other:python:jyp_steps
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other:python:jyp_steps [2022/06/15 13:05] jypeter [Extra numpy information] Added np vs np.ma warning |
other:python:jyp_steps [2023/12/14 09:25] jypeter [3D resources] |
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| You can start using python by reading the {{:other:python:python_intro_ipsl_oct2013_v2.pdf|Bien démarrer avec python}} tutorial that was used during a 2013 IPSL python class: | You can start using python by reading the {{:other:python:python_intro_ipsl_oct2013_v2.pdf|Bien démarrer avec python}} tutorial that was used during a 2013 IPSL python class: | ||
| * this tutorial is in French (my apologies for the lack of translation, but it should be easy to understand) | * this tutorial is in French (my apologies for the lack of translation, but it should be easy to understand) | ||
| - | * If you have too much trouble understanding this French Tutorial, you can read the first 6 chapters of the **Tutorial** in [[#the_official_python_documentation|the official Python documentation]] and chapters 1.2.1 to 1.2.5 in the [[#scipy_lecture_notes|Scipy Lecture Notes]]. Once you have read these, you can try to read the French tutorial again | + | * If you have too much trouble understanding this French Tutorial, you can read the first 6 chapters of the **Tutorial** in [[#the_official_python_documentation|the official Python documentation]] and chapters 1.2.1 to 1.2.5 in the [[#scientific_python_lectures|Scientific Python Lectures]]. Once you have read these, you can try to read the French tutorial again |
| * it's an introduction to python (and programming) for the climate scientist: after reading this tutorial, you should be able to do most of the things you usually do in a shell script | * it's an introduction to python (and programming) for the climate scientist: after reading this tutorial, you should be able to do most of the things you usually do in a shell script | ||
| * python types, tests, loops, reading a text file | * python types, tests, loops, reading a text file | ||
| Line 44: | Line 44: | ||
| [[https://docs.python.org/3/|html]] - [[https://docs.python.org/3/download.html|pdf (in a zip file)]] | [[https://docs.python.org/3/|html]] - [[https://docs.python.org/3/download.html|pdf (in a zip file)]] | ||
| + | |||
| + | |||
| + | ===== Scientific Python Lectures ===== | ||
| + | |||
| + | Summary: //One document to learn numerics, science, and data with Python// | ||
| + | |||
| + | Note: this used to be called //Scipy Lecture Notes// | ||
| + | |||
| + | Where: [[https://lectures.scientific-python.org/_downloads/ScientificPythonLectures-simple.pdf|pdf]] - [[https://lectures.scientific-python.org/|html]] | ||
| + | |||
| + | This is **a really nice and useful document** that is regularly updated and used for the [[https://www.euroscipy.org/|EuroScipy]] tutorials. | ||
| + | |||
| + | This document will teach you lots of things about python, numpy and matplotlib, debugging and optimizing scripts, and about using python for statistics, image processing, machine learning, washing dishes (this is just to check if you have read this page), etc... | ||
| + | * Example: the [[https://lectures.scientific-python.org/packages/statistics/index.html|Statistics in Python]] tutorial that combines [[other:python:jyp_steps#pandas|Pandas]], [[http://statsmodels.sourceforge.net/|Statsmodels]] and [[http://seaborn.pydata.org/|Seaborn]] | ||
| Line 64: | Line 78: | ||
| - Numpy Reference Guide | - Numpy Reference Guide | ||
| - Scipy Reference Guide | - Scipy Reference Guide | ||
| + | - read [[https://github.com/rougier/numpy-100/blob/master/100_Numpy_exercises.ipynb|100 numpy exercises]] | ||
| ==== Beware of the array view side effects ==== | ==== Beware of the array view side effects ==== | ||
| Line 133: | Line 148: | ||
| * {{ :other:python:indirect_indexing_2.py.txt |}}: Take a vertical slice in a 3D zyx array, along a varying y 'path' | * {{ :other:python:indirect_indexing_2.py.txt |}}: Take a vertical slice in a 3D zyx array, along a varying y 'path' | ||
| * [[https://numpy.org/doc/stable/user/basics.indexing.html|Array indexing basics (user guide)]] (//index arrays//, //boolean index arrays//, //np.newaxis//, //Ellipsis//, //variable numbers of indices//, ...) | * [[https://numpy.org/doc/stable/user/basics.indexing.html|Array indexing basics (user guide)]] (//index arrays//, //boolean index arrays//, //np.newaxis//, //Ellipsis//, //variable numbers of indices//, ...) | ||
| - | * [[https://numpy.org/doc/stable/reference/arrays.indexing.html|Array indexing (reference manual)]] | + | * [[https://numpy.org/doc/stable/reference/arrays.indexing.html|Indexing routines (reference manual)]] |
| * [[https://numpy.org/doc/stable/user/quickstart.html#advanced-indexing-and-index-tricks|Advanced indexing and index tricks]] and [[https://numpy.org/doc/stable/user/quickstart.html#the-ix-function|the ix_() function]] | * [[https://numpy.org/doc/stable/user/quickstart.html#advanced-indexing-and-index-tricks|Advanced indexing and index tricks]] and [[https://numpy.org/doc/stable/user/quickstart.html#the-ix-function|the ix_() function]] | ||
| - | * [[https://numpy.org/doc/stable/reference/routines.indexing.html#routines-indexing|Indexing routines]] | ||
| * More information about arrays: | * More information about arrays: | ||
| * [[https://numpy.org/doc/stable/reference/routines.array-creation.html|Array creation routines]] | * [[https://numpy.org/doc/stable/reference/routines.array-creation.html|Array creation routines]] | ||
| Line 149: | Line 163: | ||
| * [[https://numpy.org/doc/stable/reference/routines.err.html|Floating point error handling]] | * [[https://numpy.org/doc/stable/reference/routines.err.html|Floating point error handling]] | ||
| - | ===== NetCDF files: using cdms2, xarray and netCDF4 ===== | + | ===== Using NetCDF files with Python ===== |
| - | There is a good chance that your input array data will come from a file in the [[other:newppl:starting#netcdf_and_file_formats|NetCDF format]]. | + | <note tip>People using CMIPn and model data on the IPSL servers can easily search and process NetCDF files using: |
| + | * the [[https://climaf.readthedocs.io/|Climate Model Assessment Framework (CliMAF)]] environment | ||
| + | * and the [[https://github.com/jservonnat/C-ESM-EP/wiki|CliMAF Earth System Evaluation Platform (C-ESM-EP)]] | ||
| + | </note> | ||
| + | |||
| + | * There is a good chance that your input array data will be stored in a [[other:newppl:starting#netcdf_and_related_conventions|NetCDF]] file. | ||
| - | Depending on which [[other:python:starting#some_python_distributions|python distribution]] you are using, you can use the //cdms2//, //xarray// or //netCDF4// modules to read the data. | + | * There may be different ways of dealing with NetCDF files, depending on which [[other:python:starting#some_python_distributions|python distribution]] you have access to |
| ==== cdms2 ==== | ==== cdms2 ==== | ||
| Line 168: | Line 187: | ||
| Summary: [[http://xarray.pydata.org/en/stable/|xarray]] is an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun! [...] It is particularly tailored to working with netCDF files | Summary: [[http://xarray.pydata.org/en/stable/|xarray]] is an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun! [...] It is particularly tailored to working with netCDF files | ||
| + | |||
| + | === Some xarray related resources === | ||
| + | |||
| + | Note: more packages (than listed below) may be listed in the [[other:uvcdat:cdat_conda:cdat_8_2_1#extra_packages_list|Extra packages list]] | ||
| + | |||
| + | * [[https://xcdat.readthedocs.io/|xcdat]]: xarray extended with Climate Data Analysis Tools | ||
| + | |||
| + | * [[https://xoa.readthedocs.io/en/latest/|xoa]]: xarray-based ocean analysis library | ||
| + | |||
| + | * [[https://uxarray.readthedocs.io/|uxarray]]: provide xarray styled functionality for unstructured grid datasets following [[https://ugrid-conventions.github.io/ugrid-conventions/|UGRID Conventions]] | ||
| + | |||
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| - | ===== 3D resources ===== | + | ===== 3D plots resources ===== |
| * [[https://ipyvolume.readthedocs.io/en/latest/|Ipyvolume]] | * [[https://ipyvolume.readthedocs.io/en/latest/|Ipyvolume]] | ||
| * [[https://zulko.wordpress.com/2012/09/29/animate-your-3d-plots-with-pythons-matplotlib/|Animate your 3D plots with Python’s Matplotlib]] | * [[https://zulko.wordpress.com/2012/09/29/animate-your-3d-plots-with-pythons-matplotlib/|Animate your 3D plots with Python’s Matplotlib]] | ||
| * [[https://stackoverflow.com/questions/26796997/how-to-get-vertical-z-axis-in-3d-surface-plot-of-matplotlib|How to get vertical Z axis in 3D surface plot of Matplotlib?]] | * [[https://stackoverflow.com/questions/26796997/how-to-get-vertical-z-axis-in-3d-surface-plot-of-matplotlib|How to get vertical Z axis in 3D surface plot of Matplotlib?]] | ||
| + | |||
| + | ===== Data analysis ===== | ||
| + | |||
| ===== Data file formats ===== | ===== Data file formats ===== | ||
| Line 342: | Line 375: | ||
| * Some tutorials: | * Some tutorials: | ||
| * [[https://www.datacamp.com/community/blog/python-pandas-cheat-sheet|Pandas Cheat Sheet for Data Science in Python]] pandas introduction page | * [[https://www.datacamp.com/community/blog/python-pandas-cheat-sheet|Pandas Cheat Sheet for Data Science in Python]] pandas introduction page | ||
| - | * The [[http://www.scipy-lectures.org/packages/statistics/index.html|Statistics in Python]] tutorial that combines Pandas, [[http://statsmodels.sourceforge.net/|Statsmodels]] and [[http://seaborn.pydata.org/|Seaborn]] | + | * The [[https://lectures.scientific-python.org/packages/statistics/index.html|Statistics in Python]] tutorial that combines Pandas, [[http://statsmodels.sourceforge.net/|Statsmodels]] and [[http://seaborn.pydata.org/|Seaborn]] |
| - | + | ||
| - | ===== Scipy Lecture Notes ===== | + | |
| - | + | ||
| - | Summary: //One document to learn numerics, science, and data with Python// | + | |
| - | + | ||
| - | Where: [[http://www.scipy-lectures.org/_downloads/ScipyLectures-simple.pdf|pdf]] - [[http://www.scipy-lectures.org/|html]] | + | |
| - | + | ||
| - | This is **a really nice and useful document** that is regularly updated and used for the [[https://www.euroscipy.org/|EuroScipy]] tutorials. | + | |
| - | This document will teach you even more things about python, numpy and matplotlib, debugging and optimizing scripts, and about using python for statistics, image processing, machine learning, washing dishes (this is just to check if you have read this page), etc... | ||
| - | * Example: the [[http://www.scipy-lectures.org/packages/statistics/index.html|Statistics in Python]] tutorial that combines [[other:python:jyp_steps#pandas|Pandas]], [[http://statsmodels.sourceforge.net/|Statsmodels]] and [[http://seaborn.pydata.org/|Seaborn]] | ||
| ===== statsmodels ===== | ===== statsmodels ===== | ||
other/python/jyp_steps.txt · Last modified: 2024/03/07 10:15 by jypeter
