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updated examples

This commit is contained in:
Marco Cammarata 2017-01-27 15:42:36 +01:00
parent 4319f4e394
commit 63c07ea3f1
2 changed files with 41 additions and 30 deletions
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55
xray/example_main_salen.py
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@ -18,11 +18,12 @@ from mcutils.xray import id9
#id9 = xray.id9 #id9 = xray.id9
# use npz files (they can handle more stuff (list of arrays,unicode) than h5py) # use npz files (they can handle more stuff (list of arrays,unicode) than h5py)
id9.default_extension = '.npz' g_default_ext = '.npz'
#id9.default_extension = '.h5'
id9.default_extension = g_default_ext
g_default_mask = '../masks/fesalen1_run8_careful.edf' g_default_mask = '../masks/fesalen1_run8_careful.edf'
g_default_folder = "../fesalen/fesalen1/run%d" g_default_folder = "../fesalen/fesalen1/run%d"
runsE = collections.OrderedDict() runsE = collections.OrderedDict()
runsT = collections.OrderedDict() runsT = collections.OrderedDict()
runsE[7] = 60; runsT[7] = 135 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): def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
if isinstance(folder,int): folder = g_default_folder%folder 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: if not os.path.isfile(fname) or force:
log.info("Calling azav with default parameters") logging.info("Calling azav with default parameters")
data = azav(folder,withBaseline=False) data = azav(folder,withBaseline=True)
# first peak (around 0.6) is weak and requires special care ... # first peak (around 0.6) is weak and requires special care ...
data.q,data.data = xray.utils.removeBackground(data.q,data.data, data.q,data.data = xray.utils.removeBackground(data.q,data.data,
xlims=qlims,max_iter=max_iter,background_regions=[ (0,0.58) ]) 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, def azav(folder,nQ=3000,force=False,saveChi=True,mask=g_default_mask,
withBaseline=True): withBaseline=True):
if isinstance(folder,int): folder = g_default_folder%folder
if withBaseline: if withBaseline:
data=removeBaseline(folder)
else:
data = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask, data = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,
saveChi=saveChi) saveChi=saveChi)
else:
data=removeBaseline(folder)
return data 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, qlims=(0.5,3),withBaseline=False,forceDatared=False,
select=slice(None),**kw): select=slice(None),**kw):
if isinstance(folder,int): folder = g_default_folder%folder if isinstance(folder,int): folder = g_default_folder%folder
data = azav(folder,withBaseline=withBaseline) data = azav(folder,withBaseline=withBaseline)
extension = def_ext if withBaseline else "_nobaseline" + def_ext if withBaseline:
# storage files to use diffFile = folder + "/diffs" + g_default_ext
diffFile = folder + "/diffs" + extension else:
diffFile = folder + "/diffs_nobaseline" + g_default_ext
if not os.path.isfile(diffFile) or forceDatared: if not os.path.isfile(diffFile) or forceDatared:
data,diffs = id9.doFolder_dataRed(data,monitor=monitor, data,diffs = id9.doFolder_dataRed(data,monitor=monitor,
errMask=errMask,chi2Mask=chi2Mask,qlims=qlims, errMask=errMask,chi2Mask=chi2Mask,qlims=qlims,
outStorageFile=diffFile) outStorageFile=diffFile)
else: else:
data = xray.storage.read(azavFile)
diffs = xray.storage.read(diffFile) diffs = xray.storage.read(diffFile)
if showPlot: if showPlot:
@ -191,11 +193,11 @@ def anaAmplitue(run=12,plot=False,scaleWithE=False,withBaseline=False):
ax[num].set_title("Range %s"%(str(r))) ax[num].set_title("Range %s"%(str(r)))
return diffs.scan,amp return diffs.scan,amp
def _getPeakPos(x,y): def _getPeakPos(x,y,e=1):
if y.ndim == 1: y = (y,) if y.ndim == 1: y = (y,)
ret = dict() ret = dict()
for yy in y: for yy,ee in zip(y,e):
res = xray.peaks.fitPeak(x,yy) res = xray.peaks.fitPeak(x,yy,err=ee)
#plt.figure(); res.plot_fit(); input("ok") #plt.figure(); res.plot_fit(); input("ok")
pars = res.params.keys() pars = res.params.keys()
for p in pars: for p in pars:
@ -218,7 +220,7 @@ def anaPeakPos(run=12,plot=False,withBaseline=False):
for num,r in enumerate(ranges): for num,r in enumerate(ranges):
idx = (diffs.q>r[0]) & (diffs.q<r[1]) idx = (diffs.q>r[0]) & (diffs.q<r[1])
#amplitude = _getAmplitudeFromLinFit( diffs.data[:,idx] ) #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: if plot:
ax[num].axhline( pars[r].center.value[0] ) ax[num].axhline( pars[r].center.value[0] )
ax[num].plot(diffs.scan,pars[r].center.value,'-o') ax[num].plot(diffs.scan,pars[r].center.value,'-o')
@ -254,8 +256,8 @@ def showBaseline(N=2):
def showBaselineStability(N=100): def showBaselineStability(N=100):
# has to be done with cryo on # has to be done with cryo on
data_bs = azav("../fesalen/fesalen1/run15") data_bs = azav("../fesalen/fesalen1/run15",withBaseline=True)
data = removeBaseline("../fesalen/fesalen1/run15") data = azav("../fesalen/fesalen1/run15",withBaseline=False)
fig,ax=plt.subplots(2,2,sharey=True) fig,ax=plt.subplots(2,2,sharey=True)
i = np.arange(data.data.shape[0]) i = np.arange(data.data.shape[0])
ax[0,0].pcolormesh(i,data_bs.q,data_bs.data.T) 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.subplots_adjust( **subplots_kw )
plt.rcParams['font.size']=14 plt.rcParams['font.size']=14
if scaleWithE and not ratio: 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 scaleWithE = Fale
for run in runs: for run in runs:
t,pos = anaPeakPos(run,plot=False,withBaseline=withBaseline) t,pars = anaPeakPos(run,plot=False,withBaseline=withBaseline)
for k,a in zip(pos.keys(),ax): for k,a in zip(pars.keys(),ax):
label = "run %d %.0f uJ"%(run,runsE[run]) label = "run %d %.0f uJ"%(run,runsE[run])
if useRatio: 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 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: else:
line = a.plot(t[1:],pos[k].center.value[1:],'-o',label=label)[0] line = a.plot(t[1:],pars[k].center.value[1:],'-o',label=label)[0]
a.axhline(pos[k].center.value[0],color=line.get_color()) a.axhline(pars[k].center.value[0],color=line.get_color())
for interval,a in zip(pos.keys(),ax): a.set_title("range %s"%(str(interval))) for interval,a in zip(pars.keys(),ax): a.set_title("range %s"%(str(interval)))
if useRatio: if useRatio:
ax[0].set_ylabel("Peak Position / Peak Position(t=-5ns)") ax[0].set_ylabel("Peak Position / Peak Position(t=-5ns)")
else: else:

16
xray/example_main_tiox.py
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@ -1,13 +1,15 @@
from __future__ import print_function,division from __future__ import print_function,division
import numpy as np import numpy as np
import pylab as plt import pylab as plt
import os
import mcutils as mc import mcutils as mc
import mcutils.xray as xray import mcutils.xray as xray
from mcutils.xray import id9 from mcutils.xray import id9
id9 = xray.id9 id9 = xray.id9
g_default_ext = '.npz'
# use npz files (they can handle more stuff (list of arrays,unicode) than h5py) # 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' #id9.default_extension = '.h5'
def readCalc(): def readCalc():
@ -25,8 +27,14 @@ calc = readCalc()
def azav(folder,nQ=1500,force=False,saveChi=True,mask='y>470'): 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) return id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,saveChi=saveChi)
def datared(folder,monitor=(1,5),showPlot=True,**kw): def datared(folder,monitor=(1,5),forceDatared=False,showPlot=True,**kw):
data,diffs = id9.doFolder_dataRed(folder,monitor=monitor,**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: if showPlot:
xray.utils.plotdiffs(diffs.q,diffs.data,t=diffs.scan, xray.utils.plotdiffs(diffs.q,diffs.data,t=diffs.scan,
absSignal=diffs.dataAbsAvAll,absSignalScale=30) absSignal=diffs.dataAbsAvAll,absSignalScale=30)
@ -36,7 +44,7 @@ def datared(folder,monitor=(1,5),showPlot=True,**kw):
def doall(folder,force=False): def doall(folder,force=False):
azav(folder,force=force) azav(folder,force=force)
return datared(folder) return datared(folder,forceDatared=force)
def anaAmplitue(run=6): def anaAmplitue(run=6):
fname = "../tiox/tiox1/run%d/diffs.npz" % run fname = "../tiox/tiox1/run%d/diffs.npz" % run