Computer crashes with cnmf.run_detrend_dfof

[restrepd]

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

[kushalkolar]

This is a caiman level issue, I suspect it's related to this: flatironinstitute/CaImAn#1274

I'm going to close the issue here and refer you to that issue on caiman.

[restrepd]

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#1274<flatironinstitute/CaImAn#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 GitHub<#276 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A2FV7SB4LF3B253DY5AGABDYTQSX7AVCNFSM6AAAAABDGNLEVSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBTGAYTKMZWGI>. You are receiving this because you authored the thread.Message ID: ***@***.***>