/
ring_pattern.py
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/
ring_pattern.py
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#!/usr/bin/env python
"""
Makes ring patterns from profiles
"""
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg
from matplotlib.figure import Figure
import wx
import os
import numpy as np
import matplotlib.patches as patches
from polar_pattern import make_profile_rings
import time
class Timer():
def __enter__(self): self.start = time.time()
def __exit__(self, *args): print(time.time() - self.start)
from matplotlib import rc
rc('savefig', dpi=600)
class MyNavigationToolbar2(NavigationToolbar2WxAgg):
"""
Extend the default wx toolbar with your own event handlers
"""
def __init__(self, parent, canvas, cankill):
NavigationToolbar2WxAgg.__init__(self, canvas)
self.parent = parent
def mouse_move(self, event):
#print('mouse_move', event.button)
if event.inaxes:
try: s = event.inaxes.format_coord(event.xdata, event.ydata)
except ValueError: pass
except OverflowError: pass
else:
if len(self.mode):
self.parent.statbar.SetStatusText('%s, %s' % (self.mode, s), 1)
else:
self.parent.statbar.SetStatusText(s, 1)
else: self.parent.statbar.SetStatusText(self.mode,1)
def set_cursor(self, cursor):
cursor =wx.StockCursor(cursord[cursor])
self.canvas.SetCursor( cursor )
# cursors
class Cursors: #namespace
HAND, POINTER, SELECT_REGION, MOVE, BULLSEYE = range(5)
cursors = Cursors()
#print(cursord)
cursord = {
cursors.MOVE : wx.CURSOR_HAND,
cursors.HAND : wx.CURSOR_HAND,
cursors.POINTER : wx.CURSOR_ARROW,
cursors.SELECT_REGION : wx.CURSOR_CROSS,
cursors.BULLSEYE : wx.CURSOR_BULLSEYE,
}
print(cursord)
class ring_pattern(wx.Frame):
def __init__(self, parent):
wx.Frame.__init__(self,parent,-1,"Ring Figure - "+parent.filename ,size=(550,400))
self.parent = parent
iconFile = os.path.join(parent.parent.iconspath, "diff_profiler_ico.ico")
icon1 = wx.Icon(iconFile, wx.BITMAP_TYPE_ICO)
self.SetIcon(icon1)
self.mpl_old = self.parent.mpl_old
self.background_sub = self.parent.background_sub
self.prosim = self.parent.prosim
self.plot_sim = self.parent.plot_sim
self.ring_patt = []
self.back_patt = []
self.dirname = self.parent.dirname
self.statbar = self.CreateStatusBar() # A Statusbar in the bottom of the window
self.statbar.SetFieldsCount(2)
self.statbar.SetStatusText("None", 1)
# Setting up the menu. filemenu is a local variable at this stage.
figmenu= wx.Menu()
# use ID_ for future easy reference - much better than "48", "404" etc
# The & character indicates the short cut key
self.Save_evt = figmenu.Append(wx.NewId(), "&Save Figure","Save the figure as vestor or highres image")
self.BGSub_evt = figmenu.AppendCheckItem(wx.NewId(), "&Background Subtract","Subtract the profile fitted background from the pattern image")
self.ProSim_evt = figmenu.AppendCheckItem(wx.NewId(), "&Profile Simulation","Show the ring pattern from a profile simulation")
self.PeakSim_evt = figmenu.AppendCheckItem(wx.NewId(), "Peak &Simulation","Show a peak simulation as rings")
if self.parent.background_sub:
self.BGSub_evt.Check(True)
else:
self.BGSub_evt.Enable(False)
if self.parent.prosim:
self.ProSim_evt.Check(True)
else:
self.ProSim_evt.Enable(False)
if self.parent.plot_sim:
self.PeakSim_evt.Check(True)
else:
self.PeakSim_evt.Enable(False)
# Creating the menubar.
menuBar = wx.MenuBar()
menuBar.Append(figmenu,"&Figure") # Adding the "patternmenu" to the MenuBar
self.SetMenuBar(menuBar) # Adding the MenuBar to the Frame content.
# Note - previous line stores the whole of the menu into the current object
self.SetBackgroundColour(wx.Colour("WHITE"))
self.figure = Figure(figsize=(8,8), dpi=76)
self.axes = self.figure.add_axes([0,0,1,1],yticks=[],xticks=[],frame_on=False)#
self.canvas = FigureCanvas(self, -1, self.figure)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.canvas, 1, wx.TOP | wx.LEFT | wx.EXPAND)
# Capture the paint message
self.Bind(wx.EVT_PAINT, self.OnPaint)
self.toolbar = MyNavigationToolbar2(self, self.canvas, True)
self.toolbar.Realize()
tw, th = self.toolbar.GetSize()
fw, fh = self.canvas.GetSize()
self.toolbar.SetSize(wx.Size(fw, th))
self.sizer.Add(self.toolbar, 0, wx.LEFT | wx.EXPAND)
# update the axes menu on the toolbar
self.toolbar.update()
# Define the code to be run when a menu option is selected
if self.mpl_old:
self.Bind(wx.EVT_MENU, self.toolbar.save, self.Save_evt)
self.Bind(wx.EVT_MENU, self.toolbar.save_figure, self.Save_evt)
self.Bind(wx.EVT_MENU, self.OnBGSub, self.BGSub_evt)
self.Bind(wx.EVT_MENU, self.OnProSim, self.ProSim_evt)
self.Bind(wx.EVT_MENU, self.OnPeakSim, self.PeakSim_evt)
self.SetSizer(self.sizer)
self.Fit()
self.ring_plot()
def OnBGSub(self, event):
#self.id = event.GetId()
if self.BGSub_evt.IsChecked():
self.background_sub = 1
else:
self.background_sub = 0
self.ring_plot()
def OnProSim(self, event):
#self.id = event.GetId()
if self.ProSim_evt.IsChecked():
self.prosim = 1
else:
self.prosim = 0
self.ring_plot()
def OnPeakSim(self, event):
#self.id = event.GetId()
if self.PeakSim_evt.IsChecked():
self.plot_sim = 1
else:
self.plot_sim = 0
self.axes.cla()
self.ring_plot()
def OnPaint(self, event):
self.canvas.draw()
event.Skip()
def ring_plot(self):
#rc('font', size=16)
if self.parent.latex:
rc('text', usetex=True)
rc('font', family='serif')
else:
rc('text', usetex=False)
rc('font', family='sans-serif')
rc('mathtext', fontset = 'custom')
self.origin = [round(self.parent.C[1]), round(self.parent.C[0])]
#self.pattern_open_crop = self.parent.pattern_open[origin[0]-(self.parent.boxs-6):origin[0]+(self.parent.boxs-3),origin[1]-(self.parent.boxs-6):origin[1]+(self.parent.boxs-3)]
self.pattern_open_crop = self.parent.pattern_open[int(self.origin[0]-(self.parent.boxs)):int(self.origin[0]+(self.parent.boxs)),int(self.origin[1]-(self.parent.boxs)):int(self.origin[1]+(self.parent.boxs))]
if self.background_sub == 1:
self.do_background_sub()
self.axes.imshow(self.pattern_open_crop, cmap = 'gray', interpolation='bicubic',
extent=(-self.parent.drdf.max(), self.parent.drdf.max(), -self.parent.drdf.max(), self.parent.drdf.max()))
if self.prosim == 1:
self.do_prosim()
if self.plot_sim == 1:
self.do_plot_sim()
#self.axes.plot(0,0,'+')
#self.axes.axis('equal')
self.axes.set_xlim(-self.parent.limit, self.parent.limit)
self.axes.set_ylim(-self.parent.limit, self.parent.limit)
#self.axes.xaxis.set_ticks_position('bottom')
#self.axes.yaxis.set_ticks_position('left')
self.axes.figure.canvas.draw()
def do_background_sub(self):
if self.back_patt == []:
self.back_patt = make_profile_rings(self.parent.background - self.parent.background.min(), self.parent.drdf, self.origin, self.parent.boxs, True)
#figure()
#imshow(self.back_patt, cmap = 'gray')
#show()
print(self.pattern_open_crop.shape, self.back_patt.shape, self.origin)
print(self.parent.rdf.max(), self.back_patt.max(), self.pattern_open_crop.max(), self.parent.rdf_max)
middle_x = self.back_patt.shape[1]/2
self.back_patt = self.back_patt * self.parent.rdf_max
#figure()
#plot(self.back_patt[:,middle_x])
#plot(self.pattern_open_crop[:,middle_x])
#line = self.pattern_open_crop[:,middle_x] - self.back_patt[:,middle_x]
#plot(line)
#line[line < 0] = 0
#plot(line)
self.pattern_open_crop = self.pattern_open_crop.astype(np.float32)
self.pattern_open_crop -= self.back_patt
#plot(self.pattern_open_crop[:,middle_x])
self.pattern_open_crop[self.pattern_open_crop < 0] = 0
#plot(self.pattern_open_crop[:,middle_x])
#show()
print(self.pattern_open_crop.min(), self.pattern_open_crop.max())
def do_plot_sim(self):
sim_name = []
marks = []
color = ['#42D151','#2AA298','#E7E73C']
marker = ['o','^','s']
print(len(self.parent.simulations))#, self.srdfb
if len(self.parent.simulations) >= 3:
sim_len_i = 3
else:
sim_len_i = len(self.parent.simulations)
print(sim_len_i)#,self.srdfb[sim_len_i[0]],self.sdrdfb[sim_len_i[0]]
for col_index, simulation in enumerate(self.parent.simulations[-sim_len_i:]):
sim_color = simulation.sim_color if simulation.sim_color else color[col_index]
sim_name += [simulation.sim_label]
sim = simulation.srdf
sim_norm = sim/float(max(sim))
#print(sim, max(sim[1:]), min(sim[1:]), sim_norm)
marks += [self.axes.plot(0,0,'-',color=sim_color, zorder = -10)[0]]
rect = patches.Rectangle((-self.parent.limit,-self.parent.limit),self.parent.limit,self.parent.limit, facecolor="none", edgecolor="none")
self.axes.add_patch(rect)
if not simulation.peak_index_labels:
for radius in simulation.sdrdf:
#print(radius)
circ_mark = patches.Circle((0,0), radius, fill = 0 , color=sim_color, linewidth = 2, alpha=.7)
self.axes.add_patch(circ_mark)
circ_mark.set_clip_path(rect)
self.axes.set_autoscale_on(False)
#sim_index = nonzero(self.srdfb[i]!=0)
else:
j=0
for i,label in enumerate(simulation.peak_index_labels[::-1]):
#print(label)
if label:
circ_mark = patches.Circle((0,0), simulation.sdrdf[::-1][i], fill = 0 , color=sim_color, linewidth = 2, alpha=.7)
self.axes.add_patch(circ_mark)
circ_mark.set_clip_path(rect)
self.axes.set_autoscale_on(False)
if label.find('-') == -1:
label = r'('+label+')'
else:
label = r'$\mathsf{('+label.replace('-',r'\bar ')+')}$'
#print(label)
bbox_props = dict(boxstyle="round", fc=sim_color, ec="0.5", alpha=1, lw=1.5)
arrowprops=dict(arrowstyle="wedge,tail_width=1.",
fc=sim_color, ec="0.5",
alpha=.7,
patchA=None,
patchB=circ_mark,
relpos=(0.5, 0.5),
)
an = self.axes.annotate(label, xy=(0, 0),xytext=(.1+col_index/10.0, .1+j/15.0),textcoords='axes fraction', ha="center", va="center", size=20, rotation=0, zorder = 90-col_index, picker=True,
bbox=bbox_props, arrowprops=arrowprops)
an.draggable()
j+=1
print(sim_name, marks)
leg = self.axes.legend(marks , sim_name, loc='upper left', shadow=0, fancybox=True, numpoints=1, prop={'size':16})
frame = leg.get_frame()
frame.set_alpha(0.7)
for handle in leg.legendHandles:
handle.set_linewidth(3.0)
def do_prosim(self):
if self.ring_patt == []:
self.ring_patt = make_profile_rings(self.parent.prosim_int, self.parent.prosim_inv_d, self.origin, self.parent.boxs)
self.axes.imshow(self.ring_patt[:,:self.ring_patt.shape[1]//2], cmap='gray', origin='lower', interpolation='bicubic',
extent=(-self.parent.prosim_inv_d.max(), 0, -self.parent.prosim_inv_d.max(), self.parent.prosim_inv_d.max()))
print(self.parent.prosim_inv_d.max())