Must include label_dir as parameter, currently function does not set to default as None

[jenna-tomkinson]

Is this a duplicate of an existing idea for this project?

• I found no existing issues covering this topic.

What is your idea?

Hello!

I am excited to get to use this tool! After some testing, I realized that the current tiff to OMETIFF or OMEZARR does not have the default for labels as None, but says it is optional in the docstring.

I think it would be beneficial, since the parameter is optional, to set the default for the function as None.

Here is the error I was getting with the code:

# convert original data into OME-TIFF format through nViz
nviz_ome_tiff = nviz.tiff_to_ometiff(
    # specify an image directory (original images)
    image_dir=test_image_dir,
    # specify an output path
    output_path=output_ome_tiff_path,
    # map filename patterns to channel names
    channel_map={
        "111": "Channel A",
        "222": "Channel B",
        "333": "Channel C",
        "444": "Channel D",
        "555": "Channel E",
    },
    # set the scaling for z, y, and x
    scaling_values=scaling_values,
)

# show the filepath
nviz_ome_tiff

TypeError                                 Traceback (most recent call last)
Cell In[6], line 2
      1 # convert original data into OME-TIFF format through nViz
----> 2 nviz_ome_tiff = nviz.tiff_to_ometiff(
      3     # specify an image directory (original images)
      4     image_dir=test_image_dir,
      5     # specify an output path
      6     output_path=output_ome_tiff_path,
      7     # map filename patterns to channel names
      8     channel_map={
      9         "111": "Channel A",
     10         "222": "Channel B",
     11         "333": "Channel C",
     12         "444": "Channel D",
     13         "555": "Channel E",
     14     },
     15     # set the scaling for z, y, and x
     16     scaling_values=scaling_values,
     17 )
     19 # show the filepath
     20 nviz_ome_tiff

TypeError: tiff_to_ometiff() missing 1 required positional argument: 'label_dir'

Would you like to work on a solution for this?

• Yes I am willing to submit a PR for this!

[d33bs]

Thanks for finding this @jenna-tomkinson ! Let me know if you need any assistance as you proceed with a fix.