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# -*- coding: utf-8 -*-
""" PyCorrFit
Module tools - background
We make some background corection here.
Dimensionless representation:
unit of time : 1 ms
unit of inverse time: 10³ /s
unit of distance : 100 nm
unit of Diff.coeff : 10 µm²/s
unit of inverse area: 100 /µm²
unit of inv. volume : 1000 /µm³
Copyright (C) 2011-2012 Paul Müller
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 2 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, see <http://www.gnu.org/licenses/>.
"""
import numpy as np
import os
import sys
import traceback # for Error handling
import wx
from wx.lib.agw import floatspin # Float numbers in spin fields
import wx.lib.plot as plot
import doc
import misc
import openfile as opf # How to treat an opened file
import readfiles
# Menu entry name
MENUINFO = ["&Background correction", "Open a file for background correction."]
class BackgroundCorrection(wx.Frame):
def __init__(self, parent):
self.MyName="BACKGROUND"
# Parent is main frame
self.parent = parent
# Get the window positioning correctly
pos = self.parent.GetPosition()
pos = (pos[0]+100, pos[1]+100)
wx.Frame.__init__(self, parent=parent, title="Background correction",
pos=pos, style=wx.DEFAULT_FRAME_STYLE|wx.FRAME_FLOAT_ON_PARENT)
## MYID
# This ID is given by the parent for an instance of this class
self.MyID = None
# Current trace we are looking at
self.activetrace = None
# Importet trace
self.trace = None
# Importet trace after user decides to cange radio buttons
self.oldtrace = None
self.oldfilename = None
self.average = None
## Start drawing
# Splitter Window
self.sp = wx.SplitterWindow(self, style=wx.SP_NOBORDER)
## Controls
panel = wx.Panel(self.sp)
# text1
backgroundinit = (
"Correct the amplitude for non-correlated background.\n"+
"The background intensity <B> can be either imported\n"+
"from a blank measurement or set manually.")
textinit = wx.StaticText(panel, label=backgroundinit)
# Radio buttons
self.rbtnfile = wx.RadioButton(panel, -1, 'Blank measurement: ',
style = wx.RB_GROUP)
self.rbtnfile.SetValue(True)
self.btnbrowse = wx.Button(panel, wx.ID_ANY, 'Browse ...')
self.rbtnhand = wx.RadioButton (panel, -1, 'Manual, <B> [kHz]: ')
# Spincontrol
self.spinctrl = floatspin.FloatSpin(panel, digits=4, min_val=0,
increment=.01)
self.spinctrl.Enable(False)
# Verbose text
self.textfile = wx.StaticText(panel,
label="No blank measurement file selected.")
textmeanavg = wx.StaticText(panel,
label="Average background signal [kHz]: ")
self.textmean = wx.StaticText(panel, label="")
# name
textname = wx.StaticText(panel, label="User defined background name: ")
sizeTextn = textname.GetSize()[0]
self.bgname = wx.TextCtrl(panel, value="", size=(sizeTextn,-1))
self.bgname.Enable(False)
self.btnimport = wx.Button(panel, wx.ID_ANY, 'Import into session')
self.btnimport.Enable(False)
# Dropdown
self.BGlist = ["File/User"] # updated by self.UpdateDropdown()
textdropdown = wx.StaticText(panel, label="Show background: ")
self.dropdown = wx.ComboBox(panel, -1, "File/User", (15, -1),
wx.DefaultSize, self.BGlist, wx.CB_DROPDOWN|wx.CB_READONLY)
self.UpdateDropdown()
# Radio buttons Channel1 and 2
self.rbtnCh1 = wx.RadioButton (panel, -1, 'Ch1 ',
style = wx.RB_GROUP)
self.rbtnCh1.SetValue(True)
self.rbtnCh2 = wx.RadioButton (panel, -1, 'Ch2')
# Apply buttons
self.btnapply = wx.Button(panel, wx.ID_ANY, 'Apply')
textor = wx.StaticText(panel, label=" or ")
self.btnrem = wx.Button(panel, wx.ID_ANY, 'Dismiss')
textpages = wx.StaticText(panel, label=" correction for pages: ")
self.WXTextPages = wx.TextCtrl(panel, value="")
# Initial value for WXTextPages
pagenumlist = list()
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
pagenumlist.append(int(filter(lambda x: x.isdigit(), Page.counter)))
valstring=misc.parsePagenum2String(pagenumlist)
self.WXTextPages.SetValue(valstring)
textyma = wx.StaticText(panel, label="Shortcut - ")
self.btnapplyall = wx.Button(panel, wx.ID_ANY, 'Apply to all pages')
textor2 = wx.StaticText(panel, label=" or ")
self.btnremyall = wx.Button(panel, wx.ID_ANY, 'Dismiss from all pages')
# Bindings
self.Bind(wx.EVT_BUTTON, self.OnBrowse, self.btnbrowse)
self.Bind(wx.EVT_RADIOBUTTON, self.OnRadioFile, self.rbtnfile)
self.Bind(wx.EVT_RADIOBUTTON, self.OnRadioHand, self.rbtnhand)
self.Bind(wx.EVT_SPINCTRL, self.SpinCtrlChange, self.spinctrl)
self.Bind(wx.EVT_BUTTON, self.OnImport, self.btnimport)
self.Bind(wx.EVT_COMBOBOX, self.OnDraw, self.dropdown)
self.Bind(wx.EVT_BUTTON, self.OnApply, self.btnapply)
self.Bind(wx.EVT_BUTTON, self.OnApplyAll, self.btnapplyall)
self.Bind(wx.EVT_BUTTON, self.OnRemove, self.btnrem)
self.Bind(wx.EVT_BUTTON, self.OnRemoveAll, self.btnremyall)
# Sizers
topSizer = wx.BoxSizer(wx.VERTICAL)
text1sizer = wx.BoxSizer(wx.HORIZONTAL)
text1sizer.Add(self.rbtnfile)
text1sizer.Add(self.btnbrowse)
text2sizer = wx.BoxSizer(wx.HORIZONTAL)
text2sizer.Add(self.rbtnhand)
text2sizer.Add(self.spinctrl)
textmeansizer = wx.BoxSizer(wx.HORIZONTAL)
textmeansizer.Add(textmeanavg)
textmeansizer.Add(self.textmean)
dropsizer = wx.BoxSizer(wx.HORIZONTAL)
dropsizer.Add(textdropdown)
droprightsizer = wx.BoxSizer(wx.VERTICAL)
dropsizer.Add(droprightsizer)
droprightsizer.Add(self.dropdown)
#droprightsizer.Add(self.textafterdropdown)
applysizer = wx.BoxSizer(wx.HORIZONTAL)
applysizer.Add(self.btnapply)
applysizer.Add(textor)
applysizer.Add(self.btnrem)
applysizer.Add(textpages)
applysizer.Add(self.WXTextPages)
applysizer.Add(self.rbtnCh1)
applysizer.Add(self.rbtnCh2)
allsizer = wx.BoxSizer(wx.HORIZONTAL)
allsizer.Add(textyma)
allsizer.Add(self.btnapplyall)
allsizer.Add(textor2)
allsizer.Add(self.btnremyall)
topSizer.Add(textinit)
topSizer.Add(text1sizer)
topSizer.Add(text2sizer)
topSizer.Add(self.textfile)
topSizer.Add(textmeansizer)
topSizer.Add(textname)
topSizer.Add(self.bgname)
topSizer.Add(self.btnimport)
topSizer.Add(dropsizer)
topSizer.Add(applysizer)
topSizer.Add(allsizer)
panel.SetSizer(topSizer)
topSizer.Fit(self)
self.SetMinSize(topSizer.GetMinSizeTuple())
self.Show(True)
## Canvas
self.canvas = plot.PlotCanvas(self.sp)
# Sizes
psize = panel.GetBestSize()
initial_size = (psize[0],psize[1]+200)
self.SetSize(initial_size)
sashsize = psize[1]+3
# This is also necessary to prevent unsplitting
self.sp.SetMinimumPaneSize(sashsize)
self.sp.SplitHorizontally(panel, self.canvas, sashsize)
# If there is no page, disable ourselves:
self.OnPageChanged(self.parent.notebook.GetCurrentPage())
#Icon
if parent.MainIcon is not None:
wx.Frame.SetIcon(self, parent.MainIcon)
def OnApply(self, event):
strFull = self.WXTextPages.GetValue()
PageNumbers = misc.parseString2Pagenum(self, strFull)
if PageNumbers is None:
# Something went wrong and parseString2Pagenum already displayed
# an error message.
return
# BG number
item = self.dropdown.GetSelection()
# Apply to corresponding pages
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
j = filter(lambda x: x.isdigit(), Page.counter)
if int(j) in PageNumbers:
if self.rbtnCh1.GetValue() == True:
Page.bgselected = item
else:
Page.bg2selected = item
if Page.IsCrossCorrelation is False:
# Autocorrelation only has one background!
Page.bg2selected = None
Page.OnAmplitudeCheck("init")
Page.PlotAll()
# Clean up unused backgrounds
CleanupAutomaticBackground(self.parent)
def OnApplyAll(self, event):
self.btnrem.Enable(True)
self.btnremyall.Enable(True)
N = self.parent.notebook.GetPageCount()
item = self.dropdown.GetSelection()
for i in np.arange(N):
# Set Page
Page = self.parent.notebook.GetPage(i)
Page.bgselected = item
if Page.IsCrossCorrelation:
Page.bg2selected = item
else:
Page.bg2selected = None
try:
Page.OnAmplitudeCheck("init")
Page.PlotAll()
except OverflowError:
errstr = "Could not apply background to Page "+Page.counter+\
". \n Check the value of the trace average and the background."
dlg = wx.MessageDialog(self, errstr, "Error",
style=wx.ICON_ERROR|wx.OK|wx.STAY_ON_TOP)
dlg.ShowModal()
Page.bgselected = None
Page.bg2selected = None
# Clean up unused backgrounds
CleanupAutomaticBackground(self.parent)
def OnClose(self, event=None):
self.parent.toolmenu.Check(self.MyID, False)
self.parent.ToolsOpen.__delitem__(self.MyID)
self.Destroy()
def OnBrowse(self, event):
# opf.BGFiletypes is a dictionary with filetypes that have some
# trace signal information.
SupFiletypes = opf.BGFiletypes.keys()
SupFiletypes.sort()
filters = ""
for i in np.arange(len(SupFiletypes)):
# Add to the filetype filter
filters = filters+SupFiletypes[i]
if i+1 != len(SupFiletypes):
# Add a separator
filters = filters+"|"
dlg = wx.FileDialog(self, "Choose a data file",
self.parent.dirname, "", filters, wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
# Workaround since 0.7.5
(dirname, filename) = os.path.split(dlg.GetPath())
#filename = dlg.GetFilename()
#dirname = dlg.GetDirectory()
# Set parent dirname for user comfort
self.parent.dirname = dirname
try:
# [data, trace, curvelist]
stuff = readfiles.openAnyBG(dirname, filename)
except:
# The file does not seem to be what it seems to be.
info = sys.exc_info()
errstr = "Unknown file format:\n"
errstr += str(filename)+"\n\n"
errstr += str(info[0])+"\n"
errstr += str(info[1])+"\n"
for tb_item in traceback.format_tb(info[2]):
errstr += tb_item
wx.MessageDialog(self, errstr, "Error",
style=wx.ICON_ERROR|wx.OK|wx.STAY_ON_TOP)
return
# Usually we will get a bunch of traces. Let the user select which
# one to take.
if len(stuff["Filename"]) > 1:
choices = list()
for i2 in np.arange(len(stuff["Filename"])):
choices.append(str(i2)+". " + stuff["Filename"][i2] + " " +
stuff["Type"][i2])
dlg = wx.SingleChoiceDialog(self, "Choose a curve",
"Curve selection", choices=choices)
if dlg.ShowModal() == wx.ID_OK:
selindex = dlg.GetSelection()
else:
return
else:
selindex = 0
# If we accidentally recorded a cross correlation curve
# as the background, let the user choose which trace he wants:
channelindex = None
if ( len(stuff["Type"][selindex]) >= 2 and
stuff["Type"][selindex][0:2] == "CC" ):
choices = ["Channel 1", "Channel 2"]
label = "From which channel do you want to use the trace?"
dlg = wx.SingleChoiceDialog(self, label,
"Curve selection", choices=choices)
if dlg.ShowModal() == wx.ID_OK:
channelindex = dlg.GetSelection()
trace = stuff["Trace"][selindex][channelindex]
else:
return
else:
trace = stuff["Trace"][selindex]
if trace is None:
print "WARNING: I did not find any trace data."
return
# Display filename and some of the directory
self.textfile.SetLabel("File: ..."+dirname[-10:]+"/"+filename)
name = str(selindex)+". "+stuff["Filename"][selindex]+" "+\
stuff["Type"][selindex]
if channelindex is not None:
name += " "+str(channelindex+1)
self.bgname.SetValue(name)
self.trace = trace
# Calculate average
self.average = self.trace[:,1].mean()
# Display average
self.textmean.SetLabel(str(self.average)+" kHz")
self.spinctrl.SetValue(self.average)
# Let the user see the opened file
self.dropdown.SetSelection(0)
# show trace
self.OnDraw()
# Enable button and editable name
self.bgname.Enable(True)
self.btnimport.Enable(True)
else:
# User pressed "Abort" - do nothing.
self.parent.dirname = dlg.GetDirectory()
dlg.Destroy()
return
def OnDraw(self, event=None):
item = self.dropdown.GetSelection()
if item < 0:
# Disable Apply Buttons
self.btnapply.Enable(False)
self.btnapplyall.Enable(False)
# Draw the trace that was just imported
if self.trace != None:
# Calculate average
self.average = self.trace[:,1].mean()
self.activetrace = self.trace
#self.textafterdropdown.SetLabel(" Avg: "+str(self.average)+
# " kHz")
self.textmean.SetLabel(str(self.average))
self.spinctrl.SetValue(self.average)
else:
# Clear the canvas. Looks better.
self.canvas.Clear()
# Don't show the average
#self.textafterdropdown.SetLabel("")
self.textmean.SetLabel("")
return
else:
# Enable Apply Buttons
self.btnapply.Enable(True)
self.btnapplyall.Enable(True)
# Draw a trace from the list
self.activetrace = self.parent.Background[item-1][2]
#self.textafterdropdown.SetLabel(" Avg: "+
# str(self.parent.Background[item-1][0]))
# We want to have the trace in [s] here.
trace = 1.*self.activetrace
trace[:,0] = trace[:,0]/1000
linesig = plot.PolyLine(trace, legend='', colour='blue', width=1)
self.canvas.Draw(plot.PlotGraphics([linesig],
xLabel='time [s]',
yLabel='background signal [kHz]'))
def OnImport(self, event):
self.parent.Background.append([self.average, self.bgname.GetValue(),
self.trace])
# Next two lines are taken care of by UpdateDropdown
#name = "{} ({:.2f} kHz)".format(self.bgname.GetValue(), self.average)
#self.BGlist.append(name)
self.UpdateDropdown()
self.btnremyall.Enable(True)
self.btnrem.Enable(True)
self.btnapplyall.Enable(True)
self.btnapply.Enable(True)
self.OnDraw()
# Update BG dropdown of each page
for i in np.arange(self.parent.notebook.GetPageCount()):
self.parent.notebook.GetPage(i).OnAmplitudeCheck()
def OnPageChanged(self, page=None, trigger=None):
"""
This function is called, when something in the panel
changes. The variable `trigger` is used to prevent this
function from being executed to save stall time of the user.
Forr a list of possible triggers, see the doc string of
`tools`.
"""
# We do not need the *Range* Commands here yet.
# We open and close the SelectChannelsFrame every time we
# import some data.
if trigger in ["parm_batch", "fit_batch", "page_add_batch"]:
return
if len(self.parent.Background) == 0:
self.BGlist = list()
self.UpdateDropdown()
self.dropdown.SetValue("File/User")
if self.parent.notebook.GetPageCount() == 0:
self.sp.Disable()
return
self.sp.Enable()
if len(self.BGlist) <= 0:
self.btnrem.Enable(False)
self.btnremyall.Enable(False)
self.btnapply.Enable(False)
self.btnapplyall.Enable(False)
else:
self.btnrem.Enable(True)
self.btnremyall.Enable(True)
self.btnapply.Enable(True)
self.btnapplyall.Enable(True)
if (self.WXTextPages.GetValue() == ""
and self.parent.notebook.GetPageCount() != 0):
# Initial value for WXTextPages
pagenumlist = list()
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
pagenumlist.append(int(filter(lambda x: x.isdigit(), Page.counter)))
valstring=misc.parsePagenum2String(pagenumlist)
self.WXTextPages.SetValue(valstring)
def OnRadioFile(self, event):
# Do not let the user change the spinctrl
# setting.
self.spinctrl.Enable(False)
self.btnbrowse.Enable(True)
# Restor the old trace
self.trace = self.oldtrace
if self.oldfilename is not None:
self.textfile.SetLabel(self.oldfilename)
if self.trace is None:
# Disable button and editable name
self.bgname.Enable(False)
self.btnimport.Enable(False)
# Let us draw
self.dropdown.SetSelection(0)
self.OnDraw()
def OnRadioHand(self, event):
# Let user enter a signal.
self.spinctrl.Enable(True)
self.btnbrowse.Enable(False)
# save the old trace. We might want to switch back to it.
if self.trace is not None:
self.oldtrace = 1.*self.trace
self.oldfilename = self.textfile.GetLabel()
self.SpinCtrlChange()
# Do not show the filename
self.textfile.SetLabel("No file selected.")
# Enable button and editable name
self.bgname.Enable(True)
self.btnimport.Enable(True)
if len(self.bgname.GetValue()) == 0:
# Enter something as name
self.bgname.SetValue("User")
def OnRemove(self, event):
strFull = self.WXTextPages.GetValue()
PageNumbers = misc.parseString2Pagenum(self, strFull)
if PageNumbers is None:
# Something went wrong and parseString2Pagenum already displayed
# an error message.
return
# BG number
item = self.dropdown.GetSelection()
# Apply to corresponding pages
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
j = filter(lambda x: x.isdigit(), Page.counter)
if int(j) in PageNumbers:
if self.rbtnCh1.GetValue() == True:
Page.bgselected = None
else:
Page.bg2selected = None
Page.bgselected = None
Page.OnAmplitudeCheck("init")
Page.PlotAll()
# Clean up unused backgrounds
CleanupAutomaticBackground(self.parent)
def OnRemoveAll(self, event):
N = self.parent.notebook.GetPageCount()
for i in np.arange(N):
Page = self.parent.notebook.GetPage(i)
Page.bgselected = None
Page.bg2selected = None
Page.OnAmplitudeCheck("init")
Page.PlotAll()
# Clean up unused backgrounds
CleanupAutomaticBackground(self.parent)
def SetPageNumbers(self, pagestring):
self.WXTextPages.SetValue(pagestring)
def SpinCtrlChange(self, event=None):
# Let user see the continuous trace we will generate
self.average = self.spinctrl.GetValue()
self.trace = np.array([[0,self.average],[1,self.average]])
self.textmean.SetLabel(str(self.average))
self.OnDraw()
def UpdateDropdown(self, e=None):
self.BGlist = list()
#self.BGlist.append("File/User")
for item in self.parent.Background:
bgname = "{} ({:.2f} kHz)".format(item[1],item[0])
self.BGlist.append(bgname)
if len(self.BGlist) == 0:
ddlist = ["File/User"]
else:
ddlist = 1*self.BGlist
self.dropdown.SetItems(self.BGlist)
# Show the last item
self.dropdown.SetSelection(len(self.BGlist)-1)
def ApplyAutomaticBackground(page, bg, parent):
"""
Creates an "automatic" background with countrate in kHz *bg* and
applies it to the given *page* object. If an automatic
background with the same countrate exists, uses it.
Input:
*page* - page to which the background should be applied
*bg* - background that should be applied to that page
float or list of 1 or two elements
-> if the page is cross-correlation, the second
background will be applied as well.
*parent* - parent containing *Background* list
"""
bglist = 1*np.atleast_1d(bg)
# minus 1 to identify non-set background id
bgid = np.zeros(bglist.shape, dtype=int) - 1
for b in xrange(len(bglist)):
# Check if exists:
for i in xrange(len(parent.Background)):
if parent.Background[i][0] == bglist[b]:
bgid[b] = i
if bgid[b] == -1:
# Add new background
bgname = "AUTO: {:e} kHz \t".format(bglist[b])
trace = np.array([[0,bglist[b]],[1,bglist[b]]])
parent.Background.append([bglist[b], bgname, trace])
bgid[b] = len(parent.Background) - 1
# Apply background to page
# Last item is id of background
page.bgselected = bgid[0]
if page.IsCrossCorrelation:
if len(bgid) != 2:
raise NotImplementedError("Cross-correlation data needs"+
"exactly two signals for background-correction!")
# Apply second background
page.bg2selected = bgid[1]
else:
page.bg2selected = None
CleanupAutomaticBackground(parent)
page.OnAmplitudeCheck("init")
page.PlotAll()
def CleanupAutomaticBackground(parent):
"""
Goes through the pagelist *parent.notebook.GetPageCount()*
and checks *parent.Background* for unnused automatic
backgrounds.
Removes these and updates the references to all backgrounds
within the pages.
"""
# Create a dictionary with keys: indices of old background list -
# and elements: list of pages having this background
BGdict = dict()
BG2dict = dict() # cross-correlation
for i in xrange(len(parent.Background)):
BGdict[i] = list()
BG2dict[i] = list()
# Append pages to the lists inside the dictionary
for i in xrange(parent.notebook.GetPageCount()):
Page = parent.notebook.GetPage(i)
if Page.bgselected is not None:
BGdict[Page.bgselected].append(Page)
if Page.bg2selected is not None:
BG2dict[Page.bg2selected].append(Page)
# Sort the keys and create a new background list
NewBGlist = list()
keyID = 0
keys = BGdict.keys()
keys.sort()
for key in keys:
# Do not delete user-generated backgrounds
if len(BGdict[key]) == 0 and parent.Background[key][1][-1]=="\t":
# This discrads auto-generated backgrounds that have no
# pages assigned to them
pass
else:
for page in BGdict[key]:
page.bgselected = keyID
NewBGlist.append(parent.Background[key])
keyID += 1
# Same thing for cross-correlation (two bg signals)
#keyID = 0
keys = BG2dict.keys()
keys.sort()
for key in keys:
# Do not delete user-generated backgrounds
if len(BG2dict[key]) == 0 and parent.Background[key][1][-1]=="\t":
# This discrads auto-generated backgrounds that have no
# pages assigned to them
pass
elif parent.Background[key][1][-1]=="\t":
# We already added the user-defined backgrounds
# Therefore, we only check for aut-generated backgrounds
# ("\t")
for page in BG2dict[key]:
page.bg2selected = keyID
NewBGlist.append(parent.Background[key])
keyID += 1
# Finally, write back background list
parent.Background = NewBGlist
# If the background correction tool is open, update the list
# of backgrounds.
# (self.MyName="BACKGROUND")
toolkeys = parent.ToolsOpen.keys()
if len(toolkeys) == 0:
pass
else:
for key in toolkeys:
tool = parent.ToolsOpen[key]
try:
if tool.MyName == "BACKGROUND":
tool.UpdateDropdown()
tool.OnPageChanged()
except:
pass
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