improved plots for online analysis + new little helper functions

xray/utils.py

@@ -97,63 +97,88 @@ def removeBackground(x,data,xlims=None,max_iter=100,background_regions=[],**kw):
   return x,np.squeeze(data)
   
 
-def plotdata(q,data,x=None,plot=True,showTrend=True,title=None,clim='auto'):
+def plotdata(*args,x=None,plot=True,showTrend=True,title=None,clim='auto',fig=None):
+  if isinstance(args[0],storage.DataStorage):
+    q = args[0].q; data=args[0].data;
+    if title is None: title = args[0].folder
+  else:
+    q,data = args
   if not (plot or showTrend): return
   if x is None: x = np.arange(data.shape[0])
   if clim == 'auto': clim = np.nanpercentile(data,(1.5,98.5))
   one_plot = showTrend or plot
   two_plot = showTrend and plot
   if one_plot and not two_plot:
+    if fig is None:
       fig,ax = plt.subplots(1,1)
+    else:
+      fig.clear()
+      ax = fig.axes
   if two_plot:
-    fig,ax = plt.subplots(1,2,sharey=True)
+    if fig is None:
+      fig,ax = plt.subplots(2,1,sharex=True)
+    else:
+      ax = fig.axes
+
   ax = np.atleast_1d(ax)
   if showTrend:
-    plt.sca(ax[0])
+    plt.sca(ax[1])
-    plt.pcolormesh(x,q,data.T)
+    plt.pcolormesh(q,x,data)
-    plt.xlabel("image number, 0 being older")
+    plt.ylabel("image number, 0 being older")
-    plt.ylabel(r"q ($\AA^{-1}$)")
+    plt.xlabel(r"q ($\AA^{-1}$)")
     plt.clim( *clim )
   if plot:
-    if showTrend:
+      ax[0].plot(q,np.nanmean(data,axis=0))
-      ax[1].plot(data.mean(axis=0),q)
-    else:
-      ax[0].plot(q,data.mean(axis=0))
   if (plot or showTrend) and title is not None:
     plt.title(title)
 
 
-def plotdiffs(q,diffs,t,select=None,err=None,absSignal=None,absSignalScale=10,
+def plotdiffs(*args,select=None,err=None,absSignal=None,absSignalScale=10,
-              showErr=False,cmap=plt.cm.jet):
+              showErr=False,cmap=plt.cm.jet,fig=None,title=None):
   # this selection trick done in this way allows to keep the same colors when 
   # subselecting (because I do not change the size of diffs)
+  if isinstance(args[0],storage.DataStorage):
+    q = args[0].q; t = args[0].scan; err = args[0].err
+    diffs = args[0].data
+    diffs_abs = args[0].dataAbsAvScanPoint
+  else:
+    q,diffs,t = args
+    diffs_abs = None
   if select is not None:
     indices = range(*select.indices(t.shape[0]))
   else:
     indices = range(len(t))
-  lines = []
+
+  if fig is None: fig = plt.gcf() 
+#  fig.clear()
+
+  lines_diff = []
+  lines_abs = []
   if absSignal is not None:
     line = plt.plot(q,absSignal/absSignalScale,lw=3,
                     color='k',label="absSignal/%s"%str(absSignalScale))[0]
     lines.append(line)
-  for idiff in indices:
+  for linenum,idiff in enumerate(indices):
     color = cmap(idiff/(len(diffs)-1))
     label = timeToStr(t[idiff])
     kw = dict( color = color, label = label )
     if err is not None and showErr:
       line = plt.errorbar(q,diffs[idiff],err[idiff],**kw)[0]
+      lines_diff.append(line)
     else:
       line = plt.plot(q,diffs[idiff],**kw)[0]
-    lines.append(line)
+      lines_diff.append(line)
-
+      if diffs_abs is not None:
-  fig    = plt.gcf() 
+        line = plt.plot(q,diffs_abs[idiff],color=color)[0]
-  legend = plt.legend()
+        lines_abs.append(line)
+  if title is not None: fig.axes[0].set_title(title)
+  legend = plt.legend(loc=4)
   plt.grid()
   plt.xlabel(r"q ($\AA^{-1}$)")
   # we will set up a dict mapping legend line to orig line, and enable
   # picking on the legend line
   lined = dict()
-  for legline, origline in zip(legend.get_lines(), lines):
+  for legline, origline in zip(legend.get_lines(), lines_diff):
     legline.set_picker(5)  # 5 pts tolerance
     lined[legline] = origline
  
@@ -174,7 +199,14 @@ def plotdiffs(q,diffs,t,select=None,err=None,absSignal=None,absSignalScale=10,
     fig.canvas.draw()
 
   fig.canvas.mpl_connect('pick_event', onpick)
+  return lines_diff,lines_abs
 
+def updateLines(lines,data):
+  for l,d in zip(lines,data):
+    l.set_ydata(d)
+
+
+#def getScan
 
 def saveTxt(fname,q,data,headerv=None,info=None,overwrite=True,columns=''):
   """ Write data to file 'fname' in text format.
@@ -212,6 +244,7 @@ def reshapeToBroadcast(what,ref):
       multidimentional array 'ref'. The two arrays have to same the same 
       dimensions along the first axis
   """
+  if what.shape == ref.shape: return what
   assert what.shape[0] == ref.shape[0]
   shape  = [ref.shape[0],] + [1,]*(ref.ndim-1)
   return what.reshape(shape)
@@ -232,11 +265,72 @@ def degToQ(theta,**kw):
   return radToQ(theta,**kw)
 degToQ.__doc__ = radToQ.__doc__
 
-def qToTheta(q,**kw):
+def qToTheta(q,asDeg=False,**kw):
   """ Return scattering angle from q (given E or wavelength) """
   # Energy or wavelength should be in kw
   assert "E" in kw or "wavelength" in kw
   # but not both
   assert not ("E" in kw and "wavelength" in kw)
   if "E" in kw: kw["wavelength"] = 12.398/kw["E"]
-  return np.arcsin(q*kw["wavelength"]/4/np.pi)
+  theta = np.arcsin(q*kw["wavelength"]/4/np.pi)
+  if asDeg: theta = np.rad2deg(theta)
+  return theta
+
+def attenuation_length(compound, density=None, natural_density=None,energy=None, wavelength=None):
+  """ extend periodictable.xsf capabilities """
+  import periodictable.xsf
+  if energy is not None: wavelength = periodictable.xsf.xray_wavelength(energy)
+  assert wavelength is not None, "scattering calculation needs energy or wavelength"
+  if (np.isscalar(wavelength)): wavelength=np.array( [wavelength] )
+  n = periodictable.xsf.index_of_refraction(compound=compound,
+                           density=density, natural_density=natural_density,
+                           wavelength=wavelength)
+  attenuation_length = (wavelength*1e-10)/ (4*np.pi*np.imag(n))
+  return np.abs(attenuation_length)
+
+def transmission(material='Si',thickness=100e-6, density=None, natural_density=None,energy=None, wavelength=None):
+  """ extend periodictable.xsf capabilities """
+  att_len = attenuation_length(compound,density=density,
+            natural_density=natural_density,energy=energy,wavelength=wavelength)
+  return np.exp(-thickness/att_len)
+
+
+def chargeToPhoton(chargeOrCurrent,material="Si",thickness=100e-6,energy=10,e_hole_pair=3.6):
+  """
+    Function to convert charge (or current to number of photons (or number 
+    of photons per second)
+    
+    Parameters
+    ----------
+    
+    chargeOrCurrent: float or array
+    material : str
+       Used to calculate 
+     
+  """
+  # calculate absortption
+  A = 1-transmission(material=material,energy=energy)
+  chargeOrCurrent = chargeOrCurrent/A
+
+  e_hole_pair_energy = 3.6e-3
+  n_charge_per_photon = energy/e_hole_pair_energy
+  # convert to Q
+  charge_per_photon = n_charge_per_photon*1.60217662e-19
+  nphoton = chargeOrCurrent/charge_per_photon
+ 
+  if len(nphoton) == 1: nphoton = float(nphoton)
+  return nphoton
+
+  
+def logToScreen():
+  """ It allows printing to terminal on top of logfile """
+  # define a Handler which writes INFO messages or higher to the sys.stderr
+  console = logging.StreamHandler()
+  console.setLevel(logging.INFO)
+  # set a format which is simpler for console use
+  formatter = logging.Formatter('%(message)s')
+  # tell the handler to use this format
+  console.setFormatter(formatter)
+  # add the handler to the root logger (if needed)
+  if len(logging.getLogger('').handlers)==1:
+    logging.getLogger('').addHandler(console)