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carputils
Doxygen code documentation for the python framework controlling openCARP
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| ▼Nbin | |
| ►Nbin2h5 | Create a HDF5 repository file for the ionic models in LIMPET |
| CFileDescription | Class to hold the information about each of the binary output files generated by LIMPET/bench which contain information about the sv |
| ►Nbuild_pathway | |
| CPathway | |
| ►Nclosest_hc | |
| CMyError | |
| ►Ninsert_endo_layer | TBD |
| CTagHandler | Simple class to handle element-tag data |
| ►NplotTrace | Plot trace files |
| CFileDescription | Class to hold the information about each of the binary output files generated by LIMPET/bench which contain information about the sv |
| ►Nsurfextract | Little tool to extract surface data from a given mesh and save them as VTK files |
| CListCreator | |
| CListModifierAction | |
| CListModifier | |
| ►Nupdate-carp | |
| CBCOLORS | A simple color class |
| ▼Ncarputils | |
| ►Nbullseye | Bullseye plot generation |
| ►Nplot | |
| CBEPlot | |
| ►Nbundle | This module implements the bundle feature, which allows to easily share carputils experiments |
| ►Nbundle | Implements the BundleModule class, which is instantiated when the bundle module is loaded |
| CBundleModule | Class for global bundle object |
| ►Nparfileadjustment | Functions to adjust an openCARP parameter file to be included in a bundle |
| C_OCParam | An object of this class represents an OpenCARP parameter |
| ►Ncarpio | Each module in this package defines a class for reading and writing a specific data type |
| ►Nbin | Provides a class for bench .bin file IO to/from python numpy arrays |
| CBinFile | Bench .bin format file IO class |
| ►Ncsv | Read csv files |
| CCSVFile | Read from a csv file |
| ►Nfilelike | |
| CFileLikeMixin | Implements a file-like mixin that essentially allows self-closing when exiting a "with-block" |
| ►Nigb | Provides a class for IGB IO to/from python numpy arrays |
| CIGBFile | IGB format file IO class |
| ►Nlimpetguihdf5 | |
| CLimpetGUIHDF5File | Limpetgui HDF5 file IO class |
| ►Nlut | Read binary lookup tables into python numpy arrays |
| CLUTHeader | Describes a LUT file header |
| CLUTFile | Read from a LUT file |
| ►Nquantity | Provides a class to convert physical quantities from a string to numerical values |
| CPhysicalQuantity | Defines a physical quantity |
| ►Nsv | Functionality to read/write state variable (sv) files |
| CSVFile | Read a single state variable (sv) file |
| CSVSeries | Read a set of state variable (sv) files |
| ►Ntagdefs | Provides a class for .dat and .vec IO to/from python numpy arrays |
| Ctagsdict | Generate the tag and option dictionary for simulation based on the argument flags |
| ►Ntxt | Provides a class for .dat and .vec IO to/from python numpy arrays |
| CTxtFile | File IO class for reading ascii files with extensions |
| ►Ncli | Some argparse extensions implementing custom behaviors for carputils |
| CCallbacksMixin | |
| CGroupAccessMixin | |
| CCarputilsArgumentParser | |
| ►Ncml | |
| ►Ncmlconverter | |
| CCMLConverter | Class defining basic string conversion methods |
| CCMLConverterYAML | Class defining YAML conform string conversion methods |
| ►Ncmlparser | |
| CCMLParser | Class defining a basic parser interface |
| CCMLParserYAML | Class to parse YAML strings |
| ►Ncmltree | |
| CCMLDictOperations | Class defining dictionary operations |
| CCMLNamespace | Class defining a namespace |
| CCMLNode | Class defining a simple node object |
| CCMLLeaf | Class defining a leaf object |
| CCMLListBranch | Class defining a list-branch object |
| CCMLDictBranch | Class defining a dict-branch object |
| ►Ndataproc | |
| CDataProcessor | |
| CAverageData | |
| CLowPassBesselFilter | |
| CLowPassButterFilter | |
| CHighPassBesselFilter | |
| CHighPassButterFilter | |
| CBandStopBesselFilter | |
| CBandStopButterFilter | |
| ►Ndivertoutput | Execute external processes with output buffering and error checking |
| CDivertOutputError | |
| ►Nfigui | |
| CArtistMenu | |
| CFigureUI | |
| ►Nfitting | |
| ►Nklotz | Implementation from Klotz's paper 'A computational method of prediction of the end-diastolic pressure-volume relationship by single beat' |
| CKlotzRelation | Represents the EDPVR determined by Klotz from a single volume, pressure measurement |
| ►Nforcepss | |
| ►Nj2carp | |
| CSweepSetup | |
| CLeadfieldComputationOptions | |
| ►Nplanio | |
| Cj2cKey | |
| Cj2cError | |
| ►Nformat | Output formatting utilities |
| CCell | |
| CTable | |
| CSummary | |
| ►Njob | This package most importantly defines the :class:~carputils.job.Job class, which provides methods for executing bash commands |
| ►Ncommand | Defines several types of commands to execute |
| CCommand | Interface that commands should provide |
| CPythonCommand | A command defined by a self-contained Python function |
| CShellCommand | A command executable in the bash shell |
| CMPICommand | A shell command to be executed with MPI |
| ►Njob | Defines the Job class for executing sequences of commands in a customisable manner |
| CJob | A sequence of commands plus the tools to execute them |
| ►Noptionlist | |
| COptionList | Special type which behaves like list but stores some arguments to be kept at end |
| ►Nmachines | Platform-specific functionality such as MPI launcher generation |
| ►Narcher | ARCHER platform script |
| CArcher | Run jobs on the ARCHER UK National Supercomputing Service |
| ►Narcher2 | |
| CARCHER2 | Run on Archer2 Info https://www.archer2.ac.uk/ |
| ►Narcher24c | |
| CARCHER24C | Run on Archer2-4c Info https://www.archer2.ac.uk/ |
| ►Narcher2_e756 | |
| CARCHER2E756 | Run on Archer2 Info https://www.archer2.ac.uk/ |
| ►Narcher_camel | ARCHER project camel platform script |
| CArcherCamel | Run jobs on the ARCHER UK National Supercomputing Service |
| ►Narcher_intel | ARCHER intel platform script |
| CArcherIntel | Run jobs on the ARCHER UK National Supercomputing Service |
| ►Nbwunicluster | |
| CBwUniCluster | Run on BwUniCluster 2.0 Info https://wiki.bwhpc.de/e/Category:BwUniCluster_2.0 |
| ►Ncurie | |
| CCurie | Run on the Curie supercomputer |
| ►Ndesktop | |
| CDesktop | Desktop platform, providing extensive debugging and profiling capabilities |
| ►Ngeneral | |
| CClassPropertyDescriptor | |
| CPlatform | Generic platform oject outlying the interface |
| CBatchPlatform | Generic class for batch platforms |
| ►Nhoreka | |
| CHoreKa | Run on HoreKa Info https://www.nhr.kit.edu/userdocs/horeka/batch/ |
| ►Nmarconi | |
| CMarconi | Run jobs on the MARCONI HPC Cluster |
| ►Nmarconi_slurm | |
| CMarconiSlurm | Run jobs on the MARCONI HPC Cluster |
| CMarconiDebug | Run jobs on the MARCONI HPC Cluster |
| ►Nmedbionode | |
| CMedBioNode | Run on MedBioNode |
| ►Nmedtronic | |
| CMedtronic | Run jobs on the Medtronic HPC |
| ►Nmephisto | |
| CMephisto | Run on the local Mephisto GPU cluster |
| ►Nsupermuc | |
| CSuperMUCAbstract | |
| CSuperMUCFat | Run on fat nodes at the SuperMUC petascale system in Germany |
| CSuperMUCThin | Run on thin nodes at the SuperMUC petascale system in Germany |
| CSuperMUCInteractive | Run interatively at the SuperMUC petascale system in Germany |
| ►Nvsc2 | |
| CVSC2 | Run on VSC-2 at the Vienna Scientific Cluster |
| ►Nvsc3 | |
| CVSC3 | Run on VSC-3 at the Vienna Scientific Cluster |
| ►Nvsc4 | |
| CVSC4 | Run on VSC-4 at the Vienna Scientific Cluster |
| ►Nvsc5 | |
| CVSC5 | Run on VSC-5 at the Vienna Scientific Cluster |
| ►Nwopr | |
| CWopr | Run jobs on SCI GPU cluster wopr |
| ►Nmesh | Classes and routines for the generation of geometric meshes |
| ►Nbase | |
| CElement | Describes a mesh element |
| CElementMixinBase | Base class for element mixins, to be subclassed with element storage code |
| CElementMaskedArrayMixin | Element mixin implementing numpy masked array storage |
| CElementCompressedRowMixin | Element mixing implementing compressed row storage similar to openCARP storage |
| CMesh | Base mesh class with read functionality |
| ►Nbivslice | Generate a simple bi-ventricular slice geometry, providing a few parameters |
| CBiVSlice | |
| ►Nblock | A class and associated functions for generating geometries with mesher |
| CBlock | Generate a block mesh with the mesher command line utility |
| ►Ncable | |
| CCable | Generate a one dimensional mesh of line segments |
| ►Nellipsoid | Class for generation of an ellipsoidal shell mesh |
| CEllipsoid | Generate a mesh of an ellipsoidal shell |
| ►Nfourch | Generate a simple four-chamber like geometry, providing a few parameters |
| CFourChamber | |
| ►Ngeneral | Base framework for the mesh generation classes |
| CMesh | A generic mesh class the provides the core functionality in 1D and 3D |
| CMesh2D | A generic mesh class adding the core functionality for 2D meshes |
| CMesh3D | A generic mesh class adding the core functionality for 3D meshes |
| ►Ngrid | |
| CGrid | Generate a two dimensional mesh of a regular grid |
| ►Npipe | Generate a simple pipe geometry, providing a few parameters |
| CPipe | Generate a pipe mesh or a pipe-segment mesh |
| ►Nregion | Define some region defining objects for use with geometry classes |
| CRegion | A general region definition |
| CBoxRegion | Describe an axis-aligned cuboid for mesh tag assignment |
| CSphereRegion | Describe a sphere for mesh tag assignment |
| CCylinderRegion | Describe a cylinder for mesh tag assignment |
| ►Nring | Generate a simple ring geometry, providing a few parameters |
| CRing | Generate a mesh of a ring/cylindrical shell |
| ►Nmodel | |
| ►Nconductivity | |
| CConductivityRegion | Defines an electrical conductivity region |
| CConductivityRegionEMI | Defines an electrical conductivity region for the EMI model |
| ►Nconfig | |
| ►NERP_config | |
| CERPConfig | |
| ►Npath_config | |
| CPathConfig | |
| ►NPEERP_config | |
| CPEERPConfig | |
| ►Ngeneral | The core infrastructure of the model component classes |
| CModifier | Describes a parameter assigment modifier |
| CAddModifier | Describes a parameter add modifier |
| CMultModifier | Describes a parameter multiply modifier |
| CAbstractModelComponent | Describes an abstract model component |
| CParameterSet | Describes a set of parameters that can be generated into a single string |
| CParameterSetMixin | A mixin to add a parameter set field to a model component class |
| CRegionMixin | A mixin to add region fields to a model component class |
| CSingleIDRegionMixin | A mixin to add fields for a single-ID region to a model component class |
| CModelMixin | More concrete version of the ParameterSetMixin for ep/mechanics models |
| CDreamMixin | A mixin to extend model components with DREAM-specific parameter fields |
| CAbstractIonicModel | |
| CExternalIonicModel | Describes the passive ionic model configuration |
| CAbstractMechanicsMaterial | |
| CAbstractPlugin | |
| CNoPlugin | Placeholder representing no plugin to be used |
| ►Nionic | |
| CPassiveIonicRegion | Describes the passive ionic model configuration |
| CAlievPanfilovIonicModel | Describes the AlievPanfilov ionic model |
| CAslanidiSleimanIonicModel | Describes the AslanidiSleiman ionic model |
| CAugustinIonicModel | Describes the Augustin ionic model |
| CBondarenkoIonicModel | Describes the Bondarenko ionic model |
| CBuenoIonicModel | Describes the Bueno ionic model |
| CCamposIonicModel | Describes the Campos ionic model |
| CCourtemancheIonicModel | Describes the Courtemanche ionic model |
| CDiFrancescoNobleIonicModel | Describes the DiFrancescoNoble ionic model |
| CDrouhardRobergeIonicModel | Describes the DrouhardRoberge ionic model |
| CFabbriIonicModel | Describes the Fabbri ionic model |
| CFoxIonicModel | Describes the Fox ionic model |
| CGaurIonicModel | Describes the Gaur ionic model |
| CGattoni16Land17_DynSarcIonicModel | Describes the Gattoni16Land17_DynSarc ionic model |
| CGrandiIonicModel | Describes the Grandi ionic model |
| CGrandiPanditVoigtIonicModel | Describes the GrandiPanditVoigt ionic model |
| CHodgkinHuxleyIonicModel | Describes the HodgkinHuxley ionic model |
| CInadaIonicModel | Describes the Inada ionic model |
| CIribeKohlIonicModel | Describes the IribeKohl ionic model |
| CKurataIonicModel | Describes the Kurata ionic model |
| CLoeweIonicModel | Describes the Loewe ionic model |
| CLuoRudy91IonicModel | Describes the LuoRudy91 ionic model |
| CLuoRudy94IonicModel | Describes the LuoRudy94 ionic model |
| CMacCannellIonicModel | Describes the MacCannell ionic model |
| CMahajanShiferawIonicModel | Describes the MahajanShiferaw ionic model |
| CMaleckarIonicModel | Describes the Maleckar ionic model |
| CMitchellSchaefferIonicModel | Describes the MitchellSchaeffer ionic model |
| CNygrenIonicModel | Describes the Nygren ionic model |
| COHaraIonicModel | Describes the OHara ionic model |
| CPathmanathanIonicModel | Describes the Pathmanathan ionic model |
| CPlonseyIonicModel | Describes the Plonsey ionic model |
| CRamirezIonicModel | Describes the Ramirez ionic model |
| CSeveriIonicModel | Describes the Severi ionic model |
| CShannonIonicModel | Describes the Shannon ionic model |
| CSkibsbyeIonicModel | Describes the Skibsbye ionic model |
| CStewartIonicModel | Describes the Stewart ionic model |
| CTomekIonicModel | Describes the Tomek ionic model |
| CTomek20Land17_DynSarcIonicModel | Describes the Tomek20Land17_DynSarc ionic model |
| CWangSobieIonicModel | Describes the WangSobie ionic model |
| CtenTusscherPanfilovIonicModel | Describes the tenTusscherPanfilov ionic model |
| ►NPEERP_logger | |
| CPEERPLoggerManager | |
| ►Nstimulus | |
| CStimulus | Represents a single stimulus argument to openCARP |
| ►NTimePoints | |
| COptimizationTimePoints | |
| ►Nplot | |
| CPVPlots | Generate plots from csv data |
| ►Nsettings | This module manages and exposes carputils settings |
| ►Nbuildinfo | Load the my_switches.def settings from the CARP repository |
| CCARPUtilsMissingMakevar | |
| ►Nexceptions | |
| CCARPUtilsSettingsError | |
| CCARPUtilsMissingSettingError | |
| CCARPUtilsMissingPathError | |
| CCARPUtilsMissingLicenseError | |
| CCARPUtilsSettingsWarning | |
| ►Nnamespace | Implements the SettingsNamespace class, which provides case-insensitive namespaces |
| CSettingsNamespace | Settings namespace object |
| ►Npaths | Path handling utilities, including management of executable paths |
| CPath | |
| CPathSettingsNamespace | Modified namespace with extra error handling for paths |
| ►Nsettings | SettingsModule class and Exception for global settings object |
| CSettingsModule | |
| ►Nsolver | Generation and management of solver options |
| CSolverOptions | A container class with some convenience methods for setting up openCARP options |
| ►Nstream | Some tools for handling output streams (stdout, etc.) |
| CDummyStream | A placeholder stream that simply ignores the write instruction |
| CRegexCallbackStream | |
| CMultiStream | A stream that forwards on the write call to other streams |
| ►Ntools | Functions for creating run scripts for openCARP simulations and other tools |
| CMaxNPAction | Class to check that the maximum number of processes is not exceeded |
| CPrintAction | Class to print a unformatted message like '–help' and exit |
| ►Ntuning | Tune conductivity settings to match prescribed conduction velocities |
| CCVtuning | Class for managing CV tuning |
| Cdspace |
1.9.1