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other:python:jyp_steps [2018/02/26 14:19] – [Matplotlib] Added a ref to zorder jypeterother:python:jyp_steps [2018/08/07 16:26] – Added a projections section jypeter
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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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 ==== cdms2 ==== ==== cdms2 ====
  
-Summary: cdms2 can read/write netCDF files (and read //grads// dat+ctl files) and provides a higher level interface than netCDF4. Unfortunately, cdms2 is only available in the [[other:python:starting#uv-cdat|UV-CDAT distribution]], and distributions where somebody has installed some version of //cdat-lite//. 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#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.
  
 How to get started: How to get started:
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     - the tutorial is in French (soooorry!)     - the tutorial is in French (soooorry!)
     - 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://uv-cdat.llnl.gov/documentation/cdms/cdms.html|official cdms documentation]] +  - read the [[http://cdms.readthedocs.io/en/docstanya/index.html|official cdms documentation]] (link may change)
-  - ask questions and get answers on the [[http://uvcdat.askbot.com/questions/|UV-CDAT askbot]]+
  
  
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 Where: [[http://unidata.github.io/netcdf4-python/]] Where: [[http://unidata.github.io/netcdf4-python/]]
  
 +===== CDAT-related resources =====
 +
 +Some links, in case they can't be found easily on the [[https://uv-cdat.llnl.gov|UV-CDAT]] web site...
 +
 +  * [[https://uv-cdat.llnl.gov/tutorials.html|Tutorials in ipython notebooks]]
 +  * [[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/cdat-site/blob/master/eztemplate.md|EzTemplate Documentation]]
  
 ===== Matplotlib ===== ===== Matplotlib =====
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 ===== Graphics related resources ===== ===== Graphics related resources =====
  
 +  * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833|Ten Simple Rules for Better Figures]]
   * [[http://seaborn.pydata.org/|Seaborn]] is a library for making attractive and informative statistical graphics in Python, built on top of matplotlib   * [[http://seaborn.pydata.org/|Seaborn]] is a library for making attractive and informative statistical graphics in Python, built on top of matplotlib
     * 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]]
-  * [[http://colorbrewer2.org|ColorBrewer 2.0]] is a tool that can help you understand, and experiment with //sequential//, //diverging// and //qualitative// colormaps+  * Working with colors 
 +    * [[https://matplotlib.org/users/colormaps.html|Choosing colormaps]] 
 +    * [[https://matplotlib.org/cmocean/|Beautiful colormaps for oceanography: cmocean]] 
 +    * [[http://colorbrewer2.org|ColorBrewer 2.0]] is a tool that can help you understand, and experiment with //sequential//, //diverging// and //qualitative// colormaps
  
  
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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 =====
 +
 +  * [[https://ipyvolume.readthedocs.io/en/latest/|Ipyvolume]]
 +  * [[https://zulko.wordpress.com/2012/09/29/animate-your-3d-plots-with-pythons-matplotlib/|Animate your 3D plots with Python’s 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?]]
 +
 +=====  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 ).
 +
 +//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://realpython.com/python-json/|Working With JSON Data in Python]] tutorial
 +  * 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''
 +
 +==== 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 =====
other/python/jyp_steps.txt · Last modified: 2025/02/26 11:40 by jypeter
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