Inconsistent seg_suffix
causing error in pixel clustering notebook
#842
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bug
Something isn't working
seg_suffix
causing error in pixel clustering notebook
#842
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Describe the bug
In the pixel clustering notebook, one of the user-specified parameters is
seg_suffix = '_whole_cell.tiff'
(which I changed to '_feature_0.tif' to test on some old datasets). Thecreate_mantis_dir
function has an argumentseg_suffix_name
, which is default to'whole_cell'
, without the.tiff
extension (https://github.com/angelolab/ark-analysis/blob/main/ark/utils/plot_utils.py#L392-L399). In the Pixie notebook, I tried to addseg_suffix_name = seg_suffix
as an argument tocreate_mantix_dir
. However, doing this currently throws an error becauseseg_suffix
for the notebook requires.tif
at the end, whileseg_suffix_name
does not require an extensionExpected behavior
Add
seg_suffix_name=seg_suffix
to thecreate_mantis_dir
function in the pixel clustering notebook. I think it would probably be best to haveseg_suffix_name
increate_mantis_dir
to require an extension, just in case people are using other image formats for their segmentation.To Reproduce
![image](https://user-images.githubusercontent.com/11382352/204411797-61a16730-bbc9-42fa-b70b-2cb1611a72d9.png)
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