Vectorization & Clustering

Raster-to-vector conversion, clustering, polygonization, and translate.

pyramids.dataset.ops.vectorize.Vectorize

Mixin providing vectorization, clustering, and translate methods for Dataset.

Source code in src/pyramids/dataset/ops/vectorize.py

class Vectorize:
    """Mixin providing vectorization, clustering, and translate methods for Dataset."""

    def _band_to_polygon(self, band: int, col_name: str) -> GeoDataFrame:
        gdal_band = self.raster.GetRasterBand(band + 1)
        srs = osr.SpatialReference(wkt=self.crs)

        dst_ds = FeatureCollection.create_ds("memory")
        if dst_ds is None:
            raise RuntimeError("Failed to create in-memory OGR DataSource")
        dst_layer = dst_ds.CreateLayer(col_name, srs=srs)
        dtype = gdal_to_ogr_dtype(self.raster)
        new_field = ogr.FieldDefn(col_name, dtype)
        dst_layer.CreateField(new_field)
        gdal.Polygonize(gdal_band, gdal_band, dst_layer, 0, [], callback=None)

        vector = FeatureCollection(dst_ds)
        gdf = vector._ds_to_gdf()
        return gdf

    def to_feature_collection(
        self,
        mask: GeoDataFrame | None = None,
        add_geometry: str | None = None,
        tile: bool = False,
        tile_size: int = 256,
        touch: bool = True,
    ) -> DataFrame | GeoDataFrame:
        """Convert a dataset to a vector.

        The function does the following:
            - Flatten the array in each band in the raster then mask the values if a mask is given
                otherwise it will flatten all values.
            - Put the values for each band in a column in a dataframe under the name of the raster band,
                but if no meta-data in the raster band exists, an index number will be used [1, 2, 3, ...]
            - The function has an add_geometry parameter with two possible values ["point", "polygon"], which you can
                specify the type of shapely geometry you want to create from each cell,

                - If point is chosen, the created point will be at the center of each cell
                - If a polygon is chosen, a square polygon will be created that covers the entire cell.

        Args:
            mask (GeoDataFrame, optional):
                GeoDataFrame to clip the raster. If given, the raster will be cropped to the mask extent.
            add_geometry (str):
                "Polygon" or "Point" if you want to add a polygon geometry of the cells as column in dataframe.
                Default is None.
            tile (bool):
                True to use tiles in extracting the values from the raster. Default is False.
            tile_size (int):
                Tile size. Default is 1500.
            touch (bool):
                Include the cells that touch the polygon not only those that lie entirely inside the polygon mask.
                Default is True.

        Returns:
            DataFrame | GeoDataFrame:
                The resulting frame will have the band value under the name of the band (if the raster file has
                metadata; if not, the bands will be indexed from 1 to the number of bands).

        Examples:
            - Create a dataset from array with 2 bands and 3*3 array each:

              ```python
              >>> import numpy as np
              >>> arr = np.random.rand(2, 3, 3)
              >>> top_left_corner = (0, 0)
              >>> cell_size = 0.05
              >>> dataset = Dataset.create_from_array(arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326)
              >>> print(dataset.read_array(band=0)) # doctest: +SKIP
              [[0.88625832 0.81804328 0.99372706]
               [0.85333054 0.35448201 0.78079262]
               [0.43887136 0.68166208 0.53170966]]
              >>> print(dataset.read_array(band=1)) # doctest: +SKIP
              [[0.07051872 0.67650833 0.17625027]
               [0.41258071 0.38327938 0.18783139]
               [0.83741314 0.70446373 0.64913575]]

              ```

            - Convert the dataset to dataframe by calling the `to_feature_collection` method:

              ```python
              >>> df = dataset.to_feature_collection()
              >>> print(df) # doctest: +SKIP
                   Band_1    Band_2
              0  0.886258  0.070519
              1  0.818043  0.676508
              2  0.993727  0.176250
              3  0.853331  0.412581
              4  0.354482  0.383279
              5  0.780793  0.187831
              6  0.438871  0.837413
              7  0.681662  0.704464
              8  0.531710  0.649136

              ```

            - Convert the dataset into geodataframe with either a polygon or a point geometry that represents each cell.
                To specify the geometry type use the parameter `add_geometry`:

                  ```python
                  >>> gdf = dataset.to_feature_collection(add_geometry="point")
                  >>> print(gdf) # doctest: +SKIP
                       Band_1    Band_2                  geometry
                  0  0.886258  0.070519  POINT (0.02500 -0.02500)
                  1  0.818043  0.676508  POINT (0.07500 -0.02500)
                  2  0.993727  0.176250  POINT (0.12500 -0.02500)
                  3  0.853331  0.412581  POINT (0.02500 -0.07500)
                  4  0.354482  0.383279  POINT (0.07500 -0.07500)
                  5  0.780793  0.187831  POINT (0.12500 -0.07500)
                  6  0.438871  0.837413  POINT (0.02500 -0.12500)
                  7  0.681662  0.704464  POINT (0.07500 -0.12500)
                  8  0.531710  0.649136  POINT (0.12500 -0.12500)
                  >>> gdf = dataset.to_feature_collection(add_geometry="polygon")
                  >>> print(gdf) # doctest: +SKIP
                       Band_1    Band_2                                           geometry
                  0  0.886258  0.070519  POLYGON ((0.00000 0.00000, 0.05000 0.00000, 0....
                  1  0.818043  0.676508  POLYGON ((0.05000 0.00000, 0.10000 0.00000, 0....
                  2  0.993727  0.176250  POLYGON ((0.10000 0.00000, 0.15000 0.00000, 0....
                  3  0.853331  0.412581  POLYGON ((0.00000 -0.05000, 0.05000 -0.05000, ...
                  4  0.354482  0.383279  POLYGON ((0.05000 -0.05000, 0.10000 -0.05000, ...
                  5  0.780793  0.187831  POLYGON ((0.10000 -0.05000, 0.15000 -0.05000, ...
                  6  0.438871  0.837413  POLYGON ((0.00000 -0.10000, 0.05000 -0.10000, ...
                  7  0.681662  0.704464  POLYGON ((0.05000 -0.10000, 0.10000 -0.10000, ...
                  8  0.531710  0.649136  POLYGON ((0.10000 -0.10000, 0.15000 -0.10000, ...

                  ```

            - Use a mask to crop part of the dataset, and then convert the cropped part to a dataframe/geodataframe:

              - Create a mask that covers only the cell in the middle of the dataset.

                  ```python
                  >>> import geopandas as gpd
                  >>> from shapely.geometry import Polygon
                  >>> poly = gpd.GeoDataFrame(
                  ...             geometry=[Polygon([(0.05, -0.05), (0.05, -0.1), (0.1, -0.1), (0.1, -0.05)])], crs=4326
                  ... )
                  >>> df = dataset.to_feature_collection(mask=poly)
                  >>> print(df) # doctest: +SKIP
                       Band_1    Band_2
                  0  0.354482  0.383279

                  ```

            - If you have a big dataset, and you want to convert it to dataframe in tiles (do not read the whole dataset
                at once but in tiles), you can use the `tile` and the `tile_size` parameters. The values will be the
                same as above; the difference is reading in chunks:

                  ```python
                  >>> gdf = dataset.to_feature_collection(tile=True, tile_size=1)
                  >>> print(gdf) # doctest: +SKIP
                       Band_1    Band_2
                  0  0.886258  0.070519
                  1  0.818043  0.676508
                  2  0.993727  0.176250
                  3  0.853331  0.412581
                  4  0.354482  0.383279
                  5  0.780793  0.187831
                  6  0.438871  0.837413
                  7  0.681662  0.704464
                  8  0.531710  0.649136

                  ```

        """
        band_names = self.band_names

        if mask is not None:
            src = self.crop(mask=mask, touch=touch)
        else:
            src = self

        if tile:
            df = self._extract_values_tiled(band_names, tile_size)
        else:
            df = src._extract_values_full(band_names)

        df.drop(columns=["burn_value", "geometry"], errors="ignore", inplace=True)

        if add_geometry:
            df = self._attach_geometry(src, df, add_geometry)

        return df

    def _extract_values_tiled(self, band_names: list, tile_size: int) -> pd.DataFrame:
        """Extract raster band values into a DataFrame using tiles.

        Args:
            band_names (list): Band names for the DataFrame columns.
            tile_size (int): Tile size in pixels.

        Returns:
            pd.DataFrame: Concatenated DataFrame from all tiles.
        """
        no_data_value = self.no_data_value[0]
        df_list = []
        for arr in self.get_tile(tile_size):
            idx = (1, 2) if arr.ndim > 2 else (0, 1)
            mask_arr = np.ones((arr.shape[idx[0]], arr.shape[idx[1]]))
            pixels = get_pixels(arr, mask_arr).transpose()
            df = pd.DataFrame(pixels, columns=band_names)
            if no_data_value is not None:
                df.replace(no_data_value, np.nan, inplace=True)
            df.dropna(axis=0, inplace=True, ignore_index=True)
            if not df.empty:
                df_list.append(df)

        if not df_list:
            return pd.DataFrame(columns=band_names)

        return pd.concat(df_list, ignore_index=True)

    def _extract_values_full(self, band_names: list) -> pd.DataFrame:
        """Extract all raster band values into a DataFrame (no tiling).

        Args:
            band_names (list): Band names for the DataFrame columns.

        Returns:
            pd.DataFrame: DataFrame with one column per band, no-data rows removed.
        """
        arr = self.read_array()

        if self.band_count == 1:
            pixels = arr.flatten()
        else:
            pixels = (
                arr.flatten()
                .reshape(self.band_count, self.columns * self.rows)
                .transpose()
            )
        df = pd.DataFrame(pixels, columns=band_names)
        if self.no_data_value[0] is not None:
            df.replace(self.no_data_value[0], np.nan, inplace=True)
        df.dropna(axis=0, inplace=True, ignore_index=True)
        return df

    @staticmethod
    def _attach_geometry(
        src, df: pd.DataFrame, geometry_type: str
    ) -> gpd.GeoDataFrame:
        """Attach point or polygon geometry to a DataFrame.

        Args:
            src: The dataset to derive cell geometries from.
            df (pd.DataFrame): DataFrame with band values.
            geometry_type (str): "point" or "polygon".

        Returns:
            gpd.GeoDataFrame: GeoDataFrame with geometry column.
        """
        if geometry_type.lower() == "point":
            coords = src.get_cell_points(domain_only=True)
        else:
            coords = src.get_cell_polygons(domain_only=True)

        gdf = gpd.GeoDataFrame(df.loc[:], geometry=coords["geometry"].to_list())
        gdf = gdf.set_crs(coords.crs.to_epsg())
        return gdf

    def translate(self, path: str | Path | None = None, **kwargs) -> Dataset:
        """Translate.

        The translate function can be used to
        - Convert Between Formats: Convert a raster from one format to another (e.g., from GeoTIFF to JPEG).
        - Subset: Extract a subregion of a raster.
        - Resample: Change the resolution of a raster.
        - Reproject: Change the coordinate reference system of a raster.
        - Scale Values: Scale pixel values to a new range.
        - Change Data Type: Convert the data type of the raster.
        - Apply Compression: Apply compression to the output raster.
        - Apply No-Data Values: Define no-data values for the output raster.


        Parameters
        ----------
        path: str, optional, default is None.
            path to save the output, if None, the output will be saved in memory.
        kwargs:
            unscale:
                unscale values with scale and offset metadata.
            scaleParams:
                list of scale parameters, each of the form [src_min,src_max] or [src_min,src_max,dst_min,dst_max]
            outputType:
                output type (gdalconst.GDT_Byte, etc...)
            exponents:
                list of exponentiation parameters
            bandList:
                array of band numbers (index start at 1)
            maskBand:
                mask band to generate or not ("none", "auto", "mask", 1, ...)
            creationOptions:
                list or dict of creation options
            srcWin:
                subwindow in pixels to extract: [left_x, top_y, width, height]
            projWin:
                subwindow in projected coordinates to extract: [ulx, uly, lrx, lry]
            projWinSRS:
                SRS in which projWin is expressed
            outputBounds:
                assigned output bounds: [ulx, uly, lrx, lry]
            outputGeotransform:
                assigned geotransform matrix (array of 6 values) (mutually exclusive with outputBounds)
            metadataOptions:
                list or dict of metadata options
            outputSRS:
                assigned output SRS
            noData:
                nodata value (or "none" to unset it)
            rgbExpand:
                Color palette expansion mode: "gray", "rgb", "rgba"
            xmp:
                whether to copy XMP metadata
            resampleAlg:
                resampling mode
            overviewLevel:
                To specify which overview level of source files must be used
            domainMetadataOptions:
                list or dict of domain-specific metadata options

        Returns
        -------
        Dataset

        Examples
        --------
        Scale & offset:
            - the translate function can be used to get rid of the scale and offset that are used to manipulate the
            dataset, to get the real values of the dataset.

            Scale:
                - First we will create a dataset from a float32 array with values between 1 and 10, and then we will
                    assign a scale of 0.1 to the dataset.

                    >>> import numpy as np
                    >>> arr = np.random.randint(1, 10, size=(5, 5)).astype(np.float32)
                    >>> print(arr) # doctest: +SKIP
                    [[5. 5. 3. 4. 2.]
                     [2. 5. 5. 8. 5.]
                     [7. 5. 6. 1. 2.]
                     [6. 8. 1. 5. 8.]
                     [2. 5. 2. 2. 9.]]
                    >>> top_left_corner = (0, 0)
                    >>> cell_size = 0.05
                    >>> dataset = Dataset.create_from_array(
                    ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                    ... )
                    >>> print(dataset)
                    <BLANKLINE>
                                Top Left Corner: (0.0, 0.0)
                                Cell size: 0.05
                                Dimension: 5 * 5
                                EPSG: 4326
                                Number of Bands: 1
                                Band names: ['Band_1']
                                Band colors: {0: 'undefined'}
                                Band units: ['']
                                Scale: [1.0]
                                Offset: [0]
                                Mask: -9999.0
                                Data type: float32
                                File: ...
                    <BLANKLINE>
                    >>> dataset.scale = [0.1]

                - now lets unscale the dataset values.

                    >>> unscaled_dataset = dataset.translate(unscale=True)
                    >>> print(unscaled_dataset) # doctest: +SKIP
                    <BLANKLINE>
                                Top Left Corner: (0.0, 0.0)
                                Cell size: 0.05
                                Dimension: 5 * 5
                                EPSG: 4326
                                Number of Bands: 1
                                Band names: ['Band_1']
                                Band colors: {0: 'undefined'}
                                Band units: ['']
                                Scale: [1.0]
                                Offset: [0]
                                Mask: -9999.0
                                Data type: float32
                                File:
                    <BLANKLINE>
                    >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                    [[0.5 0.5 0.3 0.4 0.2]
                     [0.2 0.5 0.5 0.8 0.5]
                     [0.7 0.5 0.6 0.1 0.2]
                     [0.6 0.8 0.1 0.5 0.8]
                     [0.2 0.5 0.2 0.2 0.9]]

            offset:
                - You can also unshift the values of the dataset if the dataset has an offset. To remove the offset
                    from all values in the dataset, you can read the values using the `read_array` and then add the
                    offset value to the array. we will create a dataset from the same array we created above (values
                    are between 1, and 10) with an offset of 100.

                    >>> dataset = Dataset.create_from_array(
                    ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                    ... )
                    >>> print(dataset)
                    <BLANKLINE>
                                Top Left Corner: (0.0, 0.0)
                                Cell size: 0.05
                                Dimension: 5 * 5
                                EPSG: 4326
                                Number of Bands: 1
                                Band names: ['Band_1']
                                Band colors: {0: 'undefined'}
                                Band units: ['']
                                Scale: [1.0]
                                Offset: [0]
                                Mask: -9999.0
                                Data type: float32
                                File: ...
                    <BLANKLINE>

                - set the offset to 100.

                    >>> dataset.offset = [100]

                - check if the offset has been set.

                    >>> print(dataset.offset)
                    [100.0]

                - now lets unscale the dataset values.

                    >>> unscaled_dataset = dataset.translate(unscale=True)
                    >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                    [[105. 105. 103. 104. 102.]
                     [102. 105. 105. 108. 105.]
                     [107. 105. 106. 101. 102.]
                     [106. 108. 101. 105. 108.]
                     [102. 105. 102. 102. 109.]]

                - as you see, all the values have been shifted by 100. now if you check the offset of the dataset

                    >>> print(unscaled_dataset.offset)
                    [0]

            Offset and Scale together:
                - we can unscale and get rid of the offset at the same time.

                    >>> dataset = Dataset.create_from_array(
                    ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                    ... )

                - set the offset to 100, and a scale of 0.1.

                    >>> dataset.offset = [100]
                    >>> dataset.scale = [0.1]

                - check if the offset has been set.

                    >>> print(dataset.offset)
                    [100.0]
                    >>> print(dataset.scale)
                    [0.1]

                - now lets unscale the dataset values.

                    >>> unscaled_dataset = dataset.translate(unscale=True)
                    >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                    [[100.5 100.5 100.3 100.4 100.2]
                     [100.2 100.5 100.5 100.8 100.5]
                     [100.7 100.5 100.6 100.1 100.2]
                     [100.6 100.8 100.1 100.5 100.8]
                     [100.2 100.5 100.2 100.2 100.9]]

                - Now you can see that the values were multiplied first by the scale; then the offset value was added.
                    `value * scale + offset`

                    >>> print(unscaled_dataset.offset)
                    [0]
                    >>> print(unscaled_dataset.scale)
                    [1.0]

        Scale between two values:
            - you can scale the values of the dataset between two values, for example, you can scale the values
                between two values 0 and 1.

                >>> dataset = Dataset.create_from_array(
                ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                ... )
                >>> print(dataset.stats()) # doctest: +SKIP
                        min  max  mean      std
                Band_1  1.0  9.0   4.0  2.19089
                >>> scaled_dataset = dataset.translate(scaleParams=[[1, 9, 0, 255]], outputType=gdal.GDT_Byte)
                >>> print(scaled_dataset.read_array()) # doctest: +SKIP
                [[128 128  64  96  32]
                 [ 32 128 128 223 128]
                 [191 128 159   0  32]
                 [159 223   0 128 223]
                 [ 32 128  32  32 255]]


        """
        if path is None:
            driver = "MEM"
            path = ""
        else:
            driver = "GTiff"

        options = gdal.TranslateOptions(format=driver, **kwargs)
        dst = gdal.Translate(str(path), self.raster, options=options)
        result = type(self)(dst, access="write")
        return result

    @staticmethod
    def _nearest_neighbour(
        array: np.ndarray, no_data_value: float | int, rows: list, cols: list
    ) -> np.ndarray:
        """Fill specified cells with the value of the nearest neighbor.

            - The _nearest_neighbour method fills the cells with the given indices in rows and cols with the value
                of the nearest neighbor.
            - The raster grid is square, so the 4 perpendicular directions are of the same proximity; the function
                gives priority to the right, left, bottom, and then top, and similarly for 45-degree directions:
                right-bottom, left-bottom, left-top, right-top.

        Args:
            array (np.ndarray):
                Array to fill some of its cells with the nearest value.
            no_data_value (float | int):
                Value stored in cells that are out of the domain.
            rows (list[int]):
                Row indices of the cells you want to fill with the nearest neighbor.
            cols (list[int]):
                Column indices of the cells you want to fill with the nearest neighbor.

        Returns:
            np.ndarray:
                Cells of given indices filled with the value of the nearest neighbor.

        Examples:
            - Basic usage:

              ```python
              >>> import numpy as np
              >>> arr = np.random.rand(5, 5)
              >>> top_left_corner = (0, 0)
              >>> cell_size = 0.05
              >>> dataset = Dataset.create_from_array(
              ...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
              ... )
              >>> req_rows = [1,3]
              >>> req_cols = [2,4]
              >>> no_data_value = dataset.no_data_value[0]
              >>> new_array = Dataset._nearest_neighbour(arr, no_data_value, req_rows, req_cols)

              ```
        """
        if not isinstance(array, np.ndarray):
            raise TypeError(
                "src should be read using gdal (gdal dataset please read it using gdal library) "
            )
        if not isinstance(rows, list):
            raise TypeError("The `rows` input has to be of type list")
        if not isinstance(cols, list):
            raise TypeError("The `cols` input has to be of type list")

        no_rows = np.shape(array)[0]
        no_cols = np.shape(array)[1]

        for i in range(len(rows)):
            # give the cell the value of the cell that is at the right
            if cols[i] + 1 < no_cols:
                if array[rows[i], cols[i] + 1] != no_data_value:
                    array[rows[i], cols[i]] = array[rows[i], cols[i] + 1]

            elif array[rows[i], cols[i] - 1] != no_data_value and cols[i] - 1 > 0:
                # give the cell the value of the cell that is at the left
                array[rows[i], cols[i]] = array[rows[i], cols[i] - 1]

            elif array[rows[i] - 1, cols[i]] != no_data_value and rows[i] - 1 > 0:
                # give the cell the value of the cell that is at the bottom
                array[rows[i], cols[i]] = array[rows[i] - 1, cols[i]]

            elif array[rows[i] + 1, cols[i]] != no_data_value and rows[i] + 1 < no_rows:
                # give the cell the value of the cell that is at the Top
                array[rows[i], cols[i]] = array[rows[i] + 1, cols[i]]

            elif (
                array[rows[i] - 1, cols[i] + 1] != no_data_value
                and rows[i] - 1 > 0
                and cols[i] + 1 <= no_cols
            ):
                # give the cell the value of the cell that is at the right bottom
                array[rows[i], cols[i]] = array[rows[i] - 1, cols[i] + 1]

            elif (
                array[rows[i] - 1, cols[i] - 1] != no_data_value
                and rows[i] - 1 > 0
                and cols[i] - 1 > 0
            ):
                # give the cell the value of the cell that is at the left bottom
                array[rows[i], cols[i]] = array[rows[i] - 1, cols[i] - 1]

            elif (
                array[rows[i] + 1, cols[i] - 1] != no_data_value
                and rows[i] + 1 <= no_rows
                and cols[i] - 1 > 0
            ):
                # give the cell the value of the cell that is at the left Top
                array[rows[i], cols[i]] = array[rows[i] + 1, cols[i] - 1]

            elif (
                array[rows[i] + 1, cols[i] + 1] != no_data_value
                and rows[i] + 1 <= no_rows
                and cols[i] + 1 <= no_cols
            ):
                # give the cell the value of the cell that is at the right Top
                array[rows[i], cols[i]] = array[rows[i] + 1, cols[i] + 1]
            else:
                logger.warning("the cell is isolated (No surrounding cells exist)")
        return array

    @staticmethod
    def _group_neighbours(
        array, i, j, lower_bound, upper_bound, position, values, count, cluster
    ) -> None:
        """Group neighboring cells with the same values using iterative BFS.

        Uses a queue-based breadth-first search instead of recursion to avoid
        hitting Python's recursion limit on large connected regions.

        Note: The starting cell (i, j) is enqueued but not marked. When a
        discovered neighbor later checks its own neighbors, it will find (i, j)
        still unmarked and add it to position/values. Therefore the starting
        cell appears in the output whenever it has at least one in-bound
        neighbor. The caller (cluster) handles truly isolated cells separately.
        """
        rows, cols = array.shape
        queue = collections.deque()
        queue.append((i, j))

        while queue:
            ci, cj = queue.popleft()
            for di in (-1, 0, 1):
                for dj in (-1, 0, 1):
                    if di == 0 and dj == 0:
                        continue
                    ni, nj = ci + di, cj + dj
                    if 0 <= ni < rows and 0 <= nj < cols:
                        if (
                            cluster[ni, nj] == 0
                            and lower_bound <= array[ni, nj] <= upper_bound
                        ):
                            cluster[ni, nj] = count
                            position.append([ni, nj])
                            values.append(array[ni, nj])
                            queue.append((ni, nj))

    def cluster(
        self, lower_bound: Any, upper_bound: Any
    ) -> tuple[np.ndarray, int, list, list]:
        """Group all the connected values between two bounds.

        Args:
            lower_bound (Number):
                Lower bound of the cluster.
            upper_bound (Number):
                Upper bound of the cluster.

        Returns:
            tuple[np.ndarray, int, list, list]:
                - cluster (np.ndarray):
                    Array with integers representing the cluster number per cell.
                - count (int):
                    Number of clusters in the array.
                - position (list[list[int, int]]):
                    List of [row, col] indices for the position of each value.
                - values (list[Number]):
                    Values stored in each cell in the cluster.

        Examples:
            - First, we will create a dataset with 10 rows and 10 columns.

              ```python
              >>> import numpy as np
              >>> np.random.seed(10)
              >>> arr = np.random.randint(1, 5, size=(5, 5))
              >>> print(arr) # doctest: +SKIP
              [[2 3 3 2 3]
               [3 4 1 1 1]
               [1 3 3 2 2]
               [4 1 1 3 2]
               [2 4 2 3 2]]
              >>> top_left_corner = (0, 0)
              >>> cell_size = 0.05
              >>> dataset = Dataset.create_from_array(
              ...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
              ... )
              >>> dataset.plot(
              ...     color_scale=4, bounds=[1, 1.9, 4.1, 5], display_cell_value=True, num_size=12,
              ...     background_color_threshold=5
              ... )  # doctest: +SKIP

              ```
              ![cluster](./../../_images/dataset/cluster.png)

            - Now let's cluster the values in the dataset that are between 2 and 4.

              ```python
              >>> lower_value = 2
              >>> upper_value = 4
              >>> cluster_array, count, position, values = dataset.cluster(lower_value, upper_value)

              ```
            - The first returned output is a binary array with 1 indicating that the cell value is inside the
                cluster, and 0 is outside.

              ```python
              >>> print(cluster_array)  # doctest: +SKIP
              [[1. 1. 1. 1. 1.]
               [1. 1. 0. 0. 0.]
               [0. 1. 1. 1. 1.]
               [1. 0. 0. 1. 1.]
               [1. 1. 1. 1. 1.]]

              ```
            - The second returned value is the number of connected clusters.

              ```python
              >>> print(count) # doctest: +SKIP
              2

              ```
            - The third returned value is the indices of the cells that belong to the cluster.

              ```python
              >>> print(position) # doctest: +SKIP
              [[1, 0], [2, 1], [2, 2], [3, 3], [4, 3], [4, 4], [3, 4], [2, 4], [2, 3], [4, 2], [4, 1], [3, 0], [4, 0], [1, 1], [0, 2], [0, 3], [0, 4], [0, 1], [0, 0]]

              ```
            - The fourth returned value is a list of the values that are in the cluster (extracted from these cells).

              ```python
              >>> print(values) # doctest: +SKIP
              [3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 4, 4, 2, 4, 3, 2, 3, 3, 2]

              ```

        """
        data = self.read_array()
        position: list[list[int]] = []
        values: list[Any] = []
        count = 1
        cluster = np.zeros(shape=(data.shape[0], data.shape[1]))

        for i in range(data.shape[0]):
            for j in range(data.shape[1]):
                if lower_bound <= data[i, j] <= upper_bound and cluster[i, j] == 0:
                    self._group_neighbours(
                        data,
                        i,
                        j,
                        lower_bound,
                        upper_bound,
                        position,
                        values,
                        count,
                        cluster,
                    )
                    if cluster[i, j] == 0:
                        position.append([i, j])
                        values.append(data[i, j])
                        cluster[i, j] = count
                    count += 1

        return cluster, count, position, values

    def cluster2(
        self,
        band: int | list[int] | None = None,
    ) -> GeoDataFrame:
        """Cluster the connected equal cells into polygons.

        - Creates vector polygons for all connected regions of pixels in the raster sharing a common
            pixel value (group neighboring cells with the same value into one polygon).

        Args:
            band (int | List[int] | None):
                Band index 0, 1, 2, 3, ...

        Returns:
            GeoDataFrame:
                GeodataFrame containing polygon geomtries for all connected regions.

        Examples:
            - First, we will create a 10*10 dataset full of random integer between 1, and 5.

              ```python
              >>> import numpy as np
              >>> np.random.seed(200)
              >>> arr = np.random.randint(1, 5, size=(10, 10))
              >>> print(arr)  # doctest: +SKIP
              [[3 2 1 1 3 4 1 4 2 3]
               [4 2 2 4 3 3 1 2 4 4]
               [4 2 4 2 3 4 2 1 4 3]
               [3 2 1 4 3 3 4 1 1 4]
               [1 2 4 2 2 1 3 2 3 1]
               [1 4 4 4 1 1 4 2 1 1]
               [1 3 2 3 3 4 1 3 1 3]
               [4 1 3 3 3 4 1 4 1 1]
               [2 1 3 3 4 2 2 1 3 4]
               [2 3 2 2 4 2 1 3 2 2]]
              >>> top_left_corner = (0, 0)
              >>> cell_size = 0.05
              >>> dataset = Dataset.create_from_array(
              ...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
              ... )

              ```

            - Now, let's cluster the connected equal cells into polygons.
              ```python
              >>> gdf = dataset.cluster2()
              >>> print(gdf)  # doctest: +SKIP
                  Band_1                                           geometry
              0        3  POLYGON ((0 0, 0 -0.05, 0.05 -0.05, 0.05 0, 0 0))
              1        1  POLYGON ((0.1 0, 0.1 -0.05, 0.2 -0.05, 0.2 0, ...
              2        4  POLYGON ((0.25 0, 0.25 -0.05, 0.3 -0.05, 0.3 0...
              3        4  POLYGON ((0.35 0, 0.35 -0.05, 0.4 -0.05, 0.4 0...
              4        2  POLYGON ((0.4 0, 0.4 -0.05, 0.45 -0.05, 0.45 0...
              5        3  POLYGON ((0.45 0, 0.45 -0.05, 0.5 -0.05, 0.5 0...
              6        1  POLYGON ((0.3 0, 0.3 -0.1, 0.35 -0.1, 0.35 0, ...
              7        4  POLYGON ((0.15 -0.05, 0.15 -0.1, 0.2 -0.1, 0.2...
              8        2  POLYGON ((0.35 -0.05, 0.35 -0.1, 0.4 -0.1, 0.4...
              9        4  POLYGON ((0 -0.05, 0 -0.15, 0.05 -0.15, 0.05 -...
              10       4  POLYGON ((0.4 -0.05, 0.4 -0.15, 0.45 -0.15, 0....
              11       4  POLYGON ((0.1 -0.1, 0.1 -0.15, 0.15 -0.15, 0.1...

              ```

        """
        if band is None:
            band = 0

        if isinstance(band, int):
            name = self.band_names[band]
            gdf = self._band_to_polygon(band, name)
        else:
            gdfs = []
            for b in band:
                name = self.band_names[b]
                gdfs.append(self._band_to_polygon(b, name))
            gdf = gpd.GeoDataFrame(pd.concat(gdfs, ignore_index=True))

        return gdf

to_feature_collection(mask=None, add_geometry=None, tile=False, tile_size=256, touch=True)

Convert a dataset to a vector.

The function does the following

• Flatten the array in each band in the raster then mask the values if a mask is given otherwise it will flatten all values.
• Put the values for each band in a column in a dataframe under the name of the raster band, but if no meta-data in the raster band exists, an index number will be used [1, 2, 3, ...]

• The function has an add_geometry parameter with two possible values ["point", "polygon"], which you can specify the type of shapely geometry you want to create from each cell,

  • If point is chosen, the created point will be at the center of each cell
  • If a polygon is chosen, a square polygon will be created that covers the entire cell.

Parameters:

Name	Type	Description	Default
mask	GeoDataFrame	GeoDataFrame to clip the raster. If given, the raster will be cropped to the mask extent.	None
add_geometry	str	"Polygon" or "Point" if you want to add a polygon geometry of the cells as column in dataframe. Default is None.	None
tile	bool	True to use tiles in extracting the values from the raster. Default is False.	False
tile_size	int	Tile size. Default is 1500.	256
touch	bool	Include the cells that touch the polygon not only those that lie entirely inside the polygon mask. Default is True.	True

Returns:

Type	Description
DataFrame | GeoDataFrame	DataFrame | GeoDataFrame: The resulting frame will have the band value under the name of the band (if the raster file has metadata; if not, the bands will be indexed from 1 to the number of bands).

Examples:

• Create a dataset from array with 2 bands and 3*3 array each:

>>> import numpy as np
>>> arr = np.random.rand(2, 3, 3)
>>> top_left_corner = (0, 0)
>>> cell_size = 0.05
>>> dataset = Dataset.create_from_array(arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326)
>>> print(dataset.read_array(band=0)) # doctest: +SKIP
[[0.88625832 0.81804328 0.99372706]
 [0.85333054 0.35448201 0.78079262]
 [0.43887136 0.68166208 0.53170966]]
>>> print(dataset.read_array(band=1)) # doctest: +SKIP
[[0.07051872 0.67650833 0.17625027]
 [0.41258071 0.38327938 0.18783139]
 [0.83741314 0.70446373 0.64913575]]

• Convert the dataset to dataframe by calling the to_feature_collection method:

>>> df = dataset.to_feature_collection()
>>> print(df) # doctest: +SKIP
     Band_1    Band_2
0  0.886258  0.070519
1  0.818043  0.676508
2  0.993727  0.176250
3  0.853331  0.412581
4  0.354482  0.383279
5  0.780793  0.187831
6  0.438871  0.837413
7  0.681662  0.704464
8  0.531710  0.649136

• Convert the dataset into geodataframe with either a polygon or a point geometry that represents each cell. To specify the geometry type use the parameter add_geometry:

  >>> gdf = dataset.to_feature_collection(add_geometry="point")
  >>> print(gdf) # doctest: +SKIP
       Band_1    Band_2                  geometry
  0  0.886258  0.070519  POINT (0.02500 -0.02500)
  1  0.818043  0.676508  POINT (0.07500 -0.02500)
  2  0.993727  0.176250  POINT (0.12500 -0.02500)
  3  0.853331  0.412581  POINT (0.02500 -0.07500)
  4  0.354482  0.383279  POINT (0.07500 -0.07500)
  5  0.780793  0.187831  POINT (0.12500 -0.07500)
  6  0.438871  0.837413  POINT (0.02500 -0.12500)
  7  0.681662  0.704464  POINT (0.07500 -0.12500)
  8  0.531710  0.649136  POINT (0.12500 -0.12500)
  >>> gdf = dataset.to_feature_collection(add_geometry="polygon")
  >>> print(gdf) # doctest: +SKIP
       Band_1    Band_2                                           geometry
  0  0.886258  0.070519  POLYGON ((0.00000 0.00000, 0.05000 0.00000, 0....
  1  0.818043  0.676508  POLYGON ((0.05000 0.00000, 0.10000 0.00000, 0....
  2  0.993727  0.176250  POLYGON ((0.10000 0.00000, 0.15000 0.00000, 0....
  3  0.853331  0.412581  POLYGON ((0.00000 -0.05000, 0.05000 -0.05000, ...
  4  0.354482  0.383279  POLYGON ((0.05000 -0.05000, 0.10000 -0.05000, ...
  5  0.780793  0.187831  POLYGON ((0.10000 -0.05000, 0.15000 -0.05000, ...
  6  0.438871  0.837413  POLYGON ((0.00000 -0.10000, 0.05000 -0.10000, ...
  7  0.681662  0.704464  POLYGON ((0.05000 -0.10000, 0.10000 -0.10000, ...
  8  0.531710  0.649136  POLYGON ((0.10000 -0.10000, 0.15000 -0.10000, ...
  

• Use a mask to crop part of the dataset, and then convert the cropped part to a dataframe/geodataframe:

• Create a mask that covers only the cell in the middle of the dataset.

  >>> import geopandas as gpd
  >>> from shapely.geometry import Polygon
  >>> poly = gpd.GeoDataFrame(
  ...             geometry=[Polygon([(0.05, -0.05), (0.05, -0.1), (0.1, -0.1), (0.1, -0.05)])], crs=4326
  ... )
  >>> df = dataset.to_feature_collection(mask=poly)
  >>> print(df) # doctest: +SKIP
       Band_1    Band_2
  0  0.354482  0.383279
  

• If you have a big dataset, and you want to convert it to dataframe in tiles (do not read the whole dataset at once but in tiles), you can use the tile and the tile_size parameters. The values will be the same as above; the difference is reading in chunks:

  >>> gdf = dataset.to_feature_collection(tile=True, tile_size=1)
  >>> print(gdf) # doctest: +SKIP
       Band_1    Band_2
  0  0.886258  0.070519
  1  0.818043  0.676508
  2  0.993727  0.176250
  3  0.853331  0.412581
  4  0.354482  0.383279
  5  0.780793  0.187831
  6  0.438871  0.837413
  7  0.681662  0.704464
  8  0.531710  0.649136
  

Source code in src/pyramids/dataset/ops/vectorize.py

def to_feature_collection(
    self,
    mask: GeoDataFrame | None = None,
    add_geometry: str | None = None,
    tile: bool = False,
    tile_size: int = 256,
    touch: bool = True,
) -> DataFrame | GeoDataFrame:
    """Convert a dataset to a vector.

    The function does the following:
        - Flatten the array in each band in the raster then mask the values if a mask is given
            otherwise it will flatten all values.
        - Put the values for each band in a column in a dataframe under the name of the raster band,
            but if no meta-data in the raster band exists, an index number will be used [1, 2, 3, ...]
        - The function has an add_geometry parameter with two possible values ["point", "polygon"], which you can
            specify the type of shapely geometry you want to create from each cell,

            - If point is chosen, the created point will be at the center of each cell
            - If a polygon is chosen, a square polygon will be created that covers the entire cell.

    Args:
        mask (GeoDataFrame, optional):
            GeoDataFrame to clip the raster. If given, the raster will be cropped to the mask extent.
        add_geometry (str):
            "Polygon" or "Point" if you want to add a polygon geometry of the cells as column in dataframe.
            Default is None.
        tile (bool):
            True to use tiles in extracting the values from the raster. Default is False.
        tile_size (int):
            Tile size. Default is 1500.
        touch (bool):
            Include the cells that touch the polygon not only those that lie entirely inside the polygon mask.
            Default is True.

    Returns:
        DataFrame | GeoDataFrame:
            The resulting frame will have the band value under the name of the band (if the raster file has
            metadata; if not, the bands will be indexed from 1 to the number of bands).

    Examples:
        - Create a dataset from array with 2 bands and 3*3 array each:

          ```python
          >>> import numpy as np
          >>> arr = np.random.rand(2, 3, 3)
          >>> top_left_corner = (0, 0)
          >>> cell_size = 0.05
          >>> dataset = Dataset.create_from_array(arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326)
          >>> print(dataset.read_array(band=0)) # doctest: +SKIP
          [[0.88625832 0.81804328 0.99372706]
           [0.85333054 0.35448201 0.78079262]
           [0.43887136 0.68166208 0.53170966]]
          >>> print(dataset.read_array(band=1)) # doctest: +SKIP
          [[0.07051872 0.67650833 0.17625027]
           [0.41258071 0.38327938 0.18783139]
           [0.83741314 0.70446373 0.64913575]]

          ```

        - Convert the dataset to dataframe by calling the `to_feature_collection` method:

          ```python
          >>> df = dataset.to_feature_collection()
          >>> print(df) # doctest: +SKIP
               Band_1    Band_2
          0  0.886258  0.070519
          1  0.818043  0.676508
          2  0.993727  0.176250
          3  0.853331  0.412581
          4  0.354482  0.383279
          5  0.780793  0.187831
          6  0.438871  0.837413
          7  0.681662  0.704464
          8  0.531710  0.649136

          ```

        - Convert the dataset into geodataframe with either a polygon or a point geometry that represents each cell.
            To specify the geometry type use the parameter `add_geometry`:

              ```python
              >>> gdf = dataset.to_feature_collection(add_geometry="point")
              >>> print(gdf) # doctest: +SKIP
                   Band_1    Band_2                  geometry
              0  0.886258  0.070519  POINT (0.02500 -0.02500)
              1  0.818043  0.676508  POINT (0.07500 -0.02500)
              2  0.993727  0.176250  POINT (0.12500 -0.02500)
              3  0.853331  0.412581  POINT (0.02500 -0.07500)
              4  0.354482  0.383279  POINT (0.07500 -0.07500)
              5  0.780793  0.187831  POINT (0.12500 -0.07500)
              6  0.438871  0.837413  POINT (0.02500 -0.12500)
              7  0.681662  0.704464  POINT (0.07500 -0.12500)
              8  0.531710  0.649136  POINT (0.12500 -0.12500)
              >>> gdf = dataset.to_feature_collection(add_geometry="polygon")
              >>> print(gdf) # doctest: +SKIP
                   Band_1    Band_2                                           geometry
              0  0.886258  0.070519  POLYGON ((0.00000 0.00000, 0.05000 0.00000, 0....
              1  0.818043  0.676508  POLYGON ((0.05000 0.00000, 0.10000 0.00000, 0....
              2  0.993727  0.176250  POLYGON ((0.10000 0.00000, 0.15000 0.00000, 0....
              3  0.853331  0.412581  POLYGON ((0.00000 -0.05000, 0.05000 -0.05000, ...
              4  0.354482  0.383279  POLYGON ((0.05000 -0.05000, 0.10000 -0.05000, ...
              5  0.780793  0.187831  POLYGON ((0.10000 -0.05000, 0.15000 -0.05000, ...
              6  0.438871  0.837413  POLYGON ((0.00000 -0.10000, 0.05000 -0.10000, ...
              7  0.681662  0.704464  POLYGON ((0.05000 -0.10000, 0.10000 -0.10000, ...
              8  0.531710  0.649136  POLYGON ((0.10000 -0.10000, 0.15000 -0.10000, ...

              ```

        - Use a mask to crop part of the dataset, and then convert the cropped part to a dataframe/geodataframe:

          - Create a mask that covers only the cell in the middle of the dataset.

              ```python
              >>> import geopandas as gpd
              >>> from shapely.geometry import Polygon
              >>> poly = gpd.GeoDataFrame(
              ...             geometry=[Polygon([(0.05, -0.05), (0.05, -0.1), (0.1, -0.1), (0.1, -0.05)])], crs=4326
              ... )
              >>> df = dataset.to_feature_collection(mask=poly)
              >>> print(df) # doctest: +SKIP
                   Band_1    Band_2
              0  0.354482  0.383279

              ```

        - If you have a big dataset, and you want to convert it to dataframe in tiles (do not read the whole dataset
            at once but in tiles), you can use the `tile` and the `tile_size` parameters. The values will be the
            same as above; the difference is reading in chunks:

              ```python
              >>> gdf = dataset.to_feature_collection(tile=True, tile_size=1)
              >>> print(gdf) # doctest: +SKIP
                   Band_1    Band_2
              0  0.886258  0.070519
              1  0.818043  0.676508
              2  0.993727  0.176250
              3  0.853331  0.412581
              4  0.354482  0.383279
              5  0.780793  0.187831
              6  0.438871  0.837413
              7  0.681662  0.704464
              8  0.531710  0.649136

              ```

    """
    band_names = self.band_names

    if mask is not None:
        src = self.crop(mask=mask, touch=touch)
    else:
        src = self

    if tile:
        df = self._extract_values_tiled(band_names, tile_size)
    else:
        df = src._extract_values_full(band_names)

    df.drop(columns=["burn_value", "geometry"], errors="ignore", inplace=True)

    if add_geometry:
        df = self._attach_geometry(src, df, add_geometry)

    return df

translate(path=None, **kwargs)

Translate.

The translate function can be used to - Convert Between Formats: Convert a raster from one format to another (e.g., from GeoTIFF to JPEG). - Subset: Extract a subregion of a raster. - Resample: Change the resolution of a raster. - Reproject: Change the coordinate reference system of a raster. - Scale Values: Scale pixel values to a new range. - Change Data Type: Convert the data type of the raster. - Apply Compression: Apply compression to the output raster. - Apply No-Data Values: Define no-data values for the output raster.

Parameters

path: str, optional, default is None. path to save the output, if None, the output will be saved in memory. kwargs: unscale: unscale values with scale and offset metadata. scaleParams: list of scale parameters, each of the form [src_min,src_max] or [src_min,src_max,dst_min,dst_max] outputType: output type (gdalconst.GDT_Byte, etc...) exponents: list of exponentiation parameters bandList: array of band numbers (index start at 1) maskBand: mask band to generate or not ("none", "auto", "mask", 1, ...) creationOptions: list or dict of creation options srcWin: subwindow in pixels to extract: [left_x, top_y, width, height] projWin: subwindow in projected coordinates to extract: [ulx, uly, lrx, lry] projWinSRS: SRS in which projWin is expressed outputBounds: assigned output bounds: [ulx, uly, lrx, lry] outputGeotransform: assigned geotransform matrix (array of 6 values) (mutually exclusive with outputBounds) metadataOptions: list or dict of metadata options outputSRS: assigned output SRS noData: nodata value (or "none" to unset it) rgbExpand: Color palette expansion mode: "gray", "rgb", "rgba" xmp: whether to copy XMP metadata resampleAlg: resampling mode overviewLevel: To specify which overview level of source files must be used domainMetadataOptions: list or dict of domain-specific metadata options

Returns

Dataset

Examples

Scale & offset: - the translate function can be used to get rid of the scale and offset that are used to manipulate the dataset, to get the real values of the dataset.

Scale:
    - First we will create a dataset from a float32 array with values between 1 and 10, and then we will
        assign a scale of 0.1 to the dataset.

        >>> import numpy as np
        >>> arr = np.random.randint(1, 10, size=(5, 5)).astype(np.float32)
        >>> print(arr) # doctest: +SKIP
        [[5. 5. 3. 4. 2.]
         [2. 5. 5. 8. 5.]
         [7. 5. 6. 1. 2.]
         [6. 8. 1. 5. 8.]
         [2. 5. 2. 2. 9.]]
        >>> top_left_corner = (0, 0)
        >>> cell_size = 0.05
        >>> dataset = Dataset.create_from_array(
        ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
        ... )
        >>> print(dataset)
        <BLANKLINE>
                    Top Left Corner: (0.0, 0.0)
                    Cell size: 0.05
                    Dimension: 5 * 5
                    EPSG: 4326
                    Number of Bands: 1
                    Band names: ['Band_1']
                    Band colors: {0: 'undefined'}
                    Band units: ['']
                    Scale: [1.0]
                    Offset: [0]
                    Mask: -9999.0
                    Data type: float32
                    File: ...
        <BLANKLINE>
        >>> dataset.scale = [0.1]

    - now lets unscale the dataset values.

        >>> unscaled_dataset = dataset.translate(unscale=True)
        >>> print(unscaled_dataset) # doctest: +SKIP
        <BLANKLINE>
                    Top Left Corner: (0.0, 0.0)
                    Cell size: 0.05
                    Dimension: 5 * 5
                    EPSG: 4326
                    Number of Bands: 1
                    Band names: ['Band_1']
                    Band colors: {0: 'undefined'}
                    Band units: ['']
                    Scale: [1.0]
                    Offset: [0]
                    Mask: -9999.0
                    Data type: float32
                    File:
        <BLANKLINE>
        >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
        [[0.5 0.5 0.3 0.4 0.2]
         [0.2 0.5 0.5 0.8 0.5]
         [0.7 0.5 0.6 0.1 0.2]
         [0.6 0.8 0.1 0.5 0.8]
         [0.2 0.5 0.2 0.2 0.9]]

offset:
    - You can also unshift the values of the dataset if the dataset has an offset. To remove the offset
        from all values in the dataset, you can read the values using the `read_array` and then add the
        offset value to the array. we will create a dataset from the same array we created above (values
        are between 1, and 10) with an offset of 100.

        >>> dataset = Dataset.create_from_array(
        ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
        ... )
        >>> print(dataset)
        <BLANKLINE>
                    Top Left Corner: (0.0, 0.0)
                    Cell size: 0.05
                    Dimension: 5 * 5
                    EPSG: 4326
                    Number of Bands: 1
                    Band names: ['Band_1']
                    Band colors: {0: 'undefined'}
                    Band units: ['']
                    Scale: [1.0]
                    Offset: [0]
                    Mask: -9999.0
                    Data type: float32
                    File: ...
        <BLANKLINE>

    - set the offset to 100.

        >>> dataset.offset = [100]

    - check if the offset has been set.

        >>> print(dataset.offset)
        [100.0]

    - now lets unscale the dataset values.

        >>> unscaled_dataset = dataset.translate(unscale=True)
        >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
        [[105. 105. 103. 104. 102.]
         [102. 105. 105. 108. 105.]
         [107. 105. 106. 101. 102.]
         [106. 108. 101. 105. 108.]
         [102. 105. 102. 102. 109.]]

    - as you see, all the values have been shifted by 100. now if you check the offset of the dataset

        >>> print(unscaled_dataset.offset)
        [0]

Offset and Scale together:
    - we can unscale and get rid of the offset at the same time.

        >>> dataset = Dataset.create_from_array(
        ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
        ... )

    - set the offset to 100, and a scale of 0.1.

        >>> dataset.offset = [100]
        >>> dataset.scale = [0.1]

    - check if the offset has been set.

        >>> print(dataset.offset)
        [100.0]
        >>> print(dataset.scale)
        [0.1]

    - now lets unscale the dataset values.

        >>> unscaled_dataset = dataset.translate(unscale=True)
        >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
        [[100.5 100.5 100.3 100.4 100.2]
         [100.2 100.5 100.5 100.8 100.5]
         [100.7 100.5 100.6 100.1 100.2]
         [100.6 100.8 100.1 100.5 100.8]
         [100.2 100.5 100.2 100.2 100.9]]

    - Now you can see that the values were multiplied first by the scale; then the offset value was added.
        `value * scale + offset`

        >>> print(unscaled_dataset.offset)
        [0]
        >>> print(unscaled_dataset.scale)
        [1.0]

Scale between two values

• you can scale the values of the dataset between two values, for example, you can scale the values between two values 0 and 1.

  dataset = Dataset.create_from_array( ... arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326 ... ) print(dataset.stats()) # doctest: +SKIP min max mean std Band_1 1.0 9.0 4.0 2.19089 scaled_dataset = dataset.translate(scaleParams=[[1, 9, 0, 255]], outputType=gdal.GDT_Byte) print(scaled_dataset.read_array()) # doctest: +SKIP [[128 128 64 96 32] [ 32 128 128 223 128] [191 128 159 0 32] [159 223 0 128 223] [ 32 128 32 32 255]]

Source code in src/pyramids/dataset/ops/vectorize.py

def translate(self, path: str | Path | None = None, **kwargs) -> Dataset:
    """Translate.

    The translate function can be used to
    - Convert Between Formats: Convert a raster from one format to another (e.g., from GeoTIFF to JPEG).
    - Subset: Extract a subregion of a raster.
    - Resample: Change the resolution of a raster.
    - Reproject: Change the coordinate reference system of a raster.
    - Scale Values: Scale pixel values to a new range.
    - Change Data Type: Convert the data type of the raster.
    - Apply Compression: Apply compression to the output raster.
    - Apply No-Data Values: Define no-data values for the output raster.


    Parameters
    ----------
    path: str, optional, default is None.
        path to save the output, if None, the output will be saved in memory.
    kwargs:
        unscale:
            unscale values with scale and offset metadata.
        scaleParams:
            list of scale parameters, each of the form [src_min,src_max] or [src_min,src_max,dst_min,dst_max]
        outputType:
            output type (gdalconst.GDT_Byte, etc...)
        exponents:
            list of exponentiation parameters
        bandList:
            array of band numbers (index start at 1)
        maskBand:
            mask band to generate or not ("none", "auto", "mask", 1, ...)
        creationOptions:
            list or dict of creation options
        srcWin:
            subwindow in pixels to extract: [left_x, top_y, width, height]
        projWin:
            subwindow in projected coordinates to extract: [ulx, uly, lrx, lry]
        projWinSRS:
            SRS in which projWin is expressed
        outputBounds:
            assigned output bounds: [ulx, uly, lrx, lry]
        outputGeotransform:
            assigned geotransform matrix (array of 6 values) (mutually exclusive with outputBounds)
        metadataOptions:
            list or dict of metadata options
        outputSRS:
            assigned output SRS
        noData:
            nodata value (or "none" to unset it)
        rgbExpand:
            Color palette expansion mode: "gray", "rgb", "rgba"
        xmp:
            whether to copy XMP metadata
        resampleAlg:
            resampling mode
        overviewLevel:
            To specify which overview level of source files must be used
        domainMetadataOptions:
            list or dict of domain-specific metadata options

    Returns
    -------
    Dataset

    Examples
    --------
    Scale & offset:
        - the translate function can be used to get rid of the scale and offset that are used to manipulate the
        dataset, to get the real values of the dataset.

        Scale:
            - First we will create a dataset from a float32 array with values between 1 and 10, and then we will
                assign a scale of 0.1 to the dataset.

                >>> import numpy as np
                >>> arr = np.random.randint(1, 10, size=(5, 5)).astype(np.float32)
                >>> print(arr) # doctest: +SKIP
                [[5. 5. 3. 4. 2.]
                 [2. 5. 5. 8. 5.]
                 [7. 5. 6. 1. 2.]
                 [6. 8. 1. 5. 8.]
                 [2. 5. 2. 2. 9.]]
                >>> top_left_corner = (0, 0)
                >>> cell_size = 0.05
                >>> dataset = Dataset.create_from_array(
                ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                ... )
                >>> print(dataset)
                <BLANKLINE>
                            Top Left Corner: (0.0, 0.0)
                            Cell size: 0.05
                            Dimension: 5 * 5
                            EPSG: 4326
                            Number of Bands: 1
                            Band names: ['Band_1']
                            Band colors: {0: 'undefined'}
                            Band units: ['']
                            Scale: [1.0]
                            Offset: [0]
                            Mask: -9999.0
                            Data type: float32
                            File: ...
                <BLANKLINE>
                >>> dataset.scale = [0.1]

            - now lets unscale the dataset values.

                >>> unscaled_dataset = dataset.translate(unscale=True)
                >>> print(unscaled_dataset) # doctest: +SKIP
                <BLANKLINE>
                            Top Left Corner: (0.0, 0.0)
                            Cell size: 0.05
                            Dimension: 5 * 5
                            EPSG: 4326
                            Number of Bands: 1
                            Band names: ['Band_1']
                            Band colors: {0: 'undefined'}
                            Band units: ['']
                            Scale: [1.0]
                            Offset: [0]
                            Mask: -9999.0
                            Data type: float32
                            File:
                <BLANKLINE>
                >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                [[0.5 0.5 0.3 0.4 0.2]
                 [0.2 0.5 0.5 0.8 0.5]
                 [0.7 0.5 0.6 0.1 0.2]
                 [0.6 0.8 0.1 0.5 0.8]
                 [0.2 0.5 0.2 0.2 0.9]]

        offset:
            - You can also unshift the values of the dataset if the dataset has an offset. To remove the offset
                from all values in the dataset, you can read the values using the `read_array` and then add the
                offset value to the array. we will create a dataset from the same array we created above (values
                are between 1, and 10) with an offset of 100.

                >>> dataset = Dataset.create_from_array(
                ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                ... )
                >>> print(dataset)
                <BLANKLINE>
                            Top Left Corner: (0.0, 0.0)
                            Cell size: 0.05
                            Dimension: 5 * 5
                            EPSG: 4326
                            Number of Bands: 1
                            Band names: ['Band_1']
                            Band colors: {0: 'undefined'}
                            Band units: ['']
                            Scale: [1.0]
                            Offset: [0]
                            Mask: -9999.0
                            Data type: float32
                            File: ...
                <BLANKLINE>

            - set the offset to 100.

                >>> dataset.offset = [100]

            - check if the offset has been set.

                >>> print(dataset.offset)
                [100.0]

            - now lets unscale the dataset values.

                >>> unscaled_dataset = dataset.translate(unscale=True)
                >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                [[105. 105. 103. 104. 102.]
                 [102. 105. 105. 108. 105.]
                 [107. 105. 106. 101. 102.]
                 [106. 108. 101. 105. 108.]
                 [102. 105. 102. 102. 109.]]

            - as you see, all the values have been shifted by 100. now if you check the offset of the dataset

                >>> print(unscaled_dataset.offset)
                [0]

        Offset and Scale together:
            - we can unscale and get rid of the offset at the same time.

                >>> dataset = Dataset.create_from_array(
                ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
                ... )

            - set the offset to 100, and a scale of 0.1.

                >>> dataset.offset = [100]
                >>> dataset.scale = [0.1]

            - check if the offset has been set.

                >>> print(dataset.offset)
                [100.0]
                >>> print(dataset.scale)
                [0.1]

            - now lets unscale the dataset values.

                >>> unscaled_dataset = dataset.translate(unscale=True)
                >>> print(unscaled_dataset.read_array()) # doctest: +SKIP
                [[100.5 100.5 100.3 100.4 100.2]
                 [100.2 100.5 100.5 100.8 100.5]
                 [100.7 100.5 100.6 100.1 100.2]
                 [100.6 100.8 100.1 100.5 100.8]
                 [100.2 100.5 100.2 100.2 100.9]]

            - Now you can see that the values were multiplied first by the scale; then the offset value was added.
                `value * scale + offset`

                >>> print(unscaled_dataset.offset)
                [0]
                >>> print(unscaled_dataset.scale)
                [1.0]

    Scale between two values:
        - you can scale the values of the dataset between two values, for example, you can scale the values
            between two values 0 and 1.

            >>> dataset = Dataset.create_from_array(
            ...     arr, top_left_corner=top_left_corner, cell_size=cell_size,epsg=4326
            ... )
            >>> print(dataset.stats()) # doctest: +SKIP
                    min  max  mean      std
            Band_1  1.0  9.0   4.0  2.19089
            >>> scaled_dataset = dataset.translate(scaleParams=[[1, 9, 0, 255]], outputType=gdal.GDT_Byte)
            >>> print(scaled_dataset.read_array()) # doctest: +SKIP
            [[128 128  64  96  32]
             [ 32 128 128 223 128]
             [191 128 159   0  32]
             [159 223   0 128 223]
             [ 32 128  32  32 255]]


    """
    if path is None:
        driver = "MEM"
        path = ""
    else:
        driver = "GTiff"

    options = gdal.TranslateOptions(format=driver, **kwargs)
    dst = gdal.Translate(str(path), self.raster, options=options)
    result = type(self)(dst, access="write")
    return result

cluster(lower_bound, upper_bound)

Group all the connected values between two bounds.

Parameters:

Name	Type	Description	Default
lower_bound	Number	Lower bound of the cluster.	required
upper_bound	Number	Upper bound of the cluster.	required

Returns:

Type	Description
tuple[ndarray, int, list, list]	tuple[np.ndarray, int, list, list]: - cluster (np.ndarray): Array with integers representing the cluster number per cell. - count (int): Number of clusters in the array. - position (list[list[int, int]]): List of [row, col] indices for the position of each value. - values (list[Number]): Values stored in each cell in the cluster.

Examples:

• First, we will create a dataset with 10 rows and 10 columns.

>>> import numpy as np
>>> np.random.seed(10)
>>> arr = np.random.randint(1, 5, size=(5, 5))
>>> print(arr) # doctest: +SKIP
[[2 3 3 2 3]
 [3 4 1 1 1]
 [1 3 3 2 2]
 [4 1 1 3 2]
 [2 4 2 3 2]]
>>> top_left_corner = (0, 0)
>>> cell_size = 0.05
>>> dataset = Dataset.create_from_array(
...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
... )
>>> dataset.plot(
...     color_scale=4, bounds=[1, 1.9, 4.1, 5], display_cell_value=True, num_size=12,
...     background_color_threshold=5
... )  # doctest: +SKIP

• Now let's cluster the values in the dataset that are between 2 and 4.

>>> lower_value = 2
>>> upper_value = 4
>>> cluster_array, count, position, values = dataset.cluster(lower_value, upper_value)

- The first returned output is a binary array with 1 indicating that the cell value is inside the cluster, and 0 is outside.

>>> print(cluster_array)  # doctest: +SKIP
[[1. 1. 1. 1. 1.]
 [1. 1. 0. 0. 0.]
 [0. 1. 1. 1. 1.]
 [1. 0. 0. 1. 1.]
 [1. 1. 1. 1. 1.]]

- The second returned value is the number of connected clusters.

>>> print(count) # doctest: +SKIP
2

- The third returned value is the indices of the cells that belong to the cluster.

>>> print(position) # doctest: +SKIP
[[1, 0], [2, 1], [2, 2], [3, 3], [4, 3], [4, 4], [3, 4], [2, 4], [2, 3], [4, 2], [4, 1], [3, 0], [4, 0], [1, 1], [0, 2], [0, 3], [0, 4], [0, 1], [0, 0]]

- The fourth returned value is a list of the values that are in the cluster (extracted from these cells).

>>> print(values) # doctest: +SKIP
[3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 4, 4, 2, 4, 3, 2, 3, 3, 2]

Source code in src/pyramids/dataset/ops/vectorize.py

def cluster(
    self, lower_bound: Any, upper_bound: Any
) -> tuple[np.ndarray, int, list, list]:
    """Group all the connected values between two bounds.

    Args:
        lower_bound (Number):
            Lower bound of the cluster.
        upper_bound (Number):
            Upper bound of the cluster.

    Returns:
        tuple[np.ndarray, int, list, list]:
            - cluster (np.ndarray):
                Array with integers representing the cluster number per cell.
            - count (int):
                Number of clusters in the array.
            - position (list[list[int, int]]):
                List of [row, col] indices for the position of each value.
            - values (list[Number]):
                Values stored in each cell in the cluster.

    Examples:
        - First, we will create a dataset with 10 rows and 10 columns.

          ```python
          >>> import numpy as np
          >>> np.random.seed(10)
          >>> arr = np.random.randint(1, 5, size=(5, 5))
          >>> print(arr) # doctest: +SKIP
          [[2 3 3 2 3]
           [3 4 1 1 1]
           [1 3 3 2 2]
           [4 1 1 3 2]
           [2 4 2 3 2]]
          >>> top_left_corner = (0, 0)
          >>> cell_size = 0.05
          >>> dataset = Dataset.create_from_array(
          ...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
          ... )
          >>> dataset.plot(
          ...     color_scale=4, bounds=[1, 1.9, 4.1, 5], display_cell_value=True, num_size=12,
          ...     background_color_threshold=5
          ... )  # doctest: +SKIP

          ```
          ![cluster](./../../_images/dataset/cluster.png)

        - Now let's cluster the values in the dataset that are between 2 and 4.

          ```python
          >>> lower_value = 2
          >>> upper_value = 4
          >>> cluster_array, count, position, values = dataset.cluster(lower_value, upper_value)

          ```
        - The first returned output is a binary array with 1 indicating that the cell value is inside the
            cluster, and 0 is outside.

          ```python
          >>> print(cluster_array)  # doctest: +SKIP
          [[1. 1. 1. 1. 1.]
           [1. 1. 0. 0. 0.]
           [0. 1. 1. 1. 1.]
           [1. 0. 0. 1. 1.]
           [1. 1. 1. 1. 1.]]

          ```
        - The second returned value is the number of connected clusters.

          ```python
          >>> print(count) # doctest: +SKIP
          2

          ```
        - The third returned value is the indices of the cells that belong to the cluster.

          ```python
          >>> print(position) # doctest: +SKIP
          [[1, 0], [2, 1], [2, 2], [3, 3], [4, 3], [4, 4], [3, 4], [2, 4], [2, 3], [4, 2], [4, 1], [3, 0], [4, 0], [1, 1], [0, 2], [0, 3], [0, 4], [0, 1], [0, 0]]

          ```
        - The fourth returned value is a list of the values that are in the cluster (extracted from these cells).

          ```python
          >>> print(values) # doctest: +SKIP
          [3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 4, 4, 2, 4, 3, 2, 3, 3, 2]

          ```

    """
    data = self.read_array()
    position: list[list[int]] = []
    values: list[Any] = []
    count = 1
    cluster = np.zeros(shape=(data.shape[0], data.shape[1]))

    for i in range(data.shape[0]):
        for j in range(data.shape[1]):
            if lower_bound <= data[i, j] <= upper_bound and cluster[i, j] == 0:
                self._group_neighbours(
                    data,
                    i,
                    j,
                    lower_bound,
                    upper_bound,
                    position,
                    values,
                    count,
                    cluster,
                )
                if cluster[i, j] == 0:
                    position.append([i, j])
                    values.append(data[i, j])
                    cluster[i, j] = count
                count += 1

    return cluster, count, position, values

cluster2(band=None)

Cluster the connected equal cells into polygons.

• Creates vector polygons for all connected regions of pixels in the raster sharing a common pixel value (group neighboring cells with the same value into one polygon).

Parameters:

Name	Type	Description	Default
band	int | List[int] | None	Band index 0, 1, 2, 3, ...	None

Returns:

Name	Type	Description
GeoDataFrame	GeoDataFrame	GeodataFrame containing polygon geomtries for all connected regions.

Examples:

• First, we will create a 10*10 dataset full of random integer between 1, and 5.

>>> import numpy as np
>>> np.random.seed(200)
>>> arr = np.random.randint(1, 5, size=(10, 10))
>>> print(arr)  # doctest: +SKIP
[[3 2 1 1 3 4 1 4 2 3]
 [4 2 2 4 3 3 1 2 4 4]
 [4 2 4 2 3 4 2 1 4 3]
 [3 2 1 4 3 3 4 1 1 4]
 [1 2 4 2 2 1 3 2 3 1]
 [1 4 4 4 1 1 4 2 1 1]
 [1 3 2 3 3 4 1 3 1 3]
 [4 1 3 3 3 4 1 4 1 1]
 [2 1 3 3 4 2 2 1 3 4]
 [2 3 2 2 4 2 1 3 2 2]]
>>> top_left_corner = (0, 0)
>>> cell_size = 0.05
>>> dataset = Dataset.create_from_array(
...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
... )

• Now, let's cluster the connected equal cells into polygons.

  >>> gdf = dataset.cluster2()
  >>> print(gdf)  # doctest: +SKIP
      Band_1                                           geometry
  0        3  POLYGON ((0 0, 0 -0.05, 0.05 -0.05, 0.05 0, 0 0))
  1        1  POLYGON ((0.1 0, 0.1 -0.05, 0.2 -0.05, 0.2 0, ...
  2        4  POLYGON ((0.25 0, 0.25 -0.05, 0.3 -0.05, 0.3 0...
  3        4  POLYGON ((0.35 0, 0.35 -0.05, 0.4 -0.05, 0.4 0...
  4        2  POLYGON ((0.4 0, 0.4 -0.05, 0.45 -0.05, 0.45 0...
  5        3  POLYGON ((0.45 0, 0.45 -0.05, 0.5 -0.05, 0.5 0...
  6        1  POLYGON ((0.3 0, 0.3 -0.1, 0.35 -0.1, 0.35 0, ...
  7        4  POLYGON ((0.15 -0.05, 0.15 -0.1, 0.2 -0.1, 0.2...
  8        2  POLYGON ((0.35 -0.05, 0.35 -0.1, 0.4 -0.1, 0.4...
  9        4  POLYGON ((0 -0.05, 0 -0.15, 0.05 -0.15, 0.05 -...
  10       4  POLYGON ((0.4 -0.05, 0.4 -0.15, 0.45 -0.15, 0....
  11       4  POLYGON ((0.1 -0.1, 0.1 -0.15, 0.15 -0.15, 0.1...
  

Source code in src/pyramids/dataset/ops/vectorize.py

def cluster2(
    self,
    band: int | list[int] | None = None,
) -> GeoDataFrame:
    """Cluster the connected equal cells into polygons.

    - Creates vector polygons for all connected regions of pixels in the raster sharing a common
        pixel value (group neighboring cells with the same value into one polygon).

    Args:
        band (int | List[int] | None):
            Band index 0, 1, 2, 3, ...

    Returns:
        GeoDataFrame:
            GeodataFrame containing polygon geomtries for all connected regions.

    Examples:
        - First, we will create a 10*10 dataset full of random integer between 1, and 5.

          ```python
          >>> import numpy as np
          >>> np.random.seed(200)
          >>> arr = np.random.randint(1, 5, size=(10, 10))
          >>> print(arr)  # doctest: +SKIP
          [[3 2 1 1 3 4 1 4 2 3]
           [4 2 2 4 3 3 1 2 4 4]
           [4 2 4 2 3 4 2 1 4 3]
           [3 2 1 4 3 3 4 1 1 4]
           [1 2 4 2 2 1 3 2 3 1]
           [1 4 4 4 1 1 4 2 1 1]
           [1 3 2 3 3 4 1 3 1 3]
           [4 1 3 3 3 4 1 4 1 1]
           [2 1 3 3 4 2 2 1 3 4]
           [2 3 2 2 4 2 1 3 2 2]]
          >>> top_left_corner = (0, 0)
          >>> cell_size = 0.05
          >>> dataset = Dataset.create_from_array(
          ...     arr, top_left_corner=top_left_corner, cell_size=cell_size, epsg=4326
          ... )

          ```

        - Now, let's cluster the connected equal cells into polygons.
          ```python
          >>> gdf = dataset.cluster2()
          >>> print(gdf)  # doctest: +SKIP
              Band_1                                           geometry
          0        3  POLYGON ((0 0, 0 -0.05, 0.05 -0.05, 0.05 0, 0 0))
          1        1  POLYGON ((0.1 0, 0.1 -0.05, 0.2 -0.05, 0.2 0, ...
          2        4  POLYGON ((0.25 0, 0.25 -0.05, 0.3 -0.05, 0.3 0...
          3        4  POLYGON ((0.35 0, 0.35 -0.05, 0.4 -0.05, 0.4 0...
          4        2  POLYGON ((0.4 0, 0.4 -0.05, 0.45 -0.05, 0.45 0...
          5        3  POLYGON ((0.45 0, 0.45 -0.05, 0.5 -0.05, 0.5 0...
          6        1  POLYGON ((0.3 0, 0.3 -0.1, 0.35 -0.1, 0.35 0, ...
          7        4  POLYGON ((0.15 -0.05, 0.15 -0.1, 0.2 -0.1, 0.2...
          8        2  POLYGON ((0.35 -0.05, 0.35 -0.1, 0.4 -0.1, 0.4...
          9        4  POLYGON ((0 -0.05, 0 -0.15, 0.05 -0.15, 0.05 -...
          10       4  POLYGON ((0.4 -0.05, 0.4 -0.15, 0.45 -0.15, 0....
          11       4  POLYGON ((0.1 -0.1, 0.1 -0.15, 0.15 -0.15, 0.1...

          ```

    """
    if band is None:
        band = 0

    if isinstance(band, int):
        name = self.band_names[band]
        gdf = self._band_to_polygon(band, name)
    else:
        gdfs = []
        for b in band:
            name = self.band_names[b]
            gdfs.append(self._band_to_polygon(b, name))
        gdf = gpd.GeoDataFrame(pd.concat(gdfs, ignore_index=True))

    return gdf