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Merge pull request #100 from akaszynski/readers
Support all VTK readers
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,196 @@ | ||
| """ | ||
| Contains a dictionary that maps file extensions to VTK readers | ||
| """ | ||
| import os | ||
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| import vtk | ||
| import vtki | ||
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| READERS = { | ||
| # Standard dataset readers: | ||
| '.vtk': vtk.vtkDataSetReader, | ||
| '.vti': vtk.vtkXMLImageDataReader, | ||
| '.vtr': vtk.vtkXMLRectilinearGridReader, | ||
| '.vtu': vtk.vtkXMLUnstructuredGridReader, | ||
| '.ply': vtk.vtkPLYReader, | ||
| '.obj': vtk.vtkOBJReader, | ||
| '.stl': vtk.vtkSTLReader, | ||
| '.vts': vtk.vtkXMLStructuredGridReader, | ||
| '.vtm': vtk.vtkXMLMultiBlockDataReader, | ||
| '.vtmb': vtk.vtkXMLMultiBlockDataReader, | ||
| # Image formats: | ||
| '.bmp': vtk.vtkBMPReader, | ||
| '.dem': vtk.vtkDEMReader, | ||
| '.dcm': vtk.vtkDICOMImageReader, | ||
| '.jpeg': vtk.vtkJPEGReader, | ||
| '.jpg': vtk.vtkJPEGReader, | ||
| '.png': vtk.vtkPNGReader, | ||
| '.pnm': vtk.vtkPNMReader, | ||
| '.slc': vtk.vtkSLCReader, | ||
| '.tiff': vtk.vtkTIFFReader, | ||
| '.tif': vtk.vtkTIFFReader, | ||
| # ExodusII files: | ||
| #.g, .e, .ex2, .ex2v2, .exo, .gen, .exoII, .exii, .0, .00, .000 | ||
| '.g': vtk.vtkExodusIIReader, | ||
| '.e': vtk.vtkExodusIIReader, | ||
| '.ex2': vtk.vtkExodusIIReader, | ||
| '.ex2v2': vtk.vtkExodusIIReader, | ||
| '.exo': vtk.vtkExodusIIReader, | ||
| '.gen': vtk.vtkExodusIIReader, | ||
| '.exoii': vtk.vtkExodusIIReader, | ||
| '.exii': vtk.vtkExodusIIReader, | ||
| '.0': vtk.vtkExodusIIReader, | ||
| '.00': vtk.vtkExodusIIReader, | ||
| '.000': vtk.vtkExodusIIReader, | ||
| # Other formats: | ||
| '.byu': vtk.vtkBYUReader, | ||
| '.chemml': vtk.vtkCMLMoleculeReader, | ||
| '.cml': vtk.vtkCMLMoleculeReader, | ||
| # TODO: '.csv': vtk.vtkCSVReader, # vtkTables are currently not supported | ||
| '.facet': vtk.vtkFacetReader, | ||
| '.cas': vtk.vtkFLUENTReader, | ||
| '.dat': vtk.vtkFLUENTReader, | ||
| '.cube': vtk.vtkGaussianCubeReader, | ||
| '.res': vtk.vtkMFIXReader, | ||
| '.foam': vtk.vtkOpenFOAMReader, | ||
| '.pdb': vtk.vtkPDBReader, | ||
| '.p3d': vtk.vtkPlot3DMetaReader, | ||
| '.pts': vtk.vtkPTSReader, | ||
| '.particles': vtk.vtkParticleReader, | ||
| #TODO: '.pht': vtk.vtkPhasta??????, | ||
| #TODO: '.vpc': vtk.vtkVPIC?????, | ||
| '.xyz': vtk.vtkXYZMolReader, | ||
| } | ||
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| if (vtk.vtkVersion().GetVTKMajorVersion() >= 8 and | ||
| vtk.vtkVersion().GetVTKMinorVersion() >= 2): | ||
| READERS['.sgy'] = vtk.vtkSegYReader | ||
| READERS['.segy'] = vtk.vtkSegYReader | ||
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| def get_ext(filename): | ||
| """Extract the extension of the filename""" | ||
| ext = os.path.splitext(filename)[1].lower() | ||
| return ext | ||
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| def get_reader(filename): | ||
| """Gets the corresponding reader based on file extension and instantiates it | ||
| """ | ||
| ext = get_ext(filename) | ||
| return READERS[ext]() # Get and instantiate the reader | ||
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| def standard_reader_routine(reader, filename, attrs=None): | ||
| """Use a given reader from the ``READERS`` mapping in the common VTK reading | ||
| pipeline routine. | ||
| Parameters | ||
| ---------- | ||
| reader : vtkReader | ||
| Any instantiated VTK reader class | ||
| filename : str | ||
| The string filename to the data file to read. | ||
| attrs : dict, optional | ||
| A dictionary of attributes to call on the reader. Keys of dictionary are | ||
| the attribute/method names and values are the arguments passed to those | ||
| calls. If you do not have any attributes to call, pass ``None`` as the | ||
| value. | ||
| """ | ||
| if attrs is None: | ||
| attrs = {} | ||
| if not isinstance(attrs, dict): | ||
| raise TypeError('Attributes must be a dictionary of name and arguments.') | ||
| reader.SetFileName(filename) | ||
| # Apply any attributes listed | ||
| for name, args in attrs.items(): | ||
| attr = getattr(reader, name) | ||
| if args is not None: | ||
| if not isinstance(args, (list, tuple)): | ||
| args = [args] | ||
| attr(*args) | ||
| else: | ||
| attr() | ||
| # Perform the read | ||
| reader.Update() | ||
| return vtki.wrap(reader.GetOutputDataObject(0)) | ||
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| def read_legacy(filename): | ||
| """Use VTK's legacy reader to read a file""" | ||
| reader = vtk.vtkDataSetReader() | ||
| reader.SetFileName(filename) | ||
| # Ensure all data is fetched with poorly formated legacy files | ||
| reader.ReadAllScalarsOn() | ||
| reader.ReadAllColorScalarsOn() | ||
| reader.ReadAllNormalsOn() | ||
| reader.ReadAllTCoordsOn() | ||
| reader.ReadAllVectorsOn() | ||
| # Perform the read | ||
| reader.Update() | ||
| output = reader.GetOutputDataObject(0) | ||
| if output is None: | ||
| raise AssertionError('No output when using VTKs legacy reader') | ||
| return vtki.wrap(output) | ||
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| def read(filename, attrs=None): | ||
| """This will read any VTK file! It will figure out what reader to use | ||
| then wrap the VTK object for use in ``vtki``. | ||
| Parameters | ||
| ---------- | ||
| attrs : dict, optional | ||
| A dictionary of attributes to call on the reader. Keys of dictionary are | ||
| the attribute/method names and values are the arguments passed to those | ||
| calls. If you do not have any attributes to call, pass ``None`` as the | ||
| value. | ||
| """ | ||
| filename = os.path.abspath(os.path.expanduser(filename)) | ||
| ext = get_ext(filename) | ||
|
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| # From the extension, decide which reader to use | ||
| if attrs is not None: | ||
| reader = get_reader(filename) | ||
| return standard_reader_routine(reader, filename, attrs=attrs) | ||
| elif ext in '.vti': # ImageData | ||
| return vtki.UniformGrid(filename) | ||
| elif ext in '.vtr': # RectilinearGrid | ||
| return vtki.RectilinearGrid(filename) | ||
| elif ext in '.vtu': # UnstructuredGrid | ||
| return vtki.UnstructuredGrid(filename) | ||
| elif ext in ['.ply', '.obj', '.stl']: # PolyData | ||
| return vtki.PolyData(filename) | ||
| elif ext in '.vts': # StructuredGrid | ||
| return vtki.StructuredGrid(filename) | ||
| elif ext in ['.vtm', '.vtmb']: | ||
| return vtki.MultiBlock(filename) | ||
| elif ext in ['.vtk']: | ||
| # Attempt to use the legacy reader... | ||
| return read_legacy(filename) | ||
| else: | ||
| # Attempt find a reader in the readers mapping | ||
| try: | ||
| reader = get_reader(filename) | ||
| return standard_reader_routine(reader, filename) | ||
| except KeyError: | ||
| pass | ||
| raise IOError("This file was not able to be automatically read by vtki.") | ||
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| def read_texture(filename, attrs=None): | ||
| """Loads a ``vtkTexture`` from an image file.""" | ||
| filename = os.path.abspath(os.path.expanduser(filename)) | ||
| try: | ||
| # intitialize the reader using the extnesion to find it | ||
| reader = get_reader(filename) | ||
| image = standard_reader_routine(reader, filename, attrs=attrs) | ||
| return vtki.image_to_texture(image) | ||
| except KeyError: | ||
| # Otherwise, use the imageio reader | ||
| pass | ||
| return vtki.numpy_to_texture(imageio.imread(filename)) |
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