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Braph-2.0-Python README

Installation

Download or clone the repository from github.com. Make sure you have installed python 3. Python version >=3.8 not yet supported.

Ubuntu

Open a terminal window. Install Qt OpenGL for Python by typing:

sudo apt install python3-pyqt5.qtopengl

Manual installation

Go to the top level folder of the project and install dependencies:

pip3 install .

Installation script

You can also install the project by running the file install.sh, placed in the folder Braph-2.0-Python. This will install the project's dependencies and place a shortcut to the program in your applications directory. Note that this replaces only the manual installation, not the first step.

Shortcuts

Running the installation script automatically creates two desktop files and places them in the applications directory, one for starting the application and one for killing it. If you want to create your own see

https://specifications.freedesktop.org/desktop-entry-spec/latest/index.html

You can then right click the icons for the .desktop files and add them to favourites for easy access in the dock.

Windows

Install Qt for python by typing the following command in PowerShell:

pip3 install pyqt5

Go to the top level folder of the project and install dependencies:

pip3 install .

macOS

Manual installation

Go to the top level folder of the project and install dependencies by running the following command in the terminal:

pip3 install .

Installation script

You can also install the project by running the file install_macos.sh, placed in the folder Braph-2.0-Python. This will install the project's dependencies.

Run the program

To run the program, run the file braphy.sh, placed in the folder 'bin' in 'Braph-2.0-Python'.

Development

You can also run the program from the terminal, by typing

python3 braphy/gui/main_window.py

When developing the software, it is useful to add the Braph directory to your pythonpath. On Ubuntu/macOS this is done by adding the following line

export PYTHONPATH=[your braph directory]:$PYTHONPATH

e.g.

export PYTHONPATH=~/git/Braph-2.0-Python:$PYTHONPATH

at the bottom of your ~/.bashrc file (Ubuntu) or ~/.bash_profile (macOS).

On Windows this is done by adding the pythonpath to your environment variables list.

By doing so, you don't have to install the program after each change.

Tests

Unit Tests on Ubuntu

To run all tests:

python3 -m unittest

To run a single test file:

python3 -m unittest braphy.test.test_betweenness

To debug a test in Visual Studio Code:

  1. Set appropriate breakpoints
  2. Press F5
  3. Select Module
  4. Type for example braphy.test.test_distance

Controlling the brain view

This section provides a guide for controlling the brain view. You can either change the point of view by using the buttons in the toolbar, or you can use different shortcuts.

  • Zoom in/out: use the scroll function
  • Pan in x/y-plane: press and drag the scroll wheel
  • Pan in x/z-plane: press and drag ctrl + the scroll wheel
  • Rotate: press and drag left mouse click (Note that this is not available when a button in the toolbar is checked.)
  • Select brain region: right click on brain region