def execute(self, namespace):
from PYME.localization.FitFactories import GaussMultifitSR
import pandas as pd
img = namespace[self.inputImage]
img.mdh['Analysis.PSFSigma'] = self.blobSigma
res = []
for i in range(img.data.shape[2]):
md = MetaDataHandler.NestedClassMDHandler(img.mdh)
md['tIndex'] = i
ff = GaussMultifitSR.FitFactory(self.scale * img.data[:, :, i],
img.mdh,
noiseSigma=np.ones_like(
img.data[:, :, i].squeeze()))
res.append(tabular.FitResultsSource(ff.FindAndFit(self.threshold)))
#FIXME - this shouldn't be a DataFrame
res = pd.DataFrame(np.vstack(res))
res.mdh = img.mdh
namespace[self.outputName] = res
def _add_new_results(self, newResults):
if len(newResults) > 0:
if len(self.fitResults) == 0:
self.fitResults = newResults
self.ds = tabular.FitResultsSource(self.fitResults)
self.ds.mdh = self.resultsMdh
self.dsviewer.pipeline.OpenFile(
ds=self.ds, imBounds=self.dsviewer.image.imgBounds)
self.dsviewer.pipeline.mdh = self.resultsMdh
try:
self.dsviewer.LMDisplay.SetFit()
except:
pass
else:
self.fitResults = np.concatenate((self.fitResults, newResults))
self.ds.setResults(self.fitResults)
self.dsviewer.pipeline.recipe.prune_dependencies_from_namespace(
[
'Localizations',
], True)
self.dsviewer.pipeline.recipe.invalidate_data()
self.progPan.fitResults = self.fitResults
self.view.points = np.vstack((self.fitResults['fitResults']['x0'],
self.fitResults['fitResults']['y0'],
self.fitResults['tIndex'])).T
self.numEvents = len(self.fitResults)
try:
self.dsviewer.LMDisplay.RefreshView()
except:
pass
def OnGenEvents(self, event):
from PYME.simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.IO import tabular
from PYME.IO.image 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,
z=self.zp)
pylab.plot(res['fitResults']['x0'], res['fitResults']['y0'], '+')
ds = tabular.MappingFilter(tabular.FitResultsSource(res))
if isinstance(self.source, ImageSource):
pipeline.imageBounds = image.openImages[
self.source.image].imgBounds
else:
pipeline.imageBounds = ImageBounds.estimateFromSource(ds)
pipeline.addDataSource('Generated Points', ds)
pipeline.selectDataSource('Generated Points')
from PYME.IO.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
pipeline.Rebuild()
if len(self.visFr.layers) < 1:
self.visFr.add_pointcloud_layer(
) #TODO - move this logic so that layer added automatically when datasource is added?
#self.visFr.CreateFoldPanel()
self.visFr.SetFit()
def analRefresh(self):
newNumAnalysed = self.tq.getNumberTasksCompleted(self.queueName)
if newNumAnalysed > self.numAnalysed:
self.numAnalysed = newNumAnalysed
newResults = self.tq.getQueueData(self.queueName, 'FitResults',
len(self.fitResults))
if len(newResults) > 0:
if len(self.fitResults) == 0:
self.fitResults = newResults
self.ds = tabular.FitResultsSource(self.fitResults)
self.dsviewer.pipeline.OpenFile(
ds=self.ds, imBounds=self.dsviewer.image.imgBounds)
self.dsviewer.pipeline.mdh = self.resultsMdh
try:
self.dsviewer.LMDisplay.SetFit()
except:
pass
else:
self.fitResults = np.concatenate(
(self.fitResults, newResults))
self.ds.setResults(self.fitResults)
#self.dsviewer.pipeline.Rebuild()
self.dsviewer.pipeline.recipe.prune_dependencies_from_namespace(
[
'Localizations',
], True)
#logger.debug('Namespace keys (should just be Localizations): %s' % self.dsviewer.pipeline.recipe.namespace.keys())
self.dsviewer.pipeline.recipe.invalidate_data()
#self.dsviewer.pipeline.Rebuild()
self.progPan.fitResults = self.fitResults
self.view.points = np.vstack(
(self.fitResults['fitResults']['x0'],
self.fitResults['fitResults']['y0'],
self.fitResults['tIndex'])).T
self.numEvents = len(self.fitResults)
try:
self.dsviewer.LMDisplay.RefreshView()
except:
pass
if (self.tq.getNumberOpenTasks(self.queueName) +
self.tq.getNumberTasksInProgress(self.queueName)
) == 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.localization.FitFactories import DumbellFitR
from PYME.IO import MetaDataHandler
img = namespace[self.inputImage]
md = MetaDataHandler.NestedClassMDHandler()
#set metadata entries needed for fitting to suitable defaults
md['Camera.ADOffset'] = img.data[:, :, 0].min()
md['Camera.TrueEMGain'] = 1.0
md['Camera.ElectronsPerCount'] = 1.0
md['Camera.ReadNoise'] = 1.0
md['Camera.NoiseFactor'] = 1.0
md['voxelsize.x'] = .001
md['voxelsize.y'] = .001
#copy across the entries from the real image, replacing the defaults
#if necessary
md.copyEntriesFrom(img.mdh)
inp = namespace[self.inputPositions]
fitMod = __import__('PYME.localization.FitFactories.' + self.fitModule,
fromlist=['PYME', 'localization', 'FitFactories'
]) #import our fitting module
r = np.zeros(len(inp['x']), dtype=fitMod.FitResultsDType)
ff_t = -1
ps = img.pixelSize
print('pixel size: %s' % ps)
for x, y, t, i in zip(inp['x'], inp['y'], inp['t'],
range(len(inp['x']))):
if not t == ff_t:
md['tIndex'] = t
ff = fitMod.FitFactory(img.data[:, :, t, self.channel], md)
ff_t = t
#print x/ps, y/ps
r[i] = ff.FromPoint(x / ps, y / ps, roiHalfSize=self.roiHalfSize)
res = tabular.FitResultsSource(r, sort=False)
res.mdh = md
namespace[self.outputName] = res
def _OnCoalesce(self, event=None):
from PYME.IO import tabular
from PYME.Analysis.points.DeClump import pyDeClump
pipeline = self.visFr.pipeline
try:
nphotons = pipeline.selectedDataSource['nPhotons']
except KeyError:
nphotons = None
#TODO - check what nPhotons is doing here!!!
dclumped = pyDeClump.coalesceClumps(pipeline.selectedDataSource.resultsSource.fitResults,
pipeline.selectedDataSource['clumpIndex'], nphotons)
ds = tabular.FitResultsSource(dclumped)
pipeline.addDataSource('Coalesced', ds)
pipeline.selectDataSource('Coalesced')
def execute(self, namespace):
from PYME.localization.FitFactories import DumbellFitR
from PYME.IO import MetaDataHandler
img = namespace[self.inputImage]
md = MetaDataHandler.NestedClassMDHandler()
#set metadata entries needed for fitting to suitable defaults
md['Camera.ADOffset'] = img.data[:,:,0].min()
md['Camera.TrueEMGain'] = 1.0
md['Camera.ElectronsPerCount'] = 1.0
md['Camera.ReadNoise'] = 1.0
md['Camera.NoiseFactor'] = 1.0
#copy across the entries from the real image, replacing the defaults
#if necessary
md.copyEntriesFrom(img.mdh)
inp = namespace[self.inputPositions]
r = np.zeros(len(inp['x']), dtype=DumbellFitR.FitResultsDType)
ff_t = -1
ps = img.pixelSize
for x, y, t, i in zip(inp['x'], inp['y'], inp['t'], range(len(inp['x']))):
if not t == ff_t:
md['tIndex'] = t
ff = DumbellFitR.FitFactory(img.data[:,:,t], md)
ff_t = t
r[i] = ff.FromPoint(x/ps, y/ps)
res = tabular.FitResultsSource(r)
res.mdh = md
namespace[self.outputName] = res
def OnGenEvents(self, event):
from PYME.simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.IO import tabular
from PYME.IO.image import ImageBounds
# import pylab
import matplotlib.pyplot as plt
#wc = wormlike2.wormlikeChain(100)
pipeline = self.visFr.pipeline
pipeline.filename = 'Simulation'
plt.figure()
plt.plot(self.xp, self.yp, 'x') #, lw=2)
if isinstance(self.source, WormlikeSource):
plt.plot(self.xp, self.yp, lw=2)
if self.mode == 'STORM':
res = locify.eventify(self.xp,
self.yp,
self.meanIntensity,
self.meanDuration,
self.backgroundIntensity,
self.meanEventNumber,
self.scaleFactor,
self.meanTime,
z=self.zp)
else:
res = locify.eventify2(self.xp,
self.yp,
self.meanIntensity,
self.meanDuration,
self.backgroundIntensity,
self.meanEventNumber,
self.scaleFactor,
self.meanTime,
z=self.zp)
plt.plot(res['fitResults']['x0'], res['fitResults']['y0'], '+')
ds = tabular.MappingFilter(tabular.FitResultsSource(res))
try:
# some data sources (current ImageSource) have image bound info. Use this if available
# this could fail on either an AttributeError (if the data source doesn't implement bounds
# or another error if something fails in get_bounds(). Only catch the AttributeError, as we have
# should not be handling other errors here.
pipeline.imageBounds = self.source.get_bounds()
except AttributeError:
pipeline.imageBounds = ImageBounds.estimateFromSource(ds)
pipeline.addDataSource('Generated Points', ds)
pipeline.selectDataSource('Generated Points')
from PYME.IO.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
# some info about the parameters
pipeline.mdh['GeneratedPoints.MeanIntensity'] = self.meanIntensity
pipeline.mdh['GeneratedPoints.MeanDuration'] = self.meanDuration
pipeline.mdh['GeneratedPoints.MeanEventNumber'] = self.meanEventNumber
pipeline.mdh[
'GeneratedPoints.BackgroundIntensity'] = self.backgroundIntensity
pipeline.mdh['GeneratedPoints.ScaleFactor'] = self.scaleFactor
pipeline.mdh['GeneratedPoints.MeanTime'] = self.meanTime
pipeline.mdh['GeneratedPoints.Mode'] = self.mode
# the source info
self.source.genMetaData(pipeline.mdh)
try:
pipeline.filterKeys.pop('sig')
except:
pass
pipeline.Rebuild()
if len(self.visFr.layers) < 1:
self.visFr.add_pointcloud_layer(
) #TODO - move this logic so that layer added automatically when datasource is added?
#self.visFr.CreateFoldPanel()
self.visFr.SetFit()