ColumnDataWriter.cpp

/*
 
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   this list of conditions and the following disclaimer.
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   software without specific prior written permission.
 
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*/
 
#include <ctype.h>
#include <sstream>
#include <iomanip>
#include <fstream>
 
#include "ColumnDataWriter.hpp"
#include "ColumnDataConstants.hpp"
#include "Exception.hpp"
#include "Version.hpp"
 
 
ColumnDataWriter::ColumnDataWriter(const std::string& rDirectory,
                                   const std::string& rBaseName,
                                   bool cleanDirectory,
                                   unsigned precision)
    : mOutputFileHandler(rDirectory, cleanDirectory),
      mDirectory(rDirectory),
      mBaseName(rBaseName),
      mIsInDefineMode(true),
      mIsFixedDimensionSet(false),
      mIsUnlimitedDimensionSet(false),
      mUnlimitedDimensionPosition(0),
      mFixedDimensionSize(-1),
      mpCurrentOutputFile(nullptr),
      mpCurrentAncillaryFile(nullptr),
      mpUnlimitedDimensionVariable(nullptr),
      mpFixedDimensionVariable(nullptr),
      mFieldWidth(precision+8),
      mPrecision(precision),
      mHasPutVariable(false),
      mNeedAdvanceAlongUnlimitedDimension(false),
      mCommentForInfoFile("")
{
    if (mPrecision<2 || mPrecision>20)
    {
        EXCEPTION("Precision must be between 2 and 20 (inclusive)");
    }
}
 
ColumnDataWriter::~ColumnDataWriter()
{
    // Close any open output files
    Close();
 
    // Delete memory allocated for variables
    if (mpUnlimitedDimensionVariable != nullptr)
    {
        delete mpUnlimitedDimensionVariable;
    }
    if (mpFixedDimensionVariable != nullptr)
    {
        delete mpFixedDimensionVariable;
    }
}
 
std::string ColumnDataWriter::GetOutputDirectory()
{
    return mOutputFileHandler.GetOutputDirectoryFullPath();
}
 
void ColumnDataWriter::Close()
{
    if (mpCurrentOutputFile.get() != nullptr)
    {
        mpCurrentOutputFile->close();
        mpCurrentOutputFile = out_stream(nullptr);
    }
 
    if (mpCurrentAncillaryFile.get() != nullptr)
    {
        mpCurrentAncillaryFile->close();
        mpCurrentAncillaryFile = out_stream(nullptr);
    }
}
 
void ColumnDataWriter::CheckVariableName(const std::string& rName)
{
    if (rName.length() == 0)
    {
        EXCEPTION("Variable name not allowed: may not be blank.");
    }
    CheckUnitsName(rName);
}
 
void ColumnDataWriter::CheckUnitsName(const std::string& rName)
{
    for (unsigned i=0; i<rName.length(); i++)
    {
        if (!isalnum(rName[i]) && !(rName[i]=='_'))
        {
            std::string error = "Variable name/units '" + rName + "' not allowed: may only contain alphanumeric characters or '_'.";
            EXCEPTION(error);
        }
    }
}
 
int ColumnDataWriter::DefineUnlimitedDimension(const std::string& rDimensionName,
                                               const std::string& rDimensionUnits)
{
    if (mIsUnlimitedDimensionSet)
    {
        EXCEPTION("Unlimited dimension already set. Cannot be defined twice");
    }
 
    if (!mIsInDefineMode)
    {
        EXCEPTION("Cannot define variables when not in Define mode");
    }
 
    CheckVariableName(rDimensionName);
    CheckUnitsName(rDimensionUnits);
 
    mUnlimitedDimensionName = rDimensionName;
    mUnlimitedDimensionUnits = rDimensionUnits;
 
    mpUnlimitedDimensionVariable = new DataWriterVariable;
    mpUnlimitedDimensionVariable->mVariableName = rDimensionName;
    mpUnlimitedDimensionVariable->mVariableUnits = rDimensionUnits;
 
    mIsUnlimitedDimensionSet = true;
 
    return UNLIMITED_DIMENSION_VAR_ID;
}
 
int ColumnDataWriter::DefineFixedDimension(const std::string& rDimensionName,
                                           const std::string& rDimensionUnits,
                                           long dimensionSize)
{
    if (!mIsInDefineMode)
    {
        EXCEPTION("Cannot define variables when not in Define mode");
    }
    if (dimensionSize < 1)
    {
        EXCEPTION("Fixed dimension must be at least 1 long");
    }
 
    CheckVariableName(rDimensionName);
    CheckUnitsName(rDimensionUnits);
 
    mFixedDimensionName = rDimensionName;
    mFixedDimensionUnits = rDimensionUnits;
    mFixedDimensionSize = dimensionSize;
 
    mIsFixedDimensionSet = true;
 
    mpFixedDimensionVariable = new DataWriterVariable;
    mpFixedDimensionVariable->mVariableName = rDimensionName;
    mpFixedDimensionVariable->mVariableUnits = rDimensionUnits;
    return FIXED_DIMENSION_VAR_ID;
}
 
int ColumnDataWriter::DefineVariable(const std::string& rVariableName,
                                     const std::string& rVariableUnits)
{
    if (!mIsInDefineMode)
    {
        EXCEPTION("Cannot define variables when not in Define mode");
    }
 
    CheckVariableName(rVariableName);
    CheckUnitsName(rVariableUnits);
 
    int variable_id;
 
    if (rVariableName == mUnlimitedDimensionName)
    {
        EXCEPTION("Variable name: " + rVariableName + " already in use as unlimited dimension");
    }
    else if (rVariableName == mFixedDimensionName)
    {
        EXCEPTION("Variable name: " + rVariableName + " already in use as fixed dimension");
    }
    else // ordinary variable
    {
        // Add the variable to the variable vector
        DataWriterVariable new_variable;
        new_variable.mVariableName = rVariableName;
        new_variable.mVariableUnits = rVariableUnits;
        mVariables.push_back(new_variable);
 
        // Use the index of the variable vector as the variable ID.
        // This is ok since there is no way to remove variables.
        variable_id = mVariables.size()-1;
    }
 
    return variable_id;
}
 
void ColumnDataWriter::EndDefineMode()
{
    // Check that a dimension has been defined
    if (mIsFixedDimensionSet == false && mIsUnlimitedDimensionSet == false)
    {
        EXCEPTION("Cannot end define mode. No dimensions have been defined.");
    }
    // Check that at least one variable has been defined
    if (mVariables.size() < 1)
    {
        EXCEPTION("Cannot end define mode. No variables have been defined.");
    }
    // Calculate the width of each row
    int unlimited_dimension_variable = (mpUnlimitedDimensionVariable != nullptr);
    int fixed_dimension_variable = (mpFixedDimensionVariable != nullptr);
    if (mIsUnlimitedDimensionSet)
    {
        if (mIsFixedDimensionSet)
        {
            mRowWidth = (mVariables.size() + fixed_dimension_variable) * (mFieldWidth + SPACING);
            mAncillaryRowWidth = mFieldWidth + SPACING;
 
            // Write out the headers for the first position along the unlimited dimension
            std::stringstream suffix;
            suffix << std::setfill('0') << std::setw(FILE_SUFFIX_WIDTH) << mUnlimitedDimensionPosition;
 
            if (mpUnlimitedDimensionVariable != nullptr)
            {
                std::string ancillary_filename = mBaseName + "_unlimited.dat";
                mpCurrentAncillaryFile = mOutputFileHandler.OpenOutputFile(ancillary_filename, std::ios::out | std::ios::binary);
                (*mpCurrentAncillaryFile) << std::setiosflags(std::ios::scientific);
                (*mpCurrentAncillaryFile) << std::setprecision(mPrecision);
                if (mpUnlimitedDimensionVariable != nullptr)
                {
                    (*mpCurrentAncillaryFile) << mpUnlimitedDimensionVariable->mVariableName
                                              << "(" << mpUnlimitedDimensionVariable->mVariableUnits << ") ";
                }
            }
            mAncillaryRowStartPosition = mpCurrentAncillaryFile->tellp();
            std::string filename = mBaseName + "_" + suffix.str() + ".dat";
            this->CreateFixedDimensionFile(filename);
        }
        else
        {
            mRowWidth = (mVariables.size() + unlimited_dimension_variable) * (mFieldWidth + SPACING);
 
            // Write out the column headers
            std::string filename = mBaseName + ".dat";
            mpCurrentOutputFile = mOutputFileHandler.OpenOutputFile(filename, std::ios::out);
            (*mpCurrentOutputFile) << std::setiosflags(std::ios::scientific);
            (*mpCurrentOutputFile) << std::setprecision(mPrecision);
            if (mpUnlimitedDimensionVariable != nullptr)
            {
                (*mpCurrentOutputFile) << mpUnlimitedDimensionVariable->mVariableName
                                       << "(" << mpUnlimitedDimensionVariable->mVariableUnits << ") ";
            }
            /*
             * Write out header(which may contain several variables) for output file.
             * In this scope the method "CreateFixedDimensionFile" has not been invoked,
             * because there is no mFixedDimensionSize available.
             */
            for (unsigned i=0; i<mVariables.size(); i++)
            {
                (*mpCurrentOutputFile) << mVariables[i].mVariableName << "(" << mVariables[i].mVariableUnits << ")";
                if (i < mVariables.size()-1)
                {
                    (*mpCurrentOutputFile) << " ";
                }
            }
            (*mpCurrentOutputFile) << std::endl;
            mRowStartPosition = mpCurrentOutputFile->tellp();
 
            // Write out a line of blank space which is #variables * (mFieldWidth + 1) -1
            std::string blank_line(mRowWidth, ' ');
            (*mpCurrentOutputFile) << blank_line;
        }
    }
    else
    {
        // The fixed dimension must be set at this point or we wouldn't be here
        mRowWidth = (mVariables.size() + fixed_dimension_variable) * (mFieldWidth + SPACING);
        std::string filename = mBaseName + ".dat";
        this->CreateFixedDimensionFile(filename);
    }
 
    // Write info file
    std::string infoname = mBaseName + ".info";
    this->CreateInfoFile(infoname);
 
    mIsInDefineMode = false;
}
 
void ColumnDataWriter::CreateFixedDimensionFile(const std::string& rFileName)
{
    // Create new data file
    mpCurrentOutputFile = mOutputFileHandler.OpenOutputFile(rFileName, std::ios::out | std::ios::binary);
    (*mpCurrentOutputFile) << std::setiosflags(std::ios::scientific);
    (*mpCurrentOutputFile) << std::setprecision(mPrecision);
    if (mpFixedDimensionVariable != nullptr)
    {
        (*mpCurrentOutputFile) << mpFixedDimensionVariable->mVariableName
                               << "(" << mpFixedDimensionVariable->mVariableUnits << ") ";
    }
    // Write out the column headers and spaces for the rest of the file
    for (unsigned i = 0; i < mVariables.size(); i++)
    {
        (*mpCurrentOutputFile) << mVariables[i].mVariableName << "(" << mVariables[i].mVariableUnits << ")";
        if (i < mVariables.size()-1)
        {
            (*mpCurrentOutputFile) << " ";
        }
    }
    (*mpCurrentOutputFile) << std::endl;
    mRowStartPosition = mpCurrentOutputFile->tellp();
    std::string blank_line(mRowWidth, ' ');
    for (int i = 0; i < mFixedDimensionSize; i++)
    {
        (*mpCurrentOutputFile) << blank_line << std::endl;
    }
}
 
void ColumnDataWriter::CreateInfoFile(const std::string& rFileName)
{
    // Create new info file
    out_stream p_info_file = mOutputFileHandler.OpenOutputFile(rFileName, std::ios::out | std::ios::binary);
    (*p_info_file) << "FIXED " << mFixedDimensionSize << std::endl;
    (*p_info_file) << "UNLIMITED " << mIsUnlimitedDimensionSet << std::endl;
    (*p_info_file) << "VARIABLES " << mVariables.size() << std::endl;
    if (mCommentForInfoFile != "")
    {
        *p_info_file << mCommentForInfoFile << std::endl;
    }
    *p_info_file << ChasteBuildInfo::GetProvenanceString();
    p_info_file->close();
}
 
void ColumnDataWriter::DoAdvanceAlongUnlimitedDimension()
{
    mHasPutVariable = false;
    mNeedAdvanceAlongUnlimitedDimension = false;
 
    if (mIsUnlimitedDimensionSet)
    {
        if (mIsFixedDimensionSet)
        {
            //first close the current file before creating another one
            mpCurrentOutputFile->close();
            std::stringstream suffix;
            suffix << std::setfill('0') << std::setw(FILE_SUFFIX_WIDTH) << mUnlimitedDimensionPosition + 1;
 
            std::string filename = mBaseName + "_" + suffix.str() + ".dat";
            this->CreateFixedDimensionFile(filename);
        }
        else
        {
            //go to the end of the current line
            mpCurrentOutputFile->seekp(mRowStartPosition+mRowWidth);
            (*mpCurrentOutputFile) << std::endl;
            mRowStartPosition = mpCurrentOutputFile->tellp();
            std::string blank_line(mRowWidth,' ');
            (*mpCurrentOutputFile) << blank_line;
        }
    }
    else
    {
        EXCEPTION("Cannot advance along unlimited dimension if it is not defined");
    }
    mUnlimitedDimensionPosition++;
}
 
void ColumnDataWriter::AdvanceAlongUnlimitedDimension()
{
    if (mHasPutVariable)
    {
        mNeedAdvanceAlongUnlimitedDimension = true;
    }
}
 
void ColumnDataWriter::PutVariable(int variableID, double variableValue, long dimensionPosition)
{
 
    if (mNeedAdvanceAlongUnlimitedDimension)
    {
        DoAdvanceAlongUnlimitedDimension();
    }
 
    // Check that we are not in define mode
    if (mIsInDefineMode)
    {
        EXCEPTION("Cannot put variables when in Define mode");
    }
    // Check that variableID is in range (exception)
    if (variableID > (int)mVariables.size() ||
        (variableID != UNLIMITED_DIMENSION_VAR_ID &&
         variableID != FIXED_DIMENSION_VAR_ID &&
         variableID < 0))
    {
        EXCEPTION("variableID unknown");
    }
 
    if (mIsFixedDimensionSet)
    {
        if (dimensionPosition == -1 && variableID != UNLIMITED_DIMENSION_VAR_ID)
        {
            EXCEPTION("Dimension position not supplied");
        }
        if (dimensionPosition < -1 || dimensionPosition >= mFixedDimensionSize)
        {
            EXCEPTION("Dimension position out of range");
        }
        if (dimensionPosition != -1 && variableID == UNLIMITED_DIMENSION_VAR_ID)
        {
            EXCEPTION("Dimension position supplied, but not required");
        }
    }
 
    if (mIsUnlimitedDimensionSet)
    {
        if (mIsFixedDimensionSet)
        {
            // Go to the correct position in the file
            if (variableID == UNLIMITED_DIMENSION_VAR_ID)
            {
                (*mpCurrentAncillaryFile) << std::endl << " ";
                mpCurrentAncillaryFile->width(mFieldWidth);
                (*mpCurrentAncillaryFile) << variableValue;
            }
            else
            {
                int position;
                if (variableID == FIXED_DIMENSION_VAR_ID)
                {
                    position = mRowStartPosition + (mRowWidth+SPACING) * dimensionPosition;
                }
                else
                {
                    // ordinary variables
                    position = mRowStartPosition + (mRowWidth+SPACING) * dimensionPosition +
                               ((variableID + (mpFixedDimensionVariable != nullptr)) * (mFieldWidth + SPACING));
                }
 
                mpCurrentOutputFile->seekp(position);
                mpCurrentOutputFile->width(mFieldWidth);
                (*mpCurrentOutputFile) << variableValue;
            }
        }
        else
        {
            // Go to the correct position in the file
            int position;
            if (variableID == UNLIMITED_DIMENSION_VAR_ID)
            {
                position = mRowStartPosition;
            }
            else
            {
                position = (variableID + (mpUnlimitedDimensionVariable != nullptr)) * (mFieldWidth + SPACING) +
                           mRowStartPosition;
            }
 
            mpCurrentOutputFile->seekp(position);
            mpCurrentOutputFile->width(mFieldWidth);
            (*mpCurrentOutputFile) << variableValue;
 
        }
    }
    else
    {
        // Go to the correct position in the file
        int position;
        if (variableID == FIXED_DIMENSION_VAR_ID)
        {
            position = mRowStartPosition + (mRowWidth+SPACING) * dimensionPosition;
        }
        else
        {
            position = mRowStartPosition + (mRowWidth+SPACING) * dimensionPosition +
                       ((variableID + (mpFixedDimensionVariable != nullptr)) * (mFieldWidth + SPACING));
        }
        mpCurrentOutputFile->seekp(position);
        mpCurrentOutputFile->width(mFieldWidth);
        (*mpCurrentOutputFile) << variableValue;
    }
 
    mHasPutVariable = true;
}