diff --git a/cellpose/io.py b/cellpose/io.py index b77f5da8..0aa04f46 100644 --- a/cellpose/io.py +++ b/cellpose/io.py @@ -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. @@ -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]