vtu writer write only raw, vtu reader read raw and base64

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);
       

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;
 	      }
 	    }

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*>(&macroFile_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*>(&macroFile_nl), 4);
 	if (macroFile_nl > 0) { //TODO
 	  macroFilename.resize(macroFile_nl, ' ');
-	  file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
+	  file.read(&macroFilename[0], macroFile_nl);
 	}
 	file.read(reinterpret_cast<char*>(&nMacros), 4);
 	

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());
 	  

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)
 	{

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);
 	

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";