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Colormap choice guidelines in documentation - based on talk at SciPy 2014 #3301

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working on guide for choosing colormaps. Have overview section and st…
kthyng Jul 12, 2014
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added colormaps guide to beginner guide
kthyng Jul 12, 2014
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some more text to colormaps
kthyng Jul 18, 2014
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kthyng Jul 24, 2014
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working on guide for choosing colormaps. Have overview section and st… 
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.. _colormaps:

******************
Choosing Colormaps
******************


Overview
========

The idea behind choosing a good colormap is to find a good representation in 3D colorspace for your data set. The best colormap for any given data set depends on many things including:

- Whether representing form or metric data (link to C. Ware paper and explain more)
- Your knowledge of the data set (*i.e.*, is there a critical value from which the other values deviate?)
- If there is an intuitive color scheme for the parameter you are plotting
- If there is a standard in the field the audience may be expecting

For many applications, a perceptual colormap is the best choice |---| one in which equal steps in data are perceived as equal steps in the color space. Researchers have found that the human brain perceives changes in the lightness parameter as changes in the data much better than, for example, changes in hue. Therefore, colormaps which have monotonically increasing lightness through the colormap will be better interpreted by the viewer.

Color can be represented in 3D space in various ways. One way to represent color is using CIELAB (CITE). In CIELAB, color space is represented by lightness, :math:`L^*`; red-green, :math:`a`; and yellow-blue, :math:`b`. The lightness parameter :math:`L^*` can then be used to learn more about how the matplotlib colormaps will be perceived by viewers.


Sequential and diverging colormaps
==================================

STUFF


Lightness of matplotlib colormaps
=================================

.. plot:: users/plotting/colormaps/lightness.py

For the Sequential plots, the lightness value increases monotonically through the colormaps. This is good. Some of the :math:`L^*` values in the colormaps span from 0 to 100 (binary and the other grayscale), and others start around :math:`L^*=20`.

Some of the :math:`L^*` values from the Sequential2 plots are monotonically increasing, but some, such as cool and spring, plateau or even go both up and down in :math:`L^*` space. Data that is being represented in a region of the colormap that is at a plateau will lead to a perception of the data all having the same value (SHOW EXAMPLE?).

For the Diverging maps, we want to have monotonically increasing :math:`L^*` values up to a maximum, which should be close to :math:`L^*=100`, followed by monotonically decreasing :math:`L^*` values. We are looking for approximately equal minimum :math:`L^*` values at opposite ends of the colormap. Additionally, we might prefer a diverging colormap which has a rounded instead of pointed peak for retaining some spread of values around the critical point. By these measures, BrBG and RdBu are good options. coolwarm is a good option, but it doesn't span a wide range of :math:`L^*` values (see grayscale section).


:math:`L^*` function
====================

WHAT FUNCTION FOR :math:`L^*`?


References
==========

- C. Ware
- M. Niccoli
- IBM paper
- More

.. :mod:`matplotlib.pyplot` is a collection of command style functions
.. that make matplotlib work like MATLAB.
.. Each ``pyplot`` function makes
.. some change to a figure: eg, create a figure, create a plotting area
.. in a figure, plot some lines in a plotting area, decorate the plot
.. with labels, etc.... :mod:`matplotlib.pyplot` is stateful, in that it
.. keeps track of the current figure and plotting area, and the plotting
.. functions are directed to the current axes

.. .. plot:: pyplots/pyplot_simple.py
.. :include-source:

.. You may be wondering why the x-axis ranges from 0-3 and the y-axis
.. from 1-4. If you provide a single list or array to the
.. :func:`~matplotlib.pyplot.plot` command, matplotlib assumes it is a
.. sequence of y values, and automatically generates the x values for
.. you. Since python ranges start with 0, the default x vector has the
.. same length as y but starts with 0. Hence the x data are
.. ``[0,1,2,3]``.

.. :func:`~matplotlib.pyplot.plot` is a versatile command, and will take
.. an arbitrary number of arguments. For example, to plot x versus y,
.. you can issue the command::

.. plt.plot([1,2,3,4], [1,4,9,16])

.. For every x, y pair of arguments, there is an optional third argument
.. which is the format string that indicates the color and line type of
.. the plot. The letters and symbols of the format string are from
.. MATLAB, and you concatenate a color string with a line style string.
.. The default format string is 'b-', which is a solid blue line. For
.. example, to plot the above with red circles, you would issue

.. .. plot:: pyplots/pyplot_formatstr.py
.. :include-source:

.. See the :func:`~matplotlib.pyplot.plot` documentation for a complete
.. list of line styles and format strings. The
.. :func:`~matplotlib.pyplot.axis` command in the example above takes a
.. list of ``[xmin, xmax, ymin, ymax]`` and specifies the viewport of the
.. axes.

.. If matplotlib were limited to working with lists, it would be fairly
.. useless for numeric processing. Generally, you will use `numpy
.. <http://numpy.scipy.org>`_ arrays. In fact, all sequences are
.. converted to numpy arrays internally. The example below illustrates a
.. plotting several lines with different format styles in one command
.. using arrays.

.. .. plot:: pyplots/pyplot_three.py
.. :include-source:

.. .. _controlling-line-properties:

.. Controlling line properties
.. ===========================

.. Lines have many attributes that you can set: linewidth, dash style,
.. antialiased, etc; see :class:`matplotlib.lines.Line2D`. There are
.. several ways to set line properties

.. * Use keyword args::

.. plt.plot(x, y, linewidth=2.0)


.. * Use the setter methods of the ``Line2D`` instance. ``plot`` returns a list
.. of lines; eg ``line1, line2 = plot(x1,y1,x2,y2)``. Below I have only
.. one line so it is a list of length 1. I use tuple unpacking in the
.. ``line, = plot(x, y, 'o')`` to get the first element of the list::

.. line, = plt.plot(x, y, '-')
.. line.set_antialiased(False) # turn off antialising

.. * Use the :func:`~matplotlib.pyplot.setp` command. The example below
.. uses a MATLAB-style command to set multiple properties
.. on a list of lines. ``setp`` works transparently with a list of objects
.. or a single object. You can either use python keyword arguments or
.. MATLAB-style string/value pairs::

.. lines = plt.plot(x1, y1, x2, y2)
.. # use keyword args
.. plt.setp(lines, color='r', linewidth=2.0)
.. # or MATLAB style string value pairs
.. plt.setp(lines, 'color', 'r', 'linewidth', 2.0)


.. Here are the available :class:`~matplotlib.lines.Line2D` properties.

.. ====================== ==================================================
.. Property Value Type
.. ====================== ==================================================
.. alpha float
.. animated [True | False]
.. antialiased or aa [True | False]
.. clip_box a matplotlib.transform.Bbox instance
.. clip_on [True | False]
.. clip_path a Path instance and a Transform instance, a Patch
.. color or c any matplotlib color
.. contains the hit testing function
.. dash_capstyle [``'butt'`` | ``'round'`` | ``'projecting'``]
.. dash_joinstyle [``'miter'`` | ``'round'`` | ``'bevel'``]
.. dashes sequence of on/off ink in points
.. data (np.array xdata, np.array ydata)
.. figure a matplotlib.figure.Figure instance
.. label any string
.. linestyle or ls [ ``'-'`` | ``'--'`` | ``'-.'`` | ``':'`` | ``'steps'`` | ...]
.. linewidth or lw float value in points
.. lod [True | False]
.. marker [ ``'+'`` | ``','`` | ``'.'`` | ``'1'`` | ``'2'`` | ``'3'`` | ``'4'`` ]
.. markeredgecolor or mec any matplotlib color
.. markeredgewidth or mew float value in points
.. markerfacecolor or mfc any matplotlib color
.. markersize or ms float
.. markevery [ None | integer | (startind, stride) ]
.. picker used in interactive line selection
.. pickradius the line pick selection radius
.. solid_capstyle [``'butt'`` | ``'round'`` | ``'projecting'``]
.. solid_joinstyle [``'miter'`` | ``'round'`` | ``'bevel'``]
.. transform a matplotlib.transforms.Transform instance
.. visible [True | False]
.. xdata np.array
.. ydata np.array
.. zorder any number
.. ====================== ==================================================

.. To get a list of settable line properties, call the
.. :func:`~matplotlib.pyplot.setp` function with a line or lines
.. as argument

.. .. sourcecode:: ipython

.. In [69]: lines = plt.plot([1,2,3])

.. In [70]: plt.setp(lines)
.. alpha: float
.. animated: [True | False]
.. antialiased or aa: [True | False]
.. ...snip

.. .. _multiple-figs-axes:

.. Working with multiple figures and axes
.. ======================================


.. MATLAB, and :mod:`~matplotlib.pyplot`, have the concept of the current
.. figure and the current axes. All plotting commands apply to the
.. current axes. The function :func:`~matplotlib.pyplot.gca` returns the
.. current axes (a :class:`matplotlib.axes.Axes` instance), and
.. :func:`~matplotlib.pyplot.gcf` returns the current figure
.. (:class:`matplotlib.figure.Figure` instance). Normally, you don't have
.. to worry about this, because it is all taken care of behind the
.. scenes. Below is a script to create two subplots.

.. .. plot:: pyplots/pyplot_two_subplots.py
.. :include-source:

.. The :func:`~matplotlib.pyplot.figure` command here is optional because
.. ``figure(1)`` will be created by default, just as a ``subplot(111)``
.. will be created by default if you don't manually specify an axes. The
.. :func:`~matplotlib.pyplot.subplot` command specifies ``numrows,
.. numcols, fignum`` where ``fignum`` ranges from 1 to
.. ``numrows*numcols``. The commas in the ``subplot`` command are
.. optional if ``numrows*numcols<10``. So ``subplot(211)`` is identical
.. to ``subplot(2,1,1)``. You can create an arbitrary number of subplots
.. and axes. If you want to place an axes manually, ie, not on a
.. rectangular grid, use the :func:`~matplotlib.pyplot.axes` command,
.. which allows you to specify the location as ``axes([left, bottom,
.. width, height])`` where all values are in fractional (0 to 1)
.. coordinates. See :ref:`pylab_examples-axes_demo` for an example of
.. placing axes manually and :ref:`pylab_examples-subplots_demo` for an
.. example with lots-o-subplots.


.. You can create multiple figures by using multiple
.. :func:`~matplotlib.pyplot.figure` calls with an increasing figure
.. number. Of course, each figure can contain as many axes and subplots
.. as your heart desires::

.. import matplotlib.pyplot as plt
.. plt.figure(1) # the first figure
.. plt.subplot(211) # the first subplot in the first figure
.. plt.plot([1,2,3])
.. plt.subplot(212) # the second subplot in the first figure
.. plt.plot([4,5,6])


.. plt.figure(2) # a second figure
.. plt.plot([4,5,6]) # creates a subplot(111) by default

.. plt.figure(1) # figure 1 current; subplot(212) still current
.. plt.subplot(211) # make subplot(211) in figure1 current
.. plt.title('Easy as 1,2,3') # subplot 211 title

.. You can clear the current figure with :func:`~matplotlib.pyplot.clf`
.. and the current axes with :func:`~matplotlib.pyplot.cla`. If you find
.. this statefulness, annoying, don't despair, this is just a thin
.. stateful wrapper around an object oriented API, which you can use
.. instead (see :ref:`artist-tutorial`)

.. If you are making a long sequence of figures, you need to be aware of one
.. more thing: the memory required for a figure is not completely
.. released until the figure is explicitly closed with
.. :func:`~matplotlib.pyplot.close`. Deleting all references to the
.. figure, and/or using the window manager to kill the window in which
.. the figure appears on the screen, is not enough, because pyplot
.. maintains internal references until :func:`~matplotlib.pyplot.close`
.. is called.

.. .. _working-with-text:

.. Working with text
.. =================

.. The :func:`~matplotlib.pyplot.text` command can be used to add text in
.. an arbitrary location, and the :func:`~matplotlib.pyplot.xlabel`,
.. :func:`~matplotlib.pyplot.ylabel` and :func:`~matplotlib.pyplot.title`
.. are used to add text in the indicated locations (see :ref:`text-intro`
.. for a more detailed example)

.. .. plot:: pyplots/pyplot_text.py
.. :include-source:


.. All of the :func:`~matplotlib.pyplot.text` commands return an
.. :class:`matplotlib.text.Text` instance. Just as with with lines
.. above, you can customize the properties by passing keyword arguments
.. into the text functions or using :func:`~matplotlib.pyplot.setp`::

.. t = plt.xlabel('my data', fontsize=14, color='red')

.. These properties are covered in more detail in :ref:`text-properties`.


.. Using mathematical expressions in text
.. --------------------------------------

.. matplotlib accepts TeX equation expressions in any text expression.
.. For example to write the expression :math:`\sigma_i=15` in the title,
.. you can write a TeX expression surrounded by dollar signs::

.. plt.title(r'$\sigma_i=15$')

.. The ``r`` preceding the title string is important -- it signifies
.. that the string is a *raw* string and not to treat backslashes as
.. python escapes. matplotlib has a built-in TeX expression parser and
.. layout engine, and ships its own math fonts -- for details see
.. :ref:`mathtext-tutorial`. Thus you can use mathematical text across platforms
.. without requiring a TeX installation. For those who have LaTeX and
.. dvipng installed, you can also use LaTeX to format your text and
.. incorporate the output directly into your display figures or saved
.. postscript -- see :ref:`usetex-tutorial`.


.. Annotating text
.. ---------------

.. The uses of the basic :func:`~matplotlib.pyplot.text` command above
.. place text at an arbitrary position on the Axes. A common use case of
.. text is to annotate some feature of the plot, and the
.. :func:`~matplotlib.pyplot.annotate` method provides helper
.. functionality to make annotations easy. In an annotation, there are
.. two points to consider: the location being annotated represented by
.. the argument ``xy`` and the location of the text ``xytext``. Both of
.. these arguments are ``(x,y)`` tuples.

.. .. plot:: pyplots/pyplot_annotate.py
.. :include-source:

.. In this basic example, both the ``xy`` (arrow tip) and ``xytext``
.. locations (text location) are in data coordinates. There are a
.. variety of other coordinate systems one can choose -- see
.. :ref:`annotations-tutorial` and :ref:`plotting-guide-annotation` for
.. details. More examples can be found in
.. :ref:`pylab_examples-annotation_demo`.