broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments
BSD 3-Clause "New" or "Revised" License
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Bugs in 4.image-and-segmentation-qc.py #38

Closed gwaybio closed 4 years ago

gwaybio commented 4 years ago

Noting two things to be fixed in a future pull request:

force not defined

(pooled-cp) wm962-fdf:0.preprocess-sites gway$ python 4.image-and-segmentation-qc.py
Traceback (most recent call last):
  File "4.image-and-segmentation-qc.py", line 113, in <module>
    if check_if_write(output_file, force, throw_warning=True):
NameError: name 'force' is not defined

Error concatenating

Done concatenating image files
Traceback (most recent call last):
  File "4.image-and-segmentation-qc.py", line 478, in <module>
    image_corr_df = pd.concat(image_corr_list).drop_duplicates(subset="site").reset_index()
  File "/Users/gway/miniconda3/envs/pooled-cp/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 281, in concat
    sort=sort,
  File "/Users/gway/miniconda3/envs/pooled-cp/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 329, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

These should be quick fixes