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bahanonu / ciatah

CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).
https://git.io/ciatah_docs
MIT License
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Batch converting isxd to h5 specify inscopix path #130

Open rbutleriii opened 1 year ago

rbutleriii commented 1 year ago

Hi, I am batch converting many isxd movies to h5 via the command line. Is there an option to specify a path to the Inscopix software installation in my script? 

import ciapkg.inscopix.*
import ciapkg.image.*
import ciapkg.api.*

file_name = strcat(root_dir, '/ISXD_files/', arg1);
opts.maxChunkSize = 5000;
opts.downsampleFactor = 1;
opts.baseInscopixPath = strcat('path_to_inscopix/MATLAB'); % <----
opts.saveFolder = strcat(root_dir, '/HDF5');
convertInscopixIsxdToHdf5(file_name,'options',opts);
bahanonu commented 1 year ago

@rbutleriii Can either run 

ciapkg.inscopix.loadIDPS();

that will load the Inscopix IDPS from the default path or you can directly add the root IDPS folder to the path (should contain the m-file isxpublicapi.m).

pathToISX = 'YOUR_PATH';
addpath(pathToISX);

Let me know if still have issues after trying those.