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schnitzer-lab / EXTRACT-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.
MIT License
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Extractor function does not use user specified parameters #39

Open abahle opened 1 year ago

abahle commented 1 year ago

Hey, Im not sure if you guys are aware but it seems the extractor function effectively throws out the user specified config and gets defaults. After a long time of trying new parameters to no effect I finally looked at the code and saw this 

function output = extractor(M, config)
% Wrapper for EXTRACT for processing large movies

%This warning is not required thanks to Hakan's implementation of the preprocessing module.
%dispfun('Warning: If the input movie is in dfof form, please make sure to add 1 to the whole movie before running EXTRACT. \n',1)

% Get start time
start_time = posixtime(datetime);
io_time = 0;

ABS_TOL = 1e-6;
SIGNAL_LOWER_THRESHOLD = 1e-6;
PARTITION_SIDE_LEN = 250;

% Update config with defaults
**config = get_defaults(config);**

Just letting you know since I doubt this is what you want. I would also draw your attention to the fact that many of the default values talked about in your readme deviate from what is actually produced by get_defaults

fatihdinc commented 1 year ago

Dear Andrew,

Thanks for reaching out. Get Defaults does not override the user specified parameters. There may be multiple reasons to explain the situation you are describing, would you like to provide more information? Alternative, please feel free to send a movie to our email address to ask our help and/or request a tutorial session.

fatihdinc commented 10 months ago

I will update the documentation to reflect the recent default values. Thank you for bringing this up!