348 lines
12 KiB
Python
348 lines
12 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 MPLCanvasImg(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.mpl_connect('pick_event',self.OnPick) #works but locks the screed if debugging
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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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hl=[]
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hl+=ax.plot(pts[:,0],pts[:,1],'r.',label='ptsDot') #,picker=5 default value
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hl+=ax.plot(pts[:,0],pts[:,1],'y--',label='ptsLine')
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ec = mpl.collections.EllipseCollection(1, 1, 0, units='xy', offsets=pts,transOffset=ax.transData,edgecolors='g',facecolors=(1,1,0,0.3))
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ax.add_collection(ec)
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hl+=ax.plot(rec[:, 5], rec[:, 4], 'b-',label='recDesPos')
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hl+=ax.plot(rec[:,2],rec[:,1],'g-',label='recActPos')
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ax.xaxis.set_label_text('x-pos um')
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ax.yaxis.set_label_text('y-pos um')
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fig.obj=self
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self.ax=ax
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self.hl=hl
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def OnPick(self,event):
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thisline = event.artist
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xdata = thisline.get_xdata()
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ydata = thisline.get_ydata()
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ind = event.ind
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points = tuple(zip(xdata[ind], ydata[ind]))
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print('onpick points:', points)
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pass
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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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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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s=''
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for h in self.ax.get_lines(): # to get also the ellipses: self.ax.get_children()
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c=h.contains(event)
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if c[0]:
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#s = str(h)+str(c[1])
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#print "over %s" % s
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if type(h)==mpl.lines.Line2D:
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lbl=h.get_label()
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arr=h.get_data()
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idx=c[1]['ind'][0]
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s += '%s[%d] = [%.2f, %.2f]'%(lbl,idx,arr[0][idx],arr[1][idx])
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else:
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s += str(h)+str(c[1])
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self.SetStatusCB(self.Parent, 0, (x, y, s))
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#try:
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# #v=self.img.get_array()[y,x]
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# v=0;
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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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#if 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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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 MAxyPlotFrame(wx.Frame):
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def __del__(self):
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self.doc.view.remove(self)
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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 = MPLCanvasImg(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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wxAxCtrlLst=[]
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#l=len(data.shape)
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#idxXY=(l-2,l-1)
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#for idx,l in enumerate(data.shape):
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# if idx in idxXY:
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# continue
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# wxAxCtrl=ut.SliderGroup(self, label='Axis:%d'%idx,range=(0,l-1))
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# wxAxCtrl.idx=idx
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# wxAxCtrlLst.append(wxAxCtrl)
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# sizer.Add(wxAxCtrl.sizer, 0, wx.EXPAND | wx.ALIGN_CENTER | wx.ALL, border=5)
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# wxAxCtrl.SetCallback(HdfImageFrame.OnSetView,wxAxCtrl)
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#sl=ut.GetSlice(idxXY,data.shape,wxAxCtrlLst)
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#wxAxCtrl=ut.SliderGroup(self, label='Axis:%d'%1,range=(0,1000))
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#wxAxCtrl.SetCallback(MAxyPlotFrame.OnSetView,wxAxCtrl)
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#sizer.Add(wxAxCtrl.sizer, 0, wx.EXPAND | wx.ALIGN_CENTER | wx.ALL, border=5)
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canvas.InitChild(doc.fh['pts'],doc.fh['rec'])
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#self.Fit()
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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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#self.data=data
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#self.idxXY=idxXY
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#self.wxAxCtrlLst=wxAxCtrlLst
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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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#mnItem=mn.Append(wx.ID_ANY, 'Animate', 'Animate the motion');self.Bind(wx.EVT_MENU, self.OnAnimate, mnItem)
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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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if msg==0:
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canvas=self.canvas
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ax=canvas.ax
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idx=usrData
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rec=self.doc.fh['rec']
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hl=canvas.hl
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hl[2].set_data(rec[:idx+1, 5], rec[:idx+1, 4])
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hl[3].set_data(rec[:idx+1, 2], rec[:idx+1, 1])
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#ax.draw_artist(hl[2])
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x=ax.get_xlim();x=(x[1]-x[0])/2;
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y=ax.get_ylim();y=(y[1]-y[0])/2;
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ax.set_xlim(rec[idx, 2]-x,rec[idx, 2]+x)
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ax.set_ylim(rec[idx, 1]-y,rec[idx, 1]+y)
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canvas.draw()
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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=%s"%v,0)
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else:
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raise KeyError('wrong mode')
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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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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)
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return True
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frame = HdfImageFrame(None,args.elem,hid)
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frame.Show()
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self.SetTopWindow(frame)
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return True
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def OnExit(self):
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self.fid.close()
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ut.StopWatch.Start()
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app = App()
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app.MainLoop()
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