def __init__(self,parent):
"""Creates a PelvisOptionPanel"""
wx.Panel.__init__(self,parent)
sizer=wx.BoxSizer(wx.VERTICAL)
self.options={}#member which holds the created text controls
self.DEFAULTS.sort(lambda x,y: x[1]-y[1])
for option in self.DEFAULTS:
(key,_,title,val) = option
sizer.Add(wx.StaticText(self,-1,title))
self.options[key] = wx.TextCtrl(self,-1,val)
sizer.Add(self.options[key])
self.SetAutoLayout(True)
self.specDlg = SpectrumDialog(self)
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Layout()
def __init__(self,Yield):
"""Create a PELvis frame
Keyword arguments:
Yield -- A function to give control back to the main event loop
"""
wx.Frame.__init__(self,None,wx.ID_ANY,"PEL Visualizer")
self.data = PelFile()
self.Yield = Yield
self.mask = np.ones((128,16),dtype=np.bool)
#Create items in the frame
self.yPanel = GraphPanel(self,(2,8),64,GraphPanel.VERTICAL)
self.xPanel = GraphPanel(self,(8,2),64,GraphPanel.INVERTED)
self.colorbar = ColorBarPanel(self,cm.jet)
self.opPanel = PelvisOptionPanel(self)
self.posPanel = PositionPanel(self)
self.imPanel = ImagePanel(self,self.posPanel.set,
self.opPanel.setPosMin,self.opPanel.setPosMax)
self.specDlg = SpectrumDialog(self)
self.cmp = None #color map
self.imageSaveDialog=wx.FileDialog(self,"Choose graphics file",wildcard="Portable Network Graphic (png)|*.PNG|Windows Bitmap (bmp)|*.BMP|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
self.update = self.updateSingle#update the image
self.updateData = self.updateSingleData#update the data in the image
#Create the menu
menubar = wx.MenuBar()
filemenu = wx.Menu()
editmenu = wx.Menu()
scalemenu = wx.Menu()
analysismenu = wx.Menu()
noisemenu = wx.Menu()
#populate the menu
filemenu.Append(self.ID_OPEN,"&Open\tCtrl-O"," Open a PEL file")
filemenu.Append(self.ID_OPENTWO,"&Polarized Set"," Open two PEL files")
filemenu.Append(self.ID_SAVE,"&Save\tCtrl-S"," Save an image file")
filemenu.Append(self.ID_SPECTRUM,"Spectrum"," View the TOF spectrum")
filemenu.Append(self.ID_IMAGE_ARRAY,"&Export Images..."," Save a series of TOF snapshots")
filemenu.Append(self.ID_EXIT,"&Quit\tCtrl-Q"," Quit")
editmenu.Append(self.ID_COPY,"&Copy\tCtrl-c","Copy the current image to the clipboard")
scalemenu.Append(self.ID_GREY,"Greyscale\tCtrl-G","Monochrome images")
scalemenu.Append(self.ID_HUEVAL,"Hue and Value\tCtrl-H","Scaled Rainbow Images")
scalemenu.Append(self.ID_SPECTRAL,"spectral","Uses spectrum of light")
scalemenu.Append(self.ID_PICKER,"Map Picker..."," Select from the full list of colormaps")
analysismenu.Append(self.ID_POLAR,"Check Polarization\tCtrl-P","2d plot of polarization data")
analysismenu.Append(self.ID_FLIPPING,"Check Flipping Ratio\tCtrl-F","2d plot of spin up over spin down")
analysismenu.Append(self.ID_SPIN_UP,"View Spin Up State\tCtrl-U","2d plot of spin up")
analysismenu.Append(self.ID_SPIN_DOWN,"View Spin Down State\tCtrl-D","2d plot of spin down")
noisemenu.Append(self.ID_FLAT,"&Load Flat"," Load a blank run for background subtraction")
noisemenu.Append(self.ID_FAKEFLAT,"Si&mulate Flat"," Drop out background within the same image")
noisemenu.Append(self.ID_ROD,"Region of &Disinterest"," Drop out background within the same image")
noisemenu.Append(self.ID_EXPORT_ROI,"Export ROI"," Export a binary file corresponding to where the data is above the minimum intensity.")
noisemenu.Append(self.ID_IMPORT_ROI,"Import ROI"," Add another exclusion mask.")
#Bind events to the menu
self.Connect(self.ID_EXIT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExit)
self.Connect(self.ID_OPEN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpen)
self.Connect(self.ID_OPENTWO,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpenSet)
self.Connect(self.ID_SAVE,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSave)
self.Connect(self.ID_SPECTRUM,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectrum)
self.Connect(self.ID_IMAGE_ARRAY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImageArray)
self.Connect(self.ID_GREY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnGrey)
self.Connect(self.ID_HUEVAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnHueVal)
self.Connect(self.ID_SPECTRAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectral)
self.Connect(self.ID_PICKER,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPicker)
self.Connect(self.ID_POLAR,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPolar)
self.Connect(self.ID_FLIPPING,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlipping)
self.Connect(self.ID_SPIN_UP,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinUp)
self.Connect(self.ID_SPIN_DOWN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinDown)
self.Connect(self.ID_FLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlat)
self.Connect(self.ID_FAKEFLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFakeFlat)
self.Connect(self.ID_ROD,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnROD)
self.Connect(self.ID_EXPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExportROI)
self.Connect(self.ID_IMPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImportROI)
self.Connect(self.ID_COPY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnCopy)
menubar.Append(filemenu,"&File")
menubar.Append(editmenu,"&Edit")
menubar.Append(scalemenu,"&Color")
menubar.Append(analysismenu,"&Analysis")
menubar.Append(noisemenu,"&Noise")
self.SetMenuBar(menubar)
#arrange window
sizer = wx.GridBagSizer()
sizer.Add(self.colorbar,pos=wx.GBPosition(0,9),span=wx.GBSpan(9,1))
sizer.Add(self.imPanel,pos=wx.GBPosition(0,1),span=wx.GBSpan(8,8))
sizer.Add(self.yPanel,pos=wx.GBPosition(0,0),span=wx.GBSpan(8,1))
sizer.Add(self.xPanel,pos=wx.GBPosition(8,1),span=wx.GBSpan(1,8))
sizer.Add(self.opPanel,pos=wx.GBPosition(0,10),span=wx.GBSpan(8,1),flag=wx.EXPAND)
sizer.Add(self.posPanel,pos=wx.GBPosition(8,0),flag=wx.EXPAND)
self.progress = wx.Gauge(self,range=1000)
sizer.Add(self.progress,pos=wx.GBPosition(9,0),span=wx.GBSpan(1,11),flag=wx.EXPAND)
updateButton = wx.Button(self,-1,"Update")
updateButton.Bind(wx.EVT_BUTTON,self.OnUpdateButton)
sizer.Add(updateButton,flag=wx.EXPAND,pos=wx.GBPosition(8,10))
self.data = self.makePel()
self.flatrun = None#background data
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Show(True)
class PelvisFrame(wx.Frame):
"""The main application window for PELvis"""
#Menu ID constants
ID_OPEN = 100
ID_OPENTWO = 110
ID_SAVE = 130
ID_SPECTRUM=140
ID_IMAGE_ARRAY=160
ID_EXIT = 190
ID_GREY = 200
ID_HUEVAL = 220
ID_SPECTRAL = 230
ID_PICKER = 290
ID_POLAR = 300
ID_FLIPPING = 310
ID_SPIN_UP = 320
ID_SPIN_DOWN = 330
ID_FLAT = 420
ID_FAKEFLAT = 430
ID_ROD = 440
ID_EXPORT_ROI = 450
ID_IMPORT_ROI = 460
ID_COPY = 500
def __init__(self,Yield):
"""Create a PELvis frame
Keyword arguments:
Yield -- A function to give control back to the main event loop
"""
wx.Frame.__init__(self,None,wx.ID_ANY,"PEL Visualizer")
self.data = PelFile()
self.Yield = Yield
self.mask = np.ones((128,16),dtype=np.bool)
#Create items in the frame
self.yPanel = GraphPanel(self,(2,8),64,GraphPanel.VERTICAL)
self.xPanel = GraphPanel(self,(8,2),64,GraphPanel.INVERTED)
self.colorbar = ColorBarPanel(self,cm.jet)
self.opPanel = PelvisOptionPanel(self)
self.posPanel = PositionPanel(self)
self.imPanel = ImagePanel(self,self.posPanel.set,
self.opPanel.setPosMin,self.opPanel.setPosMax)
self.specDlg = SpectrumDialog(self)
self.cmp = None #color map
self.imageSaveDialog=wx.FileDialog(self,"Choose graphics file",wildcard="Portable Network Graphic (png)|*.PNG|Windows Bitmap (bmp)|*.BMP|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
self.update = self.updateSingle#update the image
self.updateData = self.updateSingleData#update the data in the image
#Create the menu
menubar = wx.MenuBar()
filemenu = wx.Menu()
editmenu = wx.Menu()
scalemenu = wx.Menu()
analysismenu = wx.Menu()
noisemenu = wx.Menu()
#populate the menu
filemenu.Append(self.ID_OPEN,"&Open\tCtrl-O"," Open a PEL file")
filemenu.Append(self.ID_OPENTWO,"&Polarized Set"," Open two PEL files")
filemenu.Append(self.ID_SAVE,"&Save\tCtrl-S"," Save an image file")
filemenu.Append(self.ID_SPECTRUM,"Spectrum"," View the TOF spectrum")
filemenu.Append(self.ID_IMAGE_ARRAY,"&Export Images..."," Save a series of TOF snapshots")
filemenu.Append(self.ID_EXIT,"&Quit\tCtrl-Q"," Quit")
editmenu.Append(self.ID_COPY,"&Copy\tCtrl-c","Copy the current image to the clipboard")
scalemenu.Append(self.ID_GREY,"Greyscale\tCtrl-G","Monochrome images")
scalemenu.Append(self.ID_HUEVAL,"Hue and Value\tCtrl-H","Scaled Rainbow Images")
scalemenu.Append(self.ID_SPECTRAL,"spectral","Uses spectrum of light")
scalemenu.Append(self.ID_PICKER,"Map Picker..."," Select from the full list of colormaps")
analysismenu.Append(self.ID_POLAR,"Check Polarization\tCtrl-P","2d plot of polarization data")
analysismenu.Append(self.ID_FLIPPING,"Check Flipping Ratio\tCtrl-F","2d plot of spin up over spin down")
analysismenu.Append(self.ID_SPIN_UP,"View Spin Up State\tCtrl-U","2d plot of spin up")
analysismenu.Append(self.ID_SPIN_DOWN,"View Spin Down State\tCtrl-D","2d plot of spin down")
noisemenu.Append(self.ID_FLAT,"&Load Flat"," Load a blank run for background subtraction")
noisemenu.Append(self.ID_FAKEFLAT,"Si&mulate Flat"," Drop out background within the same image")
noisemenu.Append(self.ID_ROD,"Region of &Disinterest"," Drop out background within the same image")
noisemenu.Append(self.ID_EXPORT_ROI,"Export ROI"," Export a binary file corresponding to where the data is above the minimum intensity.")
noisemenu.Append(self.ID_IMPORT_ROI,"Import ROI"," Add another exclusion mask.")
#Bind events to the menu
self.Connect(self.ID_EXIT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExit)
self.Connect(self.ID_OPEN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpen)
self.Connect(self.ID_OPENTWO,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpenSet)
self.Connect(self.ID_SAVE,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSave)
self.Connect(self.ID_SPECTRUM,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectrum)
self.Connect(self.ID_IMAGE_ARRAY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImageArray)
self.Connect(self.ID_GREY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnGrey)
self.Connect(self.ID_HUEVAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnHueVal)
self.Connect(self.ID_SPECTRAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectral)
self.Connect(self.ID_PICKER,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPicker)
self.Connect(self.ID_POLAR,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPolar)
self.Connect(self.ID_FLIPPING,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlipping)
self.Connect(self.ID_SPIN_UP,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinUp)
self.Connect(self.ID_SPIN_DOWN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinDown)
self.Connect(self.ID_FLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlat)
self.Connect(self.ID_FAKEFLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFakeFlat)
self.Connect(self.ID_ROD,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnROD)
self.Connect(self.ID_EXPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExportROI)
self.Connect(self.ID_IMPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImportROI)
self.Connect(self.ID_COPY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnCopy)
menubar.Append(filemenu,"&File")
menubar.Append(editmenu,"&Edit")
menubar.Append(scalemenu,"&Color")
menubar.Append(analysismenu,"&Analysis")
menubar.Append(noisemenu,"&Noise")
self.SetMenuBar(menubar)
#arrange window
sizer = wx.GridBagSizer()
sizer.Add(self.colorbar,pos=wx.GBPosition(0,9),span=wx.GBSpan(9,1))
sizer.Add(self.imPanel,pos=wx.GBPosition(0,1),span=wx.GBSpan(8,8))
sizer.Add(self.yPanel,pos=wx.GBPosition(0,0),span=wx.GBSpan(8,1))
sizer.Add(self.xPanel,pos=wx.GBPosition(8,1),span=wx.GBSpan(1,8))
sizer.Add(self.opPanel,pos=wx.GBPosition(0,10),span=wx.GBSpan(8,1),flag=wx.EXPAND)
sizer.Add(self.posPanel,pos=wx.GBPosition(8,0),flag=wx.EXPAND)
self.progress = wx.Gauge(self,range=1000)
sizer.Add(self.progress,pos=wx.GBPosition(9,0),span=wx.GBSpan(1,11),flag=wx.EXPAND)
updateButton = wx.Button(self,-1,"Update")
updateButton.Bind(wx.EVT_BUTTON,self.OnUpdateButton)
sizer.Add(updateButton,flag=wx.EXPAND,pos=wx.GBPosition(8,10))
self.data = self.makePel()
self.flatrun = None#background data
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Show(True)
def makePel(self):
"""Create a blank Pel object for loading detector data"""
data = PelFile()
def statusfunc(x):
self.progress.SetValue(x)
self.Yield()
data.statusfunc = statusfunc
return data
def loadPel(self,message):
"""Load a .pel file and its monitor data.
Keyword arguments:
message -- The title for the load file dialog.
"""
dlg=wx.FileDialog(self,message,wildcard="He3 data|*neutron_event.dat|Preformatted Histograms|*.npy",style=wx.FD_OPEN)
if dlg.ShowModal()==wx.ID_OK:
# self.SetCursor(wx.CURSOR_WAIT)
path = dlg.GetPath()
if path[-3:] == "dat":
data = self.makePel()
data.readfileimage(path)
elif path[-3:] == "npy":
data = np.load(path)
# self.SetCursor(wx.CURSOR_ARROW)
else:
return (None,None)
mon = MonFile(path[:-17]+"bmon_histo.dat")
return (data,mon)
def OnImageArray(self,event):
"""Exports the 2d detector image by wavelength"""
dlg = self.imageSaveDialog
if dlg.ShowModal()==wx.ID_OK:
path=dlg.GetPath()
ext = path[-4:]
path = path[:-4]
(lmin,lmax) = self.opPanel.getLambdaRange()
for i in range(lmin,lmax):
file=path+("%03i"%i)+ext
self.opPanel.setLambdaRange(0.1*i,0.1*(i+1))
self.updateData()
self.update()
self.imPanel.saveImage(file)
self.progress.SetValue(1000*(i-lmin)/(lmax-lmin))
self.Yield()
self.opPanel.setLambdaRange(lmin*0.1,lmax*0.1)
self.updateData()
self.progress.SetValue(0)
def loadNormPel(self,message):
"""Load a .pel file, normalize it by monitor, and subtract background"""
(data,mon) = self.loadPel(message)
if isinstance(data,PelFile):
data = np.asarray(data.make3d(),np.float32)
if mon is None:
return (data,1)
if self.flatrun != None:
flatrun = np.load(self.flatrun)
self.flatrun.seek(0)
flatrun *= mon.time
data -= flatrun
spec = mon.spec
monsum = np.sum(spec)
print("Integrated monitor counts: " + str(monsum))
data /= monsum
return (data,np.sum(mon.spec))
# def getLambdaRange(self):
# try:
# lmin = int(float(self.lambdaMin.GetValue())*10)
# except ValueError:
# lmin = 0
# try:
# lmax = int(float(self.lambdaMax.GetValue())*10)
# except ValueError:
# lmax = 200
# return (lmin,lmax)
def updateSingleData(self,event=None):
"""Update changes in wavelength on a single file"""
print("Make 2d")
(lmin,lmax) = self.opPanel.getLambdaRange()
self.flatdata = np.sum(self.data[:,:,lmin:lmax],2)
self.update()
def updateDataFlip(self,event=None):
"""Update changes in wavelength for flipping ratios"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,d3d)=self.data
u = np.sum(u3d[:,:,lmin:lmax],2)
d = np.sum(d3d[:,:,lmin:lmax],2)
self.flatdata = u/(d+1e-6)
self.update()
def updateDataPolar(self,event=None):
"""Update changes in wavelength for polarizations"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,d3d)=self.data
u = np.sum(u3d[:,:,lmin:lmax],2)
d = np.sum(d3d[:,:,lmin:lmax],2)
self.flatdata = (u-d)/(u+d+1e-6)
self.update()
def updateDataUp(self,event=None):
"""Update changes in wavelength for the spin up state"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,_)=self.data
self.flatdata = np.sum(u3d[:,:,lmin:lmax],2)
self.update()
def updateDataDown(self,event=None):
"""Update changes in wavelength for the spin down state"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(_,d3d)=self.data
self.flatdata = np.sum(d3d[:,:,lmin:lmax],2)
self.update()
def updateSingle(self,event=None):
"""Update the 2D data for the region of interest and intensity"""
(vMin,vMax) = self.opPanel.getIntensityRange()
(xMin,xMax,yMin,yMax) = self.opPanel.getRoi()
data = self.flatdata[:,:]
#Mask to zero during the summing parts
data[np.logical_not(self.mask)] = 0
self.posPanel.data = data
self.posPanel.setRange(xMin,yMin,xMax,yMax)
x=np.arange(128,0,-1)
y=np.sum(data[:,xMin:xMax],axis=1)
self.yPanel.SetPlot(x,y)
#handle the x-plot
x=np.arange(0,16,1)
y=np.sum(data[yMin:yMax,:],axis=0)
self.xPanel.SetPlot(x,y)
if vMin is None:
vMin = np.min(data)
if vMax is None:
vMax = np.max(data)
self.colorbar.setRange(vMin,vMax)
self.colorbar.update()
#mask to vmin for the plotting
data[np.logical_not(self.mask)] = vMin
self.imPanel.update(self.flatdata,vMin,vMax)
def OnUpdateButton(self,event):
"""Refresh the data when the user pushes the "Update" button"""
#This function is needed for wxWidgets to allow
#for dynamically changing the bound function
self.updateData(event)
def OnOpen(self,event):
"""Load a single .pel file for display"""
data,scale = self.loadNormPel("Choose the Pel File to Open")
if data is None:
return
self.data = data
self.scale = scale
self.progress.SetValue(0)
self.specDlg.setMode("up")
self.updateData = self.updateSingleData
self.update = self.updateSingle
self.updateData()
def OnOpenSet(self,event):
"""Load a spin flip measurement for display"""
if self.loadUpAndDown():
self.OnPolar(event)
def OnFlat(self,event):
"""Load a blank run for background subtraction"""
(data,mon) = self.loadPel("Choose a Blank Run")
if data == None:
return
if isinstance(data,PelFile):
flatrun = data.make3d()
elif isinstance(data,np.ndarray):
flatrun = data
flatrun = np.sum(flatrun,axis=2)
flatrun /= RESOLUTION
flatrun /= float(mon.time)
flatrun = np.expand_dims(flatrun,2)
self.flatrun = TemporaryFile()
np.save(self.flatrun,flatrun)
self.flatrun.seek(0)
self.progress.SetValue(0)
def OnFakeFlat(self,event):
"""Create a fake background run from outside the region of interest."""
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
totarea = 512*512
centarea = (yMax-yMin)*(xMax-xMin)
backgroundarea = totarea-centarea
if type(self.data) is tuple:
(u,d)=self.data
totu = np.sum(u)
totd = np.sum(d)
centu = np.sum(u[yMin:yMax,xMin:xMax,:])
centd = np.sum(d[yMin:yMax,xMin:xMax,:])
backgroundu = totu-centu
backgroundd = totd-centd
backgroundrateu = backgroundu/backgroundarea
backgroundrated = backgroundd/backgroundarea
backgroundrateu /= (RESOLUTION + 1) #normalize against the wavelengths
backgroundrated /= (RESOLUTION + 1) #normalize against the wavelengths
###Stupid Memory Errors
del self.data
u -= backgroundrateu
d -= backgroundrated
###
self.data=(u,d)
else:
d=self.data
tot = np.sum(d)
cent = np.sum(d[yMin:yMax,xMin:xMax,:])
background = tot-cent
backgroundrate = background/backgroundarea
backgroundrate /= (RESOLUTION + 1) #normalize against the wavelengths
self.data-=backgroundrate
self.updateData()
#Subtract out the region of disinterest
def OnROD(self,event):
"""Take the region of interest as background noise"""
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
area = (yMax-yMin)*(xMax-xMin)
if type(self.data) is tuple:
u,d=self.data
del self.data
totu = np.sum(np.sum(u[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
totd = np.sum(np.sum(d[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
totu /= area
totd /= area
u -= totu
d -= totd
self.data=(u,d)
else:
d=self.data
totd = np.sum(np.sum(d[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
#totd = np.atleast_3d(totd)
totd /= area
#print(totd.shape)
#print(self.data.shape)
self.data -= totd
self.updateData()
def OnExportROI(self,event):
"""Save a file containing a map of where the current data
image is greater than vmin"""
vMin,_ = self.opPanel.getIntensityRange()
mask = self.flatdata > vMin
# (vMin,vMax) = self.opPanel.getIntensityRange()#
# (xMin,xMax,yMin,yMax) = self.opPanel.getRoi()#
# (lMin,lMax) = self.opPanel.getLambdaRange()#
# (lMin,lMax) = (lMin/10,lMax/10)#
# mask = [["xMin",xMin], ["xMax",xMax], ["yMin",yMin], ["yMax",yMax], \
# ["lMin",lMin], ["lMax",lMax], ["vMin",vMin], ["vMax",vMax]]#
dlg = wx.FileDialog(self,
"Where to save the mask file?",
wildcard="Numpy dump (npy)|*.npy|Text (dat)|*.dat",
style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal()==wx.ID_OK:
path=dlg.GetPath()
ext = path[-4:]
if ext == ".dat":
np.savetxt(path,mask,fmt="%d")
else:
np.save(path,mask)
def OnImportROI(self,event):
"""Adds another mask to the current system mask"""
dlg = wx.FileDialog(self,
"Which Mask File?",
wildcard="Numpy dump (npy)|*.npy|Text (dat)|*.dat",
style=wx.FD_OPEN)
time.sleep(.1)
if dlg.ShowModal()==wx.ID_OK:
path = dlg.GetPath()
ext = path[-4:]
if ext == ".dat":
newmask = np.loadtxt(path,dtype=np.bool)
newmask=dict(newmask)#
else:
newmask = np.load(path)
self.mask = np.logical_and(self.mask,newmask)
#self.opPanel.setPosMin(newmask["xMin"],newmask["yMin"])#
#self.opPanel.setPosMax(newmask["xMax"],newmask["yMax"])#
#self.opPanel.setLambdaRange(newmask["lMin"],newmask["lMax"])#
#self.opPanel.setIntensityRange(newmask["vMin"],newmask["vMax"])#
self.updateData()
def OnSave(self,event):
"""Save the current 2D image to a file"""
print("OnSave")
# dlg=wx.FileDialog(self,"Choose graphics file",wildcard="Windows Bitmap (bmp)|*.BMP|Portable Network Graphic (png)|*.PNG|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
dlg = self.imageSaveDialog
if dlg.ShowModal()==wx.ID_OK:
self.imPanel.saveImage(dlg.GetPath())
def OnSpectrum(self,event):
"""Display a plot of the region of interest versus wavelength"""
print("OnSpectrum")
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
if type(self.data) is tuple:
u3d,d3d = self.data
u3d = u3d[:,:,:]
d3d = d3d[:,:,:]
u3d[np.logical_not(self.mask)] = 0
d3d[np.logical_not(self.mask)] = 0
u = np.sum(np.sum(u3d[yMin:yMax,xMin:xMax],0),0)
d = np.sum(np.sum(d3d[yMin:yMax,xMin:xMax],0),0)
uscale,dscale = self.scale
self.specDlg.setScale(uscale,dscale)
self.specDlg.setData(u,d)
else:
copy = self.data[:,:,:]
copy[np.logical_not(self.mask)] = 0
u = np.sum(np.sum(copy[yMin:yMax,xMin:xMax],0),0)
# u *= self.scale
self.specDlg.setScale(self.scale)
self.specDlg.setData(u)
self.specDlg.setIntensityRange(self.opPanel.getIntensityRange())
self.specDlg.Show()
def OnGrey(self,event):
"""Set the colormap to gray"""
self.imPanel.cmap = cm.gray
self.colorbar.setCmap(cm.gray)
self.update()
def OnHueVal(self,event):
"""Set the colormap to a rainbow"""
self.imPanel.cmap = cm.jet
self.colorbar.setCmap(cm.jet)
self.update()
def OnSpectral(self,event):
"""Set the colormap to the spectral map"""
self.imPanel.cmap = cm.spectral
self.colorbar.setCmap(cm.spectral)
self.update()
def OnPicker(self,event):
"""Let the user pick a color map from a list"""
if self.cmp is None:
self.cmp = ColorMapPicker(self,self.setColorMap)
self.cmp.Show()
def setColorMap(self,cmap):
"""Changes to the given colormap"""
self.imPanel.cmap = cmap
self.colorbar.setCmap(cmap)
self.update()
def OnExit(self,event):
"""Quit the program"""
self.Close()
def loadUpAndDown(self):
"""Read in spin flip data"""
u3d,uscale = self.loadNormPel("Spin Up State")
if u3d is None:
return False
del self.data
d3d,dscale = self.loadNormPel("Spin Down State")
self.data = (u3d,d3d)
self.scale = (uscale,dscale)
return True
def OnPolar(self,event):
"""Display neutron polarization"""
print("OnPolar")
self.specDlg.setMode("polar")
self.updateData = self.updateDataPolar
self.update = self.updateSingle
self.updateData()
def OnFlipping(self,event):
"""Display the flipping ratio"""
print("OnFlip")
self.specDlg.setMode("flipping")
self.updateData = self.updateDataFlip
self.update = self.updateSingle
self.updateData()
def OnAnalysisSpinUp(self,event):
"""Display the Spin Up data"""
print("OnSpinUp")
self.specDlg.setMode("up")
self.updateData = self.updateDataUp
self.update = self.updateSingle
self.updateData()
def OnAnalysisSpinDown(self,event):
"""Display the Spin Down data"""
print("OnSpinDown")
self.specDlg.setMode("down")
self.updateData = self.updateDataDown
self.update = self.updateSingle
self.updateData()
def OnCopy(self,event):
"""Copy the image to a clipboard"""
self.imPanel.copyToClipboard()
class PelvisOptionPanel(wx.Panel):
"""A panel for user parameters
The panel gets it's parameters and appearance from the built in
DEFAULTS variable. This was designed to allow the easy addition
of more parameters in the future.
"""
#Each parameter is a tuple
#0 - variable name
#1 - position in list
#2 - label
#3 - default value
DEFAULTS = [("lambdaMax",0,"Maximum Wavelength","20"),
("lambdaMin",10,"Minimum Wavelength","0"),
("intMax",20,"Maximum Intensity",""),
("intMin",30,"Minimum Intensity",""),
("xMin",40,"Minimun X","0"),
("xMax",50,"Maximum X","16"),
("yMin",60,"Minimun Y","0"),
("yMax",70,"Maximum Y","128")]
def __init__(self,parent):
"""Creates a PelvisOptionPanel"""
wx.Panel.__init__(self,parent)
sizer=wx.BoxSizer(wx.VERTICAL)
self.options={}#member which holds the created text controls
self.DEFAULTS.sort(lambda x,y: x[1]-y[1])
for option in self.DEFAULTS:
(key,_,title,val) = option
sizer.Add(wx.StaticText(self,-1,title))
self.options[key] = wx.TextCtrl(self,-1,val)
sizer.Add(self.options[key])
self.SetAutoLayout(True)
self.specDlg = SpectrumDialog(self)
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Layout()
def getLambdaRange(self):
"""Gives a tuple with the minimum and maximum wavelength indices"""
try:
lmin = int(float(self.options["lambdaMin"].GetValue())*10)
except ValueError:
lmin = 0
try:
lmax = int(float(self.options["lambdaMax"].GetValue())*10)
except ValueError:
lmax = RESOLUTION
return (lmin,lmax)
def setLambdaRange(self,min,max):
"""Set the minimum and maximum wavelengths"""
self.options["lambdaMin"].SetValue(str(min))
self.options["lambdaMax"].SetValue(str(max))
def getIntensityRange(self):
"""Return a tuple with the floor and ceilling for intensity
If a value isn't specified, or is not a number, None is returned
for that part of the range.
"""
try:
vMin = float(self.options["intMin"].GetValue())
except ValueError:
vMin = None
try:
vMax = float(self.options["intMax"].GetValue())
except ValueError:
vMax = None
return (vMin,vMax)
def setIntensityRange(self,min,max):
self.options["intMin"].SetValue(str(min))
self.options["intMax"].SetValue(str(max))
self.specDlg.setIntensityRange((min,max))
def getRoi(self):
"""Returns a 4-tuple with the region of interest
Returns (xmin,xmax,ymin,ymax). Minimum values, if
unspecified, are set to zero. Maximum values, if
unspecified, are set to 512.
"""
try:
xMin = int(self.options["xMin"].GetValue())
except ValueError:
xMin = 0
try:
xMax = int(self.options["xMax"].GetValue())
except ValueError:
xMax = 512
try:
yMin = int(self.options["yMin"].GetValue())
except ValueError:
yMin = 0
try:
yMax = int(self.options["yMax"].GetValue())
except ValueError:
yMax = 512
return (xMin,xMax,yMin,yMax)
def setPosMin(self,x,y):
"""Takes the x and y coordinates for the NW corner of the ROI."""
self.options["xMin"].SetValue(str(x))
self.options["yMin"].SetValue(str(y))
def setPosMax(self,x,y):
"""Takes the x and y coordinates for the SE corner of the ROI."""
self.options["xMax"].SetValue(str(x))
self.options["yMax"].SetValue(str(y))
