543 lines
18 KiB
Python
543 lines
18 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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from __future__ import print_function
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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 MouseData: #data structure for mouse events on image
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usageStr='unknown mode. available m:move t: transform'
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def __init__(self):
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self.mode=None
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def addTrfPt(self,p1):
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try:
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p0=self.btnPress
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del self.btnPress
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except AttributeError: return
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try:
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trf=self.trfPts
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except AttributeError:
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trf=self.trfPts=[]
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p=p0+p1
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print('add trf: {}'.format(p))
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trf.append(p)
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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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ax.invert_xaxis();ax.invert_yaxis()
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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.ax=ax
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self.mouseData=MouseData()
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def InitChild(self,doc):
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fig=self.figure
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ax=self.ax
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pts=doc.fh['pts']
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rec=doc.fh['rec']
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idxTrigger=doc.idxTrigger
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# idx=[]
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# for i in range(len(pts)):
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# l=rec[:,(3,2)]-pts[i,:]
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# l2=l[:,0]**2+l[:,1]**2
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# idx.extend(np.where(l2<1)[0].tolist())
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# recPts=rec[idx,:]
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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[:, 3], rec[:, 2], 'b-',label='recDesPos')
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hl+=ax.plot(rec[:,1],rec[:,0],'g-',label='recActPos')
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#hl+=ax.plot(recPts[:,1],recPts[:,0],'g.',label='recDot')
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hl+=ax.plot(rec[-1:,1],rec[-1:,0],'r.--',label='recNxt')
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#hh=ax.plot(rec[idxTrigger,1],rec[idxTrigger,0],'rx',label='trig')
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#hh[0].get_markeredgewidth();hh[0].get_markersize()
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hl+=ax.plot(rec[idxTrigger,1],rec[idxTrigger,0],'rx',label='trig',markeredgewidth=1.,markersize=6.)
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#hl+=ax.plot(recPts[:,1],recPts[:,0],'g.',label='recDot')
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fn=doc.fh.fid.name[:-4]+'.jpg'
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try:
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img=mpl.image.imread(fn)
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try:
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self.imgTrf=trf=doc.fh['imgTrf']
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except KeyError:
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mn=pts.min(0)
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mx=pts.max(0)
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ext=(mn[0], mx[0], mn[1], mx[1])
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skew=None
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else:
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xmin=trf[0, 2]
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ymin=trf[1, 2]
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xmax=trf[0, :].sum()
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ymax=trf[1, :].sum()
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xskew=trf[0, 2]+trf[0, 0]
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yskew=trf[1, 2]+trf[1, 0]
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ext=(xmin, xmax, ymin, ymax)
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skew=(xskew, yskew)
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#interpolation must be none to allow skew image
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himg=ax.imshow(img,extent=ext,interpolation='none')
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himg._image_skew_coordinate=skew
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pass
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except IOError as e:
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print(e)
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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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ax.axis('equal')
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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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md=self.mouseData
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if md.mode==2 and event.button==1 and self.toolbar.mode=='': # move
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try:
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himg=self.ax.get_images()[0]
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except IndexError:
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print('no image to transform')
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return
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trf=self.imgTrf
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xOfs=event.xdata-md.btnPress[0]
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yOfs=event.ydata-md.btnPress[1]
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xmin=trf[0, 2]+xOfs
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ymin=trf[1, 2]+yOfs
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xmax=trf[0, :].sum()+xOfs
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ymax=trf[1, :].sum()+yOfs
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xskew=trf[0, 2]+trf[0, 0]+xOfs
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yskew=trf[1, 2]+trf[1, 0]+yOfs
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himg.set_extent((xmin, xmax, ymin, ymax))
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himg._image_skew_coordinate=(xskew, yskew)
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self.figure.canvas.draw()
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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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if self.toolbar.mode!='':
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print(self.toolbar.mode)
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return
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if event.inaxes==self.ax:
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md=self.mouseData
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md.mode
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if md.mode==1:#transform
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if event.guiEvent.RightDown()==True:
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self.doTransform()
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if event.guiEvent.LeftDown()==True:
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p=(event.xdata,event.ydata)
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md.btnPress=p
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elif md.mode==2:#move
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if event.guiEvent.LeftDown()==True:
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p=(event.xdata,event.ydata)
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md.btnPress=p
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else:
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print(md.usageStr)
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#print('self.btnPress1', p)
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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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print('OnBtnRelease')
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md=self.mouseData
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if md.mode==1: #transform
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p1=(event.xdata, event.ydata)
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md.addTrfPt(p1)
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elif md.mode==2:#move
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trf=self.imgTrf
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xOfs=event.xdata-md.btnPress[0]
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yOfs=event.ydata-md.btnPress[1]
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#trf[0,2]+=xOfs
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#trf[1,2]+=yOfs
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#trf[1,2]+=yOfs
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return
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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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#self.trfPts=[(-1831.2063808574276, 1349.6011964107677, -1966.6001994017945, 1433.3499501495512), (-1830.4810087443084, 917.64916303133487, -1958.3629895701151, 870.93212944552363), (-1561.5041487047886, 917.17727380319548, -1445.8912878106089, 873.29157558622114)]
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#self.trfPts=[(-1960., 872., -1960., 872.), (-1450., 872, -1450., 872), (-1960., 1432.,-1960., 1432.)]
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#self.trfPts=[(-1960., 872., -1760., 872.), (-1450., 872, -1250., 872), (-1960., 1432.,-1760., 1432.)]
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#self.doTransform()
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md=self.mouseData
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if event.key=='t':
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md.mode=1;print('transform image mode (drag drop to add point, right mopuse to execute)')
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elif event.key=='x':
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self.doTransform()
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elif event.key=='m':
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md.mode=2;print('move image mode')
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elif event.key=='s':
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self.saveTransform()
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else:
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try:
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print('unknown mode. available m:move t: transform')
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md.mode=None
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except AttributeError:
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pass
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return
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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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def doTransform(self):
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#print('doTransform')
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try:
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trfPts=self.mouseData.trfPts
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del self.mouseData.trfPts
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except AttributeError:
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print('no transformation points')
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return
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print(trfPts)
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trfPts=np.array(trfPts)
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try:
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himg=self.ax.get_images()[0]
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except IndexError:
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print('no image to transform')
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return
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xmin,xmax,ymin,ymax=himg.get_extent()
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#himg.set_extent((xmin,xmax+10,ymin,ymax))
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skew=himg._image_skew_coordinate
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if skew is None:
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xskew=xmax
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yskew=ymin
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else:
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(xskew, yskew)=skew
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trf0=np.array([[xskew-xmin,xmax-xskew,xmin],
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[yskew-ymin,ymax-yskew,ymin],
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[0,0,1]])
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#calculate least square transformation matrix of the transformation points
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n=trfPts.shape[0]
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if n<3:
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print('tot enough points (needs at least 3)')
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return
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M=np.mat(trf0).I
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trfPtsImgI=M*np.vstack((trfPts[:,(0,1)].T,np.ones((1,n))))
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trfPtsImgO=M*np.vstack((trfPts[:,(2,3)].T,np.ones((1,n))))
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trfPtsImg=np.hstack((trfPtsImgI[0:2,:].T,trfPtsImgO[0:2,:].T))
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A=np.zeros((n*2, 6))
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A[0:n, (0, 1)]=trfPtsImg[:,(0,1)]
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A[0:n, 2]=1
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A[n:n*2, (3, 4)]=trfPtsImg[:,(0,1)]
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A[n:n*2, 5]=1
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A=np.mat(A)
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B=trfPtsImg[:,(2,3)].T.reshape(-1, 1)
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# (A'*A)^-1*A'*B
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r=(A.T*A).I*A.T*B
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trf1=np.hstack((r.T, [[0, 0, 1]])).reshape(3, -1)
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trf=np.mat(trf0)*trf1
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xmin=trf[0, 2]
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ymin=trf[1, 2]
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xmax=trf[0, :].sum()
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ymax=trf[1, :].sum()
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xskew=trf[0, 2]+trf[0, 0]
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yskew=trf[1, 2]+trf[1, 0]
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self.imgTrf=trf
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print(trf)
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himg.set_extent((xmin,xmax,ymin,ymax))
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himg._image_skew_coordinate=(xskew, yskew)
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self.figure.canvas.draw()
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def saveTransform(self):
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fhr=self.Parent.doc.fh
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fn_npz=fhr.fid.name
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fn_npzOrig=fn_npz+'.orig'
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d=dict(fhr.items())
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fhr.close()
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if not os.path.exists(fn_npzOrig):
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os.rename(fn_npz, fn_npzOrig)
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d['imgTrf']=self.imgTrf
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np.savez_compressed(fn_npz,**d)
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self.Parent.doc.fh=np.load(fn_npz)
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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)
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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)
|
|
#self.mnIDxAxis=mnItem.GetId()
|
|
#mnItem=mn.Append(wx.ID_ANY, 'Invert Y-Axis', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnInvertAxis, mnItem)
|
|
#mnItem=mn.Append(wx.ID_ANY, 'Show Moments', 'Show image moments ', kind=wx.ITEM_CHECK);self.Bind(wx.EVT_MENU, self.OnShowMoments, mnItem)
|
|
#self.mnItemShowMoment=mnItem
|
|
#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)
|
|
#self.mnItemTomoNormalize=mnItem
|
|
|
|
mnBar.Append(mn, '&Edit')
|
|
#mnItem=mn.Append(wx.ID_ANY, 'Animate', 'Animate the motion');self.Bind(wx.EVT_MENU, self.OnAnimate, mnItem)
|
|
|
|
mn = wx.Menu()
|
|
mnItem=mn.Append(wx.ID_ANY, 'Help', 'How to use the image viewer');self.Bind(wx.EVT_MENU, self.OnHelp, mnItem)
|
|
mnBar.Append(mn, '&Help')
|
|
|
|
self.SetMenuBar(mnBar)
|
|
self.CreateStatusBar()
|
|
|
|
def OnUpdate(self, msg, usrData):
|
|
# this is the model-view-control update function
|
|
#print 'OnUpdate',self, msg, usrData
|
|
if msg==0:
|
|
canvas=self.canvas
|
|
ax=canvas.ax
|
|
idx=usrData
|
|
rec=self.doc.fh['rec']
|
|
hl=canvas.hl
|
|
hl[2].set_data(rec[:idx+1, 3], rec[:idx+1, 2])
|
|
hl[3].set_data(rec[:idx+1, 1], rec[:idx+1, 0])
|
|
hl[4].set_data(rec[idx:idx+10, 1], rec[idx:idx+10, 0])
|
|
#ax.draw_artist(hl[2])
|
|
x=ax.get_xlim();x=(x[1]-x[0])/2;
|
|
y=ax.get_ylim();y=(y[1]-y[0])/2;
|
|
ax.set_xlim(rec[idx, 1]-x,rec[idx, 1]+x)
|
|
ax.set_ylim(rec[idx, 0]-y,rec[idx, 0]+y)
|
|
canvas.draw()
|
|
|
|
@staticmethod
|
|
def SetStatusCB(obj,mode,v):
|
|
if mode==0:
|
|
obj.SetStatusText( "x= %d y=%d val=%s"%v,0)
|
|
else:
|
|
raise KeyError('wrong mode')
|
|
|
|
def OnHelp(self,event):
|
|
msg='''to change the image selection:
|
|
use the toolbar at the bottom to pan and zoom the image
|
|
use the scrollbars at the bottom (if present) to select an other slice
|
|
|
|
to change the colorscale:
|
|
drag with left mouse button to move the colorbar up and down
|
|
drag with right mouse button to zoom in/out the colorbar at a given point
|
|
use mouse weel to zoom in/out the colorbar at a given point
|
|
double click left mouse button to set maximum and minimun colorbar values
|
|
use cursor up and down to use a different colormap'''
|
|
dlg = wx.MessageDialog(self, msg, 'Help', wx.OK|wx.ICON_INFORMATION)
|
|
dlg.ShowModal()
|
|
dlg.Destroy()
|
|
|
|
|
|
if __name__ == '__main__':
|
|
import os,sys,argparse #since python 2.7
|
|
def GetParser(required=True):
|
|
fnHDF='/scratch/detectorData/e14472_00033.hdf5'
|
|
#lbl='mcs'
|
|
lbl='pilatus_1'
|
|
#lbl='spec'
|
|
elem='/entry/dataScan00033/'+lbl
|
|
exampleCmd='--hdfFile='+fnHDF+' --elem='+elem
|
|
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
|
|
description=__doc__,
|
|
epilog='Example:\n'+os.path.basename(sys.argv[0])+' '+exampleCmd+'\n ')
|
|
parser.add_argument('--hdfFile', required=required, default=fnHDF, help='the hdf5 to show')
|
|
parser.add_argument('--elem', required=required, default=elem, help='the path to the element in the hdf5 file')
|
|
return parser
|
|
args = parser.parse_args()
|
|
return args
|
|
|
|
class App(wx.App):
|
|
def OnInit(self):
|
|
parser=GetParser()
|
|
#parser=GetParser(False) # debug with exampleCmd
|
|
args = parser.parse_args()
|
|
try:
|
|
self.fid=fid=h5py.h5f.open(args.hdfFile)
|
|
except IOError as e:
|
|
sys.stderr.write('Unable to open File: '+args.hdfFile+'\n')
|
|
parser.print_usage(sys.stderr)
|
|
return True
|
|
try:
|
|
hid = h5py.h5o.open(fid,args.elem)
|
|
except KeyError as e:
|
|
sys.stderr.write('Unable to open Object: '+args.elem+'\n')
|
|
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()
|