ipython extension for pyferret
Project description
ipython_ferretmagic
IPython notebook extension for ferret (a great software for Data Visualisation and Analysis from NOAA/PMEL).
Browse the demo notebooks from http://nbviewer.ipython.org/github/PBrockmann/ipython_ferretmagic/tree/master/notebooks
Combine ferret and ipython widgets and create interactive notebooks !
Browse a basic ferret tutorial using ferretmagic from: https://github.com/PBrockmann/C-CASCADES_notebooks/blob/master/ferretBasics.ipynb
Latest news
2022/08/25
- Fix to run with ipykernel 6.15.1
2020/06/03
- Update pip package to offer /outline control (now last version is 20200603 https://pypi.org/project/ferretmagic/)
2019/11/13
- Tested with python 3.7, pyferret 7.5.0
- Notebooks run with mybinder.org with 2 files (environment.yml and postBuild)
2018/12/10
- Tested with pyferret==7.44
2018/10/01
- Compatibility with python 3 with print command and base64 encoding
- Tested with pyferret==7.43, notebook==5.7.0, jupyter==1.0.0, ipython==5.8.0, ipywidgets==7.4.2
- Update pip package (now last version is 20181001 https://pypi.org/project/ferretmagic/)
2018/01/18
- a Docker image is available from https://hub.docker.com/r/pbrockmann/pyferret-7.3/
- pyferret 7.3 and ferretmagic extension can now be fully tested from binder (http://mybinder.readthedocs.io/en/latest) !
- Tested with pyferret==7.3, jupyter==4.4.0, ipython==5.5.0, ipywidgets==7.0.5
2017/03/17
- Tested with pyferret==7.1, jupyter==4.2.0, ipywidgets==6.0.0
2016/10/28
- Tested with pyferret==7.0, jupyter==4.2.0 and ipython==5.1.0
- Installation from pip
Installation
Install PyFerret following instructions from http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret It will set all directories needed to run pyferret (font, ppl, jnls, datasets, ...).
You can also install PyFerret as a conda package from https://anaconda.org/conda-forge/pyferret (no datasets distributed).
Then install the ferret magic extension (ferretmagic.py) by typing
pip install ferretmagic
Usage
In a Jupyter notebook with kernel python (previously named ipython), load the magics:
In [2]: %load_ext ferretmagic
Line magics
The %ferret_run
magic enables one-line execution of ferret command in the IPython interpreter or notebook:
In [3]: for i in [100,500,1000]:
....: %ferret_run -s 400,400 'plot sin(i[i=1:%(i)s]*0.1)' % locals()
Cell magics
Multi-line input can be entered with the %%ferret
cell magic:
In [4]: %%ferret
....: use levitus_climatology
....: shade temp[k=1] ! comments
- Control size of plot with --size, -s option.
- Create a local pdf at the same time with --pdf, -p option.
In [5]: %%ferret -s 400,300 -pdf myfig.pdf
....: shade temp[k=1]
Passing variables between Python and ferret
- Variables can be pushed from IPython into ferret with
%ferret_putdata
:
In [18]: %%ferret
....: use levitus_climatology
In [19]: %ferret_getdata tempdict = temp
....: Message: tempdict is now available in python as a dictionary containing the variable's metadata and data array.
In [20]: print tempdict.keys()
....: ['axis_coords', 'axis_types', 'data_unit', 'axis_units', 'title', 'axis_names', 'missing_value', 'data']
- Variables can be pulled from ferret into IPython with
%ferret_getdata
:
In [31]: import numpy as np
....: b = {}
....: b['name']='myvar'
....: b['name']='myvar'
....: x=np.linspace(-np.pi*4, np.pi*4, 500)
....: b['data']=np.sin(x)/x
....: b.keys()
Out[31]: ['data', 'name']
In [32]: %ferret_putdata --axis_pos (1,0,2,3,4,5) b
....: Message: b is now available in ferret as myvar
Explore notebook for examples.
Known issues and limitations
- Note that the pdf file produced by -p,--pdf option is not embedded in the notebook
- Limitations are the ones exposed from pyferret, the qualifier /pattern is not usable for example. Read http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret/known-issues
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