From 6ec60a5cc136fbdfd8938353fecee3d838a4246b Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 10:15:00 +0300
Subject: [PATCH 01/14] legacy with prototype

---
 clic/include/tier1.hpp            | 41 +++++++++++++++++++++++++++++++
 clic/src/tier1/replace_value.cpp  | 30 ----------------------
 clic/src/tier1/replace_values.cpp | 35 ++++++++++++++++++++++++++
 3 files changed, 76 insertions(+), 30 deletions(-)
 delete mode 100644 clic/src/tier1/replace_value.cpp

diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
index 91aec19f4..80caf34c3 100644
--- a/clic/include/tier1.hpp
+++ b/clic/include/tier1.hpp
@@ -2059,6 +2059,47 @@ replace_value_func(const Device::Pointer & device,
                    float                   scalar0,
                    float                   scalar1) -> Array::Pointer;
 
+/**
+ * @name replace_intensity
+ * @brief Replaces a specific intensity in an image with a given new value.
+ *
+ * @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 scalar0 Old value. [float ( = 0 )]
+ * @param scalar1 New value. [float ( = 1 )]
+ * @return Array::Pointer
+ * @see https://clij.github.io/clij2-docs/reference_replaceIntensity
+ * @deprecated This function is deprecated. Consider using replace_value() instead.
+ */
+auto
+replace_intensity_func(const Device::Pointer & device,
+                       const Array::Pointer &  src,
+                       Array::Pointer          dst,
+                       float                   scalar0,
+                       float                   scalar1) -> Array::Pointer;
+
+/**
+ * @name replace_intensities
+ * @brief Replaces integer intensities specified in a vector image. The values are passed as a vector of values.
+ * The vector index represents the old intensity and the value at that position represents the new intensity.s
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src0 Input image to process. [const Array::Pointer &]
+ * @param src1 List of intensities to replace, as a vector of values. [const Array::Pointer &]
+ * @param dst Output result image. [Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_replaceIntensities
+ * @deprecated This function is deprecated. Consider using replace_values() instead.
+ */
+auto
+replace_intensities_func(const Device::Pointer & device,
+                         const Array::Pointer &  src0,
+                         const Array::Pointer &  src1,
+                         Array::Pointer          dst) -> Array::Pointer;
+
 /**
  * @name maximum_sphere
  * @brief Computes the local maximum of a pixels spherical neighborhood. The spheres size is specified by its halfwidth,
diff --git a/clic/src/tier1/replace_value.cpp b/clic/src/tier1/replace_value.cpp
deleted file mode 100644
index 5fc464125..000000000
--- a/clic/src/tier1/replace_value.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
-#include "tier0.hpp"
-#include "tier1.hpp"
-
-#include "utils.hpp"
-
-#include "cle_replace_value.h"
-#include "cle_replace_values.h"
-
-namespace cle::tier1
-{
-
-auto
-replace_value_func(const Device::Pointer & device,
-                   const Array::Pointer &  src,
-                   Array::Pointer          dst,
-                   float                   scalar0,
-                   float                   scalar1) -> Array::Pointer
-{
-  tier0::create_like(src, dst);
-  const KernelInfo    kernel = { "replace_value", kernel::replace_value };
-  const ParameterList params = { { "src", src }, { "dst", dst }, { "scalar0", scalar0 }, { "scalar1", scalar1 } };
-  const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
-  execute(device, kernel, params, range);
-  return dst;
-}
-
-// resample_func
-// touch_matrix_to_mesh_func
-
-} // namespace cle::tier1
diff --git a/clic/src/tier1/replace_values.cpp b/clic/src/tier1/replace_values.cpp
index e6d743c84..0e35cac12 100644
--- a/clic/src/tier1/replace_values.cpp
+++ b/clic/src/tier1/replace_values.cpp
@@ -3,6 +3,7 @@
 
 #include "utils.hpp"
 
+#include "cle_replace_value.h"
 #include "cle_replace_values.h"
 
 namespace cle::tier1
@@ -22,4 +23,38 @@ replace_values_func(const Device::Pointer & device,
   return dst;
 }
 
+auto
+replace_value_func(const Device::Pointer & device,
+                   const Array::Pointer &  src,
+                   Array::Pointer          dst,
+                   float                   scalar0,
+                   float                   scalar1) -> Array::Pointer
+{
+  tier0::create_like(src, dst);
+  const KernelInfo    kernel = { "replace_value", kernel::replace_value };
+  const ParameterList params = { { "src", src }, { "dst", dst }, { "scalar0", scalar0 }, { "scalar1", scalar1 } };
+  const RangeArray    range = { dst->width(), dst->height(), dst->depth() };
+  execute(device, kernel, params, range);
+  return dst;
+}
+
+auto
+replace_intensity_func(const Device::Pointer & device,
+                       const Array::Pointer &  src,
+                       Array::Pointer          dst,
+                       float                   scalar0,
+                       float                   scalar1) -> Array::Pointer
+{
+  return replace_value_func(device, src, dst, scalar0, scalar1);
+}
+
+auto
+replace_intensities_func(const Device::Pointer & device,
+                         const Array::Pointer &  src0,
+                         const Array::Pointer &  src1,
+                         Array::Pointer          dst) -> Array::Pointer
+{
+  return replace_values_func(device, src0, src1, dst);
+}
+
 } // namespace cle::tier1

From d90255b103dec5d778232882d2a8f9cc4c0c9546 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 10:15:41 +0300
Subject: [PATCH 02/14] fix statistic function

---
 clic/include/statistics.hpp                   |  3 +-
 clic/include/tier3.hpp                        | 30 +++++++++++++++----
 clic/src/statistics.cpp                       |  5 ++--
 .../tier3/statistics_of_labelled_pixels.cpp   | 26 +++++++++++-----
 tests/tier3/test_label_statistics.cpp         |  8 ++---
 5 files changed, 50 insertions(+), 22 deletions(-)

diff --git a/clic/include/statistics.hpp b/clic/include/statistics.hpp
index 3b036dc81..a8d2365a5 100644
--- a/clic/include/statistics.hpp
+++ b/clic/include/statistics.hpp
@@ -14,8 +14,7 @@ using StatisticsMap = std::unordered_map<std::string, std::vector<float>>;
 auto
 compute_statistics_per_labels(const Device::Pointer & device,
                               const Array::Pointer &  label,
-                              const Array::Pointer &  intensity,
-                              size_t                  offset) -> StatisticsMap;
+                              const Array::Pointer &  intensity) -> StatisticsMap;
 
 auto
 _statistics_per_label(const Device::Pointer & device,
diff --git a/clic/include/tier3.hpp b/clic/include/tier3.hpp
index 423d8ca68..a4540172c 100644
--- a/clic/include/tier3.hpp
+++ b/clic/include/tier3.hpp
@@ -368,16 +368,36 @@ morphological_chan_vese_func(const Device::Pointer & device,
  * The intensity image is optional and set to 0 if not provided.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image to compute the statistics. [const Array::Pointer &]]
+ * @param label Label image to compute the statistics. [const Array::Pointer &]]
  * @param intensity Intensity image. [Array::Pointer ( = None )]
- * @param withBG Include the background label in the statistics. [bool ( = False )]
  * @return StatisticsMap
+ *
+ * @see https://clij.github.io/clij2-docs/reference_statisticsOfLabelledPixels
  */
 auto
 statistics_of_labelled_pixels_func(const Device::Pointer & device,
-                                   const Array::Pointer &  src,
-                                   Array::Pointer          intensity,
-                                   bool                    withBG) -> StatisticsMap;
+                                   const Array::Pointer &  label,
+                                   Array::Pointer          intensity) -> 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.
+ *
+ * @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 )]
+ * @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;
 
 } // namespace cle::tier3
 
diff --git a/clic/src/statistics.cpp b/clic/src/statistics.cpp
index d7baf9f5a..067ad00ed 100644
--- a/clic/src/statistics.cpp
+++ b/clic/src/statistics.cpp
@@ -77,13 +77,12 @@ _std_per_label(const Device::Pointer & device,
 auto
 compute_statistics_per_labels(const Device::Pointer & device,
                               const Array::Pointer &  label,
-                              const Array::Pointer &  intensity,
-                              size_t                  offset) -> StatisticsMap
+                              const Array::Pointer &  intensity) -> StatisticsMap
 {
 
 
   // initialize variables, output, and constants
-  // const size_t     offset= 0; // skip the bg label with value 0
+  const size_t     offset = 1;
   const size_t     nb_labels = static_cast<size_t>(tier2::maximum_of_all_pixels_func(device, label)) + offset;
   const size_t     nb_measurements = nb_labels - offset;
   const RangeArray origin = { 0, 0, 0 };
diff --git a/clic/src/tier3/statistics_of_labelled_pixels.cpp b/clic/src/tier3/statistics_of_labelled_pixels.cpp
index 96b3ec96c..3060ea2d6 100644
--- a/clic/src/tier3/statistics_of_labelled_pixels.cpp
+++ b/clic/src/tier3/statistics_of_labelled_pixels.cpp
@@ -7,22 +7,32 @@ namespace cle::tier3
 
 auto
 statistics_of_labelled_pixels_func(const Device::Pointer & device,
-                                   const Array::Pointer &  src,
-                                   Array::Pointer          intensity,
-                                   bool                    withBG) -> StatisticsMap
+                                   const Array::Pointer &  label,
+                                   Array::Pointer          intensity) -> StatisticsMap
 {
-  // create intensity if not set
   if (intensity == nullptr)
   {
     // std::cerr << "Warning: no intensity was provided. Pixels intensity will be set to their label value." <<
     // std::endl;
-    tier0::create_like(src, intensity, dType::FLOAT);
+    tier0::create_like(label, intensity, dType::FLOAT);
     intensity->fill(0);
-    // tier1::copy_func(device, label, intensity);
   }
 
-  size_t offset = (withBG) ? 0 : 1;
-  return compute_statistics_per_labels(device, src, intensity, offset);
+  return compute_statistics_per_labels(device, label, intensity);
+}
+
+
+auto
+statistics_of_background_and_labelled_pixels_func(const Device::Pointer & device,
+                                                  const Array::Pointer &  label,
+                                                  const Array::Pointer &  intensity) -> StatisticsMap
+{
+  auto               temp = tier1::add_image_and_scalar_func(device, label, nullptr, 1);
+  auto               props = tier3::statistics_of_labelled_pixels_func(device, temp, intensity);
+  std::vector<float> labels = props["label"];
+  std::transform(labels.begin(), labels.end(), labels.begin(), [](float label) { return label - 1; });
+  props["label"] = labels;
+  return props;
 }
 
 
diff --git a/tests/tier3/test_label_statistics.cpp b/tests/tier3/test_label_statistics.cpp
index b76db440e..03cdcd856 100644
--- a/tests/tier3/test_label_statistics.cpp
+++ b/tests/tier3/test_label_statistics.cpp
@@ -84,7 +84,7 @@ TEST_P(TestStatisticsOfLabelledPixels, execute2D)
   gpu_labels->writeFrom(labels.data());
 
   // passing labels also as intensity image to have a simpler test
-  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_intensity, false);
+  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_intensity);
 
   // Test bounding box min/max (x, y, z)
   std::vector<float> expected_bbox_min_x = { 0, 1, 0 };
@@ -150,7 +150,7 @@ TEST_P(TestStatisticsOfLabelledPixels, execute3D)
   auto gpu_labels = cle::Array::create(3, 2, 3, 3, cle::dType::FLOAT, cle::mType::BUFFER, device);
   gpu_labels->writeFrom(labels.data());
 
-  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_intensity, false);
+  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_intensity);
 
   // Test bounding box min/max (x, y, z)
   std::vector<float> expected_bbox_min_x = { 0, 1, 0 };
@@ -235,7 +235,7 @@ TEST_P(TestStatisticsOfLabelledPixels, shape)
   gpu_labels->writeFrom(labels.data());
 
   // passing labels also as intensity image to have a simpler test
-  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_labels, false);
+  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_labels);
 
   // Test bounding box min/max (x, y, z)
   std::vector<float> expected_bbox_min_x = { 0 };
@@ -301,7 +301,7 @@ TEST_P(TestStatisticsOfLabelledPixels, standard_deviation)
   auto gpu_labels = cle::Array::create(3, 3, 1, 3, cle::dType::FLOAT, cle::mType::BUFFER, device);
   gpu_labels->writeFrom(labels.data());
 
-  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_image, false);
+  auto region_props = cle::tier3::statistics_of_labelled_pixels_func(device, gpu_labels, gpu_image);
 
   // print_stats_dict(region_props);
 

From ea14517794671c651270cee4a4800e270243d861 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 10:15:58 +0300
Subject: [PATCH 03/14] update other filter using stats

---
 clic/src/tier4/filter_label_by_size.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clic/src/tier4/filter_label_by_size.cpp b/clic/src/tier4/filter_label_by_size.cpp
index 89a779fe2..448741bc2 100644
--- a/clic/src/tier4/filter_label_by_size.cpp
+++ b/clic/src/tier4/filter_label_by_size.cpp
@@ -18,7 +18,7 @@ filter_label_by_size_func(const Device::Pointer & device,
                           float                   max_size) -> Array::Pointer
 {
   tier0::create_like(src, dst, dType::LABEL);
-  auto stats = tier3::statistics_of_labelled_pixels_func(device, src, nullptr, true);
+  auto stats = tier3::statistics_of_background_and_labelled_pixels_func(device, src, nullptr);
 
   const auto nb_labels = stats["label"].size();
   auto       list_of_area = Array::create(nb_labels, 1, 1, 1, dType::FLOAT, mType::BUFFER, device);

From 4430a05360175c8ca22a5ea6b05952f6b0d51e10 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 10:16:13 +0300
Subject: [PATCH 04/14] add pixel count map

---
 clic/include/tier4.hpp                    | 19 ++++++++
 clic/src/tier4/label_pixel_count_map.cpp  | 48 ++++++++++++++++++++
 tests/tier4/test_label_pixelcount_map.cpp | 53 +++++++++++++++++++++++
 3 files changed, 120 insertions(+)
 create mode 100644 clic/src/tier4/label_pixel_count_map.cpp
 create mode 100644 tests/tier4/test_label_pixelcount_map.cpp

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 2e56f308a..1986dfaeb 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -126,6 +126,25 @@ filter_label_by_size_func(const Device::Pointer & device,
                           float                   max_size) -> Array::Pointer;
 
 
+/**
+ * @name label_pixel_count_map
+ * @brief Takes a label map, determines the number of pixels per label and replaces every label with the that number.
+ * This results in a parametric image expressing area or volume.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Label image to measure [const Array::Pointer &]
+ * @param dst Parametric image computed[Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'label measurement', 'map', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_pixelCountMap
+ */
+auto
+label_pixel_count_map_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst) -> Array::Pointer;
+
+
 } // namespace cle::tier4
 
 #endif // __INCLUDE_TIER4_HPP
diff --git a/clic/src/tier4/label_pixel_count_map.cpp b/clic/src/tier4/label_pixel_count_map.cpp
new file mode 100644
index 000000000..eed24658b
--- /dev/null
+++ b/clic/src/tier4/label_pixel_count_map.cpp
@@ -0,0 +1,48 @@
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+#include "tier3.hpp"
+#include "tier4.hpp"
+
+#include "utils.hpp"
+
+namespace cle::tier4
+{
+
+/**
+ * @name label_pixel_count_map
+ * @brief Takes a label map, determines the number of pixels per label and replaces every label with the that number.
+ * This results in a parametric image expressing area or volume.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Label image to measure [const Array::Pointer &]
+ * @param dst Parametric image computed[Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'label measurement', 'map', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_pixelCountMap
+ */
+auto
+label_pixel_count_map_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst) -> Array::Pointer
+{
+  tier0::create_like(src, dst, dType::FLOAT);
+  auto props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
+
+  for (auto && i : props["area"])
+  {
+    std::cout << i << std::endl;
+  }
+
+
+  auto values = cle::Array::create(props["area"].size(), 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
+  values->writeFrom(props["area"].data());
+
+  cle::print<float>(values, "values");
+  tier1::set_column_func(device, values, 0, 0);
+  return tier1::replace_values_func(device, src, values, dst);
+}
+
+
+} // namespace cle::tier4
diff --git a/tests/tier4/test_label_pixelcount_map.cpp b/tests/tier4/test_label_pixelcount_map.cpp
new file mode 100644
index 000000000..9f620c7b3
--- /dev/null
+++ b/tests/tier4/test_label_pixelcount_map.cpp
@@ -0,0 +1,53 @@
+#include "cle.hpp"
+
+#include <array>
+#include <gtest/gtest.h>
+
+class TestLabelPixelCountMap : public ::testing::TestWithParam<std::string>
+{
+protected:
+  std::array<uint32_t, 6 * 5 * 1> input = { 1, 1, 2, 0, 3, 3, 1, 1, 2, 0, 3, 3, 0, 0, 0,
+                                            0, 0, 0, 4, 4, 5, 6, 6, 6, 4, 4, 5, 6, 6, 6 };
+
+  std::array<float, 6 * 5 * 1> valid = { 4, 4, 2, 0, 4, 4, 4, 4, 2, 0, 4, 4, 0, 0, 0,
+                                         0, 0, 0, 4, 4, 2, 6, 6, 6, 4, 4, 2, 6, 6, 6 };
+};
+
+TEST_P(TestLabelPixelCountMap, execute2d)
+{
+
+  std::string param = GetParam();
+  cle::BackendManager::getInstance().setBackend(param);
+  auto device = cle::BackendManager::getInstance().getBackend().getDevice("", "all");
+  device->setWaitToFinish(true);
+
+  auto gpu_input = cle::Array::create(6, 5, 1, 2, cle::dType::LABEL, cle::mType::BUFFER, device);
+  gpu_input->writeFrom(input.data());
+
+  auto gpu_output = cle::tier4::label_pixel_count_map_func(device, gpu_input, nullptr);
+
+  cle::print<float>(gpu_output);
+
+  std::vector<float> output(gpu_output->size());
+  gpu_output->readTo(output.data());
+  //   for (int i = 0; i < output.size(); i++)
+  //   {
+  //     EXPECT_EQ(output[i], valid[i]);
+  //   }
+}
+
+
+std::vector<std::string>
+getParameters()
+{
+  std::vector<std::string> parameters;
+#if USE_OPENCL
+  parameters.push_back("opencl");
+#endif
+#if USE_CUDA
+  parameters.push_back("cuda");
+#endif
+  return parameters;
+}
+
+INSTANTIATE_TEST_SUITE_P(InstantiationName, TestLabelPixelCountMap, ::testing::ValuesIn(getParameters()));

From 0bcfe8adad18dad3b1666926f84ba920f2edc94d Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 11:42:01 +0300
Subject: [PATCH 05/14] add centroids of labels

---
 clic/include/tier4.hpp                   | 16 ++++++++
 clic/src/tier4/centroids_of_labels.cpp   | 40 +++++++++++++++++++
 tests/tier4/test_centroids_of_labels.cpp | 51 ++++++++++++++++++++++++
 3 files changed, 107 insertions(+)
 create mode 100644 clic/src/tier4/centroids_of_labels.cpp
 create mode 100644 tests/tier4/test_centroids_of_labels.cpp

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 1986dfaeb..574ed0704 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -145,6 +145,22 @@ label_pixel_count_map_func(const Device::Pointer & device,
                            Array::Pointer          dst) -> Array::Pointer;
 
 
+/**
+ * @name centroids_of_labels
+ * @brief Determines the centroids of all labels in a label image or image stack.
+ * It writes the resulting coordinates in point list image of dimensions n * d
+ * 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 withBG Determines if the background label should be included. [bool ( = false )]
+ */
+auto
+centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, bool withBG)
+  -> Array::Pointer;
+
+
 } // namespace cle::tier4
 
 #endif // __INCLUDE_TIER4_HPP
diff --git a/clic/src/tier4/centroids_of_labels.cpp b/clic/src/tier4/centroids_of_labels.cpp
new file mode 100644
index 000000000..92532d406
--- /dev/null
+++ b/clic/src/tier4/centroids_of_labels.cpp
@@ -0,0 +1,40 @@
+
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+#include "tier3.hpp"
+#include "tier4.hpp"
+
+#include "utils.hpp"
+#include <numeric>
+
+namespace cle::tier4
+{
+
+auto
+centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, bool withBG)
+  -> Array::Pointer
+{
+  cle::StatisticsMap props;
+  if (withBG)
+  {
+    props = tier3::statistics_of_background_and_labelled_pixels_func(device, src, nullptr);
+  }
+  else
+  {
+    props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
+  }
+  auto centroid_x = props["centroid_x"];
+  auto centroid_y = props["centroid_y"];
+  auto centroid_z = props["centroid_z"];
+  auto nb_labels = centroid_x.size();
+
+  auto res = Array::create(nb_labels, 3, 1, 1, dType::FLOAT, mType::BUFFER, device);
+  res->writeFrom(centroid_x.data(), { nb_labels, 1, 1 }, { 0, 0, 0 });
+  res->writeFrom(centroid_y.data(), { nb_labels, 1, 1 }, { 0, 1, 0 });
+  res->writeFrom(centroid_z.data(), { nb_labels, 1, 1 }, { 0, 2, 0 });
+  return res;
+}
+
+
+} // namespace cle::tier4
diff --git a/tests/tier4/test_centroids_of_labels.cpp b/tests/tier4/test_centroids_of_labels.cpp
new file mode 100644
index 000000000..ea189bde0
--- /dev/null
+++ b/tests/tier4/test_centroids_of_labels.cpp
@@ -0,0 +1,51 @@
+#include "cle.hpp"
+
+#include <array>
+#include <gtest/gtest.h>
+
+class TestCentroidsOfLabels : public ::testing::TestWithParam<std::string>
+{
+protected:
+  std::array<uint32_t, 6 * 5 * 1> input = { 1, 1, 2, 0, 3, 3, 1, 1, 2, 0, 3, 3, 0, 0, 0,
+                                            0, 0, 0, 4, 4, 5, 6, 6, 6, 4, 4, 5, 6, 6, 6 };
+
+  std::array<float, 7 * 3 * 1> valid = { 2.625, 0.5, 2,   4.5, 0.5, 2, 4, 1.625, 0.5, 0.5, 0.5,
+                                         3.5,   3.5, 3.5, 0,   0,   0, 0, 0,     0,   0 };
+};
+
+TEST_P(TestCentroidsOfLabels, execute2d)
+{
+
+  std::string param = GetParam();
+  cle::BackendManager::getInstance().setBackend(param);
+  auto device = cle::BackendManager::getInstance().getBackend().getDevice("", "all");
+  device->setWaitToFinish(true);
+
+  auto gpu_input = cle::Array::create(6, 5, 1, 2, cle::dType::LABEL, cle::mType::BUFFER, device);
+  gpu_input->writeFrom(input.data());
+
+  auto gpu_output = cle::tier4::centroids_of_labels_func(device, gpu_input, nullptr, true);
+
+  std::vector<float> output(gpu_output->size());
+  gpu_output->readTo(output.data());
+  for (int i = 0; i < output.size(); i++)
+  {
+    EXPECT_EQ(output[i], valid[i]);
+  }
+}
+
+
+std::vector<std::string>
+getParameters()
+{
+  std::vector<std::string> parameters;
+#if USE_OPENCL
+  parameters.push_back("opencl");
+#endif
+#if USE_CUDA
+  parameters.push_back("cuda");
+#endif
+  return parameters;
+}
+
+INSTANTIATE_TEST_SUITE_P(InstantiationName, TestCentroidsOfLabels, ::testing::ValuesIn(getParameters()));

From 6bdab9629a963b166192e550aadd2d3d720a1bed Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 17 Sep 2024 17:56:03 +0300
Subject: [PATCH 06/14] add reduce labels to centroids

---
 clic/include/tier5.hpp                        | 18 +++++++
 clic/src/tier5/reduce_labels_to_centroids.cpp | 30 +++++++++++
 .../tier5/test_reduce_labels_to_centroids.cpp | 50 +++++++++++++++++++
 3 files changed, 98 insertions(+)
 create mode 100644 clic/src/tier5/reduce_labels_to_centroids.cpp
 create mode 100644 tests/tier5/test_reduce_labels_to_centroids.cpp

diff --git a/clic/include/tier5.hpp b/clic/include/tier5.hpp
index 402c2293f..2d40ea789 100644
--- a/clic/include/tier5.hpp
+++ b/clic/include/tier5.hpp
@@ -162,6 +162,24 @@ exclude_large_labels_func(const Device::Pointer & device,
                           float                   min_size) -> Array::Pointer;
 
 
+/**
+ * @name reduce_labels_to_centroids
+ * @brief Take a label map and reduce each label to its centroid.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Label image to reduce. [const Array::Pointer &]
+ * @param dst Output label image with centroids. [Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_reduceLabelsToCentroids
+ */
+auto
+reduce_labels_to_centroids_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                Array::Pointer          dst) -> Array::Pointer;
+
+
 } // namespace cle::tier5
 
 #endif // __INCLUDE_TIER5_HPP
diff --git a/clic/src/tier5/reduce_labels_to_centroids.cpp b/clic/src/tier5/reduce_labels_to_centroids.cpp
new file mode 100644
index 000000000..5d97dc4e4
--- /dev/null
+++ b/clic/src/tier5/reduce_labels_to_centroids.cpp
@@ -0,0 +1,30 @@
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+#include "tier3.hpp"
+#include "tier4.hpp"
+#include "tier5.hpp"
+
+#include "utils.hpp"
+
+namespace cle::tier5
+{
+
+auto
+reduce_labels_to_centroids_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                Array::Pointer          dst) -> Array::Pointer
+{
+  tier0::create_like(src, dst, dType::LABEL);
+  dst->fill(0);
+
+  auto pos = tier4::centroids_of_labels_func(device, src, dst, true);
+  auto label_pos = Array::create(pos->width(), 4, 1, 2, dType::FLOAT, mType::BUFFER, device);
+  tier1::set_ramp_x_func(device, label_pos);
+  pos->copyTo(label_pos, { pos->width(), 3, 1 }, { 0, 0, 0 }, { 0, 0, 0 });
+
+  tier1::set_column_func(device, label_pos, 0, -1);
+  return tier1::write_values_to_positions_func(device, label_pos, dst);
+}
+
+} // namespace cle::tier5
diff --git a/tests/tier5/test_reduce_labels_to_centroids.cpp b/tests/tier5/test_reduce_labels_to_centroids.cpp
new file mode 100644
index 000000000..3ab68b1ad
--- /dev/null
+++ b/tests/tier5/test_reduce_labels_to_centroids.cpp
@@ -0,0 +1,50 @@
+#include "cle.hpp"
+
+#include <array>
+#include <gtest/gtest.h>
+
+class TestReduceLabelToCentroids : public ::testing::TestWithParam<std::string>
+{
+protected:
+  const std::array<uint32_t, 6 * 6 * 1> input = {
+    0, 0, 0, 1, 1, 1, 0, 2, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 3, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4,
+  };
+  const std::array<uint32_t, 6 * 6 * 1> valid = {
+    0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0,
+  };
+  std::array<uint32_t, 6 * 6 * 1> output;
+};
+
+TEST_P(TestReduceLabelToCentroids, executeBox)
+{
+  std::string param = GetParam();
+  cle::BackendManager::getInstance().setBackend(param);
+  auto device = cle::BackendManager::getInstance().getBackend().getDevice("", "all");
+  device->setWaitToFinish(true);
+
+  auto gpu_input = cle::Array::create(6, 6, 1, 3, cle::dType::LABEL, cle::mType::BUFFER, device);
+  gpu_input->writeFrom(input.data());
+
+  auto gpu_output = cle::tier5::reduce_labels_to_centroids_func(device, gpu_input, nullptr);
+
+  gpu_output->readTo(output.data());
+  for (int i = 0; i < output.size(); i++)
+  {
+    EXPECT_EQ(output[i], valid[i]);
+  }
+}
+
+std::vector<std::string>
+getParameters()
+{
+  std::vector<std::string> parameters;
+#if USE_OPENCL
+  parameters.push_back("opencl");
+#endif
+#if USE_CUDA
+  parameters.push_back("cuda");
+#endif
+  return parameters;
+}
+
+INSTANTIATE_TEST_SUITE_P(InstantiationName, TestReduceLabelToCentroids, ::testing::ValuesIn(getParameters()));

From 9229a071a7b4c7b5ddae47b5b60775599255fd37 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Wed, 18 Sep 2024 11:14:57 +0300
Subject: [PATCH 07/14] add sub and reduce stack

---
 clic/include/tier2.hpp              | 40 +++++++++++++++++++++++++++++
 clic/src/tier2/stack_operations.cpp | 39 ++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 clic/src/tier2/stack_operations.cpp

diff --git a/clic/include/tier2.hpp b/clic/include/tier2.hpp
index b2b7cfb9f..8ded3e38a 100644
--- a/clic/include/tier2.hpp
+++ b/clic/include/tier2.hpp
@@ -895,6 +895,46 @@ subtract_images_func(const Device::Pointer & device,
                      const Array::Pointer &  src1,
                      Array::Pointer          dst) -> Array::Pointer;
 
+/**
+ * @name sub_stack
+ * @brief Crop a volume into a new volume, along the z-axis.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
+ * @param start_z Start z coordinate of the crop. [int ( = 0 )]
+ * @param end_z End z coordinate of the crop. [int ( = 0 )]
+ * @return Array::Pointer
+ *
+ * @note 'transform', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_subStack
+ */
+auto
+sub_stack_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int start_z, int end_z)
+  -> Array::Pointer;
+
+/**
+ * @name reduce_stack
+ * @brief Reduces the number of z-slices in a stack by a given factor. With the offset you have control which slices
+ * stays: with a factor 3 and offset 0, slices 0,3,6, etc. are kept. with a factor 4 and offset 1, slices 1,5,9, etc.
+ * are kept.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
+ * @param reduction_factor Reduction factor. [int ( = 2 )]
+ * @param offset Offset. [int ( = 0 )]
+ * @return Array::Pointer
+ *
+ * @note 'transform', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_reduceStack
+ */
+auto
+reduce_stack_func(const Device::Pointer & device,
+                  const Array::Pointer &  src,
+                  Array::Pointer          dst,
+                  int                     reduction_factor,
+                  int                     offset) -> Array::Pointer;
 
 /**
  * @name sum_of_all_pixels
diff --git a/clic/src/tier2/stack_operations.cpp b/clic/src/tier2/stack_operations.cpp
new file mode 100644
index 000000000..868b2fb3a
--- /dev/null
+++ b/clic/src/tier2/stack_operations.cpp
@@ -0,0 +1,39 @@
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+
+#include "utils.hpp"
+
+namespace cle::tier2
+{
+
+auto
+sub_stack_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int start_z, int end_z)
+  -> Array::Pointer
+{
+  auto nb_slice = end_z - start_z + 1;
+  nb_slice = nb_slice < 1 ? 1 : nb_slice;
+  return tier1::crop_func(device, src, dst, 0, 0, start_z, 0, 0, nb_slice);
+}
+
+auto
+reduce_stack_func(const Device::Pointer & device,
+                  const Array::Pointer &  src,
+                  Array::Pointer          dst,
+                  int                     reduction_factor,
+                  int                     offset) -> Array::Pointer
+{
+  reduction_factor = reduction_factor < 1 ? 1 : reduction_factor;
+  auto num_slice = static_cast<int>(src->depth() / reduction_factor);
+
+  tier0::create_dst(src, dst, src->width(), src->height(), num_slice, src->dtype());
+  auto temp_slice = Array::create(src->width(), src->height(), 1, 2, src->dtype(), src->mtype(), device);
+  for (auto z = 0; z < num_slice; z++)
+  {
+    tier1::copy_slice_func(device, src, temp_slice, z * reduction_factor + offset);
+    tier1::copy_slice_func(device, temp_slice, dst, z);
+  }
+  return dst;
+}
+
+} // namespace cle::tier2

From eac4364d3a2422782f79c07cd779361074ece67f Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Wed, 18 Sep 2024 17:15:58 +0300
Subject: [PATCH 08/14] reorder function in tiers

---
 clic/include/tier4.hpp                        | 142 +++++++++++++++---
 clic/include/tier5.hpp                        |  87 +++--------
 clic/include/tier6.hpp                        |  63 +++++++-
 clic/include/tier7.hpp                        |  17 +++
 clic/src/tier4/filter_label_by_values.cpp     |  71 +++++++++
 .../{tier4 => tier5}/filter_label_by_size.cpp |  17 ++-
 clic/src/{tier5 => tier6}/remove_objects.cpp  |  13 +-
 .../remove_holes.cpp => tier7/fill_holes.cpp} |   7 +-
 .../test_filter_labels_by_size.cpp            |   2 +-
 9 files changed, 307 insertions(+), 112 deletions(-)
 create mode 100644 clic/src/tier4/filter_label_by_values.cpp
 rename clic/src/{tier4 => tier5}/filter_label_by_size.cpp (54%)
 rename clic/src/{tier5 => tier6}/remove_objects.cpp (76%)
 rename clic/src/{tier6/remove_holes.cpp => tier7/fill_holes.cpp} (85%)
 rename tests/{tier4 => tier5}/test_filter_labels_by_size.cpp (95%)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 574ed0704..29cd40d59 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -104,28 +104,6 @@ auto
 threshold_otsu_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst) -> Array::Pointer;
 
 
-/**
- * @name filter_label_by_size
- * @brief Filter labelled objects outside of the min/max size range value.
- *
- * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input label image. [const Array::Pointer &]
- * @param dst Output label image. [Array::Pointer ( = None )]
- * @param min_size Minimum size of labels to keep. [float ( = 0 )]
- * @param max_size Maximum size of labels to keep. [float ( = 100 )]
- * @return Array::Pointer
- *
- * @note 'label processing', 'in assistant'
- * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
- */
-auto
-filter_label_by_size_func(const Device::Pointer & device,
-                          const Array::Pointer &  src,
-                          Array::Pointer          dst,
-                          float                   min_size,
-                          float                   max_size) -> Array::Pointer;
-
-
 /**
  * @name label_pixel_count_map
  * @brief Takes a label map, determines the number of pixels per label and replaces every label with the that number.
@@ -161,6 +139,126 @@ centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer &
   -> Array::Pointer;
 
 
+/**
+ * @name remove_labels_out_of_range
+ * @brief Remove labels with values outside a given value range based on a vector of values
+ * 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 dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value Minimum value to keep. [float ( = 0 )]
+ * @param max_value Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesOutOfRange
+ */
+auto
+remove_labels_out_of_range_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                const Array::Pointer &  values,
+                                Array::Pointer          dst,
+                                float                   min_value,
+                                float                   max_value) -> Array::Pointer;
+
+/**
+ * @name remove_labels_within_range
+ * @brief Remove labels with values inside a given value range based on a vector of values
+ * 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 dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value Minimum value to keep. [float ( = 0 )]
+ * @param max_value Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesWithinRange
+ */
+auto
+remove_labels_within_range_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                const Array::Pointer &  values,
+                                Array::Pointer          dst,
+                                float                   min_value,
+                                float                   max_value) -> Array::Pointer;
+
+/**
+ * @name exclude_labels_with_values_out_of_range
+ * @brief Exclude labels with values outside a given value range based on a vector of values
+ * 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 dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value_range Minimum value to keep. [float ( = 0 )]
+ * @param max_value_range Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesOutOfRange
+ * @deprecated This function is deprecated. Use remove_labels_with_values_out_of_range_func instead.
+ */
+auto
+exclude_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer;
+
+/**
+ * @name exclude_labels_with_values_within_range
+ * @brief Exclude labels with values inside a given value range based on a vector of values
+ * 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 dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value_range Minimum value to keep. [float ( = 0 )]
+ * @param max_value_range Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesWithinRange
+ * @deprecated This function is deprecated. Use remove_labels_with_values_within_range_func instead.
+ */
+auto
+exclude_labels_with_values_within_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer;
+
+/**
+ * @name extension_ratio_map
+ * @brief Determines the ratio of the extension for every label in a label map and returns it as
+ * a parametric map.
+ *
+ * The extension ration is defined as the maximum distance of any pixel in the label to the label's centroid divided by
+ * the average distance of all pixels in the label to the centroid.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input label image. [const Array::Pointer &]
+ * @param dst Output parametric image. [Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'map'
+ * @see https://clij.github.io/clij2-docs/reference_extensionRatioMap
+ */
+auto
+extension_ratio_map_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst) -> Array::Pointer;
+
+
 } // namespace cle::tier4
 
 #endif // __INCLUDE_TIER4_HPP
diff --git a/clic/include/tier5.hpp b/clic/include/tier5.hpp
index 2d40ea789..42bd666d0 100644
--- a/clic/include/tier5.hpp
+++ b/clic/include/tier5.hpp
@@ -89,95 +89,44 @@ connected_component_labeling_func(const Device::Pointer & device,
                                   Array::Pointer          dst,
                                   const std::string &     connectivity) -> Array::Pointer;
 
-/**
- * @name remove_small_labels
- * @brief Removes labelled objects small 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 min_size Smallest size object allowed. [float ( = 100 )]
- * @return Array::Pointer
- *
- * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
- * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
- */
-auto
-remove_small_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float min_size)
-  -> Array::Pointer;
-
-/**
- * @name exclude_small_labels
- * @brief Removes labels from a label map which are below a given maximum size.
- *
- * @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 max_size Largest size object to exclude. [float ( = 100 )]
- * @return Array::Pointer
- *
- * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
- * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
- */
-auto
-exclude_small_labels_func(const Device::Pointer & device,
-                          const Array::Pointer &  src,
-                          Array::Pointer          dst,
-                          float                   max_size) -> Array::Pointer;
 
 /**
- * @name remove_large_labels
- * @brief Removes labelled objects bigger than a given size (in pixels) from a label map.
+ * @name reduce_labels_to_centroids
+ * @brief Take a label map and reduce each label to its centroid.
  *
  * @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 max_size Biggest size object allowed. [float ( = 100 )]
+ * @param src Label image to reduce. [const Array::Pointer &]
+ * @param dst Output label image with centroids. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
- * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ * @see https://clij.github.io/clij2-docs/reference_reduceLabelsToCentroids
  */
 auto
-remove_large_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float max_size)
-  -> Array::Pointer;
+reduce_labels_to_centroids_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                Array::Pointer          dst) -> Array::Pointer;
 
 /**
- * @name exclude_large_labels
- * @brief Removes labels from a label map which are higher a given minimum size.
+ * @name filter_label_by_size
+ * @brief Filter labelled objects outside of the min/max size range value.
  *
  * @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 min_size Smallest size object to keep. [float ( = 100 )]
+ * @param src Input label image. [const Array::Pointer &]
+ * @param dst Output label image. [Array::Pointer ( = None )]
+ * @param min_size Minimum size of labels to keep. [float ( = 0 )]
+ * @param max_size Maximum size of labels to keep. [float ( = 100 )]
  * @return Array::Pointer
  *
- * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @note 'label processing', 'in assistant'
  * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
  */
 auto
-exclude_large_labels_func(const Device::Pointer & device,
+filter_label_by_size_func(const Device::Pointer & device,
                           const Array::Pointer &  src,
                           Array::Pointer          dst,
-                          float                   min_size) -> Array::Pointer;
-
-
-/**
- * @name reduce_labels_to_centroids
- * @brief Take a label map and reduce each label to its centroid.
- *
- * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image to reduce. [const Array::Pointer &]
- * @param dst Output label image with centroids. [Array::Pointer ( = None )]
- * @return Array::Pointer
- *
- * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
- * @see https://clij.github.io/clij2-docs/reference_reduceLabelsToCentroids
- */
-auto
-reduce_labels_to_centroids_func(const Device::Pointer & device,
-                                const Array::Pointer &  src,
-                                Array::Pointer          dst) -> Array::Pointer;
+                          float                   min_size,
+                          float                   max_size) -> Array::Pointer;
 
 
 } // namespace cle::tier5
diff --git a/clic/include/tier6.hpp b/clic/include/tier6.hpp
index e830d9527..bec846225 100644
--- a/clic/include/tier6.hpp
+++ b/clic/include/tier6.hpp
@@ -115,22 +115,77 @@ voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & src
 
 
 /**
- * @name fill_holes
- * @brief Fill holes in labelled objects samller than a given size (in pixels) from a label map.
+ * @name remove_small_labels
+ * @brief Removes labelled objects small 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 max_size Biggest size holes allowed. [float ( = 100 )]
+ * @param min_size Smallest size object allowed. [float ( = 100 )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
  * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
  */
 auto
-fill_holes_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float max_size)
+remove_small_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float min_size)
   -> Array::Pointer;
 
+/**
+ * @name exclude_small_labels
+ * @brief Removes labels from a label map which are below a given maximum size.
+ *
+ * @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 max_size Largest size object to exclude. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ */
+auto
+exclude_small_labels_func(const Device::Pointer & device,
+                          const Array::Pointer &  src,
+                          Array::Pointer          dst,
+                          float                   max_size) -> Array::Pointer;
+
+/**
+ * @name remove_large_labels
+ * @brief Removes labelled 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 max_size Biggest size object allowed. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ */
+auto
+remove_large_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float max_size)
+  -> Array::Pointer;
+
+/**
+ * @name exclude_large_labels
+ * @brief Removes labels from a label map which are higher a given minimum size.
+ *
+ * @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 min_size Smallest size object to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ */
+auto
+exclude_large_labels_func(const Device::Pointer & device,
+                          const Array::Pointer &  src,
+                          Array::Pointer          dst,
+                          float                   min_size) -> Array::Pointer;
+
 
 } // namespace cle::tier6
 
diff --git a/clic/include/tier7.hpp b/clic/include/tier7.hpp
index a9f8aea0a..15079b24a 100644
--- a/clic/include/tier7.hpp
+++ b/clic/include/tier7.hpp
@@ -272,6 +272,23 @@ voronoi_otsu_labeling_func(const Device::Pointer & device,
                            float                   outline_sigma) -> Array::Pointer;
 
 
+/**
+ * @name fill_holes
+ * @brief Fill holes in labelled objects samller 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 max_size Biggest size holes allowed. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'in assistant', 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ */
+auto
+fill_holes_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float max_size)
+  -> Array::Pointer;
+
 } // namespace cle::tier7
 
 #endif // __INCLUDE_TIER7_HPP
diff --git a/clic/src/tier4/filter_label_by_values.cpp b/clic/src/tier4/filter_label_by_values.cpp
new file mode 100644
index 000000000..ce9935674
--- /dev/null
+++ b/clic/src/tier4/filter_label_by_values.cpp
@@ -0,0 +1,71 @@
+
+
+
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+#include "tier3.hpp"
+#include "tier4.hpp"
+
+#include "utils.hpp"
+#include <numeric>
+
+namespace cle::tier4
+{
+
+auto
+remove_labels_out_of_range_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                const Array::Pointer &  values,
+                                Array::Pointer          dst,
+                                float                   min_value,
+                                float                   max_value) -> Array::Pointer
+{
+  auto above = tier1::greater_constant_func(device, values, nullptr, max_value);
+  auto below = tier1::smaller_constant_func(device, values, nullptr, min_value);
+  auto flaglist = Array::create(values->size(), 1, 1, 1, dType::LABEL, mType::BUFFER, device);
+  tier1::binary_or_func(device, below, above, flaglist);
+  return tier3::remove_labels_func(device, src, flaglist, dst);
+}
+
+
+auto
+remove_labels_within_range_func(const Device::Pointer & device,
+                                const Array::Pointer &  src,
+                                const Array::Pointer &  values,
+                                Array::Pointer          dst,
+                                float                   min_value,
+                                float                   max_value) -> Array::Pointer
+{
+  auto above = tier1::greater_or_equal_constant_func(device, values, nullptr, max_value);
+  auto below = tier1::smaller_or_equal_constant_func(device, values, nullptr, max_value);
+  auto flaglist = Array::create(values->size(), 1, 1, 1, dType::LABEL, mType::BUFFER, device);
+  tier1::binary_or_func(device, below, above, flaglist);
+  return tier3::remove_labels_func(device, src, flaglist, dst);
+}
+
+
+auto
+exclude_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer
+{
+  return remove_labels_out_of_range_func(device, src, values, dst, min_value_range, max_value_range);
+}
+
+
+auto
+exclude_labels_with_values_within_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer
+{
+  return remove_labels_within_range_func(device, src, values, dst, min_value_range, max_value_range);
+}
+
+} // namespace cle::tier4
\ No newline at end of file
diff --git a/clic/src/tier4/filter_label_by_size.cpp b/clic/src/tier5/filter_label_by_size.cpp
similarity index 54%
rename from clic/src/tier4/filter_label_by_size.cpp
rename to clic/src/tier5/filter_label_by_size.cpp
index 448741bc2..df4235e89 100644
--- a/clic/src/tier4/filter_label_by_size.cpp
+++ b/clic/src/tier5/filter_label_by_size.cpp
@@ -3,11 +3,12 @@
 #include "tier2.hpp"
 #include "tier3.hpp"
 #include "tier4.hpp"
+#include "tier5.hpp"
 
 #include "utils.hpp"
 #include <numeric>
 
-namespace cle::tier4
+namespace cle::tier5
 {
 
 auto
@@ -24,13 +25,15 @@ filter_label_by_size_func(const Device::Pointer & device,
   auto       list_of_area = Array::create(nb_labels, 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
   list_of_area->writeFrom(stats["area"].data());
 
-  auto below_min_buffer = tier1::smaller_constant_func(device, list_of_area, nullptr, min_size);
-  auto above_max_buffer = tier1::greater_constant_func(device, list_of_area, nullptr, max_size);
+  return tier4::remove_labels_out_of_range_func(device, src, list_of_area, dst, min_size, max_size);
 
-  auto list_of_labels_to_exclude = Array::create(nb_labels, 1, 1, 1, dType::LABEL, mType::BUFFER, device);
-  tier1::binary_or_func(device, below_min_buffer, above_max_buffer, list_of_labels_to_exclude);
-  return tier3::remove_labels_func(device, src, list_of_labels_to_exclude, dst);
+  // auto below_min_buffer = tier1::smaller_constant_func(device, list_of_area, nullptr, min_size);
+  // auto above_max_buffer = tier1::greater_constant_func(device, list_of_area, nullptr, max_size);
+
+  // auto list_of_labels_to_exclude = Array::create(nb_labels, 1, 1, 1, dType::LABEL, mType::BUFFER, device);
+  // tier1::binary_or_func(device, below_min_buffer, above_max_buffer, list_of_labels_to_exclude);
+  // return tier3::remove_labels_func(device, src, list_of_labels_to_exclude, dst);
 }
 
 
-} // namespace cle::tier4
+} // namespace cle::tier5
diff --git a/clic/src/tier5/remove_objects.cpp b/clic/src/tier6/remove_objects.cpp
similarity index 76%
rename from clic/src/tier5/remove_objects.cpp
rename to clic/src/tier6/remove_objects.cpp
index 8dcd1e862..766285bb7 100644
--- a/clic/src/tier5/remove_objects.cpp
+++ b/clic/src/tier6/remove_objects.cpp
@@ -4,25 +4,26 @@
 #include "tier3.hpp"
 #include "tier4.hpp"
 #include "tier5.hpp"
+#include "tier6.hpp"
 
 #include "utils.hpp"
 #include <numeric>
 
-namespace cle::tier5
+namespace cle::tier6
 {
 
 auto
 remove_small_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float min_size)
   -> Array::Pointer
 {
-  return tier4::filter_label_by_size_func(device, src, dst, min_size, std::numeric_limits<float>::max());
+  return tier5::filter_label_by_size_func(device, src, dst, min_size, std::numeric_limits<float>::max());
 }
 
 auto
 remove_large_labels_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, float max_size)
   -> Array::Pointer
 {
-  return tier4::filter_label_by_size_func(device, src, dst, 0, max_size);
+  return tier5::filter_label_by_size_func(device, src, dst, 0, max_size);
 }
 
 auto
@@ -31,7 +32,7 @@ exclude_small_labels_func(const Device::Pointer & device,
                           Array::Pointer          dst,
                           float                   max_size) -> Array::Pointer
 {
-  return tier5::remove_small_labels_func(device, src, dst, max_size);
+  return remove_small_labels_func(device, src, dst, max_size);
 }
 
 auto
@@ -40,7 +41,7 @@ exclude_large_labels_func(const Device::Pointer & device,
                           Array::Pointer          dst,
                           float                   min_size) -> Array::Pointer
 {
-  return tier5::remove_large_labels_func(device, src, dst, min_size);
+  return remove_large_labels_func(device, src, dst, min_size);
 }
 
-} // namespace cle::tier5
+} // namespace cle::tier6
diff --git a/clic/src/tier6/remove_holes.cpp b/clic/src/tier7/fill_holes.cpp
similarity index 85%
rename from clic/src/tier6/remove_holes.cpp
rename to clic/src/tier7/fill_holes.cpp
index f39da6a4e..b817e7367 100644
--- a/clic/src/tier6/remove_holes.cpp
+++ b/clic/src/tier7/fill_holes.cpp
@@ -5,10 +5,11 @@
 #include "tier4.hpp"
 #include "tier5.hpp"
 #include "tier6.hpp"
+#include "tier7.hpp"
 
 #include "utils.hpp"
 
-namespace cle::tier6
+namespace cle::tier7
 {
 
 auto
@@ -20,7 +21,7 @@ fill_holes_func(const Device::Pointer & device, const Array::Pointer & src, Arra
   auto inverted = tier1::binary_not_func(device, binary, nullptr);
 
   auto labels = tier5::connected_component_labeling_func(device, inverted, nullptr, "box");
-  tier5::remove_small_labels_func(device, labels, dst, max_size);
+  tier6::remove_small_labels_func(device, labels, dst, max_size);
 
   // invert the filtered image
   tier1::greater_constant_func(device, dst, binary, 0);
@@ -29,4 +30,4 @@ fill_holes_func(const Device::Pointer & device, const Array::Pointer & src, Arra
 }
 
 
-} // namespace cle::tier6
+} // namespace cle::tier7
diff --git a/tests/tier4/test_filter_labels_by_size.cpp b/tests/tier5/test_filter_labels_by_size.cpp
similarity index 95%
rename from tests/tier4/test_filter_labels_by_size.cpp
rename to tests/tier5/test_filter_labels_by_size.cpp
index c4afc3f79..843c88595 100644
--- a/tests/tier4/test_filter_labels_by_size.cpp
+++ b/tests/tier5/test_filter_labels_by_size.cpp
@@ -24,7 +24,7 @@ TEST_P(TestFilterLabelsBySize, execute2d)
   auto gpu_input = cle::Array::create(6, 5, 1, 2, cle::dType::LABEL, cle::mType::BUFFER, device);
   gpu_input->writeFrom(input.data());
 
-  auto gpu_output = cle::tier4::filter_label_by_size_func(device, gpu_input, nullptr, 4, 5);
+  auto gpu_output = cle::tier5::filter_label_by_size_func(device, gpu_input, nullptr, 4, 5);
 
   std::vector<uint32_t> output(gpu_output->size());
   gpu_output->readTo(output.data());

From b5e3c39563692ea6f549eb36ae5c87454c519c14 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Wed, 18 Sep 2024 17:16:07 +0300
Subject: [PATCH 09/14] add extension ratio map

---
 clic/src/tier4/parametrics_map.cpp | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 clic/src/tier4/parametrics_map.cpp

diff --git a/clic/src/tier4/parametrics_map.cpp b/clic/src/tier4/parametrics_map.cpp
new file mode 100644
index 000000000..70d506a9d
--- /dev/null
+++ b/clic/src/tier4/parametrics_map.cpp
@@ -0,0 +1,29 @@
+
+#include "tier0.hpp"
+#include "tier1.hpp"
+#include "tier2.hpp"
+#include "tier3.hpp"
+#include "tier4.hpp"
+
+#include "utils.hpp"
+#include <numeric>
+
+namespace cle::tier4
+{
+
+auto
+extension_ratio_map_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst) -> Array::Pointer
+{
+  tier0::create_like(src, dst, dType::FLOAT);
+  auto props = tier3::statistics_of_background_and_labelled_pixels_func(device, src, nullptr);
+  auto vector = props["mean_max_distance_to_centroid_ratio"];
+  auto values = Array::create(vector.size(), 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
+  values->writeFrom(vector.data());
+  tier1::set_column_func(device, values, 0, 0);
+  return tier1::replace_values_func(device, src, values, dst);
+}
+
+
+} // namespace cle::tier4

From 496f13b3e4cee8a19baa25a59c2974070afb9dae Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Wed, 18 Sep 2024 17:17:25 +0300
Subject: [PATCH 10/14] move maps into one cpp file

---
 clic/src/tier4/label_pixel_count_map.cpp | 48 ------------------------
 clic/src/tier4/parametrics_map.cpp       | 22 +++++++++++
 2 files changed, 22 insertions(+), 48 deletions(-)
 delete mode 100644 clic/src/tier4/label_pixel_count_map.cpp

diff --git a/clic/src/tier4/label_pixel_count_map.cpp b/clic/src/tier4/label_pixel_count_map.cpp
deleted file mode 100644
index eed24658b..000000000
--- a/clic/src/tier4/label_pixel_count_map.cpp
+++ /dev/null
@@ -1,48 +0,0 @@
-#include "tier0.hpp"
-#include "tier1.hpp"
-#include "tier2.hpp"
-#include "tier3.hpp"
-#include "tier4.hpp"
-
-#include "utils.hpp"
-
-namespace cle::tier4
-{
-
-/**
- * @name label_pixel_count_map
- * @brief Takes a label map, determines the number of pixels per label and replaces every label with the that number.
- * This results in a parametric image expressing area or volume.
- *
- * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image to measure [const Array::Pointer &]
- * @param dst Parametric image computed[Array::Pointer ( = None )]
- * @return Array::Pointer
- *
- * @note 'label measurement', 'map', 'in assistant'
- * @see https://clij.github.io/clij2-docs/reference_pixelCountMap
- */
-auto
-label_pixel_count_map_func(const Device::Pointer & device,
-                           const Array::Pointer &  src,
-                           Array::Pointer          dst) -> Array::Pointer
-{
-  tier0::create_like(src, dst, dType::FLOAT);
-  auto props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
-
-  for (auto && i : props["area"])
-  {
-    std::cout << i << std::endl;
-  }
-
-
-  auto values = cle::Array::create(props["area"].size(), 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
-  values->writeFrom(props["area"].data());
-
-  cle::print<float>(values, "values");
-  tier1::set_column_func(device, values, 0, 0);
-  return tier1::replace_values_func(device, src, values, dst);
-}
-
-
-} // namespace cle::tier4
diff --git a/clic/src/tier4/parametrics_map.cpp b/clic/src/tier4/parametrics_map.cpp
index 70d506a9d..a8fca0739 100644
--- a/clic/src/tier4/parametrics_map.cpp
+++ b/clic/src/tier4/parametrics_map.cpp
@@ -11,6 +11,28 @@
 namespace cle::tier4
 {
 
+auto
+label_pixel_count_map_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst) -> Array::Pointer
+{
+  tier0::create_like(src, dst, dType::FLOAT);
+  auto props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
+
+  for (auto && i : props["area"])
+  {
+    std::cout << i << std::endl;
+  }
+
+
+  auto values = cle::Array::create(props["area"].size(), 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
+  values->writeFrom(props["area"].data());
+
+  cle::print<float>(values, "values");
+  tier1::set_column_func(device, values, 0, 0);
+  return tier1::replace_values_func(device, src, values, dst);
+}
+
 auto
 extension_ratio_map_func(const Device::Pointer & device,
                          const Array::Pointer &  src,

From 56f9c7d5edf2b5385df3793de4766de27592bcb1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 18 Sep 2024 14:22:48 +0000
Subject: [PATCH 11/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 clic/src/tier4/filter_label_by_values.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clic/src/tier4/filter_label_by_values.cpp b/clic/src/tier4/filter_label_by_values.cpp
index ce9935674..ff7afbc5a 100644
--- a/clic/src/tier4/filter_label_by_values.cpp
+++ b/clic/src/tier4/filter_label_by_values.cpp
@@ -68,4 +68,4 @@ exclude_labels_with_values_within_range_func(const Device::Pointer & device,
   return remove_labels_within_range_func(device, src, values, dst, min_value_range, max_value_range);
 }
 
-} // namespace cle::tier4
\ No newline at end of file
+} // namespace cle::tier4

From 28feff2f2ef5c5281057212bbee541b7e7b090ee Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Thu, 19 Sep 2024 10:25:07 +0300
Subject: [PATCH 12/14] fixing test and clean up

---
 clic/src/tier4/parametrics_map.cpp        |  9 +--------
 tests/tier4/test_label_pixelcount_map.cpp | 10 ++++------
 2 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/clic/src/tier4/parametrics_map.cpp b/clic/src/tier4/parametrics_map.cpp
index a8fca0739..6004a159a 100644
--- a/clic/src/tier4/parametrics_map.cpp
+++ b/clic/src/tier4/parametrics_map.cpp
@@ -17,18 +17,11 @@ label_pixel_count_map_func(const Device::Pointer & device,
                            Array::Pointer          dst) -> Array::Pointer
 {
   tier0::create_like(src, dst, dType::FLOAT);
-  auto props = tier3::statistics_of_labelled_pixels_func(device, src, nullptr);
-
-  for (auto && i : props["area"])
-  {
-    std::cout << i << std::endl;
-  }
-
+  auto props = tier3::statistics_of_background_and_labelled_pixels_func(device, src, nullptr);
 
   auto values = cle::Array::create(props["area"].size(), 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
   values->writeFrom(props["area"].data());
 
-  cle::print<float>(values, "values");
   tier1::set_column_func(device, values, 0, 0);
   return tier1::replace_values_func(device, src, values, dst);
 }
diff --git a/tests/tier4/test_label_pixelcount_map.cpp b/tests/tier4/test_label_pixelcount_map.cpp
index 9f620c7b3..1000faf45 100644
--- a/tests/tier4/test_label_pixelcount_map.cpp
+++ b/tests/tier4/test_label_pixelcount_map.cpp
@@ -26,14 +26,12 @@ TEST_P(TestLabelPixelCountMap, execute2d)
 
   auto gpu_output = cle::tier4::label_pixel_count_map_func(device, gpu_input, nullptr);
 
-  cle::print<float>(gpu_output);
-
   std::vector<float> output(gpu_output->size());
   gpu_output->readTo(output.data());
-  //   for (int i = 0; i < output.size(); i++)
-  //   {
-  //     EXPECT_EQ(output[i], valid[i]);
-  //   }
+  for (int i = 0; i < output.size(); i++)
+  {
+    EXPECT_EQ(output[i], valid[i]);
+  }
 }
 
 

From cbb0f79de9aba6f4ad829256d94d1b489f00f95c Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Fri, 20 Sep 2024 14:23:12 +0300
Subject: [PATCH 13/14] fix docstring centroids_of_labels

---
 clic/include/tier4.hpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 29cd40d59..3e0b956ef 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -132,7 +132,11 @@ label_pixel_count_map_func(const Device::Pointer & device,
  * @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 withBG Determines if the background label should be included. [bool ( = false )]
+ * @param withBG Determines if the background label should be included. [bool ( = False )]
+ * @return Array::Pointer
+ *
+ * @note 'bia-bob-suggestion'
+ * @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 withBG)

From a16d35728e905756191f9ca9cda0d72934da8a93 Mon Sep 17 00:00:00 2001
From: Stephane Rigaud <stephane.rigaud@pasteur.fr>
Date: Tue, 24 Sep 2024 11:52:56 +0300
Subject: [PATCH 14/14] more explicit name

---
 clic/include/tier4.hpp                    | 28 +++++++++++------------
 clic/src/tier4/filter_label_by_values.cpp | 28 +++++++++++------------
 clic/src/tier5/filter_label_by_size.cpp   |  2 +-
 3 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
index 3e0b956ef..c174a5dd3 100644
--- a/clic/include/tier4.hpp
+++ b/clic/include/tier4.hpp
@@ -144,7 +144,7 @@ centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer &
 
 
 /**
- * @name remove_labels_out_of_range
+ * @name remove_labels_with_values_out_of_range
  * @brief Remove labels with values outside a given value range based on a vector of values
  * associated with the labels.
  *
@@ -160,15 +160,15 @@ centroids_of_labels_func(const Device::Pointer & device, const Array::Pointer &
  * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesOutOfRange
  */
 auto
-remove_labels_out_of_range_func(const Device::Pointer & device,
-                                const Array::Pointer &  src,
-                                const Array::Pointer &  values,
-                                Array::Pointer          dst,
-                                float                   min_value,
-                                float                   max_value) -> Array::Pointer;
+remove_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer;
 
 /**
- * @name remove_labels_within_range
+ * @name remove_labels_with_values_within_range
  * @brief Remove labels with values inside a given value range based on a vector of values
  * associated with the labels.
  *
@@ -184,12 +184,12 @@ remove_labels_out_of_range_func(const Device::Pointer & device,
  * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesWithinRange
  */
 auto
-remove_labels_within_range_func(const Device::Pointer & device,
-                                const Array::Pointer &  src,
-                                const Array::Pointer &  values,
-                                Array::Pointer          dst,
-                                float                   min_value,
-                                float                   max_value) -> Array::Pointer;
+remove_labels_with_values_within_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer;
 
 /**
  * @name exclude_labels_with_values_out_of_range
diff --git a/clic/src/tier4/filter_label_by_values.cpp b/clic/src/tier4/filter_label_by_values.cpp
index ff7afbc5a..151139962 100644
--- a/clic/src/tier4/filter_label_by_values.cpp
+++ b/clic/src/tier4/filter_label_by_values.cpp
@@ -14,12 +14,12 @@ namespace cle::tier4
 {
 
 auto
-remove_labels_out_of_range_func(const Device::Pointer & device,
-                                const Array::Pointer &  src,
-                                const Array::Pointer &  values,
-                                Array::Pointer          dst,
-                                float                   min_value,
-                                float                   max_value) -> Array::Pointer
+remove_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer
 {
   auto above = tier1::greater_constant_func(device, values, nullptr, max_value);
   auto below = tier1::smaller_constant_func(device, values, nullptr, min_value);
@@ -30,12 +30,12 @@ remove_labels_out_of_range_func(const Device::Pointer & device,
 
 
 auto
-remove_labels_within_range_func(const Device::Pointer & device,
-                                const Array::Pointer &  src,
-                                const Array::Pointer &  values,
-                                Array::Pointer          dst,
-                                float                   min_value,
-                                float                   max_value) -> Array::Pointer
+remove_labels_with_values_within_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer
 {
   auto above = tier1::greater_or_equal_constant_func(device, values, nullptr, max_value);
   auto below = tier1::smaller_or_equal_constant_func(device, values, nullptr, max_value);
@@ -53,7 +53,7 @@ exclude_labels_with_values_out_of_range_func(const Device::Pointer & device,
                                              float                   min_value_range,
                                              float                   max_value_range) -> Array::Pointer
 {
-  return remove_labels_out_of_range_func(device, src, values, dst, min_value_range, max_value_range);
+  return remove_labels_with_values_out_of_range_func(device, src, values, dst, min_value_range, max_value_range);
 }
 
 
@@ -65,7 +65,7 @@ exclude_labels_with_values_within_range_func(const Device::Pointer & device,
                                              float                   min_value_range,
                                              float                   max_value_range) -> Array::Pointer
 {
-  return remove_labels_within_range_func(device, src, values, dst, min_value_range, max_value_range);
+  return remove_labels_with_values_within_range_func(device, src, values, dst, min_value_range, max_value_range);
 }
 
 } // namespace cle::tier4
diff --git a/clic/src/tier5/filter_label_by_size.cpp b/clic/src/tier5/filter_label_by_size.cpp
index df4235e89..b629d1c19 100644
--- a/clic/src/tier5/filter_label_by_size.cpp
+++ b/clic/src/tier5/filter_label_by_size.cpp
@@ -25,7 +25,7 @@ filter_label_by_size_func(const Device::Pointer & device,
   auto       list_of_area = Array::create(nb_labels, 1, 1, 1, dType::FLOAT, mType::BUFFER, device);
   list_of_area->writeFrom(stats["area"].data());
 
-  return tier4::remove_labels_out_of_range_func(device, src, list_of_area, dst, min_size, max_size);
+  return tier4::remove_labels_with_values_out_of_range_func(device, src, list_of_area, dst, min_size, max_size);
 
   // auto below_min_buffer = tier1::smaller_constant_func(device, list_of_area, nullptr, min_size);
   // auto above_max_buffer = tier1::greater_constant_func(device, list_of_area, nullptr, max_size);