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Add minisblack photometric to tiff writing #46

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merged 2 commits into from
Mar 11, 2024
Merged

Add minisblack photometric to tiff writing #46

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2109f5b
add minisblack photometric
K-Meech Mar 11, 2024
934bd03
Add default to photometric docstring
K-Meech Mar 11, 2024
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8 changes: 6 additions & 2 deletions brainglobe_utils/image_io/save.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def to_nii(img, dest_path, scale=None, affine_transform=None):
nib.save(img, dest_path)


def to_tiff(img_volume, dest_path):
def to_tiff(img_volume, dest_path, photometric="minisblack"):
"""
Save the image volume (numpy array) to a tiff stack.

Expand All @@ -51,9 +51,13 @@ def to_tiff(img_volume, dest_path):

dest_path : str
Where to save the tiff stack.

photometric: str
Color space of image (to pass to tifffile.imwrite)
Use 'minisblack' (default) for grayscale and 'rgb' for rgb
"""
dest_path = str(dest_path)
tifffile.imwrite(dest_path, img_volume)
tifffile.imwrite(dest_path, img_volume, photometric=photometric)


def to_tiffs(img_volume, path_prefix, path_suffix="", extension=".tif"):
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