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IO.cpp
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// kate: replace-tabs off; indent-width 4; indent-mode normal
// vim: ts=4:sw=4:noexpandtab
/*
Copyright (c) 2010--2012,
François Pomerleau and Stephane Magnenat, ASL, ETHZ, Switzerland
You can contact the authors at <f dot pomerleau at gmail dot com> and
<stephane at magnenat dot net>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the <organization> nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL ETH-ASL BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "IO.h"
#include "IOFunctions.h"
#include "InspectorsImpl.h"
// For logging
#include "PointMatcherPrivate.h"
#include <iostream>
#include <fstream>
#include <stdexcept>
#include <ctype.h>
#include "boost/algorithm/string.hpp"
#include "boost/filesystem.hpp"
#include "boost/filesystem/path.hpp"
#include "boost/filesystem/operations.hpp"
#include "boost/lexical_cast.hpp"
#include "boost/foreach.hpp"
#ifdef WIN32
#define strtok_r strtok_s
#endif // WIN32
namespace PointMatcherSupport {
namespace {
const int one = 1;
}
const bool isBigEndian = *reinterpret_cast<const unsigned char*>(&one) == static_cast<unsigned char>(0);
const int oneBigEndian = isBigEndian ? 1 : 1 << 8 * (sizeof(int) - 1);
}
using namespace std;
using namespace PointMatcherSupport;
// Tokenize a string, excepted if it begins with a '%' (a comment in CSV)
static std::vector<string> csvLineToVector(const char* line)
{
std::vector<string> parsedLine;
char delimiters[] = " \t,;";
char *token;
char tmpLine[1024];
char *brkt = 0;
strcpy(tmpLine, line);
token = strtok_r(tmpLine, delimiters, &brkt);
if(line[0] != '%') // Jump line if it's commented
{
while (token)
{
parsedLine.push_back(string(token));
token = strtok_r(NULL, delimiters, &brkt);
}
}
return parsedLine;
}
// Open and parse a CSV file, return the data
CsvElements parseCsvWithHeader(const std::string& fileName)
{
validateFile(fileName);
ifstream is(fileName.c_str());
unsigned elementCount=0;
std::map<string, unsigned> keywordCols;
CsvElements data;
bool firstLine(true);
unsigned lineCount=0;
string line;
while (safeGetLine(is, line))
{
if(firstLine)
{
std::vector<string> header = csvLineToVector(line.c_str());
elementCount = header.size();
for(unsigned int i = 0; i < elementCount; i++)
{
keywordCols[header[i]] = i;
}
firstLine = false;
}
else // load the rest of the file
{
std::vector<string> parsedLine = csvLineToVector(line.c_str());
if(parsedLine.size() != elementCount && parsedLine.size() !=0)
{
stringstream errorMsg;
errorMsg << "Error at line " << lineCount+1 << ": expecting " << elementCount << " columns but read " << parsedLine.size() << " elements.";
throw runtime_error(errorMsg.str());
}
for(unsigned int i = 0; i < parsedLine.size(); i++)
{
for(BOOST_AUTO(it,keywordCols.begin()); it!=keywordCols.end(); it++)
{
if(i == (*it).second)
{
data[(*it).first].push_back(parsedLine[i]);
}
}
}
}
lineCount++;
}
// Use for debug
//for(BOOST_AUTO(it,data.begin()); it!=data.end(); it++)
//{
// cout << "--------------------------" << endl;
// cout << "Header: |" << (*it).first << "|" << endl;
// //for(unsigned i=0; i<(*it).second.size(); i++)
// //{
// // cout << (*it).second[i] << endl;
// //}
//}
return data;
}
//! Constructor, leave fields blank if unused
template<typename T>
PointMatcherIO<T>::FileInfo::FileInfo(const std::string& readingFileName, const std::string& referenceFileName, const std::string& configFileName, const TransformationParameters& initialTransformation, const TransformationParameters& groundTruthTransformation, const Vector& gravity):
readingFileName(readingFileName),
referenceFileName(referenceFileName),
configFileName(configFileName),
initialTransformation(initialTransformation),
groundTruthTransformation(groundTruthTransformation),
gravity(gravity)
{}
template struct PointMatcherIO<float>::FileInfo;
template struct PointMatcherIO<double>::FileInfo;
// Empty constructor
template<typename T>
PointMatcherIO<T>::FileInfoVector::FileInfoVector()
{
}
//! Load a vector of FileInfo from a CSV file.
/**
@param fileName name of the CSV file
@param dataPath path relative to which the point cloud CSV or VTK will be resolved
@param configPath path relative to which the yaml configuration files will be resolved
The first line of the CSV file must contain a header. The supported tags are:
- reading: file name of the reading point cloud
- reference: file name of the reference point cloud
- config: file name of the YAML configuration of the ICP chain
- iTxy: initial transformation, coordinate x,y
- gTxy: ground-truth transformation, coordinate x,y
Note that the header must at least contain "reading".
*/
template<typename T>
PointMatcherIO<T>::FileInfoVector::FileInfoVector(const std::string& fileName, std::string dataPath, std::string configPath)
{
if (dataPath.empty())
{
#if BOOST_FILESYSTEM_VERSION >= 3
dataPath = boost::filesystem::path(fileName).parent_path().string();
#else
dataPath = boost::filesystem::path(fileName).parent_path().file_string();
#endif
}
if (configPath.empty())
{
#if BOOST_FILESYSTEM_VERSION >= 3
configPath = boost::filesystem::path(fileName).parent_path().string();
#else
configPath = boost::filesystem::path(fileName).parent_path().file_string();
#endif
}
const CsvElements data = parseCsvWithHeader(fileName);
// Look for transformations
const bool found3dInitialTrans(findTransform(data, "iT", 3));
bool found2dInitialTrans(findTransform(data, "iT", 2));
const bool found3dGroundTruthTrans(findTransform(data, "gT", 3));
bool found2dGroundTruthTrans(findTransform(data, "gT", 2));
if (found3dInitialTrans)
found2dInitialTrans = false;
if (found3dGroundTruthTrans)
found2dGroundTruthTrans = false;
// Check for consistency
if (found3dInitialTrans && found2dGroundTruthTrans)
throw runtime_error("Initial transformation is in 3D but ground-truth is in 2D");
if (found2dInitialTrans && found3dGroundTruthTrans)
throw runtime_error("Initial transformation is in 2D but ground-truth is in 3D");
CsvElements::const_iterator readingIt(data.find("reading"));
if (readingIt == data.end())
throw runtime_error("Error transfering CSV to structure: The header should at least contain \"reading\".");
CsvElements::const_iterator referenceIt(data.find("reference"));
CsvElements::const_iterator configIt(data.find("config"));
// Load reading
const std::vector<string>& readingFileNames = readingIt->second;
const unsigned lineCount = readingFileNames.size();
boost::optional<std::vector<string> > referenceFileNames;
boost::optional<std::vector<string> > configFileNames;
if (referenceIt != data.end())
{
referenceFileNames = referenceIt->second;
assert (referenceFileNames->size() == lineCount);
}
if (configIt != data.end())
{
configFileNames = configIt->second;
assert (configFileNames->size() == lineCount);
}
// for every lines
for(unsigned line=0; line<lineCount; line++)
{
FileInfo info;
// Files
info.readingFileName = localToGlobalFileName(dataPath, readingFileNames[line]);
if (referenceFileNames)
info.referenceFileName = localToGlobalFileName(dataPath, (*referenceFileNames)[line]);
if (configFileNames)
info.configFileName = localToGlobalFileName(configPath, (*configFileNames)[line]);
// Load transformations
if(found3dInitialTrans)
info.initialTransformation = getTransform(data, "iT", 3, line);
if(found2dInitialTrans)
info.initialTransformation = getTransform(data, "iT", 2, line);
if(found3dGroundTruthTrans)
info.groundTruthTransformation = getTransform(data, "gT", 3, line);
if(found2dGroundTruthTrans)
info.groundTruthTransformation = getTransform(data, "gT", 2, line);
// Build the list
this->push_back(info);
}
// Debug: Print the list
/*for(unsigned i=0; i<list.size(); i++)
{
cout << "\n--------------------------" << endl;
cout << "Sequence " << i << ":" << endl;
cout << "Reading path: " << list[i].readingFileName << endl;
cout << "Reference path: " << list[i].referenceFileName << endl;
cout << "Extension: " << list[i].fileExtension << endl;
cout << "Tranformation:\n" << list[i].initialTransformation << endl;
cout << "Grativity:\n" << list[i].gravity << endl;
}
*/
}
//! Join parentPath and fileName and return the result as a global path
template<typename T>
std::string PointMatcherIO<T>::FileInfoVector::localToGlobalFileName(const std::string& parentPath, const std::string& fileName)
{
std::string globalFileName(fileName);
if (!boost::filesystem::exists(globalFileName))
{
const boost::filesystem::path globalFilePath(boost::filesystem::path(parentPath) / boost::filesystem::path(fileName));
#if BOOST_FILESYSTEM_VERSION >= 3
globalFileName = globalFilePath.string();
#else
globalFileName = globalFilePath.file_string();
#endif
}
validateFile(globalFileName);
return globalFileName;
}
//! Return whether there is a valid transformation named prefix in data
template<typename T>
bool PointMatcherIO<T>::FileInfoVector::findTransform(const CsvElements& data, const std::string& prefix, unsigned dim)
{
bool found(true);
for(unsigned i=0; i<dim+1; i++)
{
for(unsigned j=0; j<dim+1; j++)
{
stringstream transName;
transName << prefix << i << j;
found = found && (data.find(transName.str()) != data.end());
}
}
return found;
}
//! Return the transformation named prefix from data
template<typename T>
typename PointMatcherIO<T>::TransformationParameters PointMatcherIO<T>::FileInfoVector::getTransform(const CsvElements& data, const std::string& prefix, unsigned dim, unsigned line)
{
TransformationParameters transformation(TransformationParameters::Identity(dim+1, dim+1));
for(unsigned i=0; i<dim+1; i++)
{
for(unsigned j=0; j<dim+1; j++)
{
stringstream transName;
transName << prefix << i << j;
CsvElements::const_iterator colIt(data.find(transName.str()));
const T value = boost::lexical_cast<T> (colIt->second[line]);
transformation(i,j) = value;
}
}
return transformation;
}
template struct PointMatcherIO<float>::FileInfoVector;
template struct PointMatcherIO<double>::FileInfoVector;
//! Throw a runtime_error exception if fileName cannot be opened
void PointMatcherSupport::validateFile(const std::string& fileName)
{
boost::filesystem::path fullPath(fileName);
ifstream ifs(fileName.c_str());
if (!ifs.good() || !boost::filesystem::is_regular_file(fullPath))
#if BOOST_FILESYSTEM_VERSION >= 3
#if BOOST_VERSION >= 105000
throw runtime_error(string("Cannot open file ") + boost::filesystem::complete(fullPath).generic_string());
#else
throw runtime_error(string("Cannot open file ") + boost::filesystem3::complete(fullPath).generic_string());
#endif
#else
throw runtime_error(string("Cannot open file ") + boost::filesystem::complete(fullPath).native_file_string());
#endif
}
//! Load a point cloud from a file, determine format from extension
template<typename T>
typename PointMatcher<T>::DataPoints PointMatcher<T>::DataPoints::load(const std::string& fileName)
{
const boost::filesystem::path path(fileName);
const string& ext(boost::filesystem::extension(path));
if (boost::iequals(ext, ".vtk"))
return PointMatcherIO<T>::loadVTK(fileName);
else if (boost::iequals(ext, ".csv"))
return PointMatcherIO<T>::loadCSV(fileName);
else if (boost::iequals(ext, ".ply"))
return PointMatcherIO<T>::loadPLY(fileName);
else if (boost::iequals(ext, ".pcd"))
return PointMatcherIO<T>::loadPCD(fileName);
else
throw runtime_error("loadAnyFormat(): Unknown extension \"" + ext + "\" for file \"" + fileName + "\", extension must be either \".vtk\" or \".csv\"");
}
template
PointMatcher<float>::DataPoints PointMatcher<float>::DataPoints::load(const std::string& fileName);
template
PointMatcher<double>::DataPoints PointMatcher<double>::DataPoints::load(const std::string& fileName);
//! @brief Load comma separated values (csv) file
//! @param fileName a string containing the path and the file name
//!
//! This loader has 3 behaviors since there is no official standard for
//! csv files. A 2D or 3D point cloud will be created automatically if:
//! - there is a header with columns named x, y and optionnaly z
//! - there are only 2 or 3 columns in the file
//!
//! Otherwise, the user is asked to enter column id manually which might
//! block automatic processing.
template<typename T>
typename PointMatcher<T>::DataPoints PointMatcherIO<T>::loadCSV(const std::string& fileName)
{
ifstream ifs(fileName.c_str());
validateFile(fileName);
return loadCSV(ifs);
}
template<typename T>
PointMatcherIO<T>::SupportedLabel::SupportedLabel(const std::string& internalName, const std::string& externalName, const PMPropTypes& type):
internalName(internalName),
externalName(externalName),
type(type)
{
}
// Class LabelGenerator
template<typename T>
void PointMatcherIO<T>::LabelGenerator::add(const std::string internalName)
{
bool findLabel = false;
for(size_t i=0; i<labels.size(); ++i)
{
if(internalName == labels[i].text)
{
labels[i].span++;
findLabel = true;
break;
}
}
if(!findLabel)
{
labels.push_back(Label(internalName,1));
}
}
template<typename T>
void PointMatcherIO<T>::LabelGenerator::add(const std::string internalName, const unsigned int dim)
{
labels.push_back(Label(internalName, dim));
}
// Class LabelGenerator
template<typename T>
typename PointMatcher<T>::DataPoints::Labels PointMatcherIO<T>::LabelGenerator::getLabels() const
{
return labels;
}
template
class PointMatcherIO<float>::LabelGenerator;
template
class PointMatcherIO<double>::LabelGenerator;
template <typename T>
std::string PointMatcherIO<T>::getColLabel(const Label& label, const int row)
{
std::string externalName;
if (label.text == "normals")
{
if (row == 0)
{
externalName = "nx";
}
if (row == 1)
{
externalName = "ny";
}
if (row == 2)
{
externalName = "nz";
}
}
else if (label.text == "color")
{
if (row == 0)
{
externalName = "red";
}
if (row == 1)
{
externalName = "green";
}
if (row == 2)
{
externalName = "blue";
}
if (row == 3)
externalName = "alpha";
}
else if (label.text == "eigValues")
{
externalName = "eigValues" + boost::lexical_cast<string>(row);
}
else if (label.text == "eigVectors")
{
// format: eigVectors<0-2><X-Z>
externalName = "eigVectors" + boost::lexical_cast<string>(row/3);
int row_mod = row % 3;
if (row_mod == 0)
externalName += "X";
else if (row_mod == 1)
externalName += "Y";
else if (row_mod == 2)
externalName += "Z";
}
else if (label.span == 1)
{
externalName = label.text;
}
else
externalName = label.text + boost::lexical_cast<std::string>(row);
return externalName;
}
//! @brief Load comma separated values (csv) file
//! @see loadCSV()
template<typename T>
typename PointMatcher<T>::DataPoints PointMatcherIO<T>::loadCSV(std::istream& is)
{
vector<GenericInputHeader> csvHeader;
LabelGenerator featLabelGen, descLabelGen, timeLabelGen;
Matrix features;
Matrix descriptors;
Int64Matrix times;
unsigned int csvCol = 0;
unsigned int csvRow = 0;
bool hasHeader(false);
bool firstLine(true);
//count lines in the file
is.unsetf(std::ios_base::skipws);
unsigned int line_count = std::count(
std::istream_iterator<char>(is),
std::istream_iterator<char>(),
'\n');
//reset the stream
is.clear();
is.seekg(0, ios::beg);
char delimiters[] = " \t,;";
char *token;
string line;
while (safeGetLine(is, line))
{
// Skip empty lines
if(line.empty())
break;
// Look for text header
unsigned int len = strspn(line.c_str(), " ,+-.1234567890Ee");
if(len != line.length())
{
//cout << "Header detected" << endl;
hasHeader = true;
}
else
{
hasHeader = false;
}
// Count dimension using first line
if(firstLine)
{
unsigned int dim = 0;
char tmpLine[1024]; //FIXME: might be problematic for large file
strcpy(tmpLine, line.c_str());
char *brkt = 0;
token = strtok_r(tmpLine, delimiters, &brkt);
//1- BUILD HEADER
while (token)
{
// Load text header
if(hasHeader)
{
csvHeader.push_back(GenericInputHeader(string(token)));
}
dim++;
token = strtok_r(NULL, delimiters, &brkt);
}
if (!hasHeader)
{
// Check if it is a simple file with only coordinates
if (!(dim == 2 || dim == 3))
{
int idX=0, idY=0, idZ=0;
cout << "WARNING: " << dim << " columns detected. Not obvious which columns to load for x, y or z." << endl;
cout << endl << "Enter column ID (starting from 0) for x: ";
cin >> idX;
cout << "Enter column ID (starting from 0) for y: ";
cin >> idY;
cout << "Enter column ID (starting from 0, -1 if 2D data) for z: ";
cin >> idZ;
// Fill with unkown column names
for(unsigned int i=0; i<dim; i++)
{
std::ostringstream os;
os << "empty" << i;
csvHeader.push_back(GenericInputHeader(os.str()));
}
// Overwrite with user inputs
csvHeader[idX] = GenericInputHeader("x");
csvHeader[idY] = GenericInputHeader("y");
if(idZ != -1)
csvHeader[idZ] = GenericInputHeader("z");
}
else
{
// Assume logical order...
csvHeader.push_back(GenericInputHeader("x"));
csvHeader.push_back(GenericInputHeader("y"));
if(dim == 3)
csvHeader.push_back(GenericInputHeader("z"));
}
}
//2- PROCESS HEADER
// Load known features, descriptors, and time
const SupportedLabels externalLabels = getSupportedExternalLabels();
// Counters
int rowIdFeatures = 0;
int rowIdDescriptors = 0;
int rowIdTime = 0;
// Loop through all known external names (ordered list)
for(size_t i=0; i<externalLabels.size(); i++)
{
const SupportedLabel supLabel = externalLabels[i];
for(size_t j=0; j < csvHeader.size(); j++)
{
if(supLabel.externalName == csvHeader[j].name)
{
csvHeader[j].matrixType = supLabel.type;
switch (supLabel.type)
{
case FEATURE:
csvHeader[j].matrixRowId = rowIdFeatures;
featLabelGen.add(supLabel.internalName);
rowIdFeatures++;
break;
case DESCRIPTOR:
csvHeader[j].matrixRowId = rowIdDescriptors;
descLabelGen.add(supLabel.internalName);
rowIdDescriptors++;
break;
case TIME:
csvHeader[j].matrixRowId = rowIdTime;
timeLabelGen.add(supLabel.internalName);
rowIdTime++;
break;
default:
throw runtime_error(string("CSV parse error: encounter a type different from FEATURE, DESCRIPTOR and TIME. Implementation not supported. See the definition of 'enum PMPropTypes'"));
break;
}
// we stop searching once we have a match
break;
}
}
}
// loop through the remaining UNSUPPORTED labels and assigned them to a descriptor row
for(unsigned int i=0; i<csvHeader.size(); i++)
{
if(csvHeader[i].matrixType == UNSUPPORTED)
{
csvHeader[i].matrixType = DESCRIPTOR; // force descriptor
csvHeader[i].matrixRowId = rowIdDescriptors;
descLabelGen.add(csvHeader[i].name); // keep original name
rowIdDescriptors++;
}
}
//3- RESERVE MEMORY
if(hasHeader && line_count > 0)
line_count--;
const unsigned int featDim = featLabelGen.getLabels().totalDim();
const unsigned int descDim = descLabelGen.getLabels().totalDim();
const unsigned int timeDim = timeLabelGen.getLabels().totalDim();
const unsigned int nbPoints = line_count;
features = Matrix(featDim, nbPoints);
descriptors = Matrix(descDim, nbPoints);
times = Int64Matrix(timeDim, nbPoints);
}
//4- LOAD DATA (this start again from the first line)
char* brkt = 0;
char line_c[1024];//FIXME: this might be a problem for large files
strcpy(line_c,line.c_str());
token = strtok_r(line_c, delimiters, &brkt);
if(!(hasHeader && firstLine))
{
// Parse a line
csvCol = 0;
while (token)
{
if(csvCol > (csvHeader.size() - 1))
{
// Error check (too much data)
throw runtime_error(
(boost::format("CSV parse error: at line %1%, too many elements to parse compare to the header number of columns (col=%2%).") % csvRow % csvHeader.size()).str());
}
// Alias
const int matrixRow = csvHeader[csvCol].matrixRowId;
const int matrixCol = csvRow;
switch (csvHeader[csvCol].matrixType)
{
case FEATURE:
features(matrixRow, matrixCol) = lexical_cast_scalar_to_string<T>(string(token));
break;
case DESCRIPTOR:
descriptors(matrixRow, matrixCol) = lexical_cast_scalar_to_string<T>(token);
break;
case TIME:
times(matrixRow, matrixCol) = lexical_cast_scalar_to_string<boost::int64_t>(token);
break;
default:
throw runtime_error(string("CSV parse error: encounter a type different from FEATURE, DESCRIPTOR and TIME. Implementation not supported. See the definition of 'enum PMPropTypes'"));
break;
}
//fetch next element
token = strtok_r(NULL, delimiters, &brkt);
csvCol++;
}
// Error check (not enough data)
if(csvCol != (csvHeader.size()))
{
throw runtime_error(
(boost::format("CSV parse error: at line %1%, not enough elements to parse compare to the header number of columns (col=%2%).") % csvRow % csvHeader.size()).str());
}
csvRow++;
}
firstLine = false;
}
// 5- ASSEMBLE FINAL DATAPOINTS
DataPoints loadedPoints(features, featLabelGen.getLabels());
if (descriptors.rows() > 0)
{
loadedPoints.descriptors = descriptors;
loadedPoints.descriptorLabels = descLabelGen.getLabels();
}
if(times.rows() > 0)
{
loadedPoints.times = times;
loadedPoints.timeLabels = timeLabelGen.getLabels();
}
// Ensure homogeous coordinates
if(!loadedPoints.featureExists("pad"))
{
loadedPoints.addFeature("pad", Matrix::Ones(1,features.cols()));
}
return loadedPoints;
}
template
PointMatcher<float>::DataPoints PointMatcherIO<float>::loadCSV(const std::string& fileName);
template
PointMatcher<double>::DataPoints PointMatcherIO<double>::loadCSV(const std::string& fileName);
//! Save a point cloud to a file, determine format from extension
template<typename T>
void PointMatcher<T>::DataPoints::save(const std::string& fileName, bool binary) const
{
const boost::filesystem::path path(fileName);
const string& ext(boost::filesystem::extension(path));
if (boost::iequals(ext, ".vtk"))
return PointMatcherIO<T>::saveVTK(*this, fileName, binary);
if (binary)
throw runtime_error("save(): Binary writing is not supported together with extension \"" + ext + "\". Currently binary writing is only supported with \".vtk\".");
if (boost::iequals(ext, ".csv"))
return PointMatcherIO<T>::saveCSV(*this, fileName);
else if (boost::iequals(ext, ".ply"))
return PointMatcherIO<T>::savePLY(*this, fileName);
else if (boost::iequals(ext, ".pcd"))
return PointMatcherIO<T>::savePCD(*this, fileName);
else
throw runtime_error("save(): Unknown extension \"" + ext + "\" for file \"" + fileName + "\", extension must be either \".vtk\", \".ply\", \".pcd\" or \".csv\"");
}
template
void PointMatcher<float>::DataPoints::save(const std::string& fileName, bool binary) const;
template
void PointMatcher<double>::DataPoints::save(const std::string& fileName, bool binary) const;
//! Save point cloud to a file as CSV
template<typename T>
void PointMatcherIO<T>::saveCSV(const DataPoints& data, const std::string& fileName)
{
ofstream ofs(fileName.c_str());
if (!ofs.good())
throw runtime_error(string("Cannot open file ") + fileName);
saveCSV(data, ofs);
}
//! Save point cloud to a stream as CSV
template<typename T>
void PointMatcherIO<T>::saveCSV(const DataPoints& data, std::ostream& os)
{
const int pointCount(data.features.cols());
const int dimCount(data.features.rows());
const int descDimCount(data.descriptors.rows());
if (pointCount == 0)
{
LOG_WARNING_STREAM( "Warning, no points, doing nothing");
return;
}
// write header
for (int i = 0; i < dimCount - 1; i++)
{
os << data.featureLabels[i].text;
if (!((i == (dimCount - 2)) && descDimCount == 0))
os << ",";
}
int n = 0;
for (size_t i = 0; i < data.descriptorLabels.size(); i++)
{
Label lab = data.descriptorLabels[i];
for (size_t s = 0; s < lab.span; s++)
{
os << getColLabel(lab,s);
if (n != (descDimCount - 1))
os << ",";
n++;
}
}
os << "\n";
// write points
for (int p = 0; p < pointCount; ++p)
{
for (int i = 0; i < dimCount-1; ++i)
{
os << data.features(i, p);
if(!((i == (dimCount - 2)) && descDimCount == 0))
os << " , ";
}
for (int i = 0; i < descDimCount; i++)
{
os << data.descriptors(i,p);
if (i != (descDimCount - 1))
os << ",";
}
os << "\n";
}
}
template
void PointMatcherIO<float>::saveCSV(const DataPoints& data, const std::string& fileName);
template
void PointMatcherIO<double>::saveCSV(const DataPoints& data, const std::string& fileName);
//! Load point cloud from a file as VTK
template<typename T>
typename PointMatcher<T>::DataPoints PointMatcherIO<T>::loadVTK(const std::string& fileName)
{
ifstream ifs(fileName.c_str());
if (!ifs.good())
throw runtime_error(string("Cannot open file ") + fileName);
return loadVTK(ifs);
}
void skipBlock(bool binary, int binarySize, std::istream & is, bool hasSeparateSizeParameter = true){
int n;
int size;
is >> n;
if(!is.good()){
throw std::runtime_error("File violates the VTK format : parameter 'n' is missing after a field name.");
}
if(hasSeparateSizeParameter) {
is >> size;
if(!is.good()){
throw std::runtime_error("File violates the VTK format : parameter 'size' is missing after a field name.");
}
} else {
size = n;
}
std::string line;
getline(is, line); // remove line end after parameters;
if(binary){
is.seekg(size * binarySize, std::ios_base::cur);
} else {
for (int p = 0; p < n; p++)
{
getline(is, line);
}
}
}
//! Load point cloud from a stream as VTK
template<typename T>
typename PointMatcher<T>::DataPoints PointMatcherIO<T>::loadVTK(std::istream& is)
{
std::map<std::string, SplitTime> labelledSplitTime;
DataPoints loadedPoints;
// parse header
string line;
getline(is, line);
if (line.find("# vtk DataFile Version") != 0)
throw runtime_error(string("Wrong magic header, found ") + line);
getline(is, line);
getline(is, line);
const bool isBinary = (line == "BINARY");
if (line != "ASCII"){
if(!isBinary){
throw runtime_error(string("Wrong file type, expecting ASCII or BINARY, found ") + line);
}
}
getline(is, line);
SupportedVTKDataTypes dataType;
if (line == "DATASET POLYDATA")
dataType = POLYDATA;
else if (line == "DATASET UNSTRUCTURED_GRID")
dataType = UNSTRUCTURED_GRID;
else
throw runtime_error(string("Wrong data type, expecting DATASET POLYDATA, found ") + line);
// parse points, descriptors and time
string fieldName;
string name;
int dim = 0;
int pointCount = 0;
string type;
while (is >> fieldName)
{
// load features
if(fieldName == "POINTS")
{
is >> pointCount;
is >> type;
getline(is, line); // remove line end after parameters!
if(!(type == "float" || type == "double"))
throw runtime_error(string("Field POINTS can only be of type double or float"));
Matrix features(4, pointCount);