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#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
#------------------------------------------------------------------------------------------
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#6, rue Jules Horowitz
#38042 Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
#aoun[at]ill.fr
#
#This library is free software; you can redistribute it and/or
#modify it under the terms of the GNU Lesser General Public
#License as published by the Free Software Foundation; either
#version 2.1 of the License, or (at your option) any later version.
#
#This library 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
#Lesser General Public License for more details.
#
#You should have received a copy of the GNU Lesser General Public
#License along with this library; if not, write to the Free Software
#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
'''
Created on Apr 10, 2015
:author: Gael Goret, Bachir Aoun, Eric C. Pellegrini
'''
import collections
import numpy
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg, NavigationToolbar2WxAgg
from matplotlib.figure import Figure
from matplotlib.colors import LogNorm, Normalize
import wx
from MDANSE.Core.Error import Error
from MDANSE.Externals.magnitude import magnitude
from MDANSE.GUI.Plugins.PlotterSettings import ImageSettingsDialog
from MDANSE.GUI.Plugins.PlotterTicker import ScaledFormatter, ScaledLocator
NORMALIZER = {'log': LogNorm(), 'auto' : Normalize()}
class CrossSlicer(object):
def __init__(self, parent, canvas, dialog, hplot, vplot, fig, color_index, hlegend, vlegend):
self.related_plot = parent
self.canvas = canvas
self.dialog = dialog
self.hplot = hplot
self.vplot = vplot
self.fig = fig
self.color_index =color_index
self.hlegend = hlegend
self.vlegend = vlegend
class Plotter2DError(Error):
pass
class Plotter2D(wx.Panel):
type = 'image'
def __init__(self, parent, data = None):
wx.Panel.__init__(self, parent, wx.ID_ANY)
self.setting = None
### Initialize variables ###
self.parent = parent
self.figure = Figure(figsize=(5,4), dpi=None)
self.axes = self.figure.add_axes( (10,10,10,10), frameon=True, facecolor='b')
self.canvas = FigureCanvasWxAgg( self, wx.ID_ANY, self.figure )
self.toolbar = NavigationToolbar2WxAgg(self.canvas)
self.ax = None
self.color_bar = None
self.slice_checkbox = wx.CheckBox(self, id=wx.ID_ANY, label="Slicing mode")
self.annotation = wx.StaticText(self, label='x : , y : , data[x,y] :' , style=wx.ALIGN_CENTER_VERTICAL)
hsizer = wx.BoxSizer()
hsizer.Add(self.toolbar, 0, flag=wx.ALL|wx.EXPAND)
hsizer.Add(self.slice_checkbox, 0, flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL )
### sizer ###
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.canvas, 1, flag=wx.EXPAND)
self.sizer.Add(hsizer, 0, flag=wx.EXPAND)
self.SetSizer(self.sizer)
### set bindings ###
self.Bind(wx.EVT_CHECKBOX, self.slice, id = self.slice_checkbox.GetId())
# Slice attributes
self.unique = False
self.slice_event_id = None
self.slice_coords = []
self.slice_widget = []
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self.cross_slice_canvas = None
self.cross_slice_dialog = None
self.h_cross_slice_plot = None
self.v_cross_slice_plot = None
self.cross_slice_fig = None
self.cross_slice_color_index = -1
self.h_cross_slice_legend = []
self.v_cross_slice_legend = []
self.color_list = collections.OrderedDict([['blue','b'],['green','g'],['red','r'],['cyan','c'],['magenta','m'],['yellow','y'],['black','k']])
self.Xmin = 0
self.Ymin = 0
self.Xmax = 0
self.Ymax = 0
self.Xunit = None
self.Yunit = None
self.Xinit_unit = None
self.Yinit_unit = None
self.Xaxis = []
self.Yaxis = []
self.Xaxis_label = ''
self.Yaxis_label = ''
self.Xticks = []
self.Yticks = []
self.Xlabel = ''
self.Ylabel = ''
self.aspect = 'equal'
self.interpolation = 'nearest'
self.normType = 'none'
hsizer = wx.BoxSizer()
hsizer.Add(self.toolbar, 0, flag=wx.ALL|wx.EXPAND)
hsizer.Add(self.slice_checkbox, 0, flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL )
hsizer.AddSpacer(25)
hsizer.Add(self.annotation, 0, flag=wx.ALIGN_CENTER_VERTICAL)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.canvas, 1, flag=wx.EXPAND)
self.sizer.Add(hsizer, 0, flag=wx.EXPAND)
self.SetSizer(self.sizer)
### set bindings ###
self.Bind(wx.EVT_CHECKBOX, self.slice, id = self.slice_checkbox.GetId())
self.menu_event_id = self.canvas.mpl_connect('button_press_event', self.on_click)
self.on_motion_id = self.canvas.mpl_connect('motion_notify_event', self.on_motion)
#### sizer automatically fitting window size ####
self.toolbar.Realize()
self.SetSizeHints(600,500,1000,1000) # SetSizeHints(minW, minH, maxW, maxH)
self.sizer.Fit(self)
self.Show(True)
@property
def dataproxy(self):
return self.parent.dataproxy
@property
def fmt_Xunit(self):
if not self.Xunit:
return ''
else:
return ' (' + self.Xunit + ')'
@property
def fmt_Yunit(self):
if not self.Yunit:
return ''
else:
return ' (' + self.Yunit + ')'
def on_click(self, event = None):
if event.button != 3:
return
popupMenu = wx.Menu()
settings = popupMenu.Append(wx.ID_ANY, "Settings")
popupMenu.Bind(wx.EVT_MENU, self.image_setting_dialog, settings)
popupMenu.AppendSeparator()
export = popupMenu.Append(wx.ID_ANY, "Export data")
popupMenu.Bind(wx.EVT_MENU, self.export_data, export)
self.canvas.ReleaseMouse()
wx.CallAfter(self.PopupMenu, popupMenu)
def on_motion(self, event):
if event.inaxes:
x = event.xdata
y = event.ydata
if self.Xmin <= x and x <= self.Xmax and self.Ymin <= y and y <= self.Ymax:
try:
dx = (self.Xmax - self.Xmin)/float(self.data.shape[1])
dy = (self.Ymax - self.Ymin)/float(self.data.shape[0])
X = numpy.floor((x - self.Xmin)/dx)
Y = numpy.floor((y - self.Ymin)/dy)
i = self.data[Y, X]
self.annotation.SetLabel('x : %g (%g), y : %g (%g), data[x,y] : %g'%(X,x*self.Xunit_conversion_factor,Y,y*self.Yunit_conversion_factor,i))
except:
self.annotation.SetLabel('') # rarely useful except outside figure
else:
self.annotation.SetLabel('')
def export_data(self, event = None):
header = '# Data : %s\n# First row : %s (%s)\n# First column : %s (%s)\n' % (self.varname,self.Xlabel,self.Xunit,self.Ylabel,self.Yunit)
output_fname = self.get_output_filename()
x = numpy.concatenate(([0],self.Xaxis))*self.Xunit_conversion_factor
data = numpy.vstack((x,numpy.hstack((self.Yaxis[:,numpy.newaxis]*self.Yunit_conversion_factor,self.data))))
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if output_fname:
with open(output_fname, 'w') as f:
f.write(header)
numpy.savetxt(f, data, fmt='%12.4e', delimiter=" ")
f.close()
def get_output_filename(self):
path = ''
dlg = wx.FileDialog(self, "Save As", '', '', "All Files|*.*", wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
dlg.Destroy()
return path
def slice(self, event):
if not event.IsChecked():
self.canvas.mpl_disconnect(self.slice_event_id)
self.slice_event_id = None
self.menu_event_id = self.canvas.mpl_connect('button_press_event', self.on_click)
self.canvas.SetCursor(wx.StockCursor(wx.CURSOR_ARROW))
for w in self.slice_widget:
w.remove()
self.slice_widget = []
self.cross_slice_fig = None
self.segment_slice_fig = None
self.segment_slice_color_index = 0
self.cross_slice_color_index = -1
self.v_cross_slice_plot = None
self.h_cross_slice_plot = None
self.segment_slice_legend = []
self.h_cross_slice_legend = []
self.v_cross_slice_legend = []
if self.cross_slice_dialog:
self.cross_slice_dialog.Close()
self.canvas.draw()
return
self.canvas.mpl_disconnect(self.menu_event_id)
self.menu_event_id = None
self.slice_event_id = self.canvas.mpl_connect('button_press_event', self.build_slice_widget)
self.canvas.SetCursor(wx.CROSS_CURSOR)
self.canvas.draw()
def build_slice_widget(self, event):
if not event.inaxes:
return
elif event.button == 1: # CROSS SLICING CASE
dx = (self.Xmax - self.Xmin)/float(self.data.shape[1])
dy = (self.Ymax - self.Ymin)/float(self.data.shape[0])
X = numpy.floor((x - self.Xmin)/dx)
Y = numpy.floor((y - self.Ymin)/dy)
vslice, hslice = self.extract_cross_slice(X, Y)
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if not self.parent.unique_slicer is None:
self.cross_slice_dialog = self.parent.unique_slicer.dialog
self.cross_slice_canvas = self.parent.unique_slicer.canvas
self.h_cross_slice_plot = self.parent.unique_slicer.hplot
self.v_cross_slice_plot = self.parent.unique_slicer.vplot
self.cross_slice_fig = self.parent.unique_slicer.fig
self.cross_slice_color_index = self.parent.unique_slicer.color_index
self.parent.unique_slicer.color_index += 1
self.h_cross_slice_legend = self.parent.unique_slicer.hlegend
self.v_cross_slice_legend = self.parent.unique_slicer.vlegend
elif self.cross_slice_fig is None or not self.cross_slice_fig:
self.cross_slice_fig = Figure()
self.v_cross_slice_plot = self.cross_slice_fig.add_subplot(211)
self.h_cross_slice_plot = self.cross_slice_fig.add_subplot(212)
if self.cross_slice_dialog is None or not self.cross_slice_dialog:
self.cross_slice_dialog = wx.Frame(self, title="Cross slicing")
self.cross_slice_canvas = FigureCanvasWxAgg(self.cross_slice_dialog, wx.ID_ANY, self.cross_slice_fig)
self.cross_slice_toolbar = NavigationToolbar2WxAgg(self.cross_slice_canvas)
self.unique_target_checkbox = wx.CheckBox(self.cross_slice_dialog, id=wx.ID_ANY, label="Single target plot")
self.Bind(wx.EVT_CHECKBOX, self.made_unique_target, id = self.unique_target_checkbox.GetId())
self.unique_target_checkbox.SetValue(self.unique)
self.auto_scale_button = wx.Button(self.cross_slice_dialog, id=wx.ID_ANY, label="Auto-Scale")
self.Bind(wx.EVT_BUTTON, self.auto_scale_cross_plot, self.auto_scale_button)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.cross_slice_canvas, 1, flag=wx.EXPAND)
hsizer = wx.BoxSizer()
hsizer.Add(self.cross_slice_toolbar, 0, flag=wx.EXPAND)
hsizer.AddSpacer(10)
hsizer.Add(self.auto_scale_button,0 ,flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL )
hsizer.AddSpacer(10)
hsizer.Add(self.unique_target_checkbox, 0, flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL )
sizer.Add(hsizer, 0, flag=wx.EXPAND)
self.cross_slice_dialog.SetSizer(sizer)
sizer.Fit(self.cross_slice_dialog)
self.cross_slice_color_index += 1
self.slice_widget.append(self.subplot.axvline(x=x, linewidth=3, color='%s'%self.get_circular_color(self.cross_slice_color_index)))
self.slice_widget.append(self.subplot.axhline(y=y, linewidth=3, color='%s'%self.get_circular_color(self.cross_slice_color_index)))
v_tmp_plot = self.v_cross_slice_plot.plot(self.Xaxis*self.Xunit_conversion_factor, vslice, color='%s'%self.get_circular_color(self.cross_slice_color_index))
h_tmp_plot = self.h_cross_slice_plot.plot(self.Yaxis*self.Yunit_conversion_factor, hslice, color='%s'%self.get_circular_color(self.cross_slice_color_index))
self.v_cross_slice_legend.append([v_tmp_plot[0],'%s = %8.3f' % (self.Ylabel,y)])
self.h_cross_slice_legend.append([h_tmp_plot[0],'%s = %8.3f' % (self.Xlabel,x)])
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self.v_cross_slice_plot.set_xlabel(self.Xlabel + self.fmt_Xunit)
self.h_cross_slice_plot.set_xlabel(self.Ylabel + self.fmt_Yunit)
self.v_cross_slice_plot.legend(tuple([e[0] for e in self.v_cross_slice_legend]), tuple([e[1] for e in self.v_cross_slice_legend]), loc = 'best', frameon = True, shadow = True)
self.h_cross_slice_plot.legend(tuple([e[0] for e in self.h_cross_slice_legend]), tuple([e[1] for e in self.h_cross_slice_legend]), loc = 'best', frameon = True, shadow = True)
if self.aspect == 'auto':
self.subplot.set_aspect("auto","datalim")
self.canvas.draw()
self.cross_slice_dialog.Show()
self.cross_slice_canvas.draw()
def made_unique_target(self, event):
self.parent.unique_slicer = CrossSlicer(self,
self.cross_slice_canvas,
self.cross_slice_dialog,
self.h_cross_slice_plot,
self.v_cross_slice_plot,
self.cross_slice_fig,
self.cross_slice_color_index,
self.h_cross_slice_legend,
self.v_cross_slice_legend)
if self.unique:
self.cross_slice_canvas = None
self.cross_slice_fig = None
self.h_cross_slice_plot = None
self.v_cross_slice_plot = None
self.cross_slice_color_index = 0
self.h_cross_slice_legend = []
self.v_cross_slice_legend = []
for w in self.slice_widget:
w.remove()
self.slice_widget = []
self.canvas.draw()
self.parent.unique_slicer = None
self.cross_slice_dialog.Close()
self.unique = not self.unique
def auto_scale_cross_plot(self, event):
norm = Normalize()
for hl in self.h_cross_slice_plot.get_lines():
d = hl.get_ydata()
norm.autoscale(d)
hl.set_ydata(norm(d))
for vl in self.v_cross_slice_plot.get_lines():
d = vl.get_ydata()
norm.autoscale(d)
vl.set_ydata(norm(d))
self.v_cross_slice_plot.relim()
self.h_cross_slice_plot.relim()
self.v_cross_slice_plot.autoscale_view(True,True,True)
self.h_cross_slice_plot.autoscale_view(True,True,True)
self.cross_slice_canvas.draw()
def get_circular_color(self, idx):
circ_idx = idx%len(self.color_list)
return self.color_list.values()[circ_idx]
def extract_cross_slice(self, x, y):
x = int(x)
y = int(y)
hslice = self.data.T[x,:]
vslice = self.data.T[:,y]
return vslice, hslice
def set_lim(self):
self.Xmin, self.Xmax = self.Xaxis[0], self.Xaxis[-1]
if self.Xmin == self.Xmax:
self.Xmin -= 1.0e-9
self.Xmax += 1.0e-9
self.Ymin, self.Ymax = self.Yaxis[0], self.Yaxis[-1]
if self.Ymin == self.Ymax:
self.Ymin -= 1.0e-9
self.Ymax += 1.0e-9
def reset_axis(self):
self.figure.gca().axis([self.Xmin, self.Xmax, self.Ymin, self.Ymax])
self.canvas.draw()
def plot(self, data, varname, Xaxis = None, Xunit = None, Yaxis = None, Yunit = None, transposition = True):
if data is None:
return
if ((Xaxis is None) or (Xunit is None) or (Yaxis is None) or (Yunit is None)):
self.set_axis_property(varname,data)
else:
self.Xaxis = Xaxis
self.Xunit = Xunit
self.Yaxis = Yaxis
self.Yunit = Yunit
if transposition:
self.data = data.T
else:
self.data = data
self.varname = varname
self.subplot = self.figure.add_subplot( 111 )
self.ax = self.subplot.imshow(self.data, interpolation=self.interpolation, origin='lower')
self.subplot.set_aspect('auto')
self.aspect = 'auto'
self.Xlabel = self.Xaxis_label
self.Ylabel = self.Yaxis_label
self.figure.gca().set_xlabel(self.Xlabel + self.fmt_Xunit )
self.figure.gca().set_ylabel(self.Ylabel + self.fmt_Yunit )
self.set_lim()
self.set_ticks()
self.reset_axis()
self.color_bar = self.figure.colorbar(self.ax)
self.canvas.draw()
def replot(self, oldinstance):
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self.data = oldinstance.data
self.Xaxis = oldinstance.Xaxis
self.Xunit = oldinstance.Xunit
self.Yaxis = oldinstance.Yaxis
self.Yunit = oldinstance.Yunit
self.varname = oldinstance.varname
self.Xaxis_label = oldinstance.Xaxis_label
self.Yaxis_label = oldinstance.Yaxis_label
self.normType = oldinstance.normType
self.aspect = oldinstance.aspect
self.subplot = self.figure.add_subplot( 111 )
self.ax = self.subplot.imshow(self.data, interpolation=self.interpolation, origin='lower')
self.subplot.set_aspect(self.aspect)
self.Xlabel = self.Xaxis_label
self.Ylabel = self.Yaxis_label
self.figure.gca().set_xlabel(self.Xlabel + self.fmt_Xunit )
self.figure.gca().set_ylabel(self.Ylabel + self.fmt_Yunit )
self.set_ticks()
self.reset_axis()
self.color_bar = self.figure.colorbar(self.ax)
self.scale(onReplot = True)
self.canvas.draw()
def scale(self, onReplot = False):
if not NORMALIZER.has_key(self.normType):
self.color_bar.set_clim(self.data.min(), self.data.max())
self.ax.set_norm(None)
return
norm = NORMALIZER[self.normType]
norm.autoscale(self.data)
try :
self.ax.set_norm(norm)
except ValueError:
raise Plotter2DError('Could not set normalization : difference between minimum and maximum values is to small')
if onReplot:
normd = norm(self.data)
self.color_bar.set_clim(normd.min(), normd.max())
def compute_conversion_factor(self):
try:
self.Xunit_conversion_factor = magnitude.mg(1., self.Xinit_unit, self.Xunit).toval()
except magnitude.MagnitudeError:
self.Xunit_conversion_factor = 1.0
try:
self.Yunit_conversion_factor = magnitude.mg(1., self.Yinit_unit, self.Yunit).toval()
except magnitude.MagnitudeError:
self.Yunit_conversion_factor = 1.0
def set_ticks(self):
self.compute_conversion_factor()
self.figure.gca().xaxis.set_major_locator(ScaledLocator(dx = self.Xunit_conversion_factor))
self.figure.gca().xaxis.set_major_formatter(ScaledFormatter(dx = self.Xunit_conversion_factor))
self.figure.gca().yaxis.set_major_locator(ScaledLocator(dx = self.Yunit_conversion_factor))
self.figure.gca().yaxis.set_major_formatter(ScaledFormatter(dx = self.Yunit_conversion_factor))
self.ax.set_extent([self.Xmin, self.Xmax, self.Ymin, self.Ymax])
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def set_axis_property(self, varname, data):
oldXunit = self.Xinit_unit
oldYunit = self.Yinit_unit
try :
self.Xaxis_label = self.dataproxy[varname]['axis'][0]
self.Xunit = self.Xinit_unit = self.dataproxy[self.Xaxis_label]['units']
self.Xaxis = self.dataproxy[self.Xaxis_label]['data']
except:
self.Xunit = self.Xinit_unit = 'au'
self.Xaxis = numpy.arange(data.shape[0])
try :
self.Yaxis_label = self.dataproxy[varname]['axis'][1]
self.Yunit = self.Yinit_unit = self.dataproxy[self.Yaxis_label]['units']
self.Yaxis = self.dataproxy[self.Yaxis_label]['data']
except:
self.Yunit = self.Yinit_unit = 'au'
self.Yaxis = numpy.arange(data.shape[1])
if not oldXunit is None:
if oldXunit != self.Xinit_unit:
raise Plotter2DError('the x axis unit (%s) of data-set %r is inconsistent with the unit (%s) of the precedent data plotted '%(self.Xinit_unit, varname, oldXunit))
if not oldYunit is None:
if oldYunit != self.Yinit_unit:
raise Plotter2DError('the y axis unit (%s) of data-set %r is inconsistent with the unit (%s) of the precedent data plotted '%(self.Yinit_unit, varname, oldYunit))
if self.Yaxis.shape[0] != data.shape[1]:
raise Plotter2DError('the y axis dimension is inconsistent with the shape of data ')
if self.Xaxis.shape[0] != data.shape[0]:
raise Plotter2DError('the x axis dimension is inconsistent with the shape of data ')
def image_setting_dialog(self, event = None):
d = ImageSettingsDialog(self)
d.SetFocus()
d.ShowModal()
d.Destroy()