def __init__(self, masterWindow, style=None, scheme=None):
self.masterWindow = masterWindow
self.legend = False
plotArea = masterWindow.ui.plotArea
#create the plotting canvas and its toolbar and add them
tfig = Figure()
tfig.set_facecolor('white')
self.canvas = FigureCanvasQTAgg(tfig)
self.navbar = AstonNavBar(self.canvas, masterWindow)
plotArea.addWidget(self.navbar)
plotArea.addWidget(self.canvas)
#TODO this next line is the slowest in this module
#self.plt = tfig.add_subplot(111, frameon=False)
self.plt = tfig.add_axes((0.05, 0.1, 0.9, 0.85), frame_on=False)
self.plt.xaxis.set_ticks_position('none')
self.plt.yaxis.set_ticks_position('none')
self.patches = []
self.cb = None
#TODO: find a way to make the axes fill the figure properly
#tfig.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
#tfig.tight_layout(pad=2)
self.canvas.setFocusPolicy(Qt.ClickFocus)
self.canvas.mpl_connect('button_press_event', self.mousedown)
self.canvas.mpl_connect('button_release_event', self.mouseup)
self.canvas.mpl_connect('scroll_event', self.mousescroll)
self.highlight = None
class Plotter(object):
def __init__(self, masterWindow, style=None, scheme=None):
self.masterWindow = masterWindow
self.legend = False
plotArea = masterWindow.ui.plotArea
#create the plotting canvas and its toolbar and add them
tfig = Figure()
tfig.set_facecolor('white')
self.canvas = FigureCanvasQTAgg(tfig)
self.navbar = AstonNavBar(self.canvas, masterWindow)
plotArea.addWidget(self.navbar)
plotArea.addWidget(self.canvas)
#TODO this next line is the slowest in this module
#self.plt = tfig.add_subplot(111, frameon=False)
self.plt = tfig.add_axes((0.05, 0.1, 0.9, 0.85), frame_on=False)
self.plt.xaxis.set_ticks_position('none')
self.plt.yaxis.set_ticks_position('none')
self.patches = []
self.cb = None
#TODO: find a way to make the axes fill the figure properly
#tfig.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
#tfig.tight_layout(pad=2)
self.canvas.setFocusPolicy(Qt.ClickFocus)
self.canvas.mpl_connect('button_press_event', self.mousedown)
self.canvas.mpl_connect('button_release_event', self.mouseup)
self.canvas.mpl_connect('scroll_event', self.mousescroll)
self.highlight = None
def availStyles(self):
l_ord = ['default', 'scaled', 'stacked', 'scaled stacked', '2d']
return [self._styles[s] for s in l_ord]
def plot_data(self, plots, update_bounds=True):
if not update_bounds:
bnds = self.plt.get_xlim(), self.plt.get_ylim()
# clean up anything on the graph already
self.plt.cla()
if self.cb is not None:
#TODO: this should work? need way to update size of mappable axes
#self.plt.figure.delaxes(self.cb.ax)
#self.cb.mappable.axes.autoscale()
#self.cb = None
#the next two lines used to work?
self.plt.figure.delaxes(self.cb.ax)
self.cb = None
tfig = self.plt.figure
tfig.clf()
self.plt = tfig.add_subplot(111, frameon=False)
self.plt.xaxis.set_ticks_position('none')
self.plt.yaxis.set_ticks_position('none')
self.cb = None
self.plt.figure.subplots_adjust(left=0.05, right=0.95)
self.patches = []
#plot all of the datafiles
if len(plots) == 0:
self.canvas.draw()
return
## make up a factor to separate plots by
#if 'stacked' in self._style:
# fts = datafils[0].trace(datafiles[0].info['traces'].split(',')[0])
# sc_factor = (max(fts.data[:, 0]) - min(fts.data[:, 0])) / 5.
## count the number of traces that will be displayed
#trs = sum(1 for x in datafiles for _ in x.info['traces'].split(','))
nplots = len(plots)
if nplots < 6:
alpha = 0.75 - nplots * 0.1
else:
alpha = 0.15
#FIXME: read this from the menu
colors = get_cmap('Spectral')
#TODO: determine the number of axes to use
#TODO: should be filtering out invalid plots before here
for pnum, plot in enumerate(plots):
if plot.style == 'auto':
#FIXME: style for auto needs to be drawn from somewhere
style = 'solid'
else:
style = plot.style
if plot.color == 'auto':
if style in {'heatmap', 'colors'}:
c = colors
elif nplots > 7:
c = colors(int(pnum % 7) / 6.0, 1)
elif nplots == 1:
c = colors(0, 1)
else:
c = colors(int(pnum % nplots) / float(nplots - 1), 1)
else:
c = plot.color
#FIXME: auto style could be "color strips"
if style == 'heatmap':
plot.plot(style=style, color=c, ax=self.plt)
if self.legend:
self.cb = self.plt.figure.colorbar(self.plt.images[0])
elif style == 'colors':
plot.plot(style=style, color=c, ax=self.plt)
else:
plot.plot(style=style, color=c, ax=self.plt)
# plot the peaks
for pk in plot.peaks:
if pk.color == 'auto':
pc = c
else:
pc = pk.color
if pk.vis:
pk_pa = pk.plot(ax=self.plt, color=pc, alpha=alpha)
self.patches.append(pk_pa)
#add a legend and make it pretty
if self.legend:
leg = self.plt.legend(frameon=False)
clrs = [i.get_color() for i in leg.get_lines()]
for i, j in enumerate(clrs):
leg.get_texts()[i].set_color(j)
for i in leg.get_lines():
i.set_linestyle('')
# if 'scaled' in self._style:
# #TODO: fails at negative chromatograms
# trace -= min(trace)
# trace /= max(trace)
# trace *= 100
# if 'stacked' in self._style:
# trace += tnum * sc_factor
# # stretch out the color spectrum if there are under 7
# if trs > 7:
# c = self._color(int(tnum % 7) / 6.0, 1)
# elif trs == 1:
# c = self._color(0, 1)
# else:
# c = self._color(int(tnum % trs) / float(trs - 1), 1)
# ls = self._linestyle[int(np.floor((tnum % 28) / 7))]
# nm = dt.info['name'].strip('_') + ' ' + ts.ions[0]
# self.plt.plot(ts.times, trace, color=c, \
# ls=ls, lw=1.2, label=nm)
# tnum += 1
## for heatmap plots
#if self.legend:
# self.cb = self.plt.figure.colorbar(img)
#update the view bounds in the navbar's history
if update_bounds:
self.navbar._views.clear()
self.navbar._positions.clear()
self.navbar.push_current()
else:
self.plt.set_xlim(bnds[0])
self.plt.set_ylim(bnds[1])
#if type(self.highlight) == Polygon:
# self.plt.add_patch(self.highlight)
#elif self.highlight is not None:
# self.plt.add_line(self.highlight)
# plot events on the bottom of the graph
#evts = []
#if self.masterWindow.ui.actionGraphFxnCollection.isChecked():
# evts += datafiles[0].events('fxn')
#if self.masterWindow.ui.actionGraphFIA.isChecked():
# evts += datafiles[0].events('fia')
#if self.masterWindow.ui.actionGraphIRMS.isChecked():
# evts += datafiles[0].events('refgas')
#if self.masterWindow.ui.actionGraph_Peaks_Found.isChecked():
# dt = self.masterWindow.obj_tab.active_file()
# tss = dt.active_plots(n=0)
# pevts = self.masterWindow.find_peaks(tss, dt)
# for i, p in enumerate(pevts[0]):
# p[2]['name'] = 'P' + str(i + 1)
# evts += pevts[0]
#if evts != []:
# # TODO: save the text and lines to delete later?
# # TODO: make this prettier
# trans = self.plt.get_xaxis_transform()
# transText = offset_copy(trans, fig=self.plt.figure, \
# x=3, units='points')
# for ev in evts:
# t0, t1, ta = ev[0], ev[1], (ev[1] + ev[0]) / 2.
# self.plt.vlines(t1, 0, 0.1, color='0.75', transform=trans)
# self.plt.vlines(t0, 0, 0.1, transform=trans)
# self.plt.text(ta, 0, ev[2]['name'], \
# ha='center', transform=transText)
# draw the y axis as log
if self.masterWindow.ui.actionGraphLogYAxis.isChecked():
self.plt.set_yscale('log')
#draw grid lines
if self.masterWindow.ui.actionGraphGrid.isChecked():
self.plt.grid(c='black', ls='-', alpha=0.05)
#update the canvas
self.canvas.draw()
def redraw(self):
self.canvas.draw()
def clear_highlight(self):
#try to remove the line from the previous spectrum (if it exists)
if self.highlight is not None:
if self.highlight in self.plt.lines:
self.plt.lines.remove(self.highlight)
if self.highlight in self.plt.patches:
self.plt.patches.remove(self.highlight)
self.redraw()
self.highlight = None
def draw_highlight(self, x1, x2, color='black', linestyle='-'):
"""
Draw the line that indicates where the spectrum came from.
"""
self.clear_highlight()
#draw a new line
if x1 is None:
self.highlight = None
elif x1 == x2:
self.highlight = self.plt.axvline(x1, color=color, ls=linestyle)
else:
self.highlight = self.plt.axvspan(x1, x2, alpha=0.25, color=color)
#redraw the canvas
self.canvas.draw()
def draw_highlight_peak(self, pk, color='white'):
coords = pk.as_poly().T
self.highlight = self.plt.fill(coords[0], coords[1], \
fc=color, alpha=0.5)[0]
#redraw the canvas
self.canvas.draw()
def mousedown(self, event):
if event.button == 3 and self.navbar.mode in ['peak', 'spectrum']:
event.button = 1
self.navbar.mode += '_pan'
self.navbar.press_pan(event)
def mouseup(self, event):
if event.button == 3 and self.navbar.mode[-4:] == '_pan':
event.button = 1
self.navbar.release_pan(event)
self.navbar.mode = self.navbar.mode[:-4]
def mousescroll(self, event):
if event.xdata is None or event.ydata is None:
return
xmin, xmax = self.plt.get_xlim()
ymin, ymax = self.plt.get_ylim()
if event.button == 'up': # zoom in
self.plt.set_xlim(event.xdata - (event.xdata - xmin) / 2.,
event.xdata + (xmax - event.xdata) / 2.)
self.plt.set_ylim(event.ydata - (event.ydata - ymin) / 2.,
event.ydata + (ymax - event.ydata) / 2.)
elif event.button == 'down': # zoom out
xmin = event.xdata - 2 * (event.xdata - xmin)
xmax = event.xdata + 2 * (xmax - event.xdata)
xmin = max(xmin, self.navbar._views.home()[0][0])
xmax = min(xmax, self.navbar._views.home()[0][1])
ymin = event.ydata - 2 * (event.ydata - ymin)
ymax = event.ydata + 2 * (ymax - event.ydata)
ymin = max(ymin, self.navbar._views.home()[0][2])
ymax = min(ymax, self.navbar._views.home()[0][3])
self.plt.axis([xmin, xmax, ymin, ymax])
self.redraw()