Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
|
#include <PostProcessingWriter.hpp>
Public Member Functions | |
PostProcessingWriter (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, const FileFinder &rDirectory, const std::string &rHdf5FileName, const std::string &rVoltageName="V", hsize_t hdf5DataWriterChunkSize=0) | |
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 | WriteGenericFileToMeshalyzer (std::vector< std::vector< double > > &rDataPayload, const std::string &rFolder, const std::string &rFileName) |
void | WriteOutputDataToHdf5 (const std::vector< std::vector< double > > &rDataPayload, const std::string &rDatasetName, const std::string &rDatasetUnit, const std::string &rUnlimitedVariableName="PaceNumber", const std::string &rUnlimitedVariableUnit="dimensionless") |
std::string | ConvertToHdf5FriendlyString (double threshold) |
Private Attributes | |
FileFinder | mDirectory |
std::string | mHdf5File |
std::string | mVoltageName |
Hdf5DataReader * | mpDataReader |
PropagationPropertiesCalculator * | mpCalculator |
unsigned | mLo |
unsigned | mHi |
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & | mrMesh |
hsize_t | mHdf5DataWriterChunkSize |
Friends | |
class | TestPostProcessingWriter |
Write out physiological parameters at the end of a simulation
N.B. You should only ever have one PostProcessingWriter around at once, as multiple Hdf5Readers (a member variable of this class) seem to cause problems.
Definition at line 57 of file PostProcessingWriter.hpp.
PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter | ( | AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh, |
const FileFinder & | rDirectory, | ||
const std::string & | rHdf5FileName, | ||
const std::string & | rVoltageName = "V" , |
||
hsize_t | hdf5DataWriterChunkSize = 0 |
||
) |
Constructor
rMesh | A reference to the mesh used to calculate the distance map to pass to the conduction velocity calculator. |
rDirectory | The directory the data is in. The output is written to <directory>/output |
rHdf5FileName | The file the data is in. |
rVoltageName | (Optional) The name of the variable representing the membrane potential. It is used in the creation of the PropagationPropertiesCalculator object. Defaults to "V". |
hdf5DataWriterChunkSize | (Optional) Chunk size and alignment parameter to pass to Hdf5DataWriter |
Definition at line 52 of file PostProcessingWriter.cpp.
References Hdf5DataReader::GetNumberOfRows(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mDirectory, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHdf5File, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mHi, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mLo, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpCalculator, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mpDataReader, PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mrMesh, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::mVoltageName.
PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::~PostProcessingWriter | ( | ) |
Destructor
Definition at line 160 of file PostProcessingWriter.cpp.
|
private |
Convert a string with numbers in it into alphanumeric plus underscores.
e.g. 20 -> "_20" -20 -> "_minus_20" 30.2 -> "_30pt20" -11.238 -> "_minus_11pt23" (always does decimals to (floor) 2d.p.)
threshold | A numerical threshold which may contain minuses or a decimal point. |
Definition at line 394 of file PostProcessingWriter.cpp.
void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteAboveThresholdDepolarisationFile | ( | double | threshold | ) |
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)
threshold | - used to signify the upstroke (mV) AND to specify above which voltage value the depolarisations are counted |
Definition at line 340 of file PostProcessingWriter.cpp.
|
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
repolarisationPercentage | eg. 90.0 for APD90 |
threshold | - Vm used to signify the upstroke (mV) |
Definition at line 248 of file PostProcessingWriter.cpp.
|
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 ...
originNode | - Node to compute the conduction velocity from |
distancesFromOriginNode | - Distance map from originNode to all the nodes in the simulation. Typically calculated with DistanceMapCalculator |
Definition at line 314 of file PostProcessingWriter.cpp.
|
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.
rDataPayload | vector data for each node. Each node's data are represented by a vector of scalars (variable length) |
rFolder | subfolder for postprocessing in which to put the data. |
rFileName | where to put the data. |
Definition at line 466 of file PostProcessingWriter.cpp.
References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::BeginRoundRobin(), PetscTools::EndRoundRobin(), ChasteBuildInfo::GetProvenanceString(), HeartConfig::Instance(), and OutputFileHandler::OpenOutputFile().
|
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
threshold | - Vm used to signify the upstroke (mV) |
Definition at line 288 of file PostProcessingWriter.cpp.
|
private |
Put the post-processed data into the main HDF5 results file.
rDataPayload | The postprocessed quantities |
rDatasetName | The name of the quantities |
rDatasetUnit | The unit of the quantities |
rUnlimitedVariableName | The name of the unlimited variable (defaults to "PaceNumber") |
rUnlimitedVariableUnit | The unlimited variable units (defaults to "dimensionless") |
Definition at line 167 of file PostProcessingWriter.cpp.
References Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), DistributedVector::Begin(), RelativeTo::ChasteTestOutput, Hdf5DataWriter::Close(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::DefineVariable(), PetscTools::Destroy(), Hdf5DataWriter::EmptyDataset(), DistributedVector::End(), Hdf5DataWriter::EndDefineMode(), Hdf5DataWriter::GetVariableByName(), Hdf5DataWriter::IsInDefineMode(), Hdf5DataWriter::PutUnlimitedVariable(), Hdf5DataWriter::PutVector(), and Hdf5DataWriter::SetTargetChunkSize().
void PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles | ( | ) |
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 72 of file PostProcessingWriter.cpp.
References DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), HeartConfig::GetApdMaps(), HeartConfig::GetConductionVelocityMaps(), HeartConfig::GetMaxUpstrokeVelocityMaps(), HeartConfig::GetNodalTimeTraceRequested(), HeartConfig::GetPseudoEcgElectrodePositions(), HeartConfig::GetUpstrokeTimeMaps(), HeartConfig::Instance(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().
|
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
threshold | - Vm used to signify the upstroke (mV) |
Definition at line 262 of file PostProcessingWriter.cpp.
|
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.
rNodeIndices | the node indices (in the unpermuted mesh) that we want the output for. |
Definition at line 419 of file PostProcessingWriter.cpp.
References PetscTools::AmMaster(), HeartConfig::GetOutputUsingOriginalNodeOrdering(), and HeartConfig::Instance().
Definition at line 59 of file PostProcessingWriter.hpp.
|
private |
The directory the HDF5 file is in
Definition at line 62 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
Chunk size parameter for Hdf5DataWriter
Definition at line 71 of file PostProcessingWriter.hpp.
|
private |
The name of the HDF5 file to post-process
Definition at line 63 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
Cache of mHi from the mesh DitributedVectorFactory
Definition at line 69 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
Cache of mLo from the mesh DitributedVectorFactory
Definition at line 68 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
PropagationPropertiesCalculator based on HDF5 data reader
Definition at line 67 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
An HDF5 reader from which to build the PropagationPropertiesCalculator
Definition at line 66 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
A mesh used to calculate the distance map to pass to the conduction velocity calculator
Definition at line 70 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().
|
private |
The name of the variable representing the membrane potential
Definition at line 64 of file PostProcessingWriter.hpp.
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter().