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other:python:jyp_steps [2019/06/03 16:12] jypeter [Useful matplotlib reference pages] Added animations |
other:python:jyp_steps [2023/03/29 13:38] jypeter [Extra numpy information] Corrected links |
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* the tutorial is very detailed about string handling, because strings offer an easy way to practice working with indices (indexing and slicing), before indexing numpy arrays. And our usual pre/post-processing scripts often need to do a lot of string handling in order to generate the file/variable/experiment names | * the tutorial is very detailed about string handling, because strings offer an easy way to practice working with indices (indexing and slicing), before indexing numpy arrays. And our usual pre/post-processing scripts often need to do a lot of string handling in order to generate the file/variable/experiment names | ||
* after reading this tutorial, you should practice with the following: | * after reading this tutorial, you should practice with the following: | ||
- | * [[https://files.lsce.ipsl.fr/public.php?service=files&t=9731fdad4521ac5fa6e84b392d3a2e44|Basic python training test (ipython notebook version)]] | + | * [[https://sharebox.lsce.ipsl.fr/index.php/s/S3EO8cLrhVDeQWA|Basic python training test (ipython notebook version)]] |
* {{:other:python:tp_intro_python_oct2013_no_solutions.pdf|Basic python training test (pdf version)}} | * {{:other:python:tp_intro_python_oct2013_no_solutions.pdf|Basic python training test (pdf version)}} | ||
* {{:other:python:tp_intro_python_oct2013_full.pdf|Basic python training test (pdf version, with answers)}} | * {{:other:python:tp_intro_python_oct2013_full.pdf|Basic python training test (pdf version, with answers)}} | ||
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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) | ||
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==== Extra numpy information ==== | ==== Extra numpy information ==== | ||
- | * More information about array indexing: | + | <WRAP center round tip 60%> |
+ | You can also check the [[other:python:misc_by_jyp#numpy_related_stuff|numpy section]] of the //Useful python stuff// page | ||
+ | </WRAP> | ||
+ | |||
+ | |||
+ | * More information about **array indexing**:\\ <wrap em>Always check what you are doing on a simple test case, when you use advanced/fancy indexing!</wrap> | ||
* 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|Array indexing basics (user guide)]] (//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/reference/arrays.indexing.html|Indexing routines (reference manual)]] |
- | * [[https://docs.scipy.org/doc/numpy/reference/arrays.indexing.html|Indexing (in the numpy 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://docs.scipy.org/doc/numpy/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|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/routines.sort.html|Sorting, searching, and counting routines]] |
- | * [[https://docs.scipy.org/doc/numpy/reference/routines.ma.html|Masked array operations]] | + | * [[https://numpy.org/doc/stable/reference/maskedarray.html|Masked arrays]] |
- | * [[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/reference/routines.ma.html|Masked array operations]] |
- | * 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://numpy.org/doc/stable/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#how-numpy-handles-numerical-exceptions|Handling numerical exceptions]] | + | * 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/reference/routines.err.html|Floating point error handling]] | + | * If you know that some of your data //may// have masked values, play safe by explicitly using ''np.ma.some_function()'' rather than just ''np.some_function()'' |
+ | * More details in the [[https://github.com/numpy/numpy/issues/18675|Why/when does np.something remove the mask of a np.ma array ?]] discussion | ||
+ | * [[https://numpy.org/doc/stable/user/misc.html#how-numpy-handles-numerical-exceptions|Handling numerical exceptions]] | ||
+ | * [[https://numpy.org/doc/stable/reference/routines.err.html|Floating point error handling]] | ||
- | ===== cdms2 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> | ||
- | Depending on which [[other:python:starting#some_python_distributions|python distribution]] you are using, you can use the //cdms2// or or //netCDF4// modules to read the data. | + | * There is a good chance that your input array data will be stored in a [[other:newppl:starting#netcdf_and_related_conventions|NetCDF]] file. |
+ | |||
+ | * 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 ==== | ||
- | Summary: cdms2 can read/write netCDF files (and read //grads// dat+ctl files) and provides a higher level interface than netCDF4. cdms2 is available in the [[other:python:starting#uv-cdat|UV-CDAT distribution]], and can theoretically be installed independently of UV-CDAT (e.g. it will be installed when you install [[https://cmor.llnl.gov/mydoc_cmor3_conda/|CMOR in conda)]]. When you can use cdms2, you also have access to //cdtime//, that is very useful for handling time axis data. | + | Summary: cdms2 can read/write netCDF files (and read //grads// dat+ctl files) and provides a higher level interface than netCDF4. cdms2 is available in the [[other:python:starting#cdat|CDAT distribution]], and can theoretically be installed independently of CDAT (e.g. it will be installed when you install [[https://cmor.llnl.gov/mydoc_cmor3_conda/|CMOR in conda)]]. When you can use cdms2, you also have access to //cdtime//, that is very useful for handling time axis data. |
How to get started: | How to get started: | ||
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- you have to replace //cdms// with **cdms2**, and //MV// with **MV2** (sooorry about that, the tutorial was written when CDAT was based on //Numeric// instead of //numpy// to handle array data) | - you have to replace //cdms// with **cdms2**, and //MV// with **MV2** (sooorry about that, the tutorial was written when CDAT was based on //Numeric// instead of //numpy// to handle array data) | ||
- read the [[http://cdms.readthedocs.io/en/docstanya/index.html|official cdms documentation]] (link may change) | - read the [[http://cdms.readthedocs.io/en/docstanya/index.html|official cdms documentation]] (link may change) | ||
+ | |||
+ | ==== xarray ==== | ||
+ | |||
+ | 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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===== CDAT-related resources ===== | ===== CDAT-related resources ===== | ||
- | Some links, in case they can't be found easily on the [[https://uv-cdat.llnl.gov|UV-CDAT]] web site... | + | Some links, in case they can't be found easily on the [[https://cdat.llnl.gov|CDAT]] web site... |
- | * [[https://uv-cdat.llnl.gov/tutorials.html|Tutorials in ipython notebooks]] | + | * [[https://cdat.llnl.gov/tutorials.html|Tutorials in ipython notebooks]] |
* [[http://cdat-vcs.readthedocs.io/en/latest/|VCS: Visualization Control System]] | * [[http://cdat-vcs.readthedocs.io/en/latest/|VCS: Visualization Control System]] | ||
* [[https://github.com/CDAT/vcs/issues/238|Colormaps in vcs examples]] | * [[https://github.com/CDAT/vcs/issues/238|Colormaps in vcs examples]] | ||
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===== Matplotlib ===== | ===== Matplotlib ===== | ||
+ | |||
+ | <note important> | ||
+ | The full content of this //matplotlib// section has been moved to\\ [[other:python:matplotlib_by_jyp|Working with matplotlib (JYP version)]]\\ after becoming too big to manage here | ||
+ | |||
+ | \\ Note: [[other:python:maps_by_jyp|Plotting maps with matplotlib+cartopy]] (examples provided by JYP) | ||
+ | </note> | ||
Summary: there are lots of python libraries that you can use for plotting, but Matplotlib has become a //de facto// standard | Summary: there are lots of python libraries that you can use for plotting, but Matplotlib has become a //de facto// standard | ||
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Help on //stack overflow//: [[https://stackoverflow.com/questions/tagged/matplotlib|matplotlib help]] | Help on //stack overflow//: [[https://stackoverflow.com/questions/tagged/matplotlib|matplotlib help]] | ||
- | |||
- | The matplotlib documentation is good, but not always easy to use. <wrap hi>A good way to start with matplotlib</wrap> is to quickly read the following, practice, and read this section again | ||
- | - Have a quick look at the [[https://matplotlib.org/gallery/index.html|matplotlib gallery]] to get an idea of all you can do with matplotlib. Later, when you need to plot something, go back to the gallery to find some examples that are close to what you need and click on them to view their source code | ||
- | * 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]]! | ||
- | - Use the free hints provided by JY! | ||
- | - You will usually **initialize matplotlib** with: ''import matplotlib.pyplot as plt'' | ||
- | * in some cases you may also need: ''import matplotlib as mpl'' | ||
- | * later, you may need other matplotlib related modules, for advanced usage | ||
- | - You need to know some **matplotlib specific vocabulary**: | ||
- | * a Matplotlib **//Figure//** (or //canvas//) is a graphical window in which you create your plots... | ||
- | * example: ''my_page = plt.figure()'' | ||
- | * if you need several display windows at the same time, create several figures | ||
- | * the [[http://matplotlib.org/faq/usage_faq.html#parts-of-a-figure|parts of a figure]] are often positioned in //normalized coordinates//: ''(0, 0)'' is the bottom left of the figure, and ''(1, 1)'' the top right | ||
- | * You don't really specify the **page orientation** (//portrait// or //landscape//) of a plot. If you want a portrait plot, it's up to you to create a plot that will look higher than it is large. The idea is not to worry about this and just check the final resulting plot: create a plot, save it, display the resulting png/pdf and then adjust the creation script | ||
- | * If you have an idea of the layout of what you want to plot, it may be easier to explicitly specify the figure size/ratio at creation time, and try to //fill// the figure | ||
- | * ''my_page = plt.figure()'': the ratio of the default figure is ''landscape'', because it is 33% larger than it is high. Creating a default figure will be OK most of the time! | ||
- | * ''my_page = plt.figure(figsize=(width, height))'': create a figure with a custom ratio (sizes are considered to be in inches) | ||
- | * ''my_page = plt.figure(figsize=(8.3, 11.7))'': create a figure that will theoretically fill an A4 size page in portrait mode (check [[https://www.papersizes.org/a-paper-sizes.htm|Dimensions Of A Series Paper Sizes]] if you need more size details) | ||
- | * a Matplotlib **//Axis//** is a plot inside a Figure... [[http://matplotlib.org/faq/usage_faq.html#parts-of-a-figure|More details]] | ||
- | * reserve space for **one plot** that will use most of the available area of the figure/page: | ||
- | * ''my_plot = my_page.add_subplot(1, 1, 1)'': syntax is ''add_subplot(nrows, ncols, index)'' | ||
- | * ''my_plot = my_page.subplot**s**()'' | ||
- | * create **3 plots on 1 column** (each plot uses the full width of the figure): | ||
- | * <code>top_plot = my_page.add_subplot(3, 1, 1) | ||
- | middle_plot = my_page.add_subplot(3, 1, 2) | ||
- | bottom_plot = my_page.add_subplot(3, 1, 3)</code> | ||
- | * the following method is more efficient than add_subplot when there are lots of plots on a page<code>plot_array = my_page.subplots(3, 1) | ||
- | top_plot = plot_array[0] | ||
- | middle_plot = plot_array[1] | ||
- | bottom_plot = plot_array[2]</code> | ||
- | * creating a figure and axes with a single line: ''my_page, plot_array = **plt**.subplots(3, 1)'' | ||
- | * a Matplotlib **//Artist//** or //Patch// is //something// (e.g a line, a group of markers, text, the legend...) plotted on the Figure/Axis | ||
- | * **clearing** the //page// (or part of it): you probably won't need that | ||
- | * ''my_page.clear()'' or ''my_page.clf()'' or ''plt.clf()'': clear the (current) figure | ||
- | * ''my_plot.clear()'' or ''my_plot.cla()'': clear the (current) axis | ||
- | - some resources for having multiple plots on the same figure | ||
- | * [[https://matplotlib.org/gallery/recipes/create_subplots.html#sphx-glr-gallery-recipes-create-subplots-py|Easily creating subplots]] | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.figure.Figure.html#matplotlib.figure.Figure.add_subplot|fig.add_subplot(...)]] | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.figure.Figure.html#matplotlib.figure.Figure.add_axes|fig.add_axes(...)]] | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.subplot.html|plt.subplot(...)]] | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.subplots.html|plt.subplots(...)]] with an **s** at the end ([[https://matplotlib.org/gallery/subplots_axes_and_figures/subplots_demo.html|demo]]) | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.subplots_adjust.html|subplots_adjust]] can be used to change the overall boundaries of the subplots on the figure, and the spacing between the subplots\\ ''plt.subplots_adjust(left=None, bottom=None, right=None, top=None, wspace=None, hspace=None)''\\ or ''my_page.subplots_adjust(left=None, bottom=None, right=None, top=None, wspace=None, hspace=None)'' | ||
- | * [[https://matplotlib.org/gallery/index.html#subplots-axes-and-figures|Subplots, axes and figures]] gallery | ||
- | * [[https://matplotlib.org/tutorials/intermediate/gridspec.html#sphx-glr-tutorials-intermediate-gridspec-py|Customizing Figure Layouts Using GridSpec and Other Functions]], [[https://matplotlib.org/tutorials/intermediate/constrainedlayout_guide.html|constrained layout]] and [[https://matplotlib.org/tutorials/intermediate/tight_layout_guide.html|tight layout]] | ||
- | - use [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html|my_page.savefig(...)]] to save a figure | ||
- | * <wrap hi>savefig(...) must be called **before** plt.show()!</wrap> | ||
- | * ''my_page.savefig('my_plot.pdf')'': save the figure to a pdf file | ||
- | * ''my_page.savefig('my_plot.png', dpi=200, transparent=True, bbox_inches='tight')'': save the figure to a png file at a higher resolution than the default (default is 100 dots per inch), with a transparent background and no extra space around the figure | ||
- | - **display** the figure and its plots, and **start interacting** (zooming, panning...) with them:\\ ''plt.show()'' | ||
- | - it may be hard to (remember how to) **work with colors**. Some examples from the [[https://matplotlib.org/gallery/index.html]] 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]] | ||
- | - 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 | ||
- | * things should automatically work //as expected// if //zorder// is not explicitly specified | ||
- | * Use the ''zorder=NN'' parameter when creating objects. ''NN'' is an integer where 0 is the lowest value (the farthest from the eye), and objects are plotted above objects with a lower //zorder// value | ||
- | * Use ''matplotlib_object.set_order(NN)'' to change the order after an object has been created | ||
- | - 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...) | ||
- | - Read the [[https://github.com/rougier/matplotlib-tutorial|Matplotlib tutorial by Nicolas Rougier]] | ||
- | - Download the [[http://matplotlib.org/contents.html|pdf version of the manual]]. **Do not print** the 2300+ 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. | ||
- | |||
- | ==== Useful matplotlib reference pages ==== | ||
- | |||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.plot.html|plot(...)]]: Plot y versus x as lines and/or markers | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.scatter.html|scatter(...)]]: A scatter plot of y vs x with varying marker size and/or color | ||
- | * The ''plot'' function will be faster for scatterplots where markers don't vary in size or color | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.lines.Line2D.html|line]] parameters | ||
- | * ''linestyle'': ''solid'', ''None'', [[https://matplotlib.org/api/_as_gen/matplotlib.lines.Line2D.html#matplotlib.lines.Line2D.set_linestyle|other]] ([[https://matplotlib.org/examples/lines_bars_and_markers/line_styles_reference.html|default styles example]], [[https://matplotlib.org/examples/lines_bars_and_markers/linestyles.html|custom styles example]]) | ||
- | * [[https://matplotlib.org/api/markers_api.html|marker types]] | ||
- | * ''fillstyle'': ''full'', ''None'', [[https://matplotlib.org/gallery/lines_bars_and_markers/marker_fillstyle_reference.html|other]] | ||
- | * Other attributes: ''markersize'', ''markerfacecolor'' (and ''markerfacecoloralt'' for dual color markers), ''markeredgecolor'', ''markeredgewidth'' | ||
- | * [[https://matplotlib.org/api/colors_api.html|colors]] | ||
- | * [[https://matplotlib.org/gallery/color/color_demo.html|color demo]] | ||
- | * [[https://matplotlib.org/examples/color/named_colors.html|named colors]] | ||
- | * [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.text.html|text(...)]] and [[https://matplotlib.org/tutorials/text/annotations.html|annotations]] | ||
- | * ''fontsize'': size in points, or (better!) string specifying a relative size (''xx-small'', ''x-small'', ''small'', ''medium'', ''large'', ''x-large'', ''xx-large'') | ||
- | * [[https://matplotlib.org/api/text_api.html#matplotlib.text.Text|all the text properties]] | ||
- | * [[https://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.legend|legend(...)]] ([[https://matplotlib.org/examples/pylab_examples/legend_demo3.html|legend demo]], [[https://matplotlib.org/users/legend_guide.html|advanced legend guide]]) | ||
- | * The legend will //show// the lines (or other objects) that were associated with a //label// with the ''label='' keyword when creating/updating a plot | ||
- | * If there are some elements of a plot that you do not want to associate with a legend (e.g. there are several lines with the same color and markers, but you want to plot the legend only once), do not specify a ''label='' keyword for these elements, or add a ''_'' at the front of the label strings | ||
- | * The legend is positioned somewhere (that can be specified) **inside** the plot. In order to place a legend **outside** the plot, use the ''bbox_to_anchor'' parameter | ||
- | * the parameters of ''bbox_to_anchor'' are in normalized coordinates of the current (sub)plot: | ||
- | * ''(0, 0)'' is the lower left corner of the plot, and ''(1, 1)'' the upper right corner | ||
- | * ''legend(... bbox_to_anchor=(1.05, 1.), loc='upper left', ...)'' will put the upper left corner of the legend slightly right (''(1.05, 1.)'') of the upper right corner (''(1, 1)'') of the plot | ||
- | * if the legend is outside of the plot, you have to **explicitly provide enough space for the legend on the page** | ||
- | * e.g. with [[https://matplotlib.org/api/_as_gen/matplotlib.pyplot.subplots_adjust.html|subplots_adjust]], ''plt.subplots_adjust(right=0.75)'' will make all the plots use 75% on the left of the page, and leave 25% on the right for the legend | ||
- | * The [[https://matplotlib.org/api/_as_gen/matplotlib.figure.Figure.html|figure(...)]] and the associated methods | ||
- | * The [[https://matplotlib.org/api/axes_api.html|axes]] and the associated methods | ||
- | * [[https://matplotlib.org/tutorials/introductory/customizing.html#matplotlib-rcparams|matplotlib default settings]] can be queried and updated | ||
- | * example: the default figure size (inches) is ''mpl.rcParams['figure.figsize']'' (''[6.4, 4.8]'') | ||
- | * current settings' file: ''mpl.matplotlib_fname()'' | ||
- | * [[https://matplotlib.org/api/animation_api.html|Animations]] ([[https://matplotlib.org/gallery/index.html#animation|demo]]) | ||
- | |||
- | ==== 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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* See also: [[https://www.datacamp.com/community/tutorials/seaborn-python-tutorial| | * See also: [[https://www.datacamp.com/community/tutorials/seaborn-python-tutorial| | ||
Python Seaborn Tutorial For Beginners]] | Python Seaborn Tutorial For Beginners]] | ||
- | * Working with colors | + | * Communicating/displaying/plotting your data (possibly for people not of your field): |
+ | * [[https://uxknowledgebase.com/introduction-to-designing-data-visualizations-part-1-31c056556133|Introduction to Designing Data Visualizations — Part 1]] | ||
+ | * [[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]] | ||
+ | * **IPCC**-related //stuff//... | ||
+ | * [[https://www.ipcc.ch/site/assets/uploads/2019/04/IPCC-visual-style-guide.pdf|IPCC Visual Style Guide for Authors]] | ||
+ | * [[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]] | ||
+ | * [[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/|Beautiful colormaps for oceanography: cmocean]] | + | * [[https://matplotlib.org/cmocean/|cmocean: Beautiful colormaps for oceanography]] |
+ | * [[https://jiffyclub.github.io/palettable/|Palettable: Color palettes for Python]] | ||
* [[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 | ||
+ | * 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]] | ||
===== 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]] | ||
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===== 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: | ||
- | * [[http://scitools.org.uk/cartopy/docs/latest/gallery.html|Gallery on the Cartopy web site]] | + | * [[other:python:maps_by_jyp|Examples provided by JYP]] |
- | * [[http://scitools.org.uk/iris/docs/latest/gallery.html|Gallery on the Iris 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/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 ===== | ||
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We list here some resources about non-NetCDF data formats that can be useful | We list here some resources about non-NetCDF data formats that can be useful | ||
+ | ==== The shelve package ==== | ||
+ | |||
+ | The [[https://docs.python.org/3/library/shelve.html|built-in shelve package]], can be easily used for storing data (python objects like lists, dictionaries, numpy arrays that are not too big, ...) on disk and retrieving them later | ||
+ | |||
+ | Use case: | ||
+ | - Use a script do to the heavy data pre-processing and store the (intermediate) results in a file using ''shelve'', or update the results | ||
+ | - Use another script for plotting the results stored with ''shelve''. This way you don't have to wait for the pre-processing step to finish each time you want to improve your plot(s) | ||
+ | |||
+ | Warning: | ||
+ | * read the [[https://docs.python.org/3/library/shelve.html|documentation]] and the example carefully (it's quite small) | ||
+ | * if you get the impression that the data is not saved correctly, re-read the parts about updating correctly the content of the shelve file | ||
+ | * you should be able to store most python objects in a shelve file, but it is safer to make tests | ||
+ | * do not forget to close the output file | ||
+ | * if you are dealing with big arrays and want to avoid performance issues, you should use netCDF files for storing the intermediate results | ||
==== json files ==== | ==== json files ==== | ||
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//json// files look basically like a **list of (nested) python dictionaries** that would have been dumped to a text file | //json// files look basically like a **list of (nested) python dictionaries** that would have been dumped to a text file | ||
- | * [[https://docs.python.org/2/library/json.html|json module]] documentation | + | * [[https://docs.python.org/3/library/json.html|json module]] documentation |
* [[https://realpython.com/python-json/|Working With JSON Data in Python]] tutorial | * [[https://realpython.com/python-json/|Working With JSON Data in Python]] tutorial | ||
* example script: ''/home/users/jypeter/CDAT/Progs/Devel/beaugendre/nc2json.py'' | * example script: ''/home/users/jypeter/CDAT/Progs/Devel/beaugendre/nc2json.py'' | ||
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Where: [[http://pandas.pydata.org|Pandas web site]] | Where: [[http://pandas.pydata.org|Pandas web site]] | ||
- | JYP's comment: pandas is supposed to be quite good for loading, processing and plotting time series, without writing custom code. You should at least have a quick look at: | + | JYP's comment: pandas is supposed to be quite good for loading, processing and plotting time series, without writing custom code. It is **very convenient for processing tables in xlsx files** (or csv, etc...). You should at least have a quick look at: |
- | * 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 cheat sheet on the [[https://www.enthought.com/services/training/pandas-mastery-workshop/|Enthought workshops advertising page]] | + | * Some //Cheat Sheets// (in the following order): |
- | * the cheat sheet on the [[https://github.com/pandas-dev/pandas/tree/master/doc/cheatsheet|github Pandas doc page]] | + | - Basics: [[http://datacamp-community-prod.s3.amazonaws.com/dbed353d-2757-4617-8206-8767ab379ab3|Pandas basics]] (associated with the [[https://www.datacamp.com/community/blog/python-pandas-cheat-sheet|Pandas Cheat Sheet for Data Science in Python]] pandas introduction page) |
+ | - Intermediate: [[https://github.com/pandas-dev/pandas/tree/master/doc/cheatsheet|github Pandas doc page]] | ||
+ | - Advanced: the cheat sheet on the [[https://www.enthought.com/services/training/pandas-mastery-workshop/|Enthought workshops advertising page]] | ||
+ | * Some tutorials: | ||
+ | * [[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]] | ||
===== Scipy Lecture Notes ===== | ===== Scipy Lecture Notes ===== | ||
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Where: [[http://www.scipy-lectures.org/_downloads/ScipyLectures-simple.pdf|pdf]] - [[http://www.scipy-lectures.org/|html]] | 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. You will learn more things about python, numpy and matplotlib, debugging and optimizing scripts, and also learn about using python for statistics, image processing, machine learning, washing dishes (this is just to check if you have read this page), etc... | + | 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 ===== | ||
+ | |||
+ | [[https://www.statsmodels.org/|statsmodels ]] is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. | ||
+ | |||
+ | ===== scikit-learn ===== | ||
+ | |||
+ | [[http://scikit-learn.org/|scikit-learn]] is an open source machine learning library that supports supervised and unsupervised learning. It also provides various tools for model fitting, data preprocessing, model selection and evaluation, and many other utilities. | ||
+ | |||
+ | ===== scikit-image ===== | ||
+ | |||
+ | [[https://scikit-image.org/|scikit-image]] is a collection of algorithms for image processing in Python | ||
===== Quick Reference and cheat sheets ===== | ===== Quick Reference and cheat sheets ===== | ||
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* [[https://www.cheatography.com/weidadeyue/cheat-sheets/jupyter-notebook/pdf_bw/|Jupyter Notebook Keyboard Shortcuts]] | * [[https://www.cheatography.com/weidadeyue/cheat-sheets/jupyter-notebook/pdf_bw/|Jupyter Notebook Keyboard Shortcuts]] | ||
+ | |||
+ | ===== Miscellaneous Python stuff ===== | ||
+ | |||
+ | Check the page about [[other:python:misc_by_jyp|useful python stuff that has not been sorted yet]] | ||
===== Misc tutorials ===== | ===== Misc tutorials ===== | ||
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Depending on the distribution, the editor and the programming environment you use, you may have access to a graphical version of the debugger. UV-CDAT users can use ''pydebug my_script.py'' | Depending on the distribution, the editor and the programming environment you use, you may have access to a graphical version of the debugger. UV-CDAT users can use ''pydebug my_script.py'' | ||
+ | |||
+ | ===== jupyter and notebook stuff ===== | ||
+ | |||
+ | FIXME Misc notes, resources and links to organize later | ||
+ | |||
+ | * [[https://beta.jupyterbook.org/|jupyter {book}]]: Jupyter Book is an open source project for building beautiful, publication-quality books and documents from computational material. | ||
===== Using a Python IDE ===== | ===== Using a Python IDE ===== | ||
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===== 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? ===== |