norm_vals_name or norm_vals_name_post_rownorm

[FaehlingT]

Describe the bug Variable error in Notebook 2:

# run pixel data preprocessing
pixie_preprocessing.create_pixel_matrix(
    fovs,
    channels,
    base_dir,
    tiff_dir,
    pixie_seg_dir,
    img_sub_folder=img_sub_folder,
    seg_suffix=seg_suffix,
    pixel_output_dir=pixel_output_dir,
    data_dir=pixel_data_dir,
    subset_dir=pixel_subset_dir,
    norm_vals_name_post_rownorm=norm_vals_name, #this variable does not exist, I think it has to be changed to norm_vals_name
    blur_factor=blur_factor,
    subset_proportion=subset_proportion,
    multiprocess=multiprocess,
    batch_size=batch_size
)

[camisowers]

Hi @FaehlingT. That variable name is correct, and was added to the notebook and create_pixel_matrix() function in PR #985. Getting a TypeError here means your code is likely out of date. If you're using a local ark_env, you'll need to git pull and update the environment.

https://github.com/angelolab/ark-analysis#installation-steps https://github.com/angelolab/ark-analysis#updating-the-repository