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lclsH5.py
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lclsH5.py
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from __future__ import print_function
import h5py
import tools
import toolsHdf5 as tH5
import time
import re
import numpy as np
from toolsLog import logbook
#import lclsH5methods as mmm
from toolsHdf5 import datasetRead as h5r
from functools import partial
import os
class lclsH5(object):
"""Class to be defined once to do all hdf5 specific stuff for lcls H5 files."""
def __init__(self,files,cnf):
self.fileNames = files
self.detectors = []
self.cnf = cnf
def checkFiles(self):
self.fileHandles = tools.iterate(self.fileNames,tH5.openOrCreateFile,"r",driver='sec2')
def close(self):
for fh in self.fileHandles:
fh.close()
def findDetectors(self,detectors=None,exclude=None):
# Detectors
# TODO
# strategy in 2 paths:
# (1) detectors are given as alias --> try to read with cached datasets/adresses --> if fails use dataset finder ONLY for defined aliases.
# (2) no detectors are given --> find all detectors for all aliases and get dataset name if alias not existing.
#
if (detectors != "parse"):
# _findDetectors tries to match datasets found in files with mnemonic given in config
t0 = time.time()
logbook("Finding data in hdf5 file ...",end="")
self.findDatasets(detectors=detectors,exclude=exclude)
logbook(" ... done (%.1f) ms" % ((time.time()-t0)*1e3),time=False)
else:
logbook("Starting to look in the file")
# parsing look in the file for dataset ...
# use first (data or cached) file to find detectors to use
h = self.fileHandles[0]
try:
cnf = parseToCnf(h)
self.cnf = tools.dictMerge(self.cnf,cnf)
self.areaDet = cnf['areaDet'].keys()
self.pointDet = cnf['pointDet'].keys()
self.detectors = cnf['areaDet'].keys()+cnf['pointDet'].keys()
except KeyError:
logbook("Failed to find detectors in ", h.filename)
def findDatasets(self,detectors=None,exclude=None):
"""finds datasets from a cnf that contains aliases, if no aliases are defined the file is parsed and the hdf5 names are returned as names.
Finds detectors in hdf5 file matching with mnemonic given in config file;
the matching mnemonic names are as dictionaries (self.pointDet and self.areaDet)
The
"""
subSelection = detectors
if (subSelection==[]) or (subSelection is None):
subSelection = self.cnf["pointDet"].keys() + self.cnf["areaDet"].keys()
if exclude is not None:
exclude = tools.iterfy(exclude)
for tex in exclude:
while True:
try:
subSelection.remove(tex)
continue
except:
break
h = self.fileHandles[0]
# Getting all Detector path strings in CCs and config
try:
# try to use only CalibCycle0
# bad for MEC as some calib cycles don't contain amything... look for longest dataset for now, later look in all
base = "Configure:0000/Run:0000/"
bases = h[base].keys()
lens = np.array([len(h[base][key].keys()) for key in bases])
base = base + bases[lens.argmax()] +'/'
h5names = tH5.getDataset_hack(h[base])
#h5names = [base+x for x in h5names]
# find all confs
base = "Configure:0000/"
confs = h[base].keys()
h5confs = []
for c in confs:
if (c.find("Run")==0):
continue
else:
temp = tH5.getDataset(h[base][c])
for t in temp:
h5confs.append(base+c+"/"+t)
except KeyError:
h5names = tH5.getDataset(h)
#raise NotImplementedError('Use the source, luke!')
ret = {}
## *** start EpicsPV *** #
## look for epics name
#epicsFound=False
#if ("epics_dset" in self.cnf):
#epicsMne = self.cnf["epics_dset"][0]
#epicsReg = self.cnf["epics_dset"][1]
#epicsH5Names=[x for x in h5names if (x.find(epicsReg)>-1)]
## common Epics path:
#ntemp = min([len(x.split("/")) for x in epicsH5Names])
#epicsCommon = "/".join(epicsH5Names[0].split("/")[0:ntemp])
## epics var
#self._epicsPaths = {}
#for d in h[epicsCommon]:
#dpath = d
#d = d.replace(':','_')
#d = d.replace('-','_')
#d = d.replace(' ','_')
#d = d.replace('.','_')
#mne = "%s.%s" % (epicsMne.split("/")[0],d)
#self._epicsPaths[mne]={}
#self._epicsPaths[mne]["data"] = epicsCommon.replace('CalibCycle:0000','CalibCycle:%04d')+"/"+dpath+"/data"
#self._epicsPaths[mne]["time"] = epicsCommon.replace('CalibCycle:0000','CalibCycle:%04d')+"/"+dpath+"/time"
#self._epicsPaths[mne]["conf"] = []
#self._epicsNames = self._epicsPaths.keys()
#else:
#self._epicsNames = []
## *** stop EpicsPV *** #
pointDet = self.cnf["pointDet"]
for (mnemonic,name) in pointDet.iteritems():
if (mnemonic.find("nops")>-1) and (mnemonic.find("*")>-1):
continue
mnemonic = mnemonic.split('_bak')[0]
# skip if not in the group we want to read
if mnemonic not in subSelection:
continue
nameData = name["data"].replace("*","\S+")
detDataset = [x for x in h5names if (re.search(nameData,x) is not None)]
nameConf = name["conf"].replace("*","\S+")
try:
detConf = [x for x in h5confs if (re.search(nameConf,x) is not None)]
except:
detConf=[]
data = [x for x in detDataset if x[-5:]=="/data" or x[-8:]=="/evrData" or x[-13:]=="/channelValue"]
time = [x for x in detDataset if x[-5:]=="/time"]
if ( (len(data) != 0) and (len(time) != 0) ):
ret[mnemonic] = {}
#ret[mnemonic]["data"] = data[0].replace('CalibCycle:0000','CalibCycle:%04d')
#ret[mnemonic]["time"] = time[0].replace('CalibCycle:0000','CalibCycle:%04d')
ret[mnemonic]["data"] = [replaceCalibCycleString(tdat) for tdat in data]
ret[mnemonic]["time"] = [replaceCalibCycleString(ttim) for ttim in time]
if len(detConf)>0:
ret[mnemonic]["conf"] = detConf[0]
self._pointDetPaths = ret
self.pointDetNames = ret.keys()
areaDet = self.cnf["areaDet"]
ret = {}
# 3D detectors need special care because data are written differently
# /data, /image, /waveform
for (mnemonic,name) in areaDet.iteritems():
mnemonic = mnemonic.split('_bak')[0]
# skip if not in the group we want to read
if mnemonic not in subSelection:
continue
name = name["data"].replace("*","\S+")
name_nodata = "/".join(name.split("/")[0:-1])
detDataset = [x for x in h5names if (re.search(name_nodata,x) is not None)]
conf = [ ]
data = [x for x in detDataset if (re.search(name,x) is not None)]
time = [x for x in detDataset if x[-5:]=="/time"]
#raise NotImplementedError('Use the source, luke!')
if ( (len(data) != 0) and (len(time) !=0) ):
ret[mnemonic] = {}
ret[mnemonic]["data"] = [replaceCalibCycleString(tdat) for tdat in data]
ret[mnemonic]["time"] = [replaceCalibCycleString(ttim) for ttim in time]
ret[mnemonic]["conf"] = conf
self._areaDetPaths = ret
self.areaDetNames = ret.keys()
self._detectorsPaths = tools.dictMerge(self._pointDetPaths,self._areaDetPaths)
self.detectorsNames = self.pointDetNames + self.areaDetNames
# *** start scan variables *** #
logbook("Finding scan variables in hdf5 file ...",end="")
temp = dict()
if (len(self.cnf["scan_step"])>0):
for scan_var in self.cnf["scan_step"]:
mne,reg = scan_var
reg = reg.replace("*","\S+")
data = [x for x in h5names if (re.search(reg,x) is not None)]
if len(data)>1:
logbook("\nWarning: in lclsH5:findDatasets, multiple path matching regex, using only first",reg)
logbook("Paths are:",data)
path = replaceCalibCycleString(data[0])
obj = scanVar(self.fileHandles,mne,path)
temp[mne] = obj
self.scanVars = temp
names_to_displ = [ x.name for x in temp.values() \
if hasattr(x,"name")]
names_to_displ = ",".join(names_to_displ)
logbook(" ... done, scanVar found:",names_to_displ, \
time=False)
# *** stop scan variables *** #
return
def initDetectors(self,detectors=None):
detectors = self.detectorsNames
# define detectors
self.detectors = {}
# START POINT DETECTORS
t0 = time.time()
logbook("defining pointDet (with memory cache) ...",end="")
#if (rdPointDetectorsImmediately):
#print " (pre-reading all) ",
for dname in self.pointDetNames:
#TODO: here dtector dependent modules from a folder are to be used in special cases, like a plugin. Not working because of importing issues. Commented out for now.
if dname in pluginNames:
tdclass = eval('detector_'+dname)
else:
tdclass = detector
det = tdclass(self.fileHandles,dname,self._detectorsPaths[dname],useMemoryCache=True,isPointDet=True)
self.detectors[dname] =det
#if (rdPointDetectorsImmediately):
#for i in range(len(self.fileHandles)):
#det.readData(stepSlice=range(det._numOfScanSteps[i]),fileSlice=i)
#tools.addToObj( self,dname,det )
logbook(" ... done (%.1f) ms, %d detectors" %
((time.time()-t0)*1e3,len(self.pointDetNames)),time=False)
# DONE POINT DETECTORS
# START AREA DETECTORS
t0 = time.time()
logbook("defining areaDet (without memory cache) ...",end="")
for dname in self.areaDetNames:
det = detector(self.fileHandles,dname,self._detectorsPaths[dname],useMemoryCache=False)
self.detectors[dname] =det
#tools.addToObj( self,dname,det )
logbook(" ... done (%.1f) ms, %d detectors" %
((time.time()-t0)*1e3,len(self.areaDetNames)),time=False)
# DONE AREA DETECTORS
# consistency check (when daq crashes, last calibs may not have all detectors)
#self._checkCalibConsistency()
# END OF DATASET.__init__
def _checkCalibConsistency(self):
import itertools
Nc = []
# upon initialization each detector check for Ncalib
tocheck = list(itertools.chain( self.detectors.values(),self._scanVars))
Nc = []
for d in tocheck:
Nc.append(d._numOfScanSteps)
Nc = np.array(Nc)
NcMin = Nc.min(axis=0)
NcMax = Nc.max(axis=0)
for d in tocheck:
# print out most limiting detector
if (list(NcMin) == list(d._numOfScanSteps)) and (list(NcMin)!=list(NcMax)):
logbook("WARNING: Detector/Scan ",d,"is limiting the number of Calybcycle to",str(NcMin),"instead of ",str(NcMax))
d._numOfScanSteps = list(NcMin)
self.numOfScanSteps = list(NcMin)
if len(NcMin) ==1:
self.numOfScanSteps = self.numOfScanSteps[0]
class detector(object):
#def __dir__(self):
#self.__init__heavy()
#return self.__dict__.keys()
def __init__(self,fhandle,name,paths,useMemoryCache=True,isauto=False,isPointDet=False):
self._h5s = tools.iterfy(fhandle)
self.name = name
self._paths = paths
self._useMemoryCache=useMemoryCache
self._isPointDet = isPointDet
self._numOfScanStepsFile = self._checkNcalib()
#if not isauto:
#self.__init__heavy()
if self._isPointDet:
self._initPointDet()
else:
self._initAreaDet()
def _getTotalNumOfSteps(self):
return np.sum(self._numOfScanStepsFile)
Nsteps = property(_getTotalNumOfSteps)
def _getFileStep(self,step):
stepout = step
fileind = 0
while stepout >= self._numOfScanStepsFile[fileind]:
stepout -= self._numOfScanStepsFile[fileind]
fileind += 1
return fileind, stepout
def _initPointDet(self):
if self._isPointDet and self._useMemoryCache:
if len(self._paths['data'])>1:
if len(self._paths['data'])>50:
# this seems the epics case
logbook("crazy amount of point counters in %s, force full reading initialization with..." %(self.name))
else:
# this might be the tt case
for datapath,timepath in zip(self._paths['data'],self._paths['time']):
datapath = getPath(datapath)
timepath = getPath(timepath)
name = getDetNamefromPath(datapath)
dat,fields = self._readPointDataGeneral(datapath)
times = self._readTime(timepath)
if not fields==[] and not hasattr(self,'fields'):
self.fields = dict()
for field,tdat in zip(fields,dat):
tname = name+'_'+field
data = [tdat,times]
self.fields[tname] = data
#memdata(tname,data)
else:
# this might be the ipm case
datapath = self._paths['data'][0]
timepath = self._paths['time'][0]
datapath = getPath(datapath)
timepath = getPath(timepath)
dat,fields = self._readPointDataGeneral(datapath)
times = self._readTime(timepath)
if not fields==[]:
self.fields = dict()
for field,tdat in zip(fields,dat):
tname = field
data = [tdat,times]
self.fields[tname] = data
def _initAreaDet(self):
self.time = self._readTime(getPath(self._paths['time'][0]))
self.readData = self._readDataGeneral
self._numOfScanStepsFile = self._checkNcalib()
self.readData = self._readDataGeneral
#######################################################################
#######################################################################
#######################################################################
def _readPointDataGeneral(self,path,field=None,stepSlice=None,shotSlice=None):
if stepSlice is None:
stepSlice = range(self.Nsteps)
stepSlice = tools.iterfy(stepSlice)
#self.readTime(stepSlice,shotSlice,fileSlice)
#if not self._existsInSelf("time"):
#timeStampObj = memdata(self,"timestamp",fileSlice[0])
##self._addToSelf("time",timeStampObj)
outS = []
for stepNum in stepSlice:
fileNum,FstepNum = self._getFileStep(stepNum)
cpath = path % FstepNum # really beautiful, same for python 3 ?
cpath = getPath(cpath)
data = h5r(self._h5s[fileNum],cpath)
try:
if (shotSlice is None):
data = data[...]
else:
data = data[shotSlice]
except:
data = np.array([])
outS.append(data)
# find structure with something in
outSind = 0
for toutS in outS:
if len(toutS)>0:
break
outSind+=1
if outS[outSind].dtype.names:
if not field is None:
index = ''
while not field in outS[outSind].dtype.names:
index = field[-1] + index
field = field[:-1]
index = int(index)
fields = [field]
else:
fields = outS[outSind].dtype.names
index = None
pret = [[dd[tfield] if len(dd)>0 else np.array([]) for dd in outS ] for tfield in fields]
ret = []
retfields = []
for tret,tfield in zip(pret,fields):
if tret[0].ndim==2:
noofvecs = np.shape(outS[0][tfield])[1]
if not index is None:
indices = [index]
else:
indices = range(noofvecs)
for tindex in indices:
strfmt = '%0' + '%dd' %(1+np.floor(np.log10(noofvecs)))
tname = tfield + strfmt %(tindex)
ret.append([sd[:,tindex] if np.ndim(sd)==2 else np.asarray([]) for sd in tret ])
retfields.append(tname)
else:
ret.append(tret)
retfields.append(tfield)
return ret,retfields
#######################################################################
#######################################################################
#######################################################################
def __init__heavy(self):
# based on det type point readData to a particular method
# container for different subfields or run
self._guessDetType()
self._numOfScanStepsFile = self._checkNcalib()
if (self._useMemoryCache):
self.readData(stepSlice=0,shotSlice=None,fileSlice=0)
#def __repr__(self):
#if (self._useMemoryCache):
#return "`detector` object: %s (w memory cache)" % self.name
#else:
#return "`detector` object: %s (w/o memory cache)" % self.name
# data object (self)manipulation
def _getFromSelf(self,what):
""" get data from object for example: d.ipm2.get("_file0.step3.channel") """
return tools.getFromObj(self,what)
def _existsInSelf(self,what):
return tools.existsInObj(self,what)
def _addToSelf(self,what,value,overWrite=True):
return tools.addToObj(self,what,value,overWrite=overWrite)
def _checkNcalib(self):
numOfScanStepsFile = []
path = tools.commonPathPrefix(self._paths["data"])
path = getPath(path)
for h in self._h5s:
n=0
while( tH5.datasetExists(h,path % n) ):
n+=1
numOfScanStepsFile.append(n)
nccs = []
for h in self._h5s:
n=0
while( tH5.datasetExists(h,'/Configure:0000/Run:0000/CalibCycle:%04d/' % n) ):
n+=1
nccs.append(n)
self._numOfScanStepsFile = []
for n in range(len(self._h5s)):
if nccs[n] > numOfScanStepsFile[n]:
logbook("More calibcycle structures than detectors, will lead to empty detector steps...")
self._numOfScanStepsFile.append(nccs[n])
else:
self._numOfScanStepsFile.append(numOfScanStepsFile[n])
return self._numOfScanStepsFile
def __getitem__(self,x):
n = self._numOfScanSteps[0]
if isinstance(x,slice):
return [self[ii] for ii in xrange(*x.indices(n))]
else:
x = tools.iterfy(x)
if (max(x)>=self._numOfScanSteps[0]):
raise IndexError
if (not self._useMemoryCache):
return self.readData(stepSlice=x)
if self._existsInSelf("_data"):
return self._getFromSelf("_data")[x]
elif self._existsInSelf("value"):
return self._getFromSelf("value")[x]
else:
return tools.getFromObj(self,x)
def _guessDetType(self):
data_type = self._h5s[0][self._paths["data"] % 0].dtype
if (data_type == np.dtype([('channel', '<f4', (4,)), ('sum', '<f4'), ('xpos', '<f4'), ('ypos', '<f4')]) ):
self._type="IPM"
self.readData = self._readDataIPM
elif self.name == "eventCode":
self._setupEventCodes()
self.readData = self._readDataEVR
else:
self._type="General"
self.readData = self._readDataGeneral
def _readTime(self,path,stepSlice=None,shotSlice=None):
if stepSlice is None:
stepSlice = range(self.Nsteps)
stepSlice = tools.iterfy(stepSlice)
times = []
for stepNum in stepSlice:
fileNum,FstepNum = self._getFileStep(stepNum)
tpath = path % FstepNum
time = h5r(self._h5s[fileNum],tpath)
try:
if (shotSlice is None):
time = time[...]
else:
time = time[shotSlice]
except:
time = np.array([])
#raise NotImplementedError('Use the source, luke!')
times.append(time)
return times
#if (shotSlice is None):
#return times
#else:
#return time[shotSlice]
def _setupEventCodes(self):
h=self._h5s[0]
codes = h[self._paths["conf"]][...]["code"]
self._addToSelf("codes",codes)
#if (EvrFound):
def _readDataEVR(self,stepSlice=0,shotSlice=None,fileSlice=0):
fileSlice = tools.iterfy(fileSlice)
stepSlice = tools.iterfy(stepSlice)
for fileNum in fileSlice:
for stepNum in stepSlice:
data= self._readDataGeneral(stepSlice=stepNum,shotSlice=shotSlice,
fileSlice=fileSlice)
timeStampObj = self._getFromSelf("time")
addr = address(fileNum,stepNum,"shotSlice")
addrCode = address(fileNum,stepNum,"code%d"%self.codes[0])
# if not read or we are asking shots outside the range of read values...
if ( (not self._existsInSelf(addrCode)) or (len(tools.iterDiff( self._getFromSelf(addr), shotSlice) )==0) ):
for code in self.codes:
nshots = len(data)
temp = np.zeros(nshots,dtype=np.bool)
for nshot in range(nshots):
if code in data[nshot][0]["eventCode"]:
temp[nshot] = True
addr = address(fileNum,stepNum,"code%d"%code)
self._addToSelf(addr,temp)
dataObj = memdata(self,"code%d"%code,fileNum,timeStampObj)
self._addToSelf("code%d"%code,dataObj)
def _readDataIPM(self,stepSlice=0,shotSlice=None,fileSlice=0,fieldName=None):
# further splits channels
fileSlice = tools.iterfy(fileSlice)
stepSlice = tools.iterfy(stepSlice)
for fileNum in fileSlice:
data= self._readDataGeneral(stepSlice=stepSlice,shotSlice=shotSlice,
fileSlice=fileNum,fieldName=fieldName)
timeStampObj = self._getFromSelf("time")
for stepNum in stepSlice:
addr = address(fileNum,stepNum,"shotSlice")
addrChannel = address(fileNum,stepNum,"channel0")
# if not read or we are asking shots outside the range of read values...
if ( (not self._existsInSelf(addrChannel)) or (len(tools.iterDiff( self._getFromSelf(addr), shotSlice) )==0) ):
# if only one step is read it does not return list ...
if isinstance(data,list):
channel_data = data[stepNum]["channel"]
else:
channel_data = data["channel"]
for i in range(4):
addr = address(fileNum,stepNum,"channel%d"%i)
self._addToSelf(addr,channel_data[:,i])
dataObj = memdata(self,"channel%d"%i,fileNum,timeStampObj)
self._addToSelf("channel%d"%i,dataObj)
def _readDataGeneral(self,stepSlice=0,shotSlice=None,fileSlice=0,fieldName=None):
fileSlice = tools.iterfy(fileSlice)
stepSlice = tools.iterfy(stepSlice)
#self.readTime(stepSlice,shotSlice,fileSlice)
#if not self._existsInSelf("time"):
#timeStampObj = memdata(self,"timestamp",fileSlice[0])
#self._addToSelf("time",timeStampObj)
outS = []
# NB: Here is an issue, doesn't make sense like it is right now...
for stepNum in stepSlice:
# check if memory chached exists and the already read values contains what we need..
#print "TODO: add slice1 in slice2 ..., the current one does not work with None ..."
#print "r1=range(5,100); r2=range(10,20); [idx for (idx,x) in zip(range(len(r1)),r1) if x in r2]"
fileNum,FstepNum = self._getFileStep(stepNum)
addr = address(fileNum,stepNum,"shotSlice")
if (not self._existsInSelf(addr)) or (len(tools.iterDiff( self._getFromSelf(addr), shotSlice) )==0):
path = self._paths["data"][0] % FstepNum
path = getPath(path)
data = h5r(self._h5s[fileNum],path)
if (shotSlice is None):
data = data[...]
else:
if isinstance(shotSlice,np.ndarray) and shotSlice.dtype is np.dtype(int):
tshotSlice = np.zeros([data.len()],dtype=bool)
tshotSlice[shotSlice]=True
shotSlice=tshotSlice
data = data[shotSlice]
else:
data = self._getFromSelf(address(fileNum,stepNum,"_data"))
# store is asked to use memory cache
if (self._useMemoryCache):
# save in .fileNum.stepNum._data
self._addToSelf(address(fileNum,stepNum,"_data"),data)
self._addToSelf(address(fileNum,stepNum,"shotSlice"),shotSlice)
if (isinstance(data.dtype.names,tuple)):
for fieldname in data.dtype.names:
self._addToSelf(address(fileNum,stepNum,fieldname),data[fieldname])
if ( not (fieldname in self.__dict__) ):
timeStampObj = memdata(self,"timestamp",fileNum)
dataObj = memdata(self,fieldname,fileNum,timeStampObj)
self._addToSelf(fieldname,dataObj)
#else:
#timeStampObj = memdata(self,"timestamp",fileNum)
#dataObj = memdata(self,"_data",fileNum,timeStampObj)
#tools.addToObj(self,"_data",dataObj)
outS.append(data)
return outS
# hack for linked calib cycles
def getPath(name):
if name[:12] == '/CalibCycle:':
return '/Configure:0000/Run:0000'+name
else:
return name
class scanVar(object):
def __init__(self,fhandle,name,paths):
self._h5s = fhandle
self._name = name
self._paths = getPath(paths)
self._checkNcalib()
self._read()
def _read(self):
names = self._h5s[0][getPath(self._paths % 0)]
if names.shape==():
return
names = names['name']
self.name = list(names)[0]
self.names = list(names)
v = []
for i in range(len(self._h5s)):
h=self._h5s[i]
for c in range(self._numOfScanSteps[i]):
val = h[self._paths % c]["value"]
v.append(val)
self.data = v
#BUGME
#for n in names:
#dhelp = memdata(self,n,0)
#self.__dict__[n,dhelp]
#tools.addToObj(self,n,dhelp)
def __repr__(self):
return "`scanVar` object: %s" % self._name
def _checkNcalib(self):
self._numOfScanSteps = []
for h in self._h5s:
n=0
while( tH5.datasetExists(h,self._paths % n) ):
n+=1
self._numOfScanSteps.append(n)
return self._numOfScanSteps
def __getitem__(self,x):
return tools.getFromObj(self,self.name)[x]
def parseToCnf(fileHandle):
cnf = dict()
cnf['areaDet'] = dict()
cnf['pointDet'] = dict()
dsets = findDatasetsInHdf5(fileHandle)
for dset in dsets:
detname = tools.varName(os.path.split(os.path.split(dset['dset_data'])[0])[1])
base = "/Configure:0000/Run:0000/"
bases = h[base].keys()
lens = np.array([len(h[base][key].keys()) for key in bases])
base = base + bases[lens.argmax()] +'/'
#ccn = '/Configure:0000/Run:0000/CalibCycle:0000/'
ccn = base
ds = fileHandle[dset['dset_data']]
if len(np.shape(ds[0]))>0:
cnf['areaDet'][detname] = dict()
cnf['areaDet'][detname]['conf'] = 'dummy'
cnf['areaDet'][detname]['timestamp'] = dset['dset_time'].split(ccn)[1]
cnf['areaDet'][detname]['data'] = dset['dset_data'].split(ccn)[1]
else:
cnf['pointDet'][detname] = dict()
cnf['pointDet'][detname]['conf'] = 'dummy'
cnf['pointDet'][detname]['timestap'] = dset['dset_time'].split(ccn)[1]
cnf['pointDet'][detname]['data'] = dset['dset_data'].split(ccn)[1]
return cnf
def getDetNamefromPath(path,lowerit=False):
name = 'data'
while name in ['waveforms','evrData','data','time','image','array','channelValue']:
path,name = os.path.split(path)
name = name.lower()
name = name.replace(':','_')
name = name.replace('.','_')
name = name.replace(' ','_')
name = name.replace('-','_')
if lowerit:
while name.find('_')>-1:
s,e = name.split('_')
name = s+e[0].upper()+e[1:]
return name
def address(fileNum,stepNum,what):
return "_file%d.step%d.%s" % (fileNum,stepNum,what)
def findDatasetsInHdf5(filehandle):
rundset = filehandle['Configure:0000']['Run:0000']
ccname = rundset.keys()[0]
dsets = crawlforDatasets(rundset[ccname])
return dsets
def crawlforDatasets(group,skipEpics = True, skipEvr = True):
found = []
if 'Epics::EpicsPv' in group.name:
return found
if 'Evr' in group.name:
return found
itemnames = group.keys()
if u'time' in itemnames:
if isinstance(group['time'],h5py.Dataset):
if u'image' in itemnames:
if isinstance(group['image'],h5py.Dataset):
if group['time'].shape[0] == group['image'].shape[0]:
dset = dict()
dset['dset_data'] = group['image'].name
dset['dset_time'] = group['time'].name
#dset['dset_type'] = 'areadet'
found.extend([dset])
elif u'data' in itemnames or u'channelValue' in itemnames:
if isinstance(group['data'],h5py.Dataset):
if group['time'].shape[0] == group['data'].shape[0]:
dset = dict()
dset['dset_data'] = group['data'].name
dset['dset_time'] = group['time'].name
#dset['dset_type'] = 'pointdet'
found.extend([dset])
else:
for itemname in itemnames:
if isinstance(group[itemname],h5py.Group):
found.extend(crawlforDatasets(group[itemname]))
return found
### Henrik: This part I think could go to some plugin directory. I put it here anyway, mainly as I failed to get it to work. The problem I ran into is cross imports, import detector class from plugin module and importing detector wrapper from here didn't work.
pluginNames = ['epics','eventCode']
#pluginNames = []
class detector_epics(detector):
def _initPointDet(self):
for datapath,timepath in zip(self._paths['data'],self._paths['time']):
name = getDetNamefromPath(datapath)
rdAllFunc = partial(self._readEpicsAllData,datapath,timepath)
if not hasattr(self,'fields'):
self.fields = dict()
self.fields[name] = rdAllFunc
def _readEpicsAllData(self,datapath,timepath):
stepSlice = range(self.Nsteps)
stepSlice = tools.iterfy(stepSlice)
outD = []
outT = []
for stepNum in stepSlice:
fileNum,FstepNum = self._getFileStep(stepNum)
cpath = datapath % FstepNum # really beautiful, same for python 3 ?
data = h5r(self._h5s[fileNum],cpath)
outD.append(data['value'])
time = data['stamp']
time.dtype.names = ('seconds','nanoseconds')
outT.append(time)
return [outD,outT]
class detector_eventCode(detector):
def _initPointDet(self):
detector._initPointDet(self)
h=self._h5s[0]
codes = h[self._paths["conf"]][...]["code"]
self._addToSelf("codes",codes)
self._getCodeFields()
#if (EvrFound):
def _getCodeFields(self):
dat = self.fields['fifoEvents'][0]
tim = self.fields['fifoEvents'][1]
dat = [[evt['eventCode'] for evt in step] for step in dat]
for code in self.codes:
name = 'code_'+str(code)
cd = [np.array([True if code in evt else False for evt in step]) for step in dat]
self.fields[name] = [cd,tim]
class detector_evts(detector):
def _initPointDet(self):
detector._initPointDet(self)
h=self._h5s[0]
codes = h[self._paths["conf"]][...]["code"]
self._addToSelf("codes",codes)
self._getCodeFields()
#if (EvrFound):
def _getCodeFields(self):
dat = self.fields['fifoEvents'][0]
tim = self.fields['fifoEvents'][1]
dat = [[evt['eventCode'] for evt in step] for step in dat]
for code in self.codes:
name = 'code_'+str(code)
cd = [np.array([True if code in evt else False for evt in step]) for step in dat]
self.fields[name] = [cd,tim]
def replaceCalibCycleString(input,digits=4):
fstr = 'CalibCycle:'
starti = input.find(fstr)
replstr = input[starti:starti+len(fstr)+digits]
input = input.replace(replstr,'CalibCycle:%04d')
return input