def analRefresh(self):
newNumAnalysed = self.tq.getNumberTasksCompleted(self.image.seriesName)
if newNumAnalysed > self.numAnalysed:
self.numAnalysed = newNumAnalysed
newResults = self.tq.getQueueData(self.image.seriesName, 'FitResults', len(self.fitResults))
if len(newResults) > 0:
if len(self.fitResults) == 0:
self.fitResults = newResults
self.ds = inpFilt.fitResultsSource(self.fitResults)
self.dsviewer.pipeline.OpenFile(ds=self.ds)
else:
self.fitResults = numpy.concatenate((self.fitResults, newResults))
self.ds.setResults(self.fitResults)
self.dsviewer.pipeline.Rebuild()
self.progPan.fitResults = self.fitResults
self.view.points = numpy.vstack((self.fitResults['fitResults']['x0'], self.fitResults['fitResults']['y0'], self.fitResults['tIndex'])).T
self.numEvents = len(self.fitResults)
if (self.tq.getNumberOpenTasks(self.image.seriesName) + self.tq.getNumberTasksInProgress(self.image.seriesName)) == 0 and 'SpoolingFinished' in self.image.mdh.getEntryNames():
self.dsviewer.statusbar.SetBackgroundColour(wx.GREEN)
self.dsviewer.statusbar.Refresh()
self.progPan.draw()
self.progPan.Refresh()
self.dsviewer.Refresh()
self.dsviewer.update()
def execute(self, namespace):
from PYME.Analysis.FitFactories import GaussMultifitSR
img = namespace[self.inputImage]
img.mdh['Analysis.PSFSigma'] = self.blobSigma
ff = GaussMultifitSR.FitFactory(self.scale*img.data[:,:,:], img.mdh, noiseSigma=np.ones_like(img.data[:,:,:].squeeze()))
res = inpFilt.fitResultsSource(ff.FindAndFit(self.threshold))
namespace[self.outputName] = res#inpFilt.mappingFilter(res, x='fitResults_x0', y='fitResults_y0')
def OnCoalesce(self, event):
from PYME.Analysis.LMVis import inpFilt
from PYME.Analysis.DeClump import pyDeClump
pipeline = self.visFr.pipeline
dclumped = pyDeClump.coalesceClumps(pipeline.selectedDataSource.resultsSource.fitResults, pipeline.selectedDataSource.clumpIndices)
ds = inpFilt.fitResultsSource(dclumped)
pipeline.selectedDataSource = ds
pipeline.dataSources.append(ds)
self.visFr.RegenFilter()
self.visFr.CreateFoldPanel()
def OnCoalesce(self, event):
from PYME.Analysis.LMVis import inpFilt
from PYME.Analysis.DeClump import pyDeClump
pipeline = self.visFr.pipeline
dclumped = pyDeClump.coalesceClumps(
pipeline.selectedDataSource.resultsSource.fitResults,
pipeline.selectedDataSource.clumpIndices)
ds = inpFilt.fitResultsSource(dclumped)
pipeline.selectedDataSource = ds
pipeline.dataSources.append(ds)
self.visFr.RegenFilter()
self.visFr.CreateFoldPanel()
def analRefresh(self):
newNumAnalysed = self.tq.getNumberTasksCompleted(self.image.seriesName)
if newNumAnalysed > self.numAnalysed:
self.numAnalysed = newNumAnalysed
newResults = self.tq.getQueueData(self.image.seriesName,
'FitResults',
len(self.fitResults))
if len(newResults) > 0:
if len(self.fitResults) == 0:
self.fitResults = newResults
self.ds = inpFilt.fitResultsSource(self.fitResults)
self.dsviewer.pipeline.OpenFile(ds=self.ds)
else:
self.fitResults = numpy.concatenate(
(self.fitResults, newResults))
self.ds.setResults(self.fitResults)
self.dsviewer.pipeline.Rebuild()
self.progPan.fitResults = self.fitResults
self.view.points = numpy.vstack(
(self.fitResults['fitResults']['x0'],
self.fitResults['fitResults']['y0'],
self.fitResults['tIndex'])).T
self.numEvents = len(self.fitResults)
if (self.tq.getNumberOpenTasks(self.image.seriesName) +
self.tq.getNumberTasksInProgress(self.image.seriesName)
) == 0 and 'SpoolingFinished' in self.image.mdh.getEntryNames():
self.dsviewer.statusbar.SetBackgroundColour(wx.GREEN)
self.dsviewer.statusbar.Refresh()
self.progPan.draw()
self.progPan.Refresh()
self.dsviewer.Refresh()
self.dsviewer.update()
def OnGenEvents(self, event):
from PYMEnf.Simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.Analysis.LMVis import inpFilt
from PYME.Analysis.LMVis.visHelpers import ImageBounds
import pylab
#wc = wormlike2.wormlikeChain(100)
pipeline = self.visFr.pipeline
pipeline.filename='Simulation'
pylab.figure()
pylab.plot(self.xp, self.yp, 'x') #, lw=2)
if isinstance(self.source, WormlikeSource):
pylab.plot(self.xp, self.yp, lw=2)
res = locify.eventify(self.xp, self.yp, self.meanIntensity, self.meanDuration, self.backgroundIntensity, self.meanEventNumber, self.scaleFactor, self.meanTime)
pylab.plot(res['fitResults']['x0'],res['fitResults']['y0'], '+')
pipeline.selectedDataSource = inpFilt.mappingFilter(inpFilt.fitResultsSource(res))
pipeline.imageBounds = ImageBounds.estimateFromSource(pipeline.selectedDataSource)
pipeline.dataSources.append(pipeline.selectedDataSource)
from PYME.Acquire.MetaDataHandler import NestedClassMDHandler
pipeline.mdh = NestedClassMDHandler()
pipeline.mdh['Camera.ElectronsPerCount'] = 1
pipeline.mdh['Camera.TrueEMGain'] = 1
pipeline.mdh['Camera.CycleTime'] = 1
pipeline.mdh['voxelsize.x'] = .110
try:
pipeline.filterKeys.pop('sig')
except:
pass
self.visFr.RegenFilter()
self.visFr.SetFit()
