diff --git a/AMDiS/src/io/Arh3Reader.cc b/AMDiS/src/io/Arh3Reader.cc
index adc1f53116e2d025ee5f3c73795437b95d8391a3..ab80858124ec6117d0e4897c7cb88a61014edfb5 100644
--- a/AMDiS/src/io/Arh3Reader.cc
+++ b/AMDiS/src/io/Arh3Reader.cc
@@ -207,7 +207,7 @@ namespace AMDiS { namespace io {
string typeId(4, ' ');
uint8_t major = 0, minor = 0;
- file.read(const_cast<char*>(typeId.data()), 4);
+ file.read(&typeId[0], 4);
file.read(reinterpret_cast<char*>(&major), 1);
file.read(reinterpret_cast<char*>(&minor), 1);
diff --git a/AMDiS/src/io/VtkReader.hh b/AMDiS/src/io/VtkReader.hh
index 874bd8d6de0e80507ea1e4b2095910aa2d876d40..36b10e2ead6bcbc0691338437b14027a735dace1 100644
--- a/AMDiS/src/io/VtkReader.hh
+++ b/AMDiS/src/io/VtkReader.hh
@@ -58,7 +58,8 @@ namespace AMDiS
TEST_EXIT(boost::filesystem::exists(filename))((filename + " does not exist!\n").c_str());
xml_document vtu;
- TEST_EXIT(vtu.load_file(filename.c_str()))("Could not load vtu file! Error in xml structure.\n");
+// TEST_EXIT(vtu.load_file(filename.c_str()))("Could not load vtu file! Error in xml structure.\n");
+ vtu.load_file(filename.c_str());
xml_node VTKFile = vtu.child("VTKFile");
string zlib = VTKFile.attribute("compressor").value();
@@ -98,14 +99,7 @@ namespace AMDiS
}
}
} else {
- string encoding = AppendedData.attribute("encoding").value();
- TEST_EXIT(encoding == "base64")
- ("Currently the encoding of AppendedData only supports base64. But it's easy to extend to raw.\n");
-
- string appendedData = AppendedData.last_child().value();
- int start = appendedData.find("_");
- appendedData = appendedData.substr(start + 1, appendedData.length() - 1);
-
+ // Get offset of all data array
vector<int> offsetVec;
int pointsIndex = 0, index = 0;
vector<pair<xml_node, int> > pointDataIndex;
@@ -121,6 +115,45 @@ namespace AMDiS
}
}
+ // Get appended data
+ string encoding = AppendedData.attribute("encoding").value();
+ string appendedData = "";
+ if (encoding == "base64") {
+ appendedData = AppendedData.last_child().value();
+ int start = appendedData.find("_");
+ appendedData = appendedData.substr(start + 1);
+ } else if (encoding == "raw") {
+ // Binary AppendedData block cannot be regonized by pugixml. So we have to
+ // extract the data manually.
+ ifstream file(filename.c_str());
+ TEST_EXIT(file.is_open())("Cannot open file: %s\n", filename.c_str());
+
+ long startPos = 0, endPos = 0;
+ string line = "";
+ while (getline(file, line))
+ if (line.find("<AppendedData") != std::string::npos)
+ break;
+
+ TEST_EXIT_DBG(!file.eof()) ("Should not happen.\n");
+ startPos = file.tellg();
+ file.seekg(offsetVec[offsetVec.size() - 1], ios_base::cur);
+
+ while (getline(file, line))
+ if (line.find("</AppendedData") != std::string::npos)
+ break;
+
+ TEST_EXIT_DBG(!file.eof()) ("Should not happen.\n");
+ file.seekg(-line.length(), ios_base::cur);
+ endPos = file.tellg();
+ appendedData.resize(endPos - startPos);
+ file.seekg(startPos);
+ file.read(&appendedData[0], endPos - startPos);
+ int start = appendedData.find("_");
+ appendedData = appendedData.substr(start + 1);
+ } else
+ ERROR_EXIT("Currently the encoding of AppendedData only supports base64 or raw.\n");
+
+ // Read appended data
string format = PointsDataArray.attribute("format").value();
string type = PointsDataArray.attribute("type").value();
TEST_EXIT(format == "appended")("The format of DataArray is not appended in appended mode. Should not happen.\n");
@@ -131,7 +164,11 @@ namespace AMDiS
offsetVec[pointsIndex + 1] - offsetVec[pointsIndex];
string points = appendedData.substr(offsetVec[pointsIndex], len);
- detail::binary2pointList(points, type, (zlib != ""), pointList);
+ detail::binary2pointList(points,
+ type,
+ (zlib != ""),
+ encoding == "base64",
+ pointList);
T test;
@@ -155,7 +192,12 @@ namespace AMDiS
nComponents = pointDataIndex[i].first.attribute("NumberOfComponents").as_int();
TEST_EXIT(nComponents == -1 || static_cast<int>(size(test)) <= nComponents)
("Can not read values in DOFVector with given value type. Too many components!\n");
- detail::binary2valueList(values, type, (zlib != ""), valueList[j], size(test), nComponents);
+ detail::binary2valueList(values, type,
+ (zlib != ""),
+ encoding == "base64",
+ valueList[j],
+ size(test),
+ nComponents);
break;
}
}
diff --git a/AMDiS/src/io/detail/Arh3Reader.cc b/AMDiS/src/io/detail/Arh3Reader.cc
index 5af58116cc9af2e699b7467097822c4bce6a184d..ff241dff9335c879b03992e6840e33f327d6073f 100644
--- a/AMDiS/src/io/detail/Arh3Reader.cc
+++ b/AMDiS/src/io/detail/Arh3Reader.cc
@@ -47,7 +47,7 @@ namespace AMDiS { namespace io {
uint8_t minor_ = 0;
string typeId(4, ' ');
- file.read(const_cast<char*>(typeId.data()), 4);
+ file.read(&typeId[0], 4);
file.read(reinterpret_cast<char*>(&major_), 1);
file.read(reinterpret_cast<char*>(&minor_), 1);
@@ -298,7 +298,7 @@ namespace AMDiS { namespace io {
{
uint32_t tmpInt = 0;
file.read(reinterpret_cast<char*>(&tmpInt), 4);
- file.read(const_cast<char*>(AFEDfileName[i].data()), tmpInt);
+ file.read(&AFEDfileName[i][0], tmpInt);
for(int j = 0; j < 4; j++)
{
file.read(reinterpret_cast<char*>(&perDOFs[j]), 4);
@@ -313,13 +313,13 @@ namespace AMDiS { namespace io {
file.read(reinterpret_cast<char*>(&tmpInt), 4);
vecsNameLen.push_back(tmpInt);
tmpString.resize(tmpInt, ' ');
- file.read(const_cast<char*>(tmpString.data()), tmpInt); //
+ file.read(&tmpString[0], tmpInt); //
vecsName.push_back(tmpString);
file.read(reinterpret_cast<char*>(&tmpInt), 4);
sortedFeSpaces[tmpInt].push_back(i);
vecsFeSpaceNum.push_back(tmpInt);
tmpString.resize(4, ' ');
- file.read(const_cast<char*>(tmpString.data()), 4);
+ file.read(&tmpString[0], 4);
dataformat.push_back(tmpString);
}
@@ -329,7 +329,7 @@ namespace AMDiS { namespace io {
if (macroFile_nl > 0) {
string tmpString("");
tmpString.resize(macroFile_nl, ' ');
- file.read(const_cast<char*>(tmpString.data()), macroFile_nl);
+ file.read(&tmpString[0], macroFile_nl);
}
//================header is over==================//
@@ -715,11 +715,11 @@ namespace AMDiS { namespace io {
uint32_t tmpInt = 0;
file.read(reinterpret_cast<char*>(&tmpInt), 4);
tmpString.resize(tmpInt, ' ');
- file.read(const_cast<char*>(tmpString.data()), tmpInt); //
+ file.read(&tmpString[0], tmpInt); //
file.read(reinterpret_cast<char*>(&tmpInt), 4);
sortedFeSpaces[tmpInt].push_back(i);
tmpString.resize(4, ' ');
- file.read(const_cast<char*>(tmpString.data()), 4);
+ file.read(&tmpString[0], 4);
dataformat.push_back(tmpString);
}
@@ -727,7 +727,7 @@ namespace AMDiS { namespace io {
uint32_t macroFile_nl = 0;
file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
string tmpString("");
- file.read(const_cast<char*>(tmpString.data()), macroFile_nl);
+ file.read(&tmpString[0], macroFile_nl);
//================header is over==================//
@@ -843,7 +843,7 @@ namespace AMDiS { namespace io {
("Cannot open file %s\n", filename.c_str());
string fd(16, ' ');
- file.read(const_cast<char*>(fd.data()), 16);
+ file.read(&fd[0], 16);
string Id = fd.substr(0, 4);
int major = boost::lexical_cast<int>(fd.substr(5, 1));
int minor = boost::lexical_cast<int>(fd.substr(7, 1));
@@ -854,12 +854,12 @@ namespace AMDiS { namespace io {
file.read(reinterpret_cast<char*>(&baseDirLen), 4);
baseDir.resize(baseDirLen, ' ');
- file.read(const_cast<char*>(baseDir.data()), baseDirLen);
+ file.read(&baseDir[0], baseDirLen);
file.read(reinterpret_cast<char*>(&nFiles), 4);
file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
if (macroFile_nl > 0) { //TODO
macroFilename.resize(macroFile_nl, ' ');
- file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
+ file.read(¯oFilename[0], macroFile_nl);
}
file.read(reinterpret_cast<char*>(&nMacros), 4);
diff --git a/AMDiS/src/io/detail/VtkReader.h b/AMDiS/src/io/detail/VtkReader.h
index 310aca401c25244b367db5a882b563f9e63793c3..8d3d0d872fe94c2d66cdb886693617a81d119787 100644
--- a/AMDiS/src/io/detail/VtkReader.h
+++ b/AMDiS/src/io/detail/VtkReader.h
@@ -108,7 +108,7 @@ namespace AMDiS
}
#endif
- inline std::string getInnerDataArray(std::string& input, bool zlib)
+ inline std::string getInnerDataArray(std::string& input, bool zlib, bool base64)
{
FUNCNAME("VtkReader::detail::getInnerDataArray()");
@@ -122,16 +122,20 @@ namespace AMDiS
if(zlib) {
#ifdef HAVE_COMPRESSION
string s = input.substr(0, 8);
- s = detail::base64ToStr(s);
- tmp = const_cast<char*>(s.c_str());
+ if (base64)
+ s = detail::base64ToStr(s);
+ tmp = const_cast<char*>(input.c_str());
ptr = reinterpret_cast<int*>(tmp);
int nBlocks = *ptr;
- int headerSize = (((4 * nBlocks + 12) % 3) > 0) ? 4 * ((4 * nBlocks + 12) / 3 + 1) : 4 * ((4 * nBlocks + 12) / 3);
+ int headerSize = (base64) ? (((4 * nBlocks + 12) % 3) > 0) ? 4 * ((4 * nBlocks + 12) / 3 + 1) : 4 * ((4 * nBlocks + 12) / 3)
+ : 4 * nBlocks + 12;
header = input.substr(0, headerSize);
body = input.substr(headerSize);
- header = detail::base64ToStr(header);
- body = detail::base64ToStr(body);
+ if (base64) {
+ header = detail::base64ToStr(header);
+ body = detail::base64ToStr(body);
+ }
int blockSize, finalSize, offset = 0;
tmp = const_cast<char*>(header.c_str());
@@ -150,7 +154,7 @@ namespace AMDiS
ERROR_EXIT("HAVE_COMPRESSION OFF. VtkReader cannot read APPENDED_COMPRESSED vtu files.\n");
#endif
} else {
- header = detail::base64ToStr(input);
+ header = (base64) ? detail::base64ToStr(input) : input;
tmp = const_cast<char*>(header.c_str());
ptr = reinterpret_cast<int*>(tmp);
nBytes = *ptr;
@@ -163,12 +167,13 @@ namespace AMDiS
inline void binary2pointList(std::string& input,
std::string type,
bool zlib,
+ bool base64,
std::vector<WorldVector<double> >& pointList)
{
int dow = Global::getGeo(WORLD);
int dowExplicit = 3;
- std::string inner = getInnerDataArray(input, zlib);
+ std::string inner = getInnerDataArray(input, zlib, base64);
int nBytes = inner.length();
char* tmp = const_cast<char*>(inner.c_str());
@@ -232,6 +237,7 @@ namespace AMDiS
void binary2valueList(std::string& input,
std::string type,
bool zlib,
+ bool base64,
std::vector<T>& valueList,
int numComponent = 1,
int numComponentMax = -1)
@@ -239,7 +245,7 @@ namespace AMDiS
if (numComponentMax < 0)
numComponentMax = numComponent;
- std::string inner = getInnerDataArray(input, zlib);
+ std::string inner = getInnerDataArray(input, zlib, base64);
int nBytes = inner.length();
char* tmp = const_cast<char*>(inner.c_str());
diff --git a/AMDiS/src/io/detail/VtkWriter.cc b/AMDiS/src/io/detail/VtkWriter.cc
index 1d834f7a22d1c3924f3b08bf77765821ef0f6ba8..d0cc250ffc64d02e3587d8243c5decdb95a74604 100644
--- a/AMDiS/src/io/detail/VtkWriter.cc
+++ b/AMDiS/src/io/detail/VtkWriter.cc
@@ -75,14 +75,14 @@ namespace AMDiS { namespace io {
using namespace std;
string result(""), header(""), body("");
-
switch(format) {
case APPENDED: {
BinaryStream hstream;
hstream << bstream.getSize();
body = bstream.str();
header = hstream.str();
- result = detail::base64Encode(header + body);
+// result = detail::base64Encode(header + body);
+ result = header + body;
break;
}
case APPENDED_COMPRESSED: {
@@ -109,7 +109,8 @@ namespace AMDiS { namespace io {
body += subData;
}
header = hstream.str();
- result = detail::base64Encode(header) + detail::base64Encode(body);
+// result = detail::base64Encode(header) + detail::base64Encode(body);
+ result = header + body;
#endif
break;
}
@@ -124,13 +125,13 @@ namespace AMDiS { namespace io {
namespace detail
{
- std::string base64Encode(std::string text)
- {
- unsigned int writePaddChars = (3-text.length()%3)%3;
- std::string base64(binary_base64(text.begin()),binary_base64(text.end()));
- base64.append(writePaddChars,'=');
- return base64;
- }
+// std::string base64Encode(std::string text)
+// {
+// unsigned int writePaddChars = (3-text.length()%3)%3;
+// std::string base64(binary_base64(text.begin()),binary_base64(text.end()));
+// base64.append(writePaddChars,'=');
+// return base64;
+// }
std::string extract_relative_path(std::string valueFilename, std::string animationFilename)
{
diff --git a/AMDiS/src/io/detail/VtkWriter.h b/AMDiS/src/io/detail/VtkWriter.h
index d65ebbf8612b015331d49eb521a7de7118e7a7d2..3ae88a2bc3b243415349c544d18a5daa98a5e2d2 100644
--- a/AMDiS/src/io/detail/VtkWriter.h
+++ b/AMDiS/src/io/detail/VtkWriter.h
@@ -28,8 +28,8 @@
#include <string>
#include <vector>
#include <sstream>
-#include <boost/archive/iterators/base64_from_binary.hpp>
-#include <boost/archive/iterators/transform_width.hpp>
+// #include <boost/archive/iterators/base64_from_binary.hpp>
+// #include <boost/archive/iterators/transform_width.hpp>
#include "AdaptInfo.h"
#include "io/DataCollector.h"
@@ -272,14 +272,14 @@ namespace AMDiS { namespace io {
namespace detail
{
- typedef
- boost::archive::iterators::base64_from_binary< // convert binary values to base64 characters
- boost::archive::iterators::transform_width< // retrieve 6 bit integers from a sequence of 8 bit bytes
- std::string::const_iterator, 6, 8
- >
- > binary_base64;
-
- std::string base64Encode(std::string text);
+// typedef
+// boost::archive::iterators::base64_from_binary< // convert binary values to base64 characters
+// boost::archive::iterators::transform_width< // retrieve 6 bit integers from a sequence of 8 bit bytes
+// std::string::const_iterator, 6, 8
+// >
+// > binary_base64;
+//
+// std::string base64Encode(std::string text);
std::string extract_relative_path(std::string valueFilename, std::string animationFilename);
diff --git a/AMDiS/src/io/detail/VtkWriter.hh b/AMDiS/src/io/detail/VtkWriter.hh
index 2752c231df417d1deb9f65af608b4556797b78ff..2ad7979d5becea7a397405413eaef31ede677405 100644
--- a/AMDiS/src/io/detail/VtkWriter.hh
+++ b/AMDiS/src/io/detail/VtkWriter.hh
@@ -232,7 +232,8 @@ namespace AMDiS { namespace io {
file << " </Cells>\n";
file << " </Piece>\n";
file << " </UnstructuredGrid>\n";
- file << " <AppendedData encoding=\"base64\">\n";
+// file << " <AppendedData encoding=\"base64\">\n";
+ file << " <AppendedData encoding=\"raw\">\n";
file << " _" << finalData << "\n";
file << " </AppendedData>\n";
file << "</VTKFile>\n";