary [const Array::Pointer &]
- * @param output_labels [Array::Pointer ( = None )]
+ * @param input_binary Input binary image  [const Array::Pointer &]
+ * @param output_labels Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label', 'in assistant', 'bia-bob-suggestion'
@@ -120,7 +120,7 @@ voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & inp
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param minimum_size Smallest size object allowed. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -139,7 +139,7 @@ remove_small_labels_func(const Device::Pointer & device,
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param maximum_size Largest size object to exclude. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -154,11 +154,11 @@ exclude_small_labels_func(const Device::Pointer & device,
 
 /**
  * @name remove_large_labels
- * @brief Removes labelled objects bigger than a given size (in pixels) from a label map.
+ * @brief Removes labeled objects bigger than a given size (in pixels) from a label map.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param maximum_size Biggest size object allowed. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -177,7 +177,7 @@ remove_large_labels_func(const Device::Pointer & device,
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param minimum_size Smallest size object to keep. [float ( = 100 )]
  * @return Array::Pointer
  *

From 45fb1ed2ad35911c30e3536aef689a1654b955f3 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:26:40 +0200
Subject: [PATCH 12/16] Documentation update tier5

---
 clic/include/tier5.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clic/include/tier5.hpp b/clic/include/tier5.hpp
index 731377a91..481f322ed 100644
--- a/clic/include/tier5.hpp
+++ b/clic/include/tier5.hpp
@@ -16,8 +16,8 @@ namespace cle::tier5
  * False. True otherwise This function is supposed to work similarly like its counterpart in numpy [1].
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First array to compare [const Array::Pointer &]
+ * @param src1 Second array to compare [const Array::Pointer &]
  * @return bool
  *
  * @note 'combine'

From 8c80092d8c04ba2db1979c93db630302e7acc1b7 Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:28:24 +0200
Subject: [PATCH 13/16] documentation update tier4

---
 clic/include/tier4.hpp | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 0df81fa9f..4297cec76 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -17,8 +17,8 @@ namespace cle::tier4
  *  an array of 6 values as follows: minX, minY, minZ, maxX, maxY, maxZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param label_id [int]
+ * @param src Label image [const Array::Pointer &]
+ * @param label_id Identifier of label [int]
  * @return std::vector<float>
  *
  * @see https://clij.github.io/clij2-docs/reference_boundingBox
@@ -33,8 +33,8 @@ label_bounding_box_func(const Device::Pointer & device, const Array::Pointer & s
  * Results table in the column 'MSE'.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First image to compare [const Array::Pointer &]
+ * @param src1 Second image to compare [const Array::Pointer &]
  * @return float
  *
  * @note 'in assistant', 'combine', 'bia-bob-suggestion'
@@ -51,8 +51,8 @@ mean_squared_error_func(const Device::Pointer & device, const Array::Pointer & s
  * pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input binary image of spots [const Array::Pointer &]
+ * @param dst Output coordinate list of spots [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_spotsToPointList
@@ -70,7 +70,7 @@ spots_to_pointlist_func(const Device::Pointer & device, const Array::Pointer & s
  * performed on the CPU.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image. [const Array::Pointer &]
+ * @param src Input label image. [const Array::Pointer &]
  * @param dst Output label image. [Array::Pointer ( = None )]
  * @param blocksize Renumbering is done in blocks for performance reasons. [int ( = 4096 )]
  * @return Array::Pointer

From 2059dcda15cf8d8937a604b3a3412ae77eb5cc6d Mon Sep 17 00:00:00 2001
From: Robert Haase <haesleinhuepf@users.noreply.github.com>
Date: Thu, 17 Oct 2024 13:32:30 +0200
Subject: [PATCH 14/16] documentation update tier3

---
 clic/include/tier3.hpp | 50 +++++++++++++++++++++---------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/clic/include/tier3.hpp b/clic/include/tier3.hpp
index 27d2303cd..844903ea1 100644
--- a/clic/include/tier3.hpp
+++ b/clic/include/tier3.hpp
@@ -17,7 +17,7 @@ namespace cle::tier3
  *  an array of 6 values as follows: minX, minY, minZ, maxX, maxY, maxZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
+ * @param src Input binary image [const Array::Pointer &]
  * @return std::vector<float>
  *
  * @see https://clij.github.io/clij2-docs/reference_boundingBox
@@ -33,7 +33,7 @@ bounding_box_func(const Device::Pointer & device, const Array::Pointer & src) ->
  * columns MassX, MassY and MassZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
+ * @param src Input image [const Array::Pointer &]
  * @return std::vector<float>
  * @see https://clij.github.io/clij2-docs/reference_centerOfMass
  *
@@ -50,9 +50,9 @@ center_of_mass_func(const Device::Pointer & device, const Array::Pointer & src)
  * renumbered to 1 and 2.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param list [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_excludeLabels
@@ -72,9 +72,9 @@ remove_labels_func(const Device::Pointer & device,
  * renumbered to 1 and 2.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param list [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_excludeLabels
@@ -92,8 +92,8 @@ exclude_labels_func(const Device::Pointer & device,
  * renumbered afterwards.
  *
  * @param device Device to perform the operation on. [const Device::Pointer & ( = None )]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image[Array::Pointer ( = None )]
  * @param exclude_x Exclude labels along min and max x [bool ( = True )]
  * @param exclude_y Exclude labels along min and max y [bool ( = True )]
  * @param exclude_z Exclude labels along min and max z [bool ( = True )]
@@ -116,8 +116,8 @@ remove_labels_on_edges_func(const Device::Pointer & device,
  * renumbered afterwards.
  *
  * @param device Device to perform the operation on. [const Device::Pointer & ( = None )]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param exclude_x Exclude labels along min and max x [bool ( = True )]
  * @param exclude_y Exclude labels along min and max y [bool ( = True )]
  * @param exclude_z Exclude labels along min and max z [bool ( = True )]
@@ -157,8 +157,8 @@ flag_existing_labels_func(const Device::Pointer & device, const Array::Pointer &
  * gamma g is computed, before normlization is reversed (^ is the power operator):f(x) = (x / max(X)) ^ gamma * max(X)
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input image [const Array::Pointer &]
+ * @param dst Output image [Array::Pointer ( = None )]
  * @param gamma [float ( = 1 )]
  * @return Array::Pointer
  *
@@ -177,9 +177,9 @@ gamma_correction_func(const Device::Pointer & device, const Array::Pointer & src
  * touching then the pixel (3,4) in the matrix will be set to 1.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src0 First input label image [const Array::Pointer &]
+ * @param src1 Second input label image [const Array::Pointer &]
+ * @param dst Output overlap matrix [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_generateBinaryOverlapMatrix
@@ -200,8 +200,8 @@ generate_binary_overlap_matrix_func(const Device::Pointer & device,
  * adjacency graph
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output touch matrix [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_generateTouchMatrix
@@ -234,8 +234,8 @@ generate_touch_matrix_func(const Device::Pointer & device, const Array::Pointer
  * http://www.openclprogrammingguide.com
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input image to derive histogram from [const Array::Pointer &]
+ * @param dst Output histogram [Array::Pointer ( = None )]
  * @param num_bins [int ( = 256 )]
  * @param minimum_intensity [float ( = None )]
  * @param maximum_intensity [float ( = None )]
@@ -261,8 +261,8 @@ histogram_func(const Device::Pointer & device,
  * + 1)</pre>
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First binary image to compare [const Array::Pointer &]
+ * @param src1 Second binary image to compare[const Array::Pointer &]
  * @return float
  *
  * @see https://clij.github.io/clij2-docs/reference_jaccardIndex
@@ -279,8 +279,8 @@ jaccard_index_func(const Device::Pointer & device, const Array::Pointer & src0,
  * contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output coordinate list [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_labelledSpotsToPointList

From 5ea536d1796749a9f80cc176f0e522d85b53ed38 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <Stephane.rigaud@pasteur.fr>
Date: Thu, 17 Oct 2024 13:59:29 +0200
Subject: [PATCH 15/16] Update clic/include/tier3.hpp

Signed-off-by: Stephane Rigaud <Stephane.rigaud@pasteur.fr>
---
 clic/include/tier3.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clic/include/tier3.hpp b/clic/include/tier3.hpp
index 844903ea1..ae84ef62e 100644
--- a/clic/include/tier3.hpp
+++ b/clic/include/tier3.hpp
@@ -262,7 +262,7 @@ histogram_func(const Device::Pointer & device,
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src0 First binary image to compare [const Array::Pointer &]
- * @param src1 Second binary image to compare[const Array::Pointer &]
+ * @param src1 Second binary image to compare [const Array::Pointer &]
  * @return float
  *
  * @see https://clij.github.io/clij2-docs/reference_jaccardIndex

From 745d8757f9baea50c0dde045fae031b8d68e07a3 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Thu, 17 Oct 2024 14:14:45 +0200
Subject: [PATCH 16/16] fix: statistic now take label as second param

---
 clic/src/tier4/centroids_of_labels.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clic/src/tier4/centroids_of_labels.cpp b/clic/src/tier4/centroids_of_labels.cpp
index 0a5439399..0c8931c67 100644
--- a/clic/src/tier4/centroids_of_labels.cpp
+++ b/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, label_image, nullptr);
+    props = tier3::statistics_of_background_and_labelled_pixels_func(device, label_image, label_image);
   }
   else
   {
-    props = tier3::statistics_of_labelled_pixels_func(device, label_image, nullptr);
+    props = tier3::statistics_of_labelled_pixels_func(device, label_image, label_image);
   }
   auto centroid_x = props["centroid_x"];
   auto centroid_y = props["centroid_y"];