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Allow fill mosaic blank pixels with specified value #141

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Allow fill mosaic blank pixels with specified value #141

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de6cdea
Remove unused argument
Yu-AnChen Sep 25, 2019
0f31b75
Merge branch 'labsyspharm:master' into master
Yu-AnChen Jun 15, 2022
eeb8c8c
Allow fill mosaic canvas with custom value
Yu-AnChen Jun 15, 2022
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8 changes: 7 additions & 1 deletion ashlar/reg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1065,10 +1065,12 @@ def _load_correction_profiles(self, dfp_path, ffp_path):
self.dfp /= np.iinfo(self.dtype).max
self.do_correction = True

def assemble_channel(self, channel, out=None):
def assemble_channel(self, channel, out=None, fill_blank_value=None):
num_tiles = len(self.aligner.positions)
if out is None:
out = np.zeros(self.shape, self.dtype)
if fill_blank_value is not None:
mask = np.ones(self.shape, bool)
else:
if out.shape != self.shape:
raise ValueError(
Expand All @@ -1082,6 +1084,10 @@ def assemble_channel(self, channel, out=None):
img = self.aligner.reader.read(c=channel, series=si)
img = self.correct_illumination(img, channel)
utils.paste(out, img, position, func=utils.pastefunc_blend)
if fill_blank_value is not None:
utils.paste(mask, np.zeros_like(img, bool), position)
if fill_blank_value is not None:
out[mask] = fill_blank_value
# Memory-conserving axis flips.
if self.flip_mosaic_x:
for i in range(len(out)):
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