def runTestCase(self, datfile, prmfile, eventPartHnd, parallel):
prm=testutil.readparams(prmfile)
dat=tsvTrajIO(fnames=[datfile], Fs=prm['Fs'], separator=',')
# sett=json.loads( "".join((open('../../.settings', 'r').readlines())) )
sett = (settings.settings('.', defaultwarn=False).settingsDict)
epartsettings = sett[eventPartHnd.__name__]
epartsettings['blockSizeSec'] = 0.006
epartsettings['meanOpenCurr'] = 1
epartsettings['sdOpenCurr'] = 0.03
epartsettings['slopeOpenCurr'] = 0
epartsettings['driftThreshold'] = 1000
epartsettings['maxDriftRate'] = 9999.0
epartsettings['eventThreshold'] = 5.0
if parallel:
epartsettings['parallelProc'] = 1
testobj=eventPartHnd(
dat,
sra.stepResponseAnalysis,
epartsettings,
sett["stepResponseAnalysis"],
json.dumps(sett, indent=4)
)
testobj.PartitionEvents()
self.assertEqual( testobj.eventcount, prm['nevents'] )
testobj.Stop()
for f in glob.glob('testdata/*.sqlite'):
os.remove(f)
def _setupTestCase(self, datfile, prmfile, algoHnd):
[self.Fs, self.dat]=testutil.readcsv(datfile)
self.prm=testutil.readparams(prmfile)
self.sett = (settings.settings('.', defaultwarn=False).settingsDict)[algoHnd.__name__]
self.dt=int(1e6/self.dat[0])
def run_eventpartition(dataPath, trajDataHnd, dataFilterHnd, eventPartHnd,
eventProcHnd, dbFilename):
# Read and parse the settings file
settingsdict = settings.settings(dataPath)
# Pull out trajectory settings to construct an IO object
trajSettings = settingsdict.getSettings(trajDataHnd.__name__)
if dataFilterHnd:
trajDataObj = trajDataHnd(datafilter=dataFilterHnd,
dirname=dataPath,
**trajSettings)
else:
trajDataObj = trajDataHnd(dirname=dataPath, **trajSettings)
if dbFilename == '':
kwargs = {}
else:
kwargs = {'dbFilename': dataPath + '/' + dbFilename}
try:
with eventPartHnd(trajDataObj, eventProcHnd,
settingsdict.getSettings(eventPartHnd.__name__),
settingsdict.getSettings(eventProcHnd.__name__),
json.dumps(settingsdict.settingsDict, indent=4),
**kwargs) as EventPartition:
EventPartition.PartitionEvents()
except KeyboardInterrupt:
raise
def runTestCase(self, datfile, prmfile, eventPartHnd, parallel):
prm=testutil.readparams(prmfile)
dat=tsvTrajIO(fnames=[datfile], Fs=prm['Fs'], separator=',')
sett = (settings.settings('.', defaultwarn=False).settingsDict)
epartsettings = sett[eventPartHnd.__name__]
epartsettings['blockSizeSec'] = 0.006
epartsettings['meanOpenCurr'] = 1
epartsettings['sdOpenCurr'] = 0.03
epartsettings['slopeOpenCurr'] = 0
epartsettings['driftThreshold'] = 1000
epartsettings['maxDriftRate'] = 9999.0
epartsettings['eventThreshold'] = 5.0
if parallel:
epartsettings['parallelProc'] = 1
testobj=eventPartHnd(
dat,
a2s.adept2State,
epartsettings,
sett["adept2State"],
json.dumps(sett, indent=4)
)
testobj.PartitionEvents()
assert testobj.eventcount == prm['nevents']
testobj.Stop()
for f in glob.glob('testdata/*.sqlite'):
os.remove(f)
def _setupTestCase(self, datfile, prmfile, algoHnd):
[self.Fs, self.dat]=testutil.readcsv(datfile)
self.prm=testutil.readparams(prmfile)
self.sett = (settings.settings('.', defaultwarn=False).settingsDict)[algoHnd.__name__]
self.dt=int(1e6/self.dat[0])
def run_eventpartition( dataPath, trajDataHnd, dataFilterHnd, eventPartHnd, eventProcHnd, dbFilename):
# Read and parse the settings file
settingsdict=settings.settings( dataPath )
# Pull out trajectory settings to construct an IO object
trajSettings=settingsdict.getSettings(trajDataHnd.__name__)
if dataFilterHnd:
trajDataObj=trajDataHnd( datafilter=dataFilterHnd, dirname=dataPath, **trajSettings )
else:
trajDataObj=trajDataHnd( dirname=dataPath, **trajSettings )
if dbFilename=='':
kwargs={}
else:
kwargs={'dbFilename': dataPath+'/'+dbFilename}
try:
with eventPartHnd(
trajDataObj,
eventProcHnd,
settingsdict.getSettings(eventPartHnd.__name__),
settingsdict.getSettings(eventProcHnd.__name__),
json.dumps(settingsdict.settingsDict, indent=4),
**kwargs
) as EventPartition:
EventPartition.PartitionEvents()
except KeyboardInterrupt:
raise
def _setupDataFilter(self):
filtsettings=settings.settings( self.datPath ).getSettings(self.datafilter.__name__)
if filtsettings=={}:
self.logger.warning("WARNING: No settings found for '{0}'. Data filtering is disabled".format(str(self.datafilter.__name__)))
self.dataFilter=False
return
return self.datafilter(**filtsettings)
def _loadSettings(self, **kwargs):
try:
self.analysisSettingsDict = json.loads(kwargs['settingsString'])
self.defaultSettings = False
except KeyError:
sObj = settings.settings(self.dataPath)
self.analysisSettingsDict = sObj.settingsDict
self.defaultSettings = sObj.defaultSettingsLoaded
def _loadSettings(self, **kwargs): try: self.analysisSettingsDict=json.loads(kwargs['settingsString']) self.defaultSettings=False except KeyError: sObj=settings.settings(self.dataPath) self.analysisSettingsDict=sObj.settingsDict self.defaultSettings=sObj.defaultSettingsLoaded
def _setupTestCase(self, datfile, prmfile, algoHnd):
self.dat=testutil.readDataRAW(datfile)
self.prm=testutil.readParametersJSON(prmfile)
self.Fs=int(self.prm['FsKHz']*1000)
self.dt=1./self.prm['FsKHz']
self.noiseRMS=self.prm['noisefArtHz']*np.sqrt(self.prm['BkHz']*1000.)/1000.
self.sett = (settings.settings('.', defaultwarn=False).settingsDict)[algoHnd.__name__]
def _setupTestCase(self, datfile, prmfile, algoHnd):
self.dat=testutil.readDataRAW(datfile)
self.prm=testutil.readParametersJSON(prmfile)
self.Fs=int(self.prm['FsKHz']*1000)
self.dt=1./self.prm['FsKHz']
self.noiseRMS=self.prm['noisefArtHz']*np.sqrt(self.prm['BkHz']*1000.)/1000.
self.sett = (settings.settings('.', defaultwarn=False).settingsDict)[algoHnd.__name__]
def runTestCase(self, datfile, prmfile, algoHnd):
self.dat=testutil.readcsv(datfile)
self.prm=testutil.readparams(prmfile)
sett = (settings.settings('.', defaultwarn=False).settingsDict)[algoHnd.__name__]
dt=int(1e6/self.dat[0])
self.testobj=algoHnd(
self.dat[1],
self.dat[0],
eventstart=int(self.prm['tau1']/dt), # event start point
eventend=int(self.prm['tau2']/dt), # event end point
baselinestats=[ 1.0, 0.01, 0.0 ],
algosettingsdict=sett,
savets=0,
absdatidx=0.0,
datafileHnd=None
)
self.testobj.processEvent()
