other:python:jyp_steps
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other:python:jyp_steps [2018/08/23 09:54] jypeter Added the 'extra numpy' section, with lots of info about indexing |
other:python:jyp_steps [2018/12/14 14:05] jypeter [Matplotlib] Added note about offline graphics |
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| * More information about array indexing: | * More information about array indexing: | ||
| + | * Examples: | ||
| + | * {{ :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://docs.scipy.org/doc/numpy/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://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://docs.scipy.org/doc/numpy/reference/arrays.indexing.html|Indexing (in the numpy reference manual)]] | * [[https://docs.scipy.org/doc/numpy/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://docs.scipy.org/doc/numpy/reference/routines.indexing.html#routines-indexing|Indexing routines]] | ||
| + | * More information about arrays: | ||
| + | * [[https://docs.scipy.org/doc/numpy/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://docs.scipy.org/doc/numpy/reference/maskedarray.html|Masked arrays]] | ||
| + | * [[https://docs.scipy.org/doc/numpy/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://docs.scipy.org/doc/numpy/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 masks | + | * 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]]! |
| * [[https://docs.scipy.org/doc/numpy/user/misc.html#how-numpy-handles-numerical-exceptions|Handling numerical exceptions]] | * [[https://docs.scipy.org/doc/numpy/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]] | ||
| ===== cdms2 and netCDF4 ===== | ===== cdms2 and netCDF4 ===== | ||
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| - a Matplotlib //Axis// is a plot inside a Figure... [[http://matplotlib.org/faq/usage_faq.html#parts-of-a-figure|More details]] | - a Matplotlib //Axis// is a plot inside a Figure... [[http://matplotlib.org/faq/usage_faq.html#parts-of-a-figure|More details]] | ||
| - some examples are more //pythonic// (ie object oriented) than others, some example mix different styles of coding, all this can be confusing. Try to [[http://matplotlib.org/faq/usage_faq.html#coding-styles|use an object oriented way of doing things]]! | - some examples are more //pythonic// (ie object oriented) than others, some example mix different styles of coding, all this can be confusing. Try to [[http://matplotlib.org/faq/usage_faq.html#coding-styles|use an object oriented way of doing things]]! | ||
| - | - sometimes the results of the python/matplolib commands are displayed directly, sometimes not. It depends if you are in [[http://matplotlib.org/faq/usage_faq.html#what-is-interactive-mode|interactive or non-interactive]] mode | + | - it may be hard to (remember how to) work with colors. Some examples from the [[http://matplotlib.org/gallery.html|Gallery]] can help you! |
| + | * [[https://matplotlib.org/examples/pylab_examples/leftventricle_bulleye.html|leftventricle_bulleye.py]]: associating different types of colormaps to a plot and colorbar | ||
| + | * [[https://matplotlib.org/examples/api/colorbar_only.html|colorbar_only.py]]: the different types of colorbars (or plotting only a colorbar) | ||
| + | * [[https://matplotlib.org/examples/color/colormaps_reference.html|colormaps_reference.py]]: pre-defined colormaps | ||
| + | * [[https://matplotlib.org/examples/color/named_colors.html|named_colors.py]]: named colors | ||
| + | * More details about the colors below, in the [[#graphics_related_resources|Resources section]] | ||
| + | - sometimes the results of the python/matplolib commands are displayed immediately, sometimes not. It depends if you are in [[http://matplotlib.org/faq/usage_faq.html#what-is-interactive-mode|interactive or non-interactive]] mode | ||
| + | - if your matplotlib is executed in a batch script, it will generate an error when trying to create (''show()'') a plot, because matplotlib expects to be able to display the figure on a screen by default. | ||
| + | * Check how you can [[https://matplotlib.org/faq/howto_faq.html?highlight=web#generate-images-without-having-a-window-appear|generate images offline]] | ||
| - the documentation may mention [[http://matplotlib.org/faq/usage_faq.html#what-is-a-backend|backends]]. What?? Basically, you use python commands to create a plot, and the backend is the //thing// that will render your plot on the screen or in a file (png, pdf, etc...) | - the documentation may mention [[http://matplotlib.org/faq/usage_faq.html#what-is-a-backend|backends]]. What?? Basically, you use python commands to create a plot, and the backend is the //thing// that will render your plot on the screen or in a file (png, pdf, etc...) | ||
| - if you don't see a part of what you have plotted, maybe it's hidden behind other elements! Use the [[https://matplotlib.org/examples/pylab_examples/zorder_demo.html|zorder parameter]] to explicitly specify the plotting order/layers | - if you don't see a part of what you have plotted, maybe it's hidden behind other elements! Use the [[https://matplotlib.org/examples/pylab_examples/zorder_demo.html|zorder parameter]] to explicitly specify the plotting order/layers | ||
| - Read the [[http://www.labri.fr/perso/nrougier/teaching/matplotlib/|Matplotlib tutorial by Nicolas Rougier]] | - Read the [[http://www.labri.fr/perso/nrougier/teaching/matplotlib/|Matplotlib tutorial by Nicolas Rougier]] | ||
| - Download the [[http://matplotlib.org/contents.html|pdf version of the manual]]. **Do not print** the 2800+ pages of the manual! Read the beginner's guide (Chapter //FIVE// of //Part II//) and have a super quick look at the table of contents of the whole document. | - Download the [[http://matplotlib.org/contents.html|pdf version of the manual]]. **Do not print** the 2800+ pages of the manual! Read the beginner's guide (Chapter //FIVE// of //Part II//) and have a super quick look at the table of contents of the whole document. | ||
| + | |||
| + | ==== Misc Matplotlib tricks ==== | ||
| + | |||
| + | * Specifying the background color of a plot (e.g. when plotting a masked variable and you don't want the masked areas to be white) | ||
| + | * ''# make the background dark gray (call this before the contourf)''\\ ''plt.gca().patch.set_color('.25')''\\ ''plt.contourf(d)''\\ ''plt.show()'' | ||
| + | * [[https://stackoverflow.com/questions/9797520/masking-part-of-a-contourf-plot-in-matplotlib|trick source]] | ||
| ===== Graphics related resources ===== | ===== Graphics related resources ===== | ||
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| * Python 3 [[https://perso.limsi.fr/pointal/python:abrege|Quick reference]] and [[https://perso.limsi.fr/pointal/python:memento|Cheat sheet]] | * Python 3 [[https://perso.limsi.fr/pointal/python:abrege|Quick reference]] and [[https://perso.limsi.fr/pointal/python:memento|Cheat sheet]] | ||
| + | ===== Misc tutorials ===== | ||
| + | |||
| + | * [[https://pyformat.info/|PyFormat]]: //With this site we try to show you the most common use-cases covered by the old and new style string formatting API with practical examples// | ||
| ===== Some good coding tips ===== | ===== Some good coding tips ===== | ||
other/python/jyp_steps.txt · Last modified: 2024/03/07 10:15 by jypeter
