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README.md

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@@ -14,68 +14,29 @@ View, curate, and share results of electrophysiological spike sorting in the bro
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pip install --upgrade sortingview
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```
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If you want to generate shareable URLs, configure your [kachery-cloud](https://github.com/scratchrealm/kachery-cloud) client
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## Kachery Setup
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```bash
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kachery-cloud-init
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# follow the instructions to associate your client with your Google user name on kachery-cloud
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```
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## Getting started
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See the [examples folder](./examples) or the [example notebook](./notebooks/sortingview_jupyter.ipynb).
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In order to use sortingview, you must configure kachery in order to share files on the kachery network.
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SortingView widgets can be viewed in any of the following modes:
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* shareable URL in the browser
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* [jupyter widget](./doc/jupyter_integration.md) (probably not working - needs to be updated)
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Visit this site to register and obtain an API key:
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## SpikeInterface Integration
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https://kachery.vercel.app
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We are working on a tight integration between SortingView and [SpikeInterface](https://spikeinterface.readthedocs.io/en/latest/).
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## Environment
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You can use environment variables to control the storage/configuration directory used by kachery-cloud, the project ID used for storing data in the cloud, and the options for creating figures.
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Then set the following environment variables
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```bash
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# Set the storage/configuration directory used by kachery-cloud
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# If unset, $HOME/.kachery-cloud will be used
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# The client ID will be determined by this directory
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# You can share the same kachery-cloud directory between multiple users,
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# but you will need to set mult-user mode for the client
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export KACHERY_CLOUD_DIR="..."
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# Set the project ID for storing data in the cloud
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# If unset, the default project associated with the client will be used
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# The default project can be configured at https://cloud.kacheryhub.org
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export KACHERY_CLOUD_PROJECT_ID="..."
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# When using local mode for figURLs, data will not be uploaded/downloaded
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# from the cloud, and the URLs will not be shareable.
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# As an alternative to using the env variable, you can also use
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# local=True as an argument to .url() in all of the views.
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# See below for more information.
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export SORTINGVIEW_LOCAL=1
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# Electron mode is similar to local mode, except instead of returning
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# a URL, an electron window will open and data will be accessed directly
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# from the file system. I.e., no browser.
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# This requires installation of figurl-electron (see below).
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# See below for more information.
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export SORTINGVIEW_ELECTRON=1 # Requires installation of figurl-electron
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export KACHERY_API_KEY = "the-api-key"
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export KACHERY_ZONE = "scratch"
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```
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It is recommend that you set these variables in your `~/.bashrc` file.
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You can use the scratch zone to get started, but the files in that zone will be cleared out periodically. For more persistent storage (which is also not guaranteed to persist forever), you'll need to set up your own zone.
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## Sharing the kachery cloud directory between multiple users
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## Getting started
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On a shared system, you may want to share your kachery cloud directory between multiple users so that
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they can utilize the same local files. Follow these steps:
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See the [examples folder](./examples).
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* Create a new kachery cloud directory in a location where the users may access it
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with read and write permissions. For example, this could be on a shared drive.
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* Have each user set the KACHERY_CLOUD_DIR environment variable to point to this
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directory on their system (see above)
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* Have the main user (the one who will own the client) initialize the client as usual via
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`kachery-cloud-init`
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* Here's the tricky part. You must configure your system such that newly created files in the directory are readable and writeable by all the users with access. This is probably best accomplished using group permissions.
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For example:
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```bash
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python examples/example_autocorrelograms.py
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```

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