Source code for pyworkflow.gui.plotter

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
"""
This module implement the classes to create plots on xmipp.
"""

try:
    import matplotlib.pyplot as plt
except ImportError:
    plt = None

from pyworkflow.viewer import View

figureCounter = 0


[docs]class Plotter(View): """ Create different types of plots using the matplotlib library. """ backend = None
[docs] @classmethod def setBackend(cls, value): """ Possible values are: - TkAgg for Tkinter - Agg for non-interactive plots. """ plt.switch_backend(value) cls.backend = value
def __init__(self, x=1, y=1, mainTitle="", figsize=None, dpi=100, windowTitle="", fontsize=8, **kwargs): """ This Plotter class has some utilities to create a Matplotlib figure and add some plots to it. Params: x, y: number of rows and columns of the grid for plots. mainTitle: figure main title. figsize: the size of the figure, if None, it will be guessed from x and y dpi: resolution, 100 by default. windowTitle: title for the whole windows. """ figure = kwargs.get('figure', None) if figure == 'active': figure = plt.gcf() if self.backend is None: Plotter.setBackend('Agg') plt.style.use(kwargs.get('style', 'default')) if figure is None: self.tightLayoutOn = True if figsize is None: # Set some defaults values if x == 1 and y == 1: figsize = (6, 5) elif x == 1 and y == 2: figsize = (4, 6) elif x == 2 and y == 1: figsize = (6, 4) else: figsize = (8, 6) # Create grid # import matplotlib.gridspec as gridspec # self.grid = gridspec.GridSpec(x, y)#, height_ratios=[7,4]) # self.grid.update(left=0.15, right=0.95, hspace=0.25, wspace=0.4)#, top=0.8, bottom=0.2) global figureCounter figureCounter += 1 self.figure = plt.figure(figureCounter, figsize=figsize, dpi=dpi) # from matplotlib.figure import Figure # self.figure = Figure(figsize=figsize, dpi=dpi) if mainTitle: self.figure.suptitle(mainTitle, fontsize=fontsize + 4) if windowTitle: self.figure.canvas.manager.set_window_title(windowTitle) self.plot_count = 0 self.last_subplot = None self.plot_yformat = '%1.2e' else: self.figure = figure self.tightLayoutOn = False self.plot_count = 0 self.fontsize = fontsize self.plot_title_fontsize = fontsize + 4 self.plot_axis_fontsize = fontsize + 2 self.plot_text_fontsize = fontsize self.gridx = x self.gridy = y
[docs] def activate(self): """ Activate this figure. """ plt.figure(self.figure.number)
[docs] def getCanvas(self): return self.figure.canvas
[docs] def getFigure(self): return self.figure
[docs] def showLegend(self, labels, loc='best'): leg = self.last_subplot.legend(tuple(labels), loc=loc) for t in leg.get_texts(): t.set_fontsize(self.plot_axis_fontsize) # the legend text fontsize
[docs] def legend(self, loc='best', **kwargs): self.last_subplot.legend(loc=loc, **kwargs)
[docs] def createSubPlot(self, title, xlabel, ylabel, xpos=None, ypos=None, yformat=False, projection='rectilinear', subtitle=None ): """ Create a subplot in the figure. You should provide plot title, and x and y axis labels. yformat True specified the use of global self.plot_yformat Possible values for projection are: 'aitoff', 'hammer', 'lambert', 'mollweide', 'polar', 'rectilinear' """ if xpos is None: self.plot_count += 1 pos = self.plot_count else: pos = xpos + (ypos - 1) * self.gridx a = self.figure.add_subplot(self.gridx, self.gridy, pos, projection=projection) # a.get_label().set_fontsize(12) a.set_title(title, fontsize=self.plot_title_fontsize) if subtitle: self.figure.text(0.5, 0.015, subtitle, horizontalalignment="center") def setTicksFont(labels): for label in labels: label.set_fontsize(self.plot_text_fontsize) # Set fontsize if xlabel is not None: # Axis setup a.set_xlabel(xlabel, fontsize=self.plot_axis_fontsize) a.xaxis.get_label().set_fontsize(self.plot_axis_fontsize) setTicksFont(a.xaxis.get_ticklabels()) if ylabel is not None: a.set_ylabel(ylabel, fontsize=self.plot_axis_fontsize) if yformat: import matplotlib.ticker as ticker formatter = ticker.FormatStrFormatter(self.plot_yformat) a.yaxis.set_major_formatter(formatter) a.yaxis.get_label().set_fontsize(self.plot_axis_fontsize) setTicksFont(a.yaxis.get_ticklabels()) if xlabel is None and ylabel is None: a.axis('off') self.last_subplot = a self.plot = a.plot self.hist = a.hist self.scatterP = a.scatter self.bar = a.bar return a
[docs] def getLastSubPlot(self): return self.last_subplot
[docs] def createCanvas(self): a = self.figure.add_subplot(111, axisbg='g') a.set_axis_off() self.figure.set_facecolor('white') return a
[docs] def getColorBar(self, plot): self.tightLayoutOn = False cax = self.figure.add_axes([0.9, 0.1, 0.03, 0.8]) cbar = self.figure.colorbar(plot, cax=cax) cbar.set_ticks(cbar.get_ticks()) cbar.ax.invert_yaxis()
[docs] def tightLayout(self): if self.tightLayoutOn: self.activate() plt.tight_layout()
[docs] def show(self, interactive=True, block=False): self.tightLayout() plt.show(block=block)
[docs] def draw(self): self.tightLayout() self.getCanvas().draw()
[docs] def clear(self): self.getFigure().clear() self.plot_count = 0 self.last_subplot = None
[docs] def savefig(self, *args, **kwargs): self.tightLayout() self.figure.savefig(*args, **kwargs)
[docs] def isClosed(self): """ Return true if the figure have been closed. """ return not plt.fignum_exists(self.figure.number)
[docs] def close(self): """ Close current Plotter figure. """ plt.close(self.figure)
[docs]def getHexColorList(numberOfColors, colorName='jet'): """ Returns a list of hexColor """ from matplotlib import cm, colors colorsList = [] colorMap = cm.get_cmap(colorName) ratio = colorMap.N / numberOfColors for index in range(numberOfColors): colorPosition = int(round((index * ratio))) rgb = colorMap(colorPosition)[:3] rgbColor = colors.rgb2hex(rgb) colorsList.append(rgbColor) return colorsList