From 63c07ea3f1f4d9d5f7d6dbbe4c589e7a70430abf Mon Sep 17 00:00:00 2001
From: Marco Cammarata <marcocamma@gmail.com>
Date: Fri, 27 Jan 2017 15:42:36 +0100
Subject: [PATCH] updated examples

---
 xray/example_main_salen.py | 55 ++++++++++++++++++++------------------
 xray/example_main_tiox.py  | 16 ++++++++---
 2 files changed, 41 insertions(+), 30 deletions(-)

diff --git a/xray/example_main_salen.py b/xray/example_main_salen.py
index cd10fad..afabf5e 100644
--- a/xray/example_main_salen.py
+++ b/xray/example_main_salen.py
@@ -18,11 +18,12 @@ from mcutils.xray import id9
 #id9 = xray.id9
 
 # use npz files (they can handle more stuff (list of arrays,unicode) than h5py)
-id9.default_extension = '.npz'
-#id9.default_extension = '.h5'
+g_default_ext = '.npz'
 
+id9.default_extension = g_default_ext
 g_default_mask = '../masks/fesalen1_run8_careful.edf'
 g_default_folder = "../fesalen/fesalen1/run%d"
+
 runsE = collections.OrderedDict()
 runsT = collections.OrderedDict()
 runsE[7]  =  60; runsT[7]  = 135
@@ -100,10 +101,10 @@ def findCenter(cen=(484,479.5),dist=0.251):
 
 def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
   if isinstance(folder,int): folder = g_default_folder%folder
-  fname    = folder + "/pyfai_1d_nobaseline"+id9.default_extension
+  fname    = folder + "/pyfai_1d_nobaseline"+g_default_ext
   if not os.path.isfile(fname) or force:
-    log.info("Calling azav with default parameters")
-    data = azav(folder,withBaseline=False)
+    logging.info("Calling azav with default parameters")
+    data = azav(folder,withBaseline=True)
     # first peak (around 0.6) is weak and requires special care ...
     data.q,data.data = xray.utils.removeBackground(data.q,data.data,
       xlims=qlims,max_iter=max_iter,background_regions=[ (0,0.58) ])
@@ -114,28 +115,29 @@ def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
 
 def azav(folder,nQ=3000,force=False,saveChi=True,mask=g_default_mask,
          withBaseline=True):
+  if isinstance(folder,int): folder = g_default_folder%folder
   if withBaseline:
-    data=removeBaseline(folder)
-  else:
     data = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,
       saveChi=saveChi)
+  else:
+    data=removeBaseline(folder)
   return data
 
-def datared(folder,monitor=(0.5,4),showPlot=True,errMask=5,chi2Mask=2,
+def datared(folder,monitor=(0.5,4),showPlot=True,errMask=5,chi2Mask=1.5,
             qlims=(0.5,3),withBaseline=False,forceDatared=False,
             select=slice(None),**kw):
   if isinstance(folder,int): folder = g_default_folder%folder
   data = azav(folder,withBaseline=withBaseline)
-  extension = def_ext if withBaseline else "_nobaseline" + def_ext
-  # storage files to use
-  diffFile = folder + "/diffs" + extension
+  if withBaseline:
+    diffFile = folder + "/diffs" + g_default_ext
+  else:
+    diffFile = folder + "/diffs_nobaseline" + g_default_ext
 
   if not os.path.isfile(diffFile) or forceDatared:
     data,diffs = id9.doFolder_dataRed(data,monitor=monitor,
                  errMask=errMask,chi2Mask=chi2Mask,qlims=qlims,
                  outStorageFile=diffFile)
   else:
-    data  = xray.storage.read(azavFile)
     diffs = xray.storage.read(diffFile)
 
   if showPlot:
@@ -191,11 +193,11 @@ def anaAmplitue(run=12,plot=False,scaleWithE=False,withBaseline=False):
       ax[num].set_title("Range %s"%(str(r)))
   return diffs.scan,amp
 
-def _getPeakPos(x,y):
+def _getPeakPos(x,y,e=1):
   if y.ndim == 1: y = (y,)
   ret = dict()
-  for yy in y:
-    res = xray.peaks.fitPeak(x,yy)
+  for yy,ee in zip(y,e):
+    res = xray.peaks.fitPeak(x,yy,err=ee)
     #plt.figure(); res.plot_fit(); input("ok")
     pars = res.params.keys()
     for p in pars:
@@ -218,7 +220,7 @@ def anaPeakPos(run=12,plot=False,withBaseline=False):
   for num,r in enumerate(ranges):
     idx = (diffs.q>r[0]) & (diffs.q<r[1])
     #amplitude = _getAmplitudeFromLinFit( diffs.data[:,idx] )
-    pars[r] = _getPeakPos( data.q[idx],diffs.dataAsAbs[:,idx] )
+    pars[r] = _getPeakPos( data.q[idx],diffs.dataAsAbs[:,idx],diffs.err[:,idx])
     if plot:
       ax[num].axhline( pars[r].center.value[0] )
       ax[num].plot(diffs.scan,pars[r].center.value,'-o')
@@ -254,8 +256,8 @@ def showBaseline(N=2):
 
 def showBaselineStability(N=100):
   # has to be done with cryo on
-  data_bs = azav("../fesalen/fesalen1/run15")
-  data    = removeBaseline("../fesalen/fesalen1/run15")
+  data_bs = azav("../fesalen/fesalen1/run15",withBaseline=True)
+  data    = azav("../fesalen/fesalen1/run15",withBaseline=False)
   fig,ax=plt.subplots(2,2,sharey=True)
   i = np.arange(data.data.shape[0])
   ax[0,0].pcolormesh(i,data_bs.q,data_bs.data.T)
@@ -333,20 +335,21 @@ def comparePosition2(runs=(11,12,8,9,10),withBaseline=False,useRatio=True,scaleW
   plt.subplots_adjust( **subplots_kw )
   plt.rcParams['font.size']=14
   if scaleWithE and not ratio:
-    log.warn("scaleWithE requires useRatio, setting scaleWithE to False")
+    logging.warn("scaleWithE requires useRatio, setting scaleWithE to False")
     scaleWithE = Fale
   for run in runs:
-    t,pos = anaPeakPos(run,plot=False,withBaseline=withBaseline)
-    for k,a in zip(pos.keys(),ax):
+    t,pars = anaPeakPos(run,plot=False,withBaseline=withBaseline)
+    for k,a in zip(pars.keys(),ax):
       label = "run %d %.0f uJ"%(run,runsE[run])
       if useRatio:
-        ratio = pos[k].center.value[1:]/pos[k].center.value[0]
+        ratio = pars[k].center.value[1:]/pars[k].center.value[0]
+        err   = pars[k].center.err[1:]/pars[k].center.value[0]
         if scaleWithE: ratio = (ratio-1)/runsE[run]+1
-        line = a.plot(t[1:],ratio,'-o',label=label)[0]
+        line = a.errorbar(t[1:],ratio,err,fmt='-o',label=label)[0]
       else:
-        line = a.plot(t[1:],pos[k].center.value[1:],'-o',label=label)[0]
-        a.axhline(pos[k].center.value[0],color=line.get_color())
-  for interval,a in zip(pos.keys(),ax): a.set_title("range %s"%(str(interval)))
+        line = a.plot(t[1:],pars[k].center.value[1:],'-o',label=label)[0]
+        a.axhline(pars[k].center.value[0],color=line.get_color())
+  for interval,a in zip(pars.keys(),ax): a.set_title("range %s"%(str(interval)))
   if useRatio:
     ax[0].set_ylabel("Peak Position / Peak Position(t=-5ns)")
   else:
diff --git a/xray/example_main_tiox.py b/xray/example_main_tiox.py
index 5670542..8b5397d 100644
--- a/xray/example_main_tiox.py
+++ b/xray/example_main_tiox.py
@@ -1,13 +1,15 @@
 from __future__ import print_function,division
 import numpy as np
 import pylab as plt
+import os
 import mcutils as mc
 import mcutils.xray as xray
 from mcutils.xray import id9
 id9 = xray.id9
 
+g_default_ext = '.npz'
 # use npz files (they can handle more stuff (list of arrays,unicode) than h5py)
-id9.default_extension = '.npz'
+id9.default_extension = g_default_ext
 #id9.default_extension = '.h5'
 
 def readCalc():
@@ -25,8 +27,14 @@ calc = readCalc()
 def azav(folder,nQ=1500,force=False,saveChi=True,mask='y>470'):
   return id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,saveChi=saveChi)
 
-def datared(folder,monitor=(1,5),showPlot=True,**kw):
-  data,diffs = id9.doFolder_dataRed(folder,monitor=monitor,**kw)
+def datared(folder,monitor=(1,5),forceDatared=False,showPlot=True,**kw):
+  azavFile = folder + "/pyfai_1d" + g_default_ext
+  diffFile = folder + "/diffs" + g_default_ext
+  if not os.path.isfile(diffFile) or forceDatared:
+    data,diffs = id9.doFolder_dataRed(folder,monitor=monitor,**kw)
+  else:
+    data = xray.storage.read(azavFile)
+    diffs = xray.storage.read(diffFile)
   if showPlot:
     xray.utils.plotdiffs(diffs.q,diffs.data,t=diffs.scan,
          absSignal=diffs.dataAbsAvAll,absSignalScale=30)
@@ -36,7 +44,7 @@ def datared(folder,monitor=(1,5),showPlot=True,**kw):
 
 def doall(folder,force=False):
   azav(folder,force=force)
-  return datared(folder)
+  return datared(folder,forceDatared=force)
 
 def anaAmplitue(run=6):
   fname = "../tiox/tiox1/run%d/diffs.npz" % run