Milad4849
commented
1 year ago Hi @eleonore-schneeg
The function that you are trying to use takes an np.ndarray as a input (see here), so you need to first read-in the mask and then pass that to the function. These recent features are not yet well documented and we will update the relevant documentation int he future.
Hi,
I've been trying to make the python function expand_mask work.
This is how I'm currently trying to implement it : (Maybe this isn't the way to implement it, but Im not sure how) I would like to expand the masks for an entire folder of tiff images.
expand_mask(mask='A138.12_001.tiff', distance=10)
Here is the error:
TypeError Traceback (most recent call last) Input In [50], in <cell line: 1>() ----> 1 expand_mask(mask='A138.12_001.tiff', distance=10)
File ~/Desktop/steinbock-main/steinbock/utils/expansion.py:12, in expand_mask(mask, distance) 11 def expand_mask(mask: np.ndarray, distance: int) -> np.ndarray: ---> 12 expanded_mask = expand_labels(mask, distance=distance) 13 return expanded_mask
File ~/opt/anaconda3/lib/python3.9/site-packages/skimage/segmentation/_expand_labels.py:104, in expand_labels(label_image, distance) 97 # build the coordinates to find nearest labels, 98 # in contrast to [1] this implementation supports label arrays 99 # of any dimension 100 masked_nearest_label_coords = [ 101 dimension_indices[dilate_mask] 102 for dimension_indices in nearest_label_coords 103 ] --> 104 nearest_labels = label_image[tuple(masked_nearest_label_coords)] 105 labels_out[dilate_mask] = nearest_labels 106 return labels_out
TypeError: string indices must be integers