diff --git a/AMDiS/src/FileWriter.cc b/AMDiS/src/FileWriter.cc
index ddb8385a881a038a8ad2776efc7abc0e9b4f0195..1f715b00c71d4b5563f0eb91451b35228e0ff7d4 100644
--- a/AMDiS/src/FileWriter.cc
+++ b/AMDiS/src/FileWriter.cc
@@ -127,6 +127,7 @@ namespace AMDiS {
writingIsDelayed_ = false;
delayedFilename_ = "";
paraViewAnimationFrames_.resize(0);
+ compression = NONE;
readParameters();
}
@@ -152,9 +153,16 @@ namespace AMDiS {
GET_PARAMETER(0, name + "->write every i-th timestep", "%d", &tsModulo);
GET_PARAMETER(0, name + "->delay", "%d", &delayWriting_);
+ std::string compressionStr = "";
+ GET_PARAMETER(0, name + "->compression", &compressionStr);
+ if ((compressionStr == "gzip") || (compressionStr == "gz")) {
+ compression = GZIP;
+ } else if ((compressionStr == "bzip2") || (compressionStr == "bz2")) {
+ compression = BZIP2;
+ }
+
TEST_EXIT(!delayWriting_ || amdisHaveOpenMP)
("Delayed writing only possible with OpenMP support!\n");
-
}
void FileWriter::writeFiles(AdaptInfo *adaptInfo,
@@ -248,7 +256,8 @@ namespace AMDiS {
if (writeParaViewFormat) {
VtkWriter vtkWriter(&dataCollectors_);
- vtkWriter.writeFile(const_cast<char*>((fn + paraViewFileExt).c_str()));
+ vtkWriter.setCompression(compression);
+ vtkWriter.writeFile(const_cast<char*>((fn + paraViewFileExt).c_str()));
MSG("ParaView file written to %s\n", (fn + paraViewFileExt).c_str());
}
diff --git a/AMDiS/src/FileWriter.h b/AMDiS/src/FileWriter.h
index 8300d3f2e489d7ea8b48bcad597fc982a00b5773..7d748f6d7df6fce755505976a823969dc0d3b1cb 100644
--- a/AMDiS/src/FileWriter.h
+++ b/AMDiS/src/FileWriter.h
@@ -44,6 +44,13 @@ namespace AMDiS {
template<typename T> class DOFVector;
+
+ typedef enum {
+ NONE = 0,
+ GZIP = 1,
+ BZIP2 = 2
+ } FileCompression;
+
// ============================================================================
// ===== class FileWriterInterface ============================================
// ============================================================================
@@ -311,6 +318,12 @@ namespace AMDiS {
* Here the filename for the file, which should be written to the next, is stored.
*/
std::string delayedFilename_;
+
+ /** \brief
+ * Defines if, and with what kind of compression, the file should be compressed
+ * during writing.
+ */
+ FileCompression compression;
};
}
diff --git a/AMDiS/src/VtkWriter.cc b/AMDiS/src/VtkWriter.cc
index f0a4a65831afd483ee3b61c6322bca11a0246615..e9ff0ce78b2d26ed890cc60023205af9c3e45ca3 100644
--- a/AMDiS/src/VtkWriter.cc
+++ b/AMDiS/src/VtkWriter.cc
@@ -13,373 +13,34 @@ namespace AMDiS {
int VtkWriter::writeFile(const char *name)
{
- int nVertices = (*dataCollector)[0]->getNumberVertices();
- int nElements = (*dataCollector)[0]->getNumberElements();
- int vertices = (*dataCollector)[0]->getMesh()->getGeo(VERTEX);
-
- if ((dim == 2) && (degree == 2)) {
- nVertices += (*dataCollector)[0]->getNumberInterpPoints();
- nElements *= 4;
- } else if ((dim == 2) && (degree == 3)) {
- nVertices += (*dataCollector)[0]->getNumberInterpPoints();
- nElements *= 9;
- } else if ((dim == 2) && (degree == 4)) {
- nVertices += (*dataCollector)[0]->getNumberInterpPoints();
- nElements *= 16;
- }
+#ifdef HAVE_BOOST
+ boost::iostreams::filtering_ostream file;
+ switch (compress) {
+ case GZIP:
+ file.push(boost::iostreams::gzip_compressor());
+ file.push(boost::iostreams::file_descriptor_sink(strcat((char*)name, ".gz")));
+ break;
+ case BZIP2:
+ file.push(boost::iostreams::bzip2_compressor());
+ file.push(boost::iostreams::file_descriptor_sink(strcat((char*)name, ".bz2")));
+ break;
+ default:
+ file.push(boost::iostreams::file_descriptor_sink(name));
+ break;
+ }
+ writeFile(file);
+
+#else
+
std::ofstream file;
file.open(name);
-
- file << "<?xml version=\"1.0\"?>\n";
- file << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";
- file << " <UnstructuredGrid>\n";
- file << " <Piece NumberOfPoints=\"" << nVertices
- << "\" NumberOfCells=\"" << nElements << "\">\n";
- file << " <Points>\n";
- file << " <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n";
-
- writeVertexCoords(file);
-
- file << " </DataArray>\n";
- file << " </Points>\n";
- file << " <Cells>\n";
- file << " <DataArray type=\"Int32\" Name=\"offsets\">\n";
-
- for (int i = 0; i < nElements; i++) {
- file << " " << (i + 1) * vertices << "\n";
- }
-
- file << " </DataArray>\n";
- file << " <DataArray type=\"UInt8\" Name=\"types\">\n";
-
- for (int i = 0; i < nElements; i++) {
- switch (vertices) {
- case 2:
- file << " 3\n";
- break;
- case 3:
- file << " 5\n";
- break;
- case 4:
- file << " 10\n";
- break;
- default:
- break;
- }
- }
-
- file << " </DataArray>\n";
- file << " <DataArray type=\"Int32\" Name=\"connectivity\">\n";
-
- writeConnectivity(file);
-
- file << " </DataArray>\n";
- file << " </Cells>\n";
- file << " <PointData>\n";
-
- for (int i = 0; i < static_cast<int>(dataCollector->size()); i++) {
- file << " <DataArray type=\"Float32\" Name=\"value" << i
- << "\" format=\"ascii\">\n";
-
- writeVertexValues(file, i);
-
- file << " </DataArray>\n";
- }
-
- file << " </PointData>\n";
- file << " </Piece>\n";
- file << " </UnstructuredGrid>\n";
- file << "</VTKFile>\n";
-
-
+ writeFile(file);
file.close();
-
- return 0;
- }
-
- void VtkWriter::writeVertexCoords(std::ofstream &file)
- {
- DOFVector< std::list<VertexInfo> > *vertexInfos = (*dataCollector)[0]->getVertexInfos();
- DOFVector< std::list<VertexInfo> >::Iterator it(vertexInfos, USED_DOFS);
- int counter = 0;
-
- // For all DOFs of vertices, write the coordinates.
- for (it.reset(); !it.end(); ++it) {
- // for all vertex infos of this DOF
- std::list<VertexInfo>::iterator it2;
- for (it2 = it->begin(); it2 != it->end(); ++it2) {
- it2->outputIndex = counter++;
- writeCoord(file, it2->coords);
- }
- }
-
- // For the second dim case, write also the interpolation points.
- if ((dim == 2) && (degree > 1)) {
- DOFVector< std::list< WorldVector<double> > > *interpPointCoords = (*dataCollector)[0]->getInterpPointCoords();
- DOFVector< std::list< WorldVector<double> > >::Iterator pointIt(interpPointCoords, USED_DOFS);
-
- for (pointIt.reset(); !pointIt.end(); ++pointIt) {
- std::list< WorldVector<double> >::iterator it2;
- for (it2 = pointIt->begin(); it2 != pointIt->end(); ++it2) {
- writeCoord(file, *it2);
- }
- }
- }
- }
-
-
- void VtkWriter::writeVertexValues(std::ofstream &file, int componentNo)
- {
- // DOFVector<int> *interpPointInd;
- // DOFVector<double> *values;
- // DOFVector< std::list<WorldVector<double> > > *dofCoords;
-
- DOFVector<int> *interpPointInd = (*dataCollector)[componentNo]->getInterpPointInd();
- DOFVector<double> *values = (*dataCollector)[componentNo]->getValues();
- DOFVector< std::list<WorldVector<double> > > *dofCoords = (*dataCollector)[componentNo]->getDofCoords();
-
- /*
-#ifdef _OPENMP
-#pragma omp critical
#endif
- {
- interpPointInd = (*dataCollector)[componentNo]->getInterpPointInd();
- values = (*dataCollector)[componentNo]->getValues();
- dofCoords = (*dataCollector)[componentNo]->getDofCoords();
- }
- */
- DOFVector<int>::Iterator intPointIt(interpPointInd, USED_DOFS);
- DOFVector<double>::Iterator valueIt(values, USED_DOFS);
- DOFVector< std::list<WorldVector<double> > >::Iterator coordIt(dofCoords, USED_DOFS);
-
- // Write the values for all vertex DOFs.
- for (intPointIt.reset(), valueIt.reset(), coordIt.reset();
- !intPointIt.end();
- ++intPointIt, ++valueIt, ++coordIt) {
-
- if (*intPointIt == -2) {
- for (int i = 0; i < static_cast<int>(coordIt->size()); i++) {
- file << " " << (fabs(*valueIt) < 1e-40 ? 0.0 : *valueIt) << "\n";
- }
- }
- }
-
- // For the second dim case, write also the values of the interpolation points.
- if ((dim == 2) && (degree > 1)) {
- DOFVector< std::list<WorldVector<double> > >::Iterator
- interpCoordIt((*dataCollector)[componentNo]->getInterpPointCoords(), USED_DOFS);
-
- for (intPointIt.reset(), valueIt.reset(), interpCoordIt.reset();
- !intPointIt.end();
- ++intPointIt, ++valueIt, ++interpCoordIt) {
-
- if (*intPointIt >= 0) {
- for (int i = 0; i < static_cast<int>(interpCoordIt->size()); i++) {
- file << " " << (fabs(*valueIt) < 1e-40 ? 0.0 : *valueIt) << "\n";
- }
- }
- }
- }
- }
-
-
- void VtkWriter::writeConnectivity(std::ofstream &file)
- {
- // For the second dim case, and if higher order Lagrange elements are used,
- // write the connectivity by extra functions.
- if ((dim == 2) && (degree == 2)) {
- writeConnectivity_dim2_degree2(file);
- } else if ((dim == 2) && (degree == 3)) {
- writeConnectivity_dim2_degree3(file);
- } else if ((dim == 2) && (degree == 4)) {
- writeConnectivity_dim2_degree4(file);
- } else {
- std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
- std::list<ElementInfo>::iterator elementIt;
- int vertices = (*dataCollector)[0]->getMesh()->getGeo(VERTEX);
-
- for (elementIt = elements->begin(); elementIt != elements->end(); ++elementIt) {
- // for all vertices
- for (int i = 0; i < vertices; i++) {
- file << " " << elementIt->vertexInfo[i]->outputIndex;
- }
- file << "\n";
- }
- }
- }
-
-
- void VtkWriter::writeConnectivity_dim2_degree2(std::ofstream &file)
- {
- std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
- std::list<ElementInfo>::iterator elementIt;
-
- std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
- std::vector< std::vector<int> >::iterator pointIt;
-
- int nVertices = (*dataCollector)[0]->getNumberVertices();
-
- for (pointIt = interpPoints->begin(), elementIt = elements->begin();
- pointIt != interpPoints->end();
- ++pointIt, ++elementIt) {
-
- file << " " << elementIt->vertexInfo[0]->outputIndex
- << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[2] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[2]->outputIndex
- << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[1] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[1]->outputIndex
- << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[2] + nVertices << "\n";
-
- file << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[2] + nVertices << "\n";
- }
-
- }
-
-
- void VtkWriter::writeConnectivity_dim2_degree3(std::ofstream &file)
- {
- std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
- std::list<ElementInfo>::iterator elementIt;
-
- std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
- std::vector< std::vector<int> >::iterator pointIt;
-
- int nVertices = (*dataCollector)[0]->getNumberVertices();
-
- for (pointIt = interpPoints->begin(), elementIt = elements->begin();
- pointIt != interpPoints->end();
- ++pointIt, ++elementIt) {
-
- file << " " << elementIt->vertexInfo[0]->outputIndex
- << " " << (*pointIt)[3] + nVertices
- << " " << (*pointIt)[4] + nVertices << "\n";
-
- file << " " << (*pointIt)[4] + nVertices
- << " " << (*pointIt)[5] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << (*pointIt)[3] + nVertices
- << " " << (*pointIt)[4] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << (*pointIt)[2] + nVertices
- << " " << (*pointIt)[3] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[1]->outputIndex
- << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[5] + nVertices << "\n";
-
- file << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[6] + nVertices
- << " " << (*pointIt)[5] + nVertices << "\n";
-
- file << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[2] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[2]->outputIndex
- << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[2] + nVertices << "\n";
-
- }
-
- }
-
-
- void VtkWriter::writeConnectivity_dim2_degree4(std::ofstream &file)
- {
- std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
- std::list<ElementInfo>::iterator elementIt;
-
- std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
- std::vector< std::vector<int> >::iterator pointIt;
-
- int nVertices = (*dataCollector)[0]->getNumberVertices();
-
- for (pointIt = interpPoints->begin(), elementIt = elements->begin();
- pointIt != interpPoints->end();
- ++pointIt, ++elementIt) {
-
- file << " " << elementIt->vertexInfo[0]->outputIndex
- << " " << (*pointIt)[5] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << (*pointIt)[5] + nVertices
- << " " << (*pointIt)[9] + nVertices
- << " " << (*pointIt)[6] + nVertices << "\n";
-
- file << " " << (*pointIt)[6] + nVertices
- << " " << (*pointIt)[7] + nVertices
- << " " << (*pointIt)[9] + nVertices << "\n";
-
- file << " " << (*pointIt)[7] + nVertices
- << " " << (*pointIt)[9] + nVertices
- << " " << (*pointIt)[10] + nVertices << "\n";
-
- file << " " << (*pointIt)[7] + nVertices
- << " " << (*pointIt)[8] + nVertices
- << " " << (*pointIt)[10] + nVertices << "\n";
-
- file << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[8] + nVertices
- << " " << (*pointIt)[10] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[1]->outputIndex
- << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[8] + nVertices << "\n";
-
- file << " " << (*pointIt)[4] + nVertices
- << " " << (*pointIt)[5] + nVertices
- << " " << (*pointIt)[9] + nVertices << "\n";
-
- file << " " << (*pointIt)[4] + nVertices
- << " " << (*pointIt)[9] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << (*pointIt)[9] + nVertices
- << " " << (*pointIt)[10] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[10] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << (*pointIt)[0] + nVertices
- << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[10] + nVertices << "\n";
-
- file << " " << (*pointIt)[3] + nVertices
- << " " << (*pointIt)[4] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << (*pointIt)[2] + nVertices
- << " " << (*pointIt)[3] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << (*pointIt)[1] + nVertices
- << " " << (*pointIt)[2] + nVertices
- << " " << (*pointIt)[11] + nVertices << "\n";
-
- file << " " << elementIt->vertexInfo[2]->outputIndex
- << " " << (*pointIt)[2] + nVertices
- << " " << (*pointIt)[3] + nVertices << "\n";
-
- }
+ return 0;
}
int VtkWriter::updateAnimationFile(std::string valueFilename,
@@ -414,18 +75,4 @@ namespace AMDiS {
}
- void VtkWriter::writeFile(DOFVector<double> *values,
- const char *filename)
- {
- DataCollector *dc = NEW DataCollector(values->getFESpace(), values);
- std::vector<DataCollector*> dcList(0);
- dcList.push_back(dc);
-
- VtkWriter *writer = NEW VtkWriter(&dcList);
- writer->writeFile(filename);
-
- DELETE writer;
- DELETE dc;
- }
-
}
diff --git a/AMDiS/src/VtkWriter.h b/AMDiS/src/VtkWriter.h
index 3443d993ed45006890031e775953adcd4e107185..1951e1d11dfbefbc171342794b7871cad6c1cf54 100644
--- a/AMDiS/src/VtkWriter.h
+++ b/AMDiS/src/VtkWriter.h
@@ -22,10 +22,17 @@
#ifndef AMDIS_VTKWRITER_H
#define AMDIS_VTKWRITER_H
-#include <fstream>
+#ifdef HAVE_BOOST
+#include <boost/iostreams/filtering_stream.hpp>
+#include <boost/iostreams/device/file_descriptor.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filter/bzip2.hpp>
+#endif
+#include <fstream>
#include "BasisFunction.h"
#include "DataCollector.h"
+#include "FileWriter.h"
namespace AMDiS {
@@ -33,7 +40,8 @@ namespace AMDiS {
{
public:
VtkWriter(std::vector<DataCollector*> *dc)
- : dataCollector(dc)
+ : dataCollector(dc),
+ compress(NONE)
{
degree = (*dataCollector)[0]->getFeSpace()->getBasisFcts()->getDegree();
dim = (*dataCollector)[0]->getMesh()->getDim();
@@ -45,11 +53,13 @@ namespace AMDiS {
*/
int writeFile(const char *name);
+
/** \brief
- * May be used to simply write ParaView files.
+ * Set a compressing method for file output.
*/
- static void writeFile(DOFVector<double> *values,
- const char *filename);
+ void setCompression(FileCompression c) {
+ compress = c;
+ }
/** \brief
* Adds a new entry to a ParaView animation file.
@@ -58,45 +68,71 @@ namespace AMDiS {
std::vector< std::string > *paraViewAnimationFrames,
const char *animationFilename);
protected:
+ /** \brief
+ * Writes the VTU file to an arbitrary stream.
+ */
+ template<typename T>
+ void writeFile(T &file);
+
/** \brief
* Writes all coordinates of vertices and interpolation points to an
* output file.
*/
- void writeVertexCoords(std::ofstream &file);
+ template<typename T>
+ void writeVertexCoords(T &file);
/** \brief
* Writes all values of vertices and interpolation point to an output
* file.
*/
- void writeVertexValues(std::ofstream &file, int componentNo);
+ template<typename T>
+ void writeVertexValues(T &file, int componentNo);
/** \brief
* Writes the connectivity of all simplices to an output file.
*/
- void writeConnectivity(std::ofstream &file);
+ template<typename T>
+ void writeConnectivity(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 2 to
* an output file.
*/
- void writeConnectivity_dim2_degree2(std::ofstream &file);
+ template<typename T>
+ void writeConnectivity_dim2_degree2(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 3 to
* an output file.
*/
- void writeConnectivity_dim2_degree3(std::ofstream &file);
+ template<typename T>
+ void writeConnectivity_dim2_degree3(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 4 to
* an output file.
*/
- void writeConnectivity_dim2_degree4(std::ofstream &file);
+ template<typename T>
+ void writeConnectivity_dim2_degree4(T &file);
+#ifdef HAVE_BOOST
+ /** \brief
+ * Writes a world coordinate to a given file.
+ */
+ inline void writeCoord(boost::iostreams::filtering_ostream &file, WorldVector<double> coord) {
+ for (int i = 0; i < Global::getGeo(WORLD); i++) {
+ file << " " << std::scientific << coord[i];
+ }
+ for (int i = Global::getGeo(WORLD); i < 3; i++) {
+ file << " 0.0";
+ }
+ file << "\n";
+ }
+#endif
/** \brief
* Writes a world coordinate to a given file.
@@ -112,12 +148,18 @@ namespace AMDiS {
}
private:
- /**
+ /** \brief
* List of DataCollectors, for each component of the problem one.
*/
std::vector<DataCollector*> *dataCollector;
+ /** \brief
+ * Defines if the file has to be compressed for ouput, and with which
+ * kind of compress method.
+ */
+ FileCompression compress;
+
/** \brief
* Degree of the basis function of the problem.
*/
@@ -131,4 +173,6 @@ namespace AMDiS {
};
}
+#include "VtkWriter.hh"
+
#endif