improved plots for online analysis + new little helper functions
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Marco Cammarata
parent
e78d5fc2ce
commit
02186d220f
140
xray/utils.py
140
xray/utils.py
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@ -97,66 +97,91 @@ def removeBackground(x,data,xlims=None,max_iter=100,background_regions=[],**kw):
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return x,np.squeeze(data)
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def plotdata(q,data,x=None,plot=True,showTrend=True,title=None,clim='auto'):
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def plotdata(*args,x=None,plot=True,showTrend=True,title=None,clim='auto',fig=None):
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if isinstance(args[0],storage.DataStorage):
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q = args[0].q; data=args[0].data;
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if title is None: title = args[0].folder
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else:
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q,data = args
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if not (plot or showTrend): return
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if x is None: x = np.arange(data.shape[0])
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if clim == 'auto': clim = np.nanpercentile(data,(1.5,98.5))
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one_plot = showTrend or plot
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two_plot = showTrend and plot
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if one_plot and not two_plot:
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fig,ax = plt.subplots(1,1)
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if fig is None:
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fig,ax = plt.subplots(1,1)
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else:
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fig.clear()
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ax = fig.axes
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if two_plot:
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fig,ax = plt.subplots(1,2,sharey=True)
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if fig is None:
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fig,ax = plt.subplots(2,1,sharex=True)
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else:
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ax = fig.axes
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ax = np.atleast_1d(ax)
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if showTrend:
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plt.sca(ax[0])
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plt.pcolormesh(x,q,data.T)
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plt.xlabel("image number, 0 being older")
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plt.ylabel(r"q ($\AA^{-1}$)")
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plt.sca(ax[1])
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plt.pcolormesh(q,x,data)
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plt.ylabel("image number, 0 being older")
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plt.xlabel(r"q ($\AA^{-1}$)")
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plt.clim( *clim )
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if plot:
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if showTrend:
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ax[1].plot(data.mean(axis=0),q)
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else:
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ax[0].plot(q,data.mean(axis=0))
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ax[0].plot(q,np.nanmean(data,axis=0))
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if (plot or showTrend) and title is not None:
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plt.title(title)
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def plotdiffs(q,diffs,t,select=None,err=None,absSignal=None,absSignalScale=10,
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showErr=False,cmap=plt.cm.jet):
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def plotdiffs(*args,select=None,err=None,absSignal=None,absSignalScale=10,
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showErr=False,cmap=plt.cm.jet,fig=None,title=None):
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# this selection trick done in this way allows to keep the same colors when
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# subselecting (because I do not change the size of diffs)
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if isinstance(args[0],storage.DataStorage):
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q = args[0].q; t = args[0].scan; err = args[0].err
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diffs = args[0].data
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diffs_abs = args[0].dataAbsAvScanPoint
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else:
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q,diffs,t = args
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diffs_abs = None
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if select is not None:
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indices = range(*select.indices(t.shape[0]))
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else:
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indices = range(len(t))
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lines = []
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if fig is None: fig = plt.gcf()
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# fig.clear()
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lines_diff = []
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lines_abs = []
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if absSignal is not None:
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line = plt.plot(q,absSignal/absSignalScale,lw=3,
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color='k',label="absSignal/%s"%str(absSignalScale))[0]
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lines.append(line)
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for idiff in indices:
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for linenum,idiff in enumerate(indices):
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color = cmap(idiff/(len(diffs)-1))
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label = timeToStr(t[idiff])
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kw = dict( color = color, label = label )
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if err is not None and showErr:
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line = plt.errorbar(q,diffs[idiff],err[idiff],**kw)[0]
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lines_diff.append(line)
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else:
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line = plt.plot(q,diffs[idiff],**kw)[0]
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lines.append(line)
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fig = plt.gcf()
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legend = plt.legend()
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lines_diff.append(line)
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if diffs_abs is not None:
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line = plt.plot(q,diffs_abs[idiff],color=color)[0]
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lines_abs.append(line)
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if title is not None: fig.axes[0].set_title(title)
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legend = plt.legend(loc=4)
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plt.grid()
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plt.xlabel(r"q ($\AA^{-1}$)")
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# we will set up a dict mapping legend line to orig line, and enable
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# picking on the legend line
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lined = dict()
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for legline, origline in zip(legend.get_lines(), lines):
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for legline, origline in zip(legend.get_lines(), lines_diff):
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legline.set_picker(5) # 5 pts tolerance
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lined[legline] = origline
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def onpick(event):
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# on the pick event, find the orig line corresponding to the
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# legend proxy line, and toggle the visibility
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@ -174,7 +199,14 @@ def plotdiffs(q,diffs,t,select=None,err=None,absSignal=None,absSignalScale=10,
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fig.canvas.draw()
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fig.canvas.mpl_connect('pick_event', onpick)
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return lines_diff,lines_abs
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def updateLines(lines,data):
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for l,d in zip(lines,data):
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l.set_ydata(d)
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#def getScan
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def saveTxt(fname,q,data,headerv=None,info=None,overwrite=True,columns=''):
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""" Write data to file 'fname' in text format.
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@ -212,6 +244,7 @@ def reshapeToBroadcast(what,ref):
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multidimentional array 'ref'. The two arrays have to same the same
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dimensions along the first axis
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"""
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if what.shape == ref.shape: return what
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assert what.shape[0] == ref.shape[0]
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shape = [ref.shape[0],] + [1,]*(ref.ndim-1)
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return what.reshape(shape)
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@ -232,11 +265,72 @@ def degToQ(theta,**kw):
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return radToQ(theta,**kw)
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degToQ.__doc__ = radToQ.__doc__
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def qToTheta(q,**kw):
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def qToTheta(q,asDeg=False,**kw):
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""" Return scattering angle from q (given E or wavelength) """
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# Energy or wavelength should be in kw
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assert "E" in kw or "wavelength" in kw
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# but not both
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assert not ("E" in kw and "wavelength" in kw)
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if "E" in kw: kw["wavelength"] = 12.398/kw["E"]
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return np.arcsin(q*kw["wavelength"]/4/np.pi)
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theta = np.arcsin(q*kw["wavelength"]/4/np.pi)
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if asDeg: theta = np.rad2deg(theta)
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return theta
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def attenuation_length(compound, density=None, natural_density=None,energy=None, wavelength=None):
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""" extend periodictable.xsf capabilities """
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import periodictable.xsf
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if energy is not None: wavelength = periodictable.xsf.xray_wavelength(energy)
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assert wavelength is not None, "scattering calculation needs energy or wavelength"
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if (np.isscalar(wavelength)): wavelength=np.array( [wavelength] )
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n = periodictable.xsf.index_of_refraction(compound=compound,
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density=density, natural_density=natural_density,
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wavelength=wavelength)
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attenuation_length = (wavelength*1e-10)/ (4*np.pi*np.imag(n))
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return np.abs(attenuation_length)
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def transmission(material='Si',thickness=100e-6, density=None, natural_density=None,energy=None, wavelength=None):
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""" extend periodictable.xsf capabilities """
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att_len = attenuation_length(compound,density=density,
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natural_density=natural_density,energy=energy,wavelength=wavelength)
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return np.exp(-thickness/att_len)
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def chargeToPhoton(chargeOrCurrent,material="Si",thickness=100e-6,energy=10,e_hole_pair=3.6):
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"""
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Function to convert charge (or current to number of photons (or number
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of photons per second)
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Parameters
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----------
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chargeOrCurrent: float or array
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material : str
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Used to calculate
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"""
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# calculate absortption
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A = 1-transmission(material=material,energy=energy)
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chargeOrCurrent = chargeOrCurrent/A
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e_hole_pair_energy = 3.6e-3
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n_charge_per_photon = energy/e_hole_pair_energy
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# convert to Q
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charge_per_photon = n_charge_per_photon*1.60217662e-19
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nphoton = chargeOrCurrent/charge_per_photon
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if len(nphoton) == 1: nphoton = float(nphoton)
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return nphoton
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def logToScreen():
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""" It allows printing to terminal on top of logfile """
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# define a Handler which writes INFO messages or higher to the sys.stderr
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console = logging.StreamHandler()
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console.setLevel(logging.INFO)
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# set a format which is simpler for console use
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formatter = logging.Formatter('%(message)s')
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# tell the handler to use this format
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console.setFormatter(formatter)
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# add the handler to the root logger (if needed)
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if len(logging.getLogger('').handlers)==1:
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logging.getLogger('').addHandler(console)
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