Source code for openpnm.io._statoil

import os
import logging
import numpy as np
from openpnm.topotools import trim, extend
from openpnm.network import Network
from pathlib import Path
from pandas import read_table, DataFrame
from tqdm.auto import tqdm


logger = logging.getLogger(__name__)



[docs]
def network_from_statoil(path, prefix):
    r"""
    Load data from the \'dat\' files located in specified folder.

    Parameters
    ----------
    path : str
        The full path to the folder containing the set of \'dat\' files.
    prefix : str
        The file name prefix on each file. The data files are stored
        as \<prefix\>_node1.dat.
    network : Network
        If given then the data will be loaded on it and returned.  If not
        given, a Network will be created and returned.

    Returns
    -------
    Project
        An OpenPNM Project containing a Network holding all the data

    Notes
    -----
    The StatOil format is used by the Maximal Ball network extraction code of
    the Imperial College London group

    This class can be used to load and work with those networks. Numerous
    datasets are available for download from the group's
    `website <http://tinyurl.com/zurko4q>`_.

    The 'Statoil' format consists of 4 different files in a single
    folder. The data is stored in columns with each corresponding to a
    specific property. Headers are not provided in the files, so one must
    refer to various theses and documents to interpret their meaning.

    """
    net = {}

    # Parse the link1 file
    path = Path(path)
    filename = Path(path.resolve(), prefix+'_link1.dat')
    with open(filename, mode='r') as f:
        link1 = read_table(filepath_or_buffer=f,
                           header=None,
                           skiprows=1,
                           sep=' ',
                           skipinitialspace=True,
                           index_col=0)
    link1.columns = ['throat.pore1', 'throat.pore2', 'throat.radius',
                     'throat.shape_factor', 'throat.total_length']
    # Add link1 props to net
    net['throat.conns'] = np.vstack((link1['throat.pore1']-1,
                                     link1['throat.pore2']-1)).T
    net['throat.conns'] = np.sort(net['throat.conns'], axis=1)
    net['throat.radius'] = np.array(link1['throat.radius'])
    net['throat.shape_factor'] = np.array(link1['throat.shape_factor'])
    net['throat.total_length'] = np.array(link1['throat.total_length'])

    filename = Path(path.resolve(), prefix+'_link2.dat')
    with open(filename, mode='r') as f:
        link2 = read_table(filepath_or_buffer=f,
                           header=None,
                           sep=' ',
                           skipinitialspace=True,
                           index_col=0)
    link2.columns = ['throat.pore1', 'throat.pore2',
                     'throat.pore1_length', 'throat.pore2_length',
                     'throat.length', 'throat.volume',
                     'throat.clay_volume']
    # Add link2 props to net
    cl_t = np.array(link2['throat.length'])
    net['throat.length'] = cl_t
    net['throat.conduit_lengths.throat'] = cl_t
    net['throat.volume'] = np.array(link2['throat.volume'])
    cl_p1 = np.array(link2['throat.pore1_length'])
    net['throat.conduit_lengths.pore1'] = cl_p1
    cl_p2 = np.array(link2['throat.pore2_length'])
    net['throat.conduit_lengths.pore2'] = cl_p2
    net['throat.clay_volume'] = np.array(link2['throat.clay_volume'])
    # ---------------------------------------------------------------------
    # Parse the node1 file
    filename = Path(path.resolve(), prefix+'_node1.dat')
    with open(filename, mode='r') as f:
        row_0 = f.readline().split()
        num_lines = int(row_0[0])
        array = np.ndarray([num_lines, 6])
        for i in range(num_lines):
            row = f.readline()\
                   .replace('\t', ' ').replace('\n', ' ').split()
            array[i, :] = row[0:6]
    node1 = DataFrame(array[:, [1, 2, 3, 4]])
    node1.columns = ['pore.x_coord', 'pore.y_coord', 'pore.z_coord',
                     'pore.coordination_number']
    # Add node1 props to net
    net['pore.coords'] = np.vstack((node1['pore.x_coord'],
                                    node1['pore.y_coord'],
                                    node1['pore.z_coord'])).T
    # ---------------------------------------------------------------------
    # Parse the node2 file
    filename = Path(path.resolve(), prefix+'_node2.dat')
    with open(filename, mode='r') as f:
        node2 = read_table(filepath_or_buffer=f,
                           header=None,
                           sep=' ',
                           skipinitialspace=True,
                           index_col=0)
    node2.columns = ['pore.volume', 'pore.radius', 'pore.shape_factor',
                     'pore.clay_volume']
    # Add node2 props to net
    net['pore.volume'] = np.array(node2['pore.volume'])
    net['pore.radius'] = np.array(node2['pore.radius'])
    net['pore.shape_factor'] = np.array(node2['pore.shape_factor'])
    net['pore.clay_volume'] = np.array(node2['pore.clay_volume'])
    net['throat.cross_sectional_area'] = ((net['throat.radius']**2)
                                          / (4.0*net['throat.shape_factor']))
    net['pore.area'] = ((net['pore.radius']**2)
                        / (4.0*net['pore.shape_factor']))

    network = Network()
    network.update(net)

    # Use OpenPNM Tools to clean up network
    # Trim throats connected to 'inlet' or 'outlet' reservoirs
    trim1 = np.where(np.any(net['throat.conns'] == -1, axis=1))[0]
    # Apply 'outlet' label to these pores
    outlets = network['throat.conns'][trim1, 1]
    network['pore.outlets'] = False
    network['pore.outlets'][outlets] = True
    trim2 = np.where(np.any(net['throat.conns'] == -2, axis=1))[0]
    # Apply 'inlet' label to these pores
    inlets = network['throat.conns'][trim2, 1]
    network['pore.inlets'] = False
    network['pore.inlets'][inlets] = True
    # Now trim the throats
    to_trim = np.hstack([trim1, trim2])
    trim(network=network, throats=to_trim)

    return network