updated examples
This commit is contained in:
Marco Cammarata
parent
4319f4e394
commit
63c07ea3f1
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@ -18,11 +18,12 @@ from mcutils.xray import id9
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#id9 = xray.id9
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# use npz files (they can handle more stuff (list of arrays,unicode) than h5py)
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id9.default_extension = '.npz'
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#id9.default_extension = '.h5'
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g_default_ext = '.npz'
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id9.default_extension = g_default_ext
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g_default_mask = '../masks/fesalen1_run8_careful.edf'
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g_default_folder = "../fesalen/fesalen1/run%d"
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runsE = collections.OrderedDict()
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runsT = collections.OrderedDict()
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runsE[7] = 60; runsT[7] = 135
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@ -100,10 +101,10 @@ def findCenter(cen=(484,479.5),dist=0.251):
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def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
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if isinstance(folder,int): folder = g_default_folder%folder
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fname = folder + "/pyfai_1d_nobaseline"+id9.default_extension
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fname = folder + "/pyfai_1d_nobaseline"+g_default_ext
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if not os.path.isfile(fname) or force:
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log.info("Calling azav with default parameters")
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data = azav(folder,withBaseline=False)
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logging.info("Calling azav with default parameters")
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data = azav(folder,withBaseline=True)
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# first peak (around 0.6) is weak and requires special care ...
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data.q,data.data = xray.utils.removeBackground(data.q,data.data,
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xlims=qlims,max_iter=max_iter,background_regions=[ (0,0.58) ])
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@ -114,28 +115,29 @@ def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
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def azav(folder,nQ=3000,force=False,saveChi=True,mask=g_default_mask,
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withBaseline=True):
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if isinstance(folder,int): folder = g_default_folder%folder
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if withBaseline:
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data=removeBaseline(folder)
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else:
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data = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,
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saveChi=saveChi)
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else:
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data=removeBaseline(folder)
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return data
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def datared(folder,monitor=(0.5,4),showPlot=True,errMask=5,chi2Mask=2,
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def datared(folder,monitor=(0.5,4),showPlot=True,errMask=5,chi2Mask=1.5,
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qlims=(0.5,3),withBaseline=False,forceDatared=False,
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select=slice(None),**kw):
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if isinstance(folder,int): folder = g_default_folder%folder
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data = azav(folder,withBaseline=withBaseline)
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extension = def_ext if withBaseline else "_nobaseline" + def_ext
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# storage files to use
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diffFile = folder + "/diffs" + extension
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if withBaseline:
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diffFile = folder + "/diffs" + g_default_ext
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else:
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diffFile = folder + "/diffs_nobaseline" + g_default_ext
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if not os.path.isfile(diffFile) or forceDatared:
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data,diffs = id9.doFolder_dataRed(data,monitor=monitor,
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errMask=errMask,chi2Mask=chi2Mask,qlims=qlims,
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outStorageFile=diffFile)
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else:
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data = xray.storage.read(azavFile)
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diffs = xray.storage.read(diffFile)
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if showPlot:
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@ -191,11 +193,11 @@ def anaAmplitue(run=12,plot=False,scaleWithE=False,withBaseline=False):
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ax[num].set_title("Range %s"%(str(r)))
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return diffs.scan,amp
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def _getPeakPos(x,y):
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def _getPeakPos(x,y,e=1):
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if y.ndim == 1: y = (y,)
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ret = dict()
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for yy in y:
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res = xray.peaks.fitPeak(x,yy)
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for yy,ee in zip(y,e):
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res = xray.peaks.fitPeak(x,yy,err=ee)
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#plt.figure(); res.plot_fit(); input("ok")
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pars = res.params.keys()
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for p in pars:
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@ -218,7 +220,7 @@ def anaPeakPos(run=12,plot=False,withBaseline=False):
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for num,r in enumerate(ranges):
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idx = (diffs.q>r[0]) & (diffs.q<r[1])
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#amplitude = _getAmplitudeFromLinFit( diffs.data[:,idx] )
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pars[r] = _getPeakPos( data.q[idx],diffs.dataAsAbs[:,idx] )
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pars[r] = _getPeakPos( data.q[idx],diffs.dataAsAbs[:,idx],diffs.err[:,idx])
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if plot:
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ax[num].axhline( pars[r].center.value[0] )
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ax[num].plot(diffs.scan,pars[r].center.value,'-o')
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@ -254,8 +256,8 @@ def showBaseline(N=2):
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def showBaselineStability(N=100):
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# has to be done with cryo on
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data_bs = azav("../fesalen/fesalen1/run15")
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data = removeBaseline("../fesalen/fesalen1/run15")
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data_bs = azav("../fesalen/fesalen1/run15",withBaseline=True)
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data = azav("../fesalen/fesalen1/run15",withBaseline=False)
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fig,ax=plt.subplots(2,2,sharey=True)
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i = np.arange(data.data.shape[0])
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ax[0,0].pcolormesh(i,data_bs.q,data_bs.data.T)
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@ -333,20 +335,21 @@ def comparePosition2(runs=(11,12,8,9,10),withBaseline=False,useRatio=True,scaleW
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plt.subplots_adjust( **subplots_kw )
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plt.rcParams['font.size']=14
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if scaleWithE and not ratio:
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log.warn("scaleWithE requires useRatio, setting scaleWithE to False")
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logging.warn("scaleWithE requires useRatio, setting scaleWithE to False")
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scaleWithE = Fale
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for run in runs:
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t,pos = anaPeakPos(run,plot=False,withBaseline=withBaseline)
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for k,a in zip(pos.keys(),ax):
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t,pars = anaPeakPos(run,plot=False,withBaseline=withBaseline)
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for k,a in zip(pars.keys(),ax):
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label = "run %d %.0f uJ"%(run,runsE[run])
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if useRatio:
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ratio = pos[k].center.value[1:]/pos[k].center.value[0]
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ratio = pars[k].center.value[1:]/pars[k].center.value[0]
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err = pars[k].center.err[1:]/pars[k].center.value[0]
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if scaleWithE: ratio = (ratio-1)/runsE[run]+1
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line = a.plot(t[1:],ratio,'-o',label=label)[0]
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line = a.errorbar(t[1:],ratio,err,fmt='-o',label=label)[0]
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else:
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line = a.plot(t[1:],pos[k].center.value[1:],'-o',label=label)[0]
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a.axhline(pos[k].center.value[0],color=line.get_color())
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for interval,a in zip(pos.keys(),ax): a.set_title("range %s"%(str(interval)))
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line = a.plot(t[1:],pars[k].center.value[1:],'-o',label=label)[0]
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a.axhline(pars[k].center.value[0],color=line.get_color())
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for interval,a in zip(pars.keys(),ax): a.set_title("range %s"%(str(interval)))
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if useRatio:
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ax[0].set_ylabel("Peak Position / Peak Position(t=-5ns)")
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else:
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@ -1,13 +1,15 @@
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from __future__ import print_function,division
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import numpy as np
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import pylab as plt
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import os
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import mcutils as mc
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import mcutils.xray as xray
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from mcutils.xray import id9
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id9 = xray.id9
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g_default_ext = '.npz'
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# use npz files (they can handle more stuff (list of arrays,unicode) than h5py)
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id9.default_extension = '.npz'
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id9.default_extension = g_default_ext
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#id9.default_extension = '.h5'
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def readCalc():
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@ -25,8 +27,14 @@ calc = readCalc()
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def azav(folder,nQ=1500,force=False,saveChi=True,mask='y>470'):
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return id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,saveChi=saveChi)
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def datared(folder,monitor=(1,5),showPlot=True,**kw):
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data,diffs = id9.doFolder_dataRed(folder,monitor=monitor,**kw)
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def datared(folder,monitor=(1,5),forceDatared=False,showPlot=True,**kw):
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azavFile = folder + "/pyfai_1d" + g_default_ext
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diffFile = folder + "/diffs" + g_default_ext
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if not os.path.isfile(diffFile) or forceDatared:
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data,diffs = id9.doFolder_dataRed(folder,monitor=monitor,**kw)
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else:
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data = xray.storage.read(azavFile)
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diffs = xray.storage.read(diffFile)
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if showPlot:
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xray.utils.plotdiffs(diffs.q,diffs.data,t=diffs.scan,
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absSignal=diffs.dataAbsAvAll,absSignalScale=30)
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@ -36,7 +44,7 @@ def datared(folder,monitor=(1,5),showPlot=True,**kw):
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def doall(folder,force=False):
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azav(folder,force=force)
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return datared(folder)
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return datared(folder,forceDatared=force)
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def anaAmplitue(run=6):
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fname = "../tiox/tiox1/run%d/diffs.npz" % run
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