PostProcessingWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <PostProcessingWriter.hpp>

Collaboration diagram for PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	PostProcessingWriter (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::string directory, std::string hdf5File, bool makeAbsolute, std::string voltageName="V")
void	WritePostProcessingFiles ()
	~PostProcessingWriter ()
void	WriteAboveThresholdDepolarisationFile (double threshold)
Private Member Functions
void	WriteVariablesOverTimeAtNodes (std::vector< unsigned > &rNodeIndices)
void	WriteApdMapFile (double repolarisationPercentage, double threshold)
void	WriteUpstrokeTimeMap (double threshold)
void	WriteMaxUpstrokeVelocityMap (double threshold)
void	WriteConductionVelocityMap (unsigned originNode, std::vector< double > distancesFromOriginNode)
void	WriteGenericFile (std::vector< std::vector< double > > &rDataPayload, std::string fileName)
Private Attributes
std::string	mDirectory
std::string	mHdf5File
bool	mMakeAbsolute
std::string	mVoltageName
Hdf5DataReader *	mpDataReader
PropagationPropertiesCalculator *	mpCalculator
unsigned	mLo
unsigned	mHi
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > &	mrMesh
Friends
class	TestPostProcessingWriter

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >

Write out physiological parameters at the end of a simulation

APD map
Upstroke time map
Upstroke Velocity map
Conduction Velocity map

Definition at line 47 of file PostProcessingWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::string	directory,
		std::string	hdf5File,
		bool	makeAbsolute,
		std::string	voltageName = `"V"`
	)			`[inline]`

Constructor

Parameters:

	rMesh	A reference to the mesh used to calculate the distance map to pass to the conduction velocity calculator.
	directory	The directory the data is in. The output is written to <directory>/output
	hdf5File	The file the data is in.
	makeAbsolute	Whether to convert the path to absolute using the OutputFileHandler (via the HdfDataReader)
	voltageName	(Optional) The name of the variable representing the membrane potential. It is used in the creation of the PropagationPropertiesCalculator object. Defaults to "V".

Definition at line 42 of file PostProcessingWriter.cpp.

References Hdf5DataReader::GetNumberOfRows(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpDataReader, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::~PostProcessingWriter ( ) [inline]

Destructor

Definition at line 137 of file PostProcessingWriter.cpp.

References PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpDataReader.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteAboveThresholdDepolarisationFile ( double threshold ) [inline]

Method for opening a file and writing one row per node: line 1: <number of upstrokes for node 0> <number of above-threshold depolarisations for node 0> line 2: <number of upstrokes for node 1> <number of above-threshold depolarisations for node 1> etc.

For the nodes where the threshold isn't crossed, the 'number of upstrokes' will be 0 (so will the number of above-threshold depolarisations for that node)

Todo:: This method ought to be private and called by the WritePostProcessingFiles method if the user requests for it. This will be possible after modifying the schema and specifying Get and Set methods in HeartConfig to check whetehr the user wants this file or not

Parameters:

threshold

- used to signify the upstroke (mV) AND to specify above which voltage value the depolarisations are counted

Definition at line 228 of file PostProcessingWriter.cpp.

References PropagationPropertiesCalculator::CalculateAllAboveThresholdDepolarisations(), PropagationPropertiesCalculator::CalculateAllMaximumUpstrokeVelocities(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteApdMapFile	(	double	repolarisationPercentage,
		double	threshold
	)			`[inline, private]`

Method for opening an APD map file and writing one row per node line 1: <first APD for node 0> <second APD for node 0> ... line 2: <first APD for node 1> <second APD for node 1> ... etc.

Nodes where there is no APD are respresented by a single 0

Parameters:

	repolarisationPercentage	eg. 90.0 for APD90
	threshold	- Vm used to signify the upstroke (mV)

Definition at line 144 of file PostProcessingWriter.cpp.

References PropagationPropertiesCalculator::CalculateAllActionPotentialDurationsForNodeRange(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteConductionVelocityMap	(	unsigned	originNode,
		std::vector< double >	distancesFromOriginNode
	)			`[inline, private]`

Write out conduction velocity map from the given node the rest of the mesh:

line 1: <conduction velocity for node 0 and AP 0> <conduction velocity for node 0 and AP 1> ... line 2: <conduction velocity for node 1 and AP 0> <conduction velocity for node 1 and AP 1> ... etc.

Note: the line corresponding to node number originNode will contain ...

Parameters:

	originNode	- Node to compute the conduction velocity from
	distancesFromOriginNode	- Distance map from originNode to all the nodes in the simulation. Tipically calculated with DistanceMapCalculator

Definition at line 203 of file PostProcessingWriter.cpp.

References PropagationPropertiesCalculator::CalculateAllConductionVelocities(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile	(	std::vector< std::vector< double > > &	rDataPayload,
		std::string	fileName
	)			`[inline, private]`

Method for opening a file and writing one row per node line 1: <first scalar data for node 0> <second scalar data for node 0> ... line 2: <first scalar data for node 1> <second scalar data for node 1> ... etc.

Parameters:

	rDataPayload	vector data for each node. Each node's data are represented by a vector of scalars (variable length)
	fileName	where to put the data.

Definition at line 327 of file PostProcessingWriter.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), PetscTools::GetMyRank(), PetscTools::GetNumProcs(), ChasteBuildInfo::GetProvenanceString(), HeartConfig::Instance(), and OutputFileHandler::OpenOutputFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteAboveThresholdDepolarisationFile(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteApdMapFile(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteConductionVelocityMap(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteMaxUpstrokeVelocityMap(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteUpstrokeTimeMap(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteMaxUpstrokeVelocityMap ( double threshold ) [inline, private]

Write out velocities of each max upstroke for each node:

line 1: <first upstroke velocity for node 0> <second upstroke velocity for node 0> ... line 2: <first upstroke velocity for node 1> <second upstroke velocity for node 1> ... etc.

If there is no upstroke then there will a blank line

Parameters:

threshold

- Vm used to signify the upstroke (mV)

Definition at line 178 of file PostProcessingWriter.cpp.

References PropagationPropertiesCalculator::CalculateAllMaximumUpstrokeVelocities(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles ( ) [inline]

Write out data files. The data that is written depends on which maps have been requested using either the XML file or HeartConfig

Definition at line 62 of file PostProcessingWriter.cpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteUpstrokeTimeMap ( double threshold ) [inline, private]

Write out times of each upstroke for each node:

line 1: <first upstroke time for node 0> <second upstroke time for node 0> ... line 2: <first upstroke time for node 1> <second upstroke time for node 1> ... etc.

If there is no upstroke then there will a blank line

Parameters:

threshold

- Vm used to signify the upstroke (mV)

Definition at line 153 of file PostProcessingWriter.cpp.

References PropagationPropertiesCalculator::CalculateUpstrokeTimes(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes ( std::vector< unsigned > & rNodeIndices ) [inline, private]

Method that extrapolates the output variables over time at specified nodes and output all to file. The use of this method is intended as follows: the user supplies a list of node indices (rNodeIndices). This method outputs the time series at each node in rNodeIndices (one time series per column). The node numbering is referred to the original mesh.

Regardless of the permutation that was used in the simulation, this method will have the same output.

There will be one file per variable contained in the hdf5 file. For each file, the name will be NodalTraces_VARIABLENAME.dat. So for example, in a bidomain simulation with default variable names, output files will be:

NodalTraces_V.dat NodalTraces_Phi_e.dat

Each output file will look like (taking variable V as an example):

Line 1: <V at time 0, Node 0> <V at time 0, Node 1> <V at time 0, Node 2> etc... Line 2: <V at time 1, Node 0> <V at time 1, Node 1> <V at time 1, Node 2> etc... etc...

where Node 0, Node 1, Node 2 are the nodes included in the rIndices vector and "V" is the name of the variable.

Parameters:

rNodeIndices

the node indices (in the unpermuted mesh) that we want the output for.

Definition at line 281 of file PostProcessingWriter.cpp.

References PetscTools::AmMaster(), HeartConfig::GetOutputUsingOriginalNodeOrdering(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableNames(), Hdf5DataReader::GetVariableOverTime(), HeartConfig::Instance(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpDataReader, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mrMesh, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().