PlotMixin

class Stoner.plot.PlotMixin(*args, **kargs)[source]

Bases: object

A mixin class that works with Stoner.Core.DataFile to add additional plotting functionality.

Parameters:
ax

The current axes on the current figure.

Type:

matplotlib.Axes

axes

A list of all the axes on the current figure

Type:

list of matplotlib.Axes

fig

The current figure object being worked with

Type:

matplotlib.figure

fignum

The current figure’s number.

Type:

int

labels

List of axis labels as aternates to the column_headers

Type:

list of string

showfig

Controls whether plot functions return a copy of the figure (True), the DataFile (False) or Nothing (None)

Type:

bool or None

subplots

essentially the same as PlotMixin.axes but ensures that the list of subplots is synchronised to the number fo Axes.

Type:

list of matplotlib.Axes

template

A plot style template subclass or object that determines the format and appearance of plots.

Type:

Sonter.plot.formats.DefaultPlotStyle or instance

Attributes Summary

ax

Return the current axis number.

axes

Return the current axes object.

cmap

Get the current cmap.

fig

Get the current figure.

fignum

Return the current figure number.

labels

Return the labels for the plot columns.

multiple

no_fmt

positional_fmt

showfig

Return either the current figure or self or None.

subplots

Return the subplot instances.

template

Return the current plot template.

Methods Summary

add_column(column_data[, header, index])

Append a column of data or inserts a column to a datafile instance.

colormap_xyz([xcol, ycol, zcol])

Make a xyz plot that forces the use of plt.colormap.

contour_xyz([xcol, ycol, zcol, shape, xlim, ...])

Make a xyz plot that forces the use of plt.contour.

figure([figure, projection])

Set the figure used by Stoner.plot.PlotMixin.

griddata([xcol, ycol, zcol, ucol, shape, ...])

Convert xyz data onto a regular grid.

image_plot([xcol, ycol, zcol, shape, xlim, ylim])

Grid up the three columns of data and plot.

inset([parent, loc, width, height])

Add a new set of axes as an inset to the current plot.

legend(*args, **kargs)

Pass Through to stop attribute access over-riding a handy method.

plot(*args, **kargs)

Try to make an appropriate plot based on the defined column assignments.

plot_matrix([xvals, yvals, rectang, cmap, ...])

Plot a surface plot by assuming that the current dataset represents a regular matrix of points.

plot_voxels([xcol, ycol, zcol, ucol, cmap])

Make a volumetric plot of data arranged as x,y,z,u.

plot_xy([xcol, ycol, fmt, xerr, yerr])

Makesa simple X-Y plot of the specified data.

plot_xyuv([xcol, ycol, ucol, vcol, wcol])

Make an overlaid image and quiver plot.

plot_xyuvw([xcol, ycol, ucol, vcol, wcol])

Make an overlaid image and quiver plot.

plot_xyz([xcol, ycol, zcol, shape, xlim, ...])

Plot a surface plot based on rows of X,Y,Z data using matplotlib.pcolor().

plot_xyzuvw([xcol, ycol, zcol, ucol, vcol, wcol])

Plot a vector field plot based on rows of X,Y,Z (U,V,W) data using ,ayavi.

quiver_plot([xcol, ycol, ucol, vcol])

Make a 2D Quiver plot from the data.

subplot(*args, **kargs)

Pass throuygh for matplotlib.pyplot.subplot().

subplot2grid(*args, **kargs)

Provide a pass through to matplotlib.pyplot.subplot2grid().

x2()

Generate a new set of axes with a second x-scale.

y2()

Generate a new set of axes with a second y-scale.

Attributes Documentation

ax

Return the current axis number.

axes

Return the current axes object.

cmap

Get the current cmap.

fig

Get the current figure.

fignum

Return the current figure number.

labels

Return the labels for the plot columns.

multiple = 'common'
no_fmt = [<function errorfill>]
positional_fmt = [<function plot>, <function semilogx>, <function semilogy>, <function loglog>]
showfig

Return either the current figure or self or None.

The return value depends on whether the attribute is True or False or None.

subplots

Return the subplot instances.

template

Return the current plot template.

Methods Documentation

add_column(column_data, header=None, index=None, **kargs)[source]

Append a column of data or inserts a column to a datafile instance.

Parameters:

column_data (numpy.array or list or callable) – Data to append or insert or a callable function that will generate new data

Keyword Arguments:

  • column_header (string) – The text to set the column header to, if not supplied then defaults to ‘col#’

  • index (int or string) – The index (numeric or string) to insert (or replace) the data

  • func_args (dict) – If column_data is a callable object, then this argument can be used to supply a dictionary of function arguments to the callable object.

  • replace (bool) – Replace the data or insert the data (default)

  • setas (str) – Set the type of column (x,y,z data etc - see Stoner.Core.DataFile.setas)

Returns:

A DataFile instance with the additional column inserted.

Note

Like most DataFile methods, this method operates in-place in that it also modifies the original DataFile Instance as well as returning it.

colormap_xyz(xcol=None, ycol=None, zcol=None, **kargs)[source]

Make a xyz plot that forces the use of plt.colormap.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

Keyword Arguments:

  • shape (two-tuple) – Number of points along x and y in the grid - defaults to a square of sidelength = square root of the length of the data.

  • xlim (tuple) – The xlimits, defaults to automatically determined from data

  • ylim (tuple) – The ylimits, defaults to automatically determined from data

  • plotter (function) – Function to use to plot data. Defaults to plt.contour

  • colorbar (bool) – Draw the z-scale color bar beside the plot (True by default)

  • show_plot (bool) – Turn on interfactive plotting and show plot when drawn

  • save_filename (string or None) – If set to a string, save the plot with this filename

  • figure (integer or matplotlib.figure or boolean) – Controls which figure is used for the plot, or if a new figure is opened.

  • **kargs (dict) – Other arguments are passed on to the plotter.

Returns:

A matplotlib figure

contour_xyz(xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim=None, plotter=None, **kargs)[source]

Make a xyz plot that forces the use of plt.contour.

Args:
xcol (index):

Xcolumn index or label

ycol (index):

Y column index or label

zcol (index):

Z column index or label

Keyword Arguments:

  • shape (two-tuple) – Number of points along x and y in the grid - defaults to a square of sidelength = square root of the length of the data.

  • xlim (tuple) – The xlimits, defaults to automatically determined from data

  • ylim (tuple) – The ylimits, defaults to automatically determined from data

  • plotter (function) – Function to use to plot data. Defaults to plt.contour

  • show_plot (bool) – Turn on interfactive plotting and show plot when drawn

  • save_filename (string or None) – If set to a string, save the plot with this filename

  • figure (integer or matplotlib.figure or boolean) – Controls which figure is used for the plot, or if a new figure is opened.

  • **kargs (dict) – Other arguments are passed on to the plotter.

Returns:

A matplotlib figure

figure(figure=None, projection='rectilinear', **kargs)[source]

Set the figure used by Stoner.plot.PlotMixin.

Parameters:

figure (matplotlib.Figure or int) – Figure to switch to

Returns:

The current Stoner.plot.PlotMixin instance

griddata(xcol=None, ycol=None, zcol=None, ucol=None, shape=None, xlim=None, ylim=None, zlim=None, method='linear', **kargs)[source]

Convert xyz data onto a regular grid.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

Keyword Arguments:

  • ucol (index) – U (magnitude) column index or label

  • shape (two-tuple, three-ruple) – Number of points along x and y in the grid - defaults to a square of sidelength = square root of the length of the data.

  • xlim (tuple) – The xlimits

  • ylim (tuple) – The ylimits

  • zlim (tuple) – The ylimits

  • method (string) – Type of interpolation to use, default is linear

  • ReturnsL –

    (X,Y,Z) or (X,Y,Z,M):

    three two dimensional arrays of the coordinates of the interpolated data or 4 three diemensional arrays of the interpolated data

Notes

Depending on whether 3 or 4 columns of data can be identified, this method will produce data for a \(Z(X,Y)\) plot or a \(M(X,Y,Z)\) volumetric plot.

image_plot(xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim=None, **kargs)[source]

Grid up the three columns of data and plot.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

Keyword Arguments:

  • shape (two-tuple) – Number of points along x and y in the grid - defaults to a square of sidelength = square root of the length of the data.

  • xlim (tuple) – The xlimits, defaults to automatically determined from data

  • ylim (tuple) – The ylimits, defaults to automatically determined from data

  • xlabel (string) – X axes label. Default is None - guess from xvals or metadata

  • ylabel (string) – Y axes label, Default is None - guess from metadata

  • zlabel (string) – Z axis label, Default is None - guess from metadata

  • plotter (function) – Function to use to plot data. Defaults to plt.contour

  • show_plot (bool) – Turn on interfactive plotting and show plot when drawn

  • save_filename (string or None) – If set to a string, save the plot with this filename

  • figure (integer or matplotlib.figure or boolean) – Controls which figure is used for the plot, or if a new figure is opened.

  • **kargs (dict) – Other arguments are passed on to the plotter.

Returns:

A matplotlib figure

inset(parent=None, loc=None, width=0.35, height=0.3, **kargs)[source]

Add a new set of axes as an inset to the current plot.

Keyword Arguments:

  • parent (matplotlib axes) – Which set of axes to add inset to, defaults to the current set

  • loc (int or string) – Inset location - can be a string like top right or upper right or a number.

  • width,height (int,float or string) – the dimensions of the inset specified as a integer %, or floating point fraction of the parent axes, or as a string measurement.

  • kargs (dictionary) – all other keywords are passed through to inset_locator.inset_axes

Returns:

A new set of axes

legend(*args, **kargs)[source]

Pass Through to stop attribute access over-riding a handy method.

plot(*args, **kargs)[source]

Try to make an appropriate plot based on the defined column assignments.

The column assignments are examined to determine whether to plot and x,y plot or an x,y,z plot and whether to plot error bars (for an x,y plot). All keyword argume nts are passed through to the selected plotting routine.

plot_matrix(xvals=None, yvals=None, rectang=None, cmap=<matplotlib.colors.ListedColormap object>, show_plot=True, title='', xlabel=None, ylabel=None, zlabel=None, figure=None, plotter=None, **kwords)[source]

Plot a surface plot by assuming that the current dataset represents a regular matrix of points.

Parameters:

  • xvals (index, list or numpy.array) – Either a column index or name or a list or numpytarray of column values. The default (None) uses the first column of data

  • yvals (int or list) – Either a row index or a list or numpy array of row values. The default (None) uses the column_ headings interpreted as floats

  • rectang (tuple) – a tuple of either 2 or 4 elements representing either the origin (row,column) or size (origin, number of rows, number of columns) of data to be used for the z0data matrix

Keyword Arguments:

  • cmap (matplotlib colour map) – Surface colour map - defaults to the jet colour map

  • show_plot (bool) – True Turns on interactive plot control

  • title (string) – Optional parameter that specifies the plot title - otherwise the current DataFile filename is used

  • xlabel (string) – X axes label. Default is None - guess from xvals or metadata

  • ylabel (string) – Y axes label, Default is None - guess from metadata

  • zlabel (string) – Z axis label, Default is None - guess from metadata

  • figure (matplotlib figure) – Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False then a new figure is always used, otherwise it will default to using the last figure used by this DataFile object.

  • plotter (callable) – Optional argument that passes a plotting function into the routine. Sensible choices might be plt.plot (default), py.semilogy, plt.semilogx

  • kwords (dict) – A dictionary of other keyword arguments to pass into the plot function.

  • Returns – The matplotib figure with the data plotted

plot_voxels(xcol=None, ycol=None, zcol=None, ucol=None, cmap=None, **kargs)[source]

Make a volumetric plot of data arranged as x,y,z,u.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

  • ucol (index) – U column index or label

Keyword Arguments:

  • visible (callable) – A function f(x,y,z) that returns True if a voxcel is to be visible

  • cmap (colourmap) – A Matplotlib colour map to apply for the magnitude (u column) data.

Returns:

(matplotlib.Figure) – The figure window contacting the plot

Example

"""3D surface plot example."""
import numpy as np
import matplotlib.cm

from Stoner import Data

x, y, z = np.meshgrid(
    np.linspace(-2, 2, 21), np.linspace(-2, 2, 21), np.linspace(-2, 2, 21)
)
x = x.ravel()
y = y.ravel()
z = z.ravel()
u = np.sin(x * y * z)

p = Data(x, y, z, u, setas="xyzu", column_headers=["X", "Y", "Z"])

p.plot_voxels(cmap=matplotlib.cm.jet, visible=lambda x, y, z: x - y + z < 2.0)
p.set_box_aspect((1, 1, 1.0))  # Passing through to the current axes
p.title = "Voxel plot"

(png, hires.png, pdf)

../_images/voxels.png
plot_xy(xcol=None, ycol=None, fmt=None, xerr=None, yerr=None, **kargs)[source]

Makesa simple X-Y plot of the specified data.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

Keyword Arguments:

  • fmt (strong or sequence of strings) – Specifies the format for the plot - see matplotlib documentation for details

  • xerr,yerr (index) – C

  • plt.errorbar (olumns of data to get x and y errorbars from. Setting these turns the default plotter to) –

  • xlabel (string) – X axes label. Default is None - guess from xvals or metadata

  • ylabel (string) – Y axes label, Default is None - guess from metadata

  • title (string) – Optional parameter that specifies the plot title - otherwise the current DataFile filename is used

  • plotter (function) – Function to use to plot data. Defaults to plt.plot unless error bars are set

  • show_plot (bool) – Turn on interfactive plotting and show plot when drawn

  • save_filename (string or None) – If set to a string, save the plot with this filename

  • figure (integer or matplotlib.figure or boolean) – Controls which figure is used for the plot, or if a new figure is opened.

  • multiple (string) –

    how to handle multiple y-axes with a common x axis. Options are:

    • common single y-axis (default)

    • panels panels sharing common x axis

    • sub plots sub plots

    • y2 single axes with 2 y scales

  • **kargs (dict) – Other arguments are passed on to the plotter.

Returns:

A matplotlib.figure instance

plot_xyuv(xcol=None, ycol=None, ucol=None, vcol=None, wcol=None, **kargs)[source]

Make an overlaid image and quiver plot.

Args:

!c xcol (index):

Xcolumn index or label

ycol (index):

Y column index or label

zcol (index):

Z column index or label

ucol (index):

U column index or label

vcol (index):

V column index or label

wcol (index):

W column index or label

Keyword Arguments:
show_plot (bool):

True Turns on interactive plot control

title (string):

Optional parameter that specifies the plot title - otherwise the current DataFile filename is used

save_filename (string):

Filename used to save the plot

figure (matplotlib figure):

Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False then a new figure is always used, otherwise it will default to using the last figure used by this DataFile object.

no_quiver (bool):

Do not overlay quiver plot (in cases of dense meshes of points)

plotter (callable):

Optional argument that passes a plotting function into the routine. Default is a 3d surface plotter, but contour plot and pcolormesh also work.

**kargs (dict):

A dictionary of other keyword arguments to pass into the plot function.

plot_xyuvw(xcol=None, ycol=None, ucol=None, vcol=None, wcol=None, **kargs)

Make an overlaid image and quiver plot.

Args:

!c xcol (index):

Xcolumn index or label

ycol (index):

Y column index or label

zcol (index):

Z column index or label

ucol (index):

U column index or label

vcol (index):

V column index or label

wcol (index):

W column index or label

Keyword Arguments:
show_plot (bool):

True Turns on interactive plot control

title (string):

Optional parameter that specifies the plot title - otherwise the current DataFile filename is used

save_filename (string):

Filename used to save the plot

figure (matplotlib figure):

Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False then a new figure is always used, otherwise it will default to using the last figure used by this DataFile object.

no_quiver (bool):

Do not overlay quiver plot (in cases of dense meshes of points)

plotter (callable):

Optional argument that passes a plotting function into the routine. Default is a 3d surface plotter, but contour plot and pcolormesh also work.

**kargs (dict):

A dictionary of other keyword arguments to pass into the plot function.

plot_xyz(xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim=None, projection='3d', **kargs)[source]

Plot a surface plot based on rows of X,Y,Z data using matplotlib.pcolor().

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

Keyword Arguments:

  • shape (tuple) – Defines the shape of the surface (i.e. the number of X and Y value. If not provided or None, then the routine will attempt to calculate these from the data provided

  • xlim (tuple) – Defines the x-axis limits and grid of the data to be plotted

  • ylim (tuple) – Defines the Y-axis limits and grid of the data data to be plotted

  • cmap (matplotlib colour map) – Surface colour map - defaults to the jet colour map

  • show_plot (bool) – True Turns on interactive plot control

  • title (string) – Optional parameter that specifies the plot title - otherwise the current DataFile filename is used

  • save_filename (string) – Filename used to save the plot

  • figure (matplotlib figure) – Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False then a new figure is always used, otherwise it will default to using the last figure used by this DataFile object.

  • plotter (callable) – Optional argument that passes a plotting function into the routine. Default is a 3d surface plotter, but contour plot and pcolormesh also work.

  • projection (string or None) – Whether to use a 3D projection or regular 2D axes (default is 3D)

  • **kargs (dict) – A dictionary of other keyword arguments to pass into the plot function.

Returns:

A matplotlib.figure instance

plot_xyzuvw(xcol=None, ycol=None, zcol=None, ucol=None, vcol=None, wcol=None, **kargs)[source]

Plot a vector field plot based on rows of X,Y,Z (U,V,W) data using ,ayavi.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

  • ucol (index) – U column index or label

  • vcol (index) – V column i ndex or label

  • wcol (index) – W column index or label

Keyword Arguments:

  • colormap (string) – Vector field colour map - defaults to the jet colour map

  • colors (column index or numpy array) – Values used to map the colors of the resultant file.

  • mode (string) – glyph type, default is “cone”

  • scale_factor (float) – Scale-size of glyphs.

  • figure (mlab figure) – Controls what mlab figure to use. Can be an integer, or a mlab.figure or False. If False then a new figure is always used, otherwise it will default to using the last figure used by this DataFile object.

  • plotter (callable) – Optional argument that passes a plotting function into the routine. Sensible choices might be plt.plot (default), py.semilogy, plt.semilogx

  • kargs (dict) – A dictionary of other keyword arguments to pass into the plot function.

Returns:

A mayavi scene instance

quiver_plot(xcol=None, ycol=None, ucol=None, vcol=None, **kargs)[source]

Make a 2D Quiver plot from the data.

Parameters:

  • xcol (index) – Xcolumn index or label

  • ycol (index) – Y column index or label

  • zcol (index) – Z column index or label

  • ucol (index) – U column index or label

  • vcol (index) – V column i ndex or label

  • wcol (index) – W column index or label

Keyword Arguments:

  • xlabel (string) – X axes label. Default is None - guess from xvals or metadata

  • ylabel (string) – Y axes label, Default is None - guess from metadata

  • zlabel (string) – Z axis label, Default is None - guess from metadata

  • plotter (function) – Function to use to plot data. Defaults to plt.contour

  • headlength,headwidth,headaxislength (float) – Controls the size of the quiver heads

  • show_plot (bool) – Turn on interfactive plotting and show plot when drawn

  • save_filename (string or None) – If set to a string, save the plot with this filename

  • figure (integer or matplotlib.figure or boolean) – Controls which figure is used for the plot, or if a new figure is opened.

  • **kargs (dict) – Other arguments are passed on to the plotter.

Returns:

A matplotlib figure instance.

Keyword arguments are all passed through to matplotlib.plt.quiver().

subplot(*args, **kargs)[source]

Pass throuygh for matplotlib.pyplot.subplot().

Parameters:

  • rows (int) – If this is the only argument, then a three digit number representing the rows,columns,index arguments. If separate rows, column and index are provided, then this is the number of rows of sub-plots in one figure.

  • columns (int) – The number of columns of sub-plots in one figure.

  • index (int) – Index (1 based) of the current sub-plot.

Returns:

A matplotlib.Axes instance representing the current sub-plot

As well as passing through to the plyplot routine of the same name, this function maintains a list of the current sub-plot axes via the subplots attribute.

subplot2grid(*args, **kargs)[source]

Provide a pass through to matplotlib.pyplot.subplot2grid().

x2()[source]

Generate a new set of axes with a second x-scale.

Returns:

The new matplotlib.axes instance.

y2()[source]

Generate a new set of axes with a second y-scale.

Returns:

The new matplotlib.axes instance