def OnTrackMolecules(self, event):
import PYME.Analysis.points.DeClump.deClumpGUI as deClumpGUI
#import PYME.Analysis.points.DeClump.deClump as deClump
import PYME.Analysis.Tracking.trackUtils as trackUtils
from PYME.LMVis.layers.tracks import TrackRenderLayer
from PYME.recipes import tracking
recipe = self.visFr.pipeline.recipe
visFr = self.visFr
pipeline = visFr.pipeline
tracking_module = tracking.FindClumps(recipe, inputName=pipeline.selectedDataSourceKey,
outputName='with_tracks',
outputClumps = 'tracks',
timeWindow=5,
clumpRadiusVariable='1.0',
clumpRadiusScale=250.,
minClumpSize=50)
if tracking_module.configure_traits(kind='modal'):
recipe.add_module(tracking_module)
recipe.execute()
self.visFr.pipeline.selectDataSource('with_tracks')
#self.visFr.CreateFoldPanel() #TODO: can we capture this some other way?
layer = TrackRenderLayer(pipeline, dsname=tracking_module.outputClumps, method='tracks')
visFr.add_layer(layer)
def OnFindClumps(self, event=None):
import PYME.Analysis.points.DeClump.deClumpGUI as deClumpGUI
#import PYME.Analysis.points.DeClump.deClump as deClump
import PYME.Analysis.Tracking.trackUtils as trackUtils
visFr = self.visFr
pipeline = visFr.pipeline
#bCurr = wx.BusyCursor()
dlg = deClumpGUI.deClumpDialog(None)
ret = dlg.ShowModal()
if ret == wx.ID_OK:
#with progress.ComputationInProgress(visFr, 'finding consecutive appearances'):
from PYME.recipes import tracking
recipe = self.visFr.pipeline.recipe
recipe.add_modules_and_execute([tracking.FindClumps(recipe, inputName=pipeline.selectedDataSourceKey, outputName='with_clumps',
timeWindow=dlg.GetClumpTimeWindow(),
clumpRadiusVariable=dlg.GetClumpRadiusVariable(),
clumpRadiusScale=dlg.GetClumpRadiusMultiplier()),])
self.visFr.pipeline.selectDataSource('with_clumps')
#self.visFr.CreateFoldPanel() #TODO: can we capture this some other way?
dlg.Destroy()
def OnTrackMolecules(self, event=None):
import PYME.Analysis.points.DeClump.deClumpGUI as deClumpGUI
#import PYME.Analysis.points.DeClump.deClump as deClump
import PYME.Analysis.Tracking.trackUtils as trackUtils
from PYME.LMVis.layers.tracks import TrackRenderLayer
from PYME.recipes import tracking
from PYME.recipes.tablefilters import FilterTable
recipe = self.visFr.pipeline.recipe
visFr = self.visFr
pipeline = visFr.pipeline # type: PYME.LMVis.pipeline.Pipeline
if hasattr(self, '_mol_tracking_module') and (self._mol_tracking_module in recipe.modules):
# We have already tracked, edit existing tracking module instead
wx.MessageBox('This dataset has already been tracked, edit parameters of existing tracking rather than starting again', 'Error', wx.OK|wx.ICON_ERROR, visFr)
self._mol_tracking_module.configure_traits(kind='modal')
return
output_name = 'with_tracks'
if output_name in recipe.namespace:
# this should take care of, e.g. having tracked with feature based tracking or something in the recipe
output_name = pipeline.new_ds_name('with_tracks')
wx.MessageBox("Another module has already created a 'with_tracks' output, using the nonstandard name '%s' instead" % output_name, 'Warning', wx.OK|wx.ICON_WARNING, visFr)
tracking_module = tracking.FindClumps(recipe, inputName=pipeline.selectedDataSourceKey,
outputName=output_name,
timeWindow=5,
clumpRadiusVariable='1.0',
clumpRadiusScale=250.,
minClumpSize=50)
if tracking_module.configure_traits(kind='modal'):
self._mol_tracking_module = tracking_module
recipe.add_modules_and_execute([tracking_module,
# Add dynamic filtering on track length, etc.
FilterTable(recipe,
inputName=tracking_module.outputName,
outputName='filtered_{}'.format(tracking_module.outputName),
filters={'clumpSize':[tracking_module.minClumpSize, 1e6]})])
self.visFr.pipeline.selectDataSource('filtered_{}'.format(tracking_module.outputName))
#self.visFr.CreateFoldPanel() #TODO: can we capture this some other way?
layer = TrackRenderLayer(pipeline, dsname='filtered_{}'.format(tracking_module.outputName), method='tracks')
visFr.add_layer(layer)
def OnTrackMolecules(self, event):
import PYME.Analysis.points.DeClump.deClumpGUI as deClumpGUI
#import PYME.Analysis.points.DeClump.deClump as deClump
import PYME.Analysis.Tracking.trackUtils as trackUtils
from PYME.recipes import tracking
recipe = self.visFr.pipeline.recipe
visFr = self.visFr
pipeline = visFr.pipeline
tracking_module = tracking.FindClumps(recipe, inputName=pipeline.selectedDataSourceKey,
outputName='with_tracks',
outputClumps = 'tracks',
timeWindow=5,
clumpRadiusVariable='1.0',
clumpRadiusScale=250.,
minClumpSize=50)
if tracking_module.configure_traits(kind='modal'):
recipe.add_module(tracking_module)
recipe.execute()
self.visFr.pipeline.selectDataSource('with_tracks')