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Update-to-0.16.0 #87

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Dec 27, 2024
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Update-to-0.16.0 #87

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update kernels
StRigaud Dec 18, 2024
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update pom
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fix html links
StRigaud Dec 18, 2024
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10 changes: 6 additions & 4 deletions README.md
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@@ -1,10 +1,12 @@
[![Build Status](https://github.com/clEsperanto/clesperantoj_prototype/actions/workflows/build.yml/badge.svg)](https://github.com/clEsperanto/clesperantoj_prototype/actions/workflows/build.yml)


[![Build Status](https://github.com/clEsperanto/clesperantoj_prototype/actions/workflows/build.yaml/badge.svg)](https://github.com/clEsperanto/clesperantoj_prototype/actions/workflows/build.yaml)
[![GitHub stars](https://img.shields.io/github/stars/clEsperanto/clesperantoj_prototype?style=social)](https://github.com/clEsperanto/clesperantoj_prototype)
[![GitHub forks](https://img.shields.io/github/forks/clEsperanto/clesperantoj_prototype?style=social)](https://github.com/clEsperanto/clesperantoj_prototype)
[![Image.sc Forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&amp;url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fclesperanto.json&amp;query=%24.topic_list.tags.0.topic_count&amp;colorB=green&amp;&amp;suffix=%20topics&amp;logo=data:image/png;base64,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)](https://forum.image.sc/tag/clesperanto)

# clEsperantoJ

clEsperantoJ is the Java package of [clEsperanto] - a multi-language framework for GPU-accelerated image processing. It relies on a familly of [OpenCL kernels] originated from [CLIJ]. This package is developped in Java and C++ wrapped using JavaCPP, and uses the C++ [CLIc] library as a processing backend.
clEsperantoJ is the Java library of [clEsperanto] - a multi-language framework for GPU-accelerated image processing.
It relies on a familly of [OpenCL kernels] originated from [CLIJ], and rely on the C++ [CLIc] library as a processing backend.

## How to Build from source

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123 changes: 66 additions & 57 deletions native/clesperantoj/include/kernelj.hpp
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136 changes: 78 additions & 58 deletions native/clesperantoj/src/tier1j.cpp
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54 changes: 37 additions & 17 deletions native/clesperantoj/src/tier2j.cpp
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Expand Up @@ -15,7 +15,7 @@ ArrayJ Tier2::add_images(DeviceJ * device, ArrayJ * src0, ArrayJ * src1, ArrayJ
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)
ArrayJ Tier2::bottom_hat_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)};
}
Expand All @@ -40,14 +40,24 @@ ArrayJ Tier2::closing_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int radi
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)
ArrayJ Tier2::closing_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::grayscale_closing(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)};
return ArrayJ{cle::tier2::grayscale_closing_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
}

ArrayJ Tier2::closing(DeviceJ * device, ArrayJ * src, ArrayJ * footprint, ArrayJ * dst)
{
return ArrayJ{cle::tier2::closing_func(device->get(), src->get(), footprint->get(), dst == nullptr ? nullptr : dst->get())};
}

ArrayJ Tier2::binary_closing(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z, std::string connectivity)
{
return ArrayJ{cle::tier2::binary_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)
Expand All @@ -65,9 +75,9 @@ ArrayJ Tier2::concatenate_along_z(DeviceJ * device, ArrayJ * src0, ArrayJ * src1
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)
ArrayJ Tier2::count_touching_neighbors(DeviceJ * device, ArrayJ * touch_matrix, ArrayJ * touching_neighbors_count_destination, bool ignore_background)
{
return ArrayJ{cle::tier2::count_touching_neighbors_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), ignore_background)};
return ArrayJ{cle::tier2::count_touching_neighbors_func(device->get(), touch_matrix->get(), touching_neighbors_count_destination == nullptr ? nullptr : touching_neighbors_count_destination->get(), ignore_background)};
}

ArrayJ Tier2::crop_border(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int border_size)
Expand All @@ -85,22 +95,22 @@ 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)
ArrayJ Tier2::detect_maxima_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::detect_maxima(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::detect_minima_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::detect_minima(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)};
}
Expand Down Expand Up @@ -145,7 +155,7 @@ float Tier2::minimum_of_masked_pixels(DeviceJ * device, ArrayJ * src, ArrayJ * m
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)
ArrayJ Tier2::opening_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z)
{
return ArrayJ{cle::tier2::opening_box_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z)};
}
Expand All @@ -155,9 +165,19 @@ ArrayJ Tier2::opening_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float
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)
ArrayJ Tier2::grayscale_opening(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float radius_z, std::string connectivity)
{
return ArrayJ{cle::tier2::grayscale_opening_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), radius_x, radius_y, radius_z, connectivity)};
}

ArrayJ Tier2::opening(DeviceJ * device, ArrayJ * src, ArrayJ * footprint, ArrayJ * dst)
{
return ArrayJ{cle::tier2::opening_func(device->get(), src->get(), footprint->get(), dst == nullptr ? nullptr : dst->get())};
}

ArrayJ Tier2::binary_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)};
return ArrayJ{cle::tier2::binary_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)
Expand Down Expand Up @@ -185,17 +205,17 @@ ArrayJ Tier2::squared_difference(DeviceJ * device, ArrayJ * src0, ArrayJ * src1,
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)
ArrayJ Tier2::standard_deviation_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::standard_deviation_sphere(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)
ArrayJ Tier2::standard_deviation(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)};
}
Expand Down Expand Up @@ -225,7 +245,7 @@ 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)
ArrayJ Tier2::top_hat_box(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float radius_x, float radius_y, float 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)};
}
Expand Down
16 changes: 8 additions & 8 deletions native/clesperantoj/src/tier3j.cpp
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Expand Up @@ -55,19 +55,19 @@ 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)
ArrayJ Tier3::histogram(DeviceJ * device, ArrayJ * src, ArrayJ * dst, int num_bins, float minimum_intensity, float maximum_intensity)
{
return ArrayJ{cle::tier3::histogram_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), nbins, min, max)};
return ArrayJ{cle::tier3::histogram_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), num_bins, minimum_intensity, maximum_intensity)};
}

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)
ArrayJ Tier3::labelled_spots_to_pointlist(DeviceJ * device, ArrayJ * label, ArrayJ * pointlist)
{
return ArrayJ{cle::tier3::labelled_spots_to_pointlist_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
return ArrayJ{cle::tier3::labelled_spots_to_pointlist_func(device->get(), label->get(), pointlist == nullptr ? nullptr : pointlist->get())};
}

std::vector<float> Tier3::maximum_position(DeviceJ * device, ArrayJ * src)
Expand All @@ -90,13 +90,13 @@ ArrayJ Tier3::morphological_chan_vese(DeviceJ * device, ArrayJ * src, ArrayJ * d
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 * label, ArrayJ * intensity)
std::unordered_map<std::string, std::vector<float>> Tier3::statistics_of_labelled_pixels(DeviceJ * device, ArrayJ * intensity, ArrayJ * label)
{
return cle::tier3::statistics_of_labelled_pixels_func(device->get(), label->get(), intensity == nullptr ? nullptr : intensity->get());
return cle::tier3::statistics_of_labelled_pixels_func(device->get(), intensity == nullptr ? nullptr : intensity->get(), label == nullptr ? nullptr : label->get());
}

std::unordered_map<std::string, std::vector<float>> Tier3::statistics_of_background_and_labelled_pixels(DeviceJ * device, ArrayJ * label, ArrayJ * intensity)
std::unordered_map<std::string, std::vector<float>> Tier3::statistics_of_background_and_labelled_pixels(DeviceJ * device, ArrayJ * intensity, ArrayJ * label)
{
return cle::tier3::statistics_of_background_and_labelled_pixels_func(device->get(), label->get(), intensity == nullptr ? nullptr : intensity->get());
return cle::tier3::statistics_of_background_and_labelled_pixels_func(device->get(), intensity == nullptr ? nullptr : intensity->get(), label == nullptr ? nullptr : label->get());
}

17 changes: 11 additions & 6 deletions native/clesperantoj/src/tier4j.cpp
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Expand Up @@ -30,6 +30,11 @@ 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::mean_intensity_map(DeviceJ * device, ArrayJ * src, ArrayJ * labels, ArrayJ * dst)
{
return ArrayJ{cle::tier4::mean_intensity_map_func(device->get(), src->get(), labels->get(), dst == nullptr ? nullptr : dst->get())};
}

ArrayJ Tier4::pixel_count_map(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
{
return ArrayJ{cle::tier4::pixel_count_map_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
Expand All @@ -40,9 +45,9 @@ ArrayJ Tier4::label_pixel_count_map(DeviceJ * device, ArrayJ * src, ArrayJ * dst
return ArrayJ{cle::tier4::label_pixel_count_map_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
}

ArrayJ Tier4::centroids_of_labels(DeviceJ * device, ArrayJ * src, ArrayJ * dst, bool withBG)
ArrayJ Tier4::centroids_of_labels(DeviceJ * device, ArrayJ * label_image, ArrayJ * centroids_coordinates, bool include_background)
{
return ArrayJ{cle::tier4::centroids_of_labels_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get(), withBG)};
return ArrayJ{cle::tier4::centroids_of_labels_func(device->get(), label_image->get(), centroids_coordinates->get(), include_background)};
}

ArrayJ Tier4::remove_labels_with_map_values_out_of_range(DeviceJ * device, ArrayJ * src, ArrayJ * values, ArrayJ * dst, float min_value, float max_value)
Expand All @@ -55,14 +60,14 @@ ArrayJ Tier4::remove_labels_with_map_values_within_range(DeviceJ * device, Array
return ArrayJ{cle::tier4::remove_labels_with_map_values_within_range_func(device->get(), src->get(), values->get(), dst == nullptr ? nullptr : dst->get(), min_value, max_value)};
}

ArrayJ Tier4::exclude_labels_with_map_values_out_of_range(DeviceJ * device, ArrayJ * src, ArrayJ * values, ArrayJ * dst, float min_value_range, float max_value_range)
ArrayJ Tier4::exclude_labels_with_map_values_out_of_range(DeviceJ * device, ArrayJ * values_map, ArrayJ * label_map_input, ArrayJ * dst, float minimum_value_range, float maximum_value_range)
{
return ArrayJ{cle::tier4::exclude_labels_with_map_values_out_of_range_func(device->get(), src->get(), values->get(), dst == nullptr ? nullptr : dst->get(), min_value_range, max_value_range)};
return ArrayJ{cle::tier4::exclude_labels_with_map_values_out_of_range_func(device->get(), values_map->get(), label_map_input->get(), dst == nullptr ? nullptr : dst->get(), minimum_value_range, maximum_value_range)};
}

ArrayJ Tier4::exclude_labels_with_map_values_within_range(DeviceJ * device, ArrayJ * src, ArrayJ * values, ArrayJ * dst, float min_value_range, float max_value_range)
ArrayJ Tier4::exclude_labels_with_map_values_within_range(DeviceJ * device, ArrayJ * values_map, ArrayJ * label_map_input, ArrayJ * dst, float minimum_value_range, float maximum_value_range)
{
return ArrayJ{cle::tier4::exclude_labels_with_map_values_within_range_func(device->get(), src->get(), values->get(), dst == nullptr ? nullptr : dst->get(), min_value_range, max_value_range)};
return ArrayJ{cle::tier4::exclude_labels_with_map_values_within_range_func(device->get(), values_map->get(), label_map_input->get(), dst == nullptr ? nullptr : dst->get(), minimum_value_range, maximum_value_range)};
}

ArrayJ Tier4::extension_ratio_map(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
Expand Down
4 changes: 2 additions & 2 deletions native/clesperantoj/src/tier6j.cpp
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Expand Up @@ -25,9 +25,9 @@ ArrayJ Tier6::masked_voronoi_labeling(DeviceJ * device, ArrayJ * src, ArrayJ * m
return ArrayJ{cle::tier6::masked_voronoi_labeling_func(device->get(), src->get(), mask->get(), dst == nullptr ? nullptr : dst->get())};
}

ArrayJ Tier6::voronoi_labeling(DeviceJ * device, ArrayJ * src, ArrayJ * dst)
ArrayJ Tier6::voronoi_labeling(DeviceJ * device, ArrayJ * input_binary, ArrayJ * output_labels)
{
return ArrayJ{cle::tier6::voronoi_labeling_func(device->get(), src->get(), dst == nullptr ? nullptr : dst->get())};
return ArrayJ{cle::tier6::voronoi_labeling_func(device->get(), input_binary->get(), output_labels == nullptr ? nullptr : output_labels->get())};
}

ArrayJ Tier6::remove_small_labels(DeviceJ * device, ArrayJ * src, ArrayJ * dst, float minimum_size)
Expand Down
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