How to get started and where to find help

Numerical and Scientific Python

While the choices for tutorials and guides on numerical and scientific python are more limited, this area has exploded in recent years and you can find lots of information through simple google searches.

Python is very modular, i.e. you include functionality by “importing” modules (similar to libraries in C or C++). Therefore much of the numerical and scientific functionality is not part of the core of python, but instead in separate modules. The four modules that are at the centre of the Python scientific stack are:

numpy

The numpy package is the fundamental package scientific work in Python. It contains the array object, which underlies most scientific computations in python, broadcasting functions and tools, some useful tools such as FFTs, basic linear algebra etc..

scipy

Scipy is the broad collection of additional tools, ranging from linear algebra routines (including BLAS routines) to signal and image processing functions.

matplotlib

Matplotlib is the main plotting tool in scientific Python. It is useful both for interactive plots when doing, e.g. analysis in the interpreter, as well as producing beautiful publication ready graphs.

IPython now part of jupyter

Ipython makes working interactively with python easy. In an interactive session either in a browser or as a console application, ipython provides a comfortable interface with command history, help, plotting etc., which makes exploring and working with data easy.

Fortunately, the anaconda distribution already includes these packages, so you do not have to worry about how to install them.

To get started programming with the scientific stack in python, it is good to begin with the numpy quickstart tutorial and the scipy getting started guide. Another great course can be found here.

Where to ask for help when you are stuck

There are many places where to ask for help, which one is best often depends on your problem. Stackoverflow is a good place to ask user questions. Remember to tag your question appropriately with e.g. python, numpy, scipy or matplotlib. For more specific questions on numpy or scipy, there are also mailing lists which can be found on this page. For other projects it is often a good idea to check on the website what their preferred way of contact is.

Starting to program

The best and easiest way to start with is using jupyter which is a tool build for letting us easily code, study and analyse data and debug our programs. It initially developed out of the ipython notebook specifically for Python, but is now capable of running other languages as well. To start working with jupyter type jupyter notebook into a commandline prompt. After that your browser should pop up with a website with a list of files (usually the directory where you typed the above command). You can start a new notebook using the button on the top right where depending if you installed Python2, Python3 or both you should see several options. Choose the Python 3 option to start a Python 3 notebook.

The notebook is an interactive programming environment in the browser. You can also write documentation along with your code using Markdown text, which can be great for documenting your work. Giving a full introduction into the notebook is well beyond this text, below you find some tutorials how to work with python and notebooks. The great thing is these are notebook files themselves, so you can view them either in the browser, or download them and use them as a starting point for getting to know python. An important thing to remember is that <Shift-Return> executes the current cell and advances to the next one.

• Programming Python Style
• Using numpy As mentioned above numpy is the most important package for numerical and scientific work in python.
• Plotting data using matplotlib
• Using scientific functions in pyhton

Some more advanced topics

I have a lot of existing Labview/Matlab code, do I need to redo everything

Fortunately there are packages that allow you to access labview and matlab code. So you don’t need to convert everything at once.

I have lots of C/Fortran code

One of the great things about python is how easy it is to integrate with C and Fortran code. The easiest way to use C-libraries is probably ctypes. However it has some performance implications, so if you need to call a C-function in a tight loop you will see a slow down. Also sometimes you only want to integrate small bits of C-code, or do some more manipulation. Cython is essentially a superset of python that can be compiled to binary. It allows easy integration of python code with C-functions or libraries and is extremely powerful. For Fortran code you should look at f2py which allows easy linking python to Fortran code (note that you can also use Cython for this). A great way of experimenting with f2py is to use fortran magic which allows you to enter Fortran code directly into the notebook.

What about instrument control?

The main package for accessing (GPIB, USB …) instruments are the python bindings to the VISA library pyvisa. Some other interesting packages that are more high-level are python-ivi which contains a lot of drivers for oscilloscopes, signal generators and more. It can also use pyvisa under the hood. You will find quite a few other higher-level projects build on top of pyvisa.

What about building a GUI?

It depends a lot what type of GUI you want. You can make interactive notebooks, by integrating widgets into the notebook using the ipywidgets. Another option for browser based interfaces is bokeh. For native GUIs we recommend to use PyQT with two great tutorials for the older qt4 and the newer qt5. For integrating plotting with you pyqt application the best is to use pyqtgraph.