error in dbscan cmd

[Z-Qing]

• Picasso version: 0.5.6
• Python version:3.8.14
• Operating System:win11

description

The command picasso dbscan asks for arguement pixelsize. But only file path, radius, density are mentioned in the help file.

What I did

I run dbscan using cmd. The cmd I typed is "picasso dbscan path 1 100"

And I get the following error message:
Traceback (most recent call last):
File "D:\Anaconda3\envs\picasso\lib\runpy.py", line 194, in _run_module_as_main
return run_code(code, main_globals, None,
File "D:\Anaconda3\envs\picasso\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "D:\Anaconda3\envs\picasso\Scripts\picasso.exe_main.py", line 7, in
File "D:\Anaconda3\envs\picasso\lib\site-packages\picasso_main.py", line 1619, in main
dbscan(args.files, args.radius, args.density)
File "D:\Anaconda3\envs\picasso\lib\site-packages\picasso_main.py", line 454, in _dbscan
clusters, locs = postprocess.dbscan(locs, radius, min_density)
TypeError: dbscan() missing 1 required positional argument: 'pixelsize'

[rafalkowalewski1]

Hello,

Thank you for raising the issue. I will fix it in the next Picasso release. If this is fine with you, you can use the following alternative in Render for now: Load the file you would like to cluster, click Postprocess in the menu bar, click Clustering > DBSCAN. The window with DBSCAN paramters will open.

Bests,
Rafal

[Z-Qing]

Thanks for the reply. I will just call postprocess.dbscan() function to work around this.
I have a separate question. Can I call the function localize.localize() and put parameters "info" and "parameters" manually to get localizations? Will this be any faster than using the localize cmd?

[rafalkowalewski1]

It should work, however, the gain in speed shouldn't be significant. Also, calling localize.localize() uses MLE fitting which is much slower that LQ gaussian fitting.
I hope this helps.
Bests,
Rafal