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allow relative savedir path #1354

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Merged
mrariden merged 1 commit into from
Oct 27, 2025
+4 −4
Merged

allow relative savedir path #1354

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8 changes: 4 additions & 4 deletions cellpose/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -692,7 +692,7 @@ def save_masks(images, masks, flows, file_names, png=True, tif=False, channels=[
save_outlines (bool, optional): Save outlines of masks. Defaults to False.
dir_above (bool, optional): Save masks/flows in directory above. Defaults to False.
in_folders (bool, optional): Save masks/flows in separate folders. Defaults to False.
savedir (str, optional): Absolute path where images will be saved. If None, saves to image directory. Defaults to None.
savedir (str, optional): Absolute or relative path where images will be saved. If None, saves to image directory. Defaults to None.
save_txt (bool, optional): Save masks as list of outlines for ImageJ. Defaults to False.
save_mpl (bool, optional): If True, saves a matplotlib figure of the original image/segmentation/flows. Does not work for 3D.
This takes a long time for large images. Defaults to False.
Expand Down Expand Up @@ -724,11 +724,11 @@ def save_masks(images, masks, flows, file_names, png=True, tif=False, channels=[

if savedir is None:
if dir_above:
savedir = Path(file_names).parent.parent.absolute(
) #go up a level to save in its own folder
savedir = Path(file_names).parent.parent#go up a level to save in its own folder
else:
savedir = Path(file_names).parent.absolute()
savedir = Path(file_names).parent

savedir = Path(savedir).resolve()
check_dir(savedir)

basename = os.path.splitext(os.path.basename(file_names))[0]
Expand Down