Exemplo n.º 1
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def _crop_img_to_shp(img: rasterio.DatasetReader, shape: shapefile.Shape,
                     out_path: _OutPath) -> bool:
    # Get the bbox to crop to
    shp_bbox = _BBox(*[round(v) for v in shape.bbox])
    img_bbox = _BBox(*list(img.bounds))
    bbox = shp_bbox.intersect(img_bbox)

    if not bbox.is_valid:
        return False

    # Crop the image
    window = bbox.to_window(img)
    data = img.read(window=window)

    # Write to the output directory
    out_path = out_path.crop_path(shp_bbox.left, shp_bbox.bottom)
    x_res, y_res = img.res
    transform = Affine.translation(bbox.left, bbox.top) * Affine.scale(
        x_res, -y_res)

    profile = img.profile
    profile.update(transform=transform,
                   height=window.height,
                   width=window.width)

    with rasterio.open(out_path, 'w', **profile) as writer:
        writer.write(data)

        # Fixes band 4 being labelled as alpha channel
        writer.colorinterp = img.colorinterp

    print(f'Created: {out_path}')
    return True
Exemplo n.º 2
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def test_complex_nodata(tmpdir):
    """A complex dataset can be created with a real nodata value"""
    import numpy as np
    import rasterio
    from rasterio.transform import Affine

    x = np.linspace(-4.0, 4.0, 240)
    y = np.linspace(-3.0, 3.0, 180)
    X, Y = np.meshgrid(x, y)
    Z1 = np.ones_like(X) + 1j

    res = (x[-1] - x[0]) / 240.0
    transform1 = Affine.translation(x[0] - res / 2,
                                    y[-1] - res / 2) * Affine.scale(res, -res)

    tempfile = str(tmpdir.join("test.tif"))
    with rasterio.open(tempfile,
                       'w',
                       driver='GTiff',
                       height=Z1.shape[0],
                       width=Z1.shape[1],
                       nodata=0,
                       count=1,
                       dtype=Z1.dtype,
                       crs='+proj=latlong',
                       transform=transform1) as dst:
        dst.write(Z1, 1)

    with rasterio.open(tempfile) as dst:
        assert dst.nodata == 0
Exemplo n.º 3
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        def __call__(self):
            with rasterio.open(input) as src:
                if bands:
                    if sampling == 1:
                        img = src.read_band(bidx)
                        transform = src.transform
                    # Decimate the band.
                    else:
                        img = numpy.zeros(
                            (src.height // sampling, src.width // sampling),
                            dtype=src.dtypes[src.indexes.index(bidx)])
                        img = src.read_band(bidx, img)
                        transform = src.affine * Affine.scale(float(sampling))
                else:
                    if sampling == 1:
                        img = src.read_mask()
                        transform = src.transform
                    # Decimate the mask.
                    else:
                        img = numpy.zeros(
                            (src.height // sampling, src.width // sampling),
                            dtype=numpy.uint8)
                        img = src.read_mask(img)
                        transform = src.affine * Affine.scale(float(sampling))

                bounds = src.bounds
                xs = [bounds[0], bounds[2]]
                ys = [bounds[1], bounds[3]]
                if projected == 'geographic':
                    xs, ys = rasterio.warp.transform(src.crs,
                                                     {'init': 'epsg:4326'}, xs,
                                                     ys)
                if precision >= 0:
                    xs = [round(v, precision) for v in xs]
                    ys = [round(v, precision) for v in ys]
                self._xs = xs
                self._ys = ys

                kwargs = {'transform': transform}
                if not bands and not with_nodata:
                    kwargs['mask'] = (img == 255)
                for g, i in rasterio.features.shapes(img, **kwargs):
                    if projected == 'geographic':
                        g = rasterio.warp.transform_geom(
                            src.crs,
                            'EPSG:4326',
                            g,
                            antimeridian_cutting=True,
                            precision=precision)
                    xs, ys = zip(*coords(g))
                    yield {
                        'type': 'Feature',
                        'id': str(i),
                        'properties': {
                            'val': i
                        },
                        'bbox': [min(xs), min(ys),
                                 max(xs), max(ys)],
                        'geometry': g
                    }
Exemplo n.º 4
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def tiffs(tmpdir):

    data = np.ones((1, 1, 1), 'uint8')

    kwargs = {
        'count': '1',
        'driver': 'GTiff',
        'dtype': 'uint8',
        'height': 1,
        'width': 1
    }

    kwargs['transform'] = Affine(1, 0, 1, 0, -1, 1)
    with rasterio.open(str(tmpdir.join('a-sw.tif')), 'w', **kwargs) as r:
        r.write(data * 40)

    kwargs['transform'] = Affine(1, 0, 2, 0, -1, 2)
    with rasterio.open(str(tmpdir.join('b-ct.tif')), 'w', **kwargs) as r:
        r.write(data * 60)

    kwargs['transform'] = Affine(2, 0, 3, 0, -2, 4)
    with rasterio.open(str(tmpdir.join('c-ne.tif')), 'w', **kwargs) as r:
        r.write(data * 90)

    kwargs['transform'] = Affine(2, 0, 2, 0, -2, 4)
    with rasterio.open(str(tmpdir.join('d-ne.tif')), 'w', **kwargs) as r:
        r.write(data * 120)

    return tmpdir
Exemplo n.º 5
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def selectInterestArea(imgName, x, y):
    out_folder = os.path.join(workingDir, 'Split', imgName[:-4])
    with rio.open(os.path.join(imageDir, imgName)) as inds:

        # tile_width, tile_height = int(inds.width/16),int(inds.height/16)
        tile_width, tile_height = 1220, 1220
        inv_transform = Affine.scale(
            1 / inds.transform.a, 1 / inds.transform.e) * Affine.translation(
                -inds.transform.xoff, -inds.transform.yoff)
        meta = inds.meta.copy()
        rasterio.warp.transform(crs0, inds.crs, [y], [x])
        a = rasterio.warp.transform(crs0, inds.crs, [y], [x])
        xPixel, yPixel = pixel_location = inv_transform * (a[0][0], a[1][0])
        print(pixel_location)
        # print(count_sliding_window(inds.read(1)))
        for window, transform in get_tiles(inds, tile_width, tile_height):
            print(window)
            meta['transform'] = transform
            meta['width'], meta['height'] = window.width, window.height
            outpath = os.path.join(
                out_folder,
                output_filename.format(int(window.col_off),
                                       int(window.row_off)))
            if ((xPixel > window.col_off) &
                (xPixel < window.col_off + window.width) &
                (yPixel > window.row_off) &
                (yPixel < window.row_off + window.height)):
                with rio.open(outpath, 'w', **meta) as outds:
                    outds.write(inds.read(window=window))
Exemplo n.º 6
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def basic_flattening(target_folder, raster, res, origin, size, tin = False):
    """Reads some pre-determined vector files, tiles them using
    Lisa's code and "burns" them into the output raster. The flat
    elevation of the polygons is estimated by Laplace-interpolating
    at the locations of the polygon vertices. The underlying TIN
    is constructed from the centre points of the raster pixels.
    Rasterisation takes place via rasterio's interface.
    """
    import startin
    from rasterio.features import rasterize
    from rasterio.transform import Affine
    transform = (Affine.translation(origin[0], origin[1])
                 * Affine.scale(size, size))
    x0, x1 = origin[0] + size / 2, origin[0] + ((res[0] - 0.5) * size)
    y0, y1 = origin[1] + size / 2, origin[1] + ((res[1] - 0.5) * size)
    poly_fpaths = [
                     'rest_bodies/bbg_rest_of_the_water.shp',
                     'sea_bodies/bbg_sea_and_big_bodies.shp',
                     # You can add more resources here.
                  ]
    wfs_urls =    [
                     #('http://3dbag.bk.tudelft.nl/data/wfs', 'BAG3D:pand3d'),
                     # You can add more resources here.
                  ]
    in_vecs = []
    for fpath in poly_fpaths:
        vec = vector_prepare([[x0, x1], [y0, y1]], target_folder + fpath)
        if len(vec) != 0: in_vecs.append(vec)
    for wfs in wfs_urls:
        vec = wfs_prepare([[x0, x1], [y0, y1]], wfs[0], wfs[1])
        if len(vec) != 0: in_vecs.append(vec)
    if len(in_vecs) == 0: return
    if tin is False:
        xs, ys = np.linspace(x0, x1, res[0]), np.linspace(y0, y1, res[1])
        xg, yg = np.meshgrid(xs, ys); xg = xg.flatten(); yg = yg.flatten()
        cs = np.vstack((xg, yg, raster.flatten())).transpose()
        data = cs[cs[:,2] != -9999]
        tin = startin.DT(); tin.insert(data)
    elevations = []
    for polys in in_vecs:
        for poly, i in zip(polys, range(len(polys))):
            els = []
            for vx in poly.exterior.coords:
                try: els += [tin.interpolate_laplace(vx[0], vx[1])]
                except: pass
            for interior in poly.interiors:
                for vx in interior.coords:
                    try: els += [tin.interpolate_laplace(vx[0], vx[1])]
                    except: pass
            elevations.append(np.median(els))
    shapes = []
    for polys in in_vecs:
        shapes += [(p, v) for p, v in zip(polys, elevations)]
    raspolys = rasterize(shapes, raster.shape, -9999, transform = transform)
    for yi in range(res[1]):
        for xi in range(res[0]):
            if raspolys[yi, xi] != -9999: raster[yi, xi] = raspolys[yi, xi]
    return tin
Exemplo n.º 7
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def latlon2transform(lat, lon, cell_center=True):
    lat = np.asarray(lat)
    lon = np.asarray(lon)
    resX = (lon[-1] - lon[0]) / (len(lon) - 1)
    resY = (lat[-1] - lat[0]) / (len(lat) - 1)
    trans = Affine.translation(lon[0] - resX / 2. * cell_center,
                               lat[0] - resY / 2. * cell_center)
    scale = Affine.scale(lon[1] - lon[0], lat[1] - lat[0])
    return trans * scale
Exemplo n.º 8
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        def __call__(self):
            with rasterio.open(input) as src:
                img = None
                nodata_mask = None
                if bands:
                    if sampling == 1:
                        img = src.read(bidx, masked=False)
                        transform = src.transform
                    # Decimate the band.
                    else:
                        img = numpy.zeros(
                            (src.height//sampling, src.width//sampling),
                            dtype=src.dtypes[src.indexes.index(bidx)])
                        img = src.read(bidx, img, masked=False)
                        transform = src.affine * Affine.scale(float(sampling))
                if not bands or not with_nodata:
                    if sampling == 1:
                        nodata_mask = src.read_masks(bidx)
                        transform = src.transform
                    # Decimate the mask.
                    else:
                        nodata_mask = numpy.zeros(
                            (src.height//sampling, src.width//sampling),
                            dtype=numpy.uint8)
                        nodata_mask = src.read_masks(bidx, nodata_mask)
                        transform = src.affine * Affine.scale(float(sampling))

                bounds = src.bounds
                xs = [bounds[0], bounds[2]]
                ys = [bounds[1], bounds[3]]
                if projection == 'geographic':
                    xs, ys = rasterio.warp.transform(
                        src.crs, {'init': 'epsg:4326'}, xs, ys)
                if precision >= 0:
                    xs = [round(v, precision) for v in xs]
                    ys = [round(v, precision) for v in ys]
                self._xs = xs
                self._ys = ys

                kwargs = {'transform': transform}
                # Default is to exclude nodata features.
                if nodata_mask is not None:
                    kwargs['mask'] = (nodata_mask==255)
                if img is None:
                    img = nodata_mask
                for g, i in rasterio.features.shapes(img, **kwargs):
                    if projection == 'geographic':
                        g = rasterio.warp.transform_geom(
                            src.crs, 'EPSG:4326', g,
                            antimeridian_cutting=True, precision=precision)
                    xs, ys = zip(*coords(g))
                    yield {
                        'type': 'Feature',
                        'id': str(i),
                        'properties': {'val': i},
                        'bbox': [min(xs), min(ys), max(xs), max(ys)],
                        'geometry': g }
Exemplo n.º 9
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def transform_lat_lon(lat, lon):
    """
    Transforms latitude and longitude arrays.
    :param lat: numpy array latitude coordinates.
    :param lon: numpy array longitude coordinates.
    :return:
    """
    lat = np.asarray(lat)
    lon = np.asarray(lon)
    trans = Affine.translation(lon[0], lat[0])
    scale = Affine.scale(lon[1] - lon[0], lat[1] - lat[0])
    return trans * scale
def pad(array, transform, pad_width, mode=None, **kwargs):
    """pad array and adjust affine transform matrix.

    Parameters
    ----------
    array: ndarray
        Numpy ndarray, for best results a 2D array
    transform: Affine transform
        transform object mapping pixel space to coordinates
    pad_width: int
        number of pixels to pad array on all four
    mode: str or function
        define the method for determining padded values

    Returns
    -------
    (array, transform): tuple
        Tuple of new array and affine transform

    Notes
    -----
    See numpy docs for details on mode and other kwargs:
    http://docs.scipy.org/doc/numpy-1.10.0/reference/generated/numpy.pad.html
    """
    import numpy as np
    transform = guard_transform(transform)
    padded_array = np.pad(array, pad_width, mode, **kwargs)
    padded_trans = list(transform)
    padded_trans[2] -= pad_width * padded_trans[0]
    padded_trans[5] -= pad_width * padded_trans[4]
    return padded_array, Affine(*padded_trans[:6])
Exemplo n.º 11
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def getTransform(xvar=None, x=None, y=None, lcheck=True):
    ''' generate an affine transformation from xarray coordinate axes '''
    from rasterio.transform import Affine # to generate Affine transform
    
    if isinstance(xvar,(xr.DataArray,xr.Dataset,nc.Dataset)):
        x,y = getGeoCoords(xvar, lraise=True)
    elif xvar is None and isinstance(x,(xr.DataArray,nc.Variable)) and isinstance(y,(xr.DataArray,nc.Variable)):
        pass # x and y axes are supplied directly
    elif xvar:
        raise TypeError('Can only infer GeoTransform from xarray Dataset or DataArray or netCDF4 Dataset\n - not from {}.'.format(xvar))
    
    # check X-axis
    if isinstance(x,xr.DataArray): x = x.data
    elif isinstance(x,nc.Variable): x = x[:]
    if not isinstance(x,np.ndarray): 
        raise TypeError(x)
    diff_x = np.diff(x); dx = diff_x.min()
    if lcheck and not np.isclose(dx, diff_x.max(), rtol=1.e-2): 
        raise ValueError("X-axis is not regular: {} - {}".format(dx, diff_x.max()))
    
    # check Y-axis
    if isinstance(y,xr.DataArray): y = y.data
    elif isinstance(y,nc.Variable): y = y[:]
    if not isinstance(y,np.ndarray): 
        raise TypeError(y)
    diff_y = np.diff(y); dy = diff_y.min()
    if lcheck and not np.isclose(dy, diff_y.max(), rtol=1.e-2): 
        raise ValueError("Y-axis is not regular. {} - {}".format(dy, diff_y.max()))
    
    # generate transform
    return Affine.from_gdal(x[0]-dx/2.,dx,0.,y[0]-dy/2.,0.,dy), (len(x),len(y))
Exemplo n.º 12
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 def __init__(self, pixel_size, raster_data=None, **kwargs):
     logger.info("Preparing a base dataframe...")
     x_min, y_min, x_max, y_max = -180, -90, 180, 90  # global
     self.pixel_size = pixel_size
     self.x_res = int((x_max - x_min) / self.pixel_size)
     self.y_res = int((y_max - y_min) / self.pixel_size)
     self.base_layer = RasterEnvironmentalLayer()
     self.base_layer.raster_affine = Affine(pixel_size, 0.0, x_min, 0.0,
                                            -pixel_size, y_max)
     logger.info("Base layer: Computing world coordinates...")
     if raster_data is not None:
         all_coordinates = self.base_layer.pixel_to_world_coordinates(
             raster_data=raster_data)
     else:
         all_coordinates = self.base_layer.pixel_to_world_coordinates(
             raster_data=np.ones((self.y_res, self.x_res), dtype=np.uint8))
     # self.base_dataframe = pd.DataFrame([all_coordinates[0], all_coordinates[1]]).T
     # self.base_dataframe.columns = ['decimallatitude', 'decimallongitude']
     self.base_dataframe = pd.DataFrame(
         columns=['decimallatitude', 'decimallongitude'])
     self.base_dataframe['decimallatitude'] = np.array(all_coordinates[0])
     self.base_dataframe['decimallongitude'] = np.array(all_coordinates[1])
     self.base_dataframe.set_index(['decimallatitude', 'decimallongitude'],
                                   inplace=True,
                                   drop=True)
     del all_coordinates
     gc.collect()
Exemplo n.º 13
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def getTransform(xvar=None, x=None, y=None, lcheck=True):
    ''' generate an affine transformation from xarray coordinate axes '''
    from rasterio.transform import Affine # to generate Affine transform
    
    if isinstance(xvar,(xr.DataArray,xr.Dataset)):
        x,y = getGeoCoords(xvar, lraise=True)
    elif xvar:
        raise TypeError('Can only infer GeoTransform from xarray Dataset or DataArray - not from {}.'.format(xvar))
    
    # check X-axis
    if isinstance(x,xr.DataArray): x = x.data
    if not isinstance(x,np.ndarray): 
        raise TypeError(x)
    diff_x = np.diff(x); dx = diff_x.min()
    if lcheck and not np.isclose(dx, diff_x.max(), rtol=1.e-2): 
        raise ValueError("X-axis is not regular: {} - {}".format(dx, diff_x.max()))
    
    # check Y-axis
    if isinstance(y,xr.DataArray): y = y.data
    if not isinstance(y,np.ndarray): 
        raise TypeError(y)
    diff_y = np.diff(y); dy = diff_y.min()
    if lcheck and not np.isclose(dy, diff_y.max(), rtol=1.e-2): 
        raise ValueError("Y-axis is not regular. {} - {}".format(dy, diff_y.max()))
    
    # generate transform
    return Affine.from_gdal(x[0]-dx/2.,dx,0.,y[0]-dy/2.,0.,dy), (len(x),len(y))
Exemplo n.º 14
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def rasterizeShapes(pshapes, geodict, all_touched=True):
    """
    Rasterizing a shape

    Args:
        pshapes: Sequence of orthographically projected shapes.
        geodict: Mapio geodictionary.
        all_touched: Turn pixel "on" if shape touches pixel, otherwise turn it
            on if the center of the pixel is contained within the shape. Note
            that the footprint of the shape is inflated and the amount of
            inflation depends on the pixel size if all_touched=True.

    Returns:
        Rasterio grid.
    """
    outshape = (geodict.ny, geodict.nx)
    txmin = geodict.xmin - geodict.dx / 2.0
    tymax = geodict.ymax + geodict.dy / 2.0
    transform = Affine.from_gdal(txmin, geodict.dx, 0.0, tymax, 0.0,
                                 -geodict.dy)
    imgs = rasterio.features.rasterize(pshapes,
                                       out_shape=outshape,
                                       fill=0.0,
                                       transform=transform,
                                       all_touched=all_touched,
                                       default_value=1.0)
    return imgs
Exemplo n.º 15
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 def preprocess_bands(self, band_stack, subset_box=None):
     bands_rescaled = band_stack[0:4].copy()
     bands_rescaled[np.isnan(bands_rescaled)] = 0
     bands_rescaled = rescale_s2(bands_rescaled)
     bands_rescaled[bands_rescaled == 0] = np.nan
     band_stack = None
     self.lat, self.lon = lat_from_meta(self.meta), lon_from_meta(self.meta)
     if subset_box is not None:
         ymin, ymax, xmin, xmax = subset_box["ymin"], subset_box[
             "ymax"], subset_box["xmin"], subset_box["xmax"]
         bands_rescaled = bands_rescaled[:, ymin:ymax, xmin:xmax]
         self.lat, self.lon = self.lat[ymin:ymax], self.lon[xmin:xmax]
         self.meta["height"], self.meta["width"] = bands_rescaled.shape[
             1], bands_rescaled.shape[2]
         t = list(self.meta["transform"])
         t[2], t[5] = self.lon[0], self.lat[0]
         self.meta["transform"] = Affine(t[0], t[1], t[2], t[3], t[4], t[5])
     bbox_epsg4326 = list(np.flip(metadata_to_bbox_epsg4326(self.meta)))
     osm_mask = self._get_osm_mask(
         bbox_epsg4326, "EPSG:" + str(self.meta["crs"].to_epsg()),
         bands_rescaled[0], {
             "lat": self.lat,
             "lon": self.lon
         }, dirs["osm"])
     if np.count_nonzero(osm_mask) == 0:
         raise ValueError("No OSM roads of requested road types in aoi")
     bands_rescaled *= osm_mask
     bands_rescaled[bands_rescaled == 0] = np.nan
     osm_mask = None
     self._build_variables(bands_rescaled)
Exemplo n.º 16
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    def download_tiles(self, scene, grid):
        bbox, shape = grid
        x, y = map(lambda coor: int(coor / self.resolution), shape)
        if scene.geometry.intersects(bbox):
            array = self.request(scene, bbox, (x, y))

            diff = bbox.difference(scene.geometry)
            if diff.area != 0:
                x0, _, _, ye = bbox.bounds
                transform = Affine(a=self.resolution,
                                   b=0,
                                   c=x0,
                                   d=0,
                                   e=-self.resolution,
                                   f=ye)
                mask = rasterize([(diff, True)],
                                 out_shape=(y, x),
                                 transform=transform,
                                 fill=False,
                                 all_touched=True)
                array = numpy.where(mask, self.nodata, array)
        else:
            array = None

        if array is not None:
            return array
        else:
            return self.nodata_tile((x, y))
Exemplo n.º 17
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def write_cog(layout, location, data, filename_template):
    """
    Write a GPS tile out as a Cloud-Optimized GeoTIFF

    Uses GDAL to write a COG out to disk, utilizing the given layout and location
    to generate the GeoTIFF header.

    Args:
        layout (``gps.LayoutDefinition``): The layout for the source layer
        location (``gps.SpatialKey`` or ``gps.SpaceTimeKey``): The cell identifier
            in the layer corresponding to the image data
        data (``gps.Tile``): The image data
        filename_template (str): A pattern giving the destination for the target
            image.  Contains two '{}' tokens which will be ``.format``ed with the
            column and row of the ``location``, in that order.  May be an S3 uri or
            local path.
    """
    bands, w, h = data.cells.shape
    nodata = data.no_data_value
    dtype = data.cells.dtype
    cw, ch = cell_size(layout)
    ex = extent_for_cell(layout, location)
    overview_level = int(log(w) / log(2) - 8)

    with rstr.io.MemoryFile() as memfile:
        with memfile.open(driver='GTiff',
                          count=bands,
                          width=w,
                          height=h,
                          transform=Affine(cw, 0.0, ex.xmin, 0.0, -ch,
                                           ex.ymax),
                          crs=rstr.crs.CRS.from_epsg(4326),
                          nodata=nodata,
                          dtype=dtype,
                          compress='lzw',
                          tiled=True) as mem:
            windows = list(mem.block_windows(1))
            for _, w in windows:
                segment = data.cells[:, w.row_off:(w.row_off + w.height),
                                     w.col_off:(w.col_off + w.width)]
                mem.write(segment, window=w)
                mask_value = np.all(segment != nodata, axis=0).astype(
                    np.uint8) * 255
                mem.write_mask(mask_value, window=w)

            overviews = [2**j for j in range(1, overview_level + 1)]
            mem.build_overviews(overviews, rwarp.Resampling.nearest)
            mem.update_tags(ns='rio_oveview',
                            resampling=rwarp.Resampling.nearest.value)

            uri = urlparse.urlparse(filename_template)
            if uri.scheme == 's3':
                boto3.resource('s3').Bucket(uri.netloc).upload_fileobj(
                    memfile,
                    uri.path.format(location.col, location.row)[1:])
            else:
                rshutil.copy(mem,
                             filename_template.format(location.col,
                                                      location.row),
                             copy_src_overviews=True)
Exemplo n.º 18
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def get_web_optimized_params(
        src_dst,
        tilesize=256,
        latitude_adjustment: bool = True,
        warp_resampling: str = "nearest",
        grid_crs=CRS.from_epsg(3857),
) -> Dict:
    """Return VRT parameters for a WebOptimized COG."""
    bounds = list(
        transform_bounds(src_dst.crs,
                         CRS.from_epsg(4326),
                         *src_dst.bounds,
                         densify_pts=21))
    center = [(bounds[0] + bounds[2]) / 2, (bounds[1] + bounds[3]) / 2]

    lat = 0 if latitude_adjustment else center[1]
    _, max_zoom = get_zooms(src_dst, lat=lat, tilesize=tilesize)

    extrema = tile_extrema(bounds, max_zoom)

    left, _, _, top = mercantile.xy_bounds(extrema["x"]["min"],
                                           extrema["y"]["min"], max_zoom)
    vrt_res = _meters_per_pixel(max_zoom, 0, tilesize=tilesize)
    vrt_transform = Affine(vrt_res, 0, left, 0, -vrt_res, top)

    vrt_width = (extrema["x"]["max"] - extrema["x"]["min"]) * tilesize
    vrt_height = (extrema["y"]["max"] - extrema["y"]["min"]) * tilesize

    return dict(
        crs=grid_crs,
        transform=vrt_transform,
        width=vrt_width,
        height=vrt_height,
        resampling=ResamplingEnums[warp_resampling],
    )
Exemplo n.º 19
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def predictFromTreeDEM(fp, dtree, outfn):
    hh_msk, hv_msk = readBands(fp)
    #print('HH read msk contains nan: '+str(np.isnan(hh_msk).any()))
    #print('HV read msk contains nan: '+str(np.isnan(hv_msk).any()))
    hh_msk_flat = hh_msk.flatten()
    hv_msk_flat = hv_msk.flatten()

    hhhvDEM_stacked = np.stack((hh_msk_flat, hv_msk_flat, dem_flat), axis=1)
    pred = dtree.predict(hhhvDEM_stacked)
    pred_reshaped = pred.reshape(-1, 11908)
    meta_outFile = {
        'driver':
        'GTiff',
        'dtype':
        'float32',
        'nodata':
        -9999.0,
        'width':
        11908,
        'height':
        12600,
        'count':
        1,
        'crs':
        CRS.from_epsg(3413),
        'transform':
        Affine(10.0, 0.0, -384702.1263054441, 0.0, -10.0, -2122443.806211936)
    }
    with rio.open(outfn, 'w', **meta_outFile) as outTif:
        outTif.write(pred_reshaped, indexes=1)
Exemplo n.º 20
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def geopandas_to_raster(gpd_frame, raster_file, gpd_column, geo_grid: GeoGrid,
                        datatype, all_touched):
    """ Write geopandas data frame to raster

    :param gpd_frame:
    :param raster_file:
    :param gpd_column:
    :param geo_grid: GeoGrid instance
    :param datatype: data type ('uint8', 'float32', etc.)
    :param all_touched:
    :return:
    """

    # _ = _create_raster_file(raster_file, geo_grid, geo_crs, 0)

    # Open temp raster file with rasterio and copy metadata
    # raster_fcn = rasterio.open(raster_temp_file.name)
    # meta = raster_fcn.meta.copy()
    # meta.update(compress='lzw')

    with rasterio.open(
            raster_file,
            'w',
            driver="GTiff",
            width=geo_grid.num_x,
            height=geo_grid.num_y,
            count=1,
            dtype=datatype,
            crs=gpd_frame.crs,
            transform=Affine.from_gdal(*geo_grid.geo_transform)) as out:

        # this is where we create a generator of geom, value pairs to use in rasterizing
        shapes = (
            (geom, value)
            for geom, value in zip(gpd_frame.geometry, gpd_frame[gpd_column]))

        burned = features.rasterize(
            shapes=shapes,
            fill=0,
            out_shape=(geo_grid.num_y, geo_grid.num_x),
            dtype=datatype,
            transform=Affine.from_gdal(*geo_grid.geo_transform),
            all_touched=all_touched)
        out.write_band(1, burned)

    return 0
Exemplo n.º 21
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def test_tiled_dataset_blocksize_guard(tmp_path):
    """Tiled datasets with dimensions less than blocksize are not permitted"""
    pytest.importorskip("pathlib")
    tmp_file = tmp_path / "test.tif"
    with pytest.raises(ValueError):
        rasterio.open(
            tmp_file, "w", driver="GTiff", count=1, height=13, width=13, dtype="uint8", crs="epsg:3857",
            transform=Affine.identity(), tiled=True, blockxsize=256, blockysize=256)
Exemplo n.º 22
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def rasterizeShapes(pshapes,geodict):
    outshape = (geodict.ny,geodict.nx)
    txmin = geodict.xmin - geodict.dx/2.0
    tymax = geodict.ymax + geodict.dy/2.0
    transform = Affine.from_gdal(txmin,geodict.dx,0.0,tymax,0.0,-geodict.dy)
    img = rasterio.features.rasterize(pshapes,out_shape=outshape,fill=0.0,transform=transform,
                                      all_touched=True,default_value=1.0)
    return img
Exemplo n.º 23
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def get_params():
    return {
        'rain': {
            'height': 129,
            'width': 135,
            'affine': Affine(0.25, 0, 66.375, 0, -0.25, 38.625)
        },
        'tmin': {
            'height': 31,
            'width': 31,
            'affine': Affine(1, 0, 67, 0, -1, 38)
        },
        'tmax': {
            'height': 31,
            'width': 31,
            'affine': Affine(1, 0, 67, 0, -1, 38)
        }
    }
Exemplo n.º 24
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def save_geotiff(img, coords, filename):
    height, width, channels = img.shape
    xres = (coords[1][0] - coords[0][0]) / width
    yres = (coords[0][1] - coords[1][1]) / height
    transform = Affine.translation(coords[0][0] - xres / 2, coords[0][1] +
                                   yres / 2) * Affine.scale(xres, -yres)
    profile = {
        'driver': 'GTiff',
        'width': width,
        'height': height,
        'count': channels,
        'crs': '+proj=latlong',
        'transform': transform,
        'dtype': img.dtype,
        'compress': 'JPEG'
    }
    with rasterio.open(filename, 'w', **profile) as f:
        f.write(img.transpose(2, 0, 1))
Exemplo n.º 25
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def read_buffered_window(uri, metadata, px_buffer, cell, resampling):
    """
    Read a region from a source image, reprojecting in the process.

    Given the metadata for a layer (including a layout), a cell id, and a buffer
    size, read a window from the supplied image while reprojecting the source image
    to the CRS specified by the metadata.

    In concept, we specify a grid in the target CRS using the cell and resolution in
    the metadata, padding with px_buffer additional cells on all sides of the cell.
    For each cell center, we read from the source image after back-projecting the
    target location to the source image's coordinate system and applying the chosen
    resampling kernel.

    Args:
        uri (str): The source image URI; any scheme interpretable by GDAL is allowed
        metadata (``gps.Metadata``): The source layer metadata
        px_buffer (int): The number of pixels worth of padding that should be added
            to the extent to be read and added to the tile.
        cell (``gps.SpatialKey`` or ``gps.SpaceTimeKey``): The key of the target
            region
        resampling (``rasterio.warp.Resampling``): The resampling method to be used
            while reading from the source image

    Returns:
        ``gps.Tile``
    """
    if ("GDAL_DATA" not in os.environ) and '_GDAL_DATA' in vars():
        os.environ["GDAL_DATA"] = _GDAL_DATA

    layout = metadata.layout_definition
    dest_bounds = buffered_cell_extent(layout, px_buffer, cell)
    res = cell_size(metadata.layout_definition)
    dest_transform = Affine(res[0], 0, dest_bounds.xmin, 0, -res[1],
                            dest_bounds.ymax)
    dest_width = max(int(ceil((dest_bounds.xmax - dest_bounds.xmin) / res[0])),
                     1)
    dest_height = max(
        int(ceil((dest_bounds.ymax - dest_bounds.ymin) / res[1])), 1)
    dest_transform, dest_width, dest_height = rwarp.aligned_target(
        dest_transform, dest_width, dest_height, res)

    with rstr.open(uri) as src:
        tile = np.zeros((src.count, layout.tileLayout.tileCols + 2 * px_buffer,
                         layout.tileLayout.tileRows + 2 * px_buffer))
        rwarp.reproject(source=rstr.band(src, list(range(1, src.count + 1))),
                        destination=tile,
                        src_transform=src.transform,
                        src_crs=src.crs,
                        src_nodata=src.nodata,
                        dst_transform=dest_transform,
                        dst_crs=CRS.from_epsg(4326),
                        dst_nodata=src.nodata,
                        resampling=resampling,
                        num_threads=1)

    return gps.Tile.from_numpy_array(tile)
Exemplo n.º 26
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def get_web_optimized_params(
    src_dst,
    zoom_level_strategy: str = "auto",
    zoom_level: Optional[int] = None,
    aligned_levels: Optional[int] = None,
    tms: morecantile.TileMatrixSet = morecantile.tms.get("WebMercatorQuad"),
) -> Dict:
    """Return VRT parameters for a WebOptimized COG."""
    if src_dst.crs != tms.rasterio_crs:
        with WarpedVRT(src_dst, crs=tms.rasterio_crs) as vrt:
            bounds = vrt.bounds
            aff = list(vrt.transform)
    else:
        bounds = src_dst.bounds
        aff = list(src_dst.transform)

    resolution = max(abs(aff[0]), abs(aff[4]))

    if zoom_level is None:
        # find max zoom (closest to the raster resolution)
        max_zoom = tms.zoom_for_res(
            resolution,
            max_z=30,
            zoom_level_strategy=zoom_level_strategy,
        )
    else:
        max_zoom = zoom_level

    # defined the zoom level we want to align the raster
    aligned_levels = aligned_levels or 0
    base_zoom = max_zoom - aligned_levels

    # find new raster bounds (bounds of UL tile / LR tile)
    ul_tile = tms._tile(bounds[0], bounds[3], base_zoom)
    w, _, _, n = tms.xy_bounds(ul_tile)

    # The output resolution should match the TMS resolution at MaxZoom
    vrt_res = tms._resolution(tms.matrix(max_zoom))

    # Output transform is built from the origin (UL tile) and output resolution
    vrt_transform = Affine(vrt_res, 0, w, 0, -vrt_res, n)

    lr_tile = tms._tile(bounds[2], bounds[1], base_zoom)
    e, _, _, s = tms.xy_bounds(
        morecantile.Tile(lr_tile.x + 1, lr_tile.y + 1, lr_tile.z)
    )

    vrt_width = max(1, round((e - w) / vrt_transform.a))
    vrt_height = max(1, round((s - n) / vrt_transform.e))

    return dict(
        crs=tms.rasterio_crs,
        transform=vrt_transform,
        width=vrt_width,
        height=vrt_height,
    )
Exemplo n.º 27
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def write_geotiff(raster, origin, size, fpath):
    """Writes data in an n by n numpy array to disk as a
    GeoTIFF raster. The header is based on the raster array
    and a manual definition of the coordinate system and an
    affine transform.
    """
    transform = (Affine.translation(origin[0], origin[1]) *
                 Affine.scale(size, size))
    with rasterio.Env():
        with rasterio.open(fpath,
                           'w',
                           driver='GTiff',
                           height=raster.shape[0],
                           width=raster.shape[1],
                           count=1,
                           dtype=rasterio.float32,
                           crs='EPSG:28992',
                           transform=transform) as out_file:
            out_file.write(raster.astype(rasterio.float32), 1)
Exemplo n.º 28
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def temp_to_tif(input, output):
    filepath = '/home/sg/Projects/FIrehub-model/Bartsotas/example.tif'
    with rasterio.open(filepath) as src:
        print(src.crs)
        metadata = src.profile
    metadata.update(transform=Affine(0.02, 0.0, 19.2, 0.0, 0.02, 34))
    with rasterio.open(
            '/home/sg/Projects/FIrehub-model/Bartsotas/dataset_07072019/' +
            output + '.tif', 'w', **metadata) as dst:
        dst.write(input.astype(rasterio.float64), 1)
Exemplo n.º 29
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def main(args):
    data = np.load(args.in_file).astype(args.type)
    if len(data.shape) > 3 or len(data.shape) < 2:
        raise UnsupportedNumberDimsError(
            f"Number of dims must be 2 or 3. Got {len(data.shape)}."
        )
    elif len(data.shape) == 3:
        nbands = data.shape[0]
    else:
        nbands = 1
        # Add extra axis for iteration purposes
        data = np.expand_dims(data, axis=0)
    trans = REGION_TO_TRANS[args.region]
    if args.mask is not None:
        mask = trans(np.load(args.mask).astype(bool))
        data[..., mask] = args.missing_value
    crs = eg.GRID_NAME_TO_V1_PROJ[eg.ML]
    x, y = [
        trans(xi)
        for xi in eg.v1_lonlat_to_meters(*eg.v1_get_full_grid_lonlat(eg.ML))
    ]
    x = x[0]
    y = y[:, 0]
    xres = (x[-1] - x[0]) / len(x)
    yres = (y[-1] - y[0]) / len(y)
    t = Affine.translation(x[0], y[0]) * Affine.scale(xres, yres)
    ds = rio.open(
        args.out_file,
        "w",
        driver="GTiff",
        height=data.shape[1],
        width=data.shape[2],
        count=nbands,
        dtype=args.type,
        crs=crs.srs,
        transform=t,
        compress="lzw",
        nodata=args.missing_value,
    )
    for i, band in enumerate(data):
        ds.write(band, i + 1)
    ds.close()
    def exec(self) -> dict:
        data_array = self.ndarray[self.data_attr].values
        x_min = min(self.ndarray.coords["X"])
        x_max = max(self.ndarray.coords["X"])
        y_min = min(self.ndarray.coords["Y"])
        y_max = max(self.ndarray.coords["Y"])
        x_res = (x_max - x_min) / len(self.ndarray.coords["X"])
        y_res = (y_max - y_min) / len(self.ndarray.coords["Y"])
        transform = Affine.translation(
            x_min - x_res / 2, y_min - y_res / 2) * Affine.scale(x_res, y_res)
        if self.is_multiple_files:
            os.makedirs(self.output_file, exist_ok=True)
            for i, time in enumerate(self.ndarray.coords["time"].values):
                with rasterio.open(
                        str(self.output_file /
                            f"{time.replace(':', '-')}.tif"),
                        'w',
                        driver='GTiff',
                        height=data_array.shape[2],
                        width=data_array.shape[1],
                        count=1,
                        dtype=data_array.dtype,
                        crs='+init=epsg:4326',
                        transform=transform,
                ) as dst:
                    array = data_array[i].transpose()
                    dst.write(np.expand_dims(array, 0))
        else:
            with rasterio.open(
                    str(self.output_file),
                    'w',
                    driver='GTiff',
                    height=data_array.shape[2],
                    width=data_array.shape[1],
                    count=12,
                    dtype=data_array.dtype,
                    crs='+init=epsg:4326',
                    transform=transform,
            ) as dst:
                dst.write(data_array.swapaxes(1, 2))

        return {"result": True}
Exemplo n.º 31
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 def test_instantiate_scene(self):
     self.assertEqual(self.l7.mtl['L1_METADATA_FILE']['PRODUCT_METADATA']['FILE_NAME_BAND_1'],
                      'LE07_L1TP_039028_20100702_20160915_01_T1_B1.TIF')
     self.assertEqual(self.l7.utm_zone, 12)
     self.assertEqual(self.l7.ex_atm_irrad, (1970.0, 1842.0, 1547.0, 1044.0,
                                             255.700, np.nan, 82.06, 1369.00))
     self.assertEqual(self.l7.rasterio_geometry['height'], 727)
     self.assertEqual(self.l7.rasterio_geometry['driver'], 'GTiff')
     self.assertEqual(self.l7.rasterio_geometry['dtype'], 'uint8')
     self.assertEqual(self.l7.rasterio_geometry['transform'], Affine(30.0, 0.0, 367035.0,
                                                                     0.0, -30.0, 5082585.0))
Exemplo n.º 32
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    def test_instantiate_scene(self):
        l8 = Landsat8(self.dirname_cloud)
        self.assertEqual(l8.mtl['L1_METADATA_FILE']['PRODUCT_METADATA']['FILE_NAME_BAND_1'],
                         'LC80400282014193LGN00_B1.TIF')
        self.assertEqual(l8.utm_zone, 12)

        self.assertEqual(l8.rasterio_geometry['height'], 727)
        self.assertEqual(l8.rasterio_geometry['driver'], 'GTiff')
        self.assertEqual(l8.rasterio_geometry['dtype'], 'uint16')
        self.assertEqual(l8.rasterio_geometry['transform'], Affine(30.0, 0.0, 367035.0,
                                                                   0.0, -30.0, 5082585.0))
Exemplo n.º 33
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def pad(array, transform, pad_width, mode=None, **kwargs):
    """Returns a padded array and shifted affine transform matrix.
    
    Array is padded using `numpy.pad()`."""
    import numpy
    transform = guard_transform(transform)
    padded_array = numpy.pad(array, pad_width, mode, **kwargs)
    padded_trans = list(transform)
    padded_trans[2] -= pad_width*padded_trans[0]
    padded_trans[5] -= pad_width*padded_trans[4]
    return padded_array, Affine(*padded_trans[:6])
Exemplo n.º 34
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def write_geotiff(raster, origin, size, fpath):
    """Writes the interpolated TIN-linear and Laplace rasters
    to disk using the GeoTIFF format. The header is based on
    the raster array and a manual definition of the coordinate
    system and an identity affine transform.
    """
    import rasterio
    from rasterio.transform import Affine
    transform = (Affine.translation(origin[0], origin[1])
                 * Affine.scale(size, size))
    with rasterio.Env():
        with rasterio.open(fpath, 'w', driver = 'GTiff',
                           height = raster.shape[0],
                           width = raster.shape[1],
                           count = 1,
                           dtype = rasterio.float32,
                           crs='EPSG:28992',
                           transform = transform
                           ) as out_file:
            out_file.write(raster.astype(rasterio.float32), 1)
Exemplo n.º 35
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def test_untiled_dataset_blocksize(tmp_path):
    """Blocksize is not relevant to untiled datasets (see #1689)"""
    pytest.importorskip("pathlib")
    tmp_file = tmp_path / "test.tif"
    with rasterio.open(
            tmp_file, "w", driver="GTiff", count=1, height=13, width=13, dtype="uint8", crs="epsg:3857",
            transform=Affine.identity(), blockxsize=256, blockysize=256) as dataset:
        pass

    with rasterio.open(tmp_file) as dataset:
        assert not dataset.profile["tiled"]
        assert dataset.shape == (13, 13)
Exemplo n.º 36
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        def __call__(self):
            with rasterio.open(input) as src:
                img = None
                msk = None
                if band:
                    if sampling == 1:
                        img = src.read(bidx, masked=False)
                        transform = src.affine
                    # Decimate the band.
                    else:
                        img = numpy.zeros(
                            (src.height//sampling, src.width//sampling),
                            dtype=src.dtypes[src.indexes.index(bidx)])
                        img = src.read(bidx, img, masked=False)
                        transform = src.affine * Affine.scale(float(sampling))
                    if as_mask:
                        tmp = numpy.ones_like(img, 'uint8') * 255
                        tmp[img == 0] = 0
                        img = tmp
                        msk = tmp
                if not band or not with_nodata:
                    if sampling == 1:
                        msk = src.read_masks(bidx)
                        if bidx is None:
                            msk = numpy.logical_or.reduce(msk).astype('uint8')
                        transform = src.affine
                    # Decimate the mask.
                    else:
                        msk_shape = src.height//sampling, src.width//sampling
                        if bidx is None:
                            msk = numpy.zeros(
                                (src.count,) + msk_shape, 'uint8')
                        else:
                            msk = numpy.zeros(msk_shape, 'uint8')
                        msk = src.read_masks(bidx, msk)
                        if bidx is None:
                            msk = numpy.logical_or.reduce(msk).astype('uint8')
                        transform = src.affine * Affine.scale(float(sampling))

                bounds = src.bounds
                xs = [bounds[0], bounds[2]]
                ys = [bounds[1], bounds[3]]
                if projection == 'geographic':
                    xs, ys = rasterio.warp.transform(
                        src.crs, {'init': 'epsg:4326'}, xs, ys)
                if precision >= 0:
                    xs = [round(v, precision) for v in xs]
                    ys = [round(v, precision) for v in ys]
                self._xs = xs
                self._ys = ys

                kwargs = {'transform': transform}
                # Default is to exclude nodata features.
                if msk is not None:
                    kwargs['mask'] = msk #(msk > 0)
                if img is None:
                    img = msk

                for g, i in rasterio.features.shapes(img, **kwargs):
                    if projection == 'geographic':
                        g = rasterio.warp.transform_geom(
                            src.crs, 'EPSG:4326', g,
                            antimeridian_cutting=True, precision=precision)
                    xs, ys = zip(*coords(g))
                    yield {
                        'type': 'Feature',
                        'id': str(i),
                        'properties': {
                            'val': i, 'filename': os.path.basename(src.name)
                        },
                        'bbox': [min(xs), min(ys), max(xs), max(ys)],
                        'geometry': g
                    }
Exemplo n.º 37
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        def __call__(self):
            with rasterio.open(input) as src:
                if bidx is not None and bidx > src.count:
                    raise ValueError('bidx is out of range for raster')

                img = None
                msk = None

                # Adjust transforms.
                transform = src.affine
                if sampling > 1:
                    # Decimation of the raster produces a georeferencing
                    # shift that we correct with a translation.
                    transform *= Affine.translation(
                                    src.width%sampling, src.height%sampling)
                    # And follow by scaling.
                    transform *= Affine.scale(float(sampling))

                # Most of the time, we'll use the valid data mask.
                # We skip reading it if we're extracting every possible
                # feature (even invalid data features) from a band.
                if not band or (band and not as_mask and not with_nodata):
                    if sampling == 1:
                        msk = src.read_masks(bidx)
                    else:
                        msk_shape = (
                            src.height//sampling, src.width//sampling)
                        if bidx is None:
                            msk = numpy.zeros(
                                (src.count,) + msk_shape, 'uint8')
                        else:
                            msk = numpy.zeros(msk_shape, 'uint8')
                        msk = src.read_masks(bidx, msk)

                    if bidx is None:
                        msk = numpy.logical_or.reduce(msk).astype('uint8')

                    # Possibly overidden below.
                    img = msk

                # Read the band data unless the --mask option is given.
                if band:
                    if sampling == 1:
                        img = src.read(bidx, masked=False)
                    else:
                        img = numpy.zeros(
                            (src.height//sampling, src.width//sampling),
                            dtype=src.dtypes[src.indexes.index(bidx)])
                        img = src.read(bidx, img, masked=False)

                # If --as-mask option was given, convert the image
                # to a binary image. This reduces the number of shape
                # categories to 2 and likely reduces the number of
                # shapes.
                if as_mask:
                    tmp = numpy.ones_like(img, 'uint8') * 255
                    tmp[img == 0] = 0
                    img = tmp
                    if not with_nodata:
                        msk = tmp

                # Transform the raster bounds.
                bounds = src.bounds
                xs = [bounds[0], bounds[2]]
                ys = [bounds[1], bounds[3]]
                if projection == 'geographic':
                    xs, ys = rasterio.warp.transform(
                        src.crs, {'init': 'epsg:4326'}, xs, ys)
                if precision >= 0:
                    xs = [round(v, precision) for v in xs]
                    ys = [round(v, precision) for v in ys]
                self._xs = xs
                self._ys = ys

                # Prepare keyword arguments for shapes().
                kwargs = {'transform': transform}
                if not with_nodata:
                    kwargs['mask'] = msk

                src_basename = os.path.basename(src.name)

                # Yield GeoJSON features.
                for i, (g, val) in enumerate(
                        rasterio.features.shapes(img, **kwargs)):
                    if projection == 'geographic':
                        g = rasterio.warp.transform_geom(
                            src.crs, 'EPSG:4326', g,
                            antimeridian_cutting=True, precision=precision)
                    xs, ys = zip(*coords(g))
                    yield {
                        'type': 'Feature',
                        'id': "{0}:{1}".format(src_basename, i),
                        'properties': {
                            'val': val, 'filename': src_basename
                        },
                        'bbox': [min(xs), min(ys), max(xs), max(ys)],
                        'geometry': g
                    }
Exemplo n.º 38
0
def merge_rgba_tool(sources, outtif, bounds=None, res=None, precision=7,
                    creation_options={}):
    """A windowed, top-down approach to merging.
    For each block window, it loops through the sources,
    reads the corresponding source window until the block
    is filled with data or we run out of sources.

    Uses more disk IO but is faster* and
    consumes significantly less memory

    * The read efficiencies comes from using
    RGBA tifs where we can assume band 4 is the sole
    determinant of nodata. This avoids the use of
    expensive masked reads but, of course, limits
    what data can used. Hence merge_rgba.
    """
    first = sources[0]
    first_res = first.res
    dtype = first.dtypes[0]
    profile = first.profile

    # Extent from option or extent of all inputs.
    if bounds:
        dst_w, dst_s, dst_e, dst_n = bounds
    else:
        # scan input files.
        # while we're at it, validate assumptions about inputs
        xs = []
        ys = []
        for src in sources:
            left, bottom, right, top = src.bounds
            xs.extend([left, right])
            ys.extend([bottom, top])
            if src.profile['count'] != 4:  # TODO, how to test for alpha?
                raise ValueError("Inputs must be 4-band RGBA rasters")
        dst_w, dst_s, dst_e, dst_n = min(xs), min(ys), max(xs), max(ys)
    logger.debug("Output bounds: %r", (dst_w, dst_s, dst_e, dst_n))
    output_transform = Affine.translation(dst_w, dst_n)
    logger.debug("Output transform, before scaling: %r", output_transform)

    # Resolution/pixel size.
    if not res:
        res = first_res
    elif not np.iterable(res):
        res = (res, res)
    elif len(res) == 1:
        res = (res[0], res[0])
    output_transform *= Affine.scale(res[0], -res[1])
    logger.debug("Output transform, after scaling: %r", output_transform)

    # Compute output array shape. We guarantee it will cover the output
    # bounds completely.
    output_width = int(math.ceil((dst_e - dst_w) / res[0]))
    output_height = int(math.ceil((dst_n - dst_s) / res[1]))

    # Adjust bounds to fit.
    dst_e, dst_s = output_transform * (output_width, output_height)
    logger.debug("Output width: %d, height: %d", output_width, output_height)
    logger.debug("Adjusted bounds: %r", (dst_w, dst_s, dst_e, dst_n))

    profile['transform'] = output_transform
    profile['height'] = output_height
    profile['width'] = output_width

    profile['nodata'] = None  # rely on alpha mask

    # Creation opts
    profile.update(creation_options)

    # create destination file
    with rasterio.open(outtif, 'w', **profile) as dstrast:

        for idx, dst_window in dstrast.block_windows():

            left, bottom, right, top = dstrast.window_bounds(dst_window)
            blocksize = ((dst_window[0][1] - dst_window[0][0]) *
                         (dst_window[1][1] - dst_window[1][0]))

            # initialize array destined for the block
            dst_count = first.count
            dst_rows, dst_cols = tuple(b - a for a, b in dst_window)
            dst_shape = (dst_count, dst_rows, dst_cols)
            logger.debug("Temp shape: %r", dst_shape)
            dstarr = np.zeros(dst_shape, dtype=dtype)

            # Read up srcs until
            # a. everything is data; i.e. no nodata
            # b. no sources left
            for src in sources:
                # The full_cover behavior is problematic here as it includes
                # extra pixels along the bottom right when the sources are
                # slightly misaligned
                #
                # src_window = get_window(left, bottom, right, top,
                #                         src.transform, precision=precision)
                #
                # With rio merge this just adds an extra row, but when the
                # imprecision occurs at each block, you get artifacts

                # Alternative, custom get_window using rounding
                window_start = rowcol(
                    src.transform, left, top, op=round, precision=precision)
                window_stop = rowcol(
                    src.transform, right, bottom, op=round, precision=precision)
                src_window = tuple(zip(window_start, window_stop))

                temp = np.zeros(dst_shape, dtype=dtype)
                temp = src.read(out=temp, window=src_window,
                                boundless=True, masked=False)

                # pixels without data yet are available to write
                write_region = np.logical_and(
                    (dstarr[3] == 0),  # 0 is nodata
                    (temp[3] != 0))
                np.copyto(dstarr, temp, where=write_region)

                # check if dest has any nodata pixels available
                if np.count_nonzero(dstarr[3]) == blocksize:
                    break

            dstrast.write(dstarr, window=dst_window)

    return output_transform
Exemplo n.º 39
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def test_open_specific_driver_with_options():
    """Open a GeoTIFF with the GTiff driver and GEOREF_SOURCES option"""
    with rasterio.open(
            'tests/data/RGB.byte.tif', driver='GTiff', GEOREF_SOURCES='NONE') as src:
        assert src.transform == Affine.identity()
Exemplo n.º 40
0
    def pixel_to_world_coordinates(self,
                                   raster_data=None,
                                   filter_no_data_value=True,
                                   no_data_value=0,
                                   band_number=1):
        """
        Map the pixel coordinates to world coordinates. The affine transformation matrix is used for this purpose.
        The convention is to reference the pixel corner. To reference the pixel center instead, we translate each pixel by 50%.
        The "no value" pixels (cells) can be filtered out.

        A dataset's pixel coordinate system has its origin at the "upper left" (imagine it displayed on your screen).
        Column index increases to the right, and row index increases downward. The mapping of these coordinates to
        "world" coordinates in the dataset's reference system is done with an affine transformation matrix.

        param string raster_data: the raster data (2-dimensional array) to translate to world coordinates. If not provided, \
        it tries to load existing rasterized data about the RasterEnvironmentalLayer.

        :param int no_data_value: The pixel values depicting non-burned cells. Default is 0.

        :param bool filter_no_data_value: Whether to filter-out the no-data pixel values. Default is true. If set to \
        false, all pixels in a 2-dimensional array will be converted to world coordinates. Typically this option is used \
        to get a "base" map of the coordinates of all pixels in an image (map).

        :returns: A tuple of numpy ndarrays. The first array contains the latitude values for each \
        non-zero cell, the second array contains the longitude values for each non-zero cell.

        TODO: document raster-affine

        :rtype: tuple(np.ndarray, np.ndarray)

        """
        if raster_data is None:
            logger.info("No raster data provided, attempting to load default...")
            try:
                raster_data = self.load_data(self.file_path).read(band_number)  # we work on one layer, the first
                logger.info("Succesfully loaded existing raster data from %s." % self.file_path)
            except AttributeError as e:
                logger.error("Could not open raster file. %s " % str(e))
                raise AttributeError(e)

        logger.info("Transforming to world coordinates...")
        # first get the original Affine transformation matrix
        if hasattr(self, "raster_affine"):
            T0 = self.raster_affine
        else:   # default from arguments
            # try to deduce it
            logger.info("No Affine translation defined for this layer, trying to deduce it.")
            x_min, y_min, x_max, y_max = -180, -90, 180, 90
            pixel_size = (x_max - x_min) / raster_data.shape[1]
            if pixel_size != (y_max - y_min) / raster_data.shape[0]:
                logger.error("Could not deduce Affine transformation...possibly the pixel is not a square.")
                return
            T0 = Affine(pixel_size, 0.0, x_min, 0.0, -pixel_size, y_max)
        # convert it to gdal format (it is otherwise flipped)
        T0 = Affine(*reversed(T0.to_gdal()))
        logger.debug("Affine transformation T0:\n %s " % (T0,))
        # shift by 50% to get the pixel center
        T1 = T0 * Affine.translation(0.5, 0.5)
        # apply the shift, filtering out no_data_value values
        logger.debug("Raster data shape: %s " % (raster_data.shape,))
        logger.debug("Affine transformation T1:\n %s " % (T1,))
        if filter_no_data_value:
            logger.info("Filtering out no_data pixels.")
            raster_data = np.where(raster_data != no_data_value, raster_data, np.nan)
            coordinates = (T1 * np.where(~np.isnan(raster_data)))
        else:
            coordinates = (T1 * np.where(raster_data))
        logger.info("Transformation to world coordinates completed.")
        return coordinates
Exemplo n.º 41
0
    def rasterize(self, raster_file=None,
                  pixel_size=None,
                  all_touched=False,
                  no_data_value=0,
                  default_value=1,
                  crs=None,
                  cropped=False,
                  classifier_column=None,
                  *args, **kwargs):
        """
        Rasterize (burn) the environment rangemaps (geometrical shapes) into pixels (cells), i.e., a 2-dimensional image array
        of type numpy ndarray. Uses the `Rasterio <https://mapbox.github.io/rasterio/_modules/rasterio/features.html>`_ library
        for this purpose. All the shapes from the ``VectorEnvironmentalLayer`` object data are burned in a single *band* of the image.
        Rasterio datasets can generally have one or more bands, or layers. Following the GDAL convention, these are indexed starting with 1.

        :param string raster_file: The full path to the targed GeoTIFF raster file (including the directory and filename in one string).

        :param int pixel_size: The size of the pixel in degrees, i.e., the resolution to use for rasterizing.

        :param bool all_touched: If true, all pixels touched by geometries, will be burned in. If false, only pixels \
        whose center is within the polygon or that are selected by Bresenham's line algorithm, will be burned in.

        :param int no_data_value: Used as value of the pixels which are not burned in. Default is 0.

        :param int default_value: Used as value of the pixels which are burned in. Default is 1.

        :param crs: The Coordinate Reference System to use. Default is "ESPG:4326"

        :param bool cropped: If true, the resulting pixel array (image) is cropped to the region borders, which contain \
        the burned pixels (i.e., an envelope within the range). Otherwise, a "global world map" is used, i.e., the boundaries \
        are set to (-180, -90, 180, 90) for the resulting array.

        :returns: Rasterio RasterReader file object which can be used to read individual bands from the raster file.

        :rtype: rasterio._io.RasterReader

        """
        if not (pixel_size or raster_file):
            raise AttributeError("Please provide pixel_size and a target raster_file.")

        if not hasattr(self, 'data_full'):
            raise AttributeError("You have not loaded the data.")

        if crs is None:
            crs = {'init': "EPSG:4326"}

        # crop to the boundaries of the shape?
        if cropped:
            # cascaded_union_geometry = shapely.ops.cascaded_union(self.data_full.geometry)
            x_min, y_min, x_max, y_max = self.data_full.geometry.total_bounds
        # else global map
        else:
            x_min, y_min, x_max, y_max = -180, -90, 180, 90

        x_res = int((x_max - x_min) / pixel_size)
        y_res = int((y_max - y_min) / pixel_size)
        logger.info("Will rasterize using pixel_size=%s, all_touched=%s, no_data_value=%s, fill_value=%s "
                    % (pixel_size, all_touched, no_data_value, default_value))
        transform = Affine.translation(x_min, y_max) * Affine.scale(pixel_size, -pixel_size)
        if classifier_column:
            logger.info("Will rasterize using classifier: %s." % classifier_column)
            classifier_categories = self.data_full[classifier_column].unique()
            stacked_layers = []
            for category_name in classifier_categories:
                if category_name:
                    logger.info("Rasterizing category %s " % category_name)
                    result = features.rasterize(self.data_full.geometry[self.data_full[classifier_column] == category_name],
                                                transform=transform,
                                                out_shape=(y_res, x_res),
                                                all_touched=all_touched,
                                                fill=no_data_value,
                                                default_value=default_value
                                                )
                    stacked_layers.append(result)

            stacked_layers = np.stack(stacked_layers)

            for i, band in enumerate(stacked_layers, 1):
                with rasterio.open(raster_file, 'w', driver='GTiff', width=x_res, height=y_res,
                                   count=stacked_layers.shape[0],
                                   dtype=np.uint8,
                                   nodata=no_data_value,
                                   transform=transform,
                                   crs=crs) as out:
                    out.write(band.astype(np.uint8), indexes=i)
            result_final = stacked_layers
        else:
            logger.info("Will rasterize everything on a single band.")
            result_final = features.rasterize(self.data_full.geometry,
                                              transform=transform,
                                              out_shape=(y_res, x_res),
                                              all_touched=all_touched,
                                              fill=no_data_value,
                                              default_value=default_value
                                              )

            with rasterio.open(raster_file, 'w', driver='GTiff', width=x_res, height=y_res,
                               count=1,
                               dtype=np.uint8,
                               nodata=no_data_value,
                               transform=transform,
                               crs=crs) as out:
                out.write(result_final.astype(np.uint8), indexes=1)
        out.close()
        logger.info("RASTERIO: Data rasterized into file %s " % raster_file)
        logger.info("RASTERIO: Resolution: x_res={0} y_res={1}".format(x_res, y_res))
        self.raster_file = raster_file
        self.raster_affine = transform
        self.stacked_layers = stacked_layers
        return result_final
Exemplo n.º 42
0
def merge(sources, bounds=None, res=None, nodata=None, precision=7):
    """Copy valid pixels from input files to an output file.

    All files must have the same number of bands, data type, and
    coordinate reference system.

    Input files are merged in their listed order using the reverse
    painter's algorithm. If the output file exists, its values will be
    overwritten by input values.

    Geospatial bounds and resolution of a new output file in the
    units of the input file coordinate reference system may be provided
    and are otherwise taken from the first input file.

    Parameters
    ----------
    sources: list of source datasets
        Open rasterio RasterReader objects to be merged.
    bounds: tuple, optional
        Bounds of the output image (left, bottom, right, top).
        If not set, bounds are determined from bounds of input rasters.
    res: tuple, optional
        Output resolution in units of coordinate reference system. If not set,
        the resolution of the first raster is used. If a single value is passed,
        output pixels will be square.
    nodata: float, optional
        nodata value to use in output file. If not set, uses the nodata value
        in the first input raster.

    Returns
    -------
    dest: numpy ndarray
        Contents of all input rasters in single array.
    out_transform: affine object
        Information for mapping pixel coordinates in `dest` to another
        coordinate system
    """
    first = sources[0]
    first_res = first.res
    nodataval = first.nodatavals[0]
    dtype = first.dtypes[0]

    # Extent from option or extent of all inputs.
    if bounds:
        dst_w, dst_s, dst_e, dst_n = bounds
    else:
        # scan input files.
        xs = []
        ys = []
        for src in sources:
            left, bottom, right, top = src.bounds
            xs.extend([left, right])
            ys.extend([bottom, top])
        dst_w, dst_s, dst_e, dst_n = min(xs), min(ys), max(xs), max(ys)

    logger.debug("Output bounds: %r", (dst_w, dst_s, dst_e, dst_n))
    output_transform = Affine.translation(dst_w, dst_n)
    logger.debug("Output transform, before scaling: %r", output_transform)

    # Resolution/pixel size.
    if not res:
        res = first_res
    elif not np.iterable(res):
        res = (res, res)
    elif len(res) == 1:
        res = (res[0], res[0])
    output_transform *= Affine.scale(res[0], -res[1])
    logger.debug("Output transform, after scaling: %r", output_transform)

    # Compute output array shape. We guarantee it will cover the output
    # bounds completely.
    output_width = int(math.ceil((dst_e - dst_w) / res[0]))
    output_height = int(math.ceil((dst_n - dst_s) / res[1]))

    # Adjust bounds to fit.
    dst_e, dst_s = output_transform * (output_width, output_height)
    logger.debug("Output width: %d, height: %d", output_width, output_height)
    logger.debug("Adjusted bounds: %r", (dst_w, dst_s, dst_e, dst_n))

    # create destination array
    dest = np.zeros((first.count, output_height, output_width), dtype=dtype)

    if nodata is not None:
        nodataval = nodata
        logger.debug("Set nodataval: %r", nodataval)

    if nodataval is not None:
        # Only fill if the nodataval is within dtype's range.
        inrange = False
        if np.dtype(dtype).kind in ('i', 'u'):
            info = np.iinfo(dtype)
            inrange = (info.min <= nodataval <= info.max)
        elif np.dtype(dtype).kind == 'f':
            info = np.finfo(dtype)
            inrange = (info.min <= nodataval <= info.max)
        if inrange:
            dest.fill(nodataval)
        else:
            warnings.warn(
                "Input file's nodata value, %s, is beyond the valid "
                "range of its data type, %s. Consider overriding it "
                "using the --nodata option for better results." % (
                    nodataval, dtype))
    else:
        nodataval = 0

    for src in sources:
        # Real World (tm) use of boundless reads.
        # This approach uses the maximum amount of memory to solve the problem.
        # Making it more efficient is a TODO.

        # 1. Compute spatial intersection of destination and source.
        src_w, src_s, src_e, src_n = src.bounds

        int_w = src_w if src_w > dst_w else dst_w
        int_s = src_s if src_s > dst_s else dst_s
        int_e = src_e if src_e < dst_e else dst_e
        int_n = src_n if src_n < dst_n else dst_n

        # 2. Compute the source window.
        src_window = get_window(
            int_w, int_s, int_e, int_n, src.affine, precision=precision)
        logger.debug("Src %s window: %r", src.name, src_window)

        # 3. Compute the destination window.
        dst_window = get_window(
            int_w, int_s, int_e, int_n, output_transform, precision=precision)
        logger.debug("Dst window: %r", dst_window)

        # 4. Initialize temp array.
        tcount = first.count
        trows, tcols = tuple(b - a for a, b in dst_window)

        temp_shape = (tcount, trows, tcols)
        logger.debug("Temp shape: %r", temp_shape)

        temp = np.zeros(temp_shape, dtype=dtype)
        temp = src.read(out=temp, window=src_window, boundless=False,
                        masked=True)

        # 5. Copy elements of temp into dest.
        roff, coff = dst_window[0][0], dst_window[1][0]

        region = dest[:, roff:roff + trows, coff:coff + tcols]
        np.copyto(
            region, temp,
            where=np.logical_and(region == nodataval, temp.mask == False))

    return dest, output_transform
Exemplo n.º 43
0
def dataset_features(
        src,
        bidx=None,
        sampling=1,
        band=True,
        as_mask=False,
        with_nodata=False,
        geographic=True,
        precision=-1):
    """Yield GeoJSON features for the dataset

    The geometries are polygons bounding contiguous regions of the same raster value.

    Parameters
    ----------
    src: Rasterio Dataset

    bidx: int
        band index

    sampling: int (DEFAULT: 1)
        Inverse of the sampling fraction; a value of 10 decimates

    band: boolean (DEFAULT: True)
        extract features from a band (True) or a mask (False)

    as_mask: boolean (DEFAULT: False)
        Interpret band as a mask and output only one class of valid data shapes?

    with_nodata: boolean (DEFAULT: False)
        Include nodata regions?

    geographic: str (DEFAULT: True)
        Output shapes in EPSG:4326? Otherwise use the native CRS.

    precision: int (DEFAULT: -1)
        Decimal precision of coordinates. -1 for full float precision output

    Yields
    ------
    GeoJSON-like Feature dictionaries for shapes found in the given band
    """
    if bidx is not None and bidx > src.count:
        raise ValueError('bidx is out of range for raster')

    img = None
    msk = None

    # Adjust transforms.
    transform = src.transform
    if sampling > 1:
        # Determine the target shape (to decimate)
        shape = (int(math.ceil(src.height / sampling)),
                 int(math.ceil(src.width / sampling)))

        # Calculate independent sampling factors
        x_sampling = src.width / shape[1]
        y_sampling = src.height / shape[0]

        # Decimation of the raster produces a georeferencing
        # shift that we correct with a translation.
        transform *= Affine.translation(
            src.width % x_sampling, src.height % y_sampling)

        # And follow by scaling.
        transform *= Affine.scale(x_sampling, y_sampling)

    # Most of the time, we'll use the valid data mask.
    # We skip reading it if we're extracting every possible
    # feature (even invalid data features) from a band.
    if not band or (band and not as_mask and not with_nodata):
        if sampling == 1:
            msk = src.read_masks(bidx)
        else:
            msk_shape = shape
            if bidx is None:
                msk = np.zeros(
                    (src.count,) + msk_shape, 'uint8')
            else:
                msk = np.zeros(msk_shape, 'uint8')
            msk = src.read_masks(bidx, msk)

        if bidx is None:
            msk = np.logical_or.reduce(msk).astype('uint8')

        # Possibly overridden below.
        img = msk

    # Read the band data unless the --mask option is given.
    if band:
        if sampling == 1:
            img = src.read(bidx, masked=False)
        else:
            img = np.zeros(
                shape,
                dtype=src.dtypes[src.indexes.index(bidx)])
            img = src.read(bidx, img, masked=False)

    # If as_mask option was given, convert the image
    # to a binary image. This reduces the number of shape
    # categories to 2 and likely reduces the number of
    # shapes.
    if as_mask:
        tmp = np.ones_like(img, 'uint8') * 255
        tmp[img == 0] = 0
        img = tmp
        if not with_nodata:
            msk = tmp

    # Prepare keyword arguments for shapes().
    kwargs = {'transform': transform}
    if not with_nodata:
        kwargs['mask'] = msk

    src_basename = os.path.basename(src.name)

    # Yield GeoJSON features.
    for i, (g, val) in enumerate(
            rasterio.features.shapes(img, **kwargs)):
        if geographic:
            g = warp.transform_geom(
                src.crs, 'EPSG:4326', g,
                antimeridian_cutting=True, precision=precision)
        xs, ys = zip(*coords(g))
        yield {
            'type': 'Feature',
            'id': "{0}:{1}".format(src_basename, i),
            'properties': {
                'val': val,
                'filename': src_basename
            },
            'bbox': [min(xs), min(ys), max(xs), max(ys)],
            'geometry': g
        }
Exemplo n.º 44
0
def affine_from_corner(ulx, uly, dx, dy):
    return Affine.translation(ulx, uly)*Affine.scale(dx, -dy)
Exemplo n.º 45
0
def merge(ctx, files, driver, bounds, res, nodata):
    """Copy valid pixels from input files to an output file.

    All files must have the same number of bands, data type, and
    coordinate reference system.

    Input files are merged in their listed order using the reverse
    painter's algorithm. If the output file exists, its values will be
    overwritten by input values.

    Geospatial bounds and resolution of a new output file in the
    units of the input file coordinate reference system may be provided
    and are otherwise taken from the first input file.
    """
    import numpy as np

    verbosity = (ctx.obj and ctx.obj.get('verbosity')) or 1
    logger = logging.getLogger('rio')

    try:
        with rasterio.drivers(CPL_DEBUG=verbosity>2):
            output = files[-1]
            files = files[:-1]

            with rasterio.open(files[0]) as first:
                first_res = first.res
                kwargs = first.meta
                kwargs.pop('affine')
                nodataval = first.nodatavals[0]
                dtype = first.dtypes[0]

            if os.path.exists(output):
                # TODO: prompt user to update existing file (-i option) like:
                # overwrite b.tif? (y/n [n]) n
                # not overwritten
                dst = rasterio.open(output, 'r+')
                nodataval = dst.nodatavals[0]
                dtype = dst.dtypes[0]
                dest = np.zeros((dst.count,) + dst.shape, dtype=dtype)
            else:
                # Create new output file.
                # Extent from option or extent of all inputs.
                if not bounds:
                    # scan input files.
                    xs = []
                    ys = []
                    for f in files:
                        with rasterio.open(f) as src:
                            left, bottom, right, top = src.bounds
                            xs.extend([left, right])
                            ys.extend([bottom, top])
                    bounds = min(xs), min(ys), max(xs), max(ys)
                output_transform = Affine.translation(bounds[0], bounds[3])

                # Resolution/pixel size.
                if not res:
                    res = first_res
                output_transform *= Affine.scale(res[0], -res[1])

                # Dataset shape.
                output_width = int(math.ceil((bounds[2]-bounds[0])/res[0]))
                output_height = int(math.ceil((bounds[3]-bounds[1])/res[1]))

                kwargs['driver'] == driver
                kwargs['transform'] = output_transform
                kwargs['width'] = output_width
                kwargs['height'] = output_height

                logger.debug("Kwargs: %r", kwargs)
                logger.debug("bounds: %r", bounds)
                logger.debug("Res: %r", res)

                dst = rasterio.open(output, 'w', **kwargs)
                dest = np.zeros((first.count, output_height, output_width),
                        dtype=dtype)

                logger.debug("In merge, dest shape: %r", dest.shape)

            if nodata is not None:
                nodataval = nodata

            if nodataval is not None:
                # Only fill if the nodataval is within dtype's range.
                inrange = False
                if np.dtype(dtype).kind in ('i', 'u'):
                    info = np.iinfo(dtype)
                    inrange = (info.min <= nodataval <= info.max)
                elif np.dtype(dtype).kind == 'f':
                    info = np.finfo(dtype)
                    inrange = (info.min <= nodataval <= info.max)
                if inrange:
                    dest.fill(nodataval)
                else:
                    warnings.warn(
                        "Input file's nodata value, %s, is beyond the valid "
                        "range of its data type, %s. Consider overriding it "
                        "using the --nodata option for better results." % (
                            nodataval, dtype))
            else:
                nodataval = 0

            dst_w, dst_s, dst_e, dst_n = dst.bounds

            for fname in reversed(files):
                with rasterio.open(fname) as src:
                    # Real World (tm) use of boundless reads.
                    # This approach uses the maximum amount of memory to solve
                    # the problem. Making it more efficient is a TODO.

                    # 1. Compute spatial intersection of destination
                    #    and source.
                    src_w, src_s, src_e, src_n = src.bounds

                    int_w = src_w if src_w > dst_w else dst_w
                    int_s = src_s if src_s > dst_s else dst_s
                    int_e = src_e if src_e < dst_e else dst_e
                    int_n = src_n if src_n < dst_n else dst_n

                    # 2. Compute the source window.
                    src_window = src.window(int_w, int_s, int_e, int_n)

                    # 3. Compute the destination window.
                    dst_window = dst.window(int_w, int_s, int_e, int_n)

                    # 4. Initialize temp array.
                    temp = np.zeros(
                            (first.count,) + tuple(b - a for a, b in dst_window),
                            dtype=dtype)

                    temp = src.read(
                            out=temp,
                            window=src_window,
                            boundless=False,
                            masked=True)

                    # 5. Copy elements of temp into dest.
                    roff, coff = dst.index(int_w, int_n)
                    h, w = temp.shape[-2:]

                    region = dest[:,roff:roff+h,coff:coff+w]
                    np.copyto(region, temp,
                        where=np.logical_and(
                        region==nodataval, temp.mask==False))

            if dst.mode == 'r+':
                temp = dst.read(masked=True)
                np.copyto(dest, temp,
                    where=np.logical_and(
                    dest==nodataval, temp.mask==False))

            dst.write(dest)
            dst.close()

        sys.exit(0)
    except Exception:
        logger.exception("Failed. Exception caught")
        sys.exit(1)