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other:python:jyp_steps [2018/05/31 14:33] jypeter Added json |
other:python:jyp_steps [2018/09/04 12:43] jypeter [Matplotlib] added note about colors |
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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 //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]]! | ||
+ | - it may be hard to (remember how to) work with colors. Some examples from the [[|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 | ||
- 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 | - 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 | ||
- 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...) | ||
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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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* [[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?]] | ||
- | ===== json files ===== | + | ===== Data file formats ===== |
+ | |||
+ | We list here some resources about non-NetCDF data formats that can be useful | ||
+ | |||
+ | ==== json files ==== | ||
More and more applications use //json files// as configuration files or as a mean to use text files to exchange data (through serialization/deserialization ). | More and more applications use //json files// as configuration files or as a mean to use text files to exchange data (through serialization/deserialization ). | ||
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* example script: ''/home/users/jypeter/CDAT/Progs/Devel/beaugendre/nc2json.py'' | * example script: ''/home/users/jypeter/CDAT/Progs/Devel/beaugendre/nc2json.py'' | ||
* A compact (not easy to read...) //json// file can be pretty-printed with\\ ''cat file.json | python -m json.tool | less'' | * A compact (not easy to read...) //json// file can be pretty-printed with\\ ''cat file.json | python -m json.tool | less'' | ||
+ | |||
+ | ==== LiPD files ==== | ||
+ | |||
+ | Resources for //Linked PaleoData//: | ||
+ | * [[http://linked.earth/projects/lipd/|LiPD]] | ||
+ | * [[https://doi.org/10.5194/cp-12-1093-2016|Technical note: The Linked Paleo Data framework – | ||
+ | a common tongue for paleoclimatology]] @ GMD | ||
+ | * [[https://github.com/nickmckay/LiPD-utilities|LiPD-utilities]] @ github | ||
+ | |||
+ | ==== BagIt files ==== | ||
+ | |||
+ | //BagIt//, a set of hierarchical file layout conventions for storage and transfer of arbitrary digital content. | ||
+ | |||
+ | * [[https://tools.ietf.org/html/draft-kunze-bagit-16|The BagIt File Packaging Format]] | ||
+ | * [[https://github.com/LibraryOfCongress/bagger|Bagger]] (BagIt GUI) | ||
+ | * [[https://github.com/LibraryOfCongress/bagit-python|bagit-python]] | ||
===== Pandas ===== | ===== Pandas ===== | ||
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* 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]] | ||
===== Some good coding tips ===== | ===== Some good coding tips ===== |