def pushImagesHDF(self, image):
dataFilename = image.seriesName
resultsFilename = _verifyResultsFilename(
genResultFileName(image.seriesName))
self.queueName = resultsFilename
self.tq.createQueue('HDFTaskQueue',
self.queueName,
dataFilename=dataFilename,
resultsFilename=resultsFilename,
startAt='notYet')
mdhQ = MetaDataHandler.QueueMDHandler(self.tq, self.queueName,
self.analysisMDH)
mdhQ['DataFileID'] = fileID.genDataSourceID(image.dataSource)
# evts = self.image.dataSource.getEvents()
# if len(evts) > 0:
# self.tq.addQueueEvents(self.image.seriesName, evts)
self.resultsMdh = mdhQ
self.tq.releaseTasks(self.queueName,
self.analysisMDH['Analysis.StartAt'])
self.onImagesPushed.send(self)
def __init__(self, filename, frameSource, frameShape, complevel=6, complib='zlib', **kwargs):
# if 'PYME_TASKQUEUENAME' in os.environ.keys():
# taskQueueName = os.environ['PYME_TASKQUEUENAME']
# else:
# taskQueueName = 'taskQueue'
import Pyro.core
from PYME.misc.computerName import GetComputerName
compName = GetComputerName()
taskQueueName = 'TaskQueues.%s' % compName
if ns:
URI = ns.resolve(taskQueueName)
else:
URI = 'PYRONAME://' + taskQueueName
self.tq = Pyro.core.getProxyForURI(URI)
self.tq._setOneway(['postTask', 'postTasks', 'addQueueEvents', 'setQueueMetaData', 'logQueueEvent'])
self.seriesName = filename
self.buffer = []
self.buflen = 30
self.tq.createQueue('HDFTaskQueue',self.seriesName, filename, frameSize = frameShape, complevel=complevel, complib=complib)
self.md = MetaDataHandler.QueueMDHandler(self.tq, self.seriesName)
self.evtLogger = EventLogger(self, self.tq, self.seriesName)
sp.Spooler.__init__(self, filename, frameSource, **kwargs)
def pushImagesHDF(startingAt=0, detThresh=.9, fitFcn='LatGaussFitFR'):
global seriesName
dataFilename = seriesName
resultsFilename = genResultFileName(seriesName)
while os.path.exists(resultsFilename):
di, fn = os.path.split(resultsFilename)
fdialog = wx.FileDialog(
None,
'Analysis file already exists, please select a new filename',
wildcard='H5R files|*.h5r',
defaultDir=di,
defaultFile=os.path.splitext(fn)[0] + '_1.h5r',
style=wx.FD_SAVE)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
resultsFilename = fdialog.GetPath()
else:
raise RuntimeError('Invalid results file - not running')
seriesName = resultsFilename
tq.createQueue('HDFTaskQueue',
seriesName,
dataFilename=dataFilename,
resultsFilename=resultsFilename,
startAt='notYet')
mdhQ = MetaDataHandler.QueueMDHandler(tq, seriesName, mdh)
mdhQ.setEntry('Analysis.DetectionThreshold', detThresh)
mdhQ.setEntry('Analysis.FitModule', fitFcn)
mdhQ.setEntry('Analysis.DataFileID', fileID.genDataSourceID(dataSource))
evts = dataSource.getEvents()
if len(evts) > 0:
tq.addQueueEvents(seriesName, evts)
tq.releaseTasks(seriesName, startingAt)
def pushImagesD(startingAt=0, detThresh=.9):
tq.createQueue('HDFResultsTaskQueue', seriesName, None)
mdhQ = MetaDataHandler.QueueMDHandler(tq, seriesName, mdh)
mdhQ.setEntry('Analysis.DetectionThreshold', detThresh)
for i in range(startingAt, ds.shape[0]):
tq.postTask(remFitBuf.fitTask(
seriesName,
i,
detThresh,
MetaDataHandler.NestedClassMDHandler(mdh),
'LatGaussFitFR',
bgindices=range(
max(i - 10, mdh.getEntry('EstimatedLaserOnFrameNo')), i),
SNThreshold=True,
driftEstInd=range(
max(i - 5, mdh.getEntry('EstimatedLaserOnFrameNo')),
min(i + 5, ds.shape[0])),
dataSourceModule=dataSource.moduleName),
queueName=seriesName)
def _loadQueue(self, filename):
"""Load data from a remote PYME.ParallelTasks.HDFTaskQueue queue using
Pyro.
Parameters:
-----------
filename : string
the name of the queue
"""
import Pyro.core
from PYME.IO.DataSources import TQDataSource
from PYME.misc.computerName import GetComputerName
compName = GetComputerName()
if self.queueURI is None:
#do a lookup
taskQueueName = 'TaskQueues.%s' % compName
try:
from PYME.misc import pyme_zeroconf
ns = pyme_zeroconf.getNS()
URI = ns.resolve(taskQueueName)
except:
URI = 'PYRONAME://' + taskQueueName
self.tq = Pyro.core.getProxyForURI(URI)
else:
self.tq = Pyro.core.getProxyForURI(self.queueURI)
self.seriesName = filename[len('QUEUE://'):]
self.dataSource = TQDataSource.DataSource(self.seriesName, self.tq)
self.data = self.dataSource #this will get replaced with a wrapped version
self.mdh = MetaDataHandler.QueueMDHandler(self.tq, self.seriesName)
MetaData.fillInBlanks(self.mdh, self.dataSource)
#self.timer.WantNotification.append(self.dsRefresh)
self.events = self.dataSource.getEvents()
self.mode = 'LM'
