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b/stackstac/rio_reader.py index 1a41532..61e44a1 100644 --- a/stackstac/rio_reader.py +++ b/stackstac/rio_reader.py @@ -103,7 +103,7 @@ def read(self, window: Window, **kwargs) -> np.ndarray: "Acquire the lock, then read from the dataset" reader = self.vrt or self.ds with self._lock, self.env.read: - return reader.read(1, window=window, **kwargs) + return reader.read(window=window, **kwargs) def close(self) -> None: "Acquire the lock, then close the dataset" @@ -173,6 +173,7 @@ def __init__( transform=vrt.transform, dtype=vrt.working_dtype, warp_extras=vrt.warp_extras, + add_alpha=vrt.nodata is None, # see `AutoParallelRioReader.read` ) # ^ copied from rioxarray # https://github.com/corteva/rioxarray/blob/0804791a44f65ac4f303dd286e94b3eaee81f72b/rioxarray/_io.py#L720-L734 @@ -224,7 +225,7 @@ def read(self, window: Window, **kwargs) -> np.ndarray: "Read from the current thread's dataset, opening a new copy of the dataset on first access from each thread." with time(f"Read {self._url!r} in {_curthread()}: {{t}}"): with self._env.read: - return self.dataset.read(1, window=window, **kwargs) + return self.dataset.read(window=window, **kwargs) def close(self) -> None: """ @@ -353,6 +354,7 @@ def _open(self) -> ThreadsafeRioDataset: ds, sharing=False, resampling=self.resampling, + add_alpha=ds.nodata is None, **self.spec.vrt_params, ) else: @@ -398,6 +400,17 @@ def read(self, window: Window, **kwargs) -> np.ndarray: raise RuntimeError(msg) from e + # When the GeoTIFF doesn't have a nodata value, and we're using a VRT, pixels + # outside the dataset don't get properly masked (they're just 0). Using `add_alpha` + # in the `WarpedVRT`, we get an explicit alpha channel, which we use as a mask instead. + # See https://github.com/gjoseph92/stackstac/issues/217. + if result.shape[0] == 2: + result = np.ma.masked_array(result[0], mask=result[1] == 0) + elif result.shape[0] == 1: + result = result[0] + else: + raise RuntimeError(f"Unexpected shape {result.shape}, expected exactly 1 band.") + scale, offset = self.scale_offset if scale != 1: