add processing of pli data

library/phx/line_segments.hpp

+
+#ifndef LIBRARY_PHX_LINE_SEGMENTS_HPP_
+#define LIBRARY_PHX_LINE_SEGMENTS_HPP_
+
+#include <vector>
+#include <glm/glm.hpp>
+
+namespace phx {
+
+	struct line_segments
+	{
+		std::vector<glm::vec3>     vertices;
+		std::vector<glm::u8vec4>   colors;
+		std::vector<std::uint32_t> indices;
+		float                      radius = 1.0f;
+
+	};
+}
+#endif
\ No newline at end of file

library/phx/pli_loader.cpp

@@ -18,8 +18,8 @@ SUPPRESS_WARNINGS_END
 
 namespace phx {
 
-	std::unique_ptr<phx::Resource> PLILoader::Load(
-		const ResourceDeclaration& declaration) {
+	std::unique_ptr<phx::Resource> PLILoader::Load(const ResourceDeclaration& declaration) 
+	{
 
 		//check for all important information
 		if (declaration.find("file_name") == declaration.end() ||
@@ -138,9 +138,11 @@ namespace phx {
 			glm::vec3(0)
 		);
 
-		tbb::parallel_for (std::size_t(0), size_vec[2], std::size_t(1), [&](std::size_t x) {
-			tbb::parallel_for (std::size_t(0), size_vec[3], std::size_t(1), [&](std::size_t y) {
-				tbb::parallel_for (std::size_t(0), size_vec[0], std::size_t(1), [&](std::size_t z) {
+		//collapse nested loops for (hopefully) better performance
+		tbb::parallel_for(tbb::blocked_range3d<int>(std::size_t(0), size_vec[2], std::size_t(0), size_vec[3], std::size_t(0), size_vec[0]), [&](const tbb::blocked_range3d<int> &r) {
+			for (int x = r.pages().begin(), x_end = r.pages().end(); x < x_end; x++) {
+				for (int y = r.rows().begin(), y_end = r.rows().end(); y < y_end; y++) {
+					for (int z = r.cols().begin(), z_end = r.cols().end(); z < z_end; z++) {
 
 						const size_t padded_coord =
 							(x + zero_pad_) + (size_vec[2] + 2 * zero_pad_) *
@@ -152,8 +154,9 @@ namespace phx {
 							glm::vec3(orientation_data[z][0][x][y],
 								orientation_data[z][1][x][y],
 								orientation_data[z][2][x][y]);
-				});
-			});
+					}
+				}
+			}
 		});
 
 		//free memory
@@ -166,6 +169,7 @@ namespace phx {
 		resource->SetRetardation(retardation_result);
 		resource->SetTransmittance(transmittance_result);
 
+		//free memory
 		orientation_result.resize(0);
 		transmittance_result.resize(0);
 		retardation_result.resize(0);

library/phx/pli_processor.cpp

+
+#include "phx/pli_processor.hpp"
+#include "phx/pli_loader.hpp"
+#include "phx/pli_region.hpp"
+#include "phx/resource_declaration.hpp"
+#include "phx/resource_manager.hpp"
+#include "phx/line_segments.hpp"
+#include "phx/resource_utils.hpp"
+
+#include <string>
+
+namespace phx {
+
+	line_segments make_hedgehog(Resource* resource, const float length = 1.0f, const float radius = 1.0f)
+	{
+		auto pli_region = dynamic_cast<PLIRegion *>(resource);
+		auto size = pli_region->GetSize();
+
+		//create return value
+		line_segments segments;
+
+		segments.radius = radius;
+
+		for (auto z = 0; z < size[0]; z++)
+		{
+			for (auto x = 0; x < size[1]; x++)
+			{
+				for (auto y = 0; y < size[2]; y++)
+				{
+					const auto center = glm::vec3(x, y, z);
+					const auto direction = glm::normalize(glm::vec3(pli_region->GetOrientation[z][0][x][y], pli_region->GetOrientation[z][1][x][y], pli_region->GetOrientation[z][2][x][y]));
+
+					segments.vertices.push_back(center + length / 2.0f * direction);
+					segments.vertices.push_back(center - length / 2.0f * direction);
+					segments.colors.push_back(glm::u8vec4(glm::abs(direction) * 255.0f, 255));
+					segments.colors.push_back(glm::u8vec4(glm::abs(direction) * 255.0f, 255));
+					segments.indices.push_back(static_cast<std::uint32_t>(segments.vertices.size() - 2));
+					segments.indices.push_back(static_cast<std::uint32_t>(segments.vertices.size() - 1));
+				}
+			}
+		}
+		return segments;
+	}
+
+
+
+	void pli_prepare_data() {
+
+		//TODO: find out how ResourceDeclaration/ nlohmann-json works
+		//TODO: find out why Load doesn't work
+		std::string addr("O:/Documents/MSA0309_s0536-0695.h5");
+		ResourceDeclaration& declaration(
+			(ResourceDeclaration)addr, { { "from",{ { "X", 0.0f },{ "Y", 0.0f },{ "Z", 0.0f } } },
+			{ "to",{ { "X", 360.0f },{ "Y", 560.0f },{ "Z", 25.0f } } },
+			{ "stride",{ { "X", 3.0f },{ "Y", 3.0f },{ "Z", 3.0f } } } },
+			false);
+
+		auto pli_resource = PLILoader::Load(declaration);
+		/*
+		auto pli_resource = ResourceUtils::LoadResourceFromFile<phx::PLIRegion>(
+			R"(O:\Documents\MSA0309_s0536-0695.h5)",
+			{ { "from",{ { "X", 0.0f },{ "Y", 0.0f },{ "Z", 0.0f } } },
+			{ "to",{ { "X", 360.0f },{ "Y", 560.0f },{ "Z", 25.0f } } },
+			{ "stride",{ { "X", 3.0f },{ "Y", 3.0f },{ "Z", 3.0f } } } });
+
+		auto resource = dynamic_cast<Resource *>(pli_resource);
+		auto mesh = make_hedgehog(pli_resource, 1.0f, 1.0f);
+		*/
+
+	}
+}
\ No newline at end of file

library/phx/pli_processor.hpp

+
+#ifndef LIBRARY_PHX_PLI_PROCESSOR_HPP_
+#define LIBRARY_PHX_PLI_PROCESSOR_HPP_
+
+
+#include "phx/pli_processor.hpp"
+#include "phx/pli_region.hpp"
+#include "phx/resource_declaration.hpp"
+#include "phx/resource_manager.hpp"
+#include "phx/line_segments.hpp"
+
+
+namespace phx{
+	line_segments make_hedgehog(Resource* resource, const float length = 1.0f, const float radius = 1.0f);
+
+}
+
+#endif
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