neutrons / ipythonnotebooktutorial

IPython Notebook Tutorial for the scientists

IPythonNotebookTutorial

IPython Notebook Tutorial for the scientists

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Contents

1. Introduction to Python with Jupyter Notebooks

• <shift>+<enter>
• <shift>+<tab>
• print
• numpy arrays
• functions
• matplotlib plot

2. Loading and plotting data from a text file

• numpy record arrays and genfromtxt
• Matplotlib: scatter, log, error bars and legend

3. Loading and viewing image data.

4. Glob:

• glob
• For loops
• os.path
• string manipulation

5. Fitting TAS data

• Defining functions
• LMFit
• Two Pannel plot

6. Loading and plotting a log from a NeXus file

• h5py

7. Working with Mantid and Python

Setup environment using conda

$ conda create -n ipythonnotebooktutorial
$ source activate ipythonnotebooktutorial
$ conda install python=3 scipy numpy matplotlib h5py astropy lmfit jupyter

Links

• A gallery of jupyter notebooks: https://github.com/jupyter/jupyter/wiki/A-gallery-of-interesting-Jupyter-Notebooks
• Coursera data science course using jupyter https://en.coursera.org/learn/python-data-analysis
• Jupyter notebook "BINARY BLACK HOLE SIGNALS IN LIGO OPEN DATA": http://nbviewer.jupyter.org/urls/losc.ligo.org/s/events/LOSC_Event_tutorial.ipynb

ipythonnotebooktutorial's Issues

Print format?

Where shall we include the python format?

https://www.python-course.eu/python3_formatted_output.php

@yxqd In the for cycle do you want to make a fancy table?
sort of print("| {:10} | {:10} |".format(1,2))

Let's split the glob notebook into 2

Let's split the Glob note book into 2

1. A notebook where you load 1 file and do all the examples of various types of plotting
2. A notebook where we add the file looping.

Fix data path

Make sure the paths are absolute paths starting with /EXAMPLES

Focus LMfitting example on lmfit

jupyter intro improvements

• Explain that onnly the last item is shown in the "output" region

We should use python 3.5+, right ?

Accessing axis object

I think we want to change to to the

f,ax= subplots()
ax.plot

syntax

subdirs

• notebooks: for "students"
• solutions

Check 7964K for number of seats

Contents

I'm adding the contents here so we don't repeat work.
This is just a draft, please edit this.

1. Intro to Jupyter @JeanBilheux

• Shift tab / Shift Enter
• cells (edit and running mode)
• Read / import files from linux (?). If so, what about a function in a file? E.g. func add(a, b)

2. Intro to Python

• Simple intro to python: var assignment, types, code formatting, etc...

3. Intro to plotting @ricleal

• os.path
• numpy arrays + recarrays
• numpy indexing
• scatter plots with log

4. Advanced plotting @yxqd

• loops
• multiple plots
• Accessing axis #5
• legend
• latex?
• table with print and format left, right precision?

5. Fitting @granrothge

• lmfit

6. HDF file reading (Andrei I believe)

7. Mantid Python @AndreiSavici

8. Notebooks and widgets (Jean) :-) (Just if we get bored at the end)

Add an "intro to jupyter" notebook

Add weighting to lmfit Tutorial

change data for fitting example