Removed <fstream> includes from headers

Applications/FileIO/AsciiRasterInterface.cpp

@@ -13,6 +13,7 @@
 
 #include "AsciiRasterInterface.h"
 
+#include <fstream>
 #include <tuple>
 
 #include "BaseLib/FileTools.h"

Applications/FileIO/AsciiRasterInterface.h

@@ -13,7 +13,6 @@
 
 #pragma once
 
-#include <fstream>
 #include <optional>
 #include <string>
 #include <vector>

Applications/FileIO/CsvInterface.cpp

@@ -14,7 +14,6 @@
 #include "CsvInterface.h"
 
 #include <algorithm>
-#include <fstream>
 #include <numeric>
 
 #include "GeoLib/Point.h"

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"

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"

Applications/FileIO/GocadIO/CoordinateSystem.h

@@ -9,7 +9,8 @@
 
 #pragma once
 
-#include <fstream>
+#include <iosfwd>
+#include <string>
 
 namespace FileIO
 {

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"

Applications/FileIO/Legacy/OGSIOVer4.cpp

@@ -14,6 +14,7 @@
 
 #include "OGSIOVer4.h"
 
+#include <fstream>
 #include <iomanip>
 #include <limits>
 #include <sstream>

Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp

@@ -18,6 +18,7 @@
 #include <mpi.h>
 #endif
 
+#include <fstream>
 #include <memory>
 
 #include "BaseLib/FileTools.h"

Applications/Utils/MeshEdit/MeshMapping.cpp

@@ -11,6 +11,7 @@
 
 #include <tclap/CmdLine.h>
 
+#include <fstream>
 #include <memory>
 #include <string>
 

Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp

@@ -17,6 +17,7 @@
 #endif
 
 #include <algorithm>
+#include <fstream>
 #include <memory>
 #include <string>
 #include <vector>

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

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.

BaseLib/Histogram.cpp

+/**
+ * \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

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

MathLib/LinAlg/Eigen/EigenMatrix.cpp

+/**
+ * \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

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_; }

MathLib/LinAlg/Eigen/EigenVector.cpp

+/**
+ * \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

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

MeshLib/IO/Legacy/MeshIO.cpp

@@ -18,6 +18,7 @@
 
 #include "MeshIO.h"
 
+#include <fstream>
 #include <iomanip>
 #include <memory>
 #include <sstream>