Update to CLIc@master

native/clesperantoj/include/kernelj.hpp

@@ -0,0 +1,17 @@
+
+/*
+ * This file is autogenerated. Do not edit manually.
+ */
+#include "kernelj.hpp"
+#include "tier8.hpp"
+
+ArrayJ Tier8::smooth_labels(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius)
+{
+    return ArrayJ{cle::tier8::smooth_labels_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius)};
+}
+
+ArrayJ Tier8::smooth_connected_labels(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius)
+{
+    return ArrayJ{cle::tier8::smooth_connected_labels_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius)};
+}
+

native/clesperantoj/src/tier2j.cpp

@@ -0,0 +1,232 @@
+
+/*
+ * This file is autogenerated. Do not edit manually.
+ */
+#include "kernelj.hpp"
+#include "tier2.hpp"
+
+ArrayJ Tier2::absolute_difference(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::absolute_difference_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::add_images(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::add_images_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::bottom_hat_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::bottom_hat_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::bottom_hat_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z)
+{
+    return ArrayJ{cle::tier2::bottom_hat_sphere_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::bottom_hat(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::bottom_hat_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::clip(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float min_intensity, float max_intensity)
+{
+    return ArrayJ{cle::tier2::clip_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), min_intensity, max_intensity)};
+}
+
+ArrayJ Tier2::closing_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::closing_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::closing_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::closing_sphere_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::closing(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::closing_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::concatenate_along_x(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::concatenate_along_x_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::concatenate_along_y(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::concatenate_along_y_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::concatenate_along_z(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::concatenate_along_z_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::count_touching_neighbors(DeviceJ * device, ArrayJ * src, ArrayJ * dst, bool ignore_background)
+{
+    return ArrayJ{cle::tier2::count_touching_neighbors_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), ignore_background)};
+}
+
+ArrayJ Tier2::crop_border(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int border_size)
+{
+    return ArrayJ{cle::tier2::crop_border_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), border_size)};
+}
+
+ArrayJ Tier2::divide_by_gaussian_background(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float sigma_x, float sigma_y, float sigma_z)
+{
+    return ArrayJ{cle::tier2::divide_by_gaussian_background_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), sigma_x, sigma_y, sigma_z)};
+}
+
+ArrayJ Tier2::degrees_to_radians(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::degrees_to_radians_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::detect_maxima_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::detect_maxima_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::detect_maxima(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::detect_maxima_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::detect_minima_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::detect_minima_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::detect_minima(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::detect_minima_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::difference_of_gaussian(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float sigma1_x, float sigma1_y, float sigma1_z, float sigma2_x, float sigma2_y, float sigma2_z)
+{
+    return ArrayJ{cle::tier2::difference_of_gaussian_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), sigma1_x, sigma1_y, sigma1_z, sigma2_x, sigma2_y, sigma2_z)};
+}
+
+ArrayJ Tier2::extend_labeling_via_voronoi(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::extend_labeling_via_voronoi_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::invert(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::invert_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::label_spots(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::label_spots_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::large_hessian_eigenvalue(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::large_hessian_eigenvalue_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+float Tier2::maximum_of_all_pixels(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier2::maximum_of_all_pixels_func(device->get(), src->get());
+}
+
+float Tier2::minimum_of_all_pixels(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier2::minimum_of_all_pixels_func(device->get(), src->get());
+}
+
+float Tier2::minimum_of_masked_pixels(DeviceJ * device, ArrayJ * src, ArrayJ * mask)
+{
+    return cle::tier2::minimum_of_masked_pixels_func(device->get(), src->get(), mask->get());
+}
+
+ArrayJ Tier2::opening_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::opening_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::opening_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z)
+{
+    return ArrayJ{cle::tier2::opening_sphere_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::opening(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::opening_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::radians_to_degrees(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::radians_to_degrees_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::reduce_labels_to_label_edges(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::reduce_labels_to_label_edges_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::small_hessian_eigenvalue(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::small_hessian_eigenvalue_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::square(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::square_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::squared_difference(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::squared_difference_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier2::standard_deviation_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::standard_deviation_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::standard_deviation_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::standard_deviation_sphere_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::standard_deviation(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::standard_deviation_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+
+ArrayJ Tier2::subtract_gaussian_background(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float sigma_x, float sigma_y, float sigma_z)
+{
+    return ArrayJ{cle::tier2::subtract_gaussian_background_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), sigma_x, sigma_y, sigma_z)};
+}
+
+ArrayJ Tier2::subtract_images(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier2::subtract_images_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+float Tier2::sum_of_all_pixels(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier2::sum_of_all_pixels_func(device->get(), src == nullptr ? nullptr : src->get());
+}
+
+ArrayJ Tier2::top_hat_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radius_x, int radius_y, int radius_z)
+{
+    return ArrayJ{cle::tier2::top_hat_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::top_hat_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z)
+{
+    return ArrayJ{cle::tier2::top_hat_sphere_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
+}
+
+ArrayJ Tier2::top_hat(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z, std::string connectivity)
+{
+    return ArrayJ{cle::tier2::top_hat_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
+}
+

native/clesperantoj/src/tier3j.cpp

@@ -0,0 +1,87 @@
+
+/*
+ * This file is autogenerated. Do not edit manually.
+ */
+#include "kernelj.hpp"
+#include "tier3.hpp"
+
+std::vector<float> Tier3::bounding_box(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier3::bounding_box_func(device->get(), src->get());
+}
+
+std::vector<float> Tier3::center_of_mass(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier3::center_of_mass_func(device->get(), src->get());
+}
+
+ArrayJ Tier3::remove_labels(DeviceJ * device, ArrayJ * src, ArrayJ * list, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier3::remove_labels_func(device->get(), src->get(), list->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier3::remove_labels_on_edges(DeviceJ * device, ArrayJ * src, ArrayJ * dst, bool exclude_x, bool exclude_y, bool exclude_z)
+{
+    return ArrayJ{cle::tier3::remove_labels_on_edges_func(device == nullptr ? nullptr : device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), exclude_x, exclude_y, exclude_z)};
+}
+
+ArrayJ Tier3::flag_existing_labels(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier3::flag_existing_labels_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier3::gamma_correction(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float gamma)
+{
+    return ArrayJ{cle::tier3::gamma_correction_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), gamma)};
+}
+
+ArrayJ Tier3::generate_binary_overlap_matrix(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier3::generate_binary_overlap_matrix_func(device->get(), src0->get(), src1->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier3::generate_touch_matrix(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier3::generate_touch_matrix_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier3::histogram(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int nbins, float min, float max)
+{
+    return ArrayJ{cle::tier3::histogram_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), nbins, min, max)};
+}
+
+float Tier3::jaccard_index(DeviceJ * device, ArrayJ * src0, ArrayJ * src1)
+{
+    return cle::tier3::jaccard_index_func(device->get(), src0->get(), src1->get());
+}
+
+ArrayJ Tier3::labelled_spots_to_pointlist(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier3::labelled_spots_to_pointlist_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+std::vector<float> Tier3::maximum_position(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier3::maximum_position_func(device->get(), src->get());
+}
+
+float Tier3::mean_of_all_pixels(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier3::mean_of_all_pixels_func(device->get(), src->get());
+}
+
+std::vector<float> Tier3::minimum_position(DeviceJ * device, ArrayJ * src)
+{
+    return cle::tier3::minimum_position_func(device->get(), src->get());
+}
+
+ArrayJ Tier3::morphological_chan_vese(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int num_iter, int smoothing, float lambda1, float lambda2)
+{
+    return ArrayJ{cle::tier3::morphological_chan_vese_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), num_iter, smoothing, lambda1, lambda2)};
+}
+
+std::unordered_map<std::string, std::vector<float>> Tier3::statistics_of_labelled_pixels(DeviceJ * device, ArrayJ * src, ArrayJ * intensity, bool withBG)
+{
+    return cle::tier3::statistics_of_labelled_pixels_func(device->get(), src->get(), intensity == nullptr ? nullptr : intensity->get(), withBG);
+}
+

native/clesperantoj/src/tier4j.cpp

@@ -0,0 +1,37 @@
+
+/*
+ * This file is autogenerated. Do not edit manually.
+ */
+#include "kernelj.hpp"
+#include "tier4.hpp"
+
+std::vector<float> Tier4::label_bounding_box(DeviceJ * device, ArrayJ * src, int label_id)
+{
+    return cle::tier4::label_bounding_box_func(device->get(), src->get(), label_id);
+}
+
+float Tier4::mean_squared_error(DeviceJ * device, ArrayJ * src0, ArrayJ * src1)
+{
+    return cle::tier4::mean_squared_error_func(device->get(), src0->get(), src1->get());
+}
+
+ArrayJ Tier4::spots_to_pointlist(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier4::spots_to_pointlist_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier4::relabel_sequential(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int blocksize)
+{
+    return ArrayJ{cle::tier4::relabel_sequential_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), blocksize)};
+}
+
+ArrayJ Tier4::threshold_otsu(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
+{
+    return ArrayJ{cle::tier4::threshold_otsu_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
+}
+
+ArrayJ Tier4::filter_label_by_size(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float min_size, float max_size)
+{
+    return ArrayJ{cle::tier4::filter_label_by_size_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), min_size, max_size)};
+}
+