jungmannlab / picasso

A collection of tools for painting super-resolution images

Home Page:https://picassosr.readthedocs.io/en/latest/?badge=latest

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Issue with localize function

Daan-Haas opened this issue · comments

commented
  • Picasso version: 0.6.1
  • Python version: 3.10.13
  • Operating System: Win10

Description

Calling picasso.localize.localize on the rawdata dataset from the git gave an error. Looking through the code, localize calls identify but doesn't pass an argument for 'box'

What I Did

params = io.load_info(infofile)
movie, info = io.load_raw(rawfile)

locs = localize.localize(movie, info, params)

and the error:

    locs = localize.localize(movie, info, params)
 line 428, in localize
    identifications = identify(movie, parameters)
TypeError: identify() missing 1 required positional argument: 'box'

Hi,

Thanks for raising the issue. This is an old piece of code which we will solve with the next Picasso release. For now, I recommend to use Picasso localize directly from the command window (not within the python script) as described here: https://picassosr.readthedocs.io/en/latest/cmd.html#localize

Bests,
Rafal

Hello again,

Apologies for the late fix. In Picasso 0.7.0, the new function will be:

def localize(movie, camera_info, parameters): identifications = identify( movie, parameters["Min. Net Gradient"], parameters["Box Size"], ) return fit(movie, camera_info, identifications, parameters["Box Size"])

Hope this helps, thank you for raising the issue.

Bests,
Rafal