Table Class Reference

#include <Table.h>

Inheritance diagram for Table:

Collaboration diagram for Table:

Public Member Functions
string	getColumnName () const
double	getDt (void) const
string	getFormat () const
string	getOutfile (void) const
double	getThreshold () const
bool	getUseSpikeMode (void) const
bool	getUseStreamer (void) const
void	input (double v)
Table &	operator= (const Table &tab)
void	process (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
	Reinitialize. More...
void	setColumnName (const string colname)
void	setFormat (const string format)
void	setOutfile (string outfilepath)
void	setThreshold (double v)
void	setUseSpikeMode (bool status)
void	setUseStreamer (bool status)
void	spike (double v)
	Table ()
void	zipWithTime (const vector< double > &yvec, vector< double > &tvec, const double &lasttime)
	Take the vector from table and timestamp it. It must only be called when packing the data for writing. More...
	~Table ()
Public Member Functions inherited from TableBase
void	clearVec ()
void	compareVec (vector< double > other, string op)
void	compareXplot (string fname, string plotname, string op)
const vector< double > &	data ()
double	getOutputValue () const
string	getPlotDump () const
vector< double >	getVec () const
unsigned int	getVecSize () const
double	getY (unsigned int index) const
double	interpolate (double x, double xmin, double xmax) const
void	linearTransform (double scale, double offset)
void	loadCSV (string fname, int startLine, int colNum, char separator)
void	loadXplot (string fname, string plotname)
void	loadXplotRange (string fname, string plotname, unsigned int start, unsigned int end)
double *	lookupVec (unsigned int index)
void	plainPlot (string file)
void	setOutputValue (double val)
void	setPlotDump (string v)
void	setVec (vector< double > val)
void	setVecSize (unsigned int num)
	TableBase ()
void	xplot (string file, string plotname)

Static Public Member Functions
static const Cinfo *	initCinfo ()
Static Public Member Functions inherited from TableBase
static const Cinfo *	initCinfo ()

Private Attributes
vector< string >	columns_
vector< double >	data_
	Keep the data, each entry is preceeded by time value. t0, v0, t1, v1, t2, v2 etc. More...
double	dt_
	dt of its clock. Needed for creating time co-ordinates, More...
bool	fired_
string	format_
	format of data. Default to csv. More...
double	input_
double	lastTime_
std::ofstream	of_
	Output stream. More...
string	outfile_
bool	outfileIsSet_
	Wheather or not outfile path is set by user. More...
string	rootdir_
	Table directory into which dump the stream data. More...
string	tableColumnName_
	Column name of this table. Use it when writing data to a datafile. More...
string	tablePath_
string	text_
	text_ to write. More...
double	threshold_
bool	useSpikeMode_
bool	useStreamer_
	If stream is set to true, then stream to outfile_. Default value of outfile_ is table path starting from pwd/_tables_ . On table, set streamToFile to true. More...

Additional Inherited Members
Protected Member Functions inherited from TableBase
vector< double > &	vec ()

Detailed Description

Receives and records inputs. Handles plot and spiking data in batch mode.

Definition at line 18 of file Table.h.

Constructor & Destructor Documentation

Table::Table

(

)

Definition at line 213 of file Table.cpp.

References format_, outfileIsSet_, rootdir_, and useStreamer_.

             : 
        threshold_( 0.0 ) , 
        lastTime_( 0.0 ) , 
        input_( 0.0 ), 
        fired_(false), 
        useSpikeMode_(false), 
        dt_( 0.0 )
{
    // Initialize the directory to which each table should stream.
    rootdir_ = "_tables";
    useStreamer_ = false;
    format_ = "csv";
    outfileIsSet_ = false;
}

Table::~Table

(

)

Definition at line 228 of file Table.cpp.

References TableBase::clearVec(), columns_, data_, format_, lastTime_, outfile_, useStreamer_, TableBase::vec(), StreamerBase::writeToOutFile(), and zipWithTime().

{
    // Make sure to write to rest of the entries to file before closing down.
    if( useStreamer_ )
    {
        zipWithTime( vec(), data_, lastTime_ );
        StreamerBase::writeToOutFile( outfile_, format_, "a", data_, columns_ );
        clearVec();
        data_.clear();
    }
}

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Member Function Documentation

string Table::getColumnName

(

void

)

const

Definition at line 389 of file Table.cpp.

References tableColumnName_.

Referenced by Streamer::addTable(), and initCinfo().

{
    return tableColumnName_;
}

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double Table::getDt

(

void

)

const

Definition at line 444 of file Table.cpp.

References dt_.

{
    return dt_;
}

string Table::getFormat

(

void

)

const

Definition at line 383 of file Table.cpp.

References format_.

Referenced by initCinfo().

{
    return format_;
}

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string Table::getOutfile

(

void

)

const

Definition at line 438 of file Table.cpp.

References outfile_.

Referenced by initCinfo().

{
    return outfile_;
}

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double Table::getThreshold

(

)

const

Definition at line 365 of file Table.cpp.

References threshold_.

Referenced by initCinfo().

{
    return threshold_;
}

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bool Table::getUseSpikeMode

(

void

)

const

Definition at line 416 of file Table.cpp.

References useSpikeMode_.

Referenced by initCinfo().

{
    return useSpikeMode_;
}

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bool Table::getUseStreamer

(

void

)

const

Definition at line 405 of file Table.cpp.

References useStreamer_.

Referenced by initCinfo().

{
    return useStreamer_;
}

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const Cinfo * Table::initCinfo ( )

static

Definition at line 42 of file Table.cpp.

References getColumnName(), getFormat(), getOutfile(), getThreshold(), getUseSpikeMode(), getUseStreamer(), handleInput(), TableBase::initCinfo(), process(), reinit(), requestOut(), setColumnName(), setFormat(), setOutfile(), setThreshold(), setUseSpikeMode(), setUseStreamer(), spike(), and tableCinfo.

{
    // Field Definitions
    static ValueFinfo< Table, double > threshold(
        "threshold"
        , "threshold used when Table acts as a buffer for spikes"
        , &Table::setThreshold
        , &Table::getThreshold
    );

    static ValueFinfo< Table, bool > useStreamer(
        "useStreamer"
        , "When set to true, write to a file instead writing in memory."
        " If `outfile` is not set, streamer writes to default path."
        , &Table::setUseStreamer
        , &Table::getUseStreamer
    );

    static ValueFinfo< Table, bool > useSpikeMode(
        "useSpikeMode"
        , "When set to true, look for spikes in a time-series."
        " Normally used for monitoring Vm for action potentials."
        " Could be used for any thresholded event. Default is False."
        , &Table::setUseSpikeMode
        , &Table::getUseSpikeMode
    );

    static ValueFinfo< Table, string > outfile(
        "outfile"
        , "Set the name of file to which data is written to. If set, "
        " streaming support is automatically enabled."
        , &Table::setOutfile
        , &Table::getOutfile
    );

    static ValueFinfo< Table, string > format(
        "format"
        , "Data format for table: default csv"
        , &Table::setFormat
        , &Table::getFormat
    );

    // relevant for Streamer class.  When data is written to a datafile, this is
    // used to create column name.
    static ValueFinfo< Table, string > columnName(
        "columnName"
        , "Name of the table written in header of data file."
        , &Table::setColumnName
        , &Table::getColumnName
    );

    // MsgDest Definitions

    static DestFinfo spike(
        "spike",
        "Fills spike timings into the Table. Signal has to exceed thresh",
        new OpFunc1< Table, double >( &Table::spike )
    );

    static DestFinfo process(
        "process",
        "Handles process call, updates internal time stamp.",
        new ProcOpFunc< Table >( &Table::process )
    );

    static DestFinfo reinit(
        "reinit",
        "Handles reinit call.",
        new ProcOpFunc< Table >( &Table::reinit )
    );

    // SharedMsg Definitions
    static Finfo* procShared[] =
    {
        &process, &reinit
    };

    static SharedFinfo proc(
        "proc"
        , "Shared message for process and reinit"
        , procShared, sizeof( procShared ) / sizeof( const Finfo* )
    );

    // Field Element for the vector data
    // Use a limit of 2^20 entries for the tables, about 1 million.

    static Finfo* tableFinfos[] =
    {
        &threshold,     // Value
        &format,                // Value
        &columnName,            // Value
        &outfile,               // Value
        &useStreamer,           // Value
        &useSpikeMode,           // Value
        handleInput(),      // DestFinfo
        &spike,         // DestFinfo
        requestOut(),       // SrcFinfo
        &proc,          // SharedFinfo
    };

    static string doc[] =
    {
        "Name", "Table",
        "Author", "Upi Bhalla",
        "Description",
        "Table for accumulating data values, or spike timings. "
        "Can either receive incoming doubles, or can explicitly "
        "request values from fields provided they are doubles. "
        "The latter mode of use is preferable if you wish to have "
        "independent control of how often you sample from the output "
        "variable. \n"
        "Typically used for storing simulation output into memory, or to file"
        " when stream is set to True \n"
        "There are two functionally identical variants of the Table "
        "class: Table and Table2. Their only difference is that the "
        "default scheduling of the Table (Clock Tick 8, dt = 0.1 ms ) "
        "makes it suitable for "
        "tracking electrical compartmental models of neurons and "
        "networks. \n"
        "Table2 (Clock Tick 18, dt = 1.0 s) is good for tracking "
        "biochemical signaling pathway outputs. \n"
        "These are just the default values and Tables can be assigned"
        " to any Clock Tick and timestep in the usual manner.",
    };

    static Dinfo< Table > dinfo;

    static Cinfo tableCinfo (
        "Table",
        TableBase::initCinfo(),
        tableFinfos,
        sizeof( tableFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc ) / sizeof( string )
    );

    static string doc2[] =
    {
        doc[0], "Table2", doc[2], doc[3], doc[4], doc[5]
    };

    doc2[1] = "Table2";

    static Cinfo table2Cinfo (
        "Table2",
        TableBase::initCinfo(),
        tableFinfos,
        sizeof( tableFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc2,
        sizeof( doc2 ) / sizeof( string )
    );

    return &tableCinfo;
}

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void Table::input

(

double

v

)

Definition at line 338 of file Table.cpp.

References TableBase::vec().

Referenced by handleInput(), and testTable().

{
    vec().push_back( v );
}

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Table & Table::operator=

(

const Table &

tab

)

Definition at line 240 of file Table.cpp.

{
    return *this;
}

void Table::process	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 250 of file Table.cpp.

References TableBase::clearVec(), columns_, ProcInfo::currTime, data_, format_, TableBase::getVecSize(), lastTime_, outfile_, requestOut(), spike(), useSpikeMode_, useStreamer_, TableBase::vec(), StreamerBase::writeToOutFile(), and zipWithTime().

Referenced by initCinfo().

{
    lastTime_ = p->currTime;

    // Copy incoming data to ret and insert into vector.
    vector< double > ret;
    requestOut()->send( e, &ret );
    if (useSpikeMode_) {
        for ( vector< double >::const_iterator
                    i = ret.begin(); i != ret.end(); ++i )
        spike( *i );
    } else {
        vec().insert( vec().end(), ret.begin(), ret.end() );
    }

    /*  If we are streaming to a file, let's write to a file. And clean the
     *  vector.
     *  Write at every 5 seconds or whenever size of vector is more than 10k.
     */
    if( useStreamer_ )
    {
        if( fmod(lastTime_, 5.0) == 0.0 or getVecSize() >= 10000 )
        {
            zipWithTime( vec(), data_, lastTime_ );
            StreamerBase::writeToOutFile( outfile_, format_ , "a", data_, columns_ );
            data_.clear();
            clearVec();
        }
    }
}

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void Table::reinit	(	const Eref &	e,
		ProcPtr	p
	)

Reinitialize.

Parameters

e
p

Create the default filepath for this table.

Definition at line 287 of file Table.cpp.

References TableBase::clearVec(), columns_, Eref::data(), data_, dt_, Eref::element(), Id::eref(), fired_, format_, Element::getTick(), Clock::getTickDt(), Eref::id(), input_, lastTime_, moose::moosePathToUserPath(), outfile_, outfileIsSet_, Id::path(), requestOut(), rootdir_, setOutfile(), spike(), tablePath_, useSpikeMode_, useStreamer_, TableBase::vec(), StreamerBase::writeToOutFile(), and zipWithTime().

Referenced by initCinfo().

{
    tablePath_ = e.id().path();
    unsigned int numTick = e.element()->getTick();
    Clock* clk = reinterpret_cast<Clock*>(Id(1).eref().data());
    dt_ = clk->getTickDt( numTick );
    fired_ = false;

    if( useStreamer_ )
    {
        // The first column is variable time.
        columns_.push_back( "time" );
        // And the second column name is the name of the table.
        columns_.push_back( moose::moosePathToUserPath( tablePath_ ) );

        // If user has not set the filepath, then use the table path prefixed
        // with rootdit as path.
        if( ! outfileIsSet_ )
            setOutfile( rootdir_ +
                    moose::moosePathToUserPath(tablePath_) + '.' + format_
                    );
    }

    input_ = 0.0;
    vec().resize( 0 );
    lastTime_ = 0;
    vector< double > ret;
    requestOut()->send( e, &ret );
    if (useSpikeMode_) {
        for ( vector< double >::const_iterator
                    i = ret.begin(); i != ret.end(); ++i )
        spike( *i );
    } else {
        vec().insert( vec().end(), ret.begin(), ret.end() );
    }

    if( useStreamer_ )
    {
        zipWithTime( vec(), data_, lastTime_ );
        StreamerBase::writeToOutFile( outfile_, format_, "w", data_, columns_);
        clearVec();
        data_.clear();
        clearVec();
    }
}

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void Table::setColumnName

(

const string

colname

)

Definition at line 394 of file Table.cpp.

References tableColumnName_.

Referenced by initCinfo().

{
    tableColumnName_ = colname ;
}

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void Table::setFormat

(

const string

format

)

Definition at line 371 of file Table.cpp.

References format_, LOG, and moose::warning.

Referenced by initCinfo().

{
    if( format == "csv" or format == "npy" )
        format_ = format;
    else
        LOG( moose::warning
                , "Unsupported format " << format
                << " only npy and csv are supported"
           );
}

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void Table::setOutfile

(

string

outfilepath

)

Definition at line 423 of file Table.cpp.

References moose::createMOOSEPath(), moose::createParentDirs(), format_, moose::getExtension(), outfile_, outfileIsSet_, setUseStreamer(), and moose::toFilename().

Referenced by initCinfo(), and reinit().

{
    outfile_ = moose::createMOOSEPath( outpath );
    if( ! moose::createParentDirs( outfile_ ) )
        outfile_ = moose::toFilename( outfile_ );

    outfileIsSet_ = true;
    setUseStreamer( true );

    // If possible get the format of file as well.
    format_ = moose::getExtension( outfile_, true );
    if( format_.size() == 0 )
        format_ = "csv";
}

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void Table::setThreshold

(

double

v

)

Definition at line 360 of file Table.cpp.

References threshold_.

Referenced by initCinfo().

{
    threshold_ = v;
}

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void Table::setUseSpikeMode

(

bool

status

)

Definition at line 411 of file Table.cpp.

References useSpikeMode_.

Referenced by initCinfo().

{
    useSpikeMode_ = useSpikeMode;
}

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void Table::setUseStreamer

(

bool

status

)

Definition at line 400 of file Table.cpp.

References useStreamer_.

Referenced by initCinfo(), and setOutfile().

{
    useStreamer_ = useStreamer;
}

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void Table::spike

(

double

v

)

Definition at line 343 of file Table.cpp.

References fired_, lastTime_, threshold_, and TableBase::vec().

Referenced by initCinfo(), process(), and reinit().

{
    if ( fired_ ) { // Wait for it to go below threshold
        if ( v < threshold_ )
            fired_ = false;
    } else {
        if ( v > threshold_ ) { // wait for it to go above threshold.
            fired_ = true;
            vec().push_back( lastTime_ );
        }
    }
}

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void Table::zipWithTime	(	const vector< double > &	yvec,
		vector< double > &	tvec,
		const double &	lasttime
	)

Take the vector from table and timestamp it. It must only be called when packing the data for writing.

Definition at line 453 of file Table.cpp.

References dt_.

Referenced by process(), reinit(), and ~Table().

{
    size_t N = v.size();
    for (size_t i = 0; i < N; i++)
    {
        tvec.push_back( currTime - (N - i - 1 ) * dt_ );
        tvec.push_back( v[i] );
    }
}

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Member Data Documentation

vector<string> Table::columns_

private

Definition at line 85 of file Table.h.

Referenced by process(), reinit(), and ~Table().

vector<double> Table::data_

private

Keep the data, each entry is preceeded by time value. t0, v0, t1, v1, t2, v2 etc.

Definition at line 84 of file Table.h.

Referenced by process(), reinit(), and ~Table().

double Table::dt_

private

dt of its clock. Needed for creating time co-ordinates,

Definition at line 129 of file Table.h.

Referenced by getDt(), reinit(), and zipWithTime().

bool Table::fired_

private

Definition at line 77 of file Table.h.

Referenced by reinit(), and spike().

string Table::format_

private

format of data. Default to csv.

Definition at line 119 of file Table.h.

Referenced by getFormat(), process(), reinit(), setFormat(), setOutfile(), Table(), and ~Table().

double Table::input_

private

Definition at line 76 of file Table.h.

Referenced by reinit().

double Table::lastTime_

private

Definition at line 75 of file Table.h.

Referenced by process(), reinit(), spike(), and ~Table().

std::ofstream Table::of_

private

Output stream.

Definition at line 134 of file Table.h.

string Table::outfile_

private

Definition at line 109 of file Table.h.

Referenced by getOutfile(), process(), reinit(), setOutfile(), and ~Table().

bool Table::outfileIsSet_

private

Wheather or not outfile path is set by user.

Definition at line 114 of file Table.h.

Referenced by reinit(), setOutfile(), and Table().

string Table::rootdir_

private

Table directory into which dump the stream data.

Definition at line 105 of file Table.h.

Referenced by reinit(), and Table().

string Table::tableColumnName_

private

Column name of this table. Use it when writing data to a datafile.

Definition at line 93 of file Table.h.

Referenced by getColumnName(), and setColumnName().

string Table::tablePath_

private

Definition at line 87 of file Table.h.

Referenced by reinit().

string Table::text_

private

text_ to write.

Definition at line 124 of file Table.h.

double Table::threshold_

private

Definition at line 74 of file Table.h.

Referenced by getThreshold(), setThreshold(), and spike().

bool Table::useSpikeMode_

private

Definition at line 78 of file Table.h.

Referenced by getUseSpikeMode(), process(), reinit(), and setUseSpikeMode().

bool Table::useStreamer_

private

If stream is set to true, then stream to outfile_. Default value of outfile_ is table path starting from pwd/_tables_ . On table, set streamToFile to true.

Definition at line 100 of file Table.h.

Referenced by getUseStreamer(), process(), reinit(), setUseStreamer(), Table(), and ~Table().

---

The documentation for this class was generated from the following files:

• moose-core/builtins/Table.h
• moose-core/builtins/Table.cpp