initial release (#1)

Author: anwarnunez

README.rst

@@ -1,17 +1,84 @@
 
+
+Welcome to fusilib!
+###################
 |Zenodo| |License|
 
 
+What is fusilib?
+=================
+``fusilib`` is a Python package for analysis of functional ultrasound and electrophysiology data.
+
+Installation
+============
+
+The following package must be installed on your system:
+
+* git
+* pip
+* python3-venv
+
+To install the `fusilib` package in a virtual environment, execute the following from the command line:
+
+.. code-block:: bash
+
+   git clone https://github.com/anwarnunez/fusi.git
+   cd fusi
+   python3 -m venv fusienv
+   source fusienv/bin/activate
+   pip install -r requirements.txt
+   pip install -e .
+  
+If you get errors from pip, try re-running the pip install commands.
+
+Getting started
+===============
+
+First, make sure everything is installed correctly by importing the package from within Python or IPython:
+
+.. code-block:: python
+
+   >>> import fusilib
+
 
-https://github.com/anwarnunez/fusi
+Checkout the figshare `project`_ and download the `dataset.zip`_ file (~15GB). Unzip the file in your local machine. Then, open the command line and navigate to the unzipped ``Subjects`` folder. You should then be able to execute the demo scripts from the command line
 
-This repository contains the code related to the article:
+.. code-block:: bash
 
-Neural correlates of blood flow measured by ultrasound. Nunez-Elizalde AO, Krumin M, Reddy CB, Montaldo G, Urban A, Harris KD, and Carandini M. (2022)
+   unzip dataset.zip
+   cd Subjects
+   python3 /path/to/repo/fusi/scripts/demo.py
 
 
+Alternatively, you can add the location of the downloaded data to the demo `scripts`_ directly. To do so, change the following lines at the top of the demo scripts:
+
+.. code-block:: python   
+
+   # Enter the path to the downloaded "Subjects" directory.
+   # By default, the path is set to the current working directory.
+   import fusilib.config
+   data_location = '/path/to/extracted/data/Subjects'
+   fusilib.config.set_dataset_path(data_location)
+
+Then, execute the demo script from the command line:
+
+.. code-block:: bash
+
+   python3 scripts/demo.py
+
+Cite as
+=======
+Neural correlates of blood flow measured by ultrasound. Nunez-Elizalde AO, Krumin M, Reddy CB, Montaldo G, Urban A, Harris KD, and Carandini M. Neuron (2022).
+
+   
 .. |Zenodo| image:: https://zenodo.org/badge/456774708.svg
    :target: https://zenodo.org/badge/latestdoi/456774708
 
 .. |License| image:: https://img.shields.io/badge/license-BSD%203--Clause-blue
    :target: https://opensource.org/licenses/BSD-3-Clause
+
+.. _project: https://figshare.com/projects/Nunez-Elizalde2022/132110
+
+.. _dataset.zip: https://figshare.com/articles/dataset/Simultaneous_functional_ultrasound_and_electrophysiology_recordings_of_neural_activity_in_awake_mice/19316228
+
+.. _scripts: https://github.com/anwarnunez/fusi/tree/main/scripts

fusilib/__init__.py

@@ -0,0 +1,12 @@
+from . import extras
+from . import io
+from . import (config,
+               align,
+               metahelper,
+               misc,
+               resampling,
+               utils)
+
+
+import warnings as _warnings
+_warnings.filterwarnings('ignore', category=RuntimeWarning)