addScalarArrayTimeSeries compiles.

CMakeLists.txt

@@ -3,36 +3,39 @@ project(VisOgsTools)
 
 include(${PROJECT_SOURCE_DIR}/cmake/CPM.cmake)
 
-CPMFindPackage(
-    NAME Boost
-    VERSION 1.69.0
-    URL https://boostorg.jfrog.io/artifactory/main/release/1.69.0/source/boost_1_69_0.tar.gz
+cpmfindpackage(
+  NAME
+  Boost
+  VERSION
+  1.69.0
+  URL
+  https://boostorg.jfrog.io/artifactory/main/release/1.69.0/source/boost_1_69_0.tar.gz
 )
 if(Boost_ADDED)
-    add_library(Boost::boost INTERFACE IMPORTED)
-    target_include_directories(Boost::boost INTERFACE "${Boost_SOURCE_DIR}")
+  add_library(Boost::boost INTERFACE IMPORTED)
+  target_include_directories(Boost::boost INTERFACE "${Boost_SOURCE_DIR}")
 endif()
-CPMAddPackage(
-    NAME tclap
-    GITHUB_REPOSITORY ufz/tclap
-    VERSION 1.2.4
-    GIT_TAG 098dd0fe07a31618f3c2a9f8727bb01c8c5d61e2
-    DOWNLOAD_ONLY YES
-)
+cpmaddpackage(
+  NAME
+  tclap
+  GITHUB_REPOSITORY
+  ufz/tclap
+  VERSION
+  1.2.4
+  GIT_TAG
+  098dd0fe07a31618f3c2a9f8727bb01c8c5d61e2
+  DOWNLOAD_ONLY
+  YES)
 if(tclap_ADDED)
-    add_library(tclap INTERFACE IMPORTED)
-    target_include_directories(
-        tclap SYSTEM INTERFACE ${tclap_SOURCE_DIR}/include
-    )
+  add_library(tclap INTERFACE IMPORTED)
+  target_include_directories(tclap SYSTEM INTERFACE ${tclap_SOURCE_DIR}/include)
 endif()
-CPMAddPackage(
+cpmaddpackage(
   "https://gitlab.opengeosys.org/ogs/ogs.git#98aeeb379ac87cc88fb71d111bcb946e2db4c16f@6.4.0-dev"
 )
 if(ogs_ADDED)
-	add_library(ogs_include INTERFACE IMPORTED)
-    target_include_directories(
-        ogs_include SYSTEM INTERFACE ${ogs_SOURCE_DIR}/
-    )
+  add_library(ogs_include INTERFACE IMPORTED)
+  target_include_directories(ogs_include SYSTEM INTERFACE ${ogs_SOURCE_DIR}/)
 endif()
 
 # find_package(Qt4)
@@ -43,6 +46,6 @@ endif()
 # ${CONAN_INCLUDE_DIRS} )
 
 add_subdirectory(addEmiDataToMesh)
-# add_subdirectory(addScalarArrayTimeSeries) add_subdirectory(EmiData2PolyData)
-# add_subdirectory(ErtData2Mesh) if (QT4_FOUND) add_subdirectory(makeBuildings)
-# endif()
+add_subdirectory(addScalarArrayTimeSeries)
+# add_subdirectory(EmiData2PolyData) add_subdirectory(ErtData2Mesh) if
+# (QT4_FOUND) add_subdirectory(makeBuildings) endif()

addEmiDataToMesh/CMakeLists.txt

 add_executable(addEmiDataToMesh addEmiDataToMesh.cpp)
-target_link_libraries(
-  addEmiDataToMesh
-  ApplicationsFileIO
-  BaseLib
-  MeshLib
-  tclap
-  ogs_include
-  Boost::boost)
+target_link_libraries(addEmiDataToMesh ApplicationsFileIO BaseLib MeshLib tclap
+                      ogs_include)
 set_target_properties(addEmiDataToMesh PROPERTIES FOLDER Utilities)

addScalarArrayTimeSeries/CMakeLists.txt

 add_executable(addScalarArrayTimeSeries addScalarArrayTimeSeries.cpp)
-target_link_libraries(addScalarArrayTimeSeries
-	logog
-	BaseLib
-	FileIO
-	InSituLib
-	${VTK_LIBRARIES}
-)
-ADD_VTK_DEPENDENCY(addScalarArrayTimeSeries)
+target_link_libraries(addScalarArrayTimeSeries ApplicationsFileIO BaseLib
+                      MeshLib tclap ogs_include)
 set_target_properties(addScalarArrayTimeSeries PROPERTIES FOLDER Utilities)

addScalarArrayTimeSeries/addScalarArrayTimeSeries.cpp

@@ -17,17 +17,13 @@
 // TCLAP
 #include "tclap/CmdLine.h"
 
-// ThirdParty/logog
-#include "logog/include/logog.hpp"
-
 // BaseLib
-#include "BaseLib/LogogSimpleFormatter.h"
 #include "BaseLib/FileTools.h"
 
 // FileIO
 #include "MeshLib/IO/VtkIO/VtuInterface.h"
-#include "FileIO/CsvInterface.h"
-#include "GeoLib/IO/AsciiRasterInterface.h"
+#include "Applications/FileIO/CsvInterface.h"
+#include "Applications/FileIO/AsciiRasterInterface.h"
 
 // GeoLib
 #include "GeoLib/Point.h"
@@ -41,11 +37,11 @@
 #include "MeshLib/Elements/Element.h"
 #include "MeshLib/Elements/Quad.h"
 
-MeshLib::Mesh*  createMesh()
+MeshLib::Mesh *createMesh()
 {
-	std::string const x_file ("utm_x.csv");
-	std::string const y_file ("utm_y.csv");
-	std::string const z_file ("Z.csv");
+	std::string const x_file("utm_x.csv");
+	std::string const y_file("utm_y.csv");
+	std::string const z_file("Z.csv");
 	std::vector<double> x;
 	int const e1 = FileIO::CsvInterface::readColumn<double>(x_file, '\t', x, 0);
 	std::vector<double> y;
@@ -53,30 +49,30 @@ MeshLib::Mesh*  createMesh()
 	std::vector<double> z;
 	int const e3 = FileIO::CsvInterface::readColumn<double>(z_file, '\t', z, 0);
 
-	if (e1!=0 || e2!=0 || e3!=0)
+	if (e1 != 0 || e2 != 0 || e3 != 0)
 		return nullptr;
 
 	if (x.size() != y.size())
 		return nullptr;
 
-	std::size_t const n_cols (x.size());
-	std::size_t const n_rows (z.size());
-	std::vector<MeshLib::Node*> nodes;
-	nodes.reserve(n_rows*n_cols);
-	for (std::size_t r=0; r<n_rows; ++r)
-		for (std::size_t c=0; c<n_cols; ++c)
+	std::size_t const n_cols(x.size());
+	std::size_t const n_rows(z.size());
+	std::vector<MeshLib::Node *> nodes;
+	nodes.reserve(n_rows * n_cols);
+	for (std::size_t r = 0; r < n_rows; ++r)
+		for (std::size_t c = 0; c < n_cols; ++c)
 			nodes.push_back(new MeshLib::Node(x[c], y[c], z[r], nodes.size()));
 
-	std::vector<MeshLib::Element*> elems;
-	elems.reserve((n_rows-1)*(n_cols-1));
+	std::vector<MeshLib::Element *> elems;
+	elems.reserve((n_rows - 1) * (n_cols - 1));
 	std::vector<std::size_t> mats;
-	mats.reserve((n_rows-1)*(n_cols-1));
-	for (std::size_t r=0; r<n_rows-2; ++r)
+	mats.reserve((n_rows - 1) * (n_cols - 1));
+	for (std::size_t r = 0; r < n_rows - 2; ++r)
 	{
-		std::size_t base_idx = r*n_cols;
-		for (std::size_t c=0; c<n_cols-1; ++c)
+		std::size_t base_idx = r * n_cols;
+		for (std::size_t c = 0; c < n_cols - 1; ++c)
 		{
-			std::array<MeshLib::Node*, 4> quad_nodes;
+			std::array<MeshLib::Node *, 4> quad_nodes;
 			quad_nodes[0] = nodes[base_idx + c];
 			quad_nodes[1] = nodes[base_idx + c + n_cols];
 			quad_nodes[2] = nodes[base_idx + c + n_cols + 1];
@@ -86,8 +82,8 @@ MeshLib::Mesh*  createMesh()
 		}
 	}
 
-	MeshLib::Mesh* mesh = new MeshLib::Mesh("Mesh", nodes, elems);
-	boost::optional<std::vector<int>&> mat_prop (mesh->getProperties().createNewPropertyVector<int>("MaterialIDs", MeshLib::MeshItemType::Cell));
+	MeshLib::Mesh *mesh = new MeshLib::Mesh("Mesh", nodes, elems);
+	auto mat_prop(mesh->getProperties().createNewPropertyVector<int>("MaterialIDs", MeshLib::MeshItemType::Cell));
 	mat_prop->insert(mat_prop->end(), mats.begin(), mats.end());
 
 	return mesh;
@@ -100,49 +96,44 @@ std::string number2str(std::size_t n)
 	return convert.str();
 }
 
-std::string output_question(std::string const& output_name)
+std::string output_question(std::string const &output_name)
 {
-	WARN ("Output file %s already exists. Overwrite? (y/n)", output_name);
+	WARN("Output file {:s} already exists. Overwrite? (y/n)", output_name);
 	std::string input;
 	std::cin >> input;
 	return input;
 }
 
-bool overwriteFiles(std::string const& output_name)
+bool overwriteFiles(std::string const &output_name)
 {
 	if (!BaseLib::IsFileExisting(output_name))
 		return true;
 
-	std::string input ("");
+	std::string input("");
 	while (input != "y" && input != "Y" && input != "n" && input != "N")
 		input = output_question(output_name);
-		
+
 	if (input == "y" || input == "Y")
 		return true;
 	return false;
 }
 
-int main (int argc, char* argv[])
+int main(int argc, char *argv[])
 {
-	LOGOG_INITIALIZE();
-	logog::Cout* logog_cout (new logog::Cout);
-	BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
-	logog_cout->SetFormatter(*custom_format);
-
 	TCLAP::CmdLine cmd("Adds a scalar array time series from a csv-file to an existing mesh or a time series of meshes.", ' ', "0.1");
 
 	// I/O params
 	TCLAP::ValueArg<std::string> mesh_new("b", "base",
-	                                      "Use this if a time series of vtu-files should be created based on a single vtu-file. If a time series *is* already existing, this parameter need not be set.",
-	                                       false, "", "base mesh input");
+										  "Use this if a time series of vtu-files should be created based on a single vtu-file. If a time series *is* already existing, this parameter need not be set.",
+										  false, "", "base mesh input");
 	cmd.add(mesh_new);
 	TCLAP::ValueArg<std::string> mesh_add("t", "output",
-	                                      "This is the base name of the output files, e.g. \'output\' will result in files called \'output0.vtu\', \'output1.vtu\', etc. If a time series is already existing, a new array will simply be added to each time step.",
-	                                       true, "", "name of mesh output");
+										  "This is the base name of the output files, e.g. \'output\' will result in files called \'output0.vtu\', \'output1.vtu\', etc. If a time series is already existing, a new array will simply be added to each time step.",
+										  true, "", "name of mesh output");
 	cmd.add(mesh_add);
 	TCLAP::ValueArg<std::string> csv_in("i", "csv",
-	                                    "CSV-file containing the input information for the scalar arrays. It is assumed that all timesteps are in one file with an empty line between timesteps and with one value per grid cell per time step.",
-	                                    true, "", "csv input file");
+										"CSV-file containing the input information for the scalar arrays. It is assumed that all timesteps are in one file with an empty line between timesteps and with one value per grid cell per time step.",
+										true, "", "csv input file");
 	cmd.add(csv_in);
 	cmd.parse(argc, argv);
 
@@ -150,18 +141,18 @@ int main (int argc, char* argv[])
 
 	if (!csv_in.isSet())
 	{
-		ERR ("Name of csv-file is missing.");
+		ERR("Name of csv-file is missing.");
 		return -5;
 	}
 
 	if (!mesh_add.isSet())
 	{
-		ERR ("Base name of output files is missing.");
+		ERR("Base name of output files is missing.");
 		return -4;
 	}
 
 	int n_rows = -1;
-	MeshLib::Mesh* mesh = nullptr;
+	MeshLib::Mesh *mesh = nullptr;
 	if (mesh_new.isSet())
 	{
 		mesh = MeshLib::IO::VtuInterface::readVTUFile(mesh_new.getValue());
@@ -170,14 +161,14 @@ int main (int argc, char* argv[])
 
 			return -1;
 		}
-		boost::optional<MeshLib::PropertyVector<int>&> materials (mesh->getProperties().getPropertyVector<int>("MaterialIDs"));
+		auto materials(mesh->getProperties().getPropertyVector<int>("MaterialIDs"));
 		n_rows = (*std::max_element(materials->cbegin(), materials->cend())) + 1;
 	}
 
-	std::ifstream in( csv_in.getValue().c_str() );
+	std::ifstream in(csv_in.getValue().c_str());
 	if (!in.is_open())
 	{
-		ERR ("Could not open CSV file.");
+		ERR("Could not open CSV file.");
 		return -2;
 	}
 
@@ -185,46 +176,46 @@ int main (int argc, char* argv[])
 
 	std::string line;
 	std::size_t file_counter(0);
-	bool overwrite (false);
+	bool overwrite(false);
 	while (getline(in, line))
 	{
 		if (!mesh_new.isSet())
 		{
 			mesh = MeshLib::IO::VtuInterface::readVTUFile(mesh_add.getValue() + number2str(file_counter) + ".vtu");
-			if (mesh==nullptr)
+			if (mesh == nullptr)
 			{
-				ERR("No base mesh given and no mesh for time step %d found.", file_counter);
+				ERR("No base mesh given and no mesh for time step {:d} found.", file_counter);
 				return -6;
 			}
-			boost::optional<MeshLib::PropertyVector<int>&> materials (mesh->getProperties().getPropertyVector<int>("MaterialIDs"));
+			auto materials(mesh->getProperties().getPropertyVector<int>("MaterialIDs"));
 			n_rows = (*std::max_element(materials->cbegin(), materials->cend())) + 1;
 		}
 		std::string const prop_name(BaseLib::extractBaseNameWithoutExtension(csv_in.getValue()));
-		boost::optional<MeshLib::PropertyVector<double>&> prop (mesh->getProperties().createNewPropertyVector<double>(prop_name, MeshLib::MeshItemType::Cell));
-		prop->resize(mesh->getNNodes(), 0);
+		auto prop(mesh->getProperties().createNewPropertyVector<double>(prop_name, MeshLib::MeshItemType::Cell));
+		prop->resize(mesh->getNumberOfNodes(), 0);
 
-		for (int i=0; i<=n_rows; ++i)
+		for (int i = 0; i <= n_rows; ++i)
 		{
 			std::list<std::string> fields = BaseLib::splitString(line, ',');
-			int const n_cols (fields.size());
-			if (n_cols != (mesh->getNElements() / n_rows) + 1)
+			int const n_cols(fields.size());
+			if (n_cols != (mesh->getNumberOfElements() / n_rows) + 1)
 				return -3;
 
-			int idx_cnt(i * (n_cols-1));
+			int idx_cnt(i * (n_cols - 1));
 			auto it = fields.cbegin();
 			it++;
 			for (; it != fields.cend(); ++it)
 			{
 				if ((*it).compare("NaN") == 0)
 					(*prop)[idx_cnt++] = nan_value;
-				else 
+				else
 					(*prop)[idx_cnt++] = std::stod(*it);
 			}
 			getline(in, line);
 		}
 
-		INFO ("Writing result #%d...", file_counter);
-		std::string output_name (mesh_add.getValue() + number2str(file_counter) + ".vtu");
+		INFO("Writing result #{:d}...", file_counter);
+		std::string output_name(mesh_add.getValue() + number2str(file_counter) + ".vtu");
 		if (overwrite == false)
 		{
 			overwrite = overwriteFiles(output_name);
@@ -235,19 +226,13 @@ int main (int argc, char* argv[])
 		MeshLib::IO::VtuInterface vtu(mesh);
 		vtu.writeToFile(output_name);
 		file_counter++;
-	
+
 		getline(in, line);
 		if (!line.empty())
 			ERR("something is wrong here.");
 	}
-	
+
 	//delete mesh;
-	delete custom_format;
-	delete logog_cout;
-	LOGOG_SHUTDOWN();
 
 	return 0;
 }
-
-
-