Source code for geoh5py.objects.geo_image

#  Copyright (c) 2023 Mira Geoscience Ltd.
#  This file is part of geoh5py.
#  geoh5py is free software: you can redistribute it and/or modify
#  it under the terms of the GNU Lesser General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#  geoh5py is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  GNU Lesser General Public License for more details.
#  You should have received a copy of the GNU Lesser General Public License
#  along with geoh5py.  If not, see <>.
from __future__ import annotations

import os
import uuid
from io import BytesIO
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import Any
from warnings import warn

import numpy as np
from PIL import Image
from PIL.TiffImagePlugin import TiffImageFile

from .. import objects
from import FilenameData
from ..shared.conversion import GeoImageConversion
from .object_base import ObjectBase, ObjectType

[docs]class GeoImage(ObjectBase): """ Image object class. .. warning:: Not yet implemented. """ __TYPE_UID = uuid.UUID( fields=(0x77AC043C, 0xFE8D, 0x4D14, 0x81, 0x67, 0x75E300FB835A) ) _converter = GeoImageConversion def __init__(self, object_type: ObjectType, **kwargs): self._vertices: None | np.ndarray = None self._cells = None self._tag: dict[int, Any] | None = None super().__init__(object_type, **kwargs) object_type.workspace._register_object(self) @property def cells(self) -> np.ndarray | None: r""" :obj:`numpy.ndarray` of :obj:`int`, shape (\*, 2): Array of indices defining segments connecting vertices. Defined based on :obj:`` if set by the user. """ if getattr(self, "_cells", None) is None: if self.on_file: self._cells = self.workspace.fetch_array_attribute(self) else: self.cells = np.c_[[0, 1, 2, 0], [0, 2, 3, 0]].T.astype("uint32") return self._cells @cells.setter def cells(self, indices): assert indices.dtype == "uint32", "Indices array must be of type 'uint32'" self._cells = indices self.workspace.update_attribute(self, "cells") @property def default_vertices(self): """ Assign the default vertices based on image pixel count """ if self.image is not None: return np.asarray( [ [0, self.image.size[1], 0], [self.image.size[0], self.image.size[1], 0], [self.image.size[0], 0, 0], [0, 0, 0], ] ) return None
[docs] @classmethod def default_type_uid(cls) -> uuid.UUID: return cls.__TYPE_UID
@property def image_data(self): """ Get the FilenameData entity holding the image. """ for child in self.children: if isinstance(child, FilenameData) and == "GeoImageMesh_Image": return child return None @property def image(self): """ Get the image as a :obj:`PIL.Image` object. """ if self.image_data is not None: return return None @image.setter def image(self, image: str | np.ndarray | BytesIO | Image.Image): """ Create a :obj:`` from dictionary of name and arguments. The provided arguments can be any property of the target Data class. :return: List of new Data objects. """ if isinstance(image, np.ndarray) and image.ndim in [2, 3]: if image.ndim == 3 and image.shape[2] != 3: raise ValueError( "Shape of the 'image' must be a 2D or " "a 3D array with shape(*,*, 3) representing 'RGB' values." ) value = image.astype(float) value -= value.min() value *= 255.0 / value.max() value = value.astype("uint8") image = Image.fromarray(value) elif isinstance(image, str): if not os.path.exists(image): raise ValueError(f"Input image file {image} does not exist.") image = # if the image is a tiff save tag information if isinstance(image, TiffImageFile): self.tag = image elif isinstance(image, bytes): image = elif isinstance(image, TiffImageFile): self.tag = image elif not isinstance(image, Image.Image): raise ValueError( "Input 'value' for the 'image' property must be " "a 2D or 3D numpy.ndarray, bytes, PIL.Image or a path to an existing image." f"Get type {type(image)} instead." ) with TemporaryDirectory() as tempdir: ext = getattr(image, "format") temp_file = os.path.join( tempdir, f"image.{ext.lower() if ext is not None else 'tiff'}" ) if self.image_data is not None: self.workspace.remove_entity(self.image_data) image = self.add_file(temp_file) = "GeoImageMesh_Image" = "GeoImageMesh_Image"
[docs] def georeference(self, reference: np.ndarray | list, locations: np.ndarray | list): """ Georeference the image vertices (corners) based on input reference and corresponding world coordinates. :param reference: Array of integers representing the reference used as reference points. :param locations: Array of floats for the corresponding world coordinates for each input pixel. :return vertices: Corners (vertices) in world coordinates. """ reference = np.asarray(reference) locations = np.asarray(locations) if self.image is None: raise AttributeError("An 'image' must be set before georeferencing.") if reference.ndim != 2 or reference.shape[0] < 3 or reference.shape[1] != 2: raise ValueError( "Input reference points must be a 2D array of shape(*, 2) " "with at least 3 control points." ) if ( locations.ndim != 2 or reference.shape[0] != locations.shape[0] or locations.shape[1] != 3 ): raise ValueError( "Input 'locations' must be a 2D array of shape(*, 3) " "with the same number of rows as the control points." ) constant = np.ones(reference.shape[0]) param_x, _, _, _ = np.linalg.lstsq( np.c_[constant, reference], locations[:, 0], rcond=None ) param_y, _, _, _ = np.linalg.lstsq( np.c_[constant, reference], locations[:, 1], rcond=None ) param_z, _, _, _ = np.linalg.lstsq( np.c_[constant, reference], locations[:, 2], rcond=None ) corners = self.default_vertices[:, :2] self.vertices = np.c_[ param_x[0] +, param_x[1:]), param_y[0] +, param_y[1:]), param_z[0] +, param_z[1:]), ] self.set_tag_from_vertices()
[docs] def set_tag_from_vertices(self): """ If tag is None, set the basic tag values based on vertices in order to export as a georeferenced .tiff. WARNING: this function must be used after georeference(). """ if self.image is None: raise AttributeError("There is no image to reference") if not isinstance(self.vertices, np.ndarray): raise AttributeError("Vertices must be set before setting tag") if self._tag is None: self._tag = {} width, height = self.image.size self._tag[256] = (width,) self._tag[257] = (height,) self._tag[33922] = ( 0.0, 0.0, 0.0, self.vertices[0, 0], self.vertices[0, 1], self.vertices[0, 2], ) self._tag[33550] = ( abs(self.vertices[1, 0] - self.vertices[0, 0]) / width, abs(self.vertices[0, 1] - self.vertices[2, 1]) / height, 0.0, )
@property def vertices(self) -> np.ndarray | None: """ :obj:`~geoh5py.objects.object_base.ObjectBase.vertices`: Defines the four corners of the geo_image """ if (getattr(self, "_vertices", None) is None) and self.on_file: self._vertices = self.workspace.fetch_array_attribute(self, "vertices") if self._vertices is None and self.image is not None: if self.tag is not None: self.vertices = self.default_vertices self.georeferencing_from_tiff() else: self.vertices = self.default_vertices if self._vertices is not None: return self._vertices.view("<f8").reshape((-1, 3)).astype(float) return self._vertices @vertices.setter def vertices(self, xyz: np.ndarray | list): if isinstance(xyz, list): xyz = np.asarray(xyz) if not isinstance(xyz, np.ndarray) or xyz.shape != (4, 3): raise ValueError("Input 'vertices' must be a numpy array of shape (4, 3)") xyz = np.asarray( np.core.records.fromarrays(xyz.T, names="x, y, z", formats="<f8, <f8, <f8") ) self._vertices = xyz self.workspace.update_attribute(self, "vertices") @property def tag(self) -> dict | None: """ Georeferencing information of a tiff image stored in the header. :return: a dictionary containing the PIL.Image.tag information. """ if self._tag: return self._tag.copy() return None @tag.setter def tag(self, image: Image.Image | dict | None): if isinstance(image, (Image.Image, TiffImageFile)): self._tag = dict(image.tag) elif isinstance(image, dict): self._tag = image elif image is None: self._tag = None else: raise ValueError("Input 'tag' must be a PIL.Image")
[docs] def georeferencing_from_tiff(self): """ Get the geographic information from the PIL Image to georeference it. Run the georeference() method of the object. """ if self.tag is None: raise AttributeError("The image is not georeferenced") try: # get geographic information u_origin = float(self.tag[33922][3]) v_origin = float(self.tag[33922][4]) u_cell_size = float(self.tag[33550][0]) v_cell_size = float(self.tag[33550][1]) u_count = float(self.tag[256][0]) v_count = float(self.tag[257][0]) u_oposite = float(u_origin + u_cell_size * u_count) v_oposite = float(v_origin - v_cell_size * v_count) # prepare georeferencing reference = np.array([[0.0, v_count], [u_count, v_count], [u_count, 0.0]]) locations = np.array( [ [u_origin, v_origin, 0.0], [u_oposite, v_origin, 0.0], [u_oposite, v_oposite, 0.0], ] ) # georeference the raster self.georeference(reference, locations) except KeyError: warn("The 'tif.' image has no referencing information")
@property def image_georeferenced(self) -> Image.Image | None: """ Get the image as a georeferenced :obj:`PIL.Image` object. """ if self.tag is not None and self.image is not None: image = self.image # modify the exif for id_ in self.tag: image.getexif()[id_] = self.tag[id_] return image return None
[docs] def save_as(self, name: str, path: str | Path = ""): """ Function to save the geoimage into an image file. It the name ends by '.tif' or '.tiff' and the tag is not None then the image is saved as georeferenced tiff image ; else, the image is save with PIL.Image's save function. :param name: the name to give to the image. :param path: the path of the file of the image, default: ''. """ # verifications if self.image is None: raise AttributeError("The object contains no image data") if not isinstance(name, str): raise TypeError( f"The 'name' has to be a string; a '{type(name)}' was entered instead" ) if not isinstance(path, (str, Path)): raise TypeError( f"The 'path' has to be a string or a Path; a '{type(name)}' was entered instead" ) if path != "" and not os.path.isdir(path): raise FileNotFoundError(f"No such file or directory: {path}") if name.endswith((".tif", ".tiff")) and self.tag is not None: # save the image image: Image = self.image_georeferenced, name), exif=image.getexif()) else:, name))
[docs] def to_grid2d( self, transform: str = "GRAY", **grid2d_kwargs, ) -> objects.Grid2D: """ Create a geoh5py :obj:geoh5py.objects.grid2d.Grid2D from the geoimage in the same workspace. :param transform: the type of transform ; if "GRAY" convert the image to grayscale ; if "RGB" every band is sent to a data of a grid. :return: the new created :obj:`geoh5py.objects.grid2d.Grid2D`. """ return self.converter.to_grid2d(self, transform, **grid2d_kwargs)