Source code for PVGeo.readers.binaries

__all__ = [
    'PackedBinariesReader',
    'MadagascarReader',
]

__displayname__ = 'Binary/Serialized File I/O'

import warnings

import numpy as np
import vtk

from .. import _helpers, interface
from ..base import ReaderBase


[docs]class PackedBinariesReader(ReaderBase): """This reads in float or double data that is packed into a binary file format. It will treat the data as one long array and make a ``vtkTable`` with one column of that data. The reader uses defaults to import as floats with native endianness. Use the Table to Uniform Grid or the Reshape Table filters to give more meaning to the data. We chose to use a ``vtkTable`` object as the output of this reader because it gives us more flexibility in the filters we can apply to this data down the pipeline and keeps thing simple when using filters in this repository. """ __displayname__ = 'Packed Binaries Reader' __category__ = 'reader' extensions = 'H@ bin rsf rsf@ HH npz' description = 'PVGeo: Packed Binaries Reader' def __init__(self, **kwargs): ReaderBase.__init__(self, nOutputPorts=1, outputType='vtkTable', **kwargs) # Other Parameters self.__data_name = kwargs.get('dataname', 'Data') self.__dtypechar = kwargs.get('dtype', 'f') self.__endian = kwargs.get('endian', '') self.__dtype, self.__vtktype = interface.get_dtypes(dtype=self.__dtypechar, endian=self.__endian) # Data objects to hold the read data for access by the pipeline methods self.__data = []
[docs] def _read_raw_file(self, filename): """Interanl helper to read the raw data from the file""" dtype = self.__dtype if dtype == np.dtype('>f'): # Checks if big-endian and fixes read dtype = np.dtype('f') try: arr = np.fromfile(filename, dtype=dtype) except (IOError, OSError) as fe: raise _helpers.PVGeoError(str(fe)) return np.asarray(arr, dtype=self.__dtype)
[docs] def _get_file_contents(self, idx=None): """Interanl helper to get all contents for all files""" if idx is not None: filenames = [self.get_file_names(idx=idx)] else: filenames = self.get_file_names() contents = [] for f in filenames: contents.append(self._read_raw_file(f)) if idx is not None: return contents[0] return contents
[docs] def _read_up_front(self): """Should not need to be overridden """ # Perform Read self.__data = self._get_file_contents() self.need_to_read(flag=False) return 1
[docs] def _get_raw_data(self, idx=0): """This will return the proper data for the given timestep """ return self.__data[idx]
[docs] def convert_array(self, arr): """Converts the numpy array to a vtkDataArray """ # Put raw data into vtk array data = interface.convert_array(arr, name=self.__data_name, deep=True, array_type=self.__vtktype) return data
[docs] def RequestData(self, request, inInfo, outInfo): """Used by pipeline to request data for current timestep """ # Get output: output = vtk.vtkTable.GetData(outInfo) if self.need_to_read(): self._read_up_front() # Get requested time index i = _helpers.get_requested_time(self, outInfo) # Generate the data object arr = self._get_raw_data(idx=i) data = self.convert_array(arr) output.AddColumn(data) return 1
#### Seters and Geters ####
[docs] def set_endian(self, endian): """Set the endianness of the data file. Args: endian (int or char): no preference = '' or 0, Little = 1 or `<` or Big = 2 `>`. """ pos = ['', '<', '>'] if isinstance(endian, int): endian = pos[endian] if endian != self.__endian: self.__endian = endian self.__dtype, self.__vtktype = interface.get_dtypes(dtype=self.__dtypechar, endian=self.__endian) self.Modified()
[docs] def get_endian(self): """Get the endianness of the data file.""" return self.__endian
[docs] def set_data_type(self, dtype): """Set the data type of the binary file: `double='d'`, `float='f'`, `int='i'` """ pos = ['d', 'f', 'i'] if isinstance(dtype, int): dtype = pos[dtype] if dtype != self.__dtype: self.__dtypechar = dtype self.__dtype, self.__vtktype = interface.get_dtypes(dtype=self.__dtypechar, endian=self.__endian) self.Modified()
[docs] def get_data_types(self): """Get the data type of the binary file""" return self.__dtype, self.__vtktype
[docs] def set_data_name(self, data_name): """The string name of the data array generated from the inut file. """ if data_name != self.__data_name: self.__data_name = data_name self.Modified(read_again=False) # Don't re-read. Just request data again
[docs] def get_data_name(self): """Get name used for the data array""" return self.__data_name
[docs]class MadagascarReader(PackedBinariesReader): """This reads in float or double data that is packed into a Madagascar binary file format with a leader header. The reader ignores all of the ascii header details by searching for the sequence of three special characters: EOL EOL EOT and it will treat the followng binary packed data as one long array and make a ``vtkTable`` with one column of that data. The reader uses defaults to import as floats with native endianness. Use the Table to Uniform Grid or the Reshape Table filters to give more meaning to the data. We will later implement the ability to create a gridded volume from the header info. This reader is a quick fix for Samir. We chose to use a ``vtkTable`` object as the output of this reader because it gives us more flexibility in the filters we can apply to this data down the pipeline and keeps thing simple when using filters in this repository. `Details Here`_. .. _Details Here: http://www.ahay.org/wiki/RSF_Comprehensive_Description#Single-stream_RSF """ __displayname__ = 'Madagascar SSRSF Reader' __category__ = 'reader' # extensions are inherrited from PackedBinariesReader description = 'PVGeo: Madagascar Single Stream RSF Files' def __init__(self, **kwargs): PackedBinariesReader.__init__(self, **kwargs)
[docs] def _read_raw_file(self, filename): """Reads the raw data from the file for Madagascar SSRSF files""" dtype, vtktype = self.get_data_types() CTLSEQ = b'\014\014\004' # The control sequence to seperate header from data rpl = b'' raw = [] with open(filename, 'rb') as file: raw = file.read() idx = raw.find(CTLSEQ) if idx == -1: warnings.warn('This is not a single stream RSF format file. Treating entire file as packed binary data.') else: raw = raw[idx:] # deletes the header raw = raw.replace(CTLSEQ, rpl) # removes the control sequence arr = np.fromstring(raw, dtype=dtype) return arr