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deepthought

This is the client side application which can connect to hard-link to get live-data from the microscope.

How to install

  1. You could optionally use a virtual environment.
$ python -m pip install virtualenv
$ python -m virtualenv deepthought
$ source deepthought/bin/activate
$ python -m pip install -U pip
  1. Install with:
    $ python -m pip install -e .

How to run

$ python run.py

Troubleshooting

  1. If you have llvm11, you might get an error while installing llvmlite, which is required by numba. Go back to llvm10.

How to access data

databroker manages access to data for us. To get started with the experimental data stored in deepthought/db_data/*.msgpack,

set-up a yml configuration file for a catalog, where databroker looks for it.

  1. Find out where databroker looks for it with python3 -c "import databroker; print(databroker.catalog_search_path())"
  2. make a copy of ./catalog.yml and edit it to point to db_data/*.msgpack correctly, and move the file to one of the catalog search paths.

to test if you have been succesfull,

  1. open terminal from the context of deepthought/deepthought,
  2. if this runs without error, you're good to go. python3 -c "from data import db"

accessing data programmatically

from data import db

# returns the databroker.Header object which can give you the data in many forms
header = db[-1]

# access data as pandas.DataFrame
df = header.table()

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