def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None ):
pool = AnimalPool( )
pool.loadAnimals( connection )
#pool.loadDetection( start = tmin, end = tmax )
rear = {}
for animal in range( 1 , 5 ):
rear[animal] = EventTimeLineCached( connection, file, "Rear isolated", animal, minFrame=tmin, maxFrame=tmax )
centerWindow = {}
for animal in range( 1 , 5 ):
centerWindow[animal] = EventTimeLineCached(connection, file, "Center Zone", animal, minFrame=tmin, maxFrame=tmax )
periphery = {}
for animal in range( 1 , 5 ):
periphery[animal] = EventTimeLineCached(connection, file, "Periphery Zone", animal, minFrame=tmin, maxFrame=tmax )
for animal in range( 1 , 5 ):
eventName1 = "Rear in centerWindow"
print ( eventName1 )
eventName2 = "Rear at periphery"
print ( eventName2 )
rearCenterTimeLine = EventTimeLine( None, eventName1 , animal , None , None , None , loadEvent=False )
rearPeripheryTimeLine = EventTimeLine( None, eventName2 , animal , None , None , None , loadEvent=False )
resultCenter={}
resultPeriphery={}
dicRear = rear[ animal ].getDictionnary()
dicCenter = centerWindow[ animal ].getDictionnary()
dicPeriphery = periphery[ animal ].getDictionnary()
for t in dicRear.keys():
if ( t in dicCenter ):
resultCenter[t] = True
if (t in dicPeriphery ):
resultPeriphery[t] = True
rearCenterTimeLine.reBuildWithDictionnary( resultCenter )
rearPeripheryTimeLine.reBuildWithDictionnary( resultPeriphery )
rearCenterTimeLine.endRebuildEventTimeLine(connection)
rearPeripheryTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger( connection )
t.addLog( "Build Event Rear in centerWindow" , tmin=tmin, tmax=tmax )
t.addLog( "Build Event Rear at periphery" , tmin=tmin, tmax=tmax )
print( "Rebuild event finished." )
def getNumberOfEventWithList( connection, file, eventName, idAnimalA , animalList, minFrame=None, maxFrame=None ):
sumOfEvent = 0
for animalCandidate in animalList:
timeLine = EventTimeLineCached( connection , file, eventName , idAnimalA , animalCandidate.baseId, minFrame=minFrame, maxFrame=maxFrame )
sumOfEvent += timeLine.getNbEvent()
return sumOfEvent
def getDurationOfEventWithList( connection, file, eventName, idAnimalA , animalList, minFrame=None, maxFrame=None ):
durationOfEvent = 0
for animalCandidate in animalList:
timeLine = EventTimeLineCached( connection , file, eventName , idAnimalA , animalCandidate.baseId, minFrame=minFrame, maxFrame=maxFrame )
durationOfEvent += timeLine.getTotalLength()
return durationOfEvent
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax, lightLoad=True)
''' load the contact timeline for each pair of animals '''
anogenitalSniffTimeLine = {}
passiveAnogenitalSniffTimeLine = {}
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
anogenitalSniffTimeLine[animal, idAnimalB] = EventTimeLineCached(
connection,
file,
"Oral-genital Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
# create an empty timeline for other contacts
passiveAnogenitalSniffTimeLine[idAnimalB, animal] = EventTimeLine(
None,
'Passive oral-genital Contact',
idAnimalB,
animal,
loadEvent=False)
anogenitalSniffDico = {}
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
anogenitalSniffDico[animal, idAnimalB] = anogenitalSniffTimeLine[
animal, idAnimalB].getDictionary(minFrame=tmin, maxFrame=tmax)
passiveAnogenitalSniffTimeLine[idAnimalB,
animal].reBuildWithDictionnary(
anogenitalSniffDico[animal,
idAnimalB])
passiveAnogenitalSniffTimeLine[
idAnimalB, animal].endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Passive oral-genital Contact", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
eventUndetected = 'Undetected exclusive'
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
''' load the existing detection timeline for animal '''
detectionTimeLine = {}
dicoDetection = {}
undetectedTimeLine = {}
for animal in range(1, pool.getNbAnimals() + 1):
detectionTimeLine[animal] = EventTimeLineCached(connection,
file,
'Detection',
animal,
minFrame=tmin,
maxFrame=tmax)
dicoDetection[animal] = detectionTimeLine[animal].getDictionary(
minFrame=tmin, maxFrame=tmax)
undetectedTimeLine[animal] = EventTimeLine(None,
eventUndetected,
animal,
loadEvent=False)
'''select the frames where the animals are not detected'''
undetectedDico = {}
for animal in range(1, pool.getNbAnimals() + 1):
undetectedDico[animal] = {}
for t in range(tmin, tmax + 1):
if t not in dicoDetection[animal]:
undetectedDico[animal][t] = True
#####################################################
#reduild all events based on dictionary
for animal in range(1, pool.getNbAnimals() + 1):
undetectedTimeLine[animal].reBuildWithDictionnary(
undetectedDico[animal])
undetectedTimeLine[animal].endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Exclusive undetected events", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
pool = AnimalPool()
pool.loadAnimals(connection)
#pool.loadDetection( start = tmin, end = tmax )
''' load contact matrix '''
contact = {}
group3In = {}
group3Out = {}
for idAnimalA in range(1, 5):
contact[idAnimalA] = EventTimeLineCached(connection,
file,
"Contact",
idAnimalA,
minFrame=tmin,
maxFrame=tmax)
group3In[idAnimalA] = EventTimeLine(connection,
"Group 3 make",
idAnimalA,
loadEvent=False)
group3Out[idAnimalA] = EventTimeLine(connection,
"Group 3 break",
idAnimalA,
loadEvent=False)
''' process group '''
for idAnimalA in range(1, 5):
for idAnimalB in range(1, 5):
for idAnimalC in range(1, 5):
''' check impossible combination (avoid 2 animals with same id) '''
test = {}
test[idAnimalA] = True
test[idAnimalB] = True
test[idAnimalC] = True
if not len(test.keys()) == 3:
continue
''' process group '''
group3 = EventTimeLineCached(connection,
file,
"Group3",
idAnimalA,
idAnimalB,
idAnimalC,
minFrame=tmin,
maxFrame=tmax)
eventList = group3.getEventList()
for event in eventList:
t = event.startFrame - 1
if (not contact[idAnimalA].hasEvent(t)):
group3In[idAnimalA].addPunctualEvent(t)
if (not contact[idAnimalB].hasEvent(t)):
group3In[idAnimalB].addPunctualEvent(t)
if (not contact[idAnimalC].hasEvent(t)):
group3In[idAnimalC].addPunctualEvent(t)
t = event.endFrame + 1
if (not contact[idAnimalA].hasEvent(t)):
group3Out[idAnimalA].addPunctualEvent(t)
if (not contact[idAnimalB].hasEvent(t)):
group3Out[idAnimalB].addPunctualEvent(t)
if (not contact[idAnimalC].hasEvent(t)):
group3Out[idAnimalC].addPunctualEvent(t)
''' save all '''
for idAnimal in range(1, 5):
group3In[idAnimal].endRebuildEventTimeLine(connection)
group3Out[idAnimal].endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Group3 Make Break", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
''' use the pool provided or create it'''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax)
'''
Event OralSide Sequence
'''
nbAnimal = pool.getNbAnimals()
contact = {}
oralOral = {}
oralGenital = {}
oralOralDico = {}
oralGenitalDico = {}
EVENT_MIN_LEN = 10
for idAnimalB in pool.animalDictionnary.keys():
print(pool.animalDictionnary[idAnimalB])
meanSizeB = pool.animalDictionnary[idAnimalB].getMeanBodyLength(
tmax=tmax)
for animal in pool.animalDictionnary.keys():
if (idAnimalB == animal):
continue
'''
contact[animal, idAnimalB] = EventTimeLine( connection, "Contact", animal, idAnimalB, minFrame=tmin, maxFrame=tmax )
'''
oralOral[animal,
idAnimalB] = EventTimeLineCached(connection,
file,
"Oral-oral Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
oralGenital[animal, idAnimalB] = EventTimeLineCached(
connection,
file,
"Oral-genital Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
oralOralDico[animal,
idAnimalB] = oralOral[animal,
idAnimalB].getDictionnary()
oralGenitalDico[animal, idAnimalB] = oralGenital[
animal, idAnimalB].getDictionnary()
window = 60
'''
oral oral followed by a oral-genital
'''
eventName = "seq oral oral - oral genital"
print(eventName)
for animal in range(1, nbAnimal + 1):
for idAnimalB in range(1, nbAnimal + 1):
if (animal == idAnimalB):
continue
selOO_OG_TimeLine = EventTimeLine(None,
eventName,
animal,
idAnimalB,
None,
None,
loadEvent=False)
print(selOO_OG_TimeLine.eventNameWithId)
oralOralTimeLine = oralOral[animal, idAnimalB]
oralGeniDico = oralGenitalDico[animal, idAnimalB]
oralGeniTimeLine = oralGenital[animal, idAnimalB]
for event in oralOralTimeLine.eventList:
endFrame = event.endFrame
if (event.duration() >= EVENT_MIN_LEN):
continue
for t in range(endFrame, endFrame + window + 1):
if (t in oralGeniDico):
event2 = oralGeniTimeLine.getEventAt(t)
if (event2.duration() >= EVENT_MIN_LEN):
start = event.startFrame
end = event2.endFrame
selOO_OG_TimeLine.addEvent(Event(start, end))
break
selOO_OG_TimeLine.endRebuildEventTimeLine(connection)
window = 60
'''
oral A genital B followed by oral oral
'''
eventName = "seq oral geni - oral oral"
print(eventName)
for animal in range(1, nbAnimal + 1):
for idAnimalB in range(1, nbAnimal + 1):
if (animal == idAnimalB):
continue
selOG_OO_TimeLine = EventTimeLine(None,
eventName,
animal,
idAnimalB,
None,
None,
loadEvent=False)
print(selOG_OO_TimeLine.eventNameWithId)
oralGenitalTimeLine = oralGenital[animal, idAnimalB]
ooDico = oralOralDico[animal, idAnimalB]
oralOralTimeLine = oralOral[animal, idAnimalB]
for event in oralGenitalTimeLine.eventList:
endFrame = event.endFrame
if (event.duration() >= EVENT_MIN_LEN):
continue
for t in range(endFrame, endFrame + window + 1):
if (t in ooDico):
event2 = oralOralTimeLine.getEventAt(t)
if (event2.duration() >= EVENT_MIN_LEN):
start = event.startFrame
end = event2.endFrame
selOG_OO_TimeLine.addEvent(Event(start, end))
break
selOG_OO_TimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Oral Side Sequence", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
''' use pool cache if available '''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax)
'''
three animals are following each others with nose-to-anogenital contacts
animals are moving
this is a combination of Train2 events (train2 events must be calculated before this event)
'''
#deleteEventTimeLineInBase(connection, "Train3" )
''' build a list of train 2 for each time point '''
time = {}
train3 = {}
for idAnimalA in range(1, 5):
for idAnimalB in range(1, 5):
if (idAnimalA == idAnimalB):
continue
train2TimeLine = EventTimeLineCached(connection,
file,
"Train2",
idAnimalA,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
for t in train2TimeLine.getDictionnary():
train = Train2(idAnimalA, idAnimalB)
if (not t in time):
time[t] = []
#print ( t , ":" , train.idA , " -> ", train.idB , "*" )
time[t].append(train)
for t in time:
trainList = time[t]
for trainSource in trainList:
for trainTarget in trainList:
if (trainSource == trainTarget):
continue
isValid = ""
''' test chain link between train2 events '''
if trainSource.idB == trainTarget.idA:
id1 = trainSource.idA
id2 = trainSource.idB
id3 = trainTarget.idB
if not (id1, id2, id3) in train3:
train3[id1, id2, id3] = {}
train3[id1, id2, id3][t] = True
isValid = ": validated train 3"
#print ( t , ":" , trainSource.idA , " -> ", trainSource.idB, "--->", trainTarget.idA , " -> ", trainTarget.idB , isValid )
''' save data '''
for idAnimalA in range(1, 5):
for idAnimalB in range(1, 5):
for idAnimalC in range(1, 5):
if (idAnimalA, idAnimalB, idAnimalC) in train3:
trainTimeLine = EventTimeLine(None,
"Train3",
idAnimalA,
idAnimalB,
idAnimalC,
loadEvent=False)
trainTimeLine.reBuildWithDictionnary(train3[idAnimalA,
idAnimalB,
idAnimalC])
#trainTimeLine.removeEventsBelowLength( 5 )
trainTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Train3", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
return
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Animal A is stopped (built-in event):
Move social: animal A is stopped and in contact with another animal.
Move isolated: animal A is stopped and not in contact with any other animal.
'''
pool = AnimalPool()
pool.loadAnimals(connection)
isInContactSourceDictionnary = {}
moveSourceTimeLine = {}
for animal in pool.animalDictionnary.keys():
''' Load source stop timeLine and revert it to get the move timeline
If the animal is not detected, this will result in a move. To avoid this we mask with the detection.
'''
moveSourceTimeLine[animal] = EventTimeLine(connection,
"Stop",
animal,
minFrame=tmin,
maxFrame=tmax,
inverseEvent=True)
detectionTimeLine = EventTimeLine(connection,
"Detection",
animal,
minFrame=tmin,
maxFrame=tmax)
moveSourceTimeLine[animal].keepOnlyEventCommonWithTimeLine(
detectionTimeLine)
''' load contact dictionnary with another animal '''
for animalB in pool.animalDictionnary.keys():
if animal == animalB:
print('Same identity')
continue
else:
isInContactSourceDictionnary[(
animal, animalB)] = EventTimeLineCached(
connection,
file,
"Contact",
animal,
animalB,
minFrame=tmin,
maxFrame=tmax).getDictionnary()
for animal in pool.animalDictionnary.keys():
#initialisation of a dic for isolated move
moveIsolatedResult = {}
for animalB in pool.animalDictionnary.keys():
# initialisation of a dic for move in contact for each individual of the cage
moveSocialResult = {}
if animal == animalB:
print('Same identity')
continue
else:
''' loop over eventlist'''
for moveEvent in moveSourceTimeLine[animal].eventList:
''' for each event we seek in t and search a match in isInContactDictionnary between animal and animalB '''
for t in range(moveEvent.startFrame,
moveEvent.endFrame + 1):
if t in isInContactSourceDictionnary[(animal,
animalB)]:
moveSocialResult[t] = True
else:
moveIsolatedResult[t] = True
''' save move social at the end of the search for each animal'''
moveSocialResultTimeLine = EventTimeLine(None,
"Move in contact",
idA=animal,
idB=animalB,
idC=None,
idD=None,
loadEvent=False)
moveSocialResultTimeLine.reBuildWithDictionnary(
moveSocialResult)
moveSocialResultTimeLine.endRebuildEventTimeLine(connection)
''' save move isolated at the end of the complete process for animalA'''
moveIsolatedResultTimeLine = EventTimeLine(None,
"Move isolated",
idA=animal,
idB=None,
idC=None,
idD=None,
loadEvent=False)
moveIsolatedResultTimeLine.reBuildWithDictionnary(moveIsolatedResult)
moveIsolatedResultTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Move", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent( connection, file, tmin=None, tmax=None , pool = None ):
'''
Nest 3
'''
print("[NEST 3] : Assume that there is no occlusion, does not work with anonymous animals")
if ( pool == None ):
pool = AnimalPool( )
pool.loadAnimals( connection )
pool.loadDetection( start = tmin, end = tmax , lightLoad=True )
if ( len ( pool.getAnimalList() ) != 4 ):
print( "[NEST3 Cancelled] 4 animals are required to build nest3.")
return
contact = {}
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if idAnimalA != idAnimalB:
contact[idAnimalA,idAnimalB] = EventTimeLineCached( connection, file, "Contact", idAnimalA, idAnimalB, minFrame=tmin, maxFrame=tmax ).getDictionnary()
stopDictionnary = {}
for idAnimalA in range( 1 , 5 ):
stopDictionnary[idAnimalA] = EventTimeLineCached( connection, file, "Stop", idAnimalA, minFrame=tmin, maxFrame=tmax ).getDictionnary()
nest3TimeLine = {}
for idAnimalA in range( 1 , 5 ):
# the id will be the one excluded from nest.
nest3TimeLine[idAnimalA] = EventTimeLine( None, "Nest3" , idAnimalA, loadEvent=False )
animalList = pool.getAnimalList()
result = {}
for idAnimalA in range( 1 , 5 ):
result[idAnimalA] = {}
for t in range( tmin, tmax+1 ):
isNest = False
nbAnimalAtT = 0
animalDetectedList = []
for animal in animalList:
if t in animal.detectionDictionnary:
nbAnimalAtT+=1
animalDetectedList.append( animal )
#print( str(t) + " : " + str( nbAnimalAtT ) )
#print("TEST")
graph = nx.Graph();
# add nodes
for animal in animalDetectedList:
graph.add_node( animal )
for animalA in animalDetectedList:
for animalB in animalDetectedList:
if animalA != animalB:
# add an edge
if t in contact[animalA.baseId,animalB.baseId]:
graph.add_edge( animalA, animalB )
# list of CC from the biggest to the smallest
listCC = sorted(nx.connected_components( graph ), key=len, reverse=True)
if ( len( listCC ) == 2 ): # we have 2 groups
# check if animals in the biggest group are stopped.
allStoppedInBiggestGroup = True
for animal in list( listCC[0] ):
if not ( t in stopDictionnary[animal.baseId] ):
allStoppedInBiggestGroup = False
break
if allStoppedInBiggestGroup:
if ( len( listCC[1] ) == 1 ): # the 2nd group (and the smallest) has only one mouse
animal = list(listCC[1])[0]
result[ animal.baseId ][ t ] = True
'''
largestCC = len ( max(nx.connected_components( graph ), key=len) )
#print( str( t ) + " : " + str ( len( largestCC ) ) )
print( str( t ) + " : " + str ( largestCC ) + " / " + str( nbAnimalAtT ) )
if largestCC == nbAnimalAtT :
isNest= True
if isNest == True:
print( "ADD PUNCTUAL")
result[t] = True;
'''
for idAnimalA in range( 1 , 5 ):
# the id will be the one excluded from nest.
nest3TimeLine[idAnimalA].reBuildWithDictionnary( result[idAnimalA] )
# remove very small events
nest3TimeLine[idAnimalA].removeEventsBelowLength( 2 )
nest3TimeLine[idAnimalA].mergeCloseEvents( 3 )
nest3TimeLine[idAnimalA].endRebuildEventTimeLine(connection)
#nest4TimeLine.reBuildWithDictionnary( result )
#nest4TimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger( connection )
t.addLog( "Build Event Nest3" , tmin=tmin, tmax=tmax )
print( "Rebuild event finished." )
def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None ):
''' use the pool provided or create it'''
if ( pool == None ):
pool = AnimalPool( )
pool.loadAnimals( connection )
pool.loadDetection( start = tmin, end = tmax )
'''
Event Rear5:
- the animal is rearing
- distinction between rearing in contact with one or several animals and rearing isolated from the others
'''
contact = {}
for idAnimalA in pool.animalDictionnary.keys():
print(pool.animalDictionnary[idAnimalA])
contact[idAnimalA] = EventTimeLineCached( connection, file, "Contact", idAnimalA, minFrame=tmin, maxFrame=tmax )
contactDico = contact[idAnimalA].getDictionnary()
eventName1 = "Rear isolated"
eventName2 = "Rear in contact"
print ( "A rears")
rearSocialTimeLine = EventTimeLine( None, eventName2 , idAnimalA , None , None , None , loadEvent=False )
rearIsolatedTimeLine = EventTimeLine( None, eventName1 , idAnimalA , None , None , None , loadEvent=False )
resultSocial={}
resultIsolated={}
animalA = pool.animalDictionnary[idAnimalA]
#print ( animalA )
dicA = animalA.detectionDictionnary
for t in dicA.keys():
slope = dicA[t].getBodySlope()
if ( slope == None):
continue
if ( abs( slope ) < BODY_SLOPE_THRESHOLD ):
continue;
if (t in contactDico.keys()):
#print("social")
resultSocial[t] = True
else:
#print("isolated")
resultIsolated[t] = True
rearSocialTimeLine.reBuildWithDictionnary( resultSocial )
rearIsolatedTimeLine.reBuildWithDictionnary( resultIsolated )
rearSocialTimeLine.endRebuildEventTimeLine( connection )
rearIsolatedTimeLine.endRebuildEventTimeLine( connection )
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger( connection )
t.addLog( "Build Event Rear5" , tmin=tmin, tmax=tmax )
print( "Rebuild event finished." )
def reBuildEvent( connection, file, tmin=None, tmax=None, pool = None ):
pool = AnimalPool( )
pool.loadAnimals( connection )
#pool.loadDetection( start = tmin, end = tmax )
contact = {}
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if ( idAnimalA == idAnimalB ):
continue
contact[idAnimalA, idAnimalB] = EventTimeLineCached( connection, file, "Contact", idAnimalA, idAnimalB, minFrame=tmin, maxFrame=tmax ) #fait une matrice de tous les contacts à deux possibles
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if( idAnimalA == idAnimalB ):
continue
for idAnimalC in range( 1 , 5 ):
if( idAnimalA == idAnimalC ):
continue
if( idAnimalB == idAnimalC ):
continue
for idAnimalD in range( 1 , 5 ):
if( idAnimalA == idAnimalD ):
continue
if( idAnimalB == idAnimalD ):
continue
if( idAnimalC == idAnimalD ):
continue
eventName = "Group2"
print ( eventName )
groupTimeLine = EventTimeLine( None, eventName , idAnimalA , idAnimalB , None , None , loadEvent=False )
result={}
dicAB = contact[ idAnimalA , idAnimalB ].getDictionnary()
dicAC = contact[ idAnimalA , idAnimalC ].getDictionnary()
dicAD = contact[ idAnimalA , idAnimalD ].getDictionnary()
dicBC = contact[ idAnimalB , idAnimalC ].getDictionnary()
dicBD = contact[ idAnimalB , idAnimalD ].getDictionnary()
for t in dicAB.keys():
if ( t in dicAC or t in dicAD or t in dicBC or t in dicBD ):
continue
else:
result[t]=True
groupTimeLine.reBuildWithDictionnary( result )
groupTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger( connection )
t.addLog( "Build Event Group 2" , tmin=tmin, tmax=tmax )
print( "Rebuild event finished." )
'''
pool.loadDetection( start = min_dur, end = max_dur)
for animal in pool.animalDictionnary.keys():
print ( pool.animalDictionnary[animal].RFID )
#total distance traveled
totalDistance = pool.animalDictionnary[animal].getDistance(tmin = min_dur, tmax = max_dur)
resTotalDistance = [file, pool.animalDictionnary[animal].RFID, min_dur, max_dur, totalDistance]
text_file.write( "{}\t{}\t{}\t{}\t{}\n".format( file, pool.animalDictionnary[animal].RFID, min_dur, max_dur, totalDistance ) )
'''
nightEventTimeLine = EventTimeLineCached(connection,
file,
"night",
minFrame=tmin,
maxFrame=tmax)
n = 1
for eventNight in nightEventTimeLine.getEventList():
startNight = eventNight.startFrame
endNight = eventNight.endFrame
print("Night: ", n)
for animal in pool.animalDictionnary.keys():
for behavEvent in behaviouralEventOneMouse:
print("computing individual event: {}".format(behavEvent))
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax, lightLoad=True)
contactDicoDico = {}
approachDico = {}
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
''' I take the dictionnary of event of the contact event, that's why I put DicoDico '''
contactDicoDico[animal, idAnimalB] = EventTimeLineCached(
connection,
file,
"Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax).getDictionnary()
''' This one is the dico of event '''
approachDico[animal, idAnimalB] = EventTimeLineCached(
connection,
file,
"Social approach",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax
) #fait une matrice de toutes les approches à deux possibles
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
eventName = "Approach contact2"
print(eventName)
appContactTimeLine = EventTimeLine(None,
eventName,
animal,
idAnimalB,
None,
None,
loadEvent=False)
for eventApp in approachDico[animal, idAnimalB].eventList:
''' new code: '''
for t in range(
eventApp.endFrame,
eventApp.endFrame + TIME_WINDOW_BEFORE_EVENT + 1):
if (t in contactDicoDico[animal, idAnimalB]):
appContactTimeLine.eventList.append(eventApp)
break
''' old code(slow)
bug: est ce que ca n aurait pas du etre eventContact.startFrame ? ou eventApp.endFrame-TIME_WINDOW_BEFORE_EVENT, eventApp.endFrame+TIME_WINDOW_BEFORE_EVENT ?
for eventContact in contactDicoDico[animal, idAnimalB].eventList:
if (eventApp.overlapInT(eventContact.endFrame-TIME_WINDOW_BEFORE_EVENT, eventContact.endFrame+TIME_WINDOW_BEFORE_EVENT) == True):
appContactTimeLine.eventList.append(eventApp)
'''
appContactTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Approach Contact2", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
''' use pool cache if available '''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax)
'''
two animals are following each others with nose-to-anogenital contacts
animals are moving
'''
#deleteEventTimeLineInBase(connection, "Train2" )
contactHeadGenital = {}
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
contactHeadGenital[animal, idAnimalB] = EventTimeLineCached(
connection,
file,
"Oral-genital Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
for animal in range(1, pool.getNbAnimals() + 1):
for idAnimalB in range(1, pool.getNbAnimals() + 1):
if (animal == idAnimalB):
continue
eventName = "Train2"
print(eventName)
trainTimeLine = EventTimeLine(None,
eventName,
animal,
idAnimalB,
loadEvent=False)
result = {}
dicAB = contactHeadGenital[animal, idAnimalB].getDictionnary()
for t in dicAB.keys():
speedA = pool.animalDictionnary[animal].getSpeed(t)
speedB = pool.animalDictionnary[idAnimalB].getSpeed(t)
if (speedA != None and speedB != None):
if (speedA > SPEED_THRESHOLD_HIGH
and speedB > SPEED_THRESHOLD_HIGH):
result[t] = True
trainTimeLine.reBuildWithDictionnary(result)
trainTimeLine.removeEventsBelowLength(5)
trainTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Train2", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Animal A is stopped (built-in event):
Stop social: animal A is stopped and in contact with any other animal.
Stop isolated: animal A is stopped and not in contact with any other animal.
'''
pool = AnimalPool()
pool.loadAnimals(connection)
#pool.loadDetection( start = tmin, end = tmax )
isInContactSourceDictionnary = {}
stopSourceTimeLine = {}
for animal in range(1, 5):
''' Load source stop timeLine '''
stopSourceTimeLine[animal] = EventTimeLineCached(connection,
file,
"Stop",
animal,
minFrame=tmin,
maxFrame=tmax)
''' load contact dictionnary with whatever animal '''
isInContactSourceDictionnary[animal] = EventTimeLineCached(
connection, file, "Contact", animal, minFrame=tmin,
maxFrame=tmax).getDictionnary()
eventName2 = "Stop in contact"
eventName1 = "Stop isolated"
for animal in range(1, 5):
print(eventName1, eventName2)
stopSocialResult = {}
stopIsolatedResult = {}
''' loop over eventlist'''
for stopEvent in stopSourceTimeLine[animal].eventList:
''' for each event we seek in t and search a match in isInContactDictionnary '''
for t in range(stopEvent.startFrame, stopEvent.endFrame + 1):
if t in isInContactSourceDictionnary[animal]:
stopSocialResult[t] = True
else:
stopIsolatedResult[t] = True
''' save stop social '''
stopSocialResultTimeLine = EventTimeLine(None,
eventName2,
animal,
None,
None,
None,
loadEvent=False)
stopSocialResultTimeLine.reBuildWithDictionnary(stopSocialResult)
stopSocialResultTimeLine.endRebuildEventTimeLine(connection)
''' save stop isolated '''
stopIsolatedResultTimeLine = EventTimeLine(None,
eventName1,
animal,
None,
None,
None,
loadEvent=False)
stopIsolatedResultTimeLine.reBuildWithDictionnary(stopIsolatedResult)
stopIsolatedResultTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Stop", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def computeProfile(file, minT, maxT, night):
connection = sqlite3.connect( file )
pool = AnimalPool( )
pool.loadAnimals( connection )
animalData = {}
for animal in pool.animalDictionnary.keys():
print( "computing individual animal: {}".format( animal ))
rfid = pool.animalDictionnary[animal].RFID
print( "RFID: {}".format( rfid ) )
animalData[rfid]= {}
animalData[rfid]["animal"] = pool.animalDictionnary[animal]
animalData[rfid]["file"] = file
genoA = None
try:
genoA=pool.animalDictionnary[animal].genotype
except:
pass
for behavEvent in behaviouralEventOneMouse[:-2]:
print( "computing individual event: {}".format(behavEvent))
behavEventTimeLine = EventTimeLineCached( connection, file, behavEvent, animal, minFrame=minT, maxFrame=maxT )
totalEventDuration = behavEventTimeLine.getTotalLength()
nbEvent = behavEventTimeLine.getNumberOfEvent(minFrame = minT, maxFrame = maxT )
print( "total event duration: " , totalEventDuration )
animalData[rfid][behavEventTimeLine.eventName+" TotalLen"] = totalEventDuration
animalData[rfid][behavEventTimeLine.eventName+" Nb"] = nbEvent
print(behavEventTimeLine.eventName, genoA, behavEventTimeLine.idA, totalEventDuration, nbEvent)
header = ["file","strain","sex","group","day","exp","RFID","genotype", "user1", "minTime","maxTime"]
for name in header:
text_file.write( "{}\t".format ( name ) )
for kAnimal in animalData:
animalData[kAnimal]["experiment"] = file
COMPUTE_TOTAL_DISTANCE = True
if ( COMPUTE_TOTAL_DISTANCE == True ):
animalData[kAnimal]["animal"].loadDetection( start=minT, end=maxT, lightLoad = True )
animalData[kAnimal]["totalDistance"] = animalData[kAnimal]["animal"].getDistance( tmin=minT,tmax=maxT)/100
else:
animalData[kAnimal]["totalDistance"] = "totalDistance"
#write event keys
firstAnimalKey = next(iter(animalData))
firstAnimal = animalData[firstAnimalKey]
for k in firstAnimal.keys():
text_file.write( "{}\t".format( k.replace(" ", "") ) )
text_file.write("\n")
for kAnimal in animalData:
text_file.write( "{}\t".format( file ) )
text_file.write( "{}\t".format( "strain" ) )
text_file.write( "{}\t".format( "sex" ) )
text_file.write( "{}\t".format( night ) )
text_file.write( "{}\t".format( "exp" ) )
text_file.write( "{}\t".format( animalData[kAnimal]["animal"].RFID ) )
text_file.write( "{}\t".format( animalData[kAnimal]["animal"].genotype ) )
text_file.write( "{}\t".format( minT ) )
text_file.write( "{}\t".format( maxT ) )
for kEvent in firstAnimal.keys():
text_file.write( "{}\t".format( animalData[kAnimal][kEvent] ) )
text_file.write( "\n" )
return animalData
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
''' use the pool provided or create it'''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax, lightLoad=True)
'''
Event Water Zone
- the animal is in the zone around the water source
- the animal is stopped in this zone for
'''
for animal in pool.animalDictionnary.keys():
print(pool.animalDictionnary[animal])
eventName1 = "Water Zone"
eventName2 = "Water Stop"
print("A is in the zone around the water source")
print(eventName1)
waterZoneTimeLine = EventTimeLine(None,
eventName1,
animal,
None,
None,
None,
loadEvent=False)
waterStopTimeLine = EventTimeLine(None,
eventName2,
animal,
None,
None,
None,
loadEvent=False)
stopTimeLine = EventTimeLineCached(connection,
file,
"Stop",
animal,
minFrame=None,
maxFrame=None)
stopTimeLineDictionary = stopTimeLine.getDictionary()
resultWaterZone = {}
resultWaterStop = {}
animalA = pool.animalDictionnary[animal]
#print ( animalA )
dicA = animalA.detectionDictionnary
for t in dicA.keys():
if (dicA[t].getDistanceToPoint(xPoint=398, yPoint=353) == None):
continue
#Check if the animal is entering the zone around the water point:
if (dicA[t].getDistanceToPoint(xPoint=398, yPoint=353) <=
MAX_DISTANCE_TO_POINT * 2):
resultWaterZone[t] = True
#Check if the animal is drinking (the animal should be in a tight zone around the water point and be stopped):
if (dicA[t].getDistanceToPoint(xPoint=398, yPoint=353) <=
MAX_DISTANCE_TO_POINT):
if t in stopTimeLineDictionary.keys():
resultWaterStop[t] = True
waterZoneTimeLine.reBuildWithDictionnary(resultWaterZone)
waterZoneTimeLine.endRebuildEventTimeLine(connection)
waterStopTimeLine.reBuildWithDictionnary(resultWaterStop)
waterStopTimeLine.removeEventsBelowLength(
maxLen=MIN_WATER_STOP_DURATION)
waterStopTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Water Point", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Nest 3
'''
print(
"[NEST 3] : Assume that there is no occlusion, does not work with anonymous animals"
)
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax, lightLoad=True)
if (len(pool.getAnimalList()) != 4):
print("[NEST3 Cancelled] 4 animals are required to build nest3.")
return
contact = {}
for idAnimalA in range(1, 5):
for idAnimalB in range(1, 5):
if idAnimalA != idAnimalB:
contact[idAnimalA, idAnimalB] = EventTimeLineCached(
connection,
file,
"Contact",
idAnimalA,
idAnimalB,
minFrame=tmin,
maxFrame=tmax).getDictionnary()
stopDictionnary = {}
for idAnimalA in range(1, 5):
stopDictionnary[idAnimalA] = EventTimeLineCached(
connection, file, "Stop", minFrame=tmin,
maxFrame=tmax).getDictionnary()
nest3TimeLine = {}
for idAnimalA in range(1, 5):
# the id will be the one excluded from nest.
nest3TimeLine[idAnimalA] = EventTimeLine(None,
"Nest3_",
idA=idAnimalA,
loadEvent=False)
pool.loadAnonymousDetection()
animalList = pool.getAnimalList()
result = {}
for idAnimalA in range(1, 5):
result[idAnimalA] = {}
#Added by Alice on 21/07/2020, to check
tmax = pool.getMaxDetectionT()
for t in range(tmin, tmax + 1):
isNest = False
nbAnimalAtT = 0
animalDetectedList = []
anonymousDetectionList = pool.getAnonymousDetection(t)
for animal in animalList:
if t in animal.detectionDictionnary:
nbAnimalAtT += 1
animalDetectedList.append(animal)
#print( str(t) + " : " + str( nbAnimalAtT ) )
#print("TEST")
graph = nx.Graph()
# add nodes
for animal in animalDetectedList:
graph.add_node(animal)
for animalA in animalDetectedList:
for animalB in animalDetectedList:
if animalA != animalB:
# add an edge
if t in contact[animalA.baseId, animalB.baseId]:
graph.add_edge(animalA, animalB)
# check with anonymous detection. Check contact
if anonymousDetectionList != None:
# manage anonymous
# print( t , "manage anonymous")
'''
# load all masks
for animal in animalDetectedList:
animal.loadMask( t )
'''
for detectionA in anonymousDetectionList: # anonymous with anonymous
for detectionB in anonymousDetectionList: # anonymous with anonymous
if detectionA != detectionB:
distance = detectionA.getDistanceTo(detectionB)
if distance != None:
if distance < DISTANCE_CONTACT_MASS_CENTER:
graph.add_edge(detectionA, detectionB)
# print("Adding edge with mask (det anonymous to det anonymous)")
for detection in anonymousDetectionList:
for animal in animalDetectedList:
distance = detection.getDistanceTo(
animal.getDetectionAt(t))
if distance != None:
if distance < DISTANCE_CONTACT_MASS_CENTER:
#if detection.getMask().isInContactWithMask( animal.getDetectionAt ( t ).getMask() ):
graph.add_edge(animal, detection)
# print("Adding edge with mask")
# list of CC from the biggest to the smallest
listCC = sorted(nx.connected_components(graph), key=len, reverse=True)
if (len(listCC) == 2): # we have 2 groups
# check if animals in the biggest group are stopped.
allStoppedInBiggestGroup = True
for animal in list(listCC[0]):
if isinstance(animal, Animal):
if not (t in stopDictionnary[animal.baseId]):
allStoppedInBiggestGroup = False
break
if allStoppedInBiggestGroup:
if (len(listCC[1]) == 1
): # the 2nd group (and the smallest) has only one mouse
animal = list(listCC[1])[0]
if isinstance(animal, Animal):
result[animal.baseId][t] = True
for idAnimalA in range(1, 5):
# the id will be the one excluded from nest.
nest3TimeLine[idAnimalA].reBuildWithDictionnary(result[idAnimalA])
# remove very small events
nest3TimeLine[idAnimalA].removeEventsBelowLength(2)
# merge flashing events
nest3TimeLine[idAnimalA].mergeCloseEvents(3)
nest3TimeLine[idAnimalA].endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Nest3", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
print(file)
connection = sqlite3.connect(file)
pool = AnimalPool()
pool.loadAnimals(connection)
MODE_MULTI_GENOTYPE = False
if (len(pool.getGenotypeList()) > 1):
MODE_MULTI_GENOTYPE = True
print("Mode multi genotype: ", MODE_MULTI_GENOTYPE)
animal = {}
nightEventTimeLine = EventTimeLineCached(connection,
file,
"night",
minFrame=tmin,
maxFrame=tmax)
n = 1
header = [
"file", "event", "RFID_A", "geno_A", "RFID_B", "geno_B", "minTime",
"maxTime", "dur", "nb"
]
for name in header:
text_file.write("{}\t".format(name))
text_file.write("{}\n".format("night"))
for eventNight in nightEventTimeLine.getEventList():
minT = eventNight.startFrame
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Animal A is stopped (built-in event): revert the event to have move events
Move social: animal A is moving and in contact with another animal.
Move isolated: animal A is moving and not in contact with any other animal.
'''
pool = AnimalPool()
pool.loadAnimals(connection)
if len(pool.animalDictionnary.keys()) == 1:
print('Only one animal in database.')
'''if the animal has been tested alone, only the move isolated event will be computed.'''
moveSourceTimeLine = {}
animal = 1
''' Load source stop timeLine and revert it to get the move timeline
If the animal is not detected, this will result in a move. To avoid this we mask with the detection.
'''
moveSourceTimeLine[animal] = EventTimeLine(connection,
"Stop",
animal,
minFrame=tmin,
maxFrame=tmax,
inverseEvent=True)
detectionTimeLine = EventTimeLine(connection,
"Detection",
animal,
minFrame=tmin,
maxFrame=tmax)
moveSourceTimeLine[animal].keepOnlyEventCommonWithTimeLine(
detectionTimeLine)
# initialisation of a dic for isolated move
moveIsolatedResult = {}
''' loop over eventlist'''
for moveEvent in moveSourceTimeLine[animal].eventList:
for t in range(moveEvent.startFrame, moveEvent.endFrame + 1):
moveIsolatedResult[t] = True
''' save move isolated at the end of the complete process for animalA'''
moveIsolatedResultTimeLine = EventTimeLine(None,
"Move isolated",
idA=animal,
idB=None,
idC=None,
idD=None,
loadEvent=False)
moveIsolatedResultTimeLine.reBuildWithDictionnary(moveIsolatedResult)
moveIsolatedResultTimeLine.endRebuildEventTimeLine(connection)
else:
print('More than one animal in database.')
isInContactSourceDictionnary = {}
moveSourceTimeLine = {}
moveIsolatedTimeLine = {}
for animal in pool.animalDictionnary.keys():
''' Load source stop timeLine and revert it to get the move timeline
If the animal is not detected, this will result in a move. To avoid this we mask with the detection.
'''
moveSourceTimeLine[animal] = EventTimeLine(connection,
"Stop",
animal,
minFrame=tmin,
maxFrame=tmax,
inverseEvent=True)
detectionTimeLine = EventTimeLine(connection,
"Detection",
animal,
minFrame=tmin,
maxFrame=tmax)
moveSourceTimeLine[animal].keepOnlyEventCommonWithTimeLine(
detectionTimeLine)
#by default let's say that all move are isolated; next we will extract frames which are in contact from this time line.
moveIsolatedTimeLine[animal] = moveSourceTimeLine[animal]
''' load contact dictionary with another animal '''
for animalB in pool.animalDictionnary.keys():
if animal == animalB:
print('Same identity')
continue
else:
isInContactSourceDictionnary[(
animal, animalB)] = EventTimeLineCached(
connection,
file,
"Contact",
animal,
animalB,
minFrame=tmin,
maxFrame=tmax).getDictionnary()
moveIsolatedDic = {}
for animal in pool.animalDictionnary.keys():
#initialisation of a dic for isolated move
moveIsolatedDic[animal] = moveIsolatedTimeLine[
animal].getDictionary()
for animalB in pool.animalDictionnary.keys():
# initialisation of a dic for move in contact for each individual of the cage
framesToRemoveFromMoveIsolatedTimeLine = []
moveSocialResult = {}
if animal == animalB:
print('Same identity')
continue
else:
''' loop over eventlist'''
for moveEvent in moveIsolatedTimeLine[animal].eventList:
''' for each event we seek in t and search a match in isInContactDictionnary between animal and animalB '''
for t in range(moveEvent.startFrame,
moveEvent.endFrame + 1):
if t in isInContactSourceDictionnary[(animal,
animalB)]:
moveSocialResult[t] = True
framesToRemoveFromMoveIsolatedTimeLine.append(
t)
''' save move social at the end of the search for each animal'''
# clean the dictionary of the move and stop events from frames that are overlapping with exclusive contacts
for t in framesToRemoveFromMoveIsolatedTimeLine:
moveIsolatedDic[animal].pop(t, None)
moveSocialResultTimeLine = EventTimeLine(None,
"Move in contact",
idA=animal,
idB=animalB,
idC=None,
idD=None,
loadEvent=False)
moveSocialResultTimeLine.reBuildWithDictionnary(
moveSocialResult)
moveSocialResultTimeLine.endRebuildEventTimeLine(
connection)
''' save move isolated at the end of the complete process for animalA'''
moveIsolatedResultTimeLine = EventTimeLine(None,
"Move isolated",
idA=animal,
idB=None,
idC=None,
idD=None,
loadEvent=False)
moveIsolatedResultTimeLine.reBuildWithDictionnary(
moveIsolatedDic[animal])
moveIsolatedResultTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Move", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
''' use the pool provided or create it'''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax)
'''
Event FollowZone:
- the two animals are moving at a speed >5 cm/s (SPEED_THRESHOLD_LOW)
- the angles between the two animals are less than 45° apart
- the mass center of the follower is within a follow zone of one mean body length of width and two mean body lengths of length
- either the animal B is in contact with another one (FollowZone Social) or the animal B is not in contact with any other animal (except A at the end of the follow event; FollowZone Isolated)
- update 17 may 2018: now works with n animals
'''
contact = {}
for idAnimalB in pool.animalDictionnary.keys():
print(pool.animalDictionnary[idAnimalB])
meanSizeB = pool.animalDictionnary[idAnimalB].getMeanBodyLength(
tmax=tmax)
for animal in pool.animalDictionnary.keys():
if (idAnimalB == animal):
continue
contact[animal, idAnimalB] = EventTimeLineCached(connection,
file,
"Contact",
animal,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
#contact[idAnimalB] = EventTimeLine( connection, "Contact", idAnimalB )
for idAnimalB in pool.animalDictionnary.keys():
for animal in pool.animalDictionnary.keys():
if (animal == idAnimalB):
continue
allAnimals = list(pool.animalDictionnary.keys())
allAnimals.remove(animal)
allAnimals.remove(idAnimalB)
allOtherAnimals = allAnimals
eventName = "FollowZone Isolated"
print("A follow B")
print(eventName)
followIsolatedTimeLine = EventTimeLine(None,
eventName,
animal,
idAnimalB,
None,
None,
loadEvent=False)
print(followIsolatedTimeLine.eventNameWithId)
resultIso = {}
animalA = pool.animalDictionnary[animal]
animalB = pool.animalDictionnary[idAnimalB]
dicA = animalA.detectionDictionnary
dicB = animalB.detectionDictionnary
dicContactBToOtherAnimal = {}
for idOtherAnimal in allOtherAnimals:
dicContactBToOtherAnimal[idOtherAnimal] = contact[
idAnimalB, idOtherAnimal].getDictionnary()
#dicContactBC = contact[ idAnimalB, idAnimalC ].getDictionnary()
#dicContactBD = contact[ idAnimalB, idAnimalD ].getDictionnary()
for t in dicB.keys():
testContactWithOtherAnimal = False
for idOtherAnimal in allOtherAnimals:
if (t in dicContactBToOtherAnimal[idOtherAnimal]):
testContactWithOtherAnimal = True
break
if testContactWithOtherAnimal == True:
continue
'''
if ( t in dicContactBC.keys() or t in dicContactBD ):
continue
'''
if (t in dicA.keys()):
speedA = pool.animalDictionnary[animal].getSpeed(t)
speedB = pool.animalDictionnary[idAnimalB].getSpeed(t)
#angleB = pool.animalList[idAnimalB].getDirection(t)
angleA = pool.animalDictionnary[animal].getDirection(t)
if (speedA == None or speedB == None):
continue
if (speedA > SPEED_THRESHOLD_LOW
and speedB > SPEED_THRESHOLD_LOW):
time = t
angleB = pool.animalDictionnary[
idAnimalB].getDirection(time)
'''
try:
if( animalA.getDistanceTo( t, animalB ) > 80 ):
continue
except:
continue
'''
for time in range(t - 15, t + 1, 2):
#time = t
try:
angleB = pool.animalDictionnary[
idAnimalB].getDirection(time)
if (checkZone(dicA[t].massX, dicA[t].massY,
angleA, meanSizeB,
dicB[time].massX,
dicB[time].massY,
angleB) == True):
resultIso[t] = True
break
except:
pass
followIsolatedTimeLine.reBuildWithDictionnary(resultIso)
followIsolatedTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Follow Zone", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def computeProfilePairs(files, tmin, tmax, text_file, animalDic):
for file in files:
print(file)
connection = sqlite3.connect(file)
pool = AnimalPool()
pool.loadAnimals(connection)
genoList = []
rfidList = []
animalDic[file] = {}
for animal in pool.animalDictionnary.keys():
print("computing individual animal: {}".format(animal))
rfid = pool.animalDictionnary[animal].RFID
print("RFID: ".format(rfid))
animalDic[file][rfid] = {}
''' store the animal '''
# animalDic[rfid]["animal"] = pool.animalDictionnary[animal]
genoA = None
try:
genoA = pool.animalDictionnary[animal].genotype
except:
pass
animalDic[file][rfid][genoA] = {}
genoList.append(genoA)
rfidList.append(rfid)
COMPUTE_TOTAL_DISTANCE = True
if (COMPUTE_TOTAL_DISTANCE == True):
pool.animalDictionnary[animal].loadDetection(lightLoad=True)
animalDic[file][rfid][genoA][
'distance'] = pool.animalDictionnary[animal].getDistance(
tmin=tmin, tmax=tmax)
for behavEvent in behaviouralEvents:
print("computing individual event: {}".format(behavEvent))
behavEventTimeLine = EventTimeLineCached(connection,
file,
behavEvent,
animal,
minFrame=tmin,
maxFrame=tmax)
totalEventDuration = behavEventTimeLine.getTotalLength()
nbEvent = behavEventTimeLine.getNumberOfEvent(minFrame=tmin,
maxFrame=tmax)
print("total event duration: ", totalEventDuration)
animalDic[file][rfid][genoA][behavEventTimeLine.eventName +
" TotalLen"] = totalEventDuration
animalDic[file][rfid][genoA][behavEventTimeLine.eventName +
" Nb"] = nbEvent
print(behavEventTimeLine.eventName, genoA,
behavEventTimeLine.idA, totalEventDuration, nbEvent)
rfidPair = '{}-{}'.format(rfidList[0], rfidList[1])
animalDic[file][rfidPair] = {}
pairType = '{}-{}'.format(genoList[0], genoList[1])
animalDic[file][rfidPair][pairType] = {}
animalDic[file][rfidPair][pairType]['distance'] = 'NA'
for behavEvent in behaviouralEvents:
print("computing individual event: {}".format(behavEvent))
behavEventTimeLine = EventTimeLineCached(connection,
file,
behavEvent,
minFrame=tmin,
maxFrame=tmax)
totalEventDuration = behavEventTimeLine.getTotalLength()
nbEvent = behavEventTimeLine.getNumberOfEvent(minFrame=tmin,
maxFrame=tmax)
print("total event duration: ", totalEventDuration)
animalDic[file][rfidPair][pairType][
behavEventTimeLine.eventName +
" TotalLen"] = totalEventDuration
animalDic[file][rfidPair][pairType][behavEventTimeLine.eventName +
" Nb"] = nbEvent
print(behavEventTimeLine.eventName, pairType, totalEventDuration,
nbEvent)
print(animalDic)
print("writing...")
'''
file strain sex genotype group day exp idA idB minTime maxTime
'''
header = [
"file", "strain", "sex", "genotype", "group", "day", "exp", "RFID",
"minTime", "maxTime"
]
for name in header:
text_file.write("{}\t".format(name))
''' write event keys '''
firstAnimalKey = next(iter(animalDic[file]))
print('firstAnimal: ', firstAnimalKey)
genoFirstAnimal = list(animalDic[file][firstAnimalKey].keys())[0]
eventDic = animalDic[file][firstAnimalKey][genoFirstAnimal]
for k in eventDic.keys():
print('k: ', k)
text_file.write("{}\t".format(k.replace(" ", "")))
text_file.write("\n")
for rfidAnimal in animalDic[file].keys():
print(rfidAnimal)
animalId = rfidAnimal
animalGeno = list(animalDic[file][rfidAnimal].keys())[0]
text_file.write("{}\t".format(file))
text_file.write("{}\t".format("strain"))
text_file.write("{}\t".format("sex"))
text_file.write("{}\t".format(animalGeno))
text_file.write("{}\t".format("group"))
text_file.write("{}\t".format("day"))
text_file.write("{}\t".format("exp"))
text_file.write("{}\t".format(animalId))
text_file.write("{}\t".format(tmin))
text_file.write("{}\t".format(tmax))
for kEvent in animalDic[file][animalId][animalGeno].keys():
text_file.write("{}\t".format(
animalDic[file][animalId][animalGeno][kEvent]))
text_file.write("\n")
text_file.write("\n")
text_file.close()
# Create a json file to store the computation
jsonFileName = 'profile_unidentified_pairs.json'
with open(jsonFileName, 'w') as fp:
json.dump(animalDic, fp, indent=4)
print("json file with acoustic measurements created for ", jsonFileName)
print("done.")
return animalDic
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Animal A is stopped (built-in event):
Move social: animal A is stopped and in contact with any other animal.
Move isolated: animal A is stopped and not in contact with any other animal.
'''
pool = AnimalPool()
pool.loadAnimals(connection)
isInContactSourceDictionnary = {}
moveSourceTimeLine = {}
for idAnimalA in range(1, pool.getNbAnimals() + 1):
''' Load source stop timeLine and revert it to get the move timeline
If the animal is not detected, this will result in a move. To avoid this we mask with the detection.
'''
moveSourceTimeLine[idAnimalA] = EventTimeLine(connection,
"Stop",
idAnimalA,
minFrame=tmin,
maxFrame=tmax,
inverseEvent=True)
detectionTimeLine = EventTimeLine(connection,
"Detection",
idAnimalA,
minFrame=tmin,
maxFrame=tmax)
moveSourceTimeLine[idAnimalA].keepOnlyEventCommonWithTimeLine(
detectionTimeLine)
''' load contact dictionnary with whatever animal '''
isInContactSourceDictionnary[idAnimalA] = EventTimeLineCached(
connection,
file,
"Contact",
idAnimalA,
minFrame=tmin,
maxFrame=tmax).getDictionnary()
for idAnimalA in range(1, pool.getNbAnimals() + 1):
moveSocialResult = {}
moveIsolatedResult = {}
''' loop over eventlist'''
for moveEvent in moveSourceTimeLine[idAnimalA].eventList:
''' for each event we seek in t and search a match in isInContactDictionnary '''
for t in range(moveEvent.startFrame, moveEvent.endFrame + 1):
if t in isInContactSourceDictionnary[idAnimalA]:
moveSocialResult[t] = True
else:
moveIsolatedResult[t] = True
''' save move '''
moveResultTimeLine = EventTimeLine(None,
"Move",
idAnimalA,
None,
None,
None,
loadEvent=False)
moveResultTimeLine.reBuildWithDictionnary(
moveSourceTimeLine[idAnimalA].getDictionnary())
moveResultTimeLine.endRebuildEventTimeLine(connection)
''' save move isolated '''
moveIsolatedResultTimeLine = EventTimeLine(None,
"Move isolated",
idAnimalA,
None,
None,
None,
loadEvent=False)
moveIsolatedResultTimeLine.reBuildWithDictionnary(moveIsolatedResult)
moveIsolatedResultTimeLine.endRebuildEventTimeLine(connection)
''' save move social '''
moveSocialResultTimeLine = EventTimeLine(None,
"Move in contact",
idAnimalA,
None,
None,
None,
loadEvent=False)
moveSocialResultTimeLine.reBuildWithDictionnary(moveSocialResult)
moveSocialResultTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Move", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def process( file ):
print(file)
mem = virtual_memory()
availableMemoryGB = mem.total / 1000000000
print( "Total memory on computer: (GB)", availableMemoryGB )
if availableMemoryGB < 10:
print( "Not enough memory to use cache load of events.")
disableEventTimeLineCache()
chronoFullFile = Chronometer("File " + file )
connection = sqlite3.connect( file )
# update missing fields
try:
connection = sqlite3.connect( file )
c = connection.cursor()
query = "ALTER TABLE EVENT ADD METADATA TEXT";
c.execute( query )
connection.commit()
except:
print( "METADATA field already exists" , file )
BuildDataBaseIndex.buildDataBaseIndex( connection, force=False )
# build sensor data
animalPool = AnimalPool( )
animalPool.loadAnimals( connection )
#animalPool.buildSensorData(file)
currentT = minT
try:
flushEvents( connection )
while currentT < maxT:
currentMinT = currentT
currentMaxT = currentT+ windowT
if ( currentMaxT > maxT ):
currentMaxT = maxT
chronoTimeWindowFile = Chronometer("File "+ file+ " currentMinT: "+ str(currentMinT)+ " currentMaxT: " + str(currentMaxT) );
processTimeWindow( connection, file, currentMinT, currentMaxT )
chronoTimeWindowFile.printTimeInS()
currentT += windowT
print("Full file process time: ")
chronoFullFile.printTimeInS()
TEST_WINDOWING_COMPUTATION = False
if ( TEST_WINDOWING_COMPUTATION ):
print("*************")
print("************* TEST START SECTION")
print("************* Test if results are the same with or without the windowing.")
# display and record to a file all events found, checking with rolling idA from None to 4. Save nbEvent and total len
eventTimeLineList = []
eventList = getAllEvents( connection )
file = open("outEvent"+str(windowT)+".txt","w")
file.write( "Event name\nnb event\ntotal duration" )
for eventName in eventList:
for animal in range( 0,5 ):
idA = animal
if idA == 0:
idA = None
timeLine = EventTimeLineCached( connection, file, eventName, idA, minFrame=minT, maxFrame=maxT )
eventTimeLineList.append( timeLine )
file.write( timeLine.eventNameWithId+"\t"+str(len(timeLine.eventList))+"\t"+str(timeLine.getTotalLength())+"\n" )
file.close()
#plotMultipleTimeLine( eventTimeLineList )
print("************* END TEST")
flushEventTimeLineCache()
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
error = ''.join('!! ' + line for line in lines)
t = TaskLogger( connection )
t.addLog( error )
flushEventTimeLineCache()
print( error, file=sys.stderr )
raise FileProcessException()
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
'''
Nest 3
Nest 4
Group 2
Group 3
Group 4
'''
print(
"[NEST 4] : Assume that there is no occlusion, does not work with anonymous animals"
)
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax, lightLoad=True)
# check if given max is more than available detection
'''
maxT = pool.getMaxDetectionT()
if ( tmax > maxT ):
tmax = maxT
'''
#pool.loadDetection( start = tmin, end = tmax )
if (len(pool.getAnimalList()) != 4):
print("[NEST4 Cancelled] 4 animals are required to build nest 4.")
return
contact = {}
for idAnimalA in range(1, 5):
for idAnimalB in range(1, 5):
if idAnimalA != idAnimalB:
contact[idAnimalA, idAnimalB] = EventTimeLineCached(
connection,
file,
"Contact",
idAnimalA,
idAnimalB,
minFrame=tmin,
maxFrame=tmax).getDictionnary(
) #fait une matrice de tous les contacts à deux possibles
stopDictionnary = {}
for idAnimalA in range(1, 5):
stopDictionnary[idAnimalA] = EventTimeLineCached(
connection, file, "Stop", idAnimalA, minFrame=tmin,
maxFrame=tmax).getDictionnary()
'''
nest3TimeLine = {}
for idAnimalA in range( 1 , 5 ):
nest3TimeLine = EventTimeLine( None, "Nest3" , idAnimalA, loadEvent=False )
'''
nest4TimeLine = EventTimeLine(None, "Nest4", loadEvent=False)
'''
group2TimeLine = {}
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if ( idAnimalA != idAnimalB ):
group2TimeLine[idAnimalA,idAnimalB] = EventTimeLine( None, "Group2" , idAnimalA , idAnimalB , loadEvent=False )
group3TimeLine = {}
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if( idAnimalA != idAnimalB ):
for idAnimalC in range( 1 , 5 ):
if ( idAnimalA != idAnimalC and idAnimalB != idAnimalC ):
group3TimeLine[idAnimalA,idAnimalB] = EventTimeLine( None, "Group3" , idAnimalA , idAnimalB , idAnimalC, loadEvent=False )
group4TimeLine = EventTimeLine( None, "Group4" , loadEvent=False )
'''
animalList = pool.getAnimalList()
result = {}
for t in range(tmin, tmax + 1):
isNest = False
nbAnimalAtT = 0
animalDetectedList = []
for animal in animalList:
if t in animal.detectionDictionnary:
nbAnimalAtT += 1
animalDetectedList.append(animal)
#print( str(t) + " : " + str( nbAnimalAtT ) )
if nbAnimalAtT == 0:
isNest = True
if not isNest:
#print("TEST")
graph = nx.Graph()
# add nodes
for animal in animalDetectedList:
graph.add_node(animal)
for animalA in animalDetectedList:
for animalB in animalDetectedList:
if animalA != animalB:
# add an edge
if t in contact[animalA.baseId, animalB.baseId]:
graph.add_edge(animalA, animalB)
# check connected components. If the biggest group gets all animal, we got a nest4
largestCC = len(max(nx.connected_components(graph), key=len))
#print( str( t ) + " : " + str ( len( largestCC ) ) )
#print( str( t ) + " : " + str ( largestCC ) + " / " + str( nbAnimalAtT ) )
if largestCC == nbAnimalAtT:
# check if animals in the nest are stopped.
allStoppedInBiggestGroup = True
for animal in animalDetectedList:
if not (t in stopDictionnary[animal.baseId]):
allStoppedInBiggestGroup = False
break
if allStoppedInBiggestGroup:
isNest = True
if isNest == True:
#print( "ADD PUNCTUAL")
result[t] = True
nest4TimeLine.reBuildWithDictionnary(result)
# remove very small events
nest4TimeLine.removeEventsBelowLength(2)
# merge flashing events
nest4TimeLine.mergeCloseEvents(3)
nest4TimeLine.endRebuildEventTimeLine(connection)
'''
for idAnimalA in range( 1 , 5 ):
for idAnimalB in range( 1 , 5 ):
if( idAnimalA == idAnimalB ):
continue
for idAnimalC in range( 1 , 5 ):
if( idAnimalA == idAnimalC ):
continue
if( idAnimalB == idAnimalC ):
continue
for idAnimalD in range( 1 , 5 ):
if( idAnimalA == idAnimalD ):
continue
if( idAnimalB == idAnimalD ):
continue
if( idAnimalC == idAnimalD ):
continue
eventName = "Group4"
print ( eventName )
groupTimeLine = EventTimeLine( None, eventName , idAnimalA , idAnimalB , idAnimalC , idAnimalD , loadEvent=False )
result={}
dicA = contact[ idAnimalA ].getDictionnary()
dicB = contact[ idAnimalB ].getDictionnary()
dicC = contact[ idAnimalC ].getDictionnary()
dicD = contact[ idAnimalD ].getDictionnary()
dicGroup2A = group2[ idAnimalA ].getDictionnary()
dicGroup2B = group2[ idAnimalB ].getDictionnary()
dicGroup2C = group2[ idAnimalC ].getDictionnary()
dicGroup2D = group2[ idAnimalD ].getDictionnary()
for t in dicA.keys():
if ( t in dicB and t in dicC and t in dicD ):
if ( t in dicGroup2A or t in dicGroup2B or t in dicGroup2C or t in dicGroup2D):
continue
else:
result[t]=True
groupTimeLine.reBuildWithDictionnary( result )
groupTimeLine.endRebuildEventTimeLine(connection)
'''
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Nest4", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
def process( file ):
print(file)
chronoFullFile = Chronometer("File " + file )
connection = sqlite3.connect( file )
BuildDataBaseIndex.buildDataBaseIndex( connection, force=False )
# TODO: flush events,
# TODO: recompute per segment of windowT.
currentT = minT
try:
flushEvents( connection )
while currentT < maxT:
currentMinT = currentT
currentMaxT = currentT+ windowT
if ( currentMaxT > maxT ):
currentMaxT = maxT
chronoTimeWindowFile = Chronometer("File "+ file+ " currentMinT: "+ str(currentMinT)+ " currentMaxT: " + str(currentMaxT) );
processTimeWindow( connection, currentMinT, currentMaxT )
chronoTimeWindowFile.printTimeInS()
currentT += windowT
print("Full file process time: ")
chronoFullFile.printTimeInS()
TEST_WINDOWING_COMPUTATION = False
if ( TEST_WINDOWING_COMPUTATION ):
print("*************")
print("************* TEST START SECTION")
print("************* Test if results are the same with or without the windowing.")
# display and record to a file all events found, checking with rolling idA from None to 4. Save nbEvent and total len
eventTimeLineList = []
eventList = getAllEvents( connection )
file = open("outEvent"+str(windowT)+".txt","w")
file.write( "Event name\nnb event\ntotal duration" )
for eventName in eventList:
for idAnimalA in range( 0,5 ):
idA = idAnimalA
if idA == 0:
idA = None
timeLine = EventTimeLineCached( connection, file, eventName, idA, minFrame=minT, maxFrame=maxT )
eventTimeLineList.append( timeLine )
file.write( timeLine.eventNameWithId+"\t"+str(len(timeLine.eventList))+"\t"+str(timeLine.getTotalLength())+"\n" )
file.close()
#plotMultipleTimeLine( eventTimeLineList )
print("************* END TEST")
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
error = ''.join('!! ' + line for line in lines)
t = TaskLogger( connection )
t.addLog( error )
print( error, file=sys.stderr )
raise FileProcessException()
def reBuildEvent(connection, file, tmin=None, tmax=None, pool=None):
print("STARTING SOCIAL ESCAPE")
''' use the pool provided or create it'''
if (pool == None):
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(start=tmin, end=tmax)
nbAnimal = pool.getNbAnimals()
# loading all the escape of animals
getAwayDico = {}
for idAnimalA in range(1, nbAnimal + 1):
for idAnimalB in range(1, nbAnimal + 1):
if (idAnimalA == idAnimalB):
continue
getAwayDico[idAnimalA,
idAnimalB] = EventTimeLineCached(connection,
file,
"Get away",
idAnimalA,
idAnimalB,
minFrame=tmin,
maxFrame=tmax)
#cache mean body len
twoMeanBodyLen = {}
for idAnimal in range(1, nbAnimal + 1):
meanBodyLength = pool.animalDictionnary[idAnimal].getMeanBodyLength()
# init value
twoMeanBodyLen[idAnimal] = None
# set value
if meanBodyLength != None:
twoMeanBodyLen[idAnimal] = 2 * meanBodyLength
for idAnimalA in range(1, nbAnimal + 1):
for idAnimalB in range(1, nbAnimal + 1):
if (idAnimalA == idAnimalB):
continue
eventName = "Social escape"
print(eventName)
socEscTimeLine = EventTimeLine(None,
eventName,
idAnimalA,
idAnimalB,
None,
None,
loadEvent=False)
result = {}
dicA = getAwayDico[idAnimalA, idAnimalB].getDictionnary()
twoMeanBodyLengthB = twoMeanBodyLen[idAnimalB]
for t in dicA.keys():
dist = pool.animalDictionnary[idAnimalA].getDistanceTo(
t, pool.animalDictionnary[idAnimalB])
if (dist == None):
continue
if (dist >= 0 and dist <= twoMeanBodyLengthB):
result[t] = True
socEscTimeLine.reBuildWithDictionnary(result)
socEscTimeLine.endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger(connection)
t.addLog("Build Event Social Escape", tmin=tmin, tmax=tmax)
print("Rebuild event finished.")
''' store the animal '''
animalDic[rfid]["animal"] = pool.animalDictionnary[animal]
genoA = None
try:
genoA = pool.animalDictionnary[animal].genotype
except:
pass
for behavEvent in behaviouralEventOneMouse:
print("computing individual event: {}".format(behavEvent))
behavEventTimeLine = EventTimeLineCached(connection,
file,
behavEvent,
animal,
minFrame=tmin,
maxFrame=tmax)
totalEventDuration = behavEventTimeLine.getTotalLength()
nbEvent = behavEventTimeLine.getNumberOfEvent(minFrame=tmin,
maxFrame=tmax)
print("total event duration: ", totalEventDuration)
animalDic[rfid][behavEventTimeLine.eventName +
" TotalLen"] = totalEventDuration
animalDic[rfid][behavEventTimeLine.eventName + " Nb"] = nbEvent
print(behavEventTimeLine.eventName, genoA,
behavEventTimeLine.idA, totalEventDuration, nbEvent)
print("writing...")
def reBuildEvent( connection, file, tmin=None, tmax=None , pool = None ):
moveEventList = ['Move isolated', 'Stop isolated']
moveEventListExclusive = exclusiveEventList[-3:-1]
eventPairs = {'Move isolated': 'Move isolated exclusive',
'Stop isolated': 'Stop isolated exclusive'}
if ( pool == None ):
pool = AnimalPool( )
pool.loadAnimals( connection )
''' load the existing timelines for animal '''
timeLine = {}
dicoContact = {}
for event in moveEventList+exclusiveEventList[:-3]:
timeLine[event] = {}
dicoContact[event] = {}
for animal in range(1, pool.getNbAnimals() + 1):
timeLine[event][animal] = EventTimeLineCached( connection, file, event, animal, minFrame=tmin, maxFrame=tmax )
dicoContact[event][animal] = timeLine[event][animal].getDictionary(minFrame=tmin, maxFrame=tmax)
''' create the timelines of the different exclusive moves '''
timeLineExclusive = {}
for event in moveEventListExclusive:
timeLineExclusive[event] = {}
for animal in range(1, pool.getNbAnimals() + 1):
timeLineExclusive[event][animal] = EventTimeLine(None, event, animal, loadEvent=False)
#generate the dico of the different move events and initiate the list of frames to remove from each timeline
moveDicoExclusive = {}
framesToRemove = {}
for event in moveEventList:
moveDicoExclusive[eventPairs[event]] = {}
framesToRemove[eventPairs[event]] = {}
for animal in range(1, pool.getNbAnimals() + 1):
moveDicoExclusive[eventPairs[event]][animal] = timeLine[event][animal].getDictionary(minFrame=tmin, maxFrame=tmax)
framesToRemove[eventPairs[event]][animal] = []
###########################################################################
#exclude the move and stop events where animals are in contacts
for animal in range(1, pool.getNbAnimals() + 1):
for moveEvent in exclusiveEventList[-3:-1]:
for t in moveDicoExclusive[moveEvent][animal].keys():
for contactEvent in exclusiveEventList[:-3]:
if t in dicoContact[contactEvent][animal].keys():
print('t = ', t, 'in', moveEvent, ' and in ', contactEvent)
framesToRemove[moveEvent][animal].append(t)
###########################################################################
# clean the dictionary of the move and stop events from frames that are overlapping with exclusive contacts
for animal in range(1, pool.getNbAnimals() + 1):
for moveEvent in exclusiveEventList[-3:-1]:
for t in framesToRemove[moveEvent][animal]:
moveDicoExclusive[moveEvent][animal].pop(t, None)
#####################################################
#reduild all events based on dictionary
for moveEvent in exclusiveEventList[-3:-1]:
for animal in range(1, pool.getNbAnimals() + 1):
timeLineExclusive[moveEvent][animal].reBuildWithDictionnary(moveDicoExclusive[moveEvent][animal])
timeLineExclusive[moveEvent][animal].endRebuildEventTimeLine(connection)
# log process
from lmtanalysis.TaskLogger import TaskLogger
t = TaskLogger( connection )
t.addLog( "Build Event Exclusive move and stop events" , tmin=tmin, tmax=tmax )
print( "Rebuild event finished." )