Project.py

import time
import h5py
import numpy as np
import openpnm
from copy import deepcopy
from openpnm.utils import SettingsDict, HealthDict, Workspace, logging
logger = logging.getLogger(__name__)
ws = Workspace()


class Project(list):
    r"""
    This class provides a container for all OpenPNM objects in a given
    simulation.

    A simulation is defined as a Network and all of it's associated objects.
    When instantiating a Network, a Project can be passed as an argument, but
    if not given one is created.  When instantiating any other object either
    a Network or a Project can be supplied.  In the former case, the
    Network's Project is retrieved and used.  The end result is that all
    objects are stored in a specific Project.

    The Project to which any object belongs can be retrieved with
    ``obj.project``.  Conversely, printing a Project displays a list of all
    objects it contains.

    Moreover, all Projects are registered with the Workspace.  Since there can
    be only instance of the Workspace it is possible to view all open Projects
    by printing the Workspace.

    See Also
    --------
    Workspace

    Notes
    -----
    The following table shows all the methods that are available on the Project
    objects along with a very brief description:

    +------------------+-------------------------------------------------+
    | Method           | Description                                     |
    +==================+=================================================+
    | export_data      | Export the pore and throat data from the giv... |
    +------------------+-------------------------------------------------+
    | import_data      |                                                 |
    +------------------+-------------------------------------------------+
    | purge_object     | Remove an object from the Project.  This rem... |
    +------------------+-------------------------------------------------+
    | load_object      | Loads a single object from a file               |
    +------------------+-------------------------------------------------+
    | save_object      | Saves the given object to a file                |
    +------------------+-------------------------------------------------+
    | find_physics     | Find the Physics object(s) associated with a... |
    +------------------+-------------------------------------------------+
    | find_geometry    | Find the Geometry associated with a given Ph... |
    +------------------+-------------------------------------------------+
    | find_phase       | Find the Phase associated with a given object.  |
    +------------------+-------------------------------------------------+
    | check_geometr... | Perform a check to find pores with overlappi... |
    +------------------+-------------------------------------------------+
    | check_physics... | Perform a check to find pores which have ove... |
    +------------------+-------------------------------------------------+

    """

    def __init__(self, *args, **kwargs):
        name = kwargs.pop('name', None)
        super().__init__(*args, **kwargs)
        # Register self with workspace
        ws[name] = self
        self.settings = SettingsDict()
        self.comments = 'Using OpenPNM ' + openpnm.__version__

    def extend(self, obj):
        r"""
        This function is used to add objects to the project.  Arguments can
        be single OpenPNM objects, an OpenPNM project list, or a plain list of
        OpenPNM objects.

        """
        if type(obj) is not list:
            obj = [obj]
        for item in obj:
            if hasattr(item, '_mro'):
                if 'GenericNetwork' in item._mro():
                    if self.network:
                        raise Exception('Project already has a network')
                # Must use append since extend breaks the dicts up into
                # separate objects, while append keeps it as a single object.
                super().append(item)
            else:
                raise Exception('Only OpenPNM objects can be added')

    def append(self, obj):
        r"""
        The Project (a list) must be kept as a flat list, so the append
        function, which can normally be used to insert a list into a list, is
        overloaded to basically prevent the normal append operation and simply
        calls ``extend``.

        """
        self.extend(obj)

    def remove(self, obj):
        r"""
        The given object is removed from the project

        This removes the object, along with all it's labels in associated
        objects, but does NOT remove the associated objects.

        See Also
        -------
        purge_object

        """
        self.purge_object(obj, deep=False)

    def pop(self, index):
        r"""
        The object at the given index is removed from the list and returned.

        Notes
        -----
        This method uses ``purge_object`` to perform the actual removal of the
        object. It is reommended to just use that directly instead.

        See Also
        --------
        purge_object

        """
        obj = self[index]
        self.purge_object(obj, deep=False)
        return obj

    def insert(self, index, obj):
        r"""
        Inserts the supplied object at the specified index in the Project list

        Notes
        -----
        The order of the objects in an OpenPNM Project lists do not matter, so
        it is recommended to just use ``append`` instead.

        See Also
        --------
        append
        extend

        """
        self.extend(obj)

    def clear(self, objtype=[]):
        r"""
        Clears objects from the project entirely or selectively, depdening on
        the received arguments.

        Parameters
        ----------
        objtype : list of strings
            A list containing the object type(s) to be removed.  If no types
            are specified, then all objects are removed.  To clear only objects
            of a specific type, use *'network'*, *'geometry'*, *'phase'*,
            *'physics'*, or *'algorithm'*.  It's also possible to use
            abbreviations, like *'geom'*.

        """
        if len(objtype) == 0:
            super().clear()
        else:
            names = [obj.name for obj in self]
            for name in names:
                try:
                    obj = self[name]
                    for t in objtype:
                        if obj._isa(t):
                            self.purge_object(obj)
                except KeyError:
                    pass

    def copy(self, name=None):
        r"""
        Creates a deep copy of the current project

        A deep copy means that new, unique versions of all the objects are
        created but with identical data and properties.

        Parameters
        ----------
        name : string
            The name to give to the new project.  If not supplied, a name
            is automatically generated.

        Returns
        -------
        proj : list
            A new Project object containing copies of all objects

        """
        if name is None:
            name = ws._gen_name()
        proj = deepcopy(self)
        ws[name] = proj
        return proj

    @property
    def workspace(self):
        return ws

    def _set_name(self, name):
        if name is None:
            name = ws._gen_name()
        ws[name] = self

    def _get_name(self):
        for key in ws.keys():
            if ws[key] is self:
                return key

    name = property(fget=_get_name, fset=_set_name)

    def __getitem__(self, key):
        if type(key) == str:
            obj = None
            for item in self:
                if item.name == key:
                    obj = item
            if obj is None:
                raise KeyError(key)
        else:
            obj = super().__getitem__(key)
        return obj

    def find_phase(self, obj):
        r"""
        Find the Phase associated with a given object.

        Parameters
        ----------
        obj : OpenPNM Object
            Can either be a Physics or Algorithm object

        Returns
        -------
        phase : OpenPNM Phase object

        Raises
        ------
        If no Phase object can be found, then an Exception is raised.
        """
        # If received phase, just return self
        if obj._isa('phase'):
            return obj
        # If phase happens to be in settings (i.e. algorithm), look it up
        if 'phase' in obj.settings.keys():
            phase = self.phases()[obj.settings['phase']]
            return phase
        # Otherwise find it using bottom-up approach (i.e. look in phase keys)
        for phase in self.phases().values():
            if ('pore.'+obj.name in phase) or ('throat.'+obj.name in phase):
                return phase
        # If all else fails, throw an exception
        raise Exception('Cannot find a phase associated with '+obj.name)

    def find_geometry(self, physics):
        r"""
        Find the Geometry associated with a given Physics

        Parameters
        ----------
        physics : OpenPNM Physics Object
            Must be a Physics object

        Returns
        -------
        geom : OpenPNM Geometry object

        Raises
        ------
        If no Geometry object can be found, then an Exception is raised.

        """
        # If geometry happens to be in settings, look it up directly
        if 'geometry' in physics.settings.keys():
            geom = self.geometries()[physics.settings['geometry']]
            return geom
        # Otherwise, use the bottom-up approach
        for geo in self.geometries().values():
            if physics in self.find_physics(geometry=geo):
                return geo
        # If all else fails, throw an exception
        raise Exception('Cannot find a geometry associated with '+physics.name)

    def find_physics(self, geometry=None, phase=None):
        r"""
        Find the Physics object(s) associated with a given Geometry, Phase,
        or combination.

        Parameters
        ----------
        geometry : OpenPNM Geometry Object
            The Geometry object for which the Physics object(s) are sought

        phase : OpenPNM Phase Object
            The Phase object for which the Physics object(s) are sought

        Returns
        -------
        physics : list
            A list containing the Physics object(s).  If only a ``geometry`` is
            specified the the Physics for all Phases is returned.  If only a
            ``phase`` is specified, then the Physics for all Geometries is
            returned.  If both ``geometry`` and ``phase`` is specified then
            the list only contains a single Physics.  If no Physics is found,
            the the list will be empty.  See the Notes section for more
            information.

        See Also
        --------
        grid

        Notes
        -----
        The Project has an ``grid`` attribute that shows the association of
        all objects.  If each Geometry represents a row and each Phase is a
        column, then each row/col intersection represents a Physics. This
        method finds the PHysics' at each intersection

        """

        if geometry and phase:
            physics = self.find_physics(geometry=geometry)
            phases = list(self.phases().values())
            phys = physics[phases.index(phase)]
            return phys
        elif geometry:
            result = []
            net = self.network
            geoPs = net['pore.'+geometry.name]
            geoTs = net['throat.'+geometry.name]
            for phase in self.phases().values():
                physics = self.find_physics(phase=phase)
                temp = None
                for phys in physics:
                    Ps = phase.map_pores(pores=phys.Ps, origin=phys)
                    physPs = phase.tomask(pores=Ps)
                    Ts = phase.map_throats(throats=phys.Ts, origin=phys)
                    physTs = phase.tomask(throats=Ts)
                    if np.all(geoPs == physPs) and np.all(geoTs == physTs):
                        temp = phys
                result.append(temp)
            return result
        elif phase:
            names = set(self.physics().keys())
            keys = set([item.split('.')[-1] for item in phase.keys()])
            hits = names.intersection(keys)
            phys = [self.physics().get(i, None) for i in hits]
            return phys
        else:
            phys = list(self.physics().values())
            return phys

    def find_full_domain(self, obj):
        r"""
        Find the full domain object associated with a given object.
        For geometry the network is found, for physics the phase is found and
        for all other objects which are defined for for the full domain,
        themselves are found.

        Parameters
        ----------
        obj : OpenPNM Object
            Can be any object

        Returns
        -------
        obj : An OpenPNM object

        """
        if 'Subdomain' not in obj._mro():
            # Network, Phase, Alg
            return obj
        else:
            if obj._isa() == 'geometry':
                # Geom
                return self.network
            else:
                # Phys
                return self.find_phase(obj)

    def _validate_name(self, name):
        if name in self.names:
            raise Exception('An object already exists named '+name)
        for item in self:
            for key in item.keys():
                if key.split('.')[1] == name:
                    raise Exception('A property/label is already named '+name)

    def _generate_name(self, obj):
        prefix = obj.settings['prefix']
        num = str(len([item for item in self if item._isa() == obj._isa()]))
        name = prefix + '_' + num.zfill(2)
        return name

    @property
    def names(self):
        names = [i.name for i in self]
        return names

    def purge_object(self, obj, deep=False):
        r"""
        Remove an object from the Project.  This removes all references to
        the object from all other objects (i.e. removes labels)

        Parameters
        ----------
        obj : OpenPNM Object
            The object to purge

        deep : boolean
            A flag that indicates whether to remove associated objects.
            If ``True``, then removing a Geometry or Phase also removes
            the associated Physics objects.  If ``False`` (default) then
            only the given object is removed, along with its labels in all
            associated objects.  Removing a Physics always keeps associated
            Geometry and Phases since they might also be associated with other
            Physics objects.

        Raises
        ------
        An Exception is raised if the object is a Network.

        Notes
        -----
        For a clearer picture of this logic, type ``print(project.grid)`` at
        the console.  A deep purge of a Geometry is like removing a row, while
        a Phase is like removing a column.

        """
        if obj._isa() in ['physics', 'algorithm']:
            self._purge(obj)
        if obj._isa() == 'geometry':
            if deep:
                physics = self.find_physics(geometry=obj)
                for phys in physics:
                    self._purge(self.physics()[phys.name])
            self._purge(obj)
        if obj._isa() == 'phase':
            if deep:
                physics = self.find_physics(phase=obj)
                for phys in physics:
                    self._purge(self.physics()[phys.name])
            self._purge(obj)
        if obj._isa() == 'network':
            raise Exception('Cannot purge a network, just make a new project')

    def _purge(self, obj):
        for item in self:
            for key in list(item.keys()):
                if key.split('.')[-1] == obj.name:
                    del item[key]
        super().remove(obj)

    def save_object(self, obj):
        r"""
        Saves the given object or list of objects to a file

        Parameters
        ----------
        obj : OpenPNM object or list of objects
            The objects to be saved.  Depending on the object type, the file
            extension will be one of 'net', 'geo', 'phase', 'phys' or 'alg'.
        """
        from openpnm.io import OpenpnmIO
        OpenpnmIO.save_object_to_file(objs=obj)

    def load_object(self, filename):
        r"""
        Loads a single object from a file

        Parameters
        ----------
        filename : string or path object
            The name of the file containing the saved object.  Can include
            an absolute or relative path as well.  If only a filename is
            given it will be saved in the current working directory.  The
            object type is inferred from

        """
        from openpnm.io import OpenpnmIO
        OpenpnmIO.load_object_from_file(filename=filename, project=self)

    def save_project(self, filename=''):
        r"""
        Save the current project to a ``pnm`` file.

        Parameters
        ----------
        filename : string or path object
            The name of the file.  Can include an absolute or relative path
            as well.  If only a filename is given it will be saved in the
            current working directory.

        """
        ws.save_project(project=self, filename=filename)

    def _new_object(self, objtype, name=None):
        r"""
        """
        if objtype.startswith('net'):
            obj = openpnm.network.GenericNetwork(project=self, name=name)
        elif objtype.startswith('geo'):
            obj = openpnm.geometry.GenericGeometry(project=self, name=name,
                                                   pores=[], throats=[])
        elif objtype.startswith('pha'):
            obj = openpnm.phases.GenericPhase(project=self, name=name)
        elif objtype.startswith('phy'):
            obj = openpnm.physics.GenericPhysics(project=self, name=name)
        elif objtype.startswith('alg'):
            obj = openpnm.algorithm.GenericAlgorithm(project=self, name=name)
        else:
            obj = openpnm.core.Base(project=self, name=name)
        return obj

    def import_data(self, filename):
        r"""
        """
        raise NotImplementedError('Use the io module to import data')

    def export_data(self, phases=[], filename=None, filetype='vtp'):
        r"""
        Export the pore and throat data from the given object(s) into the
        specified file and format.

        Parameters
        ----------
        phases : list of OpenPNM Phase Objects
            The data on each supplied phase will be added to file

        filename : string
            The file name to use.  If none is supplied then one will be
            automatically generated based on the name of the project
            containing the supplied Network, with the date and time appended.

        filetype : string
            Which file format to store the data.  If a valid extension is
            included in the ``filename``, this is ignored.  Option are:

            **'vtk'** : (default) The Visualization Toolkit format, used by
            various softwares such as Paraview.  This actually produces a 'vtp'
            file.  NOTE: This can be quite slow since all the data is written
            to a simple text file.  For large data simulations consider
            'xdmf'.

            **'csv'** : The comma-separated values format, which is easily
            openned in any spreadsheet program.  The column names represent
            the property name, including the type and name of the object to
            which they belonged, all separated by the pipe character.

            **'xmf'** : The extensible data markup format, is a very efficient
            format for large data sets.  This actually results in the creation
            of two files, the *xmf* file and an associated *hdf* file.  The
            *xmf* file contains instructions for looking into the *hdf* file
            where the data is stored. Paraview opens the *xmf* format natively,
            and is very fast.

            **'mat'** : Matlab 'mat-file', which can be openned in Matlab.

        Notes
        -----
        This is a helper function for the actual functions in the IO module.
        For more control over the format of the output, and more information
        about the format refer to ``openpnm.io``.

        """
        project = self
        network = self.network
        if filename is None:
            filename = project.name + '_' + time.strftime('%Y%b%d_%H%M%p')
        # Infer filetype from extension on file name...if given
        if '.' in filename:
            exts = ['vtk', 'vtp', 'vtu', 'csv', 'xmf', 'xdmf', 'hdf', 'hdf5',
                    'h5', 'mat']
            if filename.split('.')[-1] in exts:
                filename, filetype = filename.rsplit('.', 1)
        if filetype.lower() in ['vtk', 'vtp', 'vtu']:
            openpnm.io.VTK.save(network=network, phases=phases,
                                filename=filename)
        if filetype.lower() == 'csv':
            openpnm.io.CSV.save(network=network, phases=phases,
                                filename=filename)
        if filetype.lower() in ['xmf', 'xdmf']:
            openpnm.io.XDMF.save(network=network, phases=phases,
                                 filename=filename)
        if filetype.lower() in ['hdf5', 'hdf', 'h5']:
            f = openpnm.io.HDF5.to_hdf5(network=network, phases=phases,
                                        filename=filename)
            f.close()
        if filetype.lower() == 'mat':
            openpnm.io.MAT.save(network=network, phases=phases,
                                filename=filename)

    def _dump_data(self, mode=['props']):
        r"""
        Dump data from all objects in project to an HDF5 file.  Note that
        'pore.coords', 'throat.conns', 'pore.all', 'throat.all', and all
        labels pertaining to the linking of objects are kept.

        Parameters
        ----------
        mode : string or list of strings
            The type of data to be dumped to the HDF5 file.  Options are:

            **'props'** : Numerical data such as 'pore.diameter'.  The default
            is only 'props'.

            **'labels'** : Boolean data that are used as labels.  Since this
            is boolean data it does not consume large amounts of memory and
            probably does not need to be dumped.

        See Also
        --------
        _fetch_data

        Notes
        -----
        In principle, after data is fetched from an HDF5 file, it should
        physically stay there until it's called upon.  This let users manage
        the data as if it's in memory, even though it isn't.  This behavior
        has not been confirmed yet, which is why these functions are hidden.

        """
        with h5py.File(self.name + '.hdf5') as f:
            for obj in self:
                for key in list(obj.keys()):
                    tempname = obj.name + '|' + '_'.join(key.split('.'))
                    arr = obj[key]
                    if 'U' in str(obj[key][0].dtype):
                        pass
                    elif 'all' in key.split('.'):
                        pass
                    else:
                        f.create_dataset(name='/'+tempname, shape=arr.shape,
                                         dtype=arr.dtype, data=arr)
            for obj in self:
                obj.clear(mode=mode)

    def _fetch_data(self):
        r"""
        Retrieve data from an HDF5 file and place onto correct objects in the
        project

        See Also
        --------
        _dump_data

        Notes
        -----
        In principle, after data is fetched from and HDF5 file, it should
        physically stay there until it's called upon.  This let users manage
        the data as if it's in memory, even though it isn't.  This behavior
        has not been confirmed yet, which is why these functions are hidden.

        """
        with h5py.File(self.name + '.hdf5') as f:
            # Reload data into project
            for item in f.keys():
                obj_name, propname = item.split('|')
                propname = propname.split('_')
                propname = propname[0] + '.' + '_'.join(propname[1:])
                self[obj_name][propname] = f[item]

    @property
    def network(self):
        net = list(self._get_objects_by_type('network').values())
        if len(net) > 0:
            net = net[0]
        else:
            net = None
        return net

    def geometries(self, name=None):
        if name:
            return self._get_object_by_name(name)
        else:
            return self._get_objects_by_type('geometry')

    def phases(self, name=None):
        if name:
            return self._get_object_by_name(name)
        else:
            return self._get_objects_by_type('phase')

    def physics(self, name=None):
        if name:
            return self._get_object_by_name(name)
        else:
            return self._get_objects_by_type('physics')

    def algorithms(self, name=None):
        if name:
            return self._get_object_by_name(name)
        else:
            return self._get_objects_by_type('algorithm')

    def _get_object_by_name(self, name):
        for item in self:
            if item.name == name:
                return item
        raise Exception('An object named ' + name + ' was not found')

    def _get_objects_by_type(self, objtype):
        return {item.name: item for item in self if item._isa(objtype)}

    def _set_comments(self, string):
        if hasattr(self, '_comments') is False:
            self._comments = {}
        self._comments[time.strftime('%c')] = string

    def _get_comments(self):
        if hasattr(self, '_comments') is False:
            self._comments = {}
        for key in list(self._comments.keys()):
            print(key, ': ', self._comments[key])

    comments = property(fget=_get_comments, fset=_set_comments)

    def __str__(self):
        s = []
        hr = '―'*78
        s.append(hr)
        s.append(' {0:<15} '.format('Object Name') +
                 '{0:<65}'.format('Object ID'))
        s.append(hr)
        for item in self:
            s.append(' {0:<15} '.format(item.name) +
                     '{0:<65}'.format(item.__repr__()))
        s.append(hr)
        return '\n'.join(s)

    def check_geometry_health(self):
        r"""
        Perform a check to find pores with overlapping or undefined Geometries

        Returns
        -------
        A HealthDict
        """
        health = HealthDict()
        health['overlapping_pores'] = []
        health['undefined_pores'] = []
        health['overlapping_throats'] = []
        health['undefined_throats'] = []
        geoms = self.geometries().keys()
        if len(geoms):
            net = self.network
            Ptemp = np.zeros((net.Np,))
            Ttemp = np.zeros((net.Nt,))
            for item in geoms:
                Pind = net['pore.'+item]
                Tind = net['throat.'+item]
                Ptemp[Pind] = Ptemp[Pind] + 1
                Ttemp[Tind] = Ttemp[Tind] + 1
            health['overlapping_pores'] = np.where(Ptemp > 1)[0].tolist()
            health['undefined_pores'] = np.where(Ptemp == 0)[0].tolist()
            health['overlapping_throats'] = np.where(Ttemp > 1)[0].tolist()
            health['undefined_throats'] = np.where(Ttemp == 0)[0].tolist()
        else:
            health['undefined_pores'] = self.network.Ps
            health['undefined_throats'] = self.network.Ts
        return health

    def check_physics_health(self, phase):
        r"""
        Perform a check to find pores which have overlapping or missing Physics

        Parameters
        ----------
        phase : OpenPNM Phase object
            The Phase whose Physics should be checked

        Returns
        -------
        A HealthDict

        """
        health = HealthDict()
        health['overlapping_pores'] = []
        health['undefined_pores'] = []
        health['overlapping_throats'] = []
        health['undefined_throats'] = []
        geoms = self.geometries().keys()
        if len(geoms):
            phys = self.find_physics(phase=phase)
            if len(phys) == 0:
                raise Exception(str(len(geoms))+' geometries were found, but' +
                                ' no physics')
            if None in phys:
                raise Exception('Undefined physics found, check the grid')
            Ptemp = np.zeros((phase.Np,))
            Ttemp = np.zeros((phase.Nt,))
            for item in phys:
                    Pind = phase['pore.'+item.name]
                    Tind = phase['throat.'+item.name]
                    Ptemp[Pind] = Ptemp[Pind] + 1
                    Ttemp[Tind] = Ttemp[Tind] + 1
            health['overlapping_pores'] = np.where(Ptemp > 1)[0].tolist()
            health['undefined_pores'] = np.where(Ptemp == 0)[0].tolist()
            health['overlapping_throats'] = np.where(Ttemp > 1)[0].tolist()
            health['undefined_throats'] = np.where(Ttemp == 0)[0].tolist()
        return health

    def check_data_health(self, obj):
        r"""
        Check the health of pore and throat data arrays.

        Parameters
        ----------
        obj : OpenPNM object
            A handle of the object to be checked

        Returns
        -------
        health : dict
            Returns a HealthDict object which a basic dictionary with an added
            ``health`` attribute that is True is all entries in the dict are
            deemed healthy (empty lists), or False otherwise.

        """
        health = HealthDict()
        for item in obj.props():
            health[item] = []
            if obj[item].dtype == 'O':
                health[item] = 'No checks on object'
            elif np.sum(np.isnan(obj[item])) > 0:
                health[item] = 'Has NaNs'
            elif np.shape(obj[item])[0] != obj._count(item.split('.')[0]):
                health[item] = 'Wrong Length'
        return health

    def check_network_health(self):
        r"""
        This method check the network topological health by checking for:

            (1) Isolated pores
            (2) Islands or isolated clusters of pores
            (3) Duplicate throats
            (4) Bidirectional throats (ie. symmetrical adjacency matrix)
            (5) Headless throats

        Returns
        -------
        health : dict
            A dictionary containing the offending pores or throat numbers under
            each named key.

        Notes
        -----
        It also returns a list of which pores and throats should be trimmed
        from the network to restore health.  This list is a suggestion only,
        and is based on keeping the largest cluster and trimming the others.

        Notes
        -----
        - Does not yet check for duplicate pores
        - Does not yet suggest which throats to remove
        - This is just a 'check' and does not 'fix' the problems it finds
        """
        import scipy.sparse.csgraph as csg
        import scipy.sparse as sprs

        health = HealthDict()
        health['disconnected_clusters'] = []
        health['isolated_pores'] = []
        health['trim_pores'] = []
        health['duplicate_throats'] = []
        health['bidirectional_throats'] = []
        health['headless_throats'] = []
        health['looped_throats'] = []

        net = self.network

        # Check for headless throats
        hits = np.where(net['throat.conns'] > net.Np - 1)[0]
        if np.size(hits) > 0:
            health['headless_throats'] = np.unique(hits)
            return health

        # Check for throats that loop back onto the same pore
        P12 = net['throat.conns']
        hits = np.where(P12[:, 0] == P12[:, 1])[0]
        if np.size(hits) > 0:
            health['looped_throats'] = hits

        # Check for individual isolated pores
        Ps = net.num_neighbors(net.pores())
        if np.sum(Ps == 0) > 0:
            health['isolated_pores'] = np.where(Ps == 0)[0]

        # Check for separated clusters of pores
        temp = []
        am = net.create_adjacency_matrix(fmt='coo', triu=True)
        Cs = csg.connected_components(am, directed=False)[1]
        if np.unique(Cs).size > 1:
            for i in np.unique(Cs):
                temp.append(np.where(Cs == i)[0])
            b = np.array([len(item) for item in temp])
            c = np.argsort(b)[::-1]
            for i in range(0, len(c)):
                health['disconnected_clusters'].append(temp[c[i]])
                if i > 0:
                    health['trim_pores'].extend(temp[c[i]])

        # Check for duplicate throats
        am = net.create_adjacency_matrix(fmt='csr', triu=True).tocoo()
        hits = np.where(am.data > 1)[0]
        if len(hits):
            mergeTs = []
            hits = np.vstack((am.row[hits], am.col[hits])).T
            ihits = hits[:, 0] + 1j*hits[:, 1]
            conns = net['throat.conns']
            iconns = conns[:, 0] + 1j*conns[:, 1]  # Convert to imaginary
            for item in ihits:
                mergeTs.append(np.where(iconns == item)[0])
            health['duplicate_throats'] = mergeTs

        # Check for bidirectional throats
        adjmat = net.create_adjacency_matrix(fmt='coo')
        num_full = adjmat.sum()
        temp = sprs.triu(adjmat, k=1)
        num_upper = temp.sum()
        if num_full > num_upper:
            biTs = np.where(net['throat.conns'][:, 0] >
                            net['throat.conns'][:, 1])[0]
            health['bidirectional_throats'] = biTs.tolist()

        return health

    def _regenerate_models(self, objs=[], propnames=[]):
        r"""
        Can be used to regenerate models across all objects in the project.

        Parameters
        ----------
        objs : list of OpenPNM objects
            Can be used to specify which specific objects to regenerate.  The
            default is to regenerate all objects.  If a subset of objects is
            given, this function ensure they are generated in a sensible order
            such as any phases are done before any physics objects.

        propnames : list of strings, or string
            The specific model to regenerate.  If none are given then ALL
            models on all objects are regenerated.  If a subset is given,
            then only object that have a corresponding model are regenerated,
            to avoid any problems.  This means that a single model can be
            given, without specifying the objects.

        """
        objs = list(objs)
        if objs == []:
            objs = self
        if type(propnames) is str:
            propnames = [propnames]
        # Sort objs in the correct order (geom, phase, phys)
        net = [i for i in objs if i is self.network]
        geoms = [i for i in objs if i in self.geometries().values()]
        phases = [i for i in objs if i in self.phases().values()]
        phys = [i for i in objs if i in self.physics().values()]
        objs = net + geoms + phases + phys
        for obj in objs:
            if len(propnames):
                for model in propnames:
                    if model in obj.models.keys():
                        obj.regenerate_models(propnames=model)
            else:
                obj.regenerate_models()

    def get_grid(self, astype='table'):
        from pandas import DataFrame as df
        geoms = self.geometries().keys()
        phases = [p.name for p in self.phases().values() if not hasattr(p, 'mixture')]
        grid = df(index=geoms, columns=phases)
        for r in grid.index:
            for c in grid.columns:
                phys = self.find_physics(phase=self[c], geometry=self[r])
                if phys is not None:
                    grid.loc[r][c] = phys.name
                else:
                    grid.loc[r][c] = '---'
        if astype == 'pandas':
            pass
        elif astype == 'dict':
            grid = grid.to_dict()
        elif astype == 'table':
            from terminaltables import SingleTable
            headings = [self.network.name] + list(grid.keys())
            g = [headings]
            for row in list(grid.index):
                g.append([row] + list(grid.loc[row]))
            grid = SingleTable(g)
            grid.title = 'Project: ' + self.name
            grid.padding_left = 3
            grid.padding_right = 3
            grid.justify_columns = {col: 'center' for col in range(len(headings))}
        elif astype == 'grid':
            grid = ProjectGrid()
        return grid

    @property
    def grid(self):
        grid = self.get_grid(astype='table')
        obj = ProjectGrid(grid)
        return obj


class Grid():

    def __init__(self, table):
        self.grid = table

    def index(self):
        index = [row[0] for row in self.grid.table_data[1:]]
        return index

    def header(self):
        columns = self.grid.table_data[0][1:]
        return columns

    def row(self, name):
        for row in self.grid.table_data:
            if row[0].startswith(name):
                return row
        else:
            raise ValueError(name + 'is not in list')

    def col(self, name):
        # Find column number
        index = self.grid.table_data[0].index(name)
        col = []
        for row in self.grid.table_data:
            col.append(row[index])
        return col

    def __str__(self):
        s = self.grid.table.__str__()
        return s


class ProjectGrid(Grid):
    r"""
    This is a subclass of Grid, which adds the ability to lookup by geometries
    and phases, as more specific versions of rows and cols
    """

    def geometries(self):
        return self.index()

    def phases(self):
        return self.header()