Merge branch 'master' into v0.3.0_merge

solaris/tile/raster_tile.py

@@ -179,12 +179,12 @@ def tile(self, src, dest_dir=None, channel_idxs=None, nodata=None,
  dest.close()
  src.close()
  src = _check_rasterio_im_load(restricted_im_path) #if restrict_to_aoi, we overwrite the src to be the masked raster
-
+ 
  tile_gen = self.tile_generator(src, dest_dir, channel_idxs, nodata,
  alpha, self.aoi_boundary, restrict_to_aoi)
 
  if self.verbose:
- print('Beginning tiling...')
+ print('Beginning tiling...') 
  self.tile_paths = []
  if nodata_threshold is not None:
  if nodata_threshold > 1:
@@ -457,6 +457,49 @@ def save_tile(self, tile_data, mask, profile, dest_fname_base=None):
  # self._create_cog(os.path.join(self.dest_dir, 'tmp.tif'),
  # os.path.join(self.dest_dir, dest_fname))
  # os.remove(os.path.join(self.dest_dir, 'tmp.tif'))
+
+ def fill_all_nodata(self, nodata_fill):
+ """
+ Fills all tile nodata values with a fill value.
+ 
+ The standard workflow is to run this function only after generating label masks and using the original output 
+ from the raster tiler to filter out label pixels that overlap nodata pixels in a tile. For example, 
+ solaris.vector.mask.instance_mask will filter out nodata pixels from a label mask if a reference_im is provided,
+ and after this step nodata pixels may be filled by calling this method.
+ 
+ nodata_fill : int, float, or str, optional
+ Default is to not fill any nodata values. Otherwise, pixels outside of the aoi_boundary and pixels inside 
+ the aoi_boundary with the nodata value will be filled. "mean" will fill pixels with the channel-wise mean. 
+ Providing an int or float will fill pixels in all channels with the provided value.
+ 
+ Returns: list
+ The fill values, in case the mean of the src image should be used for normalization later.
+ """
+ src = _check_rasterio_im_load(self.src_name)
+ if nodata_fill == "mean":
+ arr = src.read()
+ arr_nan = np.where(arr!=src.nodata, arr, np.nan)
+ fill_values = np.nanmean(arr_nan, axis=tuple(range(1, arr_nan.ndim)))
+ print('Fill values set to {}'.format(fill_values))
+ elif isinstance(nodata_fill, (float, int)):
+ fill_values = src.meta['count'] * [nodata_fill]
+ print('Fill values set to {}'.format(fill_values))
+ else:
+ raise TypeError('nodata_fill must be "mean", int, or float. {} was supplied.'.format(nodata_fill))
+ src.close()
+ for tile_path in self.tile_paths:
+ tile_src = rasterio.open(tile_path, "r+")
+ tile_data = tile_src.read()
+ for i in np.arange(tile_data.shape[0]):
+ tile_data[i,...][tile_data[i,...] == tile_src.nodata] = fill_values[i] # set fill value for each band
+ if tile_src.meta['count'] == 1:
+ tile_src.write(tile_data[0, :, :], 1)
+ else:
+ for band in range(1, tile_src.meta['count'] + 1):
+ # base-1 vs. base-0 indexing...bleh
+ tile_src.write(tile_data[band-1, :, :], band)
+ tile_src.close()
+ return fill_values
 
  def fill_all_nodata(self, nodata_fill):
  """

solaris/tile/vector_tile.py

@@ -299,7 +299,7 @@ def clip_gdf(gdf, tile_bounds, min_partial_perc=0.0, geom_type="Polygon",
  gdf['origlen'] = 0
  # TODO must implement different case for lines and for spatialIndex
  # (Assume RTree is already performed)
-
+ 
  cut_gdf = gdf.copy()
  cut_gdf.geometry = gdf.intersection(tb)