Source code for PVGeo.gslib.sgems

__all__ = [

__displayname__ = 'SGeMS File I/O'

import re

import numpy as np
import pandas as pd
import vtk

from .. import _helpers, interface
from ..base import WriterBase
from .gslib import GSLibReader

[docs]class SGeMSGridReader(GSLibReader): """Generates ``vtkImageData`` from the uniform grid defined in the inout file in the SGeMS grid format. This format is simply the GSLIB format where the header line defines the dimensions of the uniform grid. """ __displayname__ = 'SGeMS Grid Reader' __category__ = 'reader' extensions = GSLibReader.extensions + 'gslibgrid mtxset' description = 'PVGeo: SGeMS Uniform Grid' def __init__(self, origin=(0.0, 0.0, 0.0), spacing=(1.0, 1.0, 1.0), **kwargs): GSLibReader.__init__(self, outputType='vtkImageData', **kwargs) self.__extent = None self.__origin = origin self.__spacing = spacing self.__mask = kwargs.get("mask", -9966699.) def __parse_extent(self, header): regex = re.compile(r'\S\s\((\d+)x(\d+)x(\d+)\)') dims = regex.findall(header) if len(dims) < 1: regex = re.compile(r'(\d+) (\d+) (\d+)') dims = regex.findall(header) if len(dims) < 1: raise _helpers.PVGeoError('File not in proper SGeMS Grid fromat.') dims = dims[0] return int(dims[0]), int(dims[1]), int(dims[2])
[docs] def _read_extent(self): """Reads the input file for the SGeMS format to get output extents. Computationally inexpensive method to discover whole output extent. Return: tuple : This returns a tuple of the whole extent for the uniform grid to be made of the input file (0,n1-1, 0,n2-1, 0,n3-1). This output should be directly passed to set the whole output extent. """ # Read first file... extent cannot vary with time # TODO: make more efficient to only reader header of file fileLines = self._get_file_contents(idx=0) h = fileLines[0+self.get_skip_rows()] n1,n2,n3 = self.__parse_extent(h) return (0,n1, 0,n2, 0,n3)
[docs] def _extract_header(self, content): """Internal helper to parse header info for the SGeMS file format""" titles, content = GSLibReader._extract_header(self, content) h = self.get_file_header() try: if self.__extent is None: self.__extent = self.__parse_extent(h) elif self.__extent != (self.__parse_extent(h)): raise _helpers.PVGeoError('Grid dimensions change in file time series.') except ValueError: raise _helpers.PVGeoError('File not in proper SGeMS Grid fromat.') return titles, content
[docs] def RequestData(self, request, inInfo, outInfo): """Used by pipeline to get output data object for given time step. Constructs the ``vtkImageData`` """ # Get output: output = vtk.vtkImageData.GetData(outInfo) # Get requested time index i = _helpers.get_requested_time(self, outInfo) if self.need_to_read(): self._read_up_front() # Generate the data object n1, n2, n3 = self.__extent dx, dy, dz = self.__spacing ox, oy, oz = self.__origin output.SetDimensions(n1+1, n2+1, n3+1) output.SetSpacing(dx, dy, dz) output.SetOrigin(ox, oy, oz) # Use table generator and convert because its easy: table = vtk.vtkTable() df = self._get_raw_data(idx=i) # Replace all masked values with NaN df.replace(self.__mask, np.nan, inplace=True) interface.data_frame_to_table(df, table) # now get arrays from table and add to point data of pdo for i in range(table.GetNumberOfColumns()): output.GetCellData().AddArray(table.GetColumn(i)) del(table) return 1
[docs] def RequestInformation(self, request, inInfo, outInfo): """Used by pipeline to set grid extents. """ # Call parent to handle time stuff GSLibReader.RequestInformation(self, request, inInfo, outInfo) # Now set whole output extent ext = self._read_extent() info = outInfo.GetInformationObject(0) # Set WHOLE_EXTENT: This is absolutely necessary info.Set(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT(), ext, 6) return 1
[docs] def set_spacing(self, dx, dy, dz): """Set the spacing for each axial direction""" spac = (dx, dy, dz) if self.__spacing != spac: self.__spacing = spac self.Modified(read_again=False)
[docs] def set_origin(self, ox, oy, oz): """Set the origin corner of the grid""" origin = (ox, oy, oz) if self.__origin != origin: self.__origin = origin self.Modified(read_again=False)
[docs]class WriteImageDataToSGeMS(WriterBase): """Writes a ``vtkImageData`` object to the SGeMS uniform grid format. This writer can only handle point data. Note that this will only handle CellData as that is convention with SGeMS. """ __displayname__ = 'Write ``vtkImageData`` To SGeMS Grid Format' __category__ = 'writer' def __init__(self, inputType='vtkImageData'): WriterBase.__init__(self, inputType=inputType, ext='SGeMS')
[docs] def perform_write_out(self, input_data_object, filename, object_name): """Write out the input ``vtkImage`` data to the SGeMS file format""" # Get the input data object grd = input_data_object # Get grid dimensions and minus one becuase this defines nodes nx, ny, nz = grd.GetDimensions() nx -= 1 ny -= 1 nz -= 1 numArrs = grd.GetCellData().GetNumberOfArrays() arrs = [] titles = [] # Get data arrays for i in range(numArrs): vtkarr = grd.GetCellData().GetArray(i) arrs.append(interface.convert_array(vtkarr)) titles.append(vtkarr.GetName()) datanames = '\n'.join(titles) df = pd.DataFrame(np.array(arrs).T) with open(filename, 'w') as f: f.write('%d %d %d\n' % (nx, ny, nz)) f.write('%d\n' % len(titles)) f.write(datanames) f.write('\n') df.to_csv(f, sep=' ', header=None, index=False, float_format=self.get_format()) return 1