Source code for PVGeo.base

__all__ = [
    'AlgorithmBase',
    'ReaderBaseBase',
    'ReaderBase',
    'FilterBase',
    'FilterPreserveTypeBase',
    'TwoFileReaderBase',
    'WriterBase',
]


__displayname__ = 'Base Classes'

import warnings

import numpy as np
# Outside Imports:
import vtk  # NOTE: This is the first import executed in the package! Keep here!!
import vtk.util.vtkAlgorithm as valg  # import VTKPythonAlgorithmBase

from . import _helpers

###############################################################################

[docs]class AlgorithmBase(valg.VTKPythonAlgorithmBase): """This is a base class to add convienace methods to the ``VTKPythonAlgorithmBase`` for all algorithms implemented in ``PVGeo``. We implement our algorithms in this manner to harness all of the backend support that the ``VTKPythonAlgorithmBase`` class provides for integrating custom algorithms on a VTK pipeline. All of the pipeline methods for setting inputs, getting outputs, making requests are handled by the super classes. For more information on what functionality is available, check out the VTK Docs for the `vtkAlgorithm`_ and then check out the following blog posts: * `vtkPythonAlgorithm is great`_ * A VTK pipeline primer `(part 1)`_, `(part 2)`_, and `(part 3)`_ * `ParaView Python Docs`_ .. _vtkAlgorithm: https://www.vtk.org/doc/nightly/html/classvtkAlgorithm.html .. _vtkPythonAlgorithm is great: https://blog.kitware.com/vtkpythonalgorithm-is-great/ .. _(part 1): https://blog.kitware.com/a-vtk-pipeline-primer-part-1/ .. _(part 2): https://blog.kitware.com/a-vtk-pipeline-primer-part-2/ .. _(part 3): https://blog.kitware.com/a-vtk-pipeline-primer-part-3/ .. _ParaView Python Docs: https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.util.vtkAlgorithm.html """ __displayname__ = 'Algorithm Base' __category__ = 'base' def __init__(self, nInputPorts=1, inputType='vtkDataSet', nOutputPorts=1, outputType='vtkTable', **kwargs): valg.VTKPythonAlgorithmBase.__init__(self, nInputPorts=nInputPorts, inputType=inputType, nOutputPorts=nOutputPorts, outputType=outputType) # Add error handler to make errors easier to deal with self.__errorObserver = _helpers.ErrorObserver() self.__errorObserver.MakeObserver(self)
[docs] def GetOutput(self, port=0): """A conveience method to get the output data object of this ``PVGeo`` algorithm. """ return self.GetOutputDataObject(port)
[docs] def ErrorOccurred(self): """A conveience method for handling errors on the VTK pipeline Return: bool: true if an error has ovvured since last checked """ return self.__errorObserver.ErrorOccurred()
[docs] def ErrorMessage(self): """A conveience method to print the error message. """ return self.__errorObserver.ErrorMessage()
[docs] def Apply(self): """Update the algorithm and get the output data object""" self.Update() return self.GetOutput()
############################################################################### # Base Base Reader
[docs]class ReaderBaseBase(AlgorithmBase): """A base class for inherrited functionality common to all reader algorithms """ __displayname__ = 'Reader Base Base' __category__ = 'base' def __init__(self, nOutputPorts=1, outputType='vtkTable', **kwargs): AlgorithmBase.__init__(self, nInputPorts=0, nOutputPorts=nOutputPorts, outputType=outputType, **kwargs) # Attributes are namemangled to ensure proper setters/getters are used # For the reader self.__fileNames = kwargs.get('filenames', []) # To know whether or not the read needs to perform self.__needToRead = True
[docs] def NeedToRead(self, flag=None): """Ask self if the reader needs to read the files again. Args: flag (bool): Set the read status Return: bool: the status of the reader. """ if flag is not None and isinstance(flag, (bool, int)): self.__needToRead = flag return self.__needToRead
[docs] def Modified(self, readAgain=True): """Call modified if the files needs to be read again again """ if readAgain: self.__needToRead = readAgain AlgorithmBase.Modified(self)
#### Methods for performing the read #### # These are meant to be overwritten by child classes
[docs] def _GetFileContents(self, idx=None): raise NotImplementedError()
[docs] def _ReadUpFront(self): raise NotImplementedError()
[docs] def _GetRawData(self, idx=0): raise NotImplementedError()
#### Seters and Geters ####
[docs] def ClearFileNames(self): """Use to clear file names of the reader. Note: This does not set the reader to need to read again as there are no files to read. """ self.__fileNames = []
[docs] def AddFileName(self, fname): """Use to set the file names for the reader. Handles singlt string or list of strings. Args: fname (str): The absolute file name with path to read. """ if fname is None: return # do nothing if None is passed by a constructor on accident if isinstance(fname, list): for f in fname: self.AddFileName(f) elif fname not in self.__fileNames: self.__fileNames.append(fname) self.Modified()
[docs] def GetFileNames(self, idx=None): """Returns the list of file names or given and index returns a specified timestep's filename. """ if self.__fileNames is None or len(self.__fileNames) < 1: raise _helpers.PVGeoError('File names are not set.') if idx is None: return self.__fileNames return self.__fileNames[idx]
[docs] def Apply(self, fname): """Given a file name (or list of file names), perfrom the read""" self.AddFileName(fname) self.Update() return self.GetOutput()
############################################################################### # Base filter to preserve input data type
[docs]class FilterBase(AlgorithmBase): """A base class for implementing filters which holds several convienace methods""" __displayname__ = 'Filter Base' __category__ = 'base' def __init__(self, nInputPorts=1, inputType='vtkDataSet', nOutputPorts=1, outputType='vtkPolyData', **kwargs): AlgorithmBase.__init__(self, nInputPorts=nInputPorts, inputType=inputType, nOutputPorts=nOutputPorts, outputType=outputType, **kwargs)
[docs] def Apply(self, inputDataObject): self.SetInputDataObject(inputDataObject) self.Update() return self.GetOutput()
############################################################################### # Base Reader
[docs]class ReaderBase(ReaderBaseBase): """A base class for inherrited functionality common to all reader algorithms that need to handle a time series. """ __displayname__ = 'Reader Base: Time Varying' __category__ = 'base' def __init__(self, nOutputPorts=1, outputType='vtkTable', **kwargs): ReaderBaseBase.__init__(self, nOutputPorts=nOutputPorts, outputType=outputType, **kwargs) # Attributes are namemangled to ensure proper setters/getters are used # For the VTK/ParaView pipeline self.__dt = kwargs.get('dt', 1.0) self.__timesteps = None
[docs] def _UpdateTimeSteps(self): """For internal use only: appropriately sets the timesteps. """ if len(self.GetFileNames()) > 1: self.__timesteps = _helpers.updateTimeSteps(self, self.GetFileNames(), self.__dt) return 1
#### Algorithm Methods ####
[docs] def RequestInformation(self, request, inInfo, outInfo): """This is a conveience method that should be overwritten when needed. This will handle setting the timesteps appropriately based on the number of file names when the pipeline needs to know the time information. """ self._UpdateTimeSteps() return 1
#### Seters and Geters ####
[docs] def GetTimestepValues(self): """Use this in ParaView decorator to register timesteps on the pipeline. """ return self.__timesteps.tolist() if self.__timesteps is not None else None
[docs] def SetTimeDelta(self, dt): """An advanced property to set the time step in seconds. """ if dt != self.__dt: self.__dt = dt self.Modified()
############################################################################### # Base filter to preserve input data type
[docs]class FilterPreserveTypeBase(FilterBase): """A Base class for implementing filters that preserve the data type of their arbitrary input. """ __displayname__ = 'Filter Preserve Type Base' __category__ = 'base' def __init__(self, nInputPorts=1, **kwargs): FilterBase.__init__(self, nInputPorts=nInputPorts, inputType='vtkDataObject', nOutputPorts=1, **kwargs) self._preservePort = 0 # This is the port to preserve data object type # THIS IS CRUCIAL to preserve data type through filter
[docs] def RequestDataObject(self, request, inInfo, outInfo): """There is no need to overwrite this. This method lets the pipeline know that the algorithm will dynamically decide the output data type based in the input data type. """ self.OutputType = self.GetInputData(inInfo, self._preservePort, 0).GetClassName() self.FillOutputPortInformation(0, outInfo.GetInformationObject(0)) return 1
############################################################################### # Two File Reader Base
[docs]class TwoFileReaderBase(AlgorithmBase): """A base clase for readers that need to handle two input files. One meta-data file and a series of data files. """ __displayname__ = 'Two File Reader Base' __category__ = 'base' def __init__(self, nOutputPorts=1, outputType='vtkUnstructuredGrid', **kwargs): AlgorithmBase.__init__(self, nInputPorts=0, nOutputPorts=nOutputPorts, outputType=outputType) self.__dt = kwargs.get('dt', 1.0) self.__timesteps = None self.__meshFileName = kwargs.get('meshfile', None) # Can only be one! modfiles = kwargs.get('modelfiles', []) # Can be many (single attribute, manytimesteps) if isinstance(modfiles, str): modfiles = [modfiles] self.__modelFileNames = modfiles self.__needToReadMesh = True self.__needToReadModels = True def __UpdateTimeSteps(self): """For internal use only """ if len(self.__modelFileNames) > 0: self.__timesteps = _helpers.updateTimeSteps(self, self.__modelFileNames, self.__dt) return 1
[docs] def NeedToReadMesh(self, flag=None): """Ask self if the reader needs to read the mesh file again. Args: flag (bool): set the status of the reader for mesh files. """ if flag is not None and isinstance(flag, (bool, int)): self.__needToReadMesh = flag return self.__needToReadMesh
[docs] def NeedToReadModels(self, flag=None): """Ask self if the reader needs to read the model files again. Args: flag (bool): set the status of the reader for model files. """ if flag is not None and isinstance(flag, (bool, int)): self.__needToReadModels = flag return self.__needToReadModels
[docs] def Modified(self, readAgainMesh=True, readAgainModels=True): """Call modified if the files needs to be read again again Args: readAgainMesh (bool): set the status of the reader for mesh files. readAgainModels (bool): set the status of the reader for model files. """ if readAgainMesh: self.NeedToReadMesh(flag=readAgainMesh) if readAgainModels: self.NeedToReadModels(flag=readAgainModels) return AlgorithmBase.Modified(self)
[docs] def RequestInformation(self, request, inInfo, outInfo): self.__UpdateTimeSteps() return 1
#### Seters and Geters ####
[docs] @staticmethod def HasModels(modelfiles): """A convienance method to see if a list contatins models filenames. """ if isinstance(modelfiles, list): return len(modelfiles) > 0 return modelfiles is not None
[docs] def ThisHasModels(self): """Ask self if the reader has model filenames set. """ return TwoFileReaderBase.HasModels(self.__modelFileNames)
[docs] def GetTimestepValues(self): """Use this in ParaView decorator to register timesteps """ return self.__timesteps.tolist() if self.__timesteps is not None else None
[docs] def SetTimeDelta(self, dt): """An advanced property for the time step in seconds. """ if dt != self.__dt: self.__dt = dt self.Modified(readAgainMesh=False, readAgainModels=False)
[docs] def ClearMesh(self): """Use to clear mesh file name """ self.__meshFileName = None self.Modified(readAgainMesh=True, readAgainModels=False)
[docs] def ClearModels(self): """Use to clear data file names """ self.__modelFileNames = [] self.Modified(readAgainMesh=False, readAgainModels=True)
[docs] def SetMeshFileName(self, fname): """Set the mesh file name. """ if self.__meshFileName != fname: self.__meshFileName = fname self.Modified(readAgainMesh=True, readAgainModels=False)
[docs] def AddModelFileName(self, fname): """Use to set the file names for the reader. Handles single string or list of strings. Args: fname (str or list(str)): the file name(s) to use for the model data. """ if fname is None: return # do nothing if None is passed by a constructor on accident if isinstance(fname, list): for f in fname: self.AddModelFileName(f) self.Modified(readAgainMesh=False, readAgainModels=True) elif fname not in self.__modelFileNames: self.__modelFileNames.append(fname) self.Modified(readAgainMesh=False, readAgainModels=True) return 1
[docs] def GetModelFileNames(self, idx=None): """Returns the list of file names or given and index returns a specified timestep's filename. """ if idx is None or not self.ThisHasModels(): return self.__modelFileNames return self.__modelFileNames[idx]
[docs] def GetMeshFileName(self): return self.__meshFileName
[docs] def Apply(self): """Perfrom the read with parameters/file names set during init or by setters""" self.Update() return self.GetOutput()
[docs]class WriterBase(AlgorithmBase): __displayname__ = 'Writer Base' __category__ = 'base' def __init__(self, nInputPorts=1, inputType='vtkPolyData', **kwargs): AlgorithmBase.__init__(self, nInputPorts=nInputPorts, inputType=inputType, nOutputPorts=0) self.__filename = kwargs.get('filename', None) self.__fmt = '%.9e' # For composite datasets: not always used self.__blockfilenames = None self.__composite = False
[docs] def FillInputPortInformation(self, port, info): """Allows us to save composite datasets as well. Note: I only care about ``vtkMultiBlockDataSet`` """ info.Set(self.INPUT_REQUIRED_DATA_TYPE(), self.InputType) info.Append(self.INPUT_REQUIRED_DATA_TYPE(), 'vtkMultiBlockDataSet') # vtkCompositeDataSet return 1
[docs] def SetFileName(self, fname): """Specify the filename for the output. Writer can only handle a single output data object/time step.""" if not isinstance(fname, str): raise RuntimeError('File name must be string. Only single file is supported.') if self.__filename != fname: self.__filename = fname self.Modified()
[docs] def GetFileName(self): """Get the set filename.""" return self.__filename
def RequestData(self, request, inInfoVec, outInfoVec): """OVERWRITE: This is executed by the pipeline and handles the write out""" raise NotImplementedError() return 1
[docs] def Write(self, inputDataObject=None): """Perfrom the write out.""" if inputDataObject: self.SetInputDataObject(inputDataObject) self.Modified() self.Update()
[docs] def PerformWriteOut(self, inputDataObject, filename, objectName): """This method must be implemented. This is automatically called by ``RequestData`` for single inputs or composite inputs.""" raise NotImplementedError('PerformWriteOut must be implemented!')
[docs] def Apply(self, inputDataObject): self.SetInputDataObject(inputDataObject) self.Modified() self.Update()
[docs] def SetFormat(self, fmt): """Use to set the ASCII format for the writer default is ``'%.9e'``""" if self.__fmt != fmt and isinstance(fmt, str): self.__fmt = fmt self.Modified()
[docs] def GetFormat(self): return self.__fmt
#### Following methods are for composite datasets ####
[docs] def UseComposite(self): """True if input dataset is a composite dataset""" return self.__composite
[docs] def SetBlockFileNames(self, n): """Gets a list of filenames based on user input filename and creates a numbered list of filenames for the reader to save out. Assumes the filename has an extension set already. """ number = n count = 0 while (number > 0): number = number // 10 count = count + 1 count = '%d' % count identifier = '_%.' + count + 'd' blocknum = [identifier % i for i in range(n)] # Check the file extension: ext = self.GetFileName().split('.')[-1] basename = self.GetFileName().replace('.%s' % ext, '') self.__blockfilenames = [basename + '%s.%s' % (blocknum[i], ext) for i in range(n)] return self.__blockfilenames
[docs] def GetBlockFileName(self, idx): return self.__blockfilenames[idx]
[docs] def RequestData(self, request, inInfoVec, outInfoVec): """Subclasses must implement a ``PerformWriteOut`` method that takes an input data object and a filename. This method will automatically handle composite data sets. """ inp = self.GetInputData(inInfoVec, 0, 0) if isinstance(inp, vtk.vtkMultiBlockDataSet): self.__composite = True # Handle composite datasets. NOTE: This only handles vtkMultiBlockDataSet if self.__composite: num = inp.GetNumberOfBlocks() self.SetBlockFileNames(num) for i in range(num): data = inp.GetBlock(i) name = inp.GetMetaData(i).Get(vtk.vtkCompositeDataSet.NAME()) if data.IsTypeOf(self.InputType): self.PerformWriteOut(data, self.GetBlockFileName(i), name) else: warnings.warn('Input block %d of type(%s) not saveable by writer.' % (i, type(data))) # Handle single input dataset else: self.PerformWriteOut(inp, self.GetFileName(), None) return 1