From 189fcd01c2bc3d10b5bef4c8dbdfe3c152dcc883 Mon Sep 17 00:00:00 2001
From: rinkk <karsten.rink@ufz.de>
Date: Thu, 1 Aug 2019 12:47:13 +0200
Subject: [PATCH] added support for GoCAD PLine data, checking for VSet and
Model3d
---
Applications/DataExplorer/mainwindow.cpp | 4 +-
...SurfaceReader.cpp => GocadAsciiReader.cpp} | 206 ++++++++++++++----
...cadTSurfaceReader.h => GocadAsciiReader.h} | 43 +++-
.../FileConverter/GocadTSurfaceReader.cpp | 9 +-
4 files changed, 204 insertions(+), 58 deletions(-)
rename Applications/FileIO/GocadIO/{GocadTSurfaceReader.cpp => GocadAsciiReader.cpp} (68%)
rename Applications/FileIO/GocadIO/{GocadTSurfaceReader.h => GocadAsciiReader.h} (68%)
diff --git a/Applications/DataExplorer/mainwindow.cpp b/Applications/DataExplorer/mainwindow.cpp
index 60810f90f78..beee85aa5a8 100644
--- a/Applications/DataExplorer/mainwindow.cpp
+++ b/Applications/DataExplorer/mainwindow.cpp
@@ -39,7 +39,7 @@
#include "Applications/FileIO/GMSInterface.h"
#include "Applications/FileIO/Gmsh/GMSHInterface.h"
#include "Applications/FileIO/Gmsh/GmshReader.h"
-#include "Applications/FileIO/GocadIO/GocadTSurfaceReader.h"
+#include "Applications/FileIO/GocadIO/GocadAsciiReader.h"
#include "Applications/FileIO/Legacy/OGSIOVer4.h"
#include "Applications/FileIO/PetrelInterface.h"
#include "Applications/FileIO/TetGenInterface.h"
@@ -687,7 +687,7 @@ void MainWindow::loadFile(ImportFileType::type t, const QString &fileName)
else if (t == ImportFileType::GOCAD_TSURF)
{
std::string file_name(fileName.toStdString());
- FileIO::Gocad::GocadTSurfaceReader gcts;
+ FileIO::Gocad::GocadAsciiReader gcts;
std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
if (gcts.readFile(file_name, meshes))
{
diff --git a/Applications/FileIO/GocadIO/GocadTSurfaceReader.cpp b/Applications/FileIO/GocadIO/GocadAsciiReader.cpp
similarity index 68%
rename from Applications/FileIO/GocadIO/GocadTSurfaceReader.cpp
rename to Applications/FileIO/GocadIO/GocadAsciiReader.cpp
index 9287c5b15ab..0f1dd070876 100644
--- a/Applications/FileIO/GocadIO/GocadTSurfaceReader.cpp
+++ b/Applications/FileIO/GocadIO/GocadAsciiReader.cpp
@@ -7,7 +7,7 @@
* http://www.opengeosys.org/LICENSE.txt
*/
-#include "GocadTSurfaceReader.h"
+#include "GocadAsciiReader.h"
#include <logog/include/logog.hpp>
@@ -16,6 +16,7 @@
#include "Applications/FileIO/GocadIO/CoordinateSystem.h"
#include "BaseLib/FileTools.h"
#include "BaseLib/StringTools.h"
+#include "MeshLib/Elements/Line.h"
#include "MeshLib/Elements/Tri.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Node.h"
@@ -27,11 +28,9 @@ namespace Gocad
const std::string mat_id_name = "MaterialIDs";
const std::string eof_error = "Error: Unexpected end of file.";
-GocadTSurfaceReader::GocadTSurfaceReader()
-{
-}
+GocadAsciiReader::GocadAsciiReader() {}
-bool GocadTSurfaceReader::readFile(
+bool GocadAsciiReader::readFile(
std::string const& file_name,
std::vector<std::unique_ptr<MeshLib::Mesh>>& meshes)
{
@@ -43,11 +42,23 @@ bool GocadTSurfaceReader::readFile(
return false;
}
- while (TSurfaceFound(in))
+ GOCAD_DATA_TYPE type;
+ while ((type = datasetFound(in)) != GOCAD_DATA_TYPE::UNDEFINED)
{
+ if (type == GOCAD_DATA_TYPE::VSET || type == GOCAD_DATA_TYPE::MODEL3D)
+ {
+ if (!skipToEND(in))
+ {
+ std::string const t = (type == GOCAD_DATA_TYPE::VSET) ? "VSet" : "Model3D";
+ ERR("Parsing of type %s is not implemented. Skipping section.", t);
+ return false;
+ }
+ continue;
+ }
+
std::string mesh_name = BaseLib::dropFileExtension(file_name) +
std::to_string(meshes.size() + 1);
- std::unique_ptr<MeshLib::Mesh> mesh(readMesh(in, mesh_name));
+ std::unique_ptr<MeshLib::Mesh> mesh(readData(in, type, mesh_name));
if (mesh == nullptr)
{
ERR("File parsing aborted...")
@@ -58,8 +69,9 @@ bool GocadTSurfaceReader::readFile(
return true;
}
-MeshLib::Mesh* GocadTSurfaceReader::readMesh(std::ifstream& in,
- std::string& mesh_name)
+MeshLib::Mesh* GocadAsciiReader::readData(std::ifstream& in,
+ GOCAD_DATA_TYPE const& type,
+ std::string& mesh_name)
{
if (!parseHeader(in, mesh_name))
{
@@ -108,7 +120,21 @@ MeshLib::Mesh* GocadTSurfaceReader::readMesh(std::ifstream& in,
return nullptr;
}
}
- else if (str[0] == "TFACE")
+ else if (type == GOCAD_DATA_TYPE::PLINE && str[0] == "ILINE")
+ {
+ std::vector<MeshLib::Node*> nodes;
+ std::vector<MeshLib::Element*> elems;
+ std::map<std::size_t, std::size_t> node_id_map;
+ INFO("Parsing line %s", mesh_name.c_str());
+ if (!parseLine(in, nodes, elems, node_id_map, mesh_prop))
+ {
+ ERR("Error parsing Line %s.", mesh_name.c_str());
+ clearData(nodes, elems);
+ return nullptr;
+ }
+ return new MeshLib::Mesh(mesh_name, nodes, elems, mesh_prop);
+ }
+ else if (type == GOCAD_DATA_TYPE::TSURF && str[0] == "TFACE")
{
std::vector<MeshLib::Node*> nodes;
std::vector<MeshLib::Element*> elems;
@@ -120,7 +146,6 @@ MeshLib::Mesh* GocadTSurfaceReader::readMesh(std::ifstream& in,
clearData(nodes, elems);
return nullptr;
}
-
return new MeshLib::Mesh(mesh_name, nodes, elems, mesh_prop);
}
else
@@ -133,7 +158,7 @@ MeshLib::Mesh* GocadTSurfaceReader::readMesh(std::ifstream& in,
return nullptr;
}
-bool GocadTSurfaceReader::TSurfaceFound(std::ifstream& in) const
+GOCAD_DATA_TYPE GocadAsciiReader::datasetFound(std::ifstream& in) const
{
std::string line;
while (std::getline(in, line))
@@ -142,35 +167,38 @@ bool GocadTSurfaceReader::TSurfaceFound(std::ifstream& in) const
{
continue;
}
- if (line.substr(0, 11) == "GOCAD TSurf")
+
+ if (line.substr(0, 10) == "GOCAD VSet")
{
- return true;
- // No idea why this is allowed in a *.ts file.
- // It should be a whole different file type.
+ return GOCAD_DATA_TYPE::VSET;
}
- if (line.substr(0, 13) == "GOCAD Model3d")
+ else if (line.substr(0, 11) == "GOCAD PLine")
{
- if (!skipModel3d(in))
- {
- ERR("Error parsing Model3d");
- return false;
- }
+ return GOCAD_DATA_TYPE::PLINE;
+ }
+ else if (line.substr(0, 11) == "GOCAD TSurf")
+ {
+ return GOCAD_DATA_TYPE::TSURF;
+ }
+ else if (line.substr(0, 13) == "GOCAD Model3d")
+ {
+ return GOCAD_DATA_TYPE::MODEL3D;
}
else
{
- ERR("No TSurf-identifier found...");
- return false;
+ ERR("No known identifier found...");
+ return GOCAD_DATA_TYPE::UNDEFINED;
}
}
- return false;
+ return GOCAD_DATA_TYPE::UNDEFINED;
}
-bool GocadTSurfaceReader::isCommentLine(std::string const& str) const
+bool GocadAsciiReader::isCommentLine(std::string const& str) const
{
return (str.substr(0, 1) == "#");
}
-bool GocadTSurfaceReader::parseHeader(std::ifstream& in, std::string& mesh_name)
+bool GocadAsciiReader::parseHeader(std::ifstream& in, std::string& mesh_name)
{
std::string line;
while (std::getline(in, line))
@@ -190,7 +218,7 @@ bool GocadTSurfaceReader::parseHeader(std::ifstream& in, std::string& mesh_name)
return false;
}
-bool GocadTSurfaceReader::parsePropertyClass(std::ifstream& in) const
+bool GocadAsciiReader::parsePropertyClass(std::ifstream& in) const
{
std::string line;
while (std::getline(in, line))
@@ -222,7 +250,7 @@ std::string propertyCheck(std::string const& strng)
return std::string("");
}
-bool GocadTSurfaceReader::parseProperties(std::ifstream& in,
+bool GocadAsciiReader::parseProperties(std::ifstream& in,
std::vector<std::string> const& names,
MeshLib::Properties& mesh_prop)
{
@@ -272,7 +300,45 @@ bool GocadTSurfaceReader::parseProperties(std::ifstream& in,
return false;
}
-bool GocadTSurfaceReader::parseSurface(
+bool GocadAsciiReader::parseLine(
+ std::ifstream& in,
+ std::vector<MeshLib::Node*>& nodes,
+ std::vector<MeshLib::Element*>& elems,
+ std::map<std::size_t, std::size_t>& node_id_map,
+ MeshLib::Properties& mesh_prop)
+{
+ if (!parseNodes(in, nodes, node_id_map, mesh_prop))
+ {
+ return false;
+ }
+ if (!parseLineSegments(in, nodes, elems, node_id_map, mesh_prop))
+ {
+ return false;
+ }
+
+ std::string line;
+ while (std::getline(in, line))
+ {
+ std::vector<std::string> str = BaseLib::splitString(line);
+ if (str[0] == "ILINE")
+ {
+ parseLine(in, nodes, elems, node_id_map, mesh_prop);
+ return true;
+ }
+ else if (line == "END")
+ {
+ return true;
+ }
+ else
+ {
+ WARN("GocadTSurfaceReader::parseLine() - Unknown keyword found: %s", line.c_str());
+ }
+ }
+ ERR("%s", eof_error.c_str());
+ return false;
+}
+
+bool GocadAsciiReader::parseSurface(
std::ifstream& in,
std::vector<MeshLib::Node*>& nodes,
std::vector<MeshLib::Element*>& elems,
@@ -311,10 +377,7 @@ bool GocadTSurfaceReader::parseSurface(
}
else
{
- WARN(
- "GocadTSurfaceReader::parseSurface() - Unknown keyword found: "
- "%s",
- line.c_str());
+ WARN("GocadTSurfaceReader::parseSurface() - Unknown keyword found: %s", line.c_str());
}
}
ERR("%s", eof_error.c_str());
@@ -330,7 +393,7 @@ MeshLib::Node* createNode(std::stringstream& sstr)
return new MeshLib::Node(data, id);
}
-bool GocadTSurfaceReader::parseNodes(
+bool GocadAsciiReader::parseNodes(
std::ifstream& in,
std::vector<MeshLib::Node*>& nodes,
std::map<std::size_t, std::size_t>& node_id_map,
@@ -345,7 +408,13 @@ bool GocadTSurfaceReader::parseNodes(
while (std::getline(in, line))
{
std::vector<std::string> str = BaseLib::splitString(line);
- if (line.substr(0, 4) == "TRGL")
+ if (line.substr(0, 3) == "SEG")
+ {
+ in.seekg(pos);
+ return true;
+ }
+
+ else if (line.substr(0, 4) == "TRGL")
{
in.seekg(pos);
return true;
@@ -358,9 +427,7 @@ bool GocadTSurfaceReader::parseNodes(
if (!(line.substr(0, 4) == "VRTX" || line.substr(0, 5) == "PVRTX" ||
line.substr(0, 4) == "ATOM"))
{
- WARN(
- "GocadTSurfaceReader::parseNodes() - Unknown keyword found: %s",
- line.c_str());
+ WARN("GocadTSurfaceReader::parseNodes() - Unknown keyword found: %s", line.c_str());
continue;
}
@@ -397,7 +464,62 @@ bool GocadTSurfaceReader::parseNodes(
return false;
}
-bool GocadTSurfaceReader::parseElements(
+bool GocadAsciiReader::parseLineSegments(
+ std::ifstream& in,
+ std::vector<MeshLib::Node*>& nodes,
+ std::vector<MeshLib::Element*>& elems,
+ std::map<std::size_t, std::size_t> const& node_id_map,
+ MeshLib::Properties& mesh_prop)
+{
+ std::string keyword;
+ std::array<std::size_t, 3> data;
+ MeshLib::PropertyVector<int>& mat_ids =
+ *mesh_prop.getPropertyVector<int>(mat_id_name);
+ int current_mat_id(0);
+ if (!mat_ids.empty())
+ {
+ current_mat_id = (*std::max_element(mat_ids.begin(), mat_ids.end()))++;
+ }
+ std::streampos pos = in.tellg();
+ std::size_t id(0);
+ std::string line;
+ while (std::getline(in, line))
+ {
+ if (line.empty() || isCommentLine(line))
+ {
+ continue;
+ }
+ if (line.substr(0, 3) == "SEG")
+ {
+ std::stringstream sstr(line);
+ sstr >> keyword >> data[0] >> data[1];
+ std::array<MeshLib::Node*, 2> elem_nodes;
+ for (std::size_t i = 0; i < 2; ++i)
+ {
+ auto const it = node_id_map.find(data[i]);
+ if (it == node_id_map.end() || it->second >= nodes.size())
+ {
+ ERR("Error: Node ID (%d) out of range (0, %d).", data[i],
+ nodes.back()->getID());
+ return false;
+ }
+ elem_nodes[i] = nodes[it->second];
+ }
+ elems.push_back(new MeshLib::Line(elem_nodes, id++));
+ mat_ids.push_back(current_mat_id);
+ }
+ else
+ {
+ in.seekg(pos);
+ return true;
+ }
+ pos = in.tellg();
+ }
+ ERR("%s", eof_error.c_str());
+ return false;
+}
+
+bool GocadAsciiReader::parseElements(
std::ifstream& in,
std::vector<MeshLib::Node*>& nodes,
std::vector<MeshLib::Element*>& elems,
@@ -452,7 +574,7 @@ bool GocadTSurfaceReader::parseElements(
return false;
}
-bool GocadTSurfaceReader::skipModel3d(std::ifstream& in) const
+bool GocadAsciiReader::skipToEND(std::ifstream& in) const
{
std::string line;
while (std::getline(in, line))
@@ -466,7 +588,7 @@ bool GocadTSurfaceReader::skipModel3d(std::ifstream& in) const
return false;
}
-void GocadTSurfaceReader::clearData(std::vector<MeshLib::Node*>& nodes,
+void GocadAsciiReader::clearData(std::vector<MeshLib::Node*>& nodes,
std::vector<MeshLib::Element*>& elems)
{
for (MeshLib::Element* e : elems)
diff --git a/Applications/FileIO/GocadIO/GocadTSurfaceReader.h b/Applications/FileIO/GocadIO/GocadAsciiReader.h
similarity index 68%
rename from Applications/FileIO/GocadIO/GocadTSurfaceReader.h
rename to Applications/FileIO/GocadIO/GocadAsciiReader.h
index 08a3bb8490a..a1f68b4441f 100644
--- a/Applications/FileIO/GocadIO/GocadTSurfaceReader.h
+++ b/Applications/FileIO/GocadIO/GocadAsciiReader.h
@@ -26,31 +26,41 @@ namespace FileIO
{
namespace Gocad
{
-class GocadTSurfaceReader final
+
+enum class GOCAD_DATA_TYPE
+{
+ UNDEFINED,
+ VSET,
+ PLINE,
+ TSURF,
+ MODEL3D
+};
+
+class GocadAsciiReader final
{
public:
/**
* Constructor takes as argument the Gocad .sg text file.
*/
- explicit GocadTSurfaceReader();
+ explicit GocadAsciiReader();
- GocadTSurfaceReader(GocadTSurfaceReader&& src) = delete;
- GocadTSurfaceReader(GocadTSurfaceReader const& src) = delete;
- GocadTSurfaceReader& operator=(GocadTSurfaceReader&& rhs) = delete;
- GocadTSurfaceReader& operator=(GocadTSurfaceReader const& rhs) = delete;
+ GocadAsciiReader(GocadAsciiReader&& src) = delete;
+ GocadAsciiReader(GocadAsciiReader const& src) = delete;
+ GocadAsciiReader& operator=(GocadAsciiReader&& rhs) = delete;
+ GocadAsciiReader& operator=(GocadAsciiReader const& rhs) = delete;
/// Reads the specified file and writes data into internal mesh vector
bool readFile(std::string const& file_name, std::vector<std::unique_ptr<MeshLib::Mesh>>& meshes);
private:
/// Reads one mesh contained in the file (there may be more than one!)
- MeshLib::Mesh* readMesh(std::ifstream& in, std::string& mesh_name);
+ MeshLib::Mesh* readData(std::ifstream& in, GOCAD_DATA_TYPE const& type, std::string& mesh_name);
/// Checks if the current line is a comment
bool isCommentLine(std::string const& str) const;
/// Checks if a TSurf identifier is found at the current stream position.
- bool TSurfaceFound(std::ifstream& in) const;
+ GOCAD_DATA_TYPE datasetFound(std::ifstream& in) const;
/// Parses the HEADER section (everything except the name is ignored right now)
bool parseHeader(std::ifstream& in, std::string& mesh_name);
@@ -65,6 +75,12 @@ private:
std::vector<std::string> const& names,
MeshLib::Properties& mesh_prop);
+ /// Parses line information (nodes, segments, properties)
+ bool parseLine(std::ifstream& in, std::vector<MeshLib::Node*>& nodes,
+ std::vector<MeshLib::Element*>& elems,
+ std::map<std::size_t, std::size_t>& node_id_map,
+ MeshLib::Properties& mesh_prop);
+
/// Parses the surface information (nodes, triangles, properties)
bool parseSurface(std::ifstream& in, std::vector<MeshLib::Node*>& nodes,
std::vector<MeshLib::Element*>& elems,
@@ -76,14 +92,20 @@ private:
std::map<std::size_t, std::size_t>& node_id_map,
MeshLib::Properties& mesh_prop);
+ /// Parses the segments of a line
+ bool parseLineSegments(std::ifstream& in, std::vector<MeshLib::Node*>& nodes,
+ std::vector<MeshLib::Element*>& elems,
+ std::map<std::size_t, std::size_t> const& node_id_map,
+ MeshLib::Properties& mesh_prop);
+
/// Parses the element data for the current mesh
bool parseElements(std::ifstream& in, std::vector<MeshLib::Node*>& nodes,
std::vector<MeshLib::Element*>& elems,
std::map<std::size_t, std::size_t> const& node_id_map,
MeshLib::Properties& mesh_prop);
- /// Skips over the Model3d sections of the file, should there be any.
- bool skipModel3d(std::ifstream& in) const;
+ /// Parses current section until END-tag is reached
+ bool skipToEND(std::ifstream& in) const;
/// Clears the memory if an error occured
void clearData(std::vector<MeshLib::Node*>& nodes,
@@ -95,7 +117,6 @@ private:
VRTX,
PVRTX
};
-
}; // end class GocadTSurfaceReader
} // end namespace Gocad
diff --git a/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp b/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp
index 48625b0dd28..f881976a6b4 100644
--- a/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp
+++ b/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp
@@ -13,7 +13,7 @@
#include "MeshLib/Mesh.h"
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "Applications/ApplicationsLib/LogogSetup.h"
-#include "Applications/FileIO/GocadIO/GocadTSurfaceReader.h"
+#include "Applications/FileIO/GocadIO/GocadAsciiReader.h"
std::string getDelim(std::string const& str)
{
@@ -27,7 +27,7 @@ int main(int argc, char* argv[])
ApplicationsLib::LogogSetup logog_setup;
TCLAP::CmdLine cmd(
- "Reads a Gocad triangular surfaces file (*.ts) and writes the "
+ "Reads Gocad ascii files (*.ts, *.pl, *.mx) and writes TSurf- and PLine"
"data into one or more VTU unstructured grids.\n\n"
"OpenGeoSys-6 software, version " +
BaseLib::BuildInfo::ogs_version +
@@ -54,18 +54,21 @@ int main(int argc, char* argv[])
cmd.parse(argc, argv);
std::string const file_name (input_arg.getValue());
- FileIO::Gocad::GocadTSurfaceReader gcts;
+ FileIO::Gocad::GocadAsciiReader gcts;
std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
if (!gcts.readFile(file_name, meshes))
{
ERR("Error reading file.");
return 1;
}
+ INFO("%d meshes found.", meshes.size());
std::string const dir = output_arg.getValue();
bool const write_binary = write_binary_arg.getValue();
std::string const delim = getDelim(dir);
for (auto& mesh : meshes)
{
+ if (mesh == nullptr)
+ continue;
INFO("Writing mesh \"%s\"", mesh->getName().c_str());
int data_mode = (write_binary) ? 2 : 0;
bool compressed = (write_binary);
--
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