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other:python:jyp_steps [2018/07/10 11:02]
jypeter [json files] Moved json to a new "Data file formats" section, and dded LiPD and BagIt
other:python:jyp_steps [2019/03/18 15:03] (current)
jypeter [Quick Reference and cheat sheets]
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     - [[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)
-  - read the [[https://​docs.scipy.org/​doc/​numpy-dev/​user/​quickstart.html|Quickstart tutorial]]+  - read the really nice [[https://​docs.scipy.org/​doc/​numpy/​user/​quickstart.html|numpy Quickstart tutorial]]
   - have a quick look at the full documentation to know where things are   - have a quick look at the full documentation to know where things are
     - Numpy User Guide     - Numpy User Guide
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        [20, 21, -1, -1, 24, 25, 26, 27, 28, 29]])        [20, 21, -1, -1, 24, 25, 26, 27, 28, 29]])
 </​code></​note>​ </​code></​note>​
 +
 +==== Extra numpy information ====
 +
 +  * 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/​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/​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//)
 +    * 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/​reference/​routines.err.html|Floating point error handling]]
  
 ===== cdms2 and netCDF4 ===== ===== cdms2 and netCDF4 =====
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     - a Matplotlib //Figure// is a graphical window in which you make your plots... ​     - a Matplotlib //Figure// is a graphical window in which you make your plots... ​
     - 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 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/​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]]
 +      * [[http://​matplotlib.org/​faq/​usage_faq.html#​parts-of-a-figure|parts of a figure]]
     - 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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 Help on //stack overflow//: [[https://​stackoverflow.com/​questions/​tagged/​cartopy|cartopy help]] Help on //stack overflow//: [[https://​stackoverflow.com/​questions/​tagged/​cartopy|cartopy help]]
 +
 +===== Maps and projections resources =====
 +
 +==== About projections ====
 +
 +  * [[https://​egsc.usgs.gov/​isb//​pubs/​MapProjections/​projections.html|Map projections from USGS poster]]
 +  * [[https://​pubs.usgs.gov/​pp/​1395/​report.pdf|Map projections - A working manual (USGS)]]
 +
 +==== Libraries ====
 +
 +  * Projections in vcs
 +  * [[http://​matplotlib.org/​basemap/​users/​mapsetup.html|Projections in basemap]]
 +  * [[https://​scitools.org.uk/​cartopy/​docs/​latest/​crs/​projections.html|Projections in cartopy]]
 +
  
 ===== 3D resources ===== ===== 3D resources =====
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 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. 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...
  
-===== Quick Reference =====+===== Quick Reference ​and cheat sheets ​=====
  
   * The nice and convenient Python 2.7 Quick Reference: [[http://​rgruet.free.fr/​PQR27/​PQR2.7_printing_a4.pdf|pdf]] - [[http://​rgruet.free.fr/​PQR27/​PQR2.7.html|html]]   * The nice and convenient Python 2.7 Quick Reference: [[http://​rgruet.free.fr/​PQR27/​PQR2.7_printing_a4.pdf|pdf]] - [[http://​rgruet.free.fr/​PQR27/​PQR2.7.html|html]]
 +    * A possibly more [[http://​iysik.com/​PQR2.7/​PQR2.7.html|up-date-version]]
 +
 +  * Python 3 [[https://​perso.limsi.fr/​pointal/​python:​abrege|Quick reference]] and [[https://​perso.limsi.fr/​pointal/​python:​memento|Cheat sheet]]
 +
 +  * [[https://​www.cheatography.com/​weidadeyue/​cheat-sheets/​jupyter-notebook/​pdf_bw/​|Jupyter Notebook Keyboard Shortcuts]]
 +
 +===== 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.1531213330.txt.gz · Last modified: 2018/07/10 11:02 by jypeter