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Widgets for visualizing electrophysiology experiments and results of spike sorting

License: Other

JavaScript 93.24% CSS 2.25% HTML 1.81% Shell 0.42% Python 1.50% TypeScript 0.78%

ephys-viz-obsolete's Introduction

Ephys-Viz

Various widgets for visualizing electrophysiology experiments and the results of spike sorting

Authors: Jeremy Magland

Installation

Use Linux (should also work in OSX, but not yet tested)

Step 0. Install the following prerequisites

A recent version of NodeJS
mountainlab-js with the ml_ephys plugin package

Step 1. Clone this repository

git clone https://github.com/flatironinstitute/ephys-viz

Install using npm:

cd ephys-viz
npm install

Add ephys-viz/bin to your PATH environment variable

Usage

View a timeseries dataset in mda format:

ev-view-timeseries --timeseries raw.mda
ev-view-timeseries --timeseries raw.mda.prv

See also the example(s) in the ephys-viz/examples directory

ephys-viz-obsolete's People

Contributors

Stargazers

Watchers

Forkers

alexmorley ecarmichael tjd2002 stjordanis

ephys-viz-obsolete's Issues

examples don't load from kbucket

although I can view my own .mda files.

Here's my errors:

alex@fiona /home/alex/SCDA/ephys-viz/examples> ./example_view_templates.sh
(node:23437) DeprecationWarning: current URL string parser is deprecated, and will be removed in a future version. To use the new parser, pass option { useNewUrlParser: true } to MongoClient.connect.
Unable to locate file.
searching kbucket...
Error checking on kbucket: Invalid URI "undefined/stat/4a724d03aed1dfd0de684548a78ff4465684ebe4"
App threw an error during load
Error: Command failed: ml-prv-locate example_templates.mda.prv --remote
Error checking on kbucket: Invalid URI "undefined/stat/4a724d03aed1dfd0de684548a78ff4465684ebe4"

at checkExecSyncError (child_process.js:613:13)
at Object.execSync (child_process.js:653:13)
at Object.childProcess.(anonymous function) [as execSync] (ELECTRON_ASAR.js:689:22)
at resolve_prv (/home/alex/SCDA/ephys-viz/electron/init_electron.js:163:43)
at resolve_prvs (/home/alex/SCDA/ephys-viz/electron/init_electron.js:148:17)
at exports.init_electron (/home/alex/SCDA/ephys-viz/electron/init_electron.js:31:3)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:30:1)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:66:3)
at Module._compile (module.js:642:30)
at Object.Module._extensions..js (module.js:653:10)

A JavaScript error occurred in the main process
Uncaught Exception:
Error: Command failed: ml-prv-locate example_templates.mda.prv --remote
Error checking on kbucket: Invalid URI "undefined/stat/4a724d03aed1dfd0de684548a78ff4465684ebe4"

at checkExecSyncError (child_process.js:613:13)
at Object.execSync (child_process.js:653:13)
at Object.childProcess.(anonymous function) [as execSync] (ELECTRON_ASAR.js:689:22)
at resolve_prv (/home/alex/SCDA/ephys-viz/electron/init_electron.js:163:43)
at resolve_prvs (/home/alex/SCDA/ephys-viz/electron/init_electron.js:148:17)
at exports.init_electron (/home/alex/SCDA/ephys-viz/electron/init_electron.js:31:3)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:30:1)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:66:3)
at Module._compile (module.js:642:30)
at Object.Module._extensions..js (module.js:653:10)

alex@fiona /home/alex/SCDA/ephys-viz/examples> ./example_view_remote_timeseries.sh
(node:23345) DeprecationWarning: current URL string parser is deprecated, and will be removed in a future version. To use the new parser, pass option { useNewUrlParser: true } to MongoClient.connect.
Unable to locate file.
searching kbucket...
Error checking on kbucket: Invalid URI "undefined/stat/9a42d2fb7d0e2cfd8c206c2ddc30640472ffab3d"
App threw an error during load
Error: Command failed: ml-prv-locate franklab_tetrode_raw.mda.prv --remote
Error checking on kbucket: Invalid URI "undefined/stat/9a42d2fb7d0e2cfd8c206c2ddc30640472ffab3d"

at checkExecSyncError (child_process.js:613:13)
at Object.execSync (child_process.js:653:13)
at Object.childProcess.(anonymous function) [as execSync] (ELECTRON_ASAR.js:689:22)
at resolve_prv (/home/alex/SCDA/ephys-viz/electron/init_electron.js:163:43)
at resolve_prvs (/home/alex/SCDA/ephys-viz/electron/init_electron.js:148:17)
at exports.init_electron (/home/alex/SCDA/ephys-viz/electron/init_electron.js:31:3)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:30:1)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:66:3)
at Module._compile (module.js:642:30)
at Object.Module._extensions..js (module.js:653:10)

A JavaScript error occurred in the main process
Uncaught Exception:
Error: Command failed: ml-prv-locate franklab_tetrode_raw.mda.prv --remote
Error checking on kbucket: Invalid URI "undefined/stat/9a42d2fb7d0e2cfd8c206c2ddc30640472ffab3d"

at checkExecSyncError (child_process.js:613:13)
at Object.execSync (child_process.js:653:13)
at Object.childProcess.(anonymous function) [as execSync] (ELECTRON_ASAR.js:689:22)
at resolve_prv (/home/alex/SCDA/ephys-viz/electron/init_electron.js:163:43)
at resolve_prvs (/home/alex/SCDA/ephys-viz/electron/init_electron.js:148:17)
at exports.init_electron (/home/alex/SCDA/ephys-viz/electron/init_electron.js:31:3)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:30:1)
at Object.<anonymous> (/home/alex/SCDA/ephys-viz/electron/openpage.js:66:3)
at Module._compile (module.js:642:30)
at Object.Module._extensions..js (module.js:653:10)

issue with libfontconfig

On Ubuntu 18.04, trying to run the example from github.com/flatironinstitute/mountainsort_examples:

ev-timeseries --timeseries output/filt.mda.prv --firings output/firings.mda --samplerate 30000

I get the following error: symbol lookup error: /home/faivre/conda/envs/mlab/lib/node_modules/ephys-viz/node_modules/electron/dist/../../../../../libfontconfig.so.1: undefined symbol: FT_Done_MM_Var

I know this is not specific to ephys-viz, and is more OS related, but that'd be nice to find a way around it for the next versions.

Thanks for all the good work!

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