From 1edb1e411f7481e599c755cc203c73c2c2659b51 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Fri, 21 Oct 2022 08:23:26 +0200
Subject: [PATCH] Removed <fstream> includes from headers
---
Applications/FileIO/AsciiRasterInterface.cpp | 1 +
Applications/FileIO/AsciiRasterInterface.h | 1 -
Applications/FileIO/CsvInterface.cpp | 1 -
.../FileIO/FEFLOW/FEFLOWGeoInterface.cpp | 1 +
.../FileIO/FEFLOW/FEFLOWMeshInterface.cpp | 1 +
.../FileIO/GocadIO/CoordinateSystem.h | 3 +-
.../FileIO/GocadIO/GocadAsciiReader.cpp | 2 +-
Applications/FileIO/Legacy/OGSIOVer4.cpp | 1 +
.../generateMatPropsFromMatID.cpp | 1 +
Applications/Utils/MeshEdit/MeshMapping.cpp | 1 +
...computeSurfaceNodeIDsInPolygonalRegion.cpp | 1 +
BaseLib/FileTools.cpp | 66 ++++++++++++++
BaseLib/FileTools.h | 55 ++----------
BaseLib/Histogram.cpp | 87 +++++++++++++++++++
BaseLib/Histogram.h | 69 ++-------------
MathLib/LinAlg/Eigen/EigenMatrix.cpp | 40 +++++++++
MathLib/LinAlg/Eigen/EigenMatrix.h | 24 +----
MathLib/LinAlg/Eigen/EigenVector.cpp | 35 ++++++++
MathLib/LinAlg/Eigen/EigenVector.h | 19 +---
MeshLib/IO/Legacy/MeshIO.cpp | 1 +
20 files changed, 260 insertions(+), 150 deletions(-)
create mode 100644 BaseLib/Histogram.cpp
create mode 100644 MathLib/LinAlg/Eigen/EigenMatrix.cpp
create mode 100644 MathLib/LinAlg/Eigen/EigenVector.cpp
diff --git a/Applications/FileIO/AsciiRasterInterface.cpp b/Applications/FileIO/AsciiRasterInterface.cpp
index c0d6495caa2..04c95d466e8 100644
--- a/Applications/FileIO/AsciiRasterInterface.cpp
+++ b/Applications/FileIO/AsciiRasterInterface.cpp
@@ -13,6 +13,7 @@
#include "AsciiRasterInterface.h"
+#include <fstream>
#include <tuple>
#include "BaseLib/FileTools.h"
diff --git a/Applications/FileIO/AsciiRasterInterface.h b/Applications/FileIO/AsciiRasterInterface.h
index f3b7d09469e..fdcc7610cbd 100644
--- a/Applications/FileIO/AsciiRasterInterface.h
+++ b/Applications/FileIO/AsciiRasterInterface.h
@@ -13,7 +13,6 @@
#pragma once
-#include <fstream>
#include <optional>
#include <string>
#include <vector>
diff --git a/Applications/FileIO/CsvInterface.cpp b/Applications/FileIO/CsvInterface.cpp
index aa61387717c..9c067d01635 100644
--- a/Applications/FileIO/CsvInterface.cpp
+++ b/Applications/FileIO/CsvInterface.cpp
@@ -14,7 +14,6 @@
#include "CsvInterface.h"
#include <algorithm>
-#include <fstream>
#include <numeric>
#include "GeoLib/Point.h"
diff --git a/Applications/FileIO/FEFLOW/FEFLOWGeoInterface.cpp b/Applications/FileIO/FEFLOW/FEFLOWGeoInterface.cpp
index 328cdd4cb4e..6f954e74000 100644
--- a/Applications/FileIO/FEFLOW/FEFLOWGeoInterface.cpp
+++ b/Applications/FileIO/FEFLOW/FEFLOWGeoInterface.cpp
@@ -13,6 +13,7 @@
#include <QtXml/QDomDocument>
#include <boost/algorithm/string/trim.hpp>
#include <cctype>
+#include <fstream>
#include <memory>
#include "BaseLib/FileTools.h"
diff --git a/Applications/FileIO/FEFLOW/FEFLOWMeshInterface.cpp b/Applications/FileIO/FEFLOW/FEFLOWMeshInterface.cpp
index 9831ecbec45..358ba141083 100644
--- a/Applications/FileIO/FEFLOW/FEFLOWMeshInterface.cpp
+++ b/Applications/FileIO/FEFLOW/FEFLOWMeshInterface.cpp
@@ -10,6 +10,7 @@
#include <boost/algorithm/string/trim.hpp>
#include <cctype>
+#include <fstream>
#include <memory>
#include "Applications/FileIO/FEFLOW/FEFLOWGeoInterface.h"
diff --git a/Applications/FileIO/GocadIO/CoordinateSystem.h b/Applications/FileIO/GocadIO/CoordinateSystem.h
index c0a5aea65b6..e29cc65a8bf 100644
--- a/Applications/FileIO/GocadIO/CoordinateSystem.h
+++ b/Applications/FileIO/GocadIO/CoordinateSystem.h
@@ -9,7 +9,8 @@
#pragma once
-#include <fstream>
+#include <iosfwd>
+#include <string>
namespace FileIO
{
diff --git a/Applications/FileIO/GocadIO/GocadAsciiReader.cpp b/Applications/FileIO/GocadIO/GocadAsciiReader.cpp
index 7bcd07b56a8..ca1d40d3f9a 100644
--- a/Applications/FileIO/GocadIO/GocadAsciiReader.cpp
+++ b/Applications/FileIO/GocadIO/GocadAsciiReader.cpp
@@ -9,7 +9,7 @@
#include "GocadAsciiReader.h"
-#include <iosfwd>
+#include <fstream>
#include "Applications/FileIO/GocadIO/CoordinateSystem.h"
#include "BaseLib/FileTools.h"
diff --git a/Applications/FileIO/Legacy/OGSIOVer4.cpp b/Applications/FileIO/Legacy/OGSIOVer4.cpp
index 763cebfd9f4..ec6808de12b 100644
--- a/Applications/FileIO/Legacy/OGSIOVer4.cpp
+++ b/Applications/FileIO/Legacy/OGSIOVer4.cpp
@@ -14,6 +14,7 @@
#include "OGSIOVer4.h"
+#include <fstream>
#include <iomanip>
#include <limits>
#include <sstream>
diff --git a/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp b/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
index 7bb834e7b28..ef556bcaa99 100644
--- a/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
+++ b/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
@@ -18,6 +18,7 @@
#include <mpi.h>
#endif
+#include <fstream>
#include <memory>
#include "BaseLib/FileTools.h"
diff --git a/Applications/Utils/MeshEdit/MeshMapping.cpp b/Applications/Utils/MeshEdit/MeshMapping.cpp
index 311000c52cc..e9ce327c60b 100644
--- a/Applications/Utils/MeshEdit/MeshMapping.cpp
+++ b/Applications/Utils/MeshEdit/MeshMapping.cpp
@@ -11,6 +11,7 @@
#include <tclap/CmdLine.h>
+#include <fstream>
#include <memory>
#include <string>
diff --git a/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp b/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp
index 355c00e3269..149aaea0c1b 100644
--- a/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp
+++ b/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp
@@ -17,6 +17,7 @@
#endif
#include <algorithm>
+#include <fstream>
#include <memory>
#include <string>
#include <vector>
diff --git a/BaseLib/FileTools.cpp b/BaseLib/FileTools.cpp
index cafbd1c6ba9..ffe7b4c32e7 100644
--- a/BaseLib/FileTools.cpp
+++ b/BaseLib/FileTools.cpp
@@ -16,6 +16,7 @@
#include <boost/algorithm/string.hpp>
#include <filesystem>
+#include <fstream>
#include <typeindex>
#include <unordered_map>
@@ -259,4 +260,69 @@ void removeFiles(std::vector<std::string> const& files)
removeFile(file);
}
}
+
+template <typename T>
+T readBinaryValue(std::istream& in)
+{
+ T v;
+ in.read(reinterpret_cast<char*>(&v), sizeof(T));
+ return v;
+}
+
+// explicit template instantiation
+template float readBinaryValue<float>(std::istream&);
+template double readBinaryValue<double>(std::istream&);
+
+template <typename T>
+std::vector<T> readBinaryArray(std::string const& filename, std::size_t const n)
+{
+ std::ifstream in(filename.c_str());
+ if (!in)
+ {
+ ERR("readBinaryArray(): Error while reading from file '{:s}'.",
+ filename);
+ ERR("Could not open file '{:s}' for input.", filename);
+ in.close();
+ return std::vector<T>();
+ }
+
+ std::vector<T> result;
+ result.reserve(n);
+
+ for (std::size_t p = 0; in && !in.eof() && p < n; ++p)
+ {
+ result.push_back(BaseLib::readBinaryValue<T>(in));
+ }
+
+ if (result.size() == n)
+ {
+ return result;
+ }
+
+ ERR("readBinaryArray(): Error while reading from file '{:s}'.", filename);
+ ERR("Read different number of values. Expected {:d}, got {:d}.",
+ n,
+ result.size());
+
+ if (!in.eof())
+ {
+ ERR("EOF reached.\n");
+ }
+
+ return std::vector<T>();
+}
+
+// explicit template instantiation
+template std::vector<float> readBinaryArray<float>(std::string const&,
+ std::size_t const);
+
+template <typename T>
+void writeValueBinary(std::ostream& out, T const& val)
+{
+ out.write(reinterpret_cast<const char*>(&val), sizeof(T));
+}
+
+// explicit template instantiation
+template void writeValueBinary<std::size_t>(std::ostream&, std::size_t const&);
+
} // end namespace BaseLib
diff --git a/BaseLib/FileTools.h b/BaseLib/FileTools.h
index 504398e1e19..6376fc1fa9b 100644
--- a/BaseLib/FileTools.h
+++ b/BaseLib/FileTools.h
@@ -14,12 +14,10 @@
#pragma once
-#include <fstream>
+#include <iosfwd>
#include <string>
#include <vector>
-#include "Logging.h"
-
namespace BaseLib
{
/**
@@ -60,10 +58,7 @@ std::string constructFormattedFileName(std::string const& format_specification,
* \param val value
*/
template <typename T>
-void writeValueBinary(std::ostream& out, T const& val)
-{
- out.write(reinterpret_cast<const char*>(&val), sizeof(T));
-}
+void writeValueBinary(std::ostream& out, T const& val);
template <typename T>
T swapEndianness(T const& v)
@@ -86,51 +81,11 @@ T swapEndianness(T const& v)
double swapEndianness(double const& v);
template <typename T>
-T readBinaryValue(std::istream& in)
-{
- T v;
- in.read(reinterpret_cast<char*>(&v), sizeof(T));
- return v;
-}
+T readBinaryValue(std::istream& in);
template <typename T>
-std::vector<T> readBinaryArray(std::string const& filename, std::size_t const n)
-{
- std::ifstream in(filename.c_str());
- if (!in)
- {
- ERR("readBinaryArray(): Error while reading from file '{:s}'.",
- filename);
- ERR("Could not open file '{:s}' for input.", filename);
- in.close();
- return std::vector<T>();
- }
-
- std::vector<T> result;
- result.reserve(n);
-
- for (std::size_t p = 0; in && !in.eof() && p < n; ++p)
- {
- result.push_back(BaseLib::readBinaryValue<T>(in));
- }
-
- if (result.size() == n)
- {
- return result;
- }
-
- ERR("readBinaryArray(): Error while reading from file '{:s}'.", filename);
- ERR("Read different number of values. Expected {:d}, got {:d}.",
- n,
- result.size());
-
- if (!in.eof())
- {
- ERR("EOF reached.\n");
- }
-
- return std::vector<T>();
-}
+std::vector<T> readBinaryArray(std::string const& filename,
+ std::size_t const n);
/**
* Extracts basename from given pathname with extension.
diff --git a/BaseLib/Histogram.cpp b/BaseLib/Histogram.cpp
new file mode 100644
index 00000000000..7d812272723
--- /dev/null
+++ b/BaseLib/Histogram.cpp
@@ -0,0 +1,87 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2022, 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 "Histogram.h"
+
+#include <fstream>
+
+#include "BaseLib/Logging.h"
+
+namespace BaseLib
+{
+
+template <typename T>
+int Histogram<T>::write(std::string const& file_name,
+ std::string const& data_set_name,
+ std::string const& param_name) const
+{
+ if (file_name.empty())
+ {
+ ERR("No file name specified.");
+ return 1;
+ }
+
+ std::ofstream out(file_name);
+ if (!out)
+ {
+ ERR("Error writing histogram: Could not open file.");
+ return 1;
+ }
+
+ out << "# Histogram for parameter " << param_name << " of data set "
+ << data_set_name << "\n";
+ std::size_t const n_bins = this->getNumberOfBins();
+ std::vector<std::size_t> const& bin_cnts(this->getBinCounts());
+ double const min(this->getMinimum());
+ double const bin_width(this->getBinWidth());
+
+ for (std::size_t k(0); k < n_bins; k++)
+ {
+ out << min + k * bin_width << " " << bin_cnts[k] << "\n";
+ }
+ out.close();
+ return 0;
+}
+
+template <typename T>
+void Histogram<T>::prettyPrint(std::ostream& os,
+ const unsigned int line_width) const
+{
+ const std::size_t count_max =
+ *std::max_element(histogram_.begin(), histogram_.end());
+ for (unsigned int bin = 0; bin < nr_bins_; ++bin)
+ {
+ os << "[" << min_ + bin * bin_width_ << ", "
+ << min_ + (bin + 1) * bin_width_ << ")\t";
+ os << histogram_[bin] << "\t";
+
+ const int n_stars = static_cast<int>(
+ std::ceil(line_width * ((double)histogram_[bin] / count_max)));
+ for (int star = 0; star < n_stars; star++)
+ {
+ os << "*";
+ }
+ os << "\n";
+ }
+}
+
+template <typename T>
+std::ostream& operator<<(std::ostream& os, const Histogram<T>& h)
+{
+ os << h.getNumberOfBins() << " " << h.getMinimum() << " " << h.getMaximum()
+ << " ";
+ std::copy(h.getBinCounts().begin(), h.getBinCounts().end(),
+ std::ostream_iterator<std::size_t>(os, " "));
+ return os << std::endl;
+}
+
+template class Histogram<double>;
+template std::ostream& operator<<(std::ostream& os, const Histogram<double>& h);
+} // namespace BaseLib
diff --git a/BaseLib/Histogram.h b/BaseLib/Histogram.h
index 031b4389556..8428c2547d0 100644
--- a/BaseLib/Histogram.h
+++ b/BaseLib/Histogram.h
@@ -14,14 +14,11 @@
#include <algorithm>
#include <cmath>
-#include <fstream>
#include <iosfwd>
-#include <iterator>
+#include <string>
#include <utility>
#include <vector>
-#include "Logging.h"
-
namespace BaseLib
{
/** Basic Histogram implementation.
@@ -115,56 +112,11 @@ public:
const T& getMaximum() const { return max_; }
const T& getBinWidth() const { return bin_width_; }
- void prettyPrint(std::ostream& os, const unsigned int line_width = 16) const
- {
- const std::size_t count_max =
- *std::max_element(histogram_.begin(), histogram_.end());
- for (unsigned int bin = 0; bin < nr_bins_; ++bin)
- {
- os << "[" << min_ + bin * bin_width_ << ", "
- << min_ + (bin + 1) * bin_width_ << ")\t";
- os << histogram_[bin] << "\t";
-
- const int n_stars =
- std::ceil(line_width * ((double)histogram_[bin] / count_max));
- for (int star = 0; star < n_stars; star++)
- {
- os << "*";
- }
- os << "\n";
- }
- }
+ void prettyPrint(std::ostream& os,
+ const unsigned int line_width = 16) const;
int write(std::string const& file_name, std::string const& data_set_name,
- std::string const& param_name) const
- {
- if (file_name.empty())
- {
- ERR("No file name specified.");
- return 1;
- }
-
- std::ofstream out(file_name);
- if (!out)
- {
- ERR("Error writing histogram: Could not open file.");
- return 1;
- }
-
- out << "# Histogram for parameter " << param_name << " of data set "
- << data_set_name << "\n";
- std::size_t const n_bins = this->getNumberOfBins();
- std::vector<std::size_t> const& bin_cnts(this->getBinCounts());
- double const min(this->getMinimum());
- double const bin_width(this->getBinWidth());
-
- for (std::size_t k(0); k < n_bins; k++)
- {
- out << min + k * bin_width << " " << bin_cnts[k] << "\n";
- }
- out.close();
- return 0;
- }
+ std::string const& param_name) const;
protected:
/** Initialize class members after constructor call.
@@ -200,12 +152,9 @@ private:
* number of bins, minimum, maximum, bin0 count, ..., binN-1 count.
*/
template <typename T>
-std::ostream& operator<<(std::ostream& os, const Histogram<T>& h)
-{
- os << h.getNumberOfBins() << " " << h.getMinimum() << " " << h.getMaximum()
- << " ";
- std::copy(h.getBinCounts().begin(), h.getBinCounts().end(),
- std::ostream_iterator<T>(os, " "));
- return os << std::endl;
-}
+std::ostream& operator<<(std::ostream& os, const Histogram<T>& h);
+
+extern template class Histogram<double>;
+extern template std::ostream& operator<<(std::ostream& os,
+ const Histogram<double>& h);
} // namespace BaseLib
diff --git a/MathLib/LinAlg/Eigen/EigenMatrix.cpp b/MathLib/LinAlg/Eigen/EigenMatrix.cpp
new file mode 100644
index 00000000000..be1aa4c9f66
--- /dev/null
+++ b/MathLib/LinAlg/Eigen/EigenMatrix.cpp
@@ -0,0 +1,40 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2022, 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 "EigenMatrix.h"
+
+#include <fstream>
+
+namespace MathLib
+{
+
+/// printout this matrix for debugging
+void EigenMatrix::write(const std::string& filename) const
+{
+ std::ofstream of(filename);
+ if (of)
+ {
+ write(of);
+ }
+}
+
+/// printout this matrix for debugging
+void EigenMatrix::write(std::ostream& os) const
+{
+ for (int k = 0; k < mat_.outerSize(); ++k)
+ {
+ for (RawMatrixType::InnerIterator it(mat_, k); it; ++it)
+ {
+ os << it.row() << " " << it.col() << ": " << it.value() << "\n";
+ }
+ }
+ os << std::endl;
+}
+} // namespace MathLib
diff --git a/MathLib/LinAlg/Eigen/EigenMatrix.h b/MathLib/LinAlg/Eigen/EigenMatrix.h
index 17e53c2f83e..b551cbc6584 100644
--- a/MathLib/LinAlg/Eigen/EigenMatrix.h
+++ b/MathLib/LinAlg/Eigen/EigenMatrix.h
@@ -11,10 +11,9 @@
#pragma once
#include <Eigen/Sparse>
-#include <fstream>
+#include <iosfwd>
#include <string>
-#include "EigenVector.h"
#include "MathLib/LinAlg/RowColumnIndices.h"
#include "MathLib/LinAlg/SetMatrixSparsity.h"
@@ -137,27 +136,10 @@ public:
static constexpr bool isAssembled() { return true; }
/// printout this matrix for debugging
- void write(const std::string& filename) const
- {
- std::ofstream of(filename);
- if (of)
- {
- write(of);
- }
- }
+ void write(const std::string& filename) const;
/// printout this matrix for debugging
- void write(std::ostream& os) const
- {
- for (int k = 0; k < mat_.outerSize(); ++k)
- {
- for (RawMatrixType::InnerIterator it(mat_, k); it; ++it)
- {
- os << it.row() << " " << it.col() << ": " << it.value() << "\n";
- }
- }
- os << std::endl;
- }
+ void write(std::ostream& os) const;
RawMatrixType& getRawMatrix() { return mat_; }
const RawMatrixType& getRawMatrix() const { return mat_; }
diff --git a/MathLib/LinAlg/Eigen/EigenVector.cpp b/MathLib/LinAlg/Eigen/EigenVector.cpp
new file mode 100644
index 00000000000..07a3b22abc7
--- /dev/null
+++ b/MathLib/LinAlg/Eigen/EigenVector.cpp
@@ -0,0 +1,35 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2022, 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 "EigenVector.h"
+
+#include "EigenMapTools.h"
+
+#ifndef NDEBUG
+#include <fstream>
+#endif
+
+namespace MathLib
+{
+void EigenVector::copyValues(std::vector<double>& u) const
+{
+ u.resize(size());
+ toVector(u) = vec_;
+}
+
+#ifndef NDEBUG
+void EigenVector::write(const std::string& filename) const
+{
+ std::ofstream os(filename);
+ os << vec_;
+}
+#endif
+
+} // namespace MathLib
diff --git a/MathLib/LinAlg/Eigen/EigenVector.h b/MathLib/LinAlg/Eigen/EigenVector.h
index 7854fd4d390..50828cf5309 100644
--- a/MathLib/LinAlg/Eigen/EigenVector.h
+++ b/MathLib/LinAlg/Eigen/EigenVector.h
@@ -11,16 +11,13 @@
#pragma once
#include <vector>
+
#ifndef NDEBUG
-#include <fstream>
#include <string>
#endif
-#include <Eigen/Core>
#include <Eigen/Sparse>
-#include "EigenMapTools.h"
-
namespace MathLib
{
/// Global vector based on Eigen vector
@@ -103,19 +100,11 @@ public:
/// Copy local entries to a vector.
/// \param u a vector for the values of local entries. It will be resized to
/// hold the current vector data.
- void copyValues(std::vector<double>& u) const
- {
- u.resize(size());
- toVector(u) = vec_;
- }
+ void copyValues(std::vector<double>& u) const;
#ifndef NDEBUG
- /// printout this equation for debugging
- void write(const std::string& filename) const
- {
- std::ofstream os(filename);
- os << vec_;
- }
+ /// write this vector to a file for debugging
+ void write(const std::string& filename) const;
#endif
/// return a raw Eigen vector object
diff --git a/MeshLib/IO/Legacy/MeshIO.cpp b/MeshLib/IO/Legacy/MeshIO.cpp
index 3eb1c38874c..6cc4a378c3a 100644
--- a/MeshLib/IO/Legacy/MeshIO.cpp
+++ b/MeshLib/IO/Legacy/MeshIO.cpp
@@ -18,6 +18,7 @@
#include "MeshIO.h"
+#include <fstream>
#include <iomanip>
#include <memory>
#include <sstream>
--
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