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Merge pull request #110 from csiro-coasts/transect
Add `emsarray.transect` module
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‎continuous-integration/environment.yaml‎

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dependencies:
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- geos ~=3.10.2
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- udunits2 >=2.2.25

‎continuous-integration/requirements.txt‎

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# pyproj
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# requests
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cftime==1.6.2
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# via netcdf4
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# via
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# cfunits
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# netcdf4
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cfunits==3.3.6
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# via emsarray (setup.cfg)
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chardet==5.2.0
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# via tox
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charset-normalizer==3.2.0
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# bottleneck
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# cartopy
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# cftime
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# cfunits
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# contourpy
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# dask
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# emsarray (setup.cfg)
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# via
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# bokeh
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# cartopy
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# cfunits
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# dask
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# distributed
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# emsarray (setup.cfg)

‎docs/_static/images/kgari-path.png‎

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‎docs/_static/images/kgari-transect.png‎

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‎docs/api/index.rst‎

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utils.rst
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tutorial.rst
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plot.rst
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transect.rst
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types.rst
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exceptions.rst

‎docs/api/transect.rst‎

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.. module:: emsarray.transect
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=================
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emsarray.transect
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=================
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.. currentmodule:: emsarray.transect
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Plot transects through your dataset.
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Transects are vertical slices along some path through your dataset.
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Examples
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--------
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.. list-table::
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* - :ref:`example-kgari-transect`
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.. image:: /_static/images/kgari-transect.png
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:width: 200
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:class: no-scaled-link
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.. autofunction:: plot
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.. autoclass:: Transect
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:members:
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.. autoclass:: TransectPoint
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.. autoclass:: TransectSegment

docs/examples.rst renamed to docs/examples/index.rst

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If you would prefer to download the examples and explore them locally,
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they are available on Github at
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`csiro-coasts/emsarray-notebooks <https://github.com/csiro-coasts/emsarray-notebooks>`_.
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Gallery
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=======
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.. toctree::
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:glob:
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:hidden:
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*
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.. list-table::
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* - :ref:`example-kgari-transect`
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.. image:: /_static/images/kgari-transect.png
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:width: 200
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:class: no-scaled-link
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‎docs/examples/kgari-transect.py‎

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import emsarray
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import shapely
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from emsarray import plot, transect
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from matplotlib import pyplot
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dataset_url = 'https://dapds00.nci.org.au/thredds/dodsC/fx3/model_data/gbr4_bgc_GBR4_H2p0_B2p0_Chyd_Dcrt.ncml'
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dataset = emsarray.open_dataset(dataset_url).isel(time=-1)
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dataset = dataset.ems.select_variables(['botz', 'temp'])
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line = shapely.LineString([
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[152.9768944, -25.4827962],
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[152.9701996, -25.4420345],
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[152.9727745, -25.3967620],
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[152.9623032, -25.3517828],
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[152.9401588, -25.3103560],
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[152.9173279, -25.2538563],
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[152.8962135, -25.1942238],
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[152.8692627, -25.0706729],
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[152.8623962, -24.9698750],
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[152.8472900, -24.8415806],
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[152.8308105, -24.6470172],
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[152.7607727, -24.3521012],
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[152.6392365, -24.1906056],
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[152.4792480, -24.0615124],
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])
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landmarks = [
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('Round Island', shapely.Point(152.9262543, -25.2878719)),
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('Lady Elliot Island', shapely.Point(152.7145958, -24.1129146)),
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]
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# Plot the transect
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figure = transect.plot(
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dataset, line, dataset['temp'],
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figsize=(7.9, 3),
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bathymetry=dataset['botz'],
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landmarks=landmarks)
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figure.savefig('kgari-transect.png')
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# Plot the path of the transect
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figure = pyplot.figure(figsize=(5, 5), dpi=100)
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axes = figure.add_subplot(projection=dataset.ems.data_crs)
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axes.set_aspect(aspect='equal', adjustable='datalim')
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axes.set_title('Transect path')
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axes.add_collection(dataset.ems.make_poly_collection(
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dataset['botz'], cmap='Blues_r', edgecolor='face',
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linewidth=0.5, zorder=0))
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plot.add_coast(axes, zorder=1)
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plot.add_gridlines(axes)
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plot.add_landmarks(axes, landmarks)
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axes = figure.axes[0]
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axes.set_extent(plot.bounds_to_extent(line.envelope.buffer(0.2).bounds))
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axes.plot(*line.coords.xy, zorder=2)
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figure.savefig('kgari-path.png')
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pyplot.show(block=True)

‎docs/examples/kgari-transect.rst‎

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.. _example-kgari-transect:
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====================
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K'gari transect plot
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====================
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The following is a :mod:`transect <emsarray.transect>` path
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starting in the Great Sandy Strait near K'gari,
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heading roughly North out to deeper waters:
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.. image:: /_static/images/kgari-path.png
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:alt: Transect of GBR1 dataset along Great Sandy Strait and past K'gari
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showing the water temperature.
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:align: center
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The temperature along this transect can be plotted:
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.. image:: /_static/images/kgari-transect.png
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:alt: Transect of GBR1 dataset along Great Sandy Strait and past K'gari
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showing the water temperature.
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Code
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====
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:download:`Download kgari-transect.py example <kgari-transect.py>`.
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.. literalinclude:: kgari-transect.py
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:language: python
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‎docs/getting-started/installing.rst‎

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Dependencies
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============
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``emsarray`` depends on
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`cartopy <https://scitools.org.uk/cartopy/docs/latest/installing.html>`_
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for plotting.
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This depends on the non-Python ``geos`` library.
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Most of the dependencies of ``emsarray`` are installable via pip,
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however some dependencies require non-Python components
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that must be installed using some other method.
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``emsarray`` uses the following libraries that can not be installed via pip:
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* ``geos``, via
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`cartopy <https://scitools.org.uk/cartopy/docs/latest/installing.html>`_.
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This is used for plotting
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* ``udunits2``, via
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* `cfunits <https://ncas-cms.github.io/cfunits/installation.html>`.
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This is used for plotting.
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These can be installed via your package manager or via ``conda``.
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Installing from ``conda`` is the recommended approach
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as these packages are often more up-to-date than the system packages
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and it guarantees that compatible versions of ``geos`` is installed.
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and it guarantees that compatible versions are installed.
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.. code-block:: shell-session
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$ conda create -n my-env
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$ conda activate my-env
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$ conda install cartopy
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$ conda install cartopy cfunits
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If ``geos`` is installed using your system package manager,
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and ``cartopy`` is installed via pip,

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