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Verified Commit df9c66e0 authored by Lars Bilke's avatar Lars Bilke
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Refactored to use CPM. addEmiDataToMesh compiles.

parent 84fa8d7e
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1 merge request!1Refactor for OGS 6.4.0
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CMakeLists.txt
+ 42
− 22
View file @ df9c66e0
cmake_minimum_required(VERSION 2.8.12)
cmake_minimum_required(VERSION 3.16)
project(VisOgsTools)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
${CMAKE_SOURCE_DIR}/ogs/scripts/cmake/cmake
${CMAKE_SOURCE_DIR}/ogs/scripts/cmake)
include(CompilerSetup)
include(ProjectSetup)
include(${PROJECT_SOURCE_DIR}/cmake/CPM.cmake)
find_package( Qt4 )
add_subdirectory(${CMAKE_SOURCE_DIR}/ogs)
include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
include_directories(
${CMAKE_SOURCE_DIR}/ogs
${CMAKE_SOURCE_DIR}/ogs/ThirdParty
${CMAKE_SOURCE_DIR}/ogs/ThirdParty/tclap/include
${Boost_INCLUDE_DIRS}
${CONAN_INCLUDE_DIRS}
CPMFindPackage(
NAME Boost
VERSION 1.69.0
URL https://boostorg.jfrog.io/artifactory/main/release/1.69.0/source/boost_1_69_0.tar.gz
)
if(Boost_ADDED)
add_library(Boost::boost INTERFACE IMPORTED)
target_include_directories(Boost::boost INTERFACE "${Boost_SOURCE_DIR}")
endif()
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
)
endif()
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 ${ogs_SOURCE_DIR}/
)
endif()
# find_package(Qt4)
# include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake) include_directories(
# ${CMAKE_SOURCE_DIR}/ogs ${CMAKE_SOURCE_DIR}/ogs/ThirdParty
# ${CMAKE_SOURCE_DIR}/ogs/ThirdParty/tclap/include ${Boost_INCLUDE_DIRS}
# ${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
+ 8
− 8
View file @ df9c66e0
add_executable(addEmiDataToMesh addEmiDataToMesh.cpp)
target_link_libraries(addEmiDataToMesh
logog
BaseLib
FileIO
InSituLib
${VTK_LIBRARIES}
)
ADD_VTK_DEPENDENCY(addEmiDataToMesh)
target_link_libraries(
addEmiDataToMesh
ApplicationsFileIO
BaseLib
MeshLib
tclap
ogs_include
Boost::boost)
set_target_properties(addEmiDataToMesh PROPERTIES FOLDER Utilities)
addEmiDataToMesh/addEmiDataToMesh.cpp
+ 54
− 71
View file @ df9c66e0
......@@ -12,56 +12,46 @@
*/
#include <algorithm>
#include <tclap/CmdLine.h>
// TCLAP
#include "tclap/CmdLine.h"
// ThirdParty/logog
#include "logog/include/logog.hpp"
// BaseLib
#include "BaseLib/LogogSimpleFormatter.h"
// FileIO
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "FileIO/CsvInterface.h"
// GeoLib
#include "GeoLib/Grid.h"
#include "Applications/FileIO/CsvInterface.h"
#include "BaseLib/Logging.h"
#include "GeoLib/AnalyticalGeometry.h"
// MeshLib
#include "GeoLib/Grid.h"
#include "MathLib/GeometricBasics.h"
#include "MeshLib/Elements/Element.h"
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Node.h"
#include "MeshLib/Properties.h"
#include "MeshLib/PropertyVector.h"
#include "MeshLib/Elements/Element.h"
#include "MeshLib/MeshEditing/projectMeshOntoPlane.h"
std::vector<double> getDataFromCSV(MeshLib::Mesh const& mesh, std::vector<GeoLib::Point*> data_points)
std::vector<double> getDataFromCSV(MeshLib::Mesh const &mesh, std::vector<GeoLib::Point *> data_points)
{
GeoLib::Point const origin(0, 0, 0);
MathLib::Vector3 const normal(0,0,-1);
MeshLib::Mesh* flat_mesh (MeshLib::projectMeshOntoPlane(mesh, origin, normal));
std::size_t n_elems (flat_mesh->getNElements());
auto nodes = mesh.getNodes();
std::vector<MeshLib::Node *> flat_nodes;
for (auto n : nodes)
{
flat_nodes.emplace_back(new MeshLib::Node((*n)[0], (*n)[1], 0));
}
std::size_t n_elems(mesh.getNumberOfElements());
std::vector<double> data(n_elems, 0.0);
std::vector<std::size_t> counter(n_elems, 0);
std::vector<MeshLib::Node*> const& nodes (flat_mesh->getNodes());
GeoLib::Grid<MeshLib::Node> grid(nodes.cbegin(), nodes.cend());
GeoLib::Grid<MeshLib::Node> grid(flat_nodes.cbegin(), flat_nodes.cend());
std::size_t const n_points (data_points.size());
for (std::size_t i=0; i<n_points; ++i)
std::size_t const n_points(data_points.size());
for (std::size_t i = 0; i < n_points; ++i)
{
MeshLib::Node const pnt((*data_points[i])[0], (*data_points[i])[1], 0.0);
MeshLib::Node const*const node = grid.getNearestPoint(pnt);
std::vector<MeshLib::Element*> const& conn_elems (node->getElements());
std::size_t const n_conn_elems (conn_elems.size());
for (std::size_t j=0; j<n_conn_elems; ++j)
MeshLib::Node const *const node = grid.getNearestPoint(pnt);
std::vector<MeshLib::Element *> const &conn_elems(node->getElements());
std::size_t const n_conn_elems(conn_elems.size());
for (std::size_t j = 0; j < n_conn_elems; ++j)
{
if (GeoLib::gaussPointInTriangle(pnt, *conn_elems[j]->getNode(0), *conn_elems[j]->getNode(1), *conn_elems[j]->getNode(2)))
if (MathLib::gaussPointInTriangle(pnt, *conn_elems[j]->getNode(0), *conn_elems[j]->getNode(1), *conn_elems[j]->getNode(2)))
{
std::size_t const idx (conn_elems[j]->getID());
std::size_t const idx(conn_elems[j]->getID());
data[idx] += ((*data_points[i])[2]);
counter[idx]++;
break;
......@@ -69,28 +59,32 @@ std::vector<double> getDataFromCSV(MeshLib::Mesh const& mesh, std::vector<GeoLib
}
}
for (std::size_t i=0; i<n_elems; ++i)
for (std::size_t i = 0; i < n_elems; ++i)
if (counter[i] > 0)
data[i] /= static_cast<double>(counter[i]);
delete flat_mesh;
for (auto n : flat_nodes)
{
delete n;
}
return data;
}
std::vector<double> addFilesAsArrays(std::string csv_base_name, MeshLib::Mesh *mesh, std::string const& name_specifier)
std::vector<double> addFilesAsArrays(std::string csv_base_name, MeshLib::Mesh *mesh, std::string const &name_specifier)
{
std::vector<GeoLib::Point*> points;
std::vector<GeoLib::Point*> points2;
std::vector<GeoLib::Point*> points3;
std::vector<GeoLib::Point *> points;
std::vector<GeoLib::Point *> points2;
std::vector<GeoLib::Point *> points3;
std::string file_name = csv_base_name + "_A_" + name_specifier + ".txt";
INFO ("Reading file %s.", file_name.c_str());
int e1 = FileIO::CsvInterface::readPoints(file_name, '\t', points, 1, 2, 3);
INFO("Reading file {:s}.", file_name.c_str());
int e1 = FileIO::CsvInterface::readPoints(file_name, '\t', points, 1, 2, 3);
file_name = csv_base_name + "_B_" + name_specifier + ".txt";
INFO ("Reading file %s.", file_name.c_str());
INFO("Reading file {:s}.", file_name.c_str());
int e2 = FileIO::CsvInterface::readPoints(file_name, '\t', points2, 1, 2, 3);
file_name = csv_base_name + "_C_" + name_specifier + ".txt";
INFO ("Reading file %s.", file_name.c_str());
INFO("Reading file {:s}.", file_name.c_str());
int e3 = FileIO::CsvInterface::readPoints(file_name, '\t', points3, 1, 2, 3);
points.insert(points.end(), points2.begin(), points2.end());
......@@ -98,7 +92,7 @@ std::vector<double> addFilesAsArrays(std::string csv_base_name, MeshLib::Mesh *m
if (e1 < 0 || e2 < 0 || e3 < 0 || points.empty())
{
ERR ("Error reading CSV-file.");
ERR("Error reading CSV-file.");
delete mesh;
std::vector<double> no_data;
return no_data;
......@@ -110,47 +104,41 @@ std::vector<double> addFilesAsArrays(std::string csv_base_name, MeshLib::Mesh *m
return data;
}
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("Add EMI data as a scalar cell array to a 2d mesh.", ' ', "0.1");
// I/O params
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
cmd.add(mesh_out);
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> csv_in("", "csv",
"csv-file containing EMI data to be added as a scalar array.",
true, "", "name of the csv input file");
"csv-file containing EMI data to be added as a scalar array.",
true, "", "name of the csv input file");
cmd.add(csv_in);
cmd.parse(argc, argv);
INFO ("Reading mesh %s.", mesh_in.getValue().c_str());
MeshLib::Mesh* mesh (MeshLib::IO::VtuInterface::readVTUFile(mesh_in.getValue()));
INFO("Reading mesh {:s}.", mesh_in.getValue().c_str());
MeshLib::Mesh *mesh(MeshLib::IO::VtuInterface::readVTUFile(mesh_in.getValue()));
if (mesh == nullptr)
{
ERR ("Error reading mesh file.");
ERR("Error reading mesh file.");
return -2;
}
if (mesh->getDimension() != 2)
{
ERR ("This utility can handle only 2d meshes at this point.");
ERR("This utility can handle only 2d meshes at this point.");
delete mesh;
return -3;
}
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
INFO("Mesh read: {:d} nodes, {:d} elements.", mesh->getNumberOfNodes(), mesh->getNumberOfElements());
/*
std::vector<GeoLib::Point*> points;
......@@ -169,26 +157,21 @@ int main (int argc, char* argv[])
if (data.empty())
return -1;
std::string const h_prop_name("TM_DD_H");
boost::optional< MeshLib::PropertyVector<double>&> h_vector = mesh->getProperties().createNewPropertyVector<double>(h_prop_name, MeshLib::MeshItemType::Cell);
auto h_vector = mesh->getProperties().createNewPropertyVector<double>(h_prop_name, MeshLib::MeshItemType::Cell);
std::copy(data.cbegin(), data.cend(), std::back_inserter(*h_vector));
data = addFilesAsArrays(csv_in.getValue(), mesh, "V");
if (data.empty())
return -1;
std::string const v_prop_name("TM_DD_V");
boost::optional< MeshLib::PropertyVector<double>&> v_vector = mesh->getProperties().createNewPropertyVector<double>(v_prop_name, MeshLib::MeshItemType::Cell);
auto v_vector = mesh->getProperties().createNewPropertyVector<double>(v_prop_name, MeshLib::MeshItemType::Cell);
std::copy(data.cbegin(), data.cend(), std::back_inserter(*v_vector));
INFO ("Writing result...");
INFO("Writing result...");
MeshLib::IO::VtuInterface vtu(mesh);
vtu.writeToFile(mesh_out.getValue());
delete mesh;
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
cmake/CPM.cmake 0 → 100644
+ 21
− 0
View file @ df9c66e0
set(CPM_DOWNLOAD_VERSION 0.32.2)
if(CPM_SOURCE_CACHE)
# Expand relative path. This is important if the provided path contains a tilde (~)
get_filename_component(CPM_SOURCE_CACHE ${CPM_SOURCE_CACHE} ABSOLUTE)
set(CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
elseif(DEFINED ENV{CPM_SOURCE_CACHE})
set(CPM_DOWNLOAD_LOCATION "$ENV{CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
else()
set(CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
endif()
if(NOT (EXISTS ${CPM_DOWNLOAD_LOCATION}))
message(STATUS "Downloading CPM.cmake to ${CPM_DOWNLOAD_LOCATION}")
file(DOWNLOAD
https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
${CPM_DOWNLOAD_LOCATION}
)
endif()
include(${CPM_DOWNLOAD_LOCATION})
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