def setup_tracking(moviefile, pre4):
"""Create all tracking objects."""
# open movie
testmovie = test_movie_for_known_movie(moviefile)
movie = movies.Movie(testmovie, interactive=False)
# create background model calculator
if pre4:
bg_model = bg_pre4.BackgroundCalculator(movie)
else:
bg_model = bg.BackgroundCalculator(movie)
bg_img_shape = (movie.get_height(), movie.get_width())
bg_model.set_buffer_maxnframes()
# open annotation file
ann_file = ann.AnnotationFile(annname(moviefile, pre4))
ann_file.InitializeData()
# calculate bg
bg_model.OnCalculate()
# estimate fly shapes
havevalue = (not params.maxshape.area == 9999.)
haveshape = (not num.isinf(params.maxshape.area))
if (not haveshape) or (not havevalue):
if pre4:
params.movie = movie
ell_pre4.est_shape(bg_model)
params.movie = None
else:
ell.est_shape(bg_model)
hindsight = hs.Hindsight(ann_file, bg_model)
return movie, bg_model, ann_file, hindsight
def DoAllPreprocessing(self):
# estimate the background
if (not self.IsBGModel()) or params.batch_autodetect_bg_model:
print "Estimating background model"
if params.interactive:
self.bg_imgs.est_bg(self.frame)
else:
self.bg_imgs.est_bg()
else:
print "Not estimating background model"
# detect arena if it has not been set yet
if params.do_set_circular_arena and params.batch_autodetect_arena:
print "Auto-detecting circular arena"
setarena.doall(self.bg_imgs.center)
else:
print "Not detecting arena"
self.bg_imgs.UpdateIsArena()
# estimate the shape
if params.batch_autodetect_shape:
print "Estimating shape model"
if params.interactive:
ell.est_shape(self.bg_imgs,self.frame)
else:
ell.est_shape(self.bg_imgs)
else:
print "Not estimating shape model"
def OnComputeShape(self,evt):
start_color = self.status.GetBackgroundColour()
if not hasattr( self.bg_imgs, 'center' ) and params.interactive:
if params.use_median:
algtxt = 'Median'
else:
algtxt = 'Mean'
msgtxt = 'Background model has not been calculated.\nCalculate now using the following parameters?\n\nAlgorithm: %s\nNumber of Frames: %d' %(algtxt,params.n_bg_frames)
if wx.MessageBox( msgtxt, "Calculate?", wx.OK|wx.CANCEL ) == wx.CANCEL:
return
else:
# set up for running background calculation
bg_calc = True
self.status.SetBackgroundColour( params.status_green )
self.status.SetStatusText( "calculating background", params.status_box )
wx.Yield()
self.bg_imgs.est_bg(self.frame)
self.status.SetBackgroundColour( params.status_red )
self.status.SetStatusText( "calculating shape", params.status_box )
wx.BeginBusyCursor()
wx.Yield()
ell.est_shape( self.bg_imgs, self.frame )
wx.EndBusyCursor()
self.status.SetBackgroundColour( start_color )
self.status.SetStatusText( "", params.status_box )
def ComputeShapeNow(self,evt):
# estimate shape now
wx.BeginBusyCursor()
wx.Yield()
succeeded = ell.est_shape( self.bg_imgs,self.frame )
wx.EndBusyCursor()
if not succeeded:
return
# copy to temporary variable
self.automatic_minshape = params.params.minshape.copy()
self.automatic_maxshape = params.params.maxshape.copy()
self.automatic_meanshape = params.params.meanshape.copy()
# show shape
self.PrintShape()
# set up to date
self.shape_uptodate = True
self.automatic_shape_text.SetLabel('')
self.RegisterParamChange()
self.ShowImage()
def ComputeShapeNow(self, evt):
# estimate shape now
wx.BeginBusyCursor()
wx.Yield()
succeeded = ell.est_shape(self.bg_imgs, self.frame)
wx.EndBusyCursor()
if not succeeded:
return
# copy to temporary variable
self.automatic_minshape = params.params.minshape.copy()
self.automatic_maxshape = params.params.maxshape.copy()
self.automatic_meanshape = params.params.meanshape.copy()
# show shape
self.PrintShape()
# set up to date
self.shape_uptodate = True
self.automatic_shape_text.SetLabel('')
self.RegisterParamChange()
self.ShowImage()
def CheckForShapeModel(self):
# already have computed the shape model
if params.have_computed_shape:
return True
haveshape = num.isinf(params.maxshape.area) == False
# have read in the shape model
if (params.movie_name == params.annotation_movie_name) and haveshape:
return True
# in non-interactive mode, automatically do the computation
if params.interactive == False:
# do the calculation
ell.est_shape( self.bg_imgs )
return True
# ask what to do
if haveshape:
msgtxt = 'Shape model has not been automatically computed for this movie. Currently:\n\nMin Area = %.2f\nMax Area = %.2f\n\nDo you want to automatically compute now with the following parameters?\n\nNumber of Frames: %d\nNumber of Standard Deviations: %.2f'%(params.minshape.area,params.maxshape.area,params.n_frames_size,params.n_std_thresh)
else:
msgtxt = 'Shape is currently unbounded. Do you want to automatically compute now with the following parameters?\n\nNumber of Frames: %d\nNumber of Standard Deviations: %.2f'%(params.n_frames_size,params.n_std_thresh)
resp = wx.MessageBox( msgtxt, "Calculate?", wx.YES_NO|wx.CANCEL )
if resp == wx.NO:
return True
elif resp == wx.CANCEL:
return False
# set up for running shape calculation
if self.status is not None:
start_color = self.status.GetBackgroundColour()
self.status.SetBackgroundColour( params.status_blue )
self.status.SetStatusText( "calculating shape", params.status_box )
wx.BeginBusyCursor()
wx.Yield()
# do the calculation
ell.est_shape(self.bg_imgs)
# return to normal
if self.status is not None:
self.status.SetBackgroundColour( start_color )
self.status.SetStatusText('',params.status_box)
wx.EndBusyCursor()
return True
def set_shape_method( self ):
"""A shape-computation method was selected. Take action."""
params.enforce_minmax_shape = True
selection = self.get_radio_control_selection()
if selection == 0:
# don't use shape bounds
params.enforce_minmax_shape = False
self.show_shape_results()
elif selection == 1:
# auto-compute shape
wx.BeginBusyCursor()
wx.Yield()
self.remember_button_states()
success = est_shape( self.bg, self.frame )
self.reset_button_states()
wx.EndBusyCursor()
if success:
self.show_shape_results()
else:
self.OnPrevButton( None )
elif selection == 2:
# launch settings for manual shape setting
self.prev_button.Enable( False )
self.next_button.Enable( False )
self.tracking_settings = TrackingSettings( self.frame, self.bg, 0 )
self.tracking_settings.frame.Bind( wx.EVT_CLOSE, self.OnQuitTrackingSettings )
self.tracking_settings.frame.Bind( wx.EVT_BUTTON, self.OnQuitTrackingSettings, id=xrc.XRCID("done") )
self.tracking_settings.frame.Show()
# hack to switch dialog to manual settings
self.tracking_settings.automatic_shape_input.SetValue( False )
self.tracking_settings.manual_shape_input.SetValue( True )
self.tracking_settings.OnAutomatic( None )