LoopStructural 1.0.4__zip

Miniconda/envs/loop/Lib/site-packages/LoopStructural/interpolators/finite_difference_interpolator.py

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+"""
+FiniteDifference interpolator
+"""
+import logging
+
+import numpy as np
+
+from LoopStructural.utils.helper import get_vectors
+from .discrete_interpolator import DiscreteInterpolator
+from .operator import Operator
+
+logger = logging.getLogger(__name__)
+
+
+class FiniteDifferenceInterpolator(DiscreteInterpolator):
+    """
+
+    """
+
+    def __init__(self, grid):
+        """
+        Finite difference interpolation on a regular cartesian grid
+
+        Parameters
+        ----------
+        grid : StructuredGrid
+        """
+        self.shape = 'rectangular'
+        DiscreteInterpolator.__init__(self, grid)
+        # default weights for the interpolation matrix are 1 in x,y,z and
+        # 1/
+        self.set_interpolation_weights({'dxy': .7,
+                                      'dyz': .7,
+                                      'dxz': .7,
+                                      'dxx': 1.,
+                                      'dyy': 1.,
+                                      'dzz': 1.,
+                                      'dx': 1.,
+                                      'dy': 1.,
+                                      'dz': 1.,
+                                      'cpw': 1.,
+                                      'gpw': 1.,
+                                      'npw': 1.,
+                                      'tpw': 1.})
+
+        self.vol = grid.step_vector[0] * grid.step_vector[1] * \
+                   grid.step_vector[2]
+
+    def _setup_interpolator(self, **kwargs):
+        """
+
+        Parameters
+        ----------
+        kwargs
+            possible kwargs are weights for the different masks and masks.
+
+        Notes
+        -----
+        Default masks are the second derivative in x,y,z direction and the second derivative of x wrt
+        y and y wrt z and z wrt x. Custom masks can be used by specifying the operator as a 3d numpy array
+        e.g. [ [ [ 0 0 0 ]
+                 [ 0 1 0 ]
+                 [ 0 0 0 ] ]
+                 [ [ 1 1 1 ]
+                 [ 1 1 1 ]
+                 [ 1 1 1 ] ]
+                 [ [ 0 0 0 ]
+                 [ 0 1 0 ]
+                 [ 0 0 0 ] ]
+
+        Returns
+        -------
+
+        """
+
+        for key in kwargs:
+            self.up_to_date = False
+            if 'regularisation' in kwargs:
+                self.interpolation_weights['dxy'] = kwargs[
+                                                        'regularisation'] * 0.7
+                self.interpolation_weights['dyz'] = kwargs[
+                                                        'regularisation'] * 0.7
+                self.interpolation_weights['dxz'] = kwargs[
+                                                        'regularisation'] * 0.7
+                self.interpolation_weights['dxx'] = kwargs[
+                                                        'regularisation'] * 1.
+                self.interpolation_weights['dyy'] = kwargs[
+                                                        'regularisation'] * 1.
+                self.interpolation_weights['dzz'] = kwargs[
+                                                        'regularisation'] * 1.
+            self.interpolation_weights[key] = kwargs[key]
+        # if we want to define the operators manually
+        if 'operators' in kwargs:
+            for n, o in kwargs['operators'].items():
+                self.assemble_inner(o[0], o[1])
+        # otherwise just use defaults
+        if 'operators' not in kwargs:
+            operator = Operator.Dxy_mask
+
+            self.assemble_inner(operator, np.sqrt(2 * self.vol) *
+                                self.interpolation_weights['dxy'])
+            operator = Operator.Dyz_mask
+            self.assemble_inner(operator, np.sqrt(2 * self.vol) *
+                                self.interpolation_weights['dyz'])
+            operator = Operator.Dxz_mask
+            self.assemble_inner(operator, np.sqrt(2 * self.vol) *
+                                self.interpolation_weights['dxz'])
+            operator = Operator.Dxx_mask
+            self.assemble_inner(operator,
+                                np.sqrt(self.vol) * self.interpolation_weights[
+                                    'dxx'])
+            operator = Operator.Dyy_mask
+            self.assemble_inner(operator,
+                                np.sqrt(self.vol) * self.interpolation_weights[
+                                    'dyy'])
+            operator = Operator.Dzz_mask
+            self.assemble_inner(operator,
+                                np.sqrt(self.vol) * self.interpolation_weights[
+                                    'dzz'])
+        self.add_norm_constraint(
+            np.sqrt(self.vol) * self.interpolation_weights['npw'])
+        self.add_gradient_constraint(
+            np.sqrt(self.vol) * self.interpolation_weights['gpw'])
+        self.add_vaue_constraint(
+            np.sqrt(self.vol) * self.interpolation_weights['cpw'])
+        self.add_tangent_ctr_pts(
+            np.sqrt(self.vol) * self.interpolation_weights['tpw']
+        )
+
+    def copy(self):
+        """
+        Create a new identical interpolator
+
+        Returns
+        -------
+        returns a new empy interpolator from the same support
+        """
+        return FiniteDifferenceInterpolator(self.support)
+
+    def add_vaue_constraint(self, w=1.):
+        """
+
+        Parameters
+        ----------
+        w : double or numpy array
+
+        Returns
+        -------
+
+        """
+
+        points = self.get_value_constraints()
+        # check that we have added some points
+        if points.shape[0] > 0:
+            node_idx, inside = self.support.position_to_cell_corners(
+                points[:, :3])
+            # print(points[inside,:].shape)
+
+            gi = np.zeros(self.support.n_nodes)
+            gi[:] = -1
+            gi[self.region] = np.arange(0, self.nx)
+            idc = np.zeros(node_idx.shape)
+            idc[:] = -1
+
+            idc[inside, :] = gi[node_idx[inside, :]]
+            inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
+            a = self.support.position_to_dof_coefs(points[inside, :3])
+            # a*=w
+
+            self.add_constraints_to_least_squares(a.T * w,
+                                                  points[inside, 3] * w,
+                                                  idc[inside, :])
+
+    def add_gradient_constraint(self, w=1.):
+        """
+
+        Parameters
+        ----------
+        w : double / numpy array
+
+        Returns
+        -------
+
+        """
+
+        points = self.get_gradient_constraints()
+        if points.shape[0] > 0:
+            # calculate unit vector for orientation data
+            # points[:,3:]/=np.linalg.norm(points[:,3:],axis=1)[:,None]
+
+            node_idx, inside = self.support.position_to_cell_corners(
+                points[:, :3])
+            # calculate unit vector for node gradients
+            # this means we are only constraining direction of grad not the
+            # magnitude
+            gi = np.zeros(self.support.n_nodes)
+            gi[:] = -1
+            gi[self.region] = np.arange(0, self.nx)
+            idc = np.zeros(node_idx.shape)
+            idc[:] = -1
+            idc[inside, :] = gi[node_idx[inside, :]]
+            inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
+
+            T = self.support.calcul_T(points[inside, :3])
+            strike_vector, dip_vector = get_vectors(points[inside, 3:6])
+            A = np.einsum('ij,ijk->ik', strike_vector.T, T)
+
+            B = np.zeros(points[inside, :].shape[0])
+            self.add_constraints_to_least_squares(A * w, B, idc[inside, :])
+            A = np.einsum('ij,ijk->ik', dip_vector.T, T)
+            self.add_constraints_to_least_squares(A * w, B, idc[inside, :])
+
+    def add_norm_constraint(self, w=1.):
+        """
+        Add constraints to control the norm of the gradient of the scalar field
+
+        Parameters
+        ----------
+        w : double
+            weighting of this constraint (double)
+
+        Returns
+        -------
+
+        """
+        points = self.get_norm_constraints()
+        if points.shape[0] > 0:
+            # calculate unit vector for orientation data
+            # points[:,3:]/=np.linalg.norm(points[:,3:],axis=1)[:,None]
+
+            node_idx, inside = self.support.position_to_cell_corners(
+                points[:, :3])
+            gi = np.zeros(self.support.n_nodes)
+            gi[:] = -1
+            gi[self.region] = np.arange(0, self.nx)
+            idc = np.zeros(node_idx.shape)
+            idc[:] = -1
+            idc[inside, :] = gi[node_idx[inside, :]]
+            inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
+
+            # calculate unit vector for node gradients
+            # this means we are only constraining direction of grad not the
+            # magnitude
+            T = self.support.calcul_T(points[inside, :3])
+
+            w /= 3
+            self.add_constraints_to_least_squares(T[:, 0, :] * w,
+                                                  points[inside, 3] * w,
+                                                  idc[inside, :])
+            self.add_constraints_to_least_squares(T[:, 1, :] * w,
+                                                  points[inside, 4] * w,
+                                                  idc[inside, :])
+            self.add_constraints_to_least_squares(T[:, 2, :] * w,
+                                                  points[inside, 5] * w,
+                                                  idc[inside, :])
+
+    def add_gradient_orthogonal_constraint(self, points, vector, w=1.0,
+                                           B=0):
+        """
+        constraints scalar field to be orthogonal to a given vector
+
+        Parameters
+        ----------
+        elements : np.array
+        normals : np.array
+        w : double
+        B : np.array
+
+        Returns
+        -------
+
+        """
+        if points.shape[0] > 0:
+            # calculate unit vector for orientation data
+            # points[:,3:]/=np.linalg.norm(points[:,3:],axis=1)[:,None]
+
+            node_idx, inside = self.support.position_to_cell_corners(
+                points[:, :3])
+            # calculate unit vector for node gradients
+            # this means we are only constraining direction of grad not the
+            # magnitude
+            gi = np.zeros(self.support.n_nodes)
+            gi[:] = -1
+            gi[self.region] = np.arange(0, self.nx)
+            idc = np.zeros(node_idx.shape)
+            idc[:] = -1
+
+            idc[inside, :] = gi[node_idx[inside, :]]
+            inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
+
+            T = self.support.calcul_T(points[inside, :3])
+            A = np.einsum('ij,ijk->ik', vector[inside, :3], T)
+
+            B = np.zeros(points[inside, :].shape[0])
+            self.add_constraints_to_least_squares(A * w, B, idc[inside, :])
+
+    def add_regularisation(self, operator, w=0.1):
+        """
+
+        Parameters
+        ----------
+        operator
+        w
+
+        Returns
+        -------
+
+        """
+        self.assemble_inner(operator)
+        # self.assemble_borders()
+
+    def assemble_inner(self, operator, w):
+        """
+
+        Parameters
+        ----------
+        operator : Operator
+        w : double
+
+        Returns
+        -------
+
+        """
+        # First get the global indicies of the pairs of neighbours this should be an
+        # Nx27 array for 3d and an Nx9 array for 2d
+
+        global_indexes = self.support.neighbour_global_indexes()  # np.array([ii,jj]))
+
+        a = np.tile(operator.flatten(), (global_indexes.shape[1], 1))
+        idc = global_indexes.T
+
+        gi = np.zeros(self.support.n_nodes)
+        gi[:] = -1
+        gi[self.region] = np.arange(0, self.nx)
+        idc = gi[idc]
+        inside = ~np.any(idc == -1, axis=1)
+        B = np.zeros(global_indexes.shape[1])
+        self.add_constraints_to_least_squares(a[inside, :] * w,
+                                              B[inside],
+                                              idc[inside, :]
+                                              )
+        return

Miniconda/envs/loop/Lib/site-packages/LoopStructural/interpolators/geological_interpolator.py

@@ -0,0 +1,190 @@
+"""
+Base geological interpolator
+"""
+import logging
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+class GeologicalInterpolator:
+    """
+    Attributes
+    ----------
+    data : dict
+        a dictionary with np.arrays for gradient, value, normal, tangent data
+    """
+    def __init__(self):
+        """
+        This class is the base class for a geological interpolator and contains all of the
+        main interface functions. Any class that is inheriting from this should be callable
+        by using any of these functions. This will enable interpolators to be interchanged.
+        """
+
+        self.data = {'gradient': np.zeros((0,7)),
+                     'value' : np.zeros((0,5)),
+                     'normal': np.zeros((0,7)),
+                     'tangent': np.zeros((0,7)),
+                     'interface' : np.zeros((0,5))
+                     }
+        self.n_g = 0
+        self.n_i = 0
+        self.n_n = 0
+        self.n_t = 0
+
+        self.type = 'undefined'
+        self.up_to_date = False
+        self.constraints = []
+        self.propertyname = 'defaultproperty'
+        self.__str = 'Base Geological Interpolator'
+
+    def __str__(self):
+        
+        return self.__str
+
+    def set_region(self,**kwargs):
+        pass
+
+    def set_property_name(self, name):
+        """
+        Set the name of the interpolated property
+        Parameters
+        ----------
+        name : string
+            name of the property to be saved on a mesh
+
+        Returns
+        -------
+
+        """
+        self.propertyname = name
+
+    def set_value_constraints(self, points):
+        """
+
+        Parameters
+        ----------
+        points
+
+        Returns
+        -------
+
+        """
+
+        self.data['value'] = points
+        self.n_i = points.shape[0]
+
+    def set_gradient_constraints(self, points):
+        """
+
+        Parameters
+        ----------
+        points
+
+        Returns
+        -------
+
+        """
+        self.n_g = points.shape[0]
+        self.data['gradient'] = points
+
+    def set_normal_constraints(self, points):
+        """
+
+        Parameters
+        ----------
+        points
+
+        Returns
+        -------
+
+        """
+        self.n_n = points.shape[0]
+        self.data['normal'] = points
+
+    def set_tangent_constraints(self, points):
+        """
+
+        Parameters
+        ----------
+        points
+
+        Returns
+        -------
+
+        """
+        self.data['tangent'] = points
+
+    def set_interface_constraints(self, points):
+        self.data['interface'] = points
+
+    def get_value_constraints(self):
+        """
+
+        Returns
+        -------
+        numpy array
+        """
+        return self.data['value']
+
+    def get_gradient_constraints(self):
+        """
+
+        Returns
+        -------
+        numpy array
+        """
+        return self.data['gradient']
+
+
+    def get_tangent_constraints(self):
+        """
+
+        Returns
+        -------
+        numpy array
+        """
+
+        return self.data['tangent']
+
+    def get_norm_constraints(self):
+        """
+
+        Returns
+        -------
+        numpy array
+        """
+        return self.data['normal']
+
+    def get_interface_constraints(self):
+        return self.data['interface']
+    def setup_interpolator(self, **kwargs):
+        """
+        Runs all of the required setting up stuff
+        """
+        self._setup_interpolator(**kwargs)
+
+    def solve_system(self, **kwargs):
+        """
+        Solves the interpolation equations
+        """
+        self._solve(**kwargs)
+        self.up_to_date = True
+
+    def update(self):
+        return False
+
+    def reset(self):
+        """
+        Removes all of the data from an interpolator
+
+        Returns
+        -------
+
+        """
+        self.n_g = 0
+        self.n_i = 0
+        self.n_n = 0
+        self.n_t = 0
+

Miniconda/envs/loop/Lib/site-packages/LoopStructural/interpolators/operator.py

@@ -0,0 +1,60 @@
+"""
+Finite difference masks
+"""
+import logging
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+class Operator(object):
+    """
+
+    """
+    z = np.zeros((3, 3))
+    Dx_mask = np.array([z, [
+        [0.0, 0.0, 0.0],
+        [-0.5, 0.0, 0.5],
+        [0.0, 0.0, 0.0]], z
+                        ])
+    Dy_mask = Dx_mask.swapaxes(1, 2)
+    Dz_mask = Dx_mask.swapaxes(0, 2)
+
+    Dxx_mask = np.array([z, [
+        [0, 0, 0],
+        [1, -2, 1],
+        [0, 0, 0]], z])
+    Dyy_mask = Dxx_mask.swapaxes(1, 2)
+    Dzz_mask = Dxx_mask.swapaxes(0, 2)
+
+    Dxy_mask = np.array([z, [
+        [-0.25, 0, 0.25],
+        [0, 0, 0],
+        [0.25, 0, -0.25]
+    ], z])
+    Dxz_mask = Dxy_mask.swapaxes(0, 1)
+    Dyz_mask = Dxy_mask.swapaxes(0, 2)
+
+    # from https://en.wikipedia.org/wiki/Discrete_Laplace_operator
+    Lapacian = np.array([[[0, 0, 0],
+                          [0, 1, 0],  # first plane
+                          [0, 0, 0]]
+                            , [[0, 1, 0],
+                               [1, -6, 1],  # second plane
+                               [0, 1, 0]],
+                         [[0, 0, 0],
+                          [0, 1, 0],  # third plane
+                          [0, 0, 0]]]
+                        )
+
+    #Hessian is 
+    # Dxx Dxy Dxz
+    # Dxy Dyy Dzy
+    # Dzx Dzy Dzz
+
+    #det of hessian
+    # Det_Hessian_operator = 
+    #             Dxx_mask.dot(Dyy_mask.dot(Dzz_mask)) - Dxx_mask.dot(Dyz_mask.dot(Dyz_mask) -
+    #             Dxy_mask.dot(Dxy_mask.dot(Dzz_mask)) - Dxy_mask.dot(Dxz_mask.dot(Dyz_mask)) +
+    #             Dxz_mask.dot(Dxy_mask.dot(Dyz_mask)) - Dxz_mask.dot(Dyy_mask.dot(Dxz_mask))