Error for running process_sample_distributions

[jianxinwang]

I'm getting this error when running my own data:

intensity_ranges, histograms, gmm_models = process_sample_distributions(
feature_input = adata,
num_bins = 1024,
plots_per_row = 4,
dpi = 100,
xlims = None,
ylims = None,
output_figure_path = "Test_feature_histogram_distributions.png",
verbose=True
)

Here is the error message:

✅ Processing BCM-3469 for marker CCNE......
✅ Processing BCM-3561 for marker CCNE......

---

ValueError Traceback (most recent call last)
/scratch/21737580/ipykernel_3365132/1758697669.py in
----> 1 intensity_ranges, histograms, gmm_models = process_sample_distributions(
2 feature_input = adata,
3 num_bins = 1024,
4 plots_per_row = 4,
5 dpi = 100,

UniFORM/preprocessing.py in process_sample_distributions(feature_input, sample_ids, all_markers, markers_to_plot, use_normalized, num_bins, plots_per_row, dpi, xlims, ylims, output_figure_path, verbose)
321 arr = feat['intensity_mean'][m_idx]
322 arr_log = log_transform_intensities(arr)
--> 323 mn, mx = arr_log.min(), arr_log.max()
324 min_list.append(mn)
325 max_list.append(mx)

uniform_env/lib/python3.9/site-packages/numpy/core/_methods.py in _amin(a, axis, out, keepdims, initial, where)
43 def _amin(a, axis=None, out=None, keepdims=False,
44 initial=_NoValue, where=True):
---> 45 return umr_minimum(a, axis, None, out, keepdims, initial, where)
46
47 def _sum(a, axis=None, dtype=None, out=None, keepdims=False,

ValueError: zero-size array to reduction operation minimum which has no identity

It worked fine for the first marker (DAPI), but not for the second marker (CCNE).