defdap.plotting module

class defdap.plotting.Plot(ax=None, axParams={}, fig=None, makeInteractive=False, title=None, **kwargs)

Bases: object

Class used for creating and manipulating plots.

checkInteractive()

Checks if current plot is interactive.

Raises:

Exception – If plot is not interactive

addEventHandler(eventName, eventHandler)

addAxes(loc, proj='2d')

Add axis to current plot

Parameters:

• loc – Location of axis.

• proj (str, {2d, 3d}) – 2D or 3D projection.

Return type:

matplotlib.Axes.axes

addButton(label, clickHandler, loc=(0.8, 0.0, 0.1, 0.07), **kwargs)

Add a button to the plot.

Parameters:

• label (str) – Label for the button.

• clickHandler – Click handler to assign.

• loc (list(float), len 4) – Left, bottom, width, height.

• kwargs – All other arguments passed to matplotlib.widgets.Button.

addTextBox(label, submitHandler=None, changeHandler=None, loc=(0.8, 0.0, 0.1, 0.07), **kwargs)

Add a text box to the plot.

Parameters:

• label (str) – Label for the button.

• submitHandler – Submit handler to assign.

• loc (list(float), len 4) – Left, bottom, width, height.

• kwargs – All other arguments passed to matplotlib.widgets.TextBox.

Return type:

matplotlotlib.widgets.TextBox

addText(ax, x, y, txt, **kwargs)

Add text to the plot.

Parameters:

• ax (matplotlib.axes.Axes) – Matplotlib axis to plot on.

• x (float) – x position.

• y (float) – y position.

• txt (str) – Text to write onto the plot.

• kwargs – All other arguments passed to matplotlib.pyplot.text().

addArrow(startEnd, persistent=False, clearPrev=True, label=None)

Add arrow to grain plot.

Parameters:

• startEnd (4-tuple) – Starting (x, y), Ending (x, y).

• persistent – If persistent, do not clear arrow with clearPrev.

• clearPrev – Clear all non-persistent arrows.

• label – Label to place near arrow.

setSize(size)

Set size of plot.

Parameters:

size (float, float) – Width and height in inches.

setTitle(txt)

Set title of plot.

Parameters:

txt (str) – Title to set.

lineSlice(event, plot, action=None)

Catch click and drag then draw an arrow.

Parameters:

• event – Click event.

• plot (defdap.plotting.Plot) – Plot to capture clicks from.

• action – Further action to perform.

Examples

To use, add a click and release event handler to your plot, pointing to this function:

>>> plot.addEventHandler('button_press_event',lambda e, p: lineSlice(e, p))
>>> plot.addEventHandler('button_release_event', lambda e, p: lineSlice(e, p))

property exists

clear()

Clear plot.

draw()

Draw plot

class defdap.plotting.MapPlot(callingMap, fig=None, ax=None, axParams={}, makeInteractive=False, **kwargs)

Bases: Plot

Class for creating a map plot.

addMap(mapData, vmin=None, vmax=None, cmap='viridis', **kwargs)

Add a map to a plot.

Parameters:

• mapData (numpy.ndarray) – Map data to plot.

• vmin (float) – Minimum value for the colour scale.

• vmax (float) – Maximum value for the colour scale.

• cmap – Colour map.

• kwargs – Other arguments are passed to matplotlib.pyplot.imshow().

Return type:

matplotlib.image.AxesImage

addColourBar(label, layer=0, **kwargs)

Add a colour bar to plot.

Parameters:

• label (str) – Label for the colour bar.

• layer (int) – Layer ID.

• kwargs – Other arguments are passed to matplotlib.pyplot.colorbar().

addScaleBar(scale=None)

Add scale bar to plot.

Parameters:

scale (float) – Size of a pixel in microns.

addGrainBoundaries(kind='pixel', boundaries=None, colour=None, dilate=False, draw=True, **kwargs)

Add grain boundaries to the plot.

Parameters:

• kind (str, {"pixel", "line"}) – Type of boundaries to plot, either a boundary image or a collection of line segments.

• boundaries (various, optional) – Boundaries to plot, either a boundary image or a list of pairs of coordinates representing the start and end of each boundary segment. If not provided the boundaries are loaded from the calling map.

• colour (various) –

  One of:

  • Colour of all boundaries as a string (only option pixel kind)

  • Colour of all boundaries as RGBA tuple

  • List of values to represent colour of each line relative to a norm and cmap

• dilate (bool) – If true, dilate the grain boundaries.

• kwargs – If line kind then other arguments are passed to matplotlib.collections.LineCollection().

Returns:

matplotlib.image.AxesImage if type is pixel

Return type:

Various

addGrainHighlights(grainIds, grainColours=None, alpha=None, newLayer=False)

Highlight grains in the plot.

Parameters:

• grainIds (list) – List of grain IDs to highlight.

• grainColours – Colour to use for grain highlight.

• alpha (float) – Alpha (transparency) to use for grain highlight.

• newLayer (bool) – If true, make a new layer in imgLayers.

Return type:

matplotlib.image.AxesImage

addGrainNumbers(fontsize=10, **kwargs)

Add grain numbers to a map.

Parameters:

• fontsize (float) – Font size.

• kwargs – Pass other arguments to matplotlib.pyplot.text().

addLegend(values, labels, layer=0, **kwargs)

Add a legend to a map.

Parameters:

• values (list) – Values to find colour patched for.

• labels (list) – Labels to assign to values.

• layer (int) – Image layer to generate legend for.

• kwargs – Pass other arguments to matplotlib.pyplot.legend().

addPoints(x, y, updateLayer=None, **kwargs)

Add points to plot.

Parameters:

• x (float) – x coordinate.

• y (float) – y coordinate.

• updateLayer (int, optional) – Layer to place points on

• kwargs – Other arguments passed to matplotlib.pyplot.scatter().

classmethod create(callingMap, mapData, fig=None, figParams={}, ax=None, axParams={}, plot=None, makeInteractive=False, plotColourBar=False, vmin=None, vmax=None, cmap=None, clabel='', plotGBs=False, dilateBoundaries=False, boundaryColour=None, plotScaleBar=False, scale=None, highlightGrains=None, highlightColours=None, highlightAlpha=None, **kwargs)

Create a plot for a map.

Parameters:

• callingMap (base.Map) – DIC or EBSD map which called this plot.

• mapData (numpy.ndarray) – Data to be plotted.

• fig (matplotlib.figure.Figure) – Matplotlib figure to plot on.

• figParams – Passed to defdap.plotting.Plot.

• ax (matplotlib.axes.Axes) – Matplotlib axis to plot on.

• axParams – Passed to defdap.plotting.Plot as axParams.

• plot (defdap.plotting.Plot) – If none, use current plot.

• makeInteractive – If true, make plot interactive

• plotColourBar (bool) – If true, plot a colour bar next to the map.

• vmin (float, optional) – Minimum value for the colour scale.

• vmax (float, optional) – Maximum value for the colour scale.

• cmap (str) – Colour map.

• clabel (str) – Label for the colour bar.

• plotGBs (bool) – If true, plot the grain boundaries on the map.

• dilateBoundaries (bool) – If true, dilate the grain boundaries.

• boundaryColour (str) – Colour to use for the grain boundaries.

• plotScaleBar (bool) – If true, plot a scale bar in the map.

• scale (float) – Size of pizel in microns.

• highlightGrains (list(int)) – List of grain IDs to highlight.

• highlightColours (str) – Colour to hightlight grains.

• highlightAlpha (float) – Alpha (transparency) by which to highlight grains.

• kwargs – All other arguments passed to defdap.plotting.MapPlot.addMap()

Return type:

defdap.plotting.MapPlot

class defdap.plotting.GrainPlot(callingGrain, fig=None, ax=None, axParams={}, makeInteractive=False, **kwargs)

Bases: Plot

Class for creating a map for a grain.

addMap(mapData, vmin=None, vmax=None, cmap='viridis', **kwargs)

Add a map to a grain plot.

Parameters:

• mapData (numpy.ndarray) – Grain data to plot

• vmin (float) – Minimum value for the colour scale.

• vmax (float) – Maximum value for the colour scale.

• cmap – Colour map to use.

• kwargs – Other arguments are passed to matplotlib.pyplot.imshow().

Return type:

matplotlib.image.AxesImage

addColourBar(label, layer=0, **kwargs)

Add colour bar to grain plot.

Parameters:

• label (str) – Label to add to colour bar.

• layer (int) – Layer on which to add colourbar.

• kwargs – Other arguments passed to matplotlib.pyplot.colorbar().

addScaleBar(scale=None)

Add scale bar to grain plot.

Parameters:

scale (float) – Size of pixel in micron.

addTraces(angles, colours, topOnly=False, pos=None, **kwargs)

Add slip trace angles to grain plot. Illustrated by lines crossing through central pivot point to create a circle.

Parameters:

• angles (list) – Angles of slip traces.

• colours (list) – Colours to plot.

• topOnly (bool, optional) – If true, plot only a semi-circle instead of a circle.

• pos (tuple) – Position of slip traces.

• kwargs – Other arguments are passed to matplotlib.pyplot.quiver()

addSlipTraces(topOnly=False, colours=None, pos=None, **kwargs)

Add slip traces to plot, based on the calling grain’s slip systems.

Parameters:

• colours (list) – Colours to plot.

• topOnly (bool, optional) – If true, plot only a semi-circle instead of a circle.

• pos (tuple) – Position of slip traces.

• kwargs – Other arguments are passed to matplotlib.pyplot.quiver()

addSlipBands(topOnly=False, grainMapData=None, angles=None, pos=None, thres=None, min_dist=None, **kwargs)

Add lines representing slip bands detected by Radon transform in calcSlipBands().

Parameters:

• topOnly (bool, optional) – If true, plot only a semi-circle instead of a circle.

• grainMapData – Map data to pass to calcSlipBands().

• angles (list(float), optional) – List of angles to plot, otherwise, use angles detected in calcSlipBands().

• pos (tuple) – Position in which to plot slip traces.

• thres (float) – Threshold to use in calcSlipBands().

• min_dist – Minimum angle between bands in calcSlipBands().

• kwargs – Other arguments are passed to matplotlib.pyplot.quiver().

classmethod create(callingGrain, mapData, fig=None, figParams={}, ax=None, axParams={}, plot=None, makeInteractive=False, plotColourBar=False, vmin=None, vmax=None, cmap=None, clabel='', plotScaleBar=False, scale=None, plotSlipTraces=False, plotSlipBands=False, **kwargs)

Create grain plot.

Parameters:

• callingGrain (base.Grain) – DIC or EBSD grain which called this plot.

• mapData – Data to be plotted.

• fig (matplotlib.figure.Figure) – Matplotlib figure to plot on.

• figParams – Passed to defdap.plotting.Plot.

• ax (matplotlib.axes.Axes) – Matplotlib axis to plot on.

• axParams – Passed to defdap.plotting.Plot as axParams.

• plot (defdap.plotting.Plot) – If none, use current plot.

• makeInteractive – If true, make plot interactive

• plotColourBar (bool) – If true, plot a colour bar next to the map.

• vmin (float) – Minimum value for the colour scale.

• vmax (float) – Maximum value for the colour scale.

• cmap – Colour map.

• clabel (str) – Label for the colour bar.

• plotScaleBar (bool) – If true, plot a scale bar in the map.

• scale (float) – Size of pizel in microns.

• plotSlipTraces (bool) – If true, plot slip traces with addSlipTraces()

• plotSlipBands (bool) – If true, plot slip traces with addSlipBands()

• kwargs – All other arguments passed to defdap.plotting.GrainPlot.addMap()

Return type:

defdap.plotting.GrainPlot

class defdap.plotting.PolePlot(plotType, crystalSym, projection=None, fig=None, ax=None, axParams={}, makeInteractive=False, **kwargs)

Bases: Plot

Class for creating an inverse pole figure plot.

addAxis()

Draw axes on the IPF based on crystal symmetry.

Raises:

NotImplementedError – If a crystal type other than ‘cubic’ or ‘hexagonal’ are selected.

addLine(startPoint, endPoint, plotSyms=False, res=100, **kwargs)

Draw lines on the IPF plot.

Parameters:

• startPoint (numpy.ndarray) – Start point in crystal coordinates (i.e. [0,0,1]).

• endPoint (numpy.ndarray) – End point in crystal coordinates, (i.e. [1,0,0]).

• plotSyms (bool, optional) – If true, plot all symmetrically equivelant points.

• res (int) – Number of points within each line to plot.

• kwargs – All other arguments are passed to matplotlib.pyplot.plot().

labelPoint(point, label, padX=0, padY=0, **kwargs)

Place a label near a coordinate in the pole plot.

Parameters:

• point (tuple) – (x, y) coordinate to place text.

• label (str) – Text to use in label.

• padX (int, optional) – Pad added to x coordinate.

• padY (int, optional) – Pad added to y coordinate.

• kwargs – Other arguments are passed to matplotlib.axes.Axes.text().

addPoints(alphaAng, betaAng, markerColour=None, markerSize=None, **kwargs)

Add a point to the pole plot.

Parameters:

• alphaAng – Inclination angle to plot.

• betaAng – Azimuthal angle (around z axis from x in anticlockwise as per ISO) to plot.

• markerColour (str or list(str), optional) – Colour of marker. If two specified, then the point will have two semicircles of different colour.

• markerSize (float) – Size of marker.

• kwargs – Other arguments are passed to matplotlib.axes.Axes.scatter().

Raises:

Exception – If more than two colours are specified

addColourBar(label, layer=0, **kwargs)

Add a colour bar to the pole plot.

Parameters:

• label (str) – Label to place next to colour bar.

• layer (int) – Layer number to add the colour bar to.

• kwargs – Other argument are passed to matplotlib.pyplot.colorbar().

addLegend(label='Grain area (μm$^2$)', number=6, layer=0, scaling=1, **kwargs)

Add a marker size legend to the pole plot.

Parameters:

• label (str) – Label to place next to legend.

• number – Number of markers to plot in legend.

• layer (int) – Layer number to add the colour bar to.

• scaling (float) – Scaling applied to the data.

• kwargs – Other argument are passed to matplotlib.pyplot.legend().

static stereoProject(*args)

Stereographic projection of pole direction or pair of polar angles.

Parameters:

args (numpy.ndarray, len 2 or 3) – 2 arguments for polar angles or 3 arguments for pole directions.

Returns:

x coordinate, y coordinate

Return type:

float, float

Raises:

Exception – If input array has incorrect length

static lambertProject(*args)

Lambert Projection of pole direction or pair of polar angles.

Parameters:

args (numpy.ndarray, len 2 or 3) – 2 arguments for polar angles or 3 arguments for pole directions.

Returns:

x coordinate, y coordinate

Return type:

float, float

Raises:

Exception – If input array has incorrect length

class defdap.plotting.HistPlot(plotType='scatter', axesType='linear', density=True, fig=None, ax=None, axParams={}, makeInteractive=False, **kwargs)

Bases: Plot

Class for creating a histogram.

addHist(histData, bins=100, range=None, line='o', label=None, **kwargs)

Add a histogram to the current plot

Parameters:

• histData (numpy.ndarray) – Data to be used in the histogram.

• bins (int) – Number of bins to use for histogram.

• range (tuple or None, optional) – The lower and upper range of the bins

• line (str, optional) – Marker or line type to be used.

• label (str, optional) – Label to use for data (used for legend).

• kwargs – Other arguments are passed to numpy.histogram()

addLegend(**kwargs)

Add legend to histogram.

Parameters:

kwargs – All arguments passed to matplotlib.axes.Axes.legend().

classmethod create(histData, fig=None, figParams={}, ax=None, axParams={}, plot=None, makeInteractive=False, plotType='scatter', axesType='linear', density=True, bins=10, range=None, line='o', label=None, **kwargs)

Create a histogram plot.

Parameters:

• histData (numpy.ndarray) – Data to be used in the histogram.

• fig (matplotlib.figure.Figure) – Matplotlib figure to plot on.

• figParams – Passed to defdap.plotting.Plot.

• ax (matplotlib.axes.Axes) – Matplotlib axis to plot on.

• axParams – Passed to defdap.plotting.Plot as axParams.

• plot (defdap.plotting.HistPlot) – Plot where histgram is created. If none, a new plot is created.

• makeInteractive (bool, optional) – If true, make plot interactive.

• plotType (str, {'scatter', 'bar', 'barfilled', 'step'}) – Type of plot to use

• axesType (str, {'linear', 'logx', 'logy', 'loglog', 'None'}, optional) – If ‘log’ is specified, logarithmic scale is used.

• density – If true, histogram is normalised such that the integral sums to 1.

• bins (int) – Number of bins to use for histogram.

• range (tuple or None, optional) – The lower and upper range of the bins

• line (str, optional) – Marker or line type to be used.

• label (str, optional) – Label to use for data (is used for legend).

• kwargs – Other arguments are passed to defdap.plotting.HistPlot.addHist()

Return type:

defdap.plotting.HistPlot

class defdap.plotting.CrystalPlot(fig=None, ax=None, axParams={}, makeInteractive=False, **kwargs)

Bases: Plot

Class for creating a 3D plot for plotting unit cells.

addVerts(verts, **kwargs)

Plots planes, defined by the vertices provided.

Parameters:

• verts (list) – List of vertices.

• kwargs – Other arguments are passed to matplotlib.collections.PolyCollection.