def OnFindObjects(self, event):
threshold = float(self.tThreshold.GetValue())
chnum = self.chChannel.GetSelection()
from PYME.Analysis.ofind3d import ObjectIdentifier
if not 'ofd' in dir(self) or not self.ofd.chnum == chnum:
#create an object identifier
self.ofd = ObjectIdentifier(self.image.data[:,:,:, chnum])
self.ofd.chnum = chnum
#and identify objects ...
if self.chMethod.GetSelection() == 1: #don't detect objects in poisson noise
fudgeFactor = 1 #to account for the fact that the blurring etc... in ofind doesn't preserve intensities - at the moment completely arbitrary so a threshold setting of 1 results in reasonable detection.
threshold = (numpy.sqrt(self.image.mdh.Camera.ReadNoise**2 + numpy.maximum(self.image.mdh.Camera.ElectronsPerCount*(self.image.mdh.Camera.NoiseFactor**2)*(self.image.data.astype('f') - self.image.mdh.Camera.ADOffset)*self.image.mdh.Camera.TrueEMGain, 1))/self.image.mdh.Camera.ElectronsPerCount)*fudgeFactor*threshold
self.ofd.FindObjects(threshold, 0)
elif self.chMethod.GetSelection() == 2:
bs = float(self.tBlurSize.GetValue())
self.ofd.FindObjects(threshold, blurRadius = bs, blurRadiusZ = bs)
else:
self.ofd.FindObjects(threshold,0)
self.dsviewer.view.points = numpy.array([[p.x, p.y, p.z] for p in self.ofd])
self.objPosRA = numpy.rec.fromrecords(self.dsviewer.view.points, names='x,y,z')
if self.vObjPos == None:
self.vObjPos = recArrayView.recArrayPanel(self.dsviewer, self.objPosRA)
self.dsviewer.AddPage(self.vObjPos, caption='Object Positions')
else:
self.vObjPos.grid.SetData(self.objPosRA)
self.dsviewer.update()
def OnObjMeasure(self, event):
om = self.pipeline.measureObjects()
if self.rav == None:
self.rav = recArrayView.recArrayPanel(self, om)
self.AddPage(self.rav, 'Measurements')
else:
self.rav.grid.SetData(om)
self.cBlobColour.Clear()
self.cBlobColour.Append('Index')
for n in om.dtype.names:
self.cBlobColour.Append(n)
self.RefreshView()
def OnObjMeasure(self, event):
om = self.pipeline.measureObjects()
if self.rav == None:
self.rav = recArrayView.recArrayPanel(self, om)
self.AddPage(self.rav, 'Measurements')
else:
self.rav.grid.SetData(om)
self.cBlobColour.Clear()
self.cBlobColour.Append('Index')
for n in om.dtype.names:
self.cBlobColour.Append(n)
self.RefreshView()
def OnFindObjects(self, event):
threshold = float(self.tThreshold.GetValue())
chnum = self.chChannel.GetSelection()
from PYME.Analysis.ofind3d import ObjectIdentifier
if not 'ofd' in dir(self) or not self.ofd.chnum == chnum:
#create an object identifier
self.ofd = ObjectIdentifier(self.image.data[:, :, :, chnum])
self.ofd.chnum = chnum
#and identify objects ...
if self.chMethod.GetSelection(
) == 1: #don't detect objects in poisson noise
fudgeFactor = 1 #to account for the fact that the blurring etc... in ofind doesn't preserve intensities - at the moment completely arbitrary so a threshold setting of 1 results in reasonable detection.
threshold = (
numpy.sqrt(self.image.mdh.Camera.ReadNoise**2 + numpy.maximum(
self.image.mdh.Camera.ElectronsPerCount *
(self.image.mdh.Camera.NoiseFactor**2) *
(self.image.data.astype('f') - self.image.mdh.Camera.
ADOffset) * self.image.mdh.Camera.TrueEMGain, 1)) /
self.image.mdh.Camera.ElectronsPerCount
) * fudgeFactor * threshold
self.ofd.FindObjects(threshold, 0)
elif self.chMethod.GetSelection() == 2:
bs = float(self.tBlurSize.GetValue())
self.ofd.FindObjects(threshold, blurRadius=bs, blurRadiusZ=bs)
else:
self.ofd.FindObjects(threshold, 0)
self.dsviewer.view.points = numpy.array([[p.x, p.y, p.z]
for p in self.ofd])
self.objPosRA = numpy.rec.fromrecords(self.dsviewer.view.points,
names='x,y,z')
if self.vObjPos == None:
self.vObjPos = recArrayView.recArrayPanel(self.dsviewer,
self.objPosRA)
self.dsviewer.AddPage(self.vObjPos, caption='Object Positions')
else:
self.vObjPos.grid.SetData(self.objPosRA)
self.dsviewer.update()
def OnFitObjects(self, event):
import PYME.Analysis.FitFactories.Gauss3DFitR as fitMod
from PYME.Acquire import MetaDataHandler
chnum = self.chChannel.GetSelection()
mdh = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
mdh['tIndex'] = 0
self.objFitRes = {}
for chnum in range(self.image.data.shape[3]):
data = self.image.data[:, :, :, chnum]
if not 'Camera.ADOffset' in mdh.getEntryNames():
mdh['Camera.ADOffset'] = data.min()
fitFac = fitMod.FitFactory(data, mdh)
self.objFitRes[chnum] = numpy.empty(len(self.ofd),
fitMod.FitResultsDType)
for i in range(len(self.ofd)):
p = self.ofd[i]
#try:
self.objFitRes[chnum][i] = fitFac.FromPoint(
round(p.x), round(p.y), round(p.z), 8)
#except:
# pass
#if self.nObjFit == None:
vObjFit = recArrayView.recArrayPanel(
self.dsviewer, self.objFitRes[chnum]['fitResults'])
self.dsviewer.AddPage(vObjFit,
caption='Fitted Positions %d - %d' %
(chnum, self.nObjFit))
self.nObjFit += 1
#else:
# self.vObjFit.grid.SetData(self.objFitRes['fitResults'])
self.dsviewer.update()
def OnFitObjects(self, event):
import PYME.Analysis.FitFactories.Gauss3DFitR as fitMod
from PYME.Acquire import MetaDataHandler
chnum = self.chChannel.GetSelection()
mdh = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
mdh['tIndex'] = 0
self.objFitRes = {}
for chnum in range(self.image.data.shape[3]):
data = self.image.data[:,:,:,chnum]
if not 'Camera.ADOffset' in mdh.getEntryNames():
mdh['Camera.ADOffset'] = data.min()
fitFac = fitMod.FitFactory(data, mdh)
self.objFitRes[chnum] = numpy.empty(len(self.ofd), fitMod.FitResultsDType)
for i in range(len(self.ofd)):
p = self.ofd[i]
#try:
self.objFitRes[chnum][i] = fitFac.FromPoint(round(p.x), round(p.y), round(p.z), 8)
#except:
# pass
#if self.nObjFit == None:
vObjFit = recArrayView.recArrayPanel(self.dsviewer, self.objFitRes[chnum]['fitResults'])
self.dsviewer.AddPage(vObjFit, caption = 'Fitted Positions %d - %d' % (chnum, self.nObjFit))
self.nObjFit += 1
#else:
# self.vObjFit.grid.SetData(self.objFitRes['fitResults'])
self.dsviewer.update()
