def listMaps(self, cells):
"""List all maps associated with the file handle for each cell in a list"""
self.ui.mapTable.clear()
self.maps = []
for cell in cells:
dbui = self.host.getElement('Database')
db = dbui.getDb()
if db is None:
logMsg("No database loaded in Data Manager.", msgType='error')
ident = self.dbIdentity+'.maps'
table = dbui.getTableName(ident)
if not db.hasTable(table):
return
if db.tableOwner(table) != ident:
raise Exception("Table %s not owned by %s" % (table, ident))
#row = db.getDirRowID(cell)
#if row is None:
#return
maps = db.select(table, ['rowid','*'], where={'cell': cell})
#print maps
for rec in maps:
scans = []
for rowid in rec['scans']:
if isinstance(rowid, tuple):
fh = db.getDir(rowid[0], rowid[1]) ## single-spot maps specify the Protocol table instead
else:
fh = db.getDir('ProtocolSequence', rowid) ## NOTE: single-spot maps use a different table!
scans.append((fh, rowid))
rec['scans'] = scans
self.newMap(rec)
def newFolder(self):
if self.ui.newFolderList.currentIndex() < 1:
return
ftype = str(self.ui.newFolderList.currentText())
self.ui.newFolderList.setCurrentIndex(0)
cdir = self.manager.getCurrentDir()
if not cdir.isManaged():
cdir.createIndex()
if ftype == 'Folder':
nd = cdir.mkdir('NewFolder', autoIncrement=True)
#item = self.model.handleIndex(nd)
self.ui.fileTreeWidget.editItem(nd)
else:
spec = self.manager.config['folderTypes'][ftype]
name = time.strftime(spec['name'])
## Determine where to put the new directory
parent = cdir
try:
checkDir = cdir
for i in range(5):
if not checkDir.isManaged():
break
inf = checkDir.info()
if 'dirType' in inf and inf['dirType'] == ftype:
parent = checkDir.parent()
break
#else:
#print "dir no match:", spec, inf
checkDir = checkDir.parent()
except:
printExc("Error while deciding where to put new folder (using currentDir by default)")
## make
nd = parent.mkdir(name, autoIncrement=True)
## Add meta-info
info = {'dirType': ftype}
if spec.get('experimentalUnit', False):
info['expUnit'] = True
nd.setInfo(info)
## set display to info
#self.showFileInfo(nd)
#index = self.model.handleIndex(nd)
#self.ui.fileTreeView.selectionModel().select(index, QtGui.QItemSelectionModel.Clear)
#self.ui.fileTreeView.selectionModel().select(index, QtGui.QItemSelectionModel.Select)
self.ui.fileTreeWidget.refresh(parent) ## fileTreeWidget waits a while before updating; force it to refresh immediately.
self.ui.fileTreeWidget.select(nd)
##self.ui.fileInfo.setCurrentFile(nd)
logMsg("Created new folder: %s" %nd.name(relativeTo=self.baseDir), msgType='status', importance=7)
self.manager.setCurrentDir(nd)
def setCommand(self, vals):
"""Requests to set the command output to the mirrors.
(The request is denied if the virtual shutter is closed)"""
with self.lock:
self.currentCommand = vals
if self.getShutterOpen():
## make sure we have not requested a command outside the allowed limits
(mn, mx) = self.config['commandLimits']
v0 = max(mn, min(mx, vals[0]))
v1 = max(mn, min(mx, vals[1]))
self.setVoltage([v0, v1])
else:
logMsg("Virtual shutter closed, not setting mirror position.", msgType='warning')
def startTask(self, task, paramSpace=None):
#print "TaskThread:startTask", self.lock.depth(), self.lock
with MutexLocker(self.lock):
#print "TaskThread:startTask got lock", self.lock.depth(), " tracebacks follow:\n==========="
#print "\n\n".join(self.lock.traceback())
#print "======================"
while self.isRunning():
#l.unlock()
raise Exception("Already running another task")
self.task = task
self.paramSpace = paramSpace
self.lastRunTime = None
#l.unlock()
#print "TaskThread:startTask starting..", self.lock.depth()
self.start() ### causes self.run() to be called from somewhere in C code
#name = '' if task.fileName is None else task.fileName
logMsg("Task started.", importance=1)
def getCalibration(self, laser, opticState=None):
with self.lock:
index = self.getCalibrationIndex()
if opticState is None:
opticState = self.getDeviceStateKey() ## this tells us about objectives, filters, etc
if laser in index:
index1 = index[laser]
else:
logMsg("Warning: No calibration found for laser %s" % laser, msgType='warning')
return None
if opticState in index1:
index2 = index1[opticState]
else:
logMsg("Warning: No calibration found for state: %s" % opticState, msgType='warning')
return None
return index2.copy()
def mcUpdate(self, state=None, mode=None):
"""MC state (or internal holding state) has changed, handle the update."""
with self.stateLock:
if state is None:
state = self.lastState[mode]
mode = state['mode']
state['holding'] = self.holding[mode]
self.lastState[mode] = state.copy()
if self.lastMode != state['mode']:
if self.lastMode is not None and state[
'mode'] != self._switchingToMode and state[
'mode'] != 'I=0':
# User changed the mode manually; we need to update the holding value immediately.
self.setHolding(state['mode'])
logMsg(
"Warning: MultiClamp mode should be changed from ACQ4, not from the MultiClamp Commander window.",
msgType='error')
self.lastMode = state['mode']
self._switchingToMode = None
self.sigStateChanged.emit(state)
def getCalibration(self, laser, opticState=None):
with self.lock:
index = self.getCalibrationIndex()
if opticState is None:
opticState = self.getDeviceStateKey(
) ## this tells us about objectives, filters, etc
if laser in index:
index1 = index[laser]
else:
logMsg("Warning: No calibration found for laser %s" % laser,
msgType='warning')
return None
if opticState in index1:
index2 = index1[opticState]
else:
logMsg("Warning: No calibration found for state: %s" % opticState,
msgType='warning')
return None
return index2.copy()
def newFolder(self):
if self.ui.newFolderList.currentIndex() < 1:
return
ftype = str(self.ui.newFolderList.currentText())
self.ui.newFolderList.setCurrentIndex(0)
cdir = self.manager.getCurrentDir()
if not cdir.isManaged():
cdir.createIndex()
if ftype == 'Folder':
nd = cdir.mkdir('NewFolder', autoIncrement=True)
#item = self.model.handleIndex(nd)
self.ui.fileTreeWidget.editItem(nd)
else:
spec = self.manager.config['folderTypes'][ftype]
name = time.strftime(spec['name'])
## Determine where to put the new directory
parent = cdir
try:
checkDir = cdir
for i in range(5):
if not checkDir.isManaged():
break
inf = checkDir.info()
if 'dirType' in inf and inf['dirType'] == ftype:
parent = checkDir.parent()
break
#else:
#print "dir no match:", spec, inf
checkDir = checkDir.parent()
except:
printExc(
"Error while deciding where to put new folder (using currentDir by default)"
)
## make
nd = parent.mkdir(name, autoIncrement=True)
## Add meta-info
info = {'dirType': ftype}
if spec.get('experimentalUnit', False):
info['expUnit'] = True
nd.setInfo(info)
## set display to info
#self.showFileInfo(nd)
#index = self.model.handleIndex(nd)
#self.ui.fileTreeView.selectionModel().select(index, QtGui.QItemSelectionModel.Clear)
#self.ui.fileTreeView.selectionModel().select(index, QtGui.QItemSelectionModel.Select)
self.ui.fileTreeWidget.refresh(
parent
) ## fileTreeWidget waits a while before updating; force it to refresh immediately.
self.ui.fileTreeWidget.select(nd)
##self.ui.fileInfo.setCurrentFile(nd)
logMsg("Created new folder: %s" % nd.name(relativeTo=self.baseDir),
msgType='status',
importance=7)
self.manager.setCurrentDir(nd)
def runSequence(self, store=True):
## Disable all start buttons
self.enableStartBtns(False)
# good time to collect garbage
gc.collect()
## Find all top-level items in the sequence parameter list
try:
## make sure all devices are reporting their correct sequence lists
items = self.ui.sequenceParamList.listParams()
#for i in self.ui.sequenceParamList.topLevelItems:
#items.append(i)
## Generate parameter space
params = OrderedDict()
paramInds = OrderedDict()
linkedParams = {}
pLen = 1
for i in items:
key = i[:2]
params[key] = i[2]
paramInds[key] = range(len(i[2]))
pLen *= len(i[2])
linkedParams[key] = i[3]
## Set storage dir
if store:
currentDir = self.manager.getCurrentDir()
name = self.currentTask.name()
if name is None:
name = 'protocol'
info = self.taskInfo(params)
info['dirType'] = 'ProtocolSequence'
dh = currentDir.mkdir(name, autoIncrement=True, info=info)
else:
dh = None
## Tell devices to prepare for task start.
for d in self.currentTask.devices:
if self.currentTask.deviceEnabled(d):
self.docks[d].widget().prepareTaskStart()
#print params, linkedParams
## Generate the complete array of command structures. This can take a long time, so we start a progress dialog.
with pg.ProgressDialog("Generating task commands..", 0, pLen) as progressDlg:
#progressDlg.setMinimumDuration(500) ## If this takes less than 500ms, progress dialog never appears.
self.lastQtProcessTime = ptime.time()
prot = runSequence(lambda p: self.generateTask(dh, p, progressDlg), paramInds, paramInds.keys(), linkedParams=linkedParams)
#progressDlg.setValue(pLen)
if dh is not None:
dh.flushSignals() ## do this now rather than later as task is running
#print "==========Sequence Task=============="
#print prot
#self.emit(QtCore.SIGNAL('taskSequenceStarted'), {})
self.sigTaskSequenceStarted.emit({})
logMsg('Started %s task sequence of length %i' %(self.currentTask.name(),pLen), importance=6)
#print 'PR task positions:
self.taskThread.startTask(prot, paramInds)
except:
self.enableStartBtns(True)
raise
def _measurePower(self):
if self.hasPowerIndicator:
## run a task that checks the power
daqName = self.getDAQName('shutter')
powerInd = self.config['powerIndicator']['channel']
rate = self.config['powerIndicator']['rate']
pConfig = getManager().getDevice(
self.config['powerIndicator']['channel'][0]).listChannels()[
self.config['powerIndicator']['channel'][1]]
sTime = pConfig.get('settlingTime', None)
mTime = pConfig.get('measurementTime', None)
if mTime is None or sTime is None:
raise Exception(
"The power indicator (%s) specified for %s needs to be configured with both a 'settlingTime' value and a 'measurementTime' value."
% (self.config['powerIndicator']['channel'], self.name()))
dur = 0.1 + (sTime + mTime)
nPts = int(dur * rate)
### create a waveform that flashes the QSwitch(or other way of turning on) the number specified by reps
waveform = np.zeros(nPts, dtype=np.byte)
#for i in range(reps):
#waveform[(i+1)/10.*rate:((i+1)/10.+sTime+mTime)*rate] = 1 ## divide i+1 by 10 to increment by hundreds of milliseconds
waveform[0.1 * rate:-2] = 1
measureMode = self.measurementMode()
cmd = {
'protocol': {
'duration': dur
},
self.name(): {
'switchWaveform': waveform,
'shutterMode': measureMode['shutter']
},
powerInd[0]: {
powerInd[1]: {
'record': True,
'recordInit': False
}
},
daqName: {
'numPts': nPts,
'rate': rate
}
}
#print "outputPowerCmd: ", cmd
task = getManager().createTask(cmd)
task.execute(
processEvents=False
) # disable event processing to prevent recurrent requests
result = task.getResult()
## pull out time that laser was on and off so that power can be measured in each state -- discard the settlingTime around each state change
#onMask = np.zeros(nPts, dtype=np.byte)
#offMask = np.zeros(nPts, dtype=np.byte)
#for i in range(reps):
#onMask[((i+1)/10+sTime)*rate:((i+1)/10+sTime+mTime)*rate] = 1
#offMask[(i/10.+2*sTime+mTime)*rate:(i+1/10.)*rate] = 1
powerIndTrace = result[powerInd[0]]
if powerIndTrace is None:
raise Exception("No data returned from power indicator")
laserOn = powerIndTrace[0][0.1 * rate:-2].asarray()
laserOff = powerIndTrace[0][:0.1 * rate].asarray()
t, prob = stats.ttest_ind(laserOn, laserOff)
if prob < 0.01: ### if powerOn is statistically different from powerOff
powerOn = laserOn.mean()
if powerOn < 0:
powerOn = 0.0
powerOff = laserOff.mean()
#self.devGui.ui.outputPowerLabel.setText(siFormat(powerOn, suffix='W')) ## NO! device does not talk to GUI!
self.setParam(currentPower=powerOn)
powerOk = self.checkPowerValidity(powerOn)
self.sigOutputPowerChanged.emit(powerOn, powerOk)
self.updateSamplePower()
return powerOn
else:
logMsg(
"No laser pulse detected by power indicator '%s' while measuring Laser.outputPower()"
% powerInd[0],
msgType='warning')
self.setParam(currentPower=0.0)
self.updateSamplePower()
return 0.0
## return the power specified in the config file if there's no powerIndicator
else:
return self.config.get('power', None)
def runSequence(self, store=True):
## Disable all start buttons
self.enableStartBtns(False)
# good time to collect garbage
gc.collect()
## Find all top-level items in the sequence parameter list
try:
## make sure all devices are reporting their correct sequence lists
items = self.ui.sequenceParamList.listParams()
## Generate parameter space
params = OrderedDict()
paramInds = OrderedDict()
linkedParams = {}
pLen = 1
for i in items:
key = i[:2]
params[key] = i[2]
paramInds[key] = range(len(i[2]))
pLen *= len(i[2])
linkedParams[key] = i[3]
## Set storage dir
if store:
currentDir = self.manager.getCurrentDir()
name = self.currentTask.name()
if name is None:
name = 'protocol'
info = self.taskInfo(params)
info['dirType'] = 'ProtocolSequence'
dh = currentDir.mkdir(name, autoIncrement=True, info=info)
else:
dh = None
## Tell devices to prepare for task start.
for d in self.currentTask.devices:
if self.currentTask.deviceEnabled(d):
self.docks[d].widget().prepareTaskStart()
#print params, linkedParams
## Generate the complete array of command structures. This can take a long time, so we start a progress dialog.
with pg.ProgressDialog("Generating task commands..", 0,
pLen) as progressDlg:
self.lastQtProcessTime = ptime.time()
prot = runSequence(
lambda p: self.generateTask(dh, p, progressDlg),
paramInds,
list(paramInds.keys()),
linkedParams=linkedParams)
if dh is not None:
dh.flushSignals(
) ## do this now rather than later when task is running
self.sigTaskSequenceStarted.emit({})
logMsg('Started %s task sequence of length %i' %
(self.currentTask.name(), pLen),
importance=6)
#print 'PR task positions:
self.taskThread.startTask(prot, paramInds)
except:
self.enableStartBtns(True)
raise
def outputPower(self):
"""
Return a tuple: (current output power, bool power within expected range)
The output power returned excludes the effect of pockel cell, shutter, etc.
This information is determined in one of a few ways:
1. The laser directly reports its power output (function needs to be reimplemented in subclass)
2. A photodiode receves a small fraction of the beam and reports an estimated power
3. The output power is specified in the config file
"""
if self.hasPowerIndicator:
## run a task that checks the power
daqName = self.getDAQName('shutter')
powerInd = self.config['powerIndicator']['channel']
rate = self.config['powerIndicator']['rate']
pConfig = getManager().getDevice(self.config['powerIndicator']['channel'][0]).listChannels()[self.config['powerIndicator']['channel'][1]]
sTime = pConfig.get('settlingTime', None)
mTime = pConfig.get('measurementTime', None)
if mTime is None or sTime is None:
raise Exception("The power indicator (%s) specified for %s needs to be configured with both a 'settlingTime' value and a 'measurementTime' value." %(self.config['powerIndicator']['channel'], self.name()))
dur = 0.1 + (sTime+mTime)
nPts = int(dur*rate)
### create a waveform that flashes the QSwitch(or other way of turning on) the number specified by reps
waveform = np.zeros(nPts, dtype=np.byte)
#for i in range(reps):
#waveform[(i+1)/10.*rate:((i+1)/10.+sTime+mTime)*rate] = 1 ## divide i+1 by 10 to increment by hundreds of milliseconds
waveform[0.1*rate:-2] = 1
cmd = {
'protocol': {'duration': dur},
self.name(): {'switchWaveform':waveform, 'shutterMode':'closed'},
powerInd[0]: {powerInd[1]: {'record':True, 'recordInit':False}},
daqName: {'numPts': nPts, 'rate': rate}
}
#print "outputPowerCmd: ", cmd
task = getManager().createTask(cmd)
task.execute()
result = task.getResult()
## pull out time that laser was on and off so that power can be measured in each state -- discard the settlingTime around each state change
#onMask = np.zeros(nPts, dtype=np.byte)
#offMask = np.zeros(nPts, dtype=np.byte)
#for i in range(reps):
#onMask[((i+1)/10+sTime)*rate:((i+1)/10+sTime+mTime)*rate] = 1
#offMask[(i/10.+2*sTime+mTime)*rate:(i+1/10.)*rate] = 1
powerIndTrace = result[powerInd[0]]
if powerIndTrace is None:
raise Exception("No data returned from power indicator")
laserOn = powerIndTrace[0][0.1*rate:-2].asarray()
laserOff = powerIndTrace[0][:0.1*rate].asarray()
t, prob = stats.ttest_ind(laserOn, laserOff)
if prob < 0.01: ### if powerOn is statistically different from powerOff
powerOn = laserOn.mean()
if powerOn < 0:
powerOn = 0.0
powerOff = laserOff.mean()
#self.devGui.ui.outputPowerLabel.setText(siFormat(powerOn, suffix='W')) ## NO! device does not talk to GUI!
self.setParam(currentPower=powerOn)
powerOk = self.checkPowerValidity(powerOn)
self.sigOutputPowerChanged.emit(powerOn, powerOk)
self.updateSamplePower()
return powerOn, powerOk
else:
logMsg("No laser pulse detected by power indicator '%s' while measuring Laser.outputPower()" % powerInd[0], msgType='warning')
self.setParam(currentPower=0.0)
self.updateSamplePower()
return 0.0, self.checkPowerValidity(0.0)
## return the power specified in the config file if there's no powerIndicator
else:
power = self.config.get('power', None)
if power is None:
return None, None
else:
return power, self.checkPowerValidity(power)