Source code for imod.gen.gen

import io
import warnings
from pathlib import Path
from typing import Optional, Tuple, Union

import numpy as np
import pandas as pd
from import FortranFile, FortranFormattingError

from imod.util import MissingOptionalModule

    import shapely.geometry as sg
except ImportError:
    sg = MissingOptionalModule("shapely")

    import geopandas as gpd
except ImportError:
    gpd = MissingOptionalModule("geopandas")

# From the iMOD User Manual
FLOAT_TYPE = np.float64
INT_TYPE = np.int32
HEADER_TYPE = np.int32
CIRCLE = 1024
POLYGON = 1025
POINT = 1027
LINE = 1028

# Map integer enumerators to strings
    CIRCLE: "circle",
    POLYGON: "polygon",
    RECTANGLE: "rectangle",
    POINT: "point",
    LINE: "line",
NAME_TO_GENTYPE = {v: k for k, v in GENTYPE_TO_NAME.items()}

# Forward references, since shapely is optional
Point = "shapely.geometry.Point"
Polygon = "shapely.geometry.Polygon"
LineString = "shapely.geometry.LineString"

# Unfortunately, the binary GEN files are written as Fortran Record files, so
# they cannot be read directly with e.g. numpy.fromfile (like direct access) The
# scipy FortranFile is mostly adequate, it just misses a method to read char
# records (always ascii encoded; note all ascii is valid utf-8, but not vice
# versa). Reading and writing methods are monkeypatched here.
def monkeypatch_method(cls):
    def decorator(func):
        setattr(cls, func.__name__, func)
        return func

    return decorator

def read_char_record(self):
    first_size = self._read_size(eof_ok=True)
    string ="utf-8")
    if len(string) != first_size:
        raise FortranFormattingError("End of file in the middle of a record")
    second_size = self._read_size(eof_ok=True)
    if first_size != second_size:
        raise IOError("Sizes do not agree in the header and footer for this record")
    return string

def write_char_record(self, string: str):
    total_size = len(string)
    bytes_string = string.encode("ascii")
    nb = np.array([total_size], dtype=self._header_dtype)

# The binary GEN file has some idiosyncratic geometries:
# * A separate circle geometry
# * A seperate rectangle geometry
# In OGC (WKT) terms, these are polygons.
# Both are defined by two vertices:
# * Circle: center and any other outside point (from which we can infer the radius)
# * Rectangle: (left, lower), (right, upper); may also be (left, upper), (right, lower)
# The other shapely geometries can be generated directly from the vertices.

def from_circle(xy: np.ndarray) -> Polygon:
    radius = np.sqrt(np.sum((xy[1] - xy[0]) ** 2))
    return sg.Point(xy[0]).buffer(radius)

def from_point(xy: np.ndarray) -> Polygon:
    return sg.Point(xy[0])

def from_rectangle(xy: np.ndarray) -> Polygon:
    return[0, 0], xy[0, 1], xy[1, 0], xy[1, 1])

def to_circle(geometry: Polygon) -> Tuple[np.ndarray, int]:
    xy = np.array([geometry.centroid.coords[0], geometry.exterior.coords[0]])
    return xy, 2

def to_rectangle(geometry: Polygon) -> Tuple[np.ndarray, int]:
    xy = np.array(geometry.exterior)
    if (geometry.area / geometry.minimum_rotated_rectangle.area) < 0.999:
        raise ValueError("Feature_type is rectangle, but geometry is not a rectangular")
    # First and third vertex will give (left, right) and (lower, upper)
    return xy[[0, 2]], 2

def to_polygon(geometry: Polygon) -> Tuple[np.ndarray, int]:
    xy = np.array(geometry.exterior)
    return xy, xy.shape[0]

def to_point(geometry: Point) -> Tuple[np.ndarray, int]:
    return np.array(geometry), 1

def to_line(geometry: LineString) -> Tuple[np.ndarray, int]:
    xy = np.array(geometry)
    return xy, xy.shape[0]

[docs]def read(path: Union[str, Path]) -> "geopandas.GeoDataFrame": # type: ignore # noqa """ Read a binary GEN file to a geopandas GeoDataFrame. Parameters ---------- path: Union[str, Path] Returns ------- geodataframe: gpd.GeoDataFrame """ # From gen itype to shapely geometry: GENTYPE_TO_GEOM = { CIRCLE: from_circle, POLYGON: sg.Polygon, RECTANGLE: from_rectangle, POINT: from_point, LINE: sg.LineString, } with warnings.catch_warnings(record=True): warnings.filterwarnings( "ignore", message="Given a dtype which is not unsigned." ) with FortranFile(path, mode="r", header_dtype=HEADER_TYPE) as f: f.read_reals(dtype=FLOAT_TYPE) # Skip the bounding box n_feature, n_column = f.read_ints(dtype=INT_TYPE) if n_column > 0: widths = f.read_ints(dtype=INT_TYPE) indices = range(0, (n_column + 1) * MAX_NAME_WIDTH, MAX_NAME_WIDTH) string = f.read_char_record() # pylint:disable=no-member names = [string[i:j].strip() for i, j in zip(indices[:-1], indices[1:])] xy = [] rows = [] feature_type = np.empty(n_feature, dtype=INT_TYPE) for i in range(n_feature): _, ftype = f.read_ints(dtype=INT_TYPE) feature_type[i] = ftype if n_column > 0: rows.append(f.read_char_record()) # pylint:disable=no-member f.read_reals(dtype=FLOAT_TYPE) # skip the bounding box xy.append(f.read_reals(dtype=FLOAT_TYPE).reshape((-1, 2))) if n_column > 0: df = pd.read_fwf( io.StringIO("\n".join(rows)), widths=widths, names=names, ) else: df = pd.DataFrame() df["feature_type"] = feature_type df["feature_type"] = df["feature_type"].replace(GENTYPE_TO_NAME) geometry = [] for ftype, geom in zip(feature_type, xy): geometry.append(GENTYPE_TO_GEOM[ftype](geom)) return gpd.GeoDataFrame(df, geometry=geometry)
def vertices( geometry: Union[Point, Polygon, LineString], ftype: str ) -> Tuple[int, np.ndarray, int]: """ Infer from geometry, or convert from string, the feature type to the GEN expected Enum (int). Convert the geometry to the GEN expected vertices, and the number of vertices. """ # Checking names with actual geometry types NAME_TO_GEOM = { "circle": sg.Polygon, "rectangle": sg.Polygon, "polygon": sg.Polygon, "point": sg.Point, "line": sg.LineString, } GENTYPE_TO_VERTICES = { CIRCLE: to_circle, RECTANGLE: to_rectangle, POLYGON: to_polygon, POINT: to_point, LINE: to_line, } # Infer gentype on the basis of shapely type GEOM_TO_GENTYPE = { sg.Polygon: POLYGON, sg.Point: POINT, sg.LineString: LINE, } if ftype != "": # Start by checking whether the feature type matches the geometry try: expected = NAME_TO_GEOM[ftype] except KeyError as e: raise ValueError( f"feature_type should be one of {set(NAME_TO_GEOM.keys())}. Got instead {ftype}" ) from e if not isinstance(geometry, expected): raise ValueError( f"Feature type is {ftype}, expected {expected}. Got instead: {type(geometry)}" ) ftype: int = NAME_TO_GENTYPE[ftype] else: try: ftype: int = GEOM_TO_GENTYPE[type(geometry)] except KeyError as e: raise TypeError( "Geometry type not allowed. Should be Polygon, Linestring, or Point." f" Got {type(geometry)} instead." ) from e xy, n_vertex = GENTYPE_TO_VERTICES[ftype](geometry) return ftype, xy, n_vertex
[docs]def write( path: Union[str, Path], geodataframe: "geopandas.GeoDataFrame", # type: ignore # noqa feature_type: Optional[str] = None, ) -> None: """ Write a GeoDataFrame to a binary GEN file. Note that the binary GEN file has two geometry types, circles and rectangles, which cannot be mapped directly from a shapely type. Points, lines, and polygons can be converted automatically. In shapely, circles and rectangles will also be represented by polygons. To specifically write circles and rectangles to a binary GEN file, an additional column of strings is required which specifies the geometry type. Parameters ---------- path : Union[str, Path] geodataframe : gpd.GeoDataFrame feature_type : Optional[str] Which column to interpret as geometry type, one of: point, line, polygon, circle, rectangle. Default value is ``None``. Returns ------- None Writes file. """ df = pd.DataFrame(geodataframe.drop(columns="geometry")).astype("string") if feature_type is not None: types = df.pop(feature_type).str.lower() else: # Create a dummy iterator types = ("" for i in range(len(df))) n_feature, n_column = df.shape # Truncate column names to 11 chars, then make everything at least 11 chars column_names = "".join([c[:11].ljust(11) for c in df]) # Get the widths of the columns. Make room for at least 11 widths = [] for column in df: width = max(11, df[column].str.len().max()) df[column] = df[column].str.pad(width, side="right") widths.append(width) with warnings.catch_warnings(record=True): warnings.filterwarnings( "ignore", message="Given a dtype which is not unsigned." ) with FortranFile(path, mode="w", header_dtype=HEADER_TYPE) as f: f.write_record(geodataframe.total_bounds.astype(FLOAT_TYPE)) f.write_record(np.array([n_feature, n_column], dtype=INT_TYPE)) if n_column > 0: f.write_record(np.array(widths).astype(INT_TYPE)) f.write_char_record(column_names) # pylint:disable=no-member for geometry, (_, row), ftype in zip( geodataframe.geometry, df.iterrows(), types ): ftype, xy, n_vertex = vertices(geometry, ftype) f.write_record(np.array([n_vertex, ftype], dtype=INT_TYPE)) if n_column > 0: f.write_char_record("".join(row.values)) # pylint:disable=no-member f.write_record(np.array(geometry.bounds).astype(FLOAT_TYPE)) f.write_record(xy.astype(FLOAT_TYPE))