geoist.vis package

Submodules

geoist.vis.giplt module

This module loads all functions from matplotlib.pyplot, adds new functions and overwrites some others (like contour(), pcolor(), etc).

Warning

This module will be removed in v0.6. We recommend the use of matplotlib.pyplot module directly. Some of the geoist specific functions will remain.

Grids

Grids are automatically reshaped and interpolated if desired or necessary.

2D objects

Interactive

Basemap (map projections)

Auxiliary

geoist.vis.giplt.basemap(area, projection, resolution='c')

Make a basemap to use when plotting with map projections.

Uses the matplotlib basemap toolkit.

Parameters:

  • area : list
    [west, east, south, north], i.e., the area of the data that is going to be plotted
  • projection : str
    The name of the projection you want to use. Choose from:
    • ‘ortho’: Orthographic
    • ‘geos’: Geostationary
    • ‘robin’: Robinson
    • ‘cass’: Cassini
    • ‘merc’: Mercator
    • ‘poly’: Polyconic
    • ‘lcc’: Lambert Conformal
    • ‘stere’: Stereographic
  • resolution : str
    The resolution for the coastlines. Can be ‘c’ for crude, ‘l’ for low, ‘i’ for intermediate, ‘h’ for high

Returns:

  • basemap : mpl_toolkits.basemap.Basemap
    The basemap
geoist.vis.giplt.contour(x, y, v, shape, levels, interp=False, extrapolate=False, color='k', label=None, clabel=True, style='solid', linewidth=1.0, basemap=None)

Make a contour plot of the data.

Parameters:

  • x, y : array
    Arrays with the x and y coordinates of the grid points. If the data is on a regular grid, then assume x varies first (ie, inner loop), then y.
  • v : array
    The scalar value assigned to the grid points.
  • shape : tuple = (ny, nx)
    Shape of the regular grid. If interpolation is not False, then will use shape to grid the data.
  • levels : int or list
    Number of contours to use or a list with the contour values.
  • interp : True or False
    Wether or not to interpolate before trying to plot. If data is not on regular grid, set to True!
  • extrapolate : True or False
    Wether or not to extrapolate the data when interp=True
  • color : str
    Color of the contour lines.
  • label : str
    String with the label of the contour that would show in a legend.
  • clabel : True or False
    Wether or not to print the numerical value of the contour lines
  • style : str
    The style of the contour lines. Can be 'dashed', 'solid' or 'mixed' (solid lines for positive contours and dashed for negative)
  • linewidth : float
    Width of the contour lines
  • basemap : mpl_toolkits.basemap.Basemap
    If not None, will use this basemap for plotting with a map projection (see basemap() for creating basemaps)

Returns:

  • levels : list
    List with the values of the contour levels
geoist.vis.giplt.contourf(x, y, v, shape, levels, interp=False, extrapolate=False, vmin=None, vmax=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, basemap=None)

Make a filled contour plot of the data.

Parameters:

  • x, y : array
    Arrays with the x and y coordinates of the grid points. If the data is on a regular grid, then assume x varies first (ie, inner loop), then y.
  • v : array
    The scalar value assigned to the grid points.
  • shape : tuple = (ny, nx)
    Shape of the regular grid. If interpolation is not False, then will use shape to grid the data.
  • levels : int or list
    Number of contours to use or a list with the contour values.
  • interp : True or False
    Wether or not to interpolate before trying to plot. If data is not on regular grid, set to True!
  • extrapolate : True or False
    Wether or not to extrapolate the data when interp=True
  • vmin, vmax
    Saturation values of the colorbar. If provided, will overwrite what is set by levels.
  • cmap : colormap
    Color map to be used. (see pyplot.cm module)
  • basemap : mpl_toolkits.basemap.Basemap
    If not None, will use this basemap for plotting with a map projection (see basemap() for creating basemaps)

Returns:

  • levels : list
    List with the values of the contour levels
geoist.vis.giplt.draw_coastlines(basemap, linewidth=1, style='solid')

Draw the coastlines using the given basemap.

Parameters:

  • basemap : mpl_toolkits.basemap.Basemap
    The basemap used for plotting (see basemap())
  • linewidth : float
    The width of the lines
  • style : str
    The style of the lines. Can be: ‘solid’, ‘dashed’, ‘dashdot’ or ‘dotted’
geoist.vis.giplt.draw_countries(basemap, linewidth=1, style='dashed')

Draw the country borders using the given basemap.

Parameters:

  • basemap : mpl_toolkits.basemap.Basemap
    The basemap used for plotting (see basemap())
  • linewidth : float
    The width of the lines
  • style : str
    The style of the lines. Can be: ‘solid’, ‘dashed’, ‘dashdot’ or ‘dotted’
geoist.vis.giplt.draw_geolines(area, dlon, dlat, basemap, linewidth=1)

Draw the parallels and meridians on a basemap plot.

Parameters:

  • area : list
    [west, east, south, north], i.e., the area where the lines will be plotted
  • dlon, dlat : float
    The spacing between the lines in the longitude and latitude directions, respectively (in decimal degrees)
  • basemap : mpl_toolkits.basemap.Basemap
    The basemap used for plotting (see basemap())
  • linewidth : float
    The width of the lines
geoist.vis.giplt.draw_layers(area, axes, style='-', marker='o', color='k', width=2)

Draw series of horizontal layers by clicking with the mouse.

The y-axis is assumed to be depth, the x-axis is the physical property of each layer.

INSTRUCTIONS:

  • Click to make a new layer;
  • Press ‘e’ to erase the last layer;
  • Close the figure window to finish;

Parameters:

  • area : list = [x1, x2, y1, y2]

    Borders of the area containing the polygon

  • axes : matplotlib Axes

    The figure to use for drawing the polygon. To get an Axes instace, just do:

    from matplotlib import pyplot
axes = pyplot.figure().add_subplot(1,1,1)

    You can plot things to axes before calling this function so that they’ll appear on the background.

  • style : str

    Line style (as in matplotlib.pyplot.plot)

  • marker : str

    Style of the point markers (as in matplotlib.pyplot.plot)

  • color : str

    Line color (as in matplotlib.pyplot.plot)

  • width : float

    The line width (as in matplotlib.pyplot.plot)

Returns:

  • layers : list = [thickness, values]

    • thickness : list
      The thickness of each layer, in order of increasing depth
    • values : list
      The physical property value of each layer, in the same order
geoist.vis.giplt.draw_polygon(area, axes, style='-', marker='o', color='k', width=2, alpha=0.5, xy2ne=False)

Draw a polygon by clicking with the mouse.

INSTRUCTIONS:

  • Left click to pick the edges of the polygon;
  • Draw edges CLOCKWISE;
  • Press ‘e’ to erase the last edge;
  • Right click to close the polygon;
  • Close the figure window to finish;

Parameters:

  • area : list = [x1, x2, y1, y2]

    Borders of the area containing the polygon

  • axes : matplotlib Axes

    The figure to use for drawing the polygon. To get an Axes instace, just do:

    from matplotlib import pyplot
axes = pyplot.figure().add_subplot(1,1,1)

    You can plot things to axes before calling this function so that they’ll appear on the background.

  • style : str

    Line style (as in matplotlib.pyplot.plot)

  • marker : str

    Style of the point markers (as in matplotlib.pyplot.plot)

  • color : str

    Line color (as in matplotlib.pyplot.plot)

  • width : float

    The line width (as in matplotlib.pyplot.plot)

  • alpha : float

    Transparency of the fill of the polygon. 0 for transparent, 1 for opaque (fills the polygon once done drawing)

  • xy2ne : True or False

    If True, will exchange the x and y axis so that x points north. Use this when drawing on a map viewed from above. If the y-axis of the plot is supposed to be z (depth), then use xy2ne=False.

Returns:

  • edges : list of lists
    List of [x, y] pairs with the edges of the polygon
geoist.vis.giplt.layers(thickness, values, style='-k', z0=0.0, linewidth=1, label=None, **kwargs)

Plot a series of layers and values associated to each layer.

Parameters:

  • thickness : list
    The thickness of each layer in order of increasing depth
  • values : list
    The value associated with each layer in order of increasing depth
  • style : str
    String with the color and line style (as in matplotlib.pyplot.plot)
  • z0 : float
    The depth of the top of the first layer
  • linewidth : float
    Line width
  • label : str
    label associated with the square.

Returns:

  • axes : matplitlib.axes

    The axes element of the plot

geoist.vis.giplt.m2km(axis=None)

Convert the x and y tick labels from meters to kilometers.

Parameters:

  • axis : matplotlib axis instance
    The plot.

Tip

Use geoist.vis.gca() to get the current axis. Or the value returned by geoist.vis.subplot or matplotlib.pyplot.subplot.

geoist.vis.giplt.paths(pts1, pts2, style='-k', linewidth=1, label=None)

Plot paths between the two sets of points.

Parameters:

  • pts1 : list of lists
    List of (x, y) pairs with the coordinates of the points
  • pts2 : list of lists
    List of (x, y) pairs with the coordinates of the points
  • style : str
    String with the color and line style (as in matplotlib.pyplot.plot)
  • linewidth : float
    The width of the lines representing the paths
  • label : str
    If not None, then the string that will show in the legend
geoist.vis.giplt.pcolor(x, y, v, shape, interp=False, extrapolate=False, cmap=<matplotlib.colors.LinearSegmentedColormap object>, vmin=None, vmax=None, basemap=None)

Make a pseudo-color plot of the data.

Parameters:

  • x, y : array
    Arrays with the x and y coordinates of the grid points. If the data is on a regular grid, then assume x varies first (ie, inner loop), then y.
  • v : array
    The scalar value assigned to the grid points.
  • shape : tuple = (ny, nx)
    Shape of the regular grid. If interpolation is not False, then will use shape to grid the data.
  • interp : True or False
    Wether or not to interpolate before trying to plot. If data is not on regular grid, set to True!
  • extrapolate : True or False
    Wether or not to extrapolate the data when interp=True
  • cmap : colormap
    Color map to be used. (see pyplot.cm module)
  • vmin, vmax
    Saturation values of the colorbar.
  • basemap : mpl_toolkits.basemap.Basemap
    If not None, will use this basemap for plotting with a map projection (see basemap() for creating basemaps)

Returns:

  • axes : matplitlib.axes

    The axes element of the plot

geoist.vis.giplt.pick_points(area, axes, marker='o', color='k', size=8, xy2ne=False)

Get the coordinates of points by clicking with the mouse.

INSTRUCTIONS:

  • Left click to pick the points;
  • Press ‘e’ to erase the last point picked;
  • Close the figure window to finish;

Parameters:

  • area : list = [x1, x2, y1, y2]

    Borders of the area containing the points

  • axes : matplotlib Axes

    The figure to use for drawing the polygon. To get an Axes instace, just do:

    from matplotlib import pyplot
axes = pyplot.figure().add_subplot(1,1,1)

    You can plot things to axes before calling this function so that they’ll appear on the background.

  • marker : str

    Style of the point markers (as in matplotlib.pyplot.plot)

  • color : str

    Line color (as in matplotlib.pyplot.plot)

  • size : float

    Marker size (as in matplotlib.pyplot.plot)

  • xy2ne : True or False

    If True, will exchange the x and y axis so that x points north. Use this when drawing on a map viewed from above. If the y-axis of the plot is supposed to be z (depth), then use xy2ne=False.

Returns:

  • points : list of lists
    List of [x, y] coordinates of the points
geoist.vis.giplt.points(pts, style='.k', size=10, label=None, xy2ne=False)

Plot a list of points.

Parameters:

  • pts : list of lists
    List of [x, y] pairs with the coordinates of the points
  • style : str
    String with the color and line style (as in matplotlib.pyplot.plot)
  • size : int
    Size of the plotted points
  • label : str
    If not None, then the string that will show in the legend
  • xy2ne : True or False
    If True, will exchange the x and y axis so that the x coordinates of the polygon are north. Use this when drawing on a map viewed from above. If the y-axis of the plot is supposed to be z (depth), then use xy2ne=False.

Returns:

  • axes : matplitlib.axes

    The axes element of the plot

geoist.vis.giplt.polygon(polygon, style='-k', linewidth=1, fill=None, alpha=1.0, label=None, xy2ne=False, linealpha=1.0)

Plot a polygon.

Parameters:

  • polygon : geoist.inversion.geometry.Polygon

    The polygon

  • style : str

    Color and line style string (as in matplotlib.pyplot.plot)

  • linewidth : float

    Line width

  • fill : str

    A color string used to fill the polygon. If None, the polygon is not filled

  • alpha : float

    Transparency of the fill (1 >= alpha >= 0). 0 is transparent and 1 is opaque

  • linealpha : float

    Transparency of the line (1 >= alpha >= 0). 0 is transparent and 1 is opaque

  • label : str

    String with the label identifying the polygon in the legend

  • xy2ne : True or False

    If True, will exchange the x and y axis so that the x coordinates of the polygon are north. Use this when drawing on a map viewed from above. If the y-axis of the plot is supposed to be z (depth), then use xy2ne=False.

Returns:

  • lines : matplotlib Line object
    Line corresponding to the polygon plotted
geoist.vis.giplt.seismic_image(section, dt, ranges=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, aspect=None, vmin=None, vmax=None)

Plot a seismic section (numpy 2D array matrix) as an image.

Parameters:

  • section : 2D array
    matrix of traces (first dimension time, second dimension traces)
  • dt : float
    sample rate in seconds
  • ranges : (x1, x2)
    min and max horizontal coordinate values (default trace number)
  • cmap : colormap
    color map to be used. (see pyplot.cm module)
  • aspect : float
    matplotlib imshow aspect parameter, ratio between axes
  • vmin, vmax : float
    min and max values for imshow
geoist.vis.giplt.seismic_wiggle(section, dt, ranges=None, scale=1.0, color='k', normalize=False)

Plot a seismic section (numpy 2D array matrix) as wiggles.

Parameters:

  • section : 2D array
    matrix of traces (first dimension time, second dimension traces)
  • dt : float
    sample rate in seconds
  • ranges : (x1, x2)
    min and max horizontal values (default trace number)
  • scale : float
    scale factor multiplied by the section values before plotting
  • color : tuple of strings
    Color for filling the wiggle, positive and negative lobes.
  • normalize :
    True to normalizes all trace in the section using global max/min data will be in the range (-0.5, 0.5) zero centered

Warning

Slow for more than 200 traces, in this case decimate your data or use seismic_image.

geoist.vis.giplt.set_area(area)

Set the area of a Matplolib plot using xlim and ylim.

Parameters:

  • area : list = [x1, x2, y1, y2]
    Coordinates of the top right and bottom left corners of the area
geoist.vis.giplt.square(area, style='-k', linewidth=1, fill=None, alpha=1.0, label=None, xy2ne=False)

Plot a square.

Parameters:

  • area : list = [x1, x2, y1, y2]
    Borders of the square
  • style : str
    String with the color and line style (as in matplotlib.pyplot.plot)
  • linewidth : float
    Line width
  • fill : str
    A color string used to fill the square. If None, the square is not filled
  • alpha : float
    Transparency of the fill (1 >= alpha >= 0). 0 is transparent and 1 is opaque
  • label : str
    label associated with the square.
  • xy2ne : True or False
    If True, will exchange the x and y axis so that the x coordinates of the polygon are north. Use this when drawing on a map viewed from above. If the y-axis of the plot is supposed to be z (depth), then use xy2ne=False.

Returns:

  • axes : matplitlib.axes

    The axes element of the plot

geoist.vis.giplt.squaremesh(mesh, prop, cmap=<matplotlib.colors.LinearSegmentedColormap object>, vmin=None, vmax=None)

Make a pseudo-color plot of a mesh of squares

Parameters:

  • mesh : geoist.mesher.SquareMesh or compatible

    The mesh (a compatible mesh must implement the methods get_xs and get_ys)

  • prop : str

    The physical property of the squares to use as the color scale.

  • cmap : colormap

    Color map to be used. (see pyplot.cm module)

  • vmin, vmax : float

    Saturation values of the colorbar.

Returns:

  • axes : matplitlib.axes

    The axes element of the plot

Module contents

Plotting utilities.

Wrappers to facilitate common plotting tasks using powerful third-party libraries.