dispersiveXanes/xanes_analyzeRun.py

import os
import sys
import numpy as np
np.warnings.simplefilter('ignore')
import time
import matplotlib.pyplot as plt
import h5py
import collections
import re

from x3py import x3py
import dispersiveXanes_alignment as alignment
import mcutils as mc

cmap = plt.cm.viridis if hasattr(plt.cm,"viridis") else plt.cm.gray
kw_2dplot = dict(
  interpolation = "none",
  aspect        = "auto",
  cmap          = cmap
  )


g_exp   = "mecl3616"
g_exp   = "xppl3716"
g_bml   = g_exp[:3]

x3py.config.updateBeamline(g_bml)

g_folder_init = g_exp+"_init_pars/"
g_folder_out  = g_exp+"_output/"
g_folder_data = "/reg/d/psdm/"+g_bml+"/"+ g_exp +"/hdf5/"

import socket
hostname = socket.gethostname()
if hostname == "x1":
  g_folder_data = "/home/marco/temp"
if hostname == "apcluster0":
  g_folder_data = "/data/marcoc/singleShotXanes/"+ g_exp +"/hdf5/"

# set defaults based on experiment
if g_bml == "xpp":
  g_roi_height = 200
  g_swapx = False
  g_swapy = False
else:
  g_roi_height = 100
  g_swapx = True
  g_swapy = False

print("Working on experiment",g_exp,"(beamline %s)"%g_bml)
print(" folder data      →",g_folder_data)
print(" folder init_pars →",g_folder_init)
print(" folder outout    →",g_folder_out)

#g_folder = "/reg/d/psdm/xpp/xppl3716/ftc/hdf5/"

def readDataset(fnameOrRun=7,
  force=False,
  doBkgSub=False):
  if isinstance(fnameOrRun,str) and (fnameOrRun[-3:]=="npz"):
    d = x3py.toolsVarious.DropObject()
    temp = np.load(fnameOrRun)
    spec1 = temp["spec1"]
    spec2 = temp["spec2"]
    nS    = spec1.shape[0]
    d.spec1 = x3py.toolsDetectors.wrapArray("spec1",spec1,time=np.arange(nS))
    d.spec2 = x3py.toolsDetectors.wrapArray("spec2",spec2,time=np.arange(nS))
  else:
    if isinstance(fnameOrRun,int):
      fnameOrRun=g_folder_data+"/"+g_exp+"-r%04d.h5" % fnameOrRun
    d = x3py.Dataset(fnameOrRun,detectors=["opal0","opal1","fee_spec","opal2","ebeam"])
    if g_bml == "xpp":
      d.spec1 = d.opal0
      d.spec2 = d.opal1
    else:
      d.spec1 = d.fee_spec
      d.spec2 = d.opal2
  if not hasattr(d,"scan"):
    d.scan = x3py.toolsVarious.DropObject()
    d.scan.scanmotor0_values = [0,]
  return d


def getCenter(img,axis=0,threshold=0.05):
  img = img.copy()
  img[img<img.max()*threshold] = 0
  if axis == 1: img=img.T
  p   = img.mean(1)
  x   = np.arange(img.shape[0])
  return int(np.sum(x*p)/np.sum(p))

def showShots(im1,im2):
  nS = im1.shape[0]
  fig,ax = plt.subplots(2,nS,sharex=True,sharey=True)
  if im1.ndim == 3:
    for a,i1,i2 in zip(ax.T,im1,im2):
      a[0].imshow(i1.T,**kw_2dplot)
      a[1].imshow(i2.T,**kw_2dplot)
  else:
    for a,p1,p2 in zip(ax.T,im1,im2):
      a[0].plot(p1)
      a[1].plot(p2)



def sliceToIndices(shot_slice,nShots):
  return list(range(*shot_slice.indices(nShots)))
 
class AnalyzeRun(object):
  def __init__(self,run,initAlign="auto",swapx=g_swapx,swapy=g_swapy):
    """ swapx → swap x axis of first spectrometer
        swapy → swap y axis of first spectrometer
        initAlign: could be:
           1. None if you want default transformation parameters
           2. a dict if you want to overwrite certain parameters of the default ones
           3. an integer (to look for xppl3716_init_pars/run????_transform.npy)
           4. a file name (that has been previosly saved with r.saveTransform(fname)
    """
    self.data = readDataset(run)
    self.scanpos = self.data.scan.scanmotor0_values
    self.nCalib  = self.data.spec1.nCalib
    self.nShotsPerCalib = self.data.spec1.lens
    if isinstance(run,str):
      run = int( re.search("\d{3,4}",run).group() )
    self.run = run
    self.results = collections.OrderedDict()
    self.swap = (swapx,swapy)
    #self.clearCache()

    d = self.data
    self.spec1 = d.spec1 ; # spec1 is the one that is moved
    self.spec2 = d.spec2 ;
    self.E = alignment.defaultE 

    try:
      self.loadTransform(initAlign)
    except (AttributeError,FileNotFoundError):
      if initAlign is None:
        print("Set to default transform")
        self.initAlign = self.setDefaultTransform()
      else:
        self.initAlign  = initAlign

  def getShots(self,shots=0,calib=None,bkgSub="line",roi=g_roi_height):
    if shots == "all":
      if calib != None:
        shots = slice(0,self.nShotsPerCalib[calib])
      else:
        shots = slice(0,self.data.spec1.nShots)
    # read data
    im1 = self.spec1.getShots(shots,calib=calib)
    im2 = self.spec2.getShots(shots,calib=calib)
    # subtractBkg bkg
    im1 = alignment.subtractBkg(im1,bkg_type=bkgSub)
    im2 = alignment.subtractBkg(im2,bkg_type=bkgSub)
    # rebin and swap im1 if necessary
    if im1.shape[-1] != 1024:
      im1 = mc.rebin(im1, (im1.shape[0],im1.shape[1],1024) )
    if self.swap[0]: im1 = im1[:,:,::-1]
    if self.swap[1]: im1 = im1[:,::-1,:]
    if roi is None:
      pass
    elif isinstance(roi,slice):
      im1 = im1[:,roi,:]
      im2 = im2[:,roi,:]
    elif isinstance(roi,int):
      if not hasattr(self,"roi1"): self.roi1 = alignment.findRoi(im1[0],roi)
      if not hasattr(self,"roi2"): self.roi2 = alignment.findRoi(im2[0],roi)
      im1 = im1[:,self.roi1,:]; im2 = im2[:,self.roi2,:]
    return im1,im2

  def guiAlign(self,shot=0,save="auto"):
    im1,im2 = self.getShot(shot)
    gui = alignment.GuiAlignment(im1[0],im2[0])
    input("Enter to start")
    gui.start()
    if save == "auto":
      fname = g_folder_init+"/run%04d_gui_align.npy" % self.run
    else:
      fname = save
    self.initAlign = gui.transform
    gui.save(fname)

  def doShot(self,shot=0,calib=None,initpars=None,im1=None,im2=None,doFit=True,show=False,showInit=False,save=False,savePlot="auto"):
    if initpars is None: initpars= self.initAlign
    if (im1 is None) or (im2 is None):
      im1,im2 = self.getShots(shot,calib=calib); im1=im1[0]; im2=im2[0]
    r = alignment.doShot(im1,im2,initpars,doFit=doFit,show=showInit)
    im1 = r.im1
    im2 = r.im2
    self.initAlign = r.final_pars
    if show:
      if savePlot == "auto":
        if not os.path.isdir(g_folder_out): os.makedirs(g_folder_out)
        savePlot = g_folder_out+"/run%04d_calib%s_shot%04d_fit.png" % (self.run,calib,shot)
      alignment.plotShot(im1,im2,res=r,save=savePlot)
    if save: self.saveTransform()
    return r

  def doShots(self,shots=slice(0,50),calib=None,initpars=None,doFit=False,returnBestTransform=False,nSaveImg=5,nInChunks=250):
    """
        shots   : slice to define shots to read, use 'all' for all shots in calibcycle
        nSaveImg : save saveImg images in memory (self.results), use 'all' for all
                                 useful for decreasing memory footprint
    """
    if initpars is None: initpars= self.initAlign
    if shots == "all": shots = list(range(self.nShotsPerCalib[calib]))
    if isinstance(shots,slice):
      nmax = self.nShotsPerCalib[calib] if calib is not None else self.data.spec1.nShots
      shots = sliceToIndices(shots,nmax)
    chunks = x3py.toolsVarious.chunk(shots,nInChunks)
    ret_chunks = []
    for chunk in chunks:
      s1,s2 = self.getShots(chunk,calib=calib)
      ret_chunk = alignment.doShots(s1,s2,initpars=initpars,doFit=doFit,\
                   returnBestTransform=False,nSaveImg=nSaveImg)
      ret_chunks.append(ret_chunk)
      if nSaveImg != 'all' and len(chunk)<nSaveImg: nSaveImg = 0
    ret = alignment.unravel_results(ret_chunks)
    bestT,fom = alignment.getBestTransform(ret)
    if doFit: self.initAlign = bestT
    # keep it for later !
    self.results[calib] = ret
    if returnBestTransform:
      return ret,bestT
    else:
      return ret

  def analyzeScan(self,initpars=None,nShotsPerCalib="all",calibs="all",calibsToFit="all",nImagesToFit=0,nSaveImg=5):
    """ nImagesToFit: number of images to Fit per calibcycle, (int or "all")
        calibs to fit could be 'all','even','odd'
    """
    if initpars is None: initpars= self.initAlign
    if calibs == "all": calibs=list(range(self.nCalib))
    if isinstance(calibs,slice): calibs=list(range(self.nCalib))[calibs]
    nC = len(calibs)
    for ic,calib in enumerate(calibs):
      shots = list(range(self.nShotsPerCalib[calib]))
      if nShotsPerCalib != "all": shots = shots[:nShotsPerCalib]
      if nImagesToFit == "all":
        nToFit = self.nShotsPerCalib[calib]
      else:
        nToFit = nImagesToFit
      if calibsToFit == 'even' and (calib%2==1): nToFit=0
      if calibsToFit == 'odd'  and (calib%2==0): nToFit=0
      print("Calib %d, tofit %d"%(calib,nToFit)) 
      ret = None
      if nToFit > 0:
        ret,bestTransf = self.doShots(shots=shots[:nToFit],calib=calib,doFit=True,\
                initpars=initpars,nSaveImg=nSaveImg,returnBestTransform=True);
        initpars = bestTransf; self.initAlign=bestTransf
      if nToFit < len(shots):
        ret2 = self.doShots(shots[nToFit:],calib=calib,initpars=initpars,
                doFit=False,nSaveImg=0)
        if ret is None:
          ret = ret2
        else:
          ret = alignment.unravel_results( (ret,ret2) )
      #print("Memory available 3",x3py.toolsOS.memAvailable())
      self.results[calib] = ret
      #print("Memory available 4",x3py.toolsOS.memAvailable())
      print("Calib cycle %d/%d -> %.3f (best FOM: %.2f)" % (ic,nC,self.scanpos[ic],np.nanmin(ret.fom)))
    return [self.results[c] for c in calibs]


  def save(self,fname="auto",overwrite=False):
    if len(self.results) == 0:
      print("self.results are empty, returning without saving")
      return
    if not os.path.isdir(g_folder_out): os.makedirs(g_folder_out)
    if fname == "auto":
      fname = g_folder_out+"/run%04d_analysis.npz" % self.run
    if os.path.exists(fname) and not overwrite:
      print("File %s exists, **NOT** saving, use overwrite=True is you want ..."%fname)
      return
    h = dict()
    h["roi1"] = (self.roi1.start,self.roi1.stop)
    h["roi2"] = (self.roi2.start,self.roi2.stop)
    if hasattr(self.data.scan,"scanmotor0"):
      h["scanmot0"] = self.data.scan.scanmotor0
    else:
      h["scanmot0"] = 'notascan'
    h["scanpos0"] = self.data.scan.scanmotor0_values
    if hasattr(self.data.scan,"scanmotor1"):
      h["scanmot1"] = self.data.scan.scanmotor1
      h["scanpos1"] = self.data.scan.scanmotor1_values
    h["results"] = self.results
    h["E"] = self.E
    np.savez(fname,**h)
     #h["transform"] = self.initAlign
    

  def load(self,fname="auto"):
    if fname == "auto": fname = g_folder_out+"/run%04d_analysis.npz" % self.run
    temp = np.load(fname)
    self.results = temp["results"].item()
    temp.close()

  def _auto_transform_name(self,run=None,calib=None):
    if run is None: run = self.run
    fname = g_folder_init+"/run%04d_transform" % run
    if calib is not None:
      fname = fname + "_c%03d" % calib
    return fname + ".npy"
    
  def saveTransform(self,fname="auto",calib=None,transform=None):
    if transform is None: transform = self.initAlign
    if fname == "auto": fname = self._auto_transform_name(calib=calib)
    print("Saving roi and transformation parameter to %s"%fname)
    alignment.saveAlignment(fname,self.initAlign,self.roi1,self.roi2,self.swap)

  def loadTransform(self,fname="auto", calib=None):
    if isinstance(fname,dict): raise FileNotFoundError
    if fname == "auto": fname = self._auto_transform_name(calib=calib)
    if isinstance(fname,int):
      fname = g_folder_init+"/run%04d_transform.npy" % fname
    if not os.path.exists(fname): print("Asked to read %s, but it does not exist"%fname)
    temp = np.load(fname).item()
    self.initAlign = temp["transform"]
    self.roi1 = temp["roi1"]
    self.roi2 = temp["roi2"]
    if 'swap' in temp: self.swap=temp['swap']
    print("init transform and ROIs from %s"%fname)


  def clearCache(self):
    del self.roi1 
    del self.roi2
    alignment.clearCache(); # nedded for multiprocessing can leave bad parameters in the cache

  def setDefaultTransform( self ):
    #dict( scalex=0.65,rotation=0.0,transx=90, iblur1=4.3,fix_iblur1=False )
    t = alignment.g_fit_default_kw
    self.initAlign = t
    return t

def quick_mec(run,ref=236,divideByRef=False,returnRes=False):
  """ useful to analyze the runs around 140 (done with the focusing """
  ref_run = 236
  h=h5py.File("mecl3616_output/run%04d_analysis.h5" %ref,"r")
  ref = np.nanmean(h["calibNone"]["ratio"][...],axis=0)
  r = AnalyzeRun(run,initAlign=ref,swapx=True,swapy=False)
  res=r.doShots(slice(5),doFit=False)
  ret = res["ratio"]/ref if divideByRef else res["ratio"]
  if returnRes:
    return ret,res
  else:
    return ret

def quickAndDirty(run,nShots=300,returnAll=True,doFit=False):
  """ useful to analyze the runs around 140 (done with the focusing """
  r = AnalyzeRun(run,swap=True,initAlign=g_folder_init+"/run0144_transform.npy")
  res=r.doShots(slice(nShots),doFit=doFit)
  o = alignment.unravel_results(res)
  ref = np.nanmedian(o["ratio"][:40],0)
  sam = np.nanmedian(o["ratio"][50:],0)
  if returnAll:
    return sam/ref,o["ratio"]/ref
  else:
    return sam/ref