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Do not apply linear stretch to alpha band #145

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Sep 27, 2023
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Do not apply linear stretch to alpha band #145

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36 changes: 36 additions & 0 deletions trollimage/tests/test_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1541,6 +1541,42 @@ def test_linear_stretch(self):

np.testing.assert_allclose(img.data.values, res, atol=1.e-6)

def test_linear_stretch_does_not_affect_alpha(self):
"""Test linear stretching with cutoffs."""
arr = np.arange(100).reshape(5, 5, 4) / 74.
arr[:, :, -1] = 1 # alpha channel, fully opaque
data = xr.DataArray(arr.copy(), dims=['y', 'x', 'bands'],
coords={'bands': ['R', 'G', 'B', 'A']})
img = xrimage.XRImage(data)
img.stretch_linear((0.005, 0.005))
res = np.array([[[-0.005051, -0.005051, -0.005051, 1.],
[0.037037, 0.037037, 0.037037, 1.],
[0.079125, 0.079125, 0.079125, 1.],
[0.121212, 0.121212, 0.121212, 1.],
[0.1633, 0.1633, 0.1633, 1.]],
[[0.205387, 0.205387, 0.205387, 1.],
[0.247475, 0.247475, 0.247475, 1.],
[0.289562, 0.289562, 0.289562, 1.],
[0.33165, 0.33165, 0.33165, 1.],
[0.373737, 0.373737, 0.373737, 1.]],
[[0.415825, 0.415825, 0.415825, 1.],
[0.457912, 0.457912, 0.457912, 1.],
[0.5, 0.5, 0.5, 1.],
[0.542088, 0.542088, 0.542088, 1.],
[0.584175, 0.584175, 0.584175, 1.]],
[[0.626263, 0.626263, 0.626263, 1.],
[0.66835, 0.66835, 0.66835, 1.],
[0.710438, 0.710438, 0.710438, 1.],
[0.752525, 0.752525, 0.752525, 1.],
[0.794613, 0.794613, 0.794613, 1.]],
[[0.8367, 0.8367, 0.8367, 1.],
[0.878788, 0.878788, 0.878788, 1.],
[0.920875, 0.920875, 0.920875, 1.],
[0.962963, 0.962963, 0.962963, 1.],
[1.005051, 1.005051, 1.005051, 1.]]])

np.testing.assert_allclose(img.data.values, res, atol=1.e-6)

def test_histogram_stretch(self):
"""Test histogram stretching."""
arr = np.arange(75).reshape(5, 5, 3) / 74.
Expand Down
38 changes: 27 additions & 11 deletions trollimage/xrimage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,7 @@ def rio_save(self, filename, fformat=None, fill_value=None,
warnings.warn(
"include_scale_offset_tags is deprecated, please use "
"scale_offset_tags to indicate tag labels",
DeprecationWarning)
DeprecationWarning, stacklevel=2)
scale_offset_tags = scale_offset_tags or ("scale", "offset")

if tags is None:
Expand Down Expand Up @@ -659,7 +659,7 @@ def _get_dtype_scale_offset(self, dtype, fill_value):
"Specified fill value will overlap with valid "
"data. To avoid this warning specify a fill_value "
"that is the minimum or maximum for the data type "
"being saved to.")
"being saved to.", stacklevel=3)
return scale, offset

def _scale_to_dtype(self, data, dtype, fill_value=None):
Expand Down Expand Up @@ -1019,29 +1019,45 @@ def stretch_linear(self, cutoffs=(0.005, 0.005)):
"""
logger.debug("Perform a linear contrast stretch.")

left, right = self._get_left_and_right_quantiles_for_linear_stretch(cutoffs)

self.crude_stretch(left, right)

def _get_left_and_right_quantiles_for_linear_stretch(self, cutoffs):
logger.debug("Calculate the histogram quantiles: ")
logger.debug("Left and right quantiles: " +
str(cutoffs[0]) + " " + str(cutoffs[1]))

cutoff_type = np.float64
# numpy percentile (which quantile calls) returns 64-bit floats
# unless the value is a higher order float
if np.issubdtype(self.data.dtype, np.floating) and \
np.dtype(self.data.dtype).itemsize > 8:
cutoff_type = self.data.dtype
left, right = dask.delayed(self._compute_quantile, nout=2)(self.data.data, self.data.dims, cutoffs)
left_data = da.from_delayed(left,
shape=(self.data.sizes['bands'],),
dtype=cutoff_type)

data = self.data
if 'A' in self.data.coords['bands'].values:
data = self.data.sel(bands=self.data.coords['bands'].values[:-1])

left_data, right_data = self._get_left_and_right_quantiles_without_alpha(data, cutoffs, cutoff_type)

if 'A' in self.data.coords['bands'].values:
left_data = np.hstack([left_data, np.array([0])])
right_data = np.hstack([right_data, np.array([1])])
left = xr.DataArray(left_data, dims=('bands',),
coords={'bands': self.data['bands']})
right_data = da.from_delayed(right,
shape=(self.data.sizes['bands'],),
dtype=cutoff_type)
right = xr.DataArray(right_data, dims=('bands',),
coords={'bands': self.data['bands']})
return left, right

self.crude_stretch(left, right)
def _get_left_and_right_quantiles_without_alpha(self, data, cutoffs, cutoff_type):
left, right = dask.delayed(self._compute_quantile, nout=2)(data.data, data.dims, cutoffs)
left_data = da.from_delayed(left,
shape=(data.sizes['bands'],),
dtype=cutoff_type)
right_data = da.from_delayed(right,
shape=(data.sizes['bands'],),
dtype=cutoff_type)
return left_data, right_data

def crude_stretch(self, min_stretch=None, max_stretch=None):
"""Perform simple linear stretching.
Expand Down