Merge branch 'TomFischer-ComputeSurfaceNodeIDsInPolygonalRegion'

Applications/Utils/CMakeLists.txt

 add_subdirectory(FileConverter)
 add_subdirectory(GeoTools)
+add_subdirectory(MeshGeoTools)
 add_subdirectory(MeshEdit)
 add_subdirectory(SimpleMeshCreation)
 

Applications/Utils/MeshGeoTools/CMakeLists.txt

+ADD_EXECUTABLE( ComputeSurfaceNodeIDsInPolygonalRegion ComputeSurfaceNodeIDsInPolygonalRegion.cpp )
+SET_TARGET_PROPERTIES( ComputeSurfaceNodeIDsInPolygonalRegion PROPERTIES FOLDER Utils)
+TARGET_LINK_LIBRARIES( ComputeSurfaceNodeIDsInPolygonalRegion
+	MeshLib
+	FileIO
+	GeoLib
+	MathLib
+	${Boost_LIBRARIES}
+	${OGS_VTK_REQUIRED_LIBS}
+)
+

Applications/Utils/MeshGeoTools/ComputeSurfaceNodeIDsInPolygonalRegion.cpp

+/**
+ * @file ComputeSurfaceNodeIDsInPolygonalRegion.cpp
+ * @brief Computes mesh node ids of mesh nodes within a polygonal region, that resides on the surface.
+ *
+ * @copyright
+ * Copyright (c) 2012-2015, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/LICENSE.txt
+ */
+
+#include <algorithm>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "tclap/CmdLine.h"
+#include "logog/include/logog.hpp"
+
+#include "Applications/ApplicationsLib/LogogSetup.h"
+
+#include "BaseLib/LogogSimpleFormatter.h"
+#include "BaseLib/StringTools.h"
+#include "BaseLib/FileTools.h"
+
+#include "FileIO/readMeshFromFile.h"
+#include "FileIO/readGeometryFromFile.h"
+
+#include "GeoLib/GEOObjects.h"
+#include "GeoLib/Polygon.h"
+
+#include "MathLib/Vector3.h"
+
+#include "MeshLib/Mesh.h"
+#include "MeshLib/Node.h"
+#include "MeshLib/MeshSurfaceExtraction.h"
+
+void writeToFile(std::string const& id_area_fname, std::string const& csv_fname,
+	std::vector<std::pair<std::size_t, double>> const& ids_and_areas,
+	std::vector<MeshLib::Node*> const& mesh_nodes)
+{
+	std::ofstream ids_and_area_out(id_area_fname);
+	if (!ids_and_area_out) {
+		ERR("Unable to open the file \"%s\" - aborting.", id_area_fname.c_str());
+		std::abort();
+	}
+	std::ofstream csv_out(csv_fname);
+	if (!csv_out) {
+		ERR("Unable to open the file \"%s\" - aborting.", csv_fname.c_str());
+		std::abort();
+	}
+
+	ids_and_area_out << std::setprecision(20);
+	csv_out << std::setprecision(20);
+
+	ids_and_area_out << ids_and_areas[0].first << " " << ids_and_areas[0].second;
+	csv_out << "ID x y z area node_id\n"; // CSV header
+	csv_out << 0 << " " << *mesh_nodes[ids_and_areas[0].first]
+			<< ids_and_areas[0].second << " " << ids_and_areas[0].first;
+	for (std::size_t k(1); k<ids_and_areas.size(); k++) {
+		ids_and_area_out << "\n"
+			<< ids_and_areas[k].first << " " << ids_and_areas[k].second;
+		csv_out << "\n" << k << " " << *mesh_nodes[ids_and_areas[k].first]
+			<< ids_and_areas[k].second << " " << ids_and_areas[k].first;
+	}
+	ids_and_area_out << "\n";
+	csv_out << "\n";
+}
+
+int main (int argc, char* argv[])
+{
+	ApplicationsLib::LogogSetup logog_setup;
+
+	TCLAP::CmdLine cmd("Computes ids of mesh nodes that are in polygonal "
+		"regions and resides on the top surface. The polygonal regions have to "
+		"be given in a gml- or gli-file. The found mesh nodes and the associated"
+		" area are written as txt and csv data.", ' ', "0.1");
+	TCLAP::ValueArg<std::string> mesh_in("m", "mesh-input-file",
+		"the name of the file containing the input mesh", true,
+		"", "file name of input mesh");
+	cmd.add(mesh_in);
+	TCLAP::ValueArg<std::string> geo_in("g", "geo-file",
+		"the name of the gml file containing the polygons", true,
+		"", "file name of input geometry");
+	cmd.add(geo_in);
+
+	cmd.parse(argc, argv);
+
+	std::unique_ptr<MeshLib::Mesh const> mesh(FileIO::readMeshFromFile(mesh_in.getValue()));
+	INFO("Mesh read: %ul nodes, %ul elements.", mesh->getNNodes(), mesh->getNElements());
+
+	GeoLib::GEOObjects geo_objs;
+	FileIO::readGeometryFromFile(geo_in.getValue(), geo_objs);
+	std::vector<std::string> geo_names;
+	geo_objs.getGeometryNames(geo_names);
+	INFO("Geometry \"%s\" read: %ul points, %ul polylines.",
+		geo_names[0].c_str(),
+		geo_objs.getPointVec(geo_names[0])->size(),
+		geo_objs.getPolylineVec(geo_names[0])->size());
+
+	MathLib::Vector3 const dir(0.0, 0.0, -1.0);
+	double angle(90);
+
+	auto computeElementTopSurfaceAreas = [](MeshLib::Mesh const& mesh,
+		MathLib::Vector3 const& d, double angle)
+	{
+		std::unique_ptr<MeshLib::Mesh> surface_mesh(
+			MeshLib::MeshSurfaceExtraction::getMeshSurface(mesh, d, angle));
+		return MeshLib::MeshSurfaceExtraction::getSurfaceAreaForNodes(
+			*surface_mesh.get());
+	};
+
+	std::vector<double> areas(computeElementTopSurfaceAreas(*mesh, dir, angle));
+	std::vector<GeoLib::Point*> all_sfc_pnts(
+		MeshLib::MeshSurfaceExtraction::getSurfaceNodes(*mesh, dir, angle)
+	);
+
+	std::for_each(all_sfc_pnts.begin(), all_sfc_pnts.end(), [](GeoLib::Point* p) { (*p)[2] = 0.0; });
+
+	std::vector<MeshLib::Node*> const& mesh_nodes(mesh->getNodes());
+	GeoLib::PolylineVec const* ply_vec(
+		geo_objs.getPolylineVecObj(geo_names[0])
+	);
+	std::vector<GeoLib::Polyline*> const& plys(*(ply_vec->getVector()));
+
+	for (std::size_t j(0); j<plys.size(); j++) {
+		if (! plys[j]->isClosed()) {
+			continue;
+		}
+		std::string polygon_name;
+		ply_vec->getNameOfElement(plys[j], polygon_name);
+		if (polygon_name.empty())
+			polygon_name = "Polygon-" + std::to_string(j);
+		// create Polygon from Polyline
+		GeoLib::Polygon const& polygon(*(plys[j]));
+		// ids of mesh nodes on surface that are within the given polygon
+		std::vector<std::pair<std::size_t, double>> ids_and_areas;
+		for (std::size_t k(0); k<all_sfc_pnts.size(); k++) {
+			GeoLib::Point const& pnt(*(all_sfc_pnts[k]));
+			if (polygon.isPntInPolygon(pnt)) {
+				ids_and_areas.push_back(std::make_pair(pnt.getID(), areas[k]));
+			}
+		}
+		if (ids_and_areas.empty()) {
+			ERR("Polygonal part of surface \"%s\" doesn't contains nodes. No "
+				"output will be generated.", polygon_name.c_str());
+			continue;
+		}
+
+		std::string const out_path(BaseLib::extractPath(geo_in.getValue()));
+		std::string id_and_area_fname(out_path + polygon_name);
+		std::string csv_fname(out_path + polygon_name);
+		id_and_area_fname += std::to_string(j) + ".txt";
+		csv_fname += std::to_string(j) + ".csv";
+		INFO("Polygonal part of surface \"%s\" contains %ul nodes. Writting to"
+			" files \"%s\" and \"%s\".",
+			polygon_name.c_str(),
+			ids_and_areas.size(),
+			id_and_area_fname.c_str(),
+			csv_fname.c_str()
+		);
+		writeToFile(id_and_area_fname, csv_fname, ids_and_areas, mesh_nodes);
+	}
+
+	std::for_each(all_sfc_pnts.begin(), all_sfc_pnts.end(), std::default_delete<GeoLib::Point>());
+
+	return 0;
+}

FileIO/CMakeLists.txt

@@ -9,6 +9,8 @@ set(SOURCES
 	GMSHInterface.cpp
 	PetrelInterface.h
 	PetrelInterface.cpp
+	readGeometryFromFile.h
+	readGeometryFromFile.cpp
 	readMeshFromFile.h
 	readMeshFromFile.cpp
 	writeGeometryToFile.h

FileIO/readGeometryFromFile.cpp

+/**
+ *
+ * \copyright
+ * Copyright (c) 2012-2015, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/project/license
+ *
+ */
+
+#include "readGeometryFromFile.h"
+
+#include <vector>
+
+#include "BaseLib/FileTools.h"
+
+#include "FileIO/XmlIO/Boost/BoostXmlGmlInterface.h"
+#include "FileIO/Legacy/OGSIOVer4.h"
+
+#include "GeoLib/GEOObjects.h"
+
+namespace FileIO
+{
+void
+readGeometryFromFile(std::string const& fname, GeoLib::GEOObjects & geo_objs)
+{
+	if (BaseLib::getFileExtension(fname).compare("gml") == 0) {
+		FileIO::BoostXmlGmlInterface xml(geo_objs);
+		xml.readFile(fname);
+	} else {
+		std::vector<std::string> errors;
+		std::string geo_name(BaseLib::extractBaseNameWithoutExtension(fname));
+		FileIO::Legacy::readGLIFileV4(fname, &geo_objs, geo_name, errors);
+	}
+}
+}

FileIO/readGeometryFromFile.h

+/**
+ *
+ * \copyright
+ * Copyright (c) 2012-2015, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/project/license
+ *
+ */
+
+#ifndef READGEOMETRYFROMFILE_H
+#define READGEOMETRYFROMFILE_H
+
+#include <string>
+
+namespace GeoLib
+{
+	class GEOObjects;
+}
+
+namespace FileIO
+{
+	void
+	readGeometryFromFile(std::string const& fname, GeoLib::GEOObjects & geo_objs);
+}
+
+#endif // READGEOMETRYFROMFILE_H