end of marion visit (main figures ready

dispersiveXanes_alignment.py

@@ -18,6 +18,7 @@ import dispersiveXanes_utils as utils
 #defaultE = np.arange(1024)*0.12+7060
 defaultE = (np.arange(1024)-512)*0.189+7123
 defaultE = 7063.5+0.1295*np.arange(1024); # done on nov 30 2016, based on xppl3716:r77
+defaultE = 7064.5-6+0.1295*np.arange(1024); # done on jun 07 2017, based on reference spectrum from ESRF
 
 __i = np.arange(1024)
 __x = (__i-512)/512

dispersiveXanes_utils.py

@@ -47,6 +47,8 @@ def maskLowIntensity(p1,p2,threshold=0.03,squeeze=True):
   if squeeze:
     p1 = np.squeeze(p1);
     p2 = np.squeeze(p2)
+  p1.fill_value=np.nan
+  p2.fill_value=np.nan
   return p1,p2
 
 def ratioOfAverage(p1,p2,threshold=0.03):

sigma_vs_shot.py

@@ -0,0 +1,43 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import xppl37_spectra
+import xanes_analyzeRun
+from datastorage import DataStorage as ds
+r=xppl37_spectra.xanes_analyzeRun.AnalyzeRun(81)
+r.load()
+if len(r.results.keys()) > 1:
+  p1 = np.vstack( ( r.results[c].p1 for c in range(0,10,2) ) )
+  p2 = np.vstack( ( r.results[c].p2 for c in range(0,10,2) ) )
+else:
+  p1 = r.results[0].p1
+  p2 = r.results[0].p2
+N = int(len(p1)/2)
+
+ref = slice(0,1000)
+sam = slice(1000,1200)
+
+#ref = slice(200)
+#sam = slice(200)
+
+ref = ds(p1=p1[ref],p2=p2[ref])
+sam = ds(p1=p1[sam],p2=p2[sam])
+
+# "ratioOfAverage medianOfRatios"
+data=xppl37_spectra.calcAbs(ref,sam,refKind="medianOfRatios")
+
+abs = data[-1]
+idx = slice(200,800)
+abs = abs[:,idx]
+
+fom = []
+fom1 = []
+x = np.arange(abs.shape[1])
+N = range(1,len(abs))
+#N = 2**np.arange(15)
+for i in N:
+  av = np.nanmean(abs[:i],axis=0)
+  p = np.polyfit(x,av,5)
+  diff = av-np.polyval(p,x)
+  fom.append( np.nanstd(av) )
+  fom1.append( np.nanstd(diff) )
+

xanes_analyzeRun.py

@@ -25,9 +25,9 @@ g_exp   = "xppl3716"
 g_bml   = g_exp[:3]
 
 x3py.config.updateBeamline(g_bml)
-
+basedir = os.path.dirname(__file__)
-g_folder_init = g_exp+"_init_pars/"
+g_folder_init = basedir + "/" +g_exp+"_init_pars/"
-g_folder_out  = g_exp+"_output/"
+g_folder_out  = basedir + "/" +g_exp+"_output/"
 g_folder_data = "/reg/d/psdm/"+g_bml+"/"+ g_exp +"/hdf5/"
 
 import socket

xppl37_spectra.py

@@ -54,7 +54,8 @@ def calcSpectraForRun(run=82,calibs="all",realign=False,init="auto",alignCalib=0
   elif isinstance(calibs,slice):
     calibsForOut = list(range(r.nCalib))[calibs]
   elif calibs == "all":
-    calibsForOut = r.results.keys()
+    calibsForOut = list(r.results.keys())
+    calibsForOut.sort()
   else:
     calibsForOut = calibs
   # focused data have one single calibcycle ...
@@ -62,9 +63,10 @@ def calcSpectraForRun(run=82,calibs="all",realign=False,init="auto",alignCalib=0
     p1 = [r.results[calib].p1 for calib in calibsForOut]
     p2 = [r.results[calib].p2 for calib in calibsForOut]
   else:
-    idx = r.results[None].fom < 0.5
+    calib = list(r.results.keys())[0]
-    p1 = [ r.results[None].p1[idx], r.results[None].p1[~idx] ]
+    idx = r.results[calib].fom < 0.5
-    p2 = [ r.results[None].p2[idx], r.results[None].p2[~idx] ]
+    p1 = [ r.results[calib].p1[idx], r.results[calib].p1[~idx] ]
+    p2 = [ r.results[calib].p2[idx], r.results[calib].p2[~idx] ]
   return profile_ret( run =r, p1 =p1, p2=p2,calibs=calibsForOut)
 
 
@@ -111,7 +113,11 @@ def calcSpectraForRefAndSample(run=82,refCalibs=slice(None,None,2),forceSpectraC
 
 def calcRef(r1,r2,calibs=None,threshold=0.05):
   """ r1 and r2 are list of 2d arrays (nShots,nPixels) for each calibcycle """
+  if not isinstance(r1,(tuple,list)): r1 = (r1,)
+  if not isinstance(r2,(tuple,list)): r2 = (r2,)
   if calibs is None: calibs = list(range(len(r1)))
+  if not isinstance(calibs,(tuple,list)): calibs = (calibs,)
+
   out = collections.OrderedDict()
   out["ratioOfAverage"] = dict()
   out["medianOfRatios"] = dict()
@@ -153,21 +159,44 @@ def showDifferentRefs(run=82,refCalibs=slice(None,None,2),threshold=0.05):
   ax[-1].legend()
   for a in ax: a.grid()
 
-def calcSampleAbs(run=82,refCalibs=slice(None,None,2),threshold=0.05,refKind="medianOfRatios",forceSpectraCalculation=False):
+def calcAbs(ref,sample=None,threshold=0.05,refKind="medianOfRatios",merge_calibs=True):
   """ example of use
-      ratio = calcSampleAbs(82)
+      ratio = calcAbsForRun(82)
-      ratio = calcSampleAbs( (155,156) )
+      ratio = calcAbsForRun( (155,156) )
   """
-  ref,sample = calcSpectraForRefAndSample(run,refCalibs=refCalibs,forceSpectraCalculation=forceSpectraCalculation)
+  if sample is None: sample=ref
-  temp  = calcRef(ref.p1,ref.p2,calibs=ref.calibs,threshold=threshold)
+  temp  = calcRef(ref.p1,ref.p2,threshold=threshold)
   ref   = temp[refKind]['all']
+  if merge_calibs:
     p1 = np.vstack( sample.p1 )
     p2 = np.vstack( sample.p2 )
-  print(p1.shape)
     p1,p2 = utils.maskLowIntensity(p1,p2,threshold=threshold)
     ratio = p2/p1
     ratio = ratio/ref
-  return p1,p2,-np.log10(ratio)
+    Abs   = -np.log10(ratio)
+  else:
+    Abs = []
+    p1 = []
+    p2 = []
+    for _p1,_p2 in zip(sample.p1,sample.p2):
+      _p1,_p2 = utils.maskLowIntensity(_p1,_p2,threshold=threshold)
+      ratio = _p2/_p1
+      ratio = ratio/ref
+      _abs  = -np.log10(ratio)
+      p1.append(_p1)
+      p2.append(_p2)
+      Abs.append(_abs)
+  return p1,p2,Abs
+
+def calcAbsForRun(run=82,refCalibs=slice(None,None,2),threshold=0.05,refKind="medianOfRatios",forceSpectraCalculation=False,merge_calibs=True):
+  """ example of use
+      ratio = calcAbsForRun(82)
+      ratio = calcAbsForRun( (155,156) )
+  """
+  ref,sample = calcSpectraForRefAndSample(run,refCalibs=refCalibs,forceSpectraCalculation=forceSpectraCalculation)
+  E = ref.run.E
+  p1,p2,Abs = calcAbs(ref,sample,threshold=threshold,refKind=refKind,merge_calibs=merge_calibs)
+  return E,p1,p2,Abs
 
 def showSpectra(run=82,shots=slice(5),calibs=0,averageEachCalib=False,
                 normalization="auto",shifty=1,xlim=(7060,7180),showAv=True):
@@ -209,7 +238,7 @@ def showAbs(run=82,shots=slice(5),normalization="auto",shifty=1,xlim=(7080,7180)
       filterShot = means that it filters out the filterShot*100 percentile
   """
   E = alignment.defaultE
-  p1,p2,abs = calcSampleAbs(run=run,threshold=threshold)
+  _,p1,p2,abs = calcAbsForRun(run=run,threshold=threshold)
   p1_sum = p1.sum(-1)
   if filterShot>0:
     idx = p1_sum>np.percentile(p1_sum,filterShot*100)
@@ -252,19 +281,23 @@ def showAbsWithSweep(run=(155,156),first=0,period=150,nSpectra=10,**kwards):
   shots = slice(first,first+period,int(period/nSpectra))
   showAbs(run=run,shots=shots,**kwards)
  
-def smoothSpectra(E,abs_spectra,res=0.5):
+def smoothSpectra(E,abs_spectra,res=0.5,skip_close=5):
   from scipy import integrate
+  if isinstance(abs_spectra,np.ma.MaskedArray): abs_spectra = abs_spectra.filled()
   if abs_spectra.ndim == 1: abs_spectra=abs_spectra[np.newaxis,:]
   out = np.empty_like(abs_spectra)
-  for ispectrum in range(abs_spectra.shape[0]):
+  for ispectrum,spectrum in enumerate(abs_spectra):
-    idx = np.isfinite(abs_spectra[ispectrum])
+    idx = np.isfinite(spectrum)
     Eclean = E[idx]
+    spectrum_clean = spectrum[idx]
     for i in range(len(E)):
-      g = 1/np.sqrt(2*np.pi)/res*np.exp(-(E-E[i])**2/2/res**2)
+      g = 1/np.sqrt(2*np.pi)/res*np.exp(-(Eclean-E[i])**2/2/res**2)
-      tointegrate = g*abs_spectra[ispectrum]
+      tointegrate = g*spectrum_clean
-      # filter out nans
-      tointegrate = tointegrate[idx]
       out[ispectrum,i] = integrate.simps(tointegrate,x=Eclean) 
+    out[ispectrum][~idx]=np.nan
+    temp = out[ispectrum].copy()
+    for i,o in enumerate(temp):
+      if np.any( np.isnan(temp[i-skip_close:i+skip_close] ) ): out[ispectrum][i] = np.nan
   return out
 
 def doLongCalc():