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| other:python:jyp_steps [2020/09/28 10:33] – Added the "jupyter and notebook stuff" section jypeter | other:python:jyp_steps [2021/06/16 18:05] – [Graphics related resources] Added Crameri and Which Blair Project references jypeter |
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| - always remember that indices start at ''0'' and that the last element of an array is at index ''-1''!\\ First learn about //indexing// and //slicing// by manipulating strings, as shown in [[#part1|Part 1]] above (try '''This document by JY is awesome!'[::-1]'' and '''This document by JY is awesome!'[slice(None, None, -1)]'') 8-) | - always remember that indices start at ''0'' and that the last element of an array is at index ''-1''!\\ First learn about //indexing// and //slicing// by manipulating strings, as shown in [[#part1|Part 1]] above (try '''This document by JY is awesome!'[::-1]'' and '''This document by JY is awesome!'[slice(None, None, -1)]'') 8-) |
| - if you are a Matlab user (but the references are interesting for others as well), you can read the following: | - if you are a **Matlab user** (but the references are interesting for others as well), you can read the following: |
| | - [[https://www.enthought.com/wp-content/uploads/2019/08/Enthought-MATLAB-to-Python-White-Paper-1.pdf|Migrating from MATLAB to Python]] on the [[https://www.enthought.com/software-development/|Enthought Software Development page]] |
| - [[https://docs.scipy.org/doc/numpy-dev/user/numpy-for-matlab-users.html|Numpy for Matlab users]] | - [[https://docs.scipy.org/doc/numpy-dev/user/numpy-for-matlab-users.html|Numpy for Matlab users]] |
| - [[http://mathesaurus.sourceforge.net/matlab-numpy.html|NumPy for MATLAB users]] (nice, but does not seem to be maintained any more) | - [[http://mathesaurus.sourceforge.net/matlab-numpy.html|NumPy for MATLAB users]] (nice, but does not seem to be maintained any more) |
| * Examples: | * Examples: |
| * {{ :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://docs.scipy.org/doc/numpy/user/basics.indexing.html|Indexing]] (//index arrays//, //boolean index arrays//, //np.newaxis//, //Ellipsis//, //variable numbers of indices//, ...) | * [[https://numpy.org/doc/stable/user/basics.indexing.html|Indexing]] (//index arrays//, //boolean index arrays//, //np.newaxis//, //Ellipsis//, //variable numbers of indices//, ...) |
| * [[https://docs.scipy.org/doc/numpy/user/quickstart.html#fancy-indexing-and-index-tricks|Fancy indexing]] and [[https://docs.scipy.org/doc/numpy/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://docs.scipy.org/doc/numpy/reference/arrays.indexing.html|Indexing (in the numpy reference manual)]] | * [[https://numpy.org/doc/stable/reference/arrays.indexing.html|Indexing (in the numpy reference manual)]] |
| * [[https://docs.scipy.org/doc/numpy/reference/routines.indexing.html#routines-indexing|Indexing routines]] | * [[https://numpy.org/doc/stable/reference/routines.indexing.html#routines-indexing|Indexing routines]] |
| * More information about arrays: | * More information about arrays: |
| * [[https://docs.scipy.org/doc/numpy/reference/routines.array-creation.html#routines-array-creation|Array creation routines]] | * [[https://numpy.org/doc/stable/reference/routines.array-creation.html#routines-array-creation|Array creation routines]] |
| * [[https://docs.scipy.org/doc/numpy/reference/routines.array-manipulation.html|Array manipulation routines]] | * [[https://numpy.org/doc/stable/reference/routines.array-manipulation.html|Array manipulation routines]] |
| * [[https://docs.scipy.org/doc/numpy/reference/maskedarray.html|Masked arrays]] | * [[https://numpy.org/doc/stable/reference/maskedarray.html|Masked arrays]] |
| * [[https://docs.scipy.org/doc/numpy/reference/routines.ma.html|Masked array operations]] | * [[https://numpy.org/doc/stable/reference/routines.ma.html|Masked array operations]] |
| * [[https://docs.scipy.org/doc/numpy/user/misc.html#ieee-754-floating-point-special-values|Dealing with special numerical values]] (//Nan//, //inf//) | * [[https://numpy.org/doc/stable/user/misc.html#ieee-754-floating-point-special-values|Dealing with special numerical values]] (//Nan//, //inf//) |
| * If you know that your data has missing values, it is cleaner and safer to handle them with [[https://docs.scipy.org/doc/numpy/reference/maskedarray.html|masked arrays]]! | * If you know that your data has missing values, it is cleaner and safer to handle them with [[https://numpy.org/doc/stable/reference/maskedarray.html|masked arrays]]! |
| * [[https://docs.scipy.org/doc/numpy/user/misc.html#how-numpy-handles-numerical-exceptions|Handling numerical exceptions]] | * [[https://numpy.org/doc/stable/user/misc.html#how-numpy-handles-numerical-exceptions|Handling numerical exceptions]] |
| * [[https://docs.scipy.org/doc/numpy/reference/routines.err.html|Floating point error handling]] | * [[https://numpy.org/doc/stable/reference/routines.err.html|Floating point error handling]] |
| |
| ===== cdms2 and netCDF4 ===== | ===== cdms2 and netCDF4 ===== |
| * [[https://uxknowledgebase.com/tables-other-charts-data-visualization-part-2-cfc582e4712c|Tables & Other Charts — Data Visualization Part 2]] | * [[https://uxknowledgebase.com/tables-other-charts-data-visualization-part-2-cfc582e4712c|Tables & Other Charts — Data Visualization Part 2]] |
| * [[https://uxknowledgebase.com/tables-other-charts-data-visualization-part-3-5bfab15ce525|Tables & Other Charts — Data Visualization Part 3]] | * [[https://uxknowledgebase.com/tables-other-charts-data-visualization-part-3-5bfab15ce525|Tables & Other Charts — Data Visualization Part 3]] |
| * Working with colors | * **IPCC**-related //stuff//... |
| * **Do not use the outdated //rainbow// colormap!** | * [[https://www.ipcc.ch/site/assets/uploads/2019/04/IPCC-visual-style-guide.pdf|IPCC Visual Style Guide for Authors]] |
| * [[http://geog.uoregon.edu/datagraphics/EOS/Light-and-Bartlein.pdf|The End of the Rainbow? Color Schemes for Improved Data Graphics]] (Light and Bartlein, EOS 2004, including replies and comments) | * [[https://wg1.ipcc.ch/sites/default/files/documents/ipcc_visual-identity_guidelines.pdf|A new assessment cycle,A new visual identity]] |
| | * [[https://link.springer.com/article/10.1007/s10584-019-02537-z|Communication of IPCC visuals: IPCC authors’ views and assessments of visual complexity]] |
| | * [[https://www.carbonbrief.org/guest-post-the-perils-of-counter-intuitive-design-in-ipcc-graphics|The perils of counter-intuitive design in IPCC graphics]] |
| | * Working with **colors** |
| | * Choosing specific colors: use [[https://www.w3schools.com/colors/colors_names.asp|HTML color names]], the [[https://www.w3schools.com/colors/colors_picker.asp|HTML color picker]], etc... |
| | * **Do not use the outdated //rainbow// and //jet// colormaps!** |
| | * [[https://pjbartlein.github.io/datagraphics/index.html|The End of the Rainbow? Color Schemes for Improved Data Graphics]] (Light and Bartlein, EOS 2004, including replies and comments) |
| * [[http://colorspace.r-forge.r-project.org/articles/endrainbow.html|Somewhere over the Rainbow]] | * [[http://colorspace.r-forge.r-project.org/articles/endrainbow.html|Somewhere over the Rainbow]] |
| | * [[https://www.nature.com/articles/s41467-020-19160-7|The misuse of colour in science communication]] |
| * [[https://matplotlib.org/users/colormaps.html|Choosing colormaps]] | * [[https://matplotlib.org/users/colormaps.html|Choosing colormaps]] |
| * [[https://matplotlib.org/cmocean/|cmocean: Beautiful colormaps for oceanography]] | * [[https://matplotlib.org/cmocean/|cmocean: Beautiful colormaps for oceanography]] |
| * [[http://colorbrewer2.org|ColorBrewer 2.0]] is a tool that can help you understand, and experiment with //sequential//, //diverging// and //qualitative// colormaps | * [[http://colorbrewer2.org|ColorBrewer 2.0]] is a tool that can help you understand, and experiment with //sequential//, //diverging// and //qualitative// colormaps |
| * The [[http://hclwizard.org/|hclwizard]] provides tools for manipulating and assessing colors and palettes based on the underlying ''colorspace'' software | * The [[http://hclwizard.org/|hclwizard]] provides tools for manipulating and assessing colors and palettes based on the underlying ''colorspace'' software |
| | * NCL (NCAR Command Language) [[https://www.ncl.ucar.edu/Document/Graphics/color_table_gallery.shtml|Color table Gallery]] |
| | * JYP's favorite title: [[https://www.researchgate.net/publication/220943662_The_Which_Blair_Project_A_Quick_Visual_Method_for_Evaluating_Perceptual_Color_Maps|The "Which Blair Project": A Quick Visual Method for Evaluating Perceptual Color Maps]] |
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| ===== Basemap ===== | ===== Basemap ===== |
| |
| <note warning>Basemap is going to be slowly phased out, in favor of [[#cartopy]]\\ More information in this: | <note warning>Basemap is going to be slowly phased out, in favor of [[#cartopy_iris|cartopy]]\\ More information in this: |
| * [[https://github.com/SciTools/cartopy/issues/920|cartopy github issue]] | * [[https://github.com/SciTools/cartopy/issues/920|cartopy github issue]] |
| * [[https://github.com/matplotlib/basemap/issues/267|basemap github issue]] | * [[https://github.com/matplotlib/basemap/issues/267|basemap github issue]] |
| ===== Cartopy + Iris ===== | ===== Cartopy + Iris ===== |
| |
| Summary: //Cartopy is a Python package for advanced map generation with a simple matplotlib interface// and //Iris is a Python package for analysing and visualising meteorological and oceanographic data sets// | Summary: |
| | * **Cartopy** is //a matplolib-based Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses// |
| | * **Iris** is //a powerful, format-agnostic, community-driven Python package for analysing and visualising Earth science data.// |
| |
| Where: [[http://scitools.org.uk/cartopy/docs/latest/|Cartopy]] and [[http://scitools.org.uk/iris/index.html|Iris]] web sites | Where: [[http://scitools.org.uk/cartopy/docs/latest/|Cartopy]] and [[https://scitools-iris.readthedocs.io/en/stable/|Iris]] web sites |
| |
| Examples: | Examples: |
| * [[other:python:maps_by_jyp|Examples provided by JYP]] | * [[other:python:maps_by_jyp|Examples provided by JYP]] |
| * [[http://scitools.org.uk/cartopy/docs/latest/gallery.html|Gallery on the Cartopy web site]] | * Official gallery pages: [[https://scitools.org.uk/cartopy/docs/latest/gallery/index.html|Cartopy]] - [[https://scitools-iris.readthedocs.io/en/stable/generated/gallery/|Iris]] |
| * [[http://scitools.org.uk/iris/docs/latest/gallery.html|Gallery on the Iris web site]] | |
| * [[http://scitools.org.uk/iris/docs/latest/examples/index.html|Examples on the Iris web site]] | |
| |
| Help on //stack overflow//: [[https://stackoverflow.com/questions/tagged/cartopy|cartopy help]] | Help on //stack overflow//: [[https://stackoverflow.com/questions/tagged/cartopy|Cartopy help]] - [[https://stackoverflow.com/questions/tagged/python-iris|Iris help]] |
| |
| ===== Maps and projections resources ===== | ===== Maps and projections resources ===== |
| ===== Python 2.7 vs Python 3 ===== | ===== Python 2.7 vs Python 3 ===== |
| |
| The official [[https://docs.python.org/2.7/howto/pyporting.html|Porting Python 2 Code to Python 3]] page gives the required information to make the transition from python 2 to python 3. It is still safe to use Python 2.7, so there is no rush to change to Python 3. | It is still safe to use Python 2.7, but **you should consider upgrading to Python 3**, unless some key modules you need are not compatible (yet) with Python 3 |
| | |
| | You should start writing code that will, when possible, work both in Python 2 and Python 3 |
| | |
| | Some interesting reading: |
| | |
| | * [[https://docs.python.org/3/whatsnew/3.0.html|What’s New In Python 3.0]].\\ Examples: |
| | * ''print'' is now a function. Use ''print('Hello')'' |
| | * You cannot test a difference with ''<>'' any longer! Use ''!='' |
| | |
| | * The official [[https://docs.python.org/2.7/howto/pyporting.html|Porting Python 2 Code to Python 3]] page gives the required information to make the transition from python 2 to python 3. |
| |
| ===== What now? ===== | ===== What now? ===== |
