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adding MAError plot

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This commit is contained in:
zamofing_t
2016-12-23 16:40:35 +01:00
parent 36a11a5657
commit c4f9813681
1 changed files with 75 additions and 258 deletions
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333
python/MAError.py
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@@ -45,136 +45,75 @@ class MPLCanvasErr(FigureCanvas):
self.fig=fig
self.ax=ax
def InitChild(self,pts,rec):
def InitChild(self,err):
fig=self.fig
ax=self.ax
err=np.sqrt((rec[:,1]-rec[:,4])**2+(rec[:,1]-rec[:,4])**2)
hl = ax.plot(err, 'r-')
errx,erry,err=err
hl = []
hl = ax.plot(errx, 'g-',label='x-error')
hl = ax.plot(erry, 'y-',label='y-error')
hl = ax.plot(err, 'r-',label='error')
ax.xaxis.set_label_text('time (10x servo cycle)')
ax.yaxis.set_label_text('pos-error um')
legend = ax.legend(loc='upper right', shadow=True)
self.ax = ax
self.hl = hl
def OnMotion(self,event):
print event,event.x,event.y,event.inaxes,event.xdata,event.ydata
return
if event.inaxes==self.ax:
x=int(round(event.xdata))
y=int(round(event.ydata))
try:
v=self.img.get_array()[y,x]
except IndexError as e:
pass
else:
#print x,y,v
self.SetStatusCB(self.Parent,0,(x,y,v))
elif event.inaxes==self.colBar.ax:
colBar=self.colBar
pt=colBar.ax.bbox.get_points()[:,1]
nrm=colBar.norm
vmin,vmax,p0,p1,pS = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
vS=0
else:#scale around point
vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
self.SetStatusCB(self.Parent,1,vS)
try:
vmin,vmax,p0,p1,pS=self.colBarPressed
except AttributeError:
return
#if event.inaxes != self.cbar.ax: return
colBar=self.colBar
#print vmin,vmax,p0,p1,pS,type(colBar.norm)
#print 'x0=%f, xpress=%f, event.xdata=%f, dx=%f, x0+dx=%f'%(x0, xpress, event.xdata, dx, x0+dx)
def OnMotion(self, event):
# print event,event.x,event.y,event.inaxes,event.xdata,event.ydata
if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
if event.button==1:
#colBar.norm.vmin=.1
colBar.norm.vmax=vmax*np.exp((pS-event.y)/100)
#scale= np.exp((event.y-pS)/100)
elif event.button==1:#move top,bottom,both
pD = event.y - pS
vD=(vmax-vmin)/(p1-p0)*(pS-event.y)
colBar.norm.vmin = vmin+vD
colBar.norm.vmax = vmax+vD
elif event.button==3:#scale around point
scale= np.exp((pS-event.y)/100)
vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
#print scale,vS
colBar.norm.vmin = vS-scale*(vS-vmin)
colBar.norm.vmax = vS-scale*(vS-vmax)
self.img.set_norm(colBar.norm)#force image to redraw
colBar.patch.figure.canvas.draw()
if event.inaxes == self.ax:
x = int(round(event.xdata))
#y = int(round(event.ydata))
y = event.ydata
s = []
for h in self.ax.get_lines(): # to get also the ellipses: self.ax.get_children()
c = h.contains(event)
if c[0]:
# s = str(h)+str(c[1])
# print "over %s" % s
if type(h) == mpl.lines.Line2D:
lbl = h.get_label()
arr = h.get_data()
idx = c[1]['ind'][0]
#s += '%s[%d] = [%.2f, %.2f]' % (lbl, idx, arr[0][idx], arr[1][idx])
s.append('%s=%.2f' % (lbl, arr[1][idx]))
else:
s += str(h) + str(c[1])
s=', '.join(s)
self.SetStatusCB(self.Parent, 0, (x, y, s))
def OnBtnPress(self, event):
"""on button press we will see if the mouse is over us and store some data"""
print dir(event.guiEvent)
return
if event.inaxes == self.colBar.ax:
#if event.guiEvent.LeftDClick()==True:
# print dlg
pt=self.colBar.ax.bbox.get_points()[:,1]
nrm=self.colBar.norm
self.colBarPressed = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
#self.colBarPressed = event.x, event.y
#print self.colBarPressed
#self.OnMouse(event)
pass
def OnBtnRelease(self, event):
"""on release we reset the press data"""
print dir(event.guiEvent)
#self.OnMouse(event)
return
try: del self.colBarPressed
except AttributeError: pass
def OnBtnScroll(self, event):
return
#self.OnMouse(event)
colBar=self.colBar
if event.inaxes==colBar.ax:
pt=colBar.ax.bbox.get_points()[:,1]
nrm=colBar.norm
vmin,vmax,p0,p1,pS = (nrm.vmin,nrm.vmax,pt[0],pt[1],event.y)
if isinstance(colBar.norm,mpl.colors.LogNorm):#type(colBar.norm)==mpl.colors.LogNorm does not work...
scale= np.exp((-event.step)/10)
colBar.norm.vmax=vmax*scale
else:#scale around point
scale= np.exp((-event.step)/10)
vS=vmin+(vmax-vmin)/(p1-p0)*(pS-p0)
#print scale,vS
colBar.norm.vmin = vS-scale*(vS-vmin)
colBar.norm.vmax = vS-scale*(vS-vmax)
self.img.set_norm(colBar.norm)#force image to redraw
colBar.patch.figure.canvas.draw()
def OnKeyPress(self, event):
return
colCycle=self.colCycle
colBar=self.colBar
if event.key=='down':
self.colIndex += 1
elif event.key=='up':
self.colIndex -= 1
self.colIndex%=len(colCycle)
cmap = colCycle[self.colIndex]
colBar.set_cmap(cmap)
colBar.draw_all()
self.img.set_cmap(cmap)
self.img.get_axes().set_title(cmap)
colBar.patch.figure.canvas.draw()
def OnMouse(self, event):
return
for k in dir(event):
if k[0]!='_':
print k,getattr(event,k)
class MAErrorFrame(wx.Frame):
def __del__(self):
self.doc.view.remove(self)
def __init__(self, parent,doc):
wx.Frame.__init__(self, parent, title='xy-Plot', size=wx.Size(850, 650))
wx.Frame.__init__(self, parent, title='error-Plot', size=wx.Size(850, 650))
self.doc=doc;doc.view.append(self)
imgDir=ut.Path.GetImage()
icon = wx.Icon(os.path.join(imgDir,'PBMA.ico'), wx.BITMAP_TYPE_ICO)
@@ -187,7 +126,16 @@ class MAErrorFrame(wx.Frame):
self.SetSizer(sizer)
toolbar=ut.AddToolbar(canvas,sizer)
canvas.InitChild(doc.fh['pts'],doc.fh['rec'])
try:
err=doc.err
except AttributeError:
rec=doc.fh['rec']
errx = abs(rec[:, 1] - rec[:, 4])
erry = abs(rec[:, 2] - rec[:, 5])
errxy = np.sqrt(errx ** 2 + erry ** 2)
doc.err = err = (errx, erry, errxy)
canvas.InitChild(err)
self.Centre()
@@ -201,15 +149,14 @@ class MAErrorFrame(wx.Frame):
#-------- Edit Menu --------
mn = wx.Menu()
mnItem=mn.Append(wx.ID_ANY, 'Setup Colormap', 'Setup the color mapping ');self.Bind(wx.EVT_MENU, self.OnColmapSetup, mnItem)
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
#mnItem=mn.Append(wx.ID_ANY, 'Setup Colormap', 'Setup the color mapping ');self.Bind(wx.EVT_MENU, self.OnColmapSetup, mnItem)
#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')
mn = wx.Menu()
@@ -222,147 +169,33 @@ class MAErrorFrame(wx.Frame):
def OnUpdate(self, msg, usrData):
# this is the model-view-control update function
print 'OnUpdate',self, msg, usrData
def SetIdxXY(self,x,y):
self.idxXY=(x,y)
# for message description s.a. class MADoc
if msg == 0:
canvas = self.canvas
ax = canvas.ax
len = usrData
err = self.doc.err
hl = canvas.hl
#hl[0].set_data(rec[:len, 4], rec[:len, 5])
#hl[3].set_data(rec[:len, 1], rec[:len, 2])
# 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(len-x, len + x,emit=True)
#ax.set_ylim(rec[len, 2] - y, rec[len, 2] + y)
canvas.draw()
@staticmethod
def SetStatusCB(obj,mode,v):
if mode==0:
obj.SetStatusText( "x= %d y=%d val=%g"%v,0)
elif mode==1:
obj.SetStatusText( "Colormap Value %d (drag to scale)"%v,0)
#obj.SetStatusText( "x= %d y=%d val=%s"%v,0)
obj.SetStatusText("x(%d,%.2f): %s" % v, 0)
else:
raise KeyError('wrong mode')
def OnShowMoments(self,event):
if event.IsChecked():
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)
if dlg.ShowModal() == wx.ID_OK:
fnMatMsk = dlg.GetPath()
print 'OnOpen',fnMatMsk
dlg.Destroy()
if not fnMatMsk:
return
#fnMatMsk='/scratch/detectorData/cSAXS_2013_10_e14608_georgiadis_3D_for_Marianne/analysis/data/pilatus_valid_mask.mat'
self.procMoment=pm=ProcMoment()
pm.SetMskMat(fnMatMsk,False)
#roi=[603, 826, 200, 200]
#pm.roi=(slice(roi[1],roi[1]+roi[3]),slice(roi[0],roi[0]+roi[2]))
#pm.shape=(roi[3],roi[2])
#pm.SetProcess('python')
#pm.SetProcess('pyFast')
pm.SetProcess('c')
self.PlotMoments()
#self.canvas.img.draw()
data=self.canvas.img.get_array()
self.canvas.img.set_array(data)
fig, ax = plt.subplots(2)
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()
ax[0].plot(v);
m=m1/m0
s=np.sqrt( (m2-(m1**2/m0))/m0)
xx=1/(s*np.sqrt(2*np.pi))*np.exp(-.5*((x-m)/s)**2)
ax[0].set_title('%g | %g | %g | %g | %g'%(m0,m1,m2,m,s))
ax[0].hold(True);ax[0].plot(xx*m0)
v=data.sum(axis=1);
ax[1].plot(v);
plt.show()
#print pm.resArr[0:3],pm.resArr[1]/pm.resArr[0],pm.resArr[2]/pm.resArr[0]
else:
for o in self.goMoment:
o.remove()
del self.goMoment
del self.procMoment
self.canvas.draw()
def PlotMoments(self):
data=self.canvas.img.get_array()
pm=self.procMoment
#data=ndi.median_filter(data, 3)
try:
data.ravel()[pm.mskIdx]=0
except AttributeError as e:
print e
try:
data=data[pm.roi]
except AttributeError as e:
print e
#data=np.log(data+1)
#data[100:110,500:510]=1000 #y,x
#data[650:850,700:850]=0 #y,x
#pm.Process(np.log(data+1))
pm.Process(data)
xbar, ybar, cov=pm.GetIntertialAxis()
m=pm.resArr
m00=m[0];m01=m[1];m10=m[2];m11=m[3];m02=m[4];m20=m[5]
xm = m10 / m00
ym = m01 / m00
u11 = (m11 - xm * m01) / m00
#u11[u11<0.]=0. #processing rounding error
u20 = (m20 - xm * m10) / m00
u02 = (m02 - ym * m01) / m00
a=(u20+u02)/2
b=np.sqrt(4*u11**2+(u20-u02)**2)/2
l0=a+b
l1=a-b
ang=0.5*np.arctan2(2*u11,(u20-u02))/(2*np.pi)*360. #orientation value 0..1
exc=np.sqrt(1-l1/l0) #eccentricity :circle=0: http://en.wikipedia.org/wiki/Eccentricity_%28mathematics%29
print 'xb:%g yb:%g cov:%g %g %g %g ang:%g exc:%g'%((xm, ym)+tuple(cov.ravel())+(ang,exc))
#fig, ax = plt.subplots()
#ax.imshow(data,vmax=100,interpolation='nearest')
#plt.show()
ax=self.canvas.img.get_axes()
try:
for o in self.goMoment:
o.remove()
except AttributeError: pass
self.goMoment=ProcMoment.PlotMoments(ax, xbar, ybar, cov)
ax.axis('image')
def OnTomoNormalize(self,event):
if event.IsChecked():
#try to find white image
#calculate average
#show white normalize factors
white=self.data.parent['data_white']
tomoNorm=white[1,:,:]
#tomoNorm=white[:,:,:].mean(axis=0)
#np.iinfo(tomoNorm.dtype).max
#tomoNorm=float(np.iinfo(tomoNorm.dtype).max/2)/tomoNorm
tomoNorm=tomoNorm.mean()/tomoNorm
#tomoNorm=tomoNorm/float(np.iinfo(tomoNorm.dtype).max)
data=self.canvas.img.get_array()
data*=tomoNorm
#data/=tomoNorm
self.tomoNorm=tomoNorm
self.canvas.img.set_array(data)
else:
tomoNorm=self.tomoNorm
data=self.canvas.img.get_array()
data/=tomoNorm
self.canvas.img.set_array(data)
del self.tomoNorm
self.canvas.draw()
def OnSetComplexData(self, event):
if event.IsChecked():
data=np.angle(self.canvas.dataRaw)
else:
data=np.absolute(self.canvas.dataRaw)
self.canvas.img.set_array(data)
self.canvas.draw()
def OnHelp(self,event):
msg='''to change the image selection:
use the toolbar at the bottom to pan and zoom the image
@@ -378,22 +211,6 @@ use cursor up and down to use a different colormap'''
dlg.ShowModal()
dlg.Destroy()
def OnColmapSetup(self,event):
dlg=DlgColBarSetup(self)
if dlg.ShowModal()==wx.ID_OK:
pass
dlg.Destroy()
def OnInvertAxis(self,event):
ax=self.canvas.ax
#event.Checked()
if self.mnIDxAxis==event.GetId():
ax.invert_xaxis()
else:
ax.invert_yaxis()
self.canvas.draw()
pass
if __name__ == '__main__':
import os,sys,argparse #since python 2.7
def GetParser(required=True):