280 lines
9.5 KiB
Python
280 lines
9.5 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 MPLCanvasVelo(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,meta,vel):
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fig=self.fig
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ax=self.ax
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velxAct,velxDes,velyAct,velyDes,velAct,velDes=vel
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l=velxAct.shape[0]
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hl = []
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hl += ax.plot(velxAct, 'b-',label='vel x act')
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hl += ax.plot(velxDes, 'b--',label='vel x des')
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hl += ax.plot(velyAct, 'g-',label='vel y act')
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hl += ax.plot(velyDes, 'g--',label='vel y des')
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hl += ax.plot(velAct, 'r-',label='vel act')
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hl += ax.plot(velDes, 'r--',label='vel des')
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ax.xaxis.set_label_text('datapoint (timebase: %g ms per data point)'%meta['timebase'])
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ax.yaxis.set_label_text('um/ms')
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legend = ax.legend(loc='upper right', shadow=True)
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#axvline(linewidth=4, color='r')
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#mpl.axvline(linewidth=4, color='r')
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#l = plt.axhline(y=.5, xmin=0.25, xmax=0.75)
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#circ = mpl.patches.Circle((0.5, 0.5), 0.25, transform=ax.transAxes,
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# facecolor='yellow', alpha=0.5)
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#ax.add_patch(circ)
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ax.plot([.5,.5],[0.01, 0.99],'k',transform=ax.transAxes)
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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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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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y = 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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s.append('%s=%.2f' % (lbl, arr[1][idx]))
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else:
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s += str(h) + str(c[1])
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s=', '.join(s)
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self.SetStatusCB(self.Parent, 0, (x, y, s))
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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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def OnBtnRelease(self, event):
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"""on release we reset the press data"""
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#print(dir(event.guiEvent))
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#self.OnMouse(event)
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return
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def OnBtnScroll(self, event):
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return
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def OnKeyPress(self, event):
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return
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def OnMouse(self, event):
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return
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class MAVelocityFrame(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='velocity-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 = MPLCanvasVelo(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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meta = doc.fh['meta'].item()
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try:
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vel=doc.vel
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except AttributeError:
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tb=meta['timebase']
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#data points are um
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#datapoint timebase: 2 ms () per data point
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#velocity: um/ms (deltatau desVel= motor units per serco cycle)
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rec=doc.fh['rec']
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velyAct = np.diff(rec[:, 0])/tb
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velxAct = np.diff(rec[:, 1])/tb
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velyDes = np.diff(rec[:, 2])/tb
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velxDes = np.diff(rec[:, 3])/tb
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velAct = np.sqrt(velxAct**2+velyAct**2)
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velDes = np.sqrt(velxDes**2+velyDes**2)
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doc.vel = vel = (velxAct,velxDes,velyAct,velyDes,velAct,velDes)
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canvas.InitChild(meta,vel)
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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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# for message description s.a. class MADoc
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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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hl = canvas.hl
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#hl[0].set_data(rec[:len, 4], rec[:len, 5])
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#hl[3].set_data(rec[:len, 1], rec[:len, 2])
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# ax.draw_artist(hl[2])
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x = ax.get_xlim();
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x = (x[1] - x[0]) / 2;
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#y = ax.get_ylim();
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#y = (y[1] - y[0]) / 2;
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ax.set_xlim(idx-x, idx + x,emit=True)
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#ax.set_ylim(rec[len, 2] - y, rec[len, 2] + 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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obj.SetStatusText("x(%d,%.2f): %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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