xtgeo 4.13.1__cp310-cp310-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl

xtgeo/well/wells.py

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+"""Wells module, which has the Wells class (collection of Well objects)"""
+
+from __future__ import annotations
+
+import pandas as pd
+
+from xtgeo.common.log import null_logger
+from xtgeo.common.xtgeo_dialog import XTGDescription, XTGeoDialog
+
+from . import _wells_utils
+from .well1 import Well, well_from_file
+
+xtg = XTGeoDialog()
+logger = null_logger(__name__)
+
+
+def wells_from_files(filelist, *args, **kwargs):
+    """Import wells from a list of files (filelist).
+
+    Creates a Wells object from a list of filenames. Remaining arguments are
+        the same as :func:`xtgeo.well_from_file`.
+
+    Args:
+        filelist (list of filenames): List with file names
+
+    Example:
+        Here the from_file method is used to initiate the object
+        directly::
+
+            >>> mywells = Wells(
+            ...     [well_dir + '/OP_1.w', well_dir + '/OP_2.w']
+            ... )
+    """
+    return Wells([well_from_file(wfile, *args, **kwargs) for wfile in filelist])
+
+
+class Wells:
+    """Class for a collection of Well objects, for operations that involves
+    a number of wells.
+
+    See also the :class:`xtgeo.well.Well` class.
+
+    Args:
+        wells: The list of Well objects.
+    """
+
+    def __init__(self, wells: list[Well] = None):
+        if wells is None:
+            self._wells = []
+        else:
+            self._wells = wells
+
+    @property
+    def names(self):
+        """Returns a list of well names (read only).
+
+        Example::
+
+            namelist = wells.names
+            for prop in namelist:
+                print ('Well name is {}'.format(name))
+
+        """
+        return [w.name for w in self._wells]
+
+    @property
+    def wells(self):
+        """Returns or sets a list of XTGeo Well objects, None if empty."""
+        if not self._wells:
+            return None
+
+        return self._wells
+
+    @wells.setter
+    def wells(self, well_list):
+        for well in well_list:
+            if not isinstance(well, Well):
+                raise ValueError("Well in list not valid Well object")
+
+        self._wells = well_list
+
+    def describe(self, flush=True):
+        """Describe an instance by printing to stdout"""
+
+        dsc = XTGDescription()
+        dsc.title(f"Description of {self.__class__.__name__} instance")
+        dsc.txt("Object ID", id(self))
+
+        dsc.txt("Wells", self.names)
+
+        if flush:
+            dsc.flush()
+            return None
+
+        return dsc.astext()
+
+    def __iter__(self):
+        return iter(self.wells)
+
+    def copy(self):
+        """Copy a Wells instance to a new unique instance (a deep copy)."""
+
+        return Wells(self._wells.copy())
+
+    def get_well(self, name):
+        """Get a Well() instance by name, or None"""
+
+        logger.debug("Asking for a well with name %s", name)
+        for well in self._wells:
+            if well.name == name:
+                return well
+        return None
+
+    # not having this as property but a get_ .. is intended, for flexibility
+    def get_dataframe(self, filled=False, fill_value1=-999, fill_value2=-9999):
+        """Get a big dataframe for all wells or blocked wells in instance,
+        with well name as first column
+
+        Args:
+            filled (bool): If True, then NaN's are replaces with values
+            fill_value1 (int): Only applied if filled=True, for logs that
+                have missing values
+            fill_value2 (int): Only applied if filled=True, when logs
+                are missing completely for that well.
+        """
+        logger.debug("Ask for big dataframe for all wells")
+
+        bigdflist = []
+        for well in self._wells:
+            dfr = well.get_dataframe()
+            dfr["WELLNAME"] = well.name
+            logger.debug(well.name)
+            if filled:
+                dfr = dfr.fillna(fill_value1)
+            bigdflist.append(dfr)
+
+        dfr = pd.concat(bigdflist, ignore_index=True, sort=True)
+        # the concat itself may lead to NaN's:
+        if filled:
+            dfr = dfr.fillna(fill_value2)
+
+        spec_order = [
+            "WELLNAME",
+            self._wells[0].xname,  # use the names in the first well as column names
+            self._wells[0].yname,
+            self._wells[0].zname,
+        ]
+        return dfr[spec_order + [col for col in dfr if col not in spec_order]]
+
+    def quickplot(self, filename=None, title="QuickPlot"):
+        """Fast plot of wells using matplotlib.
+
+        Args:
+            filename (str): Name of plot file; None will plot to screen.
+            title (str): Title of plot
+
+        """
+        import xtgeoviz.plot
+
+        mymap = xtgeoviz.plot.Map()
+
+        mymap.canvas(title=title)
+
+        mymap.plot_wells(self)
+
+        if filename is None:
+            mymap.show()
+        else:
+            mymap.savefig(filename)
+
+    def limit_tvd(self, tvdmin, tvdmax):
+        """Limit TVD to be in range tvdmin, tvdmax for all wells"""
+        for well in self.wells:
+            well.limit_tvd(tvdmin, tvdmax)
+
+    def downsample(self, interval=4, keeplast=True):
+        """Downsample by sampling every N'th element (coarsen only), all
+        wells.
+        """
+
+        for well in self.wells:
+            well.downsample(interval=interval, keeplast=keeplast)
+
+    def wellintersections(self, wfilter=None, showprogress=False):
+        """Get intersections between wells, return as dataframe table.
+
+        Notes on wfilter: A wfilter is settings to improve result. In
+        particular to remove parts of trajectories that are parallel.
+
+        wfilter = {'parallel': {'xtol': 4.0, 'ytol': 4.0, 'ztol':2.0,
+                                'itol':10, 'atol':2}}
+
+        Here xtol is tolerance in X coordinate; further Y tolerance,
+        Z tolerance, (I)nclination tolerance, and (A)zimuth tolerance.
+
+        Args:
+            tvdrange (tuple of floats): Search interval. One is often just
+                interested in the reservoir section.
+            wfilter (dict): A dictionrary for filter options, in order to
+                improve result. See example above.
+            showprogress (bool): Will show progress to screen if enabled.
+
+        Returns:
+            A Pandas dataframe object, with columns WELL, CWELL and UTMX UTMY
+                TVD coordinates for CWELL where CWELL crosses WELL,
+                and also MDEPTH for the WELL.
+        """
+
+        return _wells_utils.wellintersections(
+            self, wfilter=wfilter, showprogress=showprogress
+        )

xtgeo/xyz/__init__.py

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+"""The XTGeo xyz (points and polygons) package."""
+
+# flake8: noqa
+from xtgeo.xyz._xyz import XYZ
+from xtgeo.xyz.points import Points
+from xtgeo.xyz.polygons import Polygons

xtgeo/xyz/_polygons_oper.py

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+"""Various operations dedicated to Polygons class.
+
+First order functions here are:
+
+* boundary_from_points (input to class method)
+* simplify_polygons (instance method)
+
+
+Functions starting with '_' are local helper functions
+"""
+
+from __future__ import annotations
+
+from math import ceil
+
+import numpy as np
+import pandas as pd
+import shapely
+import shapely.geometry as sg
+from scipy.spatial import Delaunay, cKDTree
+from shapely.ops import polygonize
+
+import xtgeo
+from xtgeo.common.log import null_logger
+
+logger = null_logger(__name__)
+MINIMUM_NUMBER_POINTS = 4
+
+
+class BoundaryError(ValueError):
+    """Get error on not able to create a boundary."""
+
+
+def boundary_from_points(points, alpha_factor=1.0, alpha=None, concave=False):
+    """From a Point instance, make boundary polygons (generic)."""
+    if not isinstance(points, xtgeo.Points):
+        raise ValueError("The input points is not an instance of xtgeo.Points")
+
+    if points.nrow < MINIMUM_NUMBER_POINTS:
+        logger.info("No. points is %s, need >= %s", points.nrow, MINIMUM_NUMBER_POINTS)
+        raise ValueError(
+            "Too few points to derive a boundary, present is "
+            f"{points.nrow}, need at least {MINIMUM_NUMBER_POINTS}"
+        )
+
+    if alpha_factor <= 0.0:
+        raise ValueError("The alpha_factor value must be greater than 0.0")
+
+    if alpha is not None and alpha <= 0.0:
+        raise ValueError("The alpha value must be greater than 0.0")
+
+    if concave:
+        alpha_factor = 0
+        alpha = 999  # dummy
+
+    usepoints = points.copy()  # make a copy since points may be filtered
+
+    xvec = usepoints.get_dataframe(copy=False)[usepoints.xname].values
+    yvec = usepoints.get_dataframe(copy=False)[usepoints.yname].values
+    zvec = usepoints.get_dataframe(copy=False)[usepoints.zname].values
+
+    if alpha is None:
+        # use scipy to detect average distance; 30 points should be sufficient
+        xyv = np.column_stack((xvec, yvec))
+        use_npoints = 30 if xvec.size >= 30 else xvec.size
+        kdtree = cKDTree(xyv)
+        dist, _ = kdtree.query(xyv, k=use_npoints)
+        auto_alpha = np.mean(dist)
+        logger.info("Proposed auto alpha is %s", auto_alpha)
+
+        # now try this auto_alpha, and iterate to a gradually larger alpha proposal
+        # if still no success in creating a boundary
+        try:
+            return_values = _create_boundary_polygon(
+                xvec, yvec, zvec, auto_alpha * alpha_factor
+            )
+        except BoundaryError as berr:
+            # iterate and propose a new alpha value while raising an exception
+            propose_alpha = _propose_new_alpha(
+                xvec, yvec, zvec, alpha_factor, auto_alpha
+            )
+            propose_alpha_factor = alpha_factor * propose_alpha / auto_alpha
+            msg = (
+                "Your alpha_factor or alpha is too low. Set the alpha_factor to "
+                f"approx. {propose_alpha_factor:.3f}\n"
+            )
+            raise BoundaryError(msg) from berr
+    else:
+        return_values = _create_boundary_polygon(xvec, yvec, zvec, alpha * alpha_factor)
+
+    # return the class parameters to populate the Polygons instance
+    if return_values is None:
+        raise BoundaryError("Cannot create a a boundary, too few points?")
+
+    return return_values
+
+
+def _propose_new_alpha(xvec, yvec, zvec, alpha_factor, alpha):
+    """The current combination of alpha_factor and alpha did not get produce a result.
+
+    Do an iteration here and propose a new alpha_value, given that the user insists
+    on keeping the current alpha_factor.
+    """
+    trials = 0
+    max_trials = 1000
+    multiplier = 1.1
+
+    proposed_alpha = alpha * multiplier
+    while trials < max_trials:
+        trials += 1
+        logger.info("Proposed alpha is %s in trial %s", proposed_alpha, trials)
+        try:
+            _create_boundary_polygon(xvec, yvec, zvec, proposed_alpha * alpha_factor)
+            print("Trial number:", trials)
+            return ceil(proposed_alpha)
+        except BoundaryError:
+            proposed_alpha *= multiplier
+
+    raise RuntimeError(f"Not able to estimate an alpha in {max_trials} iterations!")
+
+
+def _create_boundary_polygon(
+    xvec: np.ndarray,
+    yvec: np.ndarray,
+    zvec: np.ndarray,
+    alpha: float,
+) -> list[list[float | int]] | None:
+    xy = np.column_stack((xvec, yvec))
+    coords = np.column_stack((xy, zvec))
+
+    # return None if too few points
+    if len(xy) < MINIMUM_NUMBER_POINTS:
+        logger.info("Too few points to derive boundary, need at least 4")
+        return None
+
+    edges = _alpha_shape(xy, alpha=alpha)
+    if not edges:
+        raise BoundaryError(
+            "Your alpha or alpha_factor value is too low, try increasing it!"
+        )
+
+    pol_coords = _get_polygon_coords_from_edges_shapely(coords, edges)
+    if not pol_coords:
+        raise BoundaryError("Could not create a valid Polygons instance for boundary.")
+
+    # sort polygons by their size to get the largest polygons first
+    pol_coords = sorted(pol_coords, key=len, reverse=True)
+
+    data = []
+    for polid, polcoord in enumerate(pol_coords):
+        for coord in polcoord:
+            data.append(list(coord) + [polid])
+
+    return data
+
+
+def _alpha_shape(points: np.ndarray, alpha: float) -> set[tuple[int, int]]:
+    """Compute the alpha shape (concave hull) of a set of points.
+
+    Args:
+        points: np.array of shape (n,2) points.
+        alpha: alpha value.
+    Returns:
+        Set of (i,j) pairs representing edges of the alpha-shape. (i,j) are
+            the indices in the points array.
+    """
+
+    def add_edge(edges: set[tuple[int, int]], icv: int, jcv: int) -> None:
+        """Add an edge between the i-th and j-th points, if not in the list already."""
+        if (icv, jcv) in edges or (jcv, icv) in edges:
+            # if both neighboring triangles are in shape, it is not a boundary edge
+            edges.remove((jcv, icv))
+            return
+        edges.add((icv, jcv))
+
+    tri = Delaunay(points)
+
+    edges = set()
+
+    # Loop over triangles: ia, ib, ic = indices of corner points of the triangle
+    for ia, ib, ic in tri.simplices:
+        pa, pb, pc = points[ia], points[ib], points[ic]
+
+        # Computing radius of triangle circumcircle
+        # www.mathalino.com/reviewer/derivation-of-formulas/derivation-of-formula-\
+        # for-radius-of-circumcircle
+        avv = np.sqrt((pa[0] - pb[0]) ** 2 + (pa[1] - pb[1]) ** 2)
+        bvv = np.sqrt((pb[0] - pc[0]) ** 2 + (pb[1] - pc[1]) ** 2)
+        cvv = np.sqrt((pc[0] - pa[0]) ** 2 + (pc[1] - pa[1]) ** 2)
+
+        svv = (avv + bvv + cvv) / 2.0
+        partial = svv * (svv - avv) * (svv - bvv) * (svv - cvv)
+        partial = partial[partial > 0.0]  # to avoid sqrt of negative number
+        area = np.sqrt(partial)
+
+        if area.size > 0:
+            # radius of circumcircle
+            circum_r = avv * bvv * cvv / (4.0 * area)
+
+            # if radius less then alpha then add outer edge
+            if circum_r < alpha or alpha == 0:
+                add_edge(edges, ia, ib)
+                add_edge(edges, ib, ic)
+                add_edge(edges, ic, ia)
+
+    return edges
+
+
+def _get_polygon_coords_from_edges_shapely(
+    coords: np.ndarray, edges: set[tuple[int, int]]
+) -> list[shapely.coords.CoordinateSequence]:
+    """Split and connect edges into shapely polygons"""
+    logger.info("Getting polygon coordinates using shapely")
+    lines = sg.MultiLineString([(coords[e[0]], coords[e[1]]) for e in edges])
+    # Need to use node workaround here to handle crossing lines
+    # see https://github.com/shapely/shapely/issues/1736
+    noded = shapely.node(shapely.GeometryCollection(lines))
+    polygons = polygonize(noded.geoms)
+    return [pol.exterior.coords for pol in polygons]
+
+
+def simplify_polygons(self, tolerance: float, preserve_topology: bool) -> bool:
+    """Use Shapely's 'simplify' method to reduce points.
+
+    Note that attributes are not yet supported (perhaps impossible?)
+
+    For Args, see Shapely
+    """
+    try:
+        if self.attributes:
+            raise UserWarning(
+                "Attributes are present, but they will be lost when simplifying"
+            )
+    except AttributeError:
+        pass
+
+    recompute_hlen = self.hname in self.get_dataframe(copy=False)
+    recompute_tlen = self.tname in self.get_dataframe(copy=False)
+
+    orig_len = len(self.get_dataframe(copy=False))
+
+    idgroups = self.get_dataframe(copy=False).groupby(self.pname)
+    dfrlist = []
+    for idx, grp in idgroups:
+        if len(grp.index) < 2:
+            logger.warning("Cannot simplify polygons with less than two points. Skip")
+            continue
+
+        pxcor = grp[self.xname].values
+        pycor = grp[self.yname].values
+        pzcor = grp[self.zname].values
+        spoly = sg.LineString(np.stack([pxcor, pycor, pzcor], axis=1))
+
+        new_spoly = spoly.simplify(tolerance, preserve_topology=preserve_topology)
+        dfr = pd.DataFrame(
+            np.array(new_spoly.coords), columns=[self.xname, self.yname, self.zname]
+        )
+
+        dfr[self.pname] = idx
+        dfrlist.append(dfr)
+
+    dfr = pd.concat(dfrlist)
+    self.set_dataframe(dfr.reset_index(drop=True))
+
+    if recompute_hlen:
+        self.hlen()
+    if recompute_tlen:
+        self.tlen()
+
+    new_len = len(self.get_dataframe(copy=False))
+
+    return new_len < orig_len