error in dbscan cmd
Z-Qing opened this issue · comments
- 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'
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
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?
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