Skip to content

Error in xb.formatting.batch_prep_xenium_data_for_baysor #13

@dertrotl

Description

@dertrotl

Dear authors,

thanks for your excellent work!

The batch function (xb.formatting.batch_prep_xenium_data_for_baysor(files, outpath, CROP=True, COORDS=[1000, 5000, 1000, 5000])) is not working correctly, since in uses as an argument "outpath" instead of output_path as in the prep_xenium_data_for_baysor(f, output_path,CROP=False) function.

One is getting therefore the following error:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[23], line 1
----> 1 batch_prep_xenium_data_for_baysor(files=files, outpath=output_path)

File [~/git_repos/Xenium_benchmarking/xb/formatting.py:775](http://localhost:8888/lab/tree/~/git_repos/Xenium_benchmarking/xb/formatting.py#line=774), in batch_prep_xenium_data_for_baysor(files, outpath, CROP, COORDS)
    773 def batch_prep_xenium_data_for_baysor(files,outpath,CROP=True, COORDS=[1000, 5000, 1000, 5000]):
    774     for f in files:
--> 775         prep_xenium_data_for_baysor(f, output_path,CROP=False)

NameError: name 'output_path' is not defined

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions