443 lines
14 KiB
Python
443 lines
14 KiB
Python
#!/usr/bin/env python
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#*-----------------------------------------------------------------------*
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#| |
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#| Copyright (c) 2013 by Paul Scherrer Institute (http://www.psi.ch) |
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#| |
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#| Author Thierry Zamofing (thierry.zamofing@psi.ch) |
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#*-----------------------------------------------------------------------*
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'''
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implements an image view to show a colored image of a hdf5 dataset.
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'''
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if __name__ == '__main__':
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#Used to guarantee to use at least Wx2.8
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import wxversion
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wxversion.ensureMinimal('2.8')
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import wx
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import matplotlib as mpl
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if __name__ == '__main__':
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mpl.use('WXAgg')
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#or mpl.use('WX')
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#matplotlib.get_backend()
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import wxutils as ut
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import os
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import numpy as np
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from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
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import pylab as plt #used for the colormaps
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#or from matplotlib.backends.backend_wx import FigureCanvasWx as FigureCanvas
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#The source of the DraggableColorbar is from:
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#http://www.ster.kuleuven.be/~pieterd/python/html/plotting/interactive_colorbar.html
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class MPLCanvasErr(FigureCanvas):
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def __init__(self,parent,SetStatusCB=None):
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if SetStatusCB:
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self.SetStatusCB=SetStatusCB
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fig = mpl.figure.Figure()
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ax = fig.add_axes([0.075,0.075,0.85,0.85])
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FigureCanvas.__init__(self,parent, -1, fig)
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self.mpl_connect('motion_notify_event', self.OnMotion)
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self.mpl_connect('button_press_event', self.OnBtnPress)
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self.mpl_connect('button_release_event', self.OnBtnRelease)
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self.mpl_connect('scroll_event', self.OnBtnScroll)
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self.mpl_connect('key_press_event',self.OnKeyPress)
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self.fig=fig
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self.ax=ax
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def InitChild(self,pts,rec):
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fig=self.fig
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ax=self.ax
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err=np.sqrt((rec[:,1]-rec[:,4])**2+(rec[:,1]-rec[:,4])**2)
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hl = ax.plot(err, 'r-')
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ax.xaxis.set_label_text('time (10x servo cycle)')
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ax.yaxis.set_label_text('pos-error um')
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self.ax = ax
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self.hl = hl
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def OnMotion(self,event):
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print event,event.x,event.y,event.inaxes,event.xdata,event.ydata
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return
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if event.inaxes==self.ax:
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x=int(round(event.xdata))
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y=int(round(event.ydata))
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try:
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v=self.img.get_array()[y,x]
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except IndexError as e:
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pass
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else:
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#print x,y,v
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self.SetStatusCB(self.Parent,0,(x,y,v))
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elif event.inaxes==self.colBar.ax:
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colBar=self.colBar
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pt=colBar.ax.bbox.get_points()[:,1]
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nrm=colBar.norm
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vmin,vmax,p0,p1,pS = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
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if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
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vS=0
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else:#scale around point
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vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
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self.SetStatusCB(self.Parent,1,vS)
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try:
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vmin,vmax,p0,p1,pS=self.colBarPressed
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except AttributeError:
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return
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#if event.inaxes != self.cbar.ax: return
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colBar=self.colBar
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#print vmin,vmax,p0,p1,pS,type(colBar.norm)
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#print 'x0=%f, xpress=%f, event.xdata=%f, dx=%f, x0+dx=%f'%(x0, xpress, event.xdata, dx, x0+dx)
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if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
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if event.button==1:
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#colBar.norm.vmin=.1
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colBar.norm.vmax=vmax*np.exp((pS-event.y)/100)
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#scale= np.exp((event.y-pS)/100)
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elif event.button==1:#move top,bottom,both
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pD = event.y - pS
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vD=(vmax-vmin)/(p1-p0)*(pS-event.y)
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colBar.norm.vmin = vmin+vD
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colBar.norm.vmax = vmax+vD
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elif event.button==3:#scale around point
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scale= np.exp((pS-event.y)/100)
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vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
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#print scale,vS
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colBar.norm.vmin = vS-scale*(vS-vmin)
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colBar.norm.vmax = vS-scale*(vS-vmax)
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self.img.set_norm(colBar.norm)#force image to redraw
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colBar.patch.figure.canvas.draw()
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def OnBtnPress(self, event):
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"""on button press we will see if the mouse is over us and store some data"""
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print dir(event.guiEvent)
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return
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if event.inaxes == self.colBar.ax:
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#if event.guiEvent.LeftDClick()==True:
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# print dlg
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pt=self.colBar.ax.bbox.get_points()[:,1]
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nrm=self.colBar.norm
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self.colBarPressed = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
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#self.colBarPressed = event.x, event.y
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#print self.colBarPressed
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#self.OnMouse(event)
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pass
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def OnBtnRelease(self, event):
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"""on release we reset the press data"""
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#self.OnMouse(event)
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return
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try: del self.colBarPressed
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except AttributeError: pass
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def OnBtnScroll(self, event):
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return
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#self.OnMouse(event)
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colBar=self.colBar
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if event.inaxes==colBar.ax:
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pt=colBar.ax.bbox.get_points()[:,1]
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nrm=colBar.norm
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vmin,vmax,p0,p1,pS = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
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if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
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scale= np.exp((-event.step)/10)
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colBar.norm.vmax=vmax*scale
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else:#scale around point
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scale= np.exp((-event.step)/10)
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vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
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#print scale,vS
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colBar.norm.vmin = vS-scale*(vS-vmin)
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colBar.norm.vmax = vS-scale*(vS-vmax)
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self.img.set_norm(colBar.norm)#force image to redraw
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colBar.patch.figure.canvas.draw()
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def OnKeyPress(self, event):
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return
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colCycle=self.colCycle
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colBar=self.colBar
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if event.key=='down':
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self.colIndex += 1
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elif event.key=='up':
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self.colIndex -= 1
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self.colIndex%=len(colCycle)
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cmap = colCycle[self.colIndex]
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colBar.set_cmap(cmap)
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colBar.draw_all()
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self.img.set_cmap(cmap)
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self.img.get_axes().set_title(cmap)
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colBar.patch.figure.canvas.draw()
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def OnMouse(self, event):
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return
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for k in dir(event):
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if k[0]!='_':
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print k,getattr(event,k)
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class MAErrorFrame(wx.Frame):
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def __init__(self, parent,doc):
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wx.Frame.__init__(self, parent, title='xy-Plot', size=wx.Size(850, 650))
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self.doc=doc;doc.view.append(self)
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imgDir=ut.Path.GetImage()
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icon = wx.Icon(os.path.join(imgDir,'PBMA.ico'), wx.BITMAP_TYPE_ICO)
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self.SetIcon(icon)
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canvas = MPLCanvasErr(self,self.SetStatusCB)
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sizer = wx.BoxSizer(wx.VERTICAL)
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sizer.Add(canvas, 1, wx.LEFT | wx.TOP | wx.GROW)
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self.SetSizer(sizer)
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toolbar=ut.AddToolbar(canvas,sizer)
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canvas.InitChild(doc.fh['pts'],doc.fh['rec'])
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self.Centre()
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self.BuildMenu()
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self.canvas=canvas
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self.sizer=sizer
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self.toolbar=toolbar
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def BuildMenu(self):
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mnBar = wx.MenuBar()
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#-------- Edit Menu --------
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mn = wx.Menu()
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mnItem=mn.Append(wx.ID_ANY, 'Setup Colormap', 'Setup the color mapping ');self.Bind(wx.EVT_MENU, self.OnColmapSetup, mnItem)
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mnItem=mn.Append(wx.ID_ANY, 'Invert X-Axis', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnInvertAxis, mnItem)
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self.mnIDxAxis=mnItem.GetId()
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mnItem=mn.Append(wx.ID_ANY, 'Invert Y-Axis', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnInvertAxis, mnItem)
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mnItem=mn.Append(wx.ID_ANY, 'Show Moments', 'Show image moments ', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnShowMoments, mnItem)
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self.mnItemShowMoment=mnItem
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mnItem=mn.Append(wx.ID_ANY, 'Tomo Normalize', 'Multiplies each pixel with a normalization factor. Assumes there exist an array exchange/data_white', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnTomoNormalize, mnItem)
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self.mnItemTomoNormalize=mnItem
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mnBar.Append(mn, '&Edit')
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mn = wx.Menu()
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mnItem=mn.Append(wx.ID_ANY, 'Help', 'How to use the image viewer');self.Bind(wx.EVT_MENU, self.OnHelp, mnItem)
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mnBar.Append(mn, '&Help')
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self.SetMenuBar(mnBar)
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self.CreateStatusBar()
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def OnUpdate(self, msg, usrData):
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# this is the model-view-control update function
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print 'OnUpdate',self, msg, usrData
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def SetIdxXY(self,x,y):
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self.idxXY=(x,y)
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@staticmethod
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def SetStatusCB(obj,mode,v):
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if mode==0:
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obj.SetStatusText( "x= %d y=%d val=%g"%v,0)
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elif mode==1:
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obj.SetStatusText( "Colormap Value %d (drag to scale)"%v,0)
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else:
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raise KeyError('wrong mode')
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def OnShowMoments(self,event):
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if event.IsChecked():
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dlg = wx.FileDialog(self, "Choose valid mask file (e.g. pilatus_valid_mask.mat)", os.getcwd(), '','MATLAB files (*.mat)|*.mat|all (*.*)|*.*', wx.OPEN|wx.FD_CHANGE_DIR)
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if dlg.ShowModal() == wx.ID_OK:
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fnMatMsk = dlg.GetPath()
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print 'OnOpen',fnMatMsk
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dlg.Destroy()
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if not fnMatMsk:
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return
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#fnMatMsk='/scratch/detectorData/cSAXS_2013_10_e14608_georgiadis_3D_for_Marianne/analysis/data/pilatus_valid_mask.mat'
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self.procMoment=pm=ProcMoment()
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pm.SetMskMat(fnMatMsk,False)
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#roi=[603, 826, 200, 200]
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#pm.roi=(slice(roi[1],roi[1]+roi[3]),slice(roi[0],roi[0]+roi[2]))
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#pm.shape=(roi[3],roi[2])
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#pm.SetProcess('python')
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#pm.SetProcess('pyFast')
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pm.SetProcess('c')
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self.PlotMoments()
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#self.canvas.img.draw()
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data=self.canvas.img.get_array()
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self.canvas.img.set_array(data)
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fig, ax = plt.subplots(2)
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v=data.sum(axis=0); x=np.arange(v.size); x0=x.sum(); m0=v.sum(); m1=(v*x).sum(); m2=(v*x*x).sum()
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ax[0].plot(v);
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m=m1/m0
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s=np.sqrt( (m2-(m1**2/m0))/m0)
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xx=1/(s*np.sqrt(2*np.pi))*np.exp(-.5*((x-m)/s)**2)
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ax[0].set_title('%g | %g | %g | %g | %g'%(m0,m1,m2,m,s))
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ax[0].hold(True);ax[0].plot(xx*m0)
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v=data.sum(axis=1);
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ax[1].plot(v);
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plt.show()
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#print pm.resArr[0:3],pm.resArr[1]/pm.resArr[0],pm.resArr[2]/pm.resArr[0]
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else:
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for o in self.goMoment:
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o.remove()
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del self.goMoment
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del self.procMoment
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self.canvas.draw()
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def PlotMoments(self):
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data=self.canvas.img.get_array()
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pm=self.procMoment
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#data=ndi.median_filter(data, 3)
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try:
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data.ravel()[pm.mskIdx]=0
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except AttributeError as e:
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print e
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try:
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data=data[pm.roi]
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except AttributeError as e:
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print e
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#data=np.log(data+1)
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#data[100:110,500:510]=1000 #y,x
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#data[650:850,700:850]=0 #y,x
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#pm.Process(np.log(data+1))
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pm.Process(data)
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xbar, ybar, cov=pm.GetIntertialAxis()
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m=pm.resArr
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m00=m[0];m01=m[1];m10=m[2];m11=m[3];m02=m[4];m20=m[5]
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xm = m10 / m00
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ym = m01 / m00
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u11 = (m11 - xm * m01) / m00
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#u11[u11<0.]=0. #processing rounding error
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u20 = (m20 - xm * m10) / m00
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u02 = (m02 - ym * m01) / m00
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a=(u20+u02)/2
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b=np.sqrt(4*u11**2+(u20-u02)**2)/2
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l0=a+b
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l1=a-b
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ang=0.5*np.arctan2(2*u11,(u20-u02))/(2*np.pi)*360. #orientation value 0..1
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exc=np.sqrt(1-l1/l0) #eccentricity :circle=0: http://en.wikipedia.org/wiki/Eccentricity_%28mathematics%29
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print 'xb:%g yb:%g cov:%g %g %g %g ang:%g exc:%g'%((xm, ym)+tuple(cov.ravel())+(ang,exc))
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#fig, ax = plt.subplots()
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#ax.imshow(data,vmax=100,interpolation='nearest')
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#plt.show()
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ax=self.canvas.img.get_axes()
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try:
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for o in self.goMoment:
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o.remove()
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except AttributeError: pass
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self.goMoment=ProcMoment.PlotMoments(ax, xbar, ybar, cov)
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ax.axis('image')
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def OnTomoNormalize(self,event):
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if event.IsChecked():
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#try to find white image
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#calculate average
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#show white normalize factors
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white=self.data.parent['data_white']
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tomoNorm=white[1,:,:]
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#tomoNorm=white[:,:,:].mean(axis=0)
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#np.iinfo(tomoNorm.dtype).max
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#tomoNorm=float(np.iinfo(tomoNorm.dtype).max/2)/tomoNorm
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tomoNorm=tomoNorm.mean()/tomoNorm
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#tomoNorm=tomoNorm/float(np.iinfo(tomoNorm.dtype).max)
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data=self.canvas.img.get_array()
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data*=tomoNorm
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#data/=tomoNorm
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self.tomoNorm=tomoNorm
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self.canvas.img.set_array(data)
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else:
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tomoNorm=self.tomoNorm
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data=self.canvas.img.get_array()
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data/=tomoNorm
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self.canvas.img.set_array(data)
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del self.tomoNorm
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self.canvas.draw()
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def OnSetComplexData(self, event):
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if event.IsChecked():
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data=np.angle(self.canvas.dataRaw)
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else:
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data=np.absolute(self.canvas.dataRaw)
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self.canvas.img.set_array(data)
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self.canvas.draw()
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def OnHelp(self,event):
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msg='''to change the image selection:
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use the toolbar at the bottom to pan and zoom the image
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use the scrollbars at the bottom (if present) to select an other slice
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to change the colorscale:
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drag with left mouse button to move the colorbar up and down
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drag with right mouse button to zoom in/out the colorbar at a given point
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use mouse weel to zoom in/out the colorbar at a given point
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double click left mouse button to set maximum and minimun colorbar values
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use cursor up and down to use a different colormap'''
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dlg = wx.MessageDialog(self, msg, 'Help', wx.OK|wx.ICON_INFORMATION)
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dlg.ShowModal()
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dlg.Destroy()
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def OnColmapSetup(self,event):
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dlg=DlgColBarSetup(self)
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if dlg.ShowModal()==wx.ID_OK:
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pass
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dlg.Destroy()
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def OnInvertAxis(self,event):
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ax=self.canvas.ax
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#event.Checked()
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if self.mnIDxAxis==event.GetId():
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ax.invert_xaxis()
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else:
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ax.invert_yaxis()
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self.canvas.draw()
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pass
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if __name__ == '__main__':
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import os,sys,argparse #since python 2.7
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def GetParser(required=True):
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fnHDF='/scratch/detectorData/e14472_00033.hdf5'
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#lbl='mcs'
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lbl='pilatus_1'
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#lbl='spec'
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elem='/entry/dataScan00033/'+lbl
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exampleCmd='--hdfFile='+fnHDF+' --elem='+elem
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parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
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description=__doc__,
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epilog='Example:\n'+os.path.basename(sys.argv[0])+' '+exampleCmd+'\n ')
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parser.add_argument('--hdfFile', required=required, default=fnHDF, help='the hdf5 to show')
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parser.add_argument('--elem', required=required, default=elem, help='the path to the element in the hdf5 file')
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return parser
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args = parser.parse_args()
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return args
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class App(wx.App):
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def OnInit(self):
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parser=GetParser()
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#parser=GetParser(False) # debug with exampleCmd
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args = parser.parse_args()
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try:
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self.fid=fid=h5py.h5f.open(args.hdfFile)
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except IOError as e:
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sys.stderr.write('Unable to open File: '+args.hdfFile+'\n')
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parser.print_usage(sys.stderr)
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return True
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try:
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hid = h5py.h5o.open(fid,args.elem)
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except KeyError as e:
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sys.stderr.write('Unable to open Object: '+args.elem+'\n')
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|
parser.print_usage(sys.stderr)
|
|
return True
|
|
frame = HdfImageFrame(None,args.elem,hid)
|
|
frame.Show()
|
|
self.SetTopWindow(frame)
|
|
return True
|
|
|
|
def OnExit(self):
|
|
self.fid.close()
|
|
|
|
ut.StopWatch.Start()
|
|
app = App()
|
|
app.MainLoop()
|