Installation and Getting Started¶
Installation¶
Even if you know no python you should have no problems setting this up with the instructions below and this should run on any system. It can be run with 2 lines of code! If you encounter problems please report them via the issues tracker on the github page
https://github.com/MikeSmithLabTeam/particletracker/issues
An additional feature of this project, is that we have tried to make extending it as easy as possible. It might mean as little as adding a few lines of python code into a preconfigured template.
The software should work on all operating systems (Windows, Linux, Mac). It has only been thoroughly tested on Windows 10 and Ubuntu Linux.
To install here is a step by step recommended guide to setting things up. In case you are coming to this new to python or new to programming we provide the steps in a lot of detail. If you are comfortable in python skip through!
Download and install miniconda (https://docs.conda.io/en/latest/miniconda.html)
Open a conda terminal:
On Windows type Anaconda at the windows search and then select “Anaconda Prompt” On Linux and Mac open a terminal.
Create a conda environment by typing “conda create -n particle” where particle here is the name of the environment.
Type “conda activate particle”
conda install git
conda install pyqt
conda install pytables
pip install git+https://github.com/MikeSmithLabTeam/particletracker
On Windows we sometimes ran into an error at this point concerning the hdflib that can be resolved by installing the Microsoft Visual Studio Build tools. Once you’ve installed them restart computer, open anaconda terminal, activate environment (step 2 above) Rerun the final command above. The build tools can be installed from here:
https://visualstudio.microsoft.com/visual-cpp-build-tools/
(Optional - nice way to work with the final data in a jupyter notebook) - conda install jupyterlab - conda install openpyxl
to upgrade use:
pip install –upgrade git+https://github.com/MikeSmithLabTeam/particletracker
Once installed you will need some way to write simple code and execute it. The bare bones approach is to use a notepad and write the few lines of code as detailed in “Getting started”. Save the file as eg. testscript.py and then from the conda command prompt navigate to the correct folder and run this script using “python testscript.py”. Alternatively and far better in the long run is to install a python IDE and learn how to run code in the conda environment you’ve just created. Good IDEs include among others:
PyCharm (https://www.jetbrains.com/pycharm/download/),
Instructions abound on Google.
Verifying the installation¶
To verify that the installation is working correctly you should read the getting started section which explains how to launch the software. Once you have done this there are 5 example videos which also act as tutorials which should enable you to verify and test the core functionality of the software.