Error at Intensity Feature extraction

[QuyANgo]

Hello,

Thank you very much for this very nice NMCO pipeline.

When I ran your notebook Nuclear_Feature.ipynb, at the step of extracting Intensity features, I got the following error. Could you please check it and provide a fix for it?

Many thanks!

---

IndexError Traceback (most recent call last)
in <cell line: 2>()
1 # Below are the features computed for 4 nuclei.
----> 2 Int_feat= pd.concat([IDF.measure_intensity_features(props[nuc_of_interest[0]].image,props[nuc_of_interest[0]].intensity_image),
3 IDF.measure_intensity_features(props[nuc_of_interest[1]].image,props[nuc_of_interest[1]].intensity_image),
4 IDF.measure_intensity_features(props[nuc_of_interest[2]].image,props[nuc_of_interest[2]].intensity_image),
5 IDF.measure_intensity_features(props[nuc_of_interest[3]].image,props[nuc_of_interest[3]].intensity_image)])

1 frames
/usr/local/lib/python3.10/dist-packages/nmco/nuclear_features/int_dist_features.py in intensity_histogram_measures(regionmask, intensity)
63 "int_max": np.percentile(intensity[regionmask], 100),
64 "int_mean": np.mean(intensity[regionmask]),
---> 65 "int_mode": stats.mode(intensity[regionmask], axis=None)[0][0],
66 "int_sd": np.std(intensity[regionmask]),
67 "kurtosis": float(kurtosis(intensity[regionmask].ravel())),

IndexError: invalid index to scalar variable.

[dpaysan]

This issue is likely due to the fact that you have a newer version of the stats package installed. Please try changing the line indicated in the error message in the file int_dist_features.py to

"int_mode": stats.mode(intensity[regionmask], axis=None)[0]