LoopStructural 1.0.9__cp36-cp36m-win32.whl

LoopStructural/modelling/features/geological_feature_builder.py

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+"""
+Feature builder
+"""
+import copy
+import logging
+
+import numpy as np
+import pandas as pd
+
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
+
+from LoopStructural.utils.helper import xyz_names, val_name, normal_vec_names, \
+    weight_name, gradient_vec_names, tangent_vec_names, interface_name
+from LoopStructural.modelling.features import GeologicalFeature
+from LoopStructural.utils.helper import get_data_bounding_box_map as get_data_bounding_box
+from LoopStructural.utils import get_data_axis_aligned_bounding_box
+from LoopStructural.utils import RegionEverywhere
+
+class GeologicalFeatureInterpolator:
+    """[summary]
+
+    [extended_summary]
+    """
+    def __init__(self, interpolator, name='Feature', region=None, **kwargs):
+        """
+        Constructor for a GeologicalFeatureInterpolator
+
+        Parameters
+        ----------
+        interpolator : GeologicalInterpolator
+            An empty GeologicalInterpolator
+        region : lambda function
+            defining whether the location (xyz) should be included in the
+        kwargs - name of the feature, region to interpolate the feature
+        """
+        self._interpolator = interpolator
+        self._name = name
+        self._interpolator.set_property_name(self._name)
+        # everywhere region is just a lambda that returns true for all locations
+        if region is None:
+            self.region = RegionEverywhere()
+        else:
+            self.region = region
+        header = xyz_names()+val_name()+gradient_vec_names()+\
+                 normal_vec_names()+tangent_vec_names()+weight_name()
+        self.data = pd.DataFrame(columns=header)
+        self.faults = []
+        self.data_added = False
+        self._interpolator.set_region(region=self.region)
+        self._feature = None
+        self._up_to_date = False
+        self._build_arguments = {}
+        self.fold = None
+        self._feature = GeologicalFeature(self._name,
+                                 self._interpolator,
+                                 builder=self, 
+                                 region=self.region,
+                                 faults=self.faults,
+                                 fold = self.fold
+                                 )
+        self._orthogonal_features = {}
+    @property
+    def feature(self):
+        return self._feature
+
+    @property
+    def build_arguments(self):
+        return self._build_arguments 
+    
+    @build_arguments.setter
+    def build_arguments(self, build_arguments):
+        # self._build_arguments = {}
+        for k, i in build_arguments.items():
+            self._build_arguments[k] = i
+
+    def update(self):
+        self.build(**self.build_arguments)
+    @property
+    def name(self):
+        return self._name
+    @property
+    def interpolator(self):
+        return self._interpolator
+
+    def up_to_date(self):
+        #has anything changed in the builder since we built the feature? if so update
+        if self._up_to_date == False:
+            self.update()
+        #check if the interpolator is up to date, if not solve
+        if self._interpolator.up_to_date == False:
+            self.update()
+        
+        
+    def add_fault(self, fault):
+        """
+        Add a fault to the geological feature builder
+
+        Parameters
+        ----------
+        fault : FaultSegment
+            A faultsegment to add to the geological feature
+
+        Returns
+        -------
+
+        """
+        self._up_to_date = False
+        self.faults.append(fault)
+
+    def add_data_from_data_frame(self, data_frame, overwrite = False):
+        """
+        Extract data from a pandas dataframe with columns for
+
+        Parameters
+        ----------
+        data_frame : pd.DataFrame
+            a dataframe containing the data to be added
+
+        Returns
+        -------
+
+        """
+        self.data = data_frame.copy()
+
+    def add_orthogonal_feature(self, feature, w=1., region=None,step=1,B=0):
+        """
+        Add a constraint to the interpolator so that the gradient of an exisitng feature is orthogonal
+        to the feature being built. E.g. dot product between gradients should be = 0
+
+        Parameters
+        ----------
+        feature : GeologicalFeature
+            feature which we want to be orthogonal to
+        w :  double
+            how much to weight in least squares sense
+        region : unused
+        step : int
+            numpy slicing step size to see how many tetras to add
+        
+        Returns
+        -------
+
+        Notes
+        -----
+        The constraint can be applied to a random subset of the tetrahedral elements in the mesh
+        in theory this shu
+        """
+        self._orthogonal_features[feature.name] = [feature,w,region,step,B]
+        self._up_to_date = False
+        
+    
+    def add_data_to_interpolator(self, constrained=False, force_constrained=False, **kwargs):
+        """
+        Iterates through the list of data and applies any faults active on the
+        data in the order they are added
+
+        Parameters
+        -----------
+        constrained : boolean
+        force_constrained : boolean
+
+        Returns
+        -------
+
+        """
+        # first move the data for the fault
+        logger.info("Adding %i faults to %s" % (len(self.faults), self.name))
+        data = self.data.copy()
+        # convert data locations to numpy array and then update
+        for f in self.faults:
+            data.loc[:,xyz_names()] = f.apply_to_points(
+                self.get_data_locations())
+        # Now check whether there are enough constraints for the
+        # interpolator to be able to solve
+        # we need at least 2 different value points or a single norm
+        # constraint. If there are not enough
+        # try converting grad to norms, if still not enough send user an error
+        if constrained:
+            # Change normals to gradients
+            mask = np.all(~np.isnan(data.loc[:, normal_vec_names()]),axis=1)
+            if mask.shape[0] > 0:
+                data.loc[mask, gradient_vec_names()] = data.loc[mask,
+                                                            normal_vec_names()].to_numpy()
+                data.loc[mask, normal_vec_names()] = np.nan
+        if self.get_norm_constraints().shape[0] > 0:
+            constrained = True
+
+        if np.unique(self.get_value_constraints()[:,3]).shape[0]>1:
+            constrained = True
+
+        if not constrained or force_constrained:
+            # change gradient constraints to normal vector constraints
+            mask = np.all(~np.isnan(data.loc[:, gradient_vec_names()]), axis=1)
+            if mask.shape[0] > 0:
+
+                data.loc[mask, normal_vec_names()] = data.loc[mask,
+                                                            gradient_vec_names()].to_numpy()
+                data.loc[mask, gradient_vec_names()] = np.nan
+                logger.info(
+                    "Setting gradient points to norm constraints")
+                constrained = True
+                mask = np.all(
+                    ~np.isnan(data.loc[:, normal_vec_names()].to_numpy()),
+                    axis=1)
+
+        if not constrained:
+            logger.error("Not enough constraints for scalar field add more")
+        # self.interpolator.reset()
+        mask = ~np.isnan(data.loc[:,val_name()].to_numpy())
+        # add value constraints
+        if mask.shape[0]>0:
+            value_data = data.loc[mask[:,0],xyz_names()+val_name()+weight_name()].to_numpy()
+            self.interpolator.set_value_constraints(value_data)
+
+        # add gradient constraints
+        mask = np.all(~np.isnan(data.loc[:, gradient_vec_names()].to_numpy()), axis=1)
+        if mask.shape[0]>0:
+            gradient_data = data.loc[
+            mask, xyz_names() + gradient_vec_names() + weight_name()].to_numpy()
+            self.interpolator.set_gradient_constraints(gradient_data)
+
+        # add normal vector data
+        mask = np.all(~np.isnan(data.loc[:, normal_vec_names()].to_numpy()), axis=1)
+        if mask.shape[0]>0:
+            normal_data = data.loc[
+                mask, xyz_names() + normal_vec_names() + weight_name()].to_numpy()
+            self.interpolator.set_normal_constraints(normal_data)
+
+        # add tangent data
+        mask = np.all(~np.isnan(data.loc[:, tangent_vec_names()].to_numpy()), axis=1)
+        if mask.shape[0]>0:
+            tangent_data = data.loc[
+                mask, xyz_names() + tangent_vec_names() + weight_name()].to_numpy()
+            self.interpolator.set_tangent_constraints(tangent_data)
+
+        # add interface constraints
+        mask = np.all(~np.isnan(data.loc[:, interface_name()].to_numpy()), axis=1)
+        if mask.shape[0] > 0:
+            interface_data = data.loc[
+                mask, xyz_names() + interface_name() + weight_name()].to_numpy()
+            self.interpolator.set_interface_constraints(interface_data)
+
+        self.data_added = True
+        self._up_to_date = False
+    
+    def install_gradient_constraint(self):
+        for g in self._orthogonal_features.values():
+            feature,w,region,step,B = g
+            vector = feature.evaluate_gradient(self.interpolator.support.barycentre())
+            vector /= np.linalg.norm(vector,axis=1)[:,None]
+            element_idx = np.arange(self.interpolator.support.n_elements)
+            np.random.shuffle(element_idx)
+            self.interpolator.add_gradient_orthogonal_constraint(
+                self.interpolator.support.barycentre()[element_idx[::step],:],
+                vector[element_idx[::step],:],
+                w=w,
+                B=B
+            )
+    def get_value_constraints(self):
+        """
+        Get the value constraints for this geological feature
+
+        Returns
+        -------
+        np.array((N,4),dtype=double)
+        """
+        header = xyz_names()+val_name()+weight_name()
+        mask = ~np.isnan(self.data.loc[:,val_name()].to_numpy())
+        return self.data.loc[mask[:,0],header].to_numpy()
+
+    def get_gradient_constraints(self):
+        """
+        Get the gradient direction constraints
+
+        Returns
+        -------
+        numpy array
+        """
+        mask = np.all(
+            ~np.isnan(self.data.loc[:, gradient_vec_names()].to_numpy()),
+            axis=1)
+        if mask.shape[0] > 0:
+            return self.data.loc[
+                mask, xyz_names() + gradient_vec_names() + weight_name(
+                )].to_numpy()
+        else:
+            return np.zeros((0, 7))
+
+    def get_tangent_constraints(self):
+        """
+
+        Returns
+        -------
+        numpy array
+        """
+        mask = np.all(
+            ~np.isnan(self.data.loc[:, tangent_vec_names()].to_numpy()),
+            axis=1)
+        if mask.shape[0] > 0:
+            return self.data.loc[
+                mask, xyz_names() + tangent_vec_names() + weight_name(
+                )].to_numpy()
+        else:
+            return np.zeros((0, 7))
+
+    def get_norm_constraints(self):
+        """
+        Get the gradient norm constraints
+
+        Returns
+        -------
+        numpy array
+        """
+        mask = np.all(~np.isnan(self.data.loc[:, normal_vec_names()].to_numpy()),
+                      axis=1)
+        if mask.shape[0] > 0:
+            return self.data.loc[
+                mask, xyz_names() + normal_vec_names() + weight_name(
+
+                )].to_numpy()
+        else:
+            return np.zeros((0,7))
+
+    def get_interface_constraints(self):
+        mask = np.all(~np.isnan(self.data.loc[:, interface_name()].to_numpy()), axis=1)
+        if mask.shape[0] > 0:
+            return self.data.loc[
+                mask, xyz_names() + interface_name() + weight_name()].to_numpy()
+        else:
+            return np.zeros((0,5))
+
+    def get_data_locations(self):
+        """
+        Get only the location for all data points
+
+        Returns
+        -------
+
+        """
+        return self.data.loc[:, xyz_names()].to_numpy()
+    def set_interpolation_geometry(self,origin,maximum):
+        """Update the interpolation support geometry to new bounding box
+
+        Parameters
+        ----------
+        origin : np.array(3)
+            origin vector
+        maximum : np.array(3)
+            maximum vector
+        """
+        logger.info("Setting mesh origin: {} {} {} ".format(origin[0],origin[1],origin[2]))
+        logger.info("Setting mesh maximum: {} {} {}".format(maximum[0],maximum[1],maximum[2]))
+        self.interpolator.support.origin = origin
+        self.interpolator.support.maximum = maximum
+
+
+        self._up_to_date = False
+
+    def build(self, fold=None, fold_weights={}, data_region=None, **kwargs):
+        """
+        Runs the interpolation and builds the geological feature
+
+        Parameters
+        ----------
+        fold : FoldEvent
+        fold_weights : dict
+        data_region : double <1
+            If not none adds a region around the data points to the interpolation
+            with data_region as a buffer
+        kwargs
+
+        Returns
+        -------
+
+        """
+
+
+        self.add_data_to_interpolator(**kwargs)
+        if data_region is not None:
+            xyz = self.interpolator.get_data_locations()
+            bb, region = get_data_bounding_box(xyz, data_region)    
+            # if self.model.reuse_supports == False:
+            if np.any(np.min(bb[0,:])< self.interpolator.support.origin):
+                neworigin = np.min([self.interpolator.support.origin,bb[0,:]],axis=0)
+                logger.info("Changing origin of support for {} from {} {} {} to {} {} {}"\
+                                .format(self.name,self.interpolator.support.origin[0],\
+                                    self.interpolator.support.origin[1],self.interpolator.support.origin[2],\
+                                                neworigin[0],neworigin[1],neworigin[2]))
+                self.interpolator.support.origin = neworigin
+            if np.any(np.max(bb[0,:])< self.interpolator.support.maximum):
+                newmax = np.max([self.interpolator.support.maximum,bb[0,:]],axis=0)
+                logger.info("Changing origin of support for {} from {} {} {} to {} {} {}"\
+                        .format(self.name,self.interpolator.support.maximum[0],
+                        self.interpolator.support.maximum[1],self.interpolator.support.maximum[2],\
+                                                newmax[0],newmax[1],newmax[2]))
+
+                self.interpolator.support.maximum = newmax
+            self.interpolator.set_region(region=region)
+        # moving this to init because it needs to be done before constraints
+        # are added?
+        if fold is not None:
+            logger.info("Adding fold to %s" % self.name)
+            self.interpolator.fold = fold
+            # if we have fold weights use those, otherwise just use default
+            self.interpolator.add_fold_constraints(**fold_weights)
+            if 'cgw' not in kwargs:
+                # try adding very small cg
+                kwargs['cgw'] = 0.0
+        self.install_gradient_constraint()
+        self.interpolator.setup_interpolator(**kwargs)
+        self.interpolator.solve_system(**kwargs)
+        self._up_to_date = True
+        return self._feature

LoopStructural/modelling/features/lambda_geological_feature.py

@@ -0,0 +1,36 @@
+"""
+Geological features
+"""
+import logging
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+class LambdaGeologicalFeature:
+    def __init__(self,function = None,name = 'unnamed_lambda', gradient_function = None, model = None):
+        self.function = function
+        self.name = name
+        self.gradient_function = gradient_function
+        self.model = model
+    def evaluate_value(self, xyz):
+        v = np.zeros((xyz.shape[0]))
+        if self.function is None:
+            v[:] =  np.nan
+        else:
+            v[:] = self.function(xyz)
+        return v
+    def evaluate_gradient(self,xyz):
+        v = np.zeros((xyz.shape[0],3))
+        if self.gradient_function is None:
+            v[:,:] =  np.nan
+        else:
+            v[:,:] = self.gradient_function(xyz)
+        return v
+    def min(self):
+        return 0
+    def max(self):
+        return 0
+
+    

LoopStructural/modelling/features/region_feature.py

@@ -0,0 +1,34 @@
+class RegionFeature:
+    """
+    """
+    def __init__(self, function):
+        """
+        Create a GeologicalFeature to represent a region in a model
+        The region is defined by a boolean function on position.
+
+        Parameters
+        ----------
+        function lambda function
+            lambda function true inside region, false outside region
+        
+        """
+        self.function = function
+        self.name = 'region'
+
+    def evaluate_value(self, pos):
+        return self.function(pos).astype(float)
+
+    def mean(self):
+        return 0
+
+    def max(self):
+        return 1
+
+    def min(self):
+        return -1
+
+    def name(self):
+        return self.name
+
+# class VectorFeature:
+#     def __init__(self, function)

LoopStructural/modelling/features/structural_frame.py

@@ -0,0 +1,133 @@
+"""
+Structural frames
+"""
+import logging
+import numpy as np
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
+
+
+class StructuralFrame:
+    """[summary]
+
+    [extended_summary]
+    """
+    def __init__(self, name, features, fold=None):
+        """
+        Structural frame is a curvilinear coordinate system defined by
+        structural observations associated with a fault or fold.
+
+        Parameters
+        ----------
+        name - name of the structural frame
+        features - list of features to build the frame with
+        """
+        self.name = name
+        self.features = features
+        self.data = None
+        self.fold = fold
+
+    def __getitem__(self, item):
+        """
+
+        Parameters
+        ----------
+        item index of feature to access
+
+        Returns
+        -------
+        the structural frame geological feature
+        """
+        return self.features[item]
+
+    def set_model(self, model):
+        """Link the model that created the frame to the frame
+        and the features that make up the frame 
+
+        Parameters
+        ----------
+        model : GeologicalModel
+            the geological model that created the fold frame
+        """
+        self.model = model
+        for f in self.features:
+            if f is None:
+                continue    
+            f.set_model(model)
+
+    def add_region(self, region):
+        for i in range(3):
+            self.features[i].add_region(region)
+
+    def get_feature(self, i):
+        """
+        Return the ith feature
+
+        Parameters
+        ----------
+        i
+
+        Returns
+        -------
+
+        """
+        return self.features[i]
+
+    def set_data(self, data):
+        """
+        Associate data with structural frame
+
+        Parameters
+        ----------
+        data
+
+        Returns
+        -------
+
+        """
+        self.data = data
+
+    def evaluate_value(self, evaluation_points):
+        """
+        Evaluate the value of the structural frame for the points.
+        Can optionally only evaluate one coordinate
+
+        Parameters
+        ----------
+        evaluation_points
+        i
+
+        Returns
+        -------
+
+        """
+        v = np.zeros(evaluation_points.shape) #create new 3d array of correct length
+        v[:] = np.nan
+        v[:,0] = self.features[0].evaluate_value(evaluation_points)
+        v[:,1] = self.features[1].evaluate_value(evaluation_points)
+        v[:,2] = self.features[2].evaluate_value(evaluation_points)
+        return v
+        
+    def evaluate_gradient(self, evaluation_points, i=None):
+        """
+        Evaluate the gradient of the structural frame.
+        Can optionally only evaluate the ith coordinate
+
+        Parameters
+        ----------
+        evaluation_points
+        i
+
+        Returns
+        -------
+
+        """
+        if i is not None:
+            return self.features[i].support.evaluate_gradient(
+                evaluation_points)
+        return (self.features[0].support.evaluate_gradient(evaluation_points),
+                self.features[1].support.evaluate_gradient(evaluation_points),
+                self.features[2].support.evaluate_gradient(evaluation_points))
+
+
+