#scanCCD data processing
'''
'''
import os
import os.path as ospath
import sys
import math
import time
import numpy as np
import numpy.linalg as nl
import numpy.ma as ma
import wx
import matplotlib as mpl
import GSASIIpath
import GSASIIIO as G2IO
import GSASIIimage as G2img
import GSASIIplot as G2plt
import GSASIIfiles as G2fil
npsind = lambda x: np.sin(x*np.pi/180.)
npcosd = lambda x: np.cos(x*np.pi/180.)
npacosd = lambda x: 180.*np.arccos(x)/np.pi
npasind = lambda x: 180.*np.arcsin(x)/np.pi
try:
wx.NewIdRef
wx.NewId = wx.NewIdRef
except AttributeError:
pass
def create(parent):
return scanCCD(parent)
[wxID_FILEEXIT, wxID_FILEOPEN, wxID_INTEGRATE, wxID_OUTPUT,
] = [wx.NewId() for _init_coll_File_Items in range(4)]
def FileDlgFixExt(dlg,file): #this is needed to fix a problem in linux wx.FileDialog
ext = dlg.GetWildcard().split('|')[2*dlg.GetFilterIndex()+1].strip('*')
if ext not in file:
file += ext
return file
[docs]
class scanCCD(wx.Frame):
def _init_ctrls(self, parent):
wx.Frame.__init__(self, name='scanCCD', parent=parent,
size=wx.Size(460, 250),style=wx.DEFAULT_FRAME_STYLE, title='scanCCD')
self._init_Imports()
self.scanCCDMenu = wx.MenuBar()
self.File = wx.Menu(title='')
self.File.Append(wxID_FILEOPEN,'Open scanCCD files','Open scanCCD image files (*.tif)')
self.File.Append(wxID_INTEGRATE,'Integrate scanCCD images','Integrate scanCCD images')
self.File.Append(wxID_OUTPUT,'Output pattern','Output fxye file from integration')
self.File.Append(wxID_FILEEXIT,'Exit','Exit from scanCCD')
self.Bind(wx.EVT_MENU, self.OnImageRead, id=wxID_FILEOPEN)
self.Bind(wx.EVT_MENU,self.OnImageIntegrate,id=wxID_INTEGRATE)
self.Bind(wx.EVT_MENU,self.OnOutput,id=wxID_OUTPUT)
self.Bind(wx.EVT_MENU, self.OnFileExit, id=wxID_FILEEXIT)
self.scanCCDMenu.Append(menu=self.File, title='File')
self.SetMenuBar(self.scanCCDMenu)
self.SCCDPanel = wx.Panel(self)
plotFrame = wx.Frame(None,-1,'scanCCD Plots',size=wx.Size(700,600), \
style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
self.plotNB = G2plt.G2PlotNoteBook(plotFrame)
plotFrame.Show()
def __init__(self, parent):
self._init_ctrls(parent)
self.Bind(wx.EVT_CLOSE, self.ExitMain)
self.dirname = ''
self.imagefiles = []
self.dataFrame = None
self.itemPicked = None
self.Image = []
self.Hxyw = []
self.data = {'color':'GSPaired','range':[[0,1000],[0,1000]]}
self.ImportImageReaderlist = G2fil.LoadImportRoutines('img','Images')
def _init_Imports(self):
self.ImportImageReaderlist = G2fil.LoadImportRoutines('img','Images')
self.ImportMenuId = {} # needed?
def ExitMain(self, event):
sys.exit()
def OnFileExit(self,event):
if self.dataFrame:
self.dataFrame.Clear()
self.dataFrame.Destroy()
self.Close()
def OnImageRead(self,event):
dlg = wx.FileDialog(self, 'Choose scanCCD image files', '.', '',\
'Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|\
All files (*.*)|*.*',
wx.FD_OPEN | wx.FD_MULTIPLE)
if self.dirname:
dlg.SetDirectory(self.dirname)
try:
self.imagefiles = []
if dlg.ShowModal() == wx.ID_OK:
self.dirname = dlg.GetDirectory()
self.imagefiles = dlg.GetPaths()
self.imagefiles.sort()
self.data['imScale'] = 8
self.Image = []
for imagefile in self.imagefiles:
Comments,Data,Npix,image = G2IO.GetImageData(self,imagefile)
if Comments:
A = G2img.ImageCompress(image,self.data['imScale'])
if len(self.Image):
self.Image = np.concatenate((self.Image,A))
else:
self.Image = A
self.data['range'][0] = self.data['range'][1] = np.max(self.Image)
self.data['pixel'] = Data['pixelSize']
self.data['size'] = self.Image.shape
self.data['Zmin'] = np.min(self.Image)
self.data['Zmax'] = np.max(self.Image)
self.data['Zeros'] = [-15.3096,16.4] #for bob1-3 files
self.data['mm/deg'] = 15.56012 #from bob1 fit to 2333 peak positions
self.data['radius'] = 180.0*self.data['mm/deg']/math.pi
self.data['TBlimits'] = [0,len(image)]
self.data['LRlimits'] = [0,len(image)*len(self.imagefiles)]
self.data['PtScan'] = len(image)/2
self.data['2thScan'] = [0.0,90.0,0.001]
self.data['showBlk'] = False
self.data['skip'] = 1 #default - skip ramp block
if len(self.imagefiles) == 1:
self.data['skip'] = 0
self.UpdateControls(event)
self.PlotImage()
finally:
dlg.Destroy()
def OnImageIntegrate(self,event):
def Make2ThetaMap(data,iLim,jLim):
#transforms scanCCD image from x,y space to 2-theta,y space
pixelSize = data['pixel']
scalex = pixelSize[0]/1000.
scaley = pixelSize[1]/1000.
vecA = np.asfarray([1.,0.,0.],dtype=np.float32)
tay,tax = np.mgrid[jLim[0]+.5:jLim[1]+.5,iLim[0]+.5:iLim[1]+.5] #bin centers not corners
tax = np.asfarray((tax*scalex-data['Zeros'][0])/data['mm/deg'],dtype=np.float32) #scanCCD 2-thetas
tay = np.asfarray(tay*scaley-data['Zeros'][1],dtype=np.float32)
vecB = np.array([npcosd(tax)*data['radius'],npsind(tax)*data['radius'],tay])
norm = np.sqrt(np.sum((vecB.T*vecB.T),axis=2))
vecB /= norm.T
tax = npacosd(np.dot(vecB.T,vecA))*tax/np.abs(tax) #to get sign of 2-theta
tay += data['Zeros'][1]
return tax,tay.T #2-theta arrays & turn y array around!!
def Fill2ThetaMap(data,TA,image):
import numpy.ma as ma
Zmin = data['Zmin']
Zmax = data['Zmax']
tax,tay = TA # 2-theta & yaxis
taz = ma.masked_outside(image.flatten()-Zmin,0,Zmax-Zmin)
tam = ma.getmask(taz)
tax = ma.compressed(ma.array(tax.flatten(),mask=tam))
tay = ma.compressed(ma.array(tay.flatten(),mask=tam))
taz = ma.compressed(ma.array(taz.flatten(),mask=tam))
del(tam)
return tax,tay,taz
import histosigma2d as h2d
print('Begin image integration')
scaley = self.data['pixel'][1]/1000.
tthStart,tthEnd,tthStep = self.data['2thScan']
LUtth = [tthStart,tthEnd]
TBlim = np.array(self.data['TBlimits'],dtype=np.float32)
nYpix = TBlim[1]-TBlim[0]
TBlim *= scaley
TBdelt = TBlim[1]-TBlim[0]
nTB = 1
numChans = (tthEnd-tthStart)/tthStep
NST = np.zeros(shape=(numChans,1),order='F',dtype=np.float32)
H0 = np.zeros(shape=(numChans,1),order='F',dtype=np.float32)
Amat = np.zeros(shape=(numChans,1),order='F',dtype=np.float32)
Qmat = np.zeros(shape=(numChans,1),order='F',dtype=np.float32)
imSize = np.array(self.data['size'])*self.data['imScale']
H1 = [tth for tth in np.linspace(LUtth[0],LUtth[1],numChans)]
blkSize = 2048
N = 4096/blkSize
nBlk = N**2*len(self.imagefiles) #assume 4Kx4K CCD images - done in 1Kx1K blocks
t0 = time.time()
dlg = wx.ProgressDialog("Elapsed time","2D image integration",nBlk,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
try:
nBlk = 0
iBegi = 0
iFin = 0
GoOn = True
for ifile,imagefile in enumerate(self.imagefiles):
if ifile >= self.data['skip']:
image = G2IO.GetImageData(self,imagefile)[3]
image = np.fliplr(image)
for iBlk in range(N):
iBeg = iBegi+iBlk*blkSize
iFin = iBeg+blkSize
for jBlk in range(N):
jBeg = jBlk*blkSize
jFin = jBeg+blkSize
print('Process map block:',nBlk,iBlk,jBlk,' offset:',iBegi,' limits:',iBeg,iFin,jBeg,jFin)
TA = Make2ThetaMap(self.data,(iBeg,iFin),(jBeg,jFin)) #2-theta & Y arrays & create position mask
Block = image[iBeg-iBegi:iFin-iBegi,jBeg:jFin]
tax,tay,taz = Fill2ThetaMap(self.data,TA,Block) #and apply masks
NST,H0,Amat,Qmat = h2d.histosigma2d(len(tax),tax,tay,taz,numChans,nTB,LUtth,TBlim,tthStep,TBdelt,NST,H0,Amat,Qmat)
H0temp = np.nan_to_num(np.divide(H0,NST))
Qtemp = np.nan_to_num(np.divide(Qmat,NST))
if self.data['showBlk']:
self.PlotBlock(Block.T,'%s %d %d'%('Block',iBlk,jBlk))
OKdlg = wx.MessageDialog(self,'','Continue',wx.OK)
try:
result = OKdlg.ShowModal()
finally:
OKdlg.Destroy()
del tax,tay,taz
nBlk += 1
GoOn = dlg.Update(nBlk)[0]
if not GoOn:
break
else:
print('file '+imagefile+' skipped')
nBlk += N*N
GoOn = dlg.Update(nBlk)[0]
iFin += N*blkSize
if not GoOn:
break
iBegi = iFin
H0 = np.divide(H0,NST)
H0 = np.nan_to_num(H0)
Qmat = np.divide(Qmat,NST)
Qmat = np.nan_to_num(Qmat)
del NST
t1 = time.time()
finally:
dlg.Destroy()
Scale = np.sum(Qmat)/np.sum(H0)
print('SumI: ',np.sum(H0),' SumV: ',np.sum(Qmat),' Scale:',Scale)
print('Integration complete')
print("Elapsed time:","%8.3f"%(t1-t0), "s")
self.Hxyw = [H1,Scale*H0.T[0],np.sqrt(Qmat.T[0])]
print()
self.PlotXY(self.Hxyw,True,type='Integration result')
def OnOutput(self,event):
def powderSave(self,powderfile,Fxye=False):
file = open(powderfile,'w')
file.write('#%s\n'%('from scanCCD image '+self.imagefiles[0]))
print('save powder pattern to file: ',powderfile)
wx.BeginBusyCursor()
try:
x,y,e = self.Hxyw
if Fxye:
file.write(powderfile+'\n')
file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
100.*x[0],100.*(x[1]-x[0])))
XYE = zip(x,y,e)
for X,Y,E in XYE:
if Fxye:
file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(E,1.0)))
else:
file.write("%15.6g %15.6g %15.6g\n" % (X,Y,max(E,1.0)))
file.close()
finally:
wx.EndBusyCursor()
print('powder pattern file written')
if not self.Hxyw:
return
dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '',
'GSAS fxye file (*.fxye)|*.fxye|xye file (*.xye)|*.xye',
wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if self.dirname:
dlg.SetDirectory(self.dirname)
try:
if dlg.ShowModal() == wx.ID_OK:
print(dlg.GetFilename())
powderfile = dlg.GetPath()
if 'fxye' in powderfile:
powderSave(self,powderfile,Fxye=True)
else: #just xye
powderSave(self,powderfile)
self.dirname = dlg.GetDirectory()
finally:
dlg.Destroy()
def UpdateControls(self,event):
ObjIndx = {}
self.SCCDPanel.DestroyChildren()
def ColorSizer(data):
def OnNewColorBar(event):
colSel = event.GetEventObject()
data['color'] = colSel.GetValue()
self.PlotImage()
def OnShowBlk(event):
data['showBlk'] = shoBlk.GetValue()
def OnSkipFiles(event):
data['skip'] = int(skipFile.GetValue())
colorList = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]+['GSPaired','GSPaired_r',]
colorSizer = wx.FlexGridSizer(0,5,5,5)
colorSizer.Add(wx.StaticText(self.SCCDPanel,label=' Color bar '),0,wx.ALIGN_CENTER_VERTICAL)
colSel = wx.ComboBox(self.SCCDPanel,value=data['color'],choices=colorList,
style=wx.CB_READONLY|wx.CB_DROPDOWN|wx.CB_SORT)
colSel.Bind(wx.EVT_COMBOBOX, OnNewColorBar)
colorSizer.Add(colSel,0,wx.ALIGN_CENTER_VERTICAL)
colorSizer.Add(wx.StaticText(self.SCCDPanel,label='image files to skip:'),0,wx.ALIGN_CENTER_VERTICAL)
skipFile = wx.ComboBox(self.SCCDPanel,value=str(data['skip']),
choices=[str(i) for i in range(len(self.imagefiles))],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
skipFile.Bind(wx.EVT_COMBOBOX,OnSkipFiles)
colorSizer.Add(skipFile,0,wx.ALIGN_CENTER_VERTICAL)
shoBlk = wx.CheckBox(self.SCCDPanel,-1,label='Show image blocks?')
shoBlk.SetValue(data['showBlk'])
shoBlk.Bind(wx.EVT_CHECKBOX, OnShowBlk)
colorSizer.Add(shoBlk,0,wx.ALIGN_CENTER_VERTICAL)
return colorSizer
def MaxSizer(data):
def OnMaxSlider(event):
imax = int(self.maxSel.GetValue())*data['range'][0]/100.
data['range'][1] = imax
self.maxVal.SetValue('%d'%(data['range'][1]))
self.PlotImage()
def OnMaxValue(event):
try:
value = int(self.maxVal.GetValue())
if value < 0 or value > data['range'][0]:
raise ValueError
except ValueError:
value = data['range'][1]
data['range'][1] = value
self.maxSel.SetValue(int(100*value/data['range'][0]))
self.PlotImage()
maxSizer = wx.FlexGridSizer(0,3,0,5)
maxSizer.AddGrowableCol(1,1)
maxSizer.SetFlexibleDirection(wx.HORIZONTAL)
maxSizer.Add(wx.StaticText(parent=self.SCCDPanel,label=' Max intensity'),0,
wx.ALIGN_CENTER_VERTICAL)
self.maxSel = wx.Slider(parent=self.SCCDPanel,style=wx.SL_HORIZONTAL,
value=int(100*data['range'][1]/data['range'][0]))
maxSizer.Add(self.maxSel,1,wx.EXPAND)
self.maxSel.Bind(wx.EVT_SLIDER, OnMaxSlider)
self.maxVal = wx.TextCtrl(parent=self.SCCDPanel,value='%d'%(data['range'][1]),style=wx.TE_PROCESS_ENTER)
self.maxVal.Bind(wx.EVT_TEXT_ENTER,OnMaxValue)
self.maxVal.Bind(wx.EVT_KILL_FOCUS,OnMaxValue)
maxSizer.Add(self.maxVal,0,wx.ALIGN_CENTER_VERTICAL)
return maxSizer
def ZSizer(data):
def OnZValue(event):
Obj = event.GetEventObject()
try:
value = int(Obj.GetValue())
except ValueError:
value = data[ObjIndx[Obj.GetId()]]
data[ObjIndx[Obj.GetId()]] = value
self.PlotImage()
zSizer = wx.FlexGridSizer(0,4,5,5)
zSizer.Add(wx.StaticText(self.SCCDPanel,label='Upper intensity mask:'),0,wx.ALIGN_CENTER_VERTICAL)
zMax = wx.TextCtrl(self.SCCDPanel,value='%d'%(data['Zmax']),style=wx.TE_PROCESS_ENTER)
zMax.Bind(wx.EVT_TEXT_ENTER,OnZValue)
zMax.Bind(wx.EVT_KILL_FOCUS,OnZValue)
ObjIndx[zMax.GetId()] = 'Zmax'
zSizer.Add(zMax)
zSizer.Add(wx.StaticText(self.SCCDPanel,label='Intensity subtraction:'),0,wx.ALIGN_CENTER_VERTICAL)
zMin = wx.TextCtrl(self.SCCDPanel,value='%d'%(data['Zmin']),style=wx.TE_PROCESS_ENTER)
ObjIndx[zMin.GetId()] = 'Zmin'
zMin.Bind(wx.EVT_TEXT_ENTER,OnZValue)
zMin.Bind(wx.EVT_KILL_FOCUS,OnZValue)
zSizer.Add(zMin)
return zSizer
def ZeroSizer(data):
def OnZeroValue(event):
Obj = event.GetEventObject()
item = ObjIndx[Obj.GetId()]
try:
value = float(Obj.GetValue())
except ValueError:
value = data[item[0]][item[1]]
data[item[0]][item[1]] = value
Obj.SetValue('%.3f'%(value))
self.PlotImage()
def OnZpdgValue(event):
Obj = event.GetEventObject()
item = ObjIndx[Obj.GetId()]
try:
value = float(Obj.GetValue())
except ValueError:
value = self.data[item[0]]
self.data[item[0]] = value
self.data['radius'] = 180.0*value/math.pi
Obj.SetValue('%.3f'%(value))
self.PlotImage()
zeroSizer = wx.FlexGridSizer(0,6,5,5)
zeroSizer.Add(wx.StaticText(self.SCCDPanel,label='X-zero:'),0,wx.ALIGN_CENTER_VERTICAL)
zMax = wx.TextCtrl(self.SCCDPanel,value='%.3f'%(data['Zeros'][0]),style=wx.TE_PROCESS_ENTER)
zMax.Bind(wx.EVT_TEXT_ENTER,OnZeroValue)
zMax.Bind(wx.EVT_KILL_FOCUS,OnZeroValue)
ObjIndx[zMax.GetId()] = ['Zeros',0]
zeroSizer.Add(zMax)
zeroSizer.Add(wx.StaticText(self.SCCDPanel,label='Y-zero:'),0,wx.ALIGN_CENTER_VERTICAL)
zMin = wx.TextCtrl(self.SCCDPanel,value='%.3f'%(data['Zeros'][1]),style=wx.TE_PROCESS_ENTER)
ObjIndx[zMin.GetId()] = ['Zeros',1]
zMin.Bind(wx.EVT_TEXT_ENTER,OnZeroValue)
zMin.Bind(wx.EVT_KILL_FOCUS,OnZeroValue)
zeroSizer.Add(zMin)
zeroSizer.Add(wx.StaticText(self.SCCDPanel,label='mm per deg:'),0,wx.ALIGN_CENTER_VERTICAL)
zpdeg = wx.TextCtrl(self.SCCDPanel,value='%.3f'%(data['mm/deg']),style=wx.TE_PROCESS_ENTER)
ObjIndx[zpdeg.GetId()] = ['mm/deg']
zpdeg.Bind(wx.EVT_TEXT_ENTER,OnZpdgValue)
zpdeg.Bind(wx.EVT_KILL_FOCUS,OnZpdgValue)
zeroSizer.Add(zpdeg)
return zeroSizer
def TBLRSizer(data):
def OnTBLRValue(event):
Obj = event.GetEventObject()
item = ObjIndx[Obj.GetId()]
try:
value = int(Obj.GetValue())
except ValueError:
value = data[item[0]][item[1]]
data[item[0]][item[1]] = value
Obj.SetValue('%d'%(value))
self.PlotImage()
TBLRsizer = wx.FlexGridSizer(0,4,5,5)
for i,item in enumerate(['Bottom','Top']):
TBLRsizer.Add(wx.StaticText(self.SCCDPanel,label=item+' limit, pixels:'),0,wx.ALIGN_CENTER_VERTICAL)
TBlim = wx.TextCtrl(self.SCCDPanel,value='%d'%(data['TBlimits'][i]),style=wx.TE_PROCESS_ENTER)
TBlim.Bind(wx.EVT_TEXT_ENTER,OnTBLRValue)
TBlim.Bind(wx.EVT_KILL_FOCUS,OnTBLRValue)
ObjIndx[TBlim.GetId()] = ['TBlimits',i]
TBLRsizer.Add(TBlim)
return TBLRsizer
def ScanSizer(data):
def OnScanValue(event):
Obj = event.GetEventObject()
item = ObjIndx[Obj.GetId()][0]
try:
value = float(Obj.GetValue())
except ValueError:
value = self.data['2thScan'][item]
data['2thScan'][item] = value
Obj.SetValue('%.3f'%(value))
if item in [0,1]:
pixel = data['pixel']
zero = data['Zeros'][0]
tthscale = data['mm/deg']
npixel = (value*tthscale+zero)*1000/pixel[0]
data['LRlimits'][item] = npixel
self.PlotImage()
scanSizer = wx.FlexGridSizer(0,6,5,5)
for i,item in enumerate(['Lower 2-th','Upper 2-th','2-th step']):
scanSizer.Add(wx.StaticText(self.SCCDPanel,label=item+':'))
scanParm = wx.TextCtrl(self.SCCDPanel,value='%.3f'%(data['2thScan'][i]),style=wx.TE_PROCESS_ENTER)
scanParm.Bind(wx.EVT_TEXT_ENTER,OnScanValue)
scanParm.Bind(wx.EVT_KILL_FOCUS,OnScanValue)
ObjIndx[scanParm.GetId()] = [i]
scanSizer.Add(scanParm)
return scanSizer
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(ColorSizer(self.data))
mainSizer.Add(MaxSizer(self.data))
mainSizer.Add(ZSizer(self.data))
mainSizer.Add(ZeroSizer(self.data))
mainSizer.Add(ScanSizer(self.data))
mainSizer.Add(TBLRSizer(self.data))
self.SCCDPanel.SetSizer(mainSizer)
mainSizer.Layout()
fitSize = mainSizer.Fit(self.SCCDPanel)
# self.SCCDPanel.GetParent().SetSize(fitSize)
def PlotImage(self):
pixel = self.data['pixel']
scalex = pixel[0]/1000.
scaley = pixel[1]/1000.
def OnMotion(event):
Page.canvas.SetToolTipString('')
sizexy = self.data['size']
if event.xdata and event.ydata: #avoid out of frame errors
Page.canvas.SetCursor(wx.CROSS_CURSOR)
item = self.itemPicked
if item:
if 'Line' in str(item):
Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
else:
xpos = event.xdata
ypos = event.ydata
xpix = xpos/(self.data['imScale']*scalex)
ypix = sizexy[1]-ypos/(self.data['imScale']*scaley)
Int = 0
if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
Int = self.Image[xpix][ypix]-self.data['Zmin']
tth = (xpos-self.data['Zeros'][0])/self.data['mm/deg']
vecA = np.array([1.0,0,0])
vecB = np.array([npcosd(tth)*self.data['radius'],npsind(tth)*self.data['radius'],(ypos-self.data['Zeros'][1])])
vecB /= nl.norm(vecB)
tth2 = npacosd(np.dot(vecA,vecB))*tth/abs(tth)
self.plotNB.status.SetStatusText('Detector x,y =%9.3fmm %9.3fmm, 2-th =%9.3f I = %6d'%(xpos,ypos,tth2,Int),1)
def OnPick(event):
if self.itemPicked is not None: return
self.itemPicked = event.artist
self.mousePicked = event.mouseevent
def OnRelease(event):
if self.itemPicked is None: return
xpos,ypos = [event.xdata,event.ydata]
if '_line0' in str(self.itemPicked): #X-zero
self.data['Zeros'][0] = xpos
elif '_line1' in str(self.itemPicked): #Y-zero
self.data['Zeros'][1] = ypos
elif '_line2' in str(self.itemPicked): #Y-lower limit
self.data['TBlimits'][0] = int(ypos/scaley)
elif '_line3' in str(self.itemPicked): #Y-upper limit
self.data['TBlimits'][1] = int(ypos/scaley)
elif '_line4' in str(self.itemPicked): #X-lower limit
self.data['LRlimits'][0] = int(xpos/scalex)
elif '_line5' in str(self.itemPicked): #X-upper limit
self.data['LRlimits'][1] = int(xpos/scalex)
self.itemPicked = None
self.PlotImage()
self.UpdateControls(event)
try:
plotNum = self.plotNB.plotList.index('scanCCD image')
Page = self.plotNB.nb.GetPage(plotNum)
Plot = Page.figure.gca() #get previous powder plot & get limits
xylim = Plot.get_xlim(),Plot.get_ylim()
Page.figure.clf()
Plot = Page.figure.gca()
if not Page.IsShown():
Page.Show()
except ValueError:
Plot = self.plotNB.addMpl('scanCCD image').gca()
plotNum = self.plotNB.plotList.index('scanCCD image')
Page = self.plotNB.nb.GetPage(plotNum)
Page.canvas.mpl_connect('motion_notify_event', OnMotion)
Page.canvas.mpl_connect('pick_event', OnPick)
Page.canvas.mpl_connect('button_release_event', OnRelease)
xylim = []
xlim,ylim = self.data['size']
Imin,Imax = [0,self.data['range'][1]]
Xmax = scalex*xlim*self.data['imScale']
Ymax = scaley*ylim*self.data['imScale']
TBlimit = np.array(self.data['TBlimits'])*scalex
LRlimit = np.array(self.data['LRlimits'])*scaley
self.plotNB.status.SetStatusText('',1)
Zmin = self.data['Zmin']
Zmax = self.data['Zmax']
Zeros = self.data['Zeros']
Lines = []
# MA = ma.masked_greater(ma.masked_less(self.Image.T,Zmin),Zmax)
# MaskA = ma.getmaskarray(MA)
# ImgM = Plot.imshow(MaskA,aspect='auto',cmap='Reds',
# interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,0,Ymax])
Img = Plot.imshow(self.Image.T-Zmin,interpolation='nearest',vmin=Imin,vmax=Imax,
aspect='auto',cmap=self.data['color'],extent=[0,Xmax,0,Ymax])
Lines.append(Plot.axvline(Zeros[0],color='b',dashes=(5,5),picker=3.))
Lines.append(Plot.axhline(Zeros[1],color='b',dashes=(5,5),picker=3.))
Lines.append(Plot.axhline(TBlimit[0],color='g',dashes=(5,5),picker=3.))
Lines.append(Plot.axhline(TBlimit[1],color='r',dashes=(5,5),picker=3.))
Lines.append(Plot.axvline(LRlimit[0],color='g',dashes=(5,5),picker=3.))
Lines.append(Plot.axvline(LRlimit[1],color='r',dashes=(5,5),picker=3.))
for blk in range(len(self.imagefiles)):
Lines.append(Plot.axvline(blk*4096*scalex,color='k'))
Plot.set_title('')
Plot.set_xlabel('Scan, mm')
Plot.set_ylabel('Detector Y, mm')
if xylim:
Page.toolbar.push_current()
Plot.set_xlim(xylim[0])
Plot.set_ylim(xylim[1])
xylim = []
Page.toolbar.push_current()
Page.toolbar.draw()
else:
Page.canvas.draw()
def PlotBlock(self,block,title):
try:
plotNum = self.plotNB.plotList.index('Block')
Page = self.plotNB.nb.GetPage(plotNum)
Plot = Page.figure.gca() #get previous powder plot & get limits
xylim = Plot.get_xlim(),Plot.get_ylim()
Page.figure.clf()
Plot = Page.figure.gca()
if not Page.IsShown():
Page.Show()
except ValueError:
Plot = self.plotNB.addMpl('Block').gca()
plotNum = self.plotNB.plotList.index('Block')
Page = self.plotNB.nb.GetPage(plotNum)
xylim = []
Img = Plot.imshow(block,interpolation='nearest',aspect='equal',cmap=self.data['color'])
Plot.invert_yaxis()
Plot.set_title(title)
if xylim:
Page.toolbar.push_current()
Plot.set_xlim(xylim[0])
Plot.set_ylim(xylim[1])
xylim = []
Page.toolbar.push_current()
Page.toolbar.draw()
else:
Page.canvas.draw()
[docs]
def PlotXY(self,XY,newPlot=False,type=''):
'''simple plot of xy data, used for diagnostic purposes
'''
def OnMotion(event):
xpos = event.xdata
if xpos: #avoid out of frame mouse position
ypos = event.ydata
Page.canvas.SetCursor(wx.CROSS_CURSOR)
try:
self.plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
except TypeError:
self.plotNB.status.SetStatusText('Select '+type+' pattern first',1)
try:
plotNum = self.plotNB.plotList.index(type)
Page = self.plotNB.nb.GetPage(plotNum)
if not newPlot:
Plot = Page.figure.gca()
xylim = Plot.get_xlim(),Plot.get_ylim()
Page.figure.clf()
Plot = Page.figure.gca()
except ValueError:
newPlot = True
Plot = self.plotNB.addMpl(type).gca()
plotNum = self.plotNB.plotList.index(type)
Page = self.plotNB.nb.GetPage(plotNum)
Page.canvas.mpl_connect('motion_notify_event', OnMotion)
Page.SetFocus()
self.plotNB.status.DestroyChildren()
Plot.set_title(type)
if type == 'line scan':
Plot.set_xlabel(r'image x, mm',fontsize=14)
else:
Plot.set_xlabel(r'2-theta, deg',fontsize=14)
Plot.set_ylabel(r''+type,fontsize=14)
colors=['b','g','r','c','m','k']
lenX = 0
X,Y,S = XY
Plot.plot(X,Y,'k',picker=False)
Plot.plot(X,S,'r',picker=False)
if not newPlot:
Page.toolbar.push_current()
Plot.set_xlim(xylim[0])
Plot.set_ylim(xylim[1])
xylim = []
Page.toolbar.push_current()
Page.toolbar.draw()
else:
Page.canvas.draw()
[docs]
class scanCCDmain(wx.App):
[docs]
def OnInit(self):
self.main = scanCCD(None)
self.main.Show()
self.SetTopWindow(self.main)
return True
[docs]
def main():
'starts main application to merge data from scanning CCD'
application = scanCCDmain(0)
application.MainLoop()
if __name__ == '__main__':
main()