ssb-sgis 1.0.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

sgis/raster/raster.py

@@ -88,7 +88,7 @@ class Raster:
 
 
     Examples:
-    --------
+    ---------
     Read tif file.
 
     >>> import sgis as sg
@@ -102,8 +102,8 @@ class Raster:
     The array is stored in the array attribute.
 
     >>> raster.load()
-    >>> raster.array[raster.array < 0] = 0
-    >>> raster.array
+    >>> raster.values[raster.values < 0] = 0
+    >>> raster.values
     [[[  0.    0.    0.  ... 158.4 155.6 152.6]
     [  0.    0.    0.  ... 158.  154.8 151.9]
     [  0.    0.    0.  ... 158.5 155.1 152.3]
@@ -194,7 +194,12 @@ class Raster:
             **kwargs: Arguments concerning file metadata or
                 spatial properties of the image.
         """
+        warnings.warn("This class is deprecated in favor of Band", stacklevel=1)
         self.filename_regex = filename_regex
+        if filename_regex:
+            self.filename_pattern = re.compile(self.filename_regex, re.VERBOSE)
+        else:
+            self.filename_pattern = None
 
         if isinstance(data, Raster):
             for key, value in data.__dict__.items():
@@ -208,9 +213,9 @@ class Raster:
             self.path = None
 
         if isinstance(data, (np.ndarray)):
-            self.array = data
+            self.values = data
         else:
-            self.array = None
+            self.values = None
 
         if self.path is None and not any(
             [kwargs.get("transform"), kwargs.get("bounds")]
@@ -457,24 +462,25 @@ class Raster:
                 Thise will override the items in the Raster's profile,
                 if overlapping.
         """
-        if self.array is None:
+        if self.values is None:
             raise AttributeError("The image hasn't been loaded.")
 
         profile = self.profile | kwargs
 
-        with opener(path, file_system=self.file_system) as file:
+        with opener(path, "wb", file_system=self.file_system) as file:
             with rasterio.open(file, "w", **profile) as dst:
                 self._write(dst, window)
 
         self.path = str(path)
 
-    def load(self, **kwargs) -> Self:
+    def load(self, reload: bool = False, **kwargs) -> Self:
         """Load the entire image as an np.array.
 
         The array is stored in the 'array' attribute
         of the Raster.
 
         Args:
+            reload: Whether to reload the array if already loaded.
             **kwargs: Keyword arguments passed to the rasterio read
                 method.
         """
@@ -483,7 +489,8 @@ class Raster:
         if "window" in kwargs:
             raise ValueError("Got an unexpected keyword argument 'window'")
 
-        self._read_tif(**kwargs)
+        if reload or self.values is None:
+            self._read_tif(**kwargs)
 
         return self
 
@@ -575,10 +582,12 @@ class Raster:
         aggregated = []
         for i, poly in poly_iter:
             clipped = self.clip(poly)
-            if not np.size(clipped.array):
+            if not np.size(clipped.values):
                 aggregated.append(_no_overlap_df(func_names, i, date=self.date))
             aggregated.append(
-                _aggregate(clipped.array, array_func, aggfunc, func_names, self.date, i)
+                _aggregate(
+                    clipped.values, array_func, aggfunc, func_names, self.date, i
+                )
             )
 
         return _zonal_post(
@@ -589,74 +598,23 @@ class Raster:
             dropna=dropna,
         )
 
-    def gradient(self, degrees: bool = False, copy: bool = False) -> Self:
-        """Get the slope of an elevation raster.
-
-        Calculates the absolute slope between the grid cells
-        based on the image resolution.
-
-        For multiband images, the calculation is done for each band.
-
-        Args:
-            degrees: If False (default), the returned values will be in ratios,
-                where a value of 1 means 1 meter up per 1 meter forward. If True,
-                the values will be in degrees from 0 to 90.
-            copy: Whether to copy or overwrite the original Raster.
-                Defaults to False to save memory.
-
-        Returns:
-            The class instance with new array values, or a copy if copy is True.
-
-        Examples:
-        --------
-        Making an array where the gradient to the center is always 10.
-
-        >>> import sgis as sg
-        >>> import numpy as np
-        >>> arr = np.array(
-        ...         [
-        ...             [100, 100, 100, 100, 100],
-        ...             [100, 110, 110, 110, 100],
-        ...             [100, 110, 120, 110, 100],
-        ...             [100, 110, 110, 110, 100],
-        ...             [100, 100, 100, 100, 100],
-        ...         ]
-        ...     )
-
-        Now let's create a Raster from this array with a resolution of 10.
-
-        >>> r = sg.Raster.from_array(arr, crs=None, bounds=(0, 0, 50, 50))
-
-        The gradient will be 1 (1 meter up for every meter forward).
-        The calculation is by default done in place to save memory.
-
-        >>> r.gradient()
-        >>> r.array
-        array([[0., 1., 1., 1., 0.],
-            [1., 1., 1., 1., 1.],
-            [1., 1., 0., 1., 1.],
-            [1., 1., 1., 1., 1.],
-            [0., 1., 1., 1., 0.]])
-        """
-        return get_gradient(self, degrees=degrees, copy=copy)
-
     def to_xarray(self) -> DataArray:
         """Convert the raster to  an xarray.DataArray."""
         self._check_for_array()
         self.name = self.name or self.__class__.__name__.lower()
         coords = _generate_spatial_coords(self.transform, self.width, self.height)
-        if len(self.array.shape) == 2:
+        if len(self.values.shape) == 2:
             dims = ["y", "x"]
             # dims = ["band", "y", "x"]
-            # array = np.array([self.array])
+            # array = np.array([self.values])
             # assert len(array.shape) == 3
-        elif len(self.array.shape) == 3:
+        elif len(self.values.shape) == 3:
             dims = ["band", "y", "x"]
-            # array = self.array
+            # array = self.values
         else:
             raise ValueError("Array must be 2 or 3 dimensional.")
         return xr.DataArray(
-            self.array,
+            self.values,
             coords=coords,
             dims=dims,
             name=self.name,
@@ -728,7 +686,7 @@ class Raster:
         if not allow_override and self.crs is not None:
             raise ValueError("Cannot overwrite crs when allow_override is False.")
 
-        if self.array is None:
+        if self.values is None:
             raise ValueError("array must be loaded/clipped before set_crs")
 
         self._crs = pyproj.CRS(crs)
@@ -750,7 +708,7 @@ class Raster:
         # ):
         #     return self
 
-        if self.array is None:
+        if self.values is None:
             project = pyproj.Transformer.from_crs(
                 pyproj.CRS(self._prev_crs), pyproj.CRS(crs), always_xy=True
             ).transform
@@ -782,16 +740,16 @@ class Raster:
             # self._bounds = shapely.transform(old_box, project)
         else:
             was_2d = len(self.shape) == 2
-            self.array, transform = reproject(
-                source=self.array,
+            self.values, transform = reproject(
+                source=self.values,
                 src_crs=self._prev_crs,
                 src_transform=self.transform,
                 dst_crs=pyproj.CRS(crs),
                 **kwargs,
             )
-            if was_2d and len(self.array.shape) == 3:
-                assert self.array.shape[0] == 1
-                self.array = self.array[0]
+            if was_2d and len(self.values.shape) == 3:
+                assert self.values.shape[0] == 1
+                self.values = self.values[0]
 
             self._bounds = rasterio.transform.array_bounds(
                 self.height, self.width, transform
@@ -811,9 +769,9 @@ class Raster:
             raster = self
 
         if len(raster.shape) == 2:
-            array = np.array([raster.array])
+            array = np.array([raster.values])
         else:
-            array = raster.array
+            array = raster.values
 
         for arr in array:
             ax = plt.axes()
@@ -824,31 +782,31 @@ class Raster:
 
     def astype(self, dtype: type) -> Self:
         """Convert the datatype of the array."""
-        if self.array is None:
+        if self.values is None:
             raise ValueError("Array is not loaded.")
-        if not rasterio.dtypes.can_cast_dtype(self.array, dtype):
-            min_dtype = rasterio.dtypes.get_minimum_dtype(self.array)
+        if not rasterio.dtypes.can_cast_dtype(self.values, dtype):
+            min_dtype = rasterio.dtypes.get_minimum_dtype(self.values)
             raise ValueError(f"Cannot cast to dtype. Minimum dtype is {min_dtype}")
-        self.array = self.array.astype(dtype)
+        self.values = self.values.astype(dtype)
         self._dtype = dtype
         return self
 
     def as_minimum_dtype(self) -> Self:
         """Convert the array to the minimum dtype without overflow."""
-        min_dtype = rasterio.dtypes.get_minimum_dtype(self.array)
-        self.array = self.array.astype(min_dtype)
+        min_dtype = rasterio.dtypes.get_minimum_dtype(self.values)
+        self.values = self.values.astype(min_dtype)
         return self
 
     def min(self) -> int | None:
         """Minimum value in the array."""
-        if np.size(self.array):
-            return np.min(self.array)
+        if np.size(self.values):
+            return np.min(self.values)
         return None
 
     def max(self) -> int | None:
         """Maximum value in the array."""
-        if np.size(self.array):
-            return np.max(self.array)
+        if np.size(self.values):
+            return np.max(self.values)
         return None
 
     def _add_meta(self) -> Self:
@@ -867,10 +825,10 @@ class Raster:
     def array_list(self) -> list[np.ndarray]:
         """Get a list of 2D arrays."""
         self._check_for_array()
-        if len(self.array.shape) == 2:
-            return [self.array]
-        elif len(self.array.shape) == 3:
-            return list(self.array)
+        if len(self.values.shape) == 2:
+            return [self.values]
+        elif len(self.values.shape) == 3:
+            return list(self.values)
         else:
             raise ValueError
 
@@ -898,8 +856,7 @@ class Raster:
     def date(self) -> str | None:
         """Date in the image file name, if filename_regex is present."""
         try:
-            pattern = re.compile(self.filename_regex, re.VERBOSE)
-            return re.match(pattern, Path(self.path).name).group("date")
+            return re.match(self.filename_pattern, Path(self.path).name).group("date")
         except (AttributeError, TypeError):
             return None
 
@@ -907,8 +864,7 @@ class Raster:
     def band(self) -> str | None:
         """Band name of the image file name, if filename_regex is present."""
         try:
-            pattern = re.compile(self.filename_regex, re.VERBOSE)
-            return re.match(pattern, Path(self.path).name).group("band")
+            return re.match(self.filename_pattern, Path(self.path).name).group("band")
         except (AttributeError, TypeError):
             return None
 
@@ -916,7 +872,7 @@ class Raster:
     def dtype(self) -> Any:
         """Data type of the array."""
         try:
-            return self.array.dtype
+            return self.values.dtype
         except AttributeError:
             try:
                 return self._dtype
@@ -925,7 +881,7 @@ class Raster:
 
     @dtype.setter
     def dtype(self, new_dtype: Any) -> None:
-        self.array = self.array.astype(new_dtype)
+        self.values = self.values.astype(new_dtype)
 
     @property
     def nodata(self) -> int | None:
@@ -937,10 +893,11 @@ class Raster:
 
     @property
     def tile(self) -> str | None:
-        """The lower left corner (minx, miny) of the image as a string."""
-        if self.bounds is None:
+        """Tile name from regex."""
+        try:
+            return re.match(self.filename_pattern, Path(self.path).name).group("tile")
+        except (AttributeError, TypeError):
             return None
-        return f"{int(self.bounds[0])}_{int(self.bounds[1])}"
 
     @property
     def meta(self) -> dict:
@@ -976,7 +933,7 @@ class Raster:
         return {
             "indexes": self.indexes,
             "fill_value": self.nodata,
-            "masked": True,
+            "masked": False,
         }
 
     @property
@@ -992,18 +949,18 @@ class Raster:
     @property
     def height(self) -> int | None:
         """Get the height of the image as number of pixels."""
-        if self.array is None:
+        if self.values is None:
             try:
                 return self._height
             except AttributeError:
                 return None
-        i = 1 if len(self.array.shape) == 3 else 0
-        return self.array.shape[i]
+        i = 1 if len(self.values.shape) == 3 else 0
+        return self.values.shape[i]
 
     @property
     def width(self) -> int | None:
         """Get the width of the image as number of pixels."""
-        if self.array is None:
+        if self.values is None:
             try:
                 return self._width
             except AttributeError:
@@ -1014,16 +971,16 @@ class Raster:
                     return self._width
                 except Exception:
                     return None
-        i = 2 if len(self.array.shape) == 3 else 1
-        return self.array.shape[i]
+        i = 2 if len(self.values.shape) == 3 else 1
+        return self.values.shape[i]
 
     @property
     def count(self) -> int:
         """Get the number of bands in the image."""
-        if self.array is not None:
-            if len(self.array.shape) == 3:
-                return self.array.shape[0]
-            if len(self.array.shape) == 2:
+        if self.values is not None:
+            if len(self.values.shape) == 3:
+                return self.values.shape[0]
+            if len(self.values.shape) == 2:
                 return 1
         if not hasattr(self._indexes, "__iter__"):
             return 1
@@ -1032,8 +989,8 @@ class Raster:
     @property
     def shape(self) -> tuple[int]:
         """Shape that is consistent with the array, whether it is loaded or not."""
-        if self.array is not None:
-            return self.array.shape
+        if self.values is not None:
+            return self.values.shape
         if hasattr(self._indexes, "__iter__"):
             return self.count, self.width, self.height
         return self.width, self.height
@@ -1123,9 +1080,9 @@ class Raster:
             raise NotImplementedError("other must be of type Raster")
         if type(other) != type(self):
             return False
-        if self.array is None and other.array is not None:
+        if self.values is None and other.values is not None:
             return False
-        if self.array is not None and other.array is None:
+        if self.values is not None and other.values is None:
             return False
 
         for method in dir(self):
@@ -1134,7 +1091,7 @@ class Raster:
             if getattr(self, method) != getattr(other, method):
                 return False
 
-        return np.array_equal(self.array, other.array)
+        return np.array_equal(self.values, other.values)
 
     def __repr__(self) -> str:
         """The print representation."""
@@ -1144,52 +1101,52 @@ class Raster:
             res = int(self.res)
         except TypeError:
             res = None
-        return f"{self.__class__.__name__}(shape=({shp}), res={res}, name={self.name}, path={self.path})"
+        return f"{self.__class__.__name__}(shape=({shp}), res={res}, band={self.band})"
 
     def __iter__(self) -> Iterator[np.ndarray]:
         """Iterate over the arrays."""
-        if len(self.array.shape) == 2:
-            return iter([self.array])
-        if len(self.array.shape) == 3:
-            return iter(self.array)
+        if len(self.values.shape) == 2:
+            return iter([self.values])
+        if len(self.values.shape) == 3:
+            return iter(self.values)
         raise ValueError(
-            f"Array should have shape length 2 or 3. Got {len(self.array.shape)}"
+            f"Array should have shape length 2 or 3. Got {len(self.values.shape)}"
         )
 
     def __mul__(self, scalar: int | float) -> "Raster":
         """Multiply the array values with *."""
         self._check_for_array()
-        self.array = self.array * scalar
+        self.values = self.values * scalar
         return self
 
     def __add__(self, scalar: int | float) -> "Raster":
         """Add to the array values with +."""
         self._check_for_array()
-        self.array = self.array + scalar
+        self.values = self.values + scalar
         return self
 
     def __sub__(self, scalar: int | float) -> "Raster":
         """Subtract the array values with -."""
         self._check_for_array()
-        self.array = self.array - scalar
+        self.values = self.values - scalar
         return self
 
     def __truediv__(self, scalar: int | float) -> "Raster":
         """Divide the array values with /."""
         self._check_for_array()
-        self.array = self.array / scalar
+        self.values = self.values / scalar
         return self
 
     def __floordiv__(self, scalar: int | float) -> "Raster":
         """Floor divide the array values with //."""
         self._check_for_array()
-        self.array = self.array // scalar
+        self.values = self.values // scalar
         return self
 
     def __pow__(self, exponent: int | float) -> "Raster":
         """Exponentiate the array values with **."""
         self._check_for_array()
-        self.array = self.array**exponent
+        self.values = self.values**exponent
         return self
 
     def _has_nessecary_attrs(self, dict_like: dict) -> bool:
@@ -1204,11 +1161,11 @@ class Raster:
 
     def _return_self_or_copy(self, array: np.ndarray, copy: bool) -> "Raster":
         if not copy:
-            self.array = array
+            self.values = array
             return self
         else:
             copy = self.copy()
-            copy.array = array
+            copy.values = array
             return copy
 
     @classmethod
@@ -1251,35 +1208,35 @@ class Raster:
     def _write(
         self, dst: rasterio.io.DatasetReader, window: rasterio.windows.Window
     ) -> None:
-        if np.ma.is_masked(self.array):
-            if len(self.array.shape) == 2:
+        if np.ma.is_masked(self.values):
+            if len(self.values.shape) == 2:
                 return dst.write(
-                    self.array.filled(self.nodata), indexes=1, window=window
+                    self.values.filled(self.nodata), indexes=1, window=window
                 )
 
             for i in range(len(self.indexes_as_tuple())):
                 dst.write(
-                    self.array[i].filled(self.nodata),
+                    self.values[i].filled(self.nodata),
                     indexes=i + 1,
                     window=window,
                 )
 
         else:
-            if len(self.array.shape) == 2:
-                return dst.write(self.array, indexes=1, window=window)
+            if len(self.values.shape) == 2:
+                return dst.write(self.values, indexes=1, window=window)
 
             for i, idx in enumerate(self.indexes_as_tuple()):
-                dst.write(self.array[i], indexes=idx, window=window)
+                dst.write(self.values[i], indexes=idx, window=window)
 
     def _get_indexes(self, indexes: int | tuple[int] | None) -> int | tuple[int] | None:
         if isinstance(indexes, numbers.Number):
             return int(indexes)
         if indexes is None:
-            if self.array is not None and len(self.array.shape) == 3:
-                return tuple(i + 1 for i in range(self.array.shape[0]))
-            elif self.array is not None and len(self.array.shape) == 2:
+            if self.values is not None and len(self.values.shape) == 3:
+                return tuple(i + 1 for i in range(self.values.shape[0]))
+            elif self.values is not None and len(self.values.shape) == 2:
                 return 1
-            elif self.array is not None:
+            elif self.values is not None:
                 raise ValueError("Array must be 2 or 3 dimensional.")
             else:
                 return None
@@ -1320,24 +1277,30 @@ class Raster:
 
     @staticmethod
     def _array_to_geojson(array: np.ndarray, transform: Affine) -> list[tuple]:
+        if np.ma.is_masked(array):
+            array = array.data
         try:
             return [
                 (value, shape(geom))
-                for geom, value in features.shapes(array, transform=transform)
+                for geom, value in features.shapes(
+                    array, transform=transform, mask=None
+                )
             ]
         except ValueError:
             array = array.astype(np.float32)
             return [
                 (value, shape(geom))
-                for geom, value in features.shapes(array, transform=transform)
+                for geom, value in features.shapes(
+                    array, transform=transform, mask=None
+                )
             ]
 
     def _add_indexes_from_array(self, indexes: int | tuple[int]) -> int | tuple[int]:
         if indexes is not None:
             return indexes
-        elif len(self.array.shape) == 3:
-            return tuple(x + 1 for x in range(len(self.array)))
-        elif len(self.array.shape) == 2:
+        elif len(self.values.shape) == 3:
+            return tuple(x + 1 for x in range(len(self.values)))
+        elif len(self.values.shape) == 2:
             return 1
         else:
             raise ValueError
@@ -1364,10 +1327,15 @@ class Raster:
         #     except AttributeError:
         #         pass
 
-        for attr in ["_indexes", "_nodata"]:
-            if not hasattr(self, attr) or getattr(self, attr) is None:
-                new_value = getattr(src, attr.replace("_", ""))
-                setattr(self, attr, new_value)
+        if not hasattr(self, "_indexes") or self._indexes is None:
+            new_value = src.indexes
+            if new_value == 1 or new_value == (1,):
+                new_value = 1
+            self._indexes = new_value
+
+        if not hasattr(self, "_nodata") or self._nodata is None:
+            new_value = src.nodata
+            self._nodata = new_value
 
         # if not hasattr(self, "_indexes") or self._indexes is None:
         #     self._indexes = src.indexes
@@ -1407,7 +1375,7 @@ class Raster:
                 if hasattr(self, "_warped_crs"):
                     src = WarpedVRT(src, crs=self.crs)
 
-                self.array = src.read(
+                self.values = src.read(
                     out_shape=out_shape,
                     **(self.read_kwargs | kwargs),
                 )
@@ -1439,11 +1407,17 @@ class Raster:
             if hasattr(self, "_warped_crs"):
                 src = WarpedVRT(src, crs=self.crs)
 
-            self.array = src.read(out_shape=out_shape, **kwargs)
+            self.values = src.read(out_shape=out_shape, **kwargs)
 
             if not masked:
-                self.array[self.array.mask] = self.nodata
-                self.array = self.array.data
+                try:
+                    self.values[self.values.mask] = self.nodata
+                    self.values = self.values.data
+                except AttributeError:
+                    pass
+                    # self.values = np.ma.masked_array(self.values, mask=mask)
+                    # self.values[self.values.mask] = self.nodata
+                    # self.values = self.values.data
 
             if boundless:
                 self._bounds = src.window_bounds(window=window)
@@ -1454,7 +1428,7 @@ class Raster:
                 else:
                     self._bounds = intersected.bounds
 
-            if not np.size(self.array):
+            if not np.size(self.values):
                 return
 
             if self._dtype:
@@ -1462,8 +1436,8 @@ class Raster:
             else:
                 self = self.as_minimum_dtype()
 
-        if self.array is not None:
-            with memfile_from_array(self.array, **self.profile) as src:
+        if self.values is not None:
+            with memfile_from_array(self.values, **self.profile) as src:
                 _read(self, src, **kwargs)
         else:
             with opener(self.path, file_system=self.file_system) as file:
@@ -1471,7 +1445,7 @@ class Raster:
                     _read(self, src, **kwargs)
 
     def _check_for_array(self, text=""):
-        if self.array is None:
+        if self.values is None:
             raise ValueError("Arrays are not loaded. " + text)
 
 
@@ -1499,82 +1473,3 @@ def get_shape_from_bounds(
     width = int(diffx / resx)
     heigth = int(diffy / resy)
     return heigth, width
-
-
-def get_gradient(raster: Raster, degrees: bool = False, copy: bool = False) -> Raster:
-    """Get the slope of an elevation raster.
-
-    Calculates the absolute slope between the grid cells
-    based on the image resolution.
-
-    For multiband images, the calculation is done for each band.
-
-    Args:
-        raster: Raster instance.
-        degrees: If False (default), the returned values will be in ratios,
-            where a value of 1 means 1 meter up per 1 meter forward. If True,
-            the values will be in degrees from 0 to 90.
-        copy: Whether to copy or overwrite the original Raster.
-            Defaults to False to save memory.
-
-    Returns:
-        The class instance with new array values, or a copy if copy is True.
-
-    Examples:
-    --------
-    Making an array where the gradient to the center is always 10.
-
-    >>> import sgis as sg
-    >>> import numpy as np
-    >>> arr = np.array(
-    ...         [
-    ...             [100, 100, 100, 100, 100],
-    ...             [100, 110, 110, 110, 100],
-    ...             [100, 110, 120, 110, 100],
-    ...             [100, 110, 110, 110, 100],
-    ...             [100, 100, 100, 100, 100],
-    ...         ]
-    ...     )
-
-    Now let's create a Raster from this array with a resolution of 10.
-
-    >>> r = sg.Raster.from_array(arr, crs=None, bounds=(0, 0, 50, 50), res=10)
-
-    The gradient will be 1 (1 meter up for every meter forward).
-    The calculation is by default done in place to save memory.
-
-    >>> r.gradient()
-    >>> r.array
-    array([[0., 1., 1., 1., 0.],
-        [1., 1., 1., 1., 1.],
-        [1., 1., 0., 1., 1.],
-        [1., 1., 1., 1., 1.],
-        [0., 1., 1., 1., 0.]])
-    """
-    out_array = []
-    for array in raster:
-        results = _slope_2d(array, raster.res, degrees=degrees)
-        out_array.append(results)
-
-    if len(raster.shape) == 2:
-        out_array = out_array[0]
-    else:
-        out_array = np.array(out_array)
-
-    return raster._return_self_or_copy(out_array, copy)
-
-
-def _slope_2d(array: np.ndarray, res: int, degrees: int) -> np.ndarray:
-    gradient_x, gradient_y = np.gradient(array, res, res)
-
-    gradient = abs(gradient_x) + abs(gradient_y)
-
-    if not degrees:
-        return gradient
-
-    radians = np.arctan(gradient)
-    degrees = np.degrees(radians)
-
-    assert np.max(degrees) <= 90
-
-    return degrees