Closed restrepd closed 6 months ago
This is a caiman level issue, I suspect it's related to this: https://github.com/flatironinstitute/CaImAn/issues/1274
I'm going to close the issue here and refer you to that issue on caiman.
Thanks!
Diego
Diego Restrepo, PhD Professor of Cell and Developmental Biology http://www.restrepolab.org/ University of Colorado Anschutz Medical Campus Department of Cell and Developmental Biology MS 8108 Bldg RC1 South, Room L18-11119 12801 E 17th Ave Aurora, CO 80045
Tel: 303-724-3405 Fax:303-724-3420
From: Kushal Kolar @.> Date: Tuesday, February 13, 2024 at 8:05 PM To: nel-lab/mesmerize-core @.> Cc: Restrepo, Diego @.>, Author @.> Subject: Re: [nel-lab/mesmerize-core] Computer crashes with cnmf.run_detrend_dfof (Issue #276) [External Email - Use Caution]
This is a caiman level issue, I suspect it's related to this: flatironinstitute/CaImAn#1274https://github.com/flatironinstitute/CaImAn/issues/1274
I'm going to close the issue here and refer you to that issue on caiman.
— Reply to this email directly, view it on GitHubhttps://github.com/nel-lab/mesmerize-core/issues/276#issuecomment-1943015362, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2FV7SB4LF3B253DY5AGABDYTQSX7AVCNFSM6AAAAABDGNLEVSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBTGAYTKMZWGI. You are receiving this because you authored the thread.Message ID: @.***>
I am trying to get dFF and my computer crashes
I run mcorr_cnmf.ipynb. The code below calls
df.iloc[index].cnmf.run_detrend_dfof(quantileMin=8, frames_window=250, flag_auto=True, use_fast=True, use_residuals=True, detrend_only=False)
The computer becomes busy and gives this message several times: "WARNING:root:Percentile computation failed. Duplicating and trying again."
It then crashes and re-starts.
Our computer runs Ubuntu:
No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy
Jupyter lab python 3.11.7
I also need information on how to read your hdf5 file in matlab.
Thanks!
Diego Restrepo