Source code for tyssue.geometry.base_geometry

import numpy as np

from ..utils.utils import to_nd


class BaseGeometry:
    """ """

    @staticmethod
    def update_all(sheet):
        raise NotImplementedError

    @staticmethod
    def scale(sheet, delta, coords):
        """Scales the coordinates `coords`
        by a factor `delta`
        """
        sheet.vert_df[coords] = sheet.vert_df[coords] * delta

    @staticmethod
    def update_dcoords(sheet):
        """
        Update the edge vector coordinates  on the
        `coords` basis (`default_coords` by default).
        Modifies the corresponding
        columns (i.e `['dx', 'dy', 'dz']`) in sheet.edge_df.

        Also updates the upcasted coordinates of the source and target
        vertices
        """
        if sheet.settings.get("boundaries") is None:
            data = sheet.vert_df[sheet.coords]
            srce_pos = sheet.upcast_srce(data)
            trgt_pos = sheet.upcast_trgt(data)
            sheet.edge_df[["s" + c for c in sheet.coords]] = srce_pos
            sheet.edge_df[["t" + c for c in sheet.coords]] = trgt_pos
            sheet.edge_df[sheet.dcoords] = trgt_pos - srce_pos
        else:
            update_periodic_dcoords(sheet)

    @staticmethod
    def update_ucoords(sheet):
        sheet.edge_df[sheet.ucoords] = sheet.edge_df[sheet.dcoords] / to_nd(
            sheet.edge_df["length"], sheet.dim
        )

    @staticmethod
    def update_length(sheet):
        """
        Updates the edge_df `length` column on the `coords` basis
        """
        sheet.edge_df["length"] = np.linalg.norm(sheet.edge_df[sheet.dcoords], axis=1)

    @staticmethod
    def update_perimeters(sheet):
        """
        Updates the perimeter of each face.
        """
        sheet.face_df["perimeter"] = sheet.sum_face(sheet.edge_df["length"])

    @staticmethod
    def update_centroid(sheet):
        """
        Updates the face_df `coords` columns as the face's vertices
        center of mass. Also updates the edge_df fx, fy, fz columns
        with their upcasted values
        """
        scoords = ["s" + c for c in sheet.coords]
        sheet.face_df[sheet.coords] = sheet.edge_df.groupby("face")[scoords].mean()
        face_pos = sheet.upcast_face(sheet.face_df[sheet.coords])
        for c in sheet.coords:
            sheet.edge_df["f" + c] = face_pos[c]
            sheet.edge_df["r" + c] = sheet.edge_df["s" + c] - sheet.edge_df["f" + c]

    @staticmethod
    def center(eptm):
        """
        Transates the epithelium vertices so that the center
        of mass is at the center of the coordinate system,
        and updates the geometry
        """

        eptm.vert_df[eptm.coords] = (
            eptm.vert_df[eptm.coords].values
            - eptm.vert_df[eptm.coords].mean(axis=0).values[np.newaxis, :]
        )

    @staticmethod
    def dist_to_point(vert_df, point, coords):
        """
        Returns the distance of all vertices from point over the
        coordinates

        Parameters
        ----------
        vert_df: a :class:`pandas.DataFrame` with the points coordinates
          in the columns given by the `coords` argument

        point: a doublet (in 2D) or triplet (in 3D) giving the reference point
          coordinates

        coords: list of 2 or 3 strings giving the column names

        Returns
        -------

        distance: a :class:`pandas.Series` with the same length
          as the input `vert_df`
        """
        return sum(((vert_df[c] - u) ** 2 for c, u in zip(coords, point))) ** 0.5


def update_periodic_dcoords(sheet):
    """Updates the coordinates for periodic boundary conditions."""
    for u, boundary in sheet.settings["boundaries"].items():
        period = boundary[1] - boundary[0]
        shift = period * (
            -(sheet.vert_df[u] > boundary[1]).astype(float)
            + (sheet.vert_df[u] <= boundary[0]).astype(float)
        )
        sheet.vert_df[u] = sheet.vert_df[u] + shift

    srce_pos = sheet.upcast_srce(sheet.vert_df[sheet.coords])
    trgt_pos = sheet.upcast_trgt(sheet.vert_df[sheet.coords])
    sheet.edge_df[["s" + u for u in sheet.coords]] = srce_pos
    sheet.edge_df[["t" + u for u in sheet.coords]] = trgt_pos
    sheet.edge_df[sheet.dcoords] = trgt_pos - srce_pos
    for u, boundary in sheet.settings["boundaries"].items():
        period = boundary[1] - boundary[0]
        center = boundary[1] - period / 2
        shift = period * (
            -(sheet.edge_df["d" + u] >= period / 2).astype(float)
            + (sheet.edge_df["d" + u] < -period / 2).astype(float)
        )
        sheet.edge_df["d" + u] = sheet.edge_df["d" + u] + shift
        sheet.edge_df[f"at_{u}_boundary"] = shift != 0

        sheet.face_df[f"at_{u}_boundary"] = sheet.edge_df.groupby("face")[
            f"at_{u}_boundary"
        ].apply(any)
        f_at_boundary = sheet.upcast_face(sheet.face_df[f"at_{u}_boundary"]).astype(int)
        period = boundary[1] - boundary[0]
        srce_shift = f_at_boundary * (sheet.edge_df["s" + u] < center) * period
        trgt_shift = f_at_boundary * (sheet.edge_df["t" + u] < center) * period
        sheet.edge_df["s" + u] += srce_shift
        sheet.edge_df["t" + u] += trgt_shift