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
maxT = eventNight.endFrame
print("Night: ", n)
for behavEvent in behaviouralEventTwoMice:
print("computing {} density".format(behavEvent))
for animal in pool.animalDictionnary:
animalDiffGeno = []
animalSameGeno = []
for animal in pool.animalDictionnary:
if (pool.animalDictionnary[animal].baseId ==
pool.loadAnimals( connection )
if nightComputation == "T":
minT = tmin
maxT = tmax
n = 0
#Compute profile data and save them in a text file
profileData[file][n] = computeProfile(file = file, minT=minT, maxT=maxT, night=n)
text_file.write( "\n" )
print("Profile data saved.")
elif nightComputation == "N":
nightEventTimeLine = EventTimeLineCached( connection, file, "night", minFrame=tmin, maxFrame=tmax )
n = 1
for eventNight in nightEventTimeLine.getEventList():
minT = eventNight.startFrame
maxT = eventNight.endFrame
print("Night: ", n)
#Compute profile data and save them in a text file
profileData[file][n] = computeProfile(file=file, minT=minT, maxT=maxT, night=n)
text_file.write( "\n" )
n+=1
print("Profile data saved.")
elif nightComputation == "D":
dayEventTimeLine = EventTimeLineCached( connection, file, "day", minFrame=tmin, maxFrame=tmax )
d = 1
for eventDay in dayEventTimeLine.getEventList():
minT = eventDay.startFrame
maxT = eventDay.endFrame
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 computeSpeedDurationPerEvent(animalData,
files,
tmin,
tmax,
eventToTest=None):
print("Compute the speed and duration of specific events ")
for file in files:
connection = sqlite3.connect(file)
pool = AnimalPool()
pool.loadAnimals(connection)
pool.loadDetection(tmin, tmax, lightLoad=True)
rfidList = []
for animal in pool.animalDictionnary.keys():
print("computing individual animal: {}".format(animal))
rfid = pool.animalDictionnary[animal].RFID
rfidList.append(rfid)
group = rfidList[0]
for n in range(1, len(rfidList)):
group = group + '-' + rfidList[n]
animalData[file] = {}
nightEventTimeLine = EventTimeLineCached(connection,
file,
"night",
minFrame=tmin,
maxFrame=tmax)
n = 1
for eventNight in nightEventTimeLine.getEventList():
minT = eventNight.startFrame
maxT = eventNight.endFrame
print("Night: ", n)
animalData[file][n] = {}
for animal in pool.animalDictionnary.keys():
print("computing individual animal: {}".format(animal))
rfid = pool.animalDictionnary[animal].RFID
print("RFID: {}".format(rfid))
animalData[file][n][rfid] = {}
# store the animal
animalData[file][n][rfid]["animal"] = pool.animalDictionnary[
animal].name
animalObject = pool.animalDictionnary[animal]
animalData[file][n][rfid]["file"] = file
animalData[file][n][rfid]['genotype'] = pool.animalDictionnary[
animal].genotype
animalData[file][n][rfid]['sex'] = pool.animalDictionnary[
animal].sex
animalData[file][n][rfid]['strain'] = pool.animalDictionnary[
animal].strain
animalData[file][n][rfid]['age'] = pool.animalDictionnary[
animal].age
animalData[file][n][rfid]['group'] = group
print("computing individual event: {}".format(eventToTest))
behavEventTimeLine = EventTimeLineCached(connection,
file,
eventToTest,
animal,
minFrame=minT,
maxFrame=maxT)
animalData[file][n][rfid]['DurationSpeed'] = []
animalData[file][n][rfid]['speed'] = []
for event in behavEventTimeLine.getEventList():
results = getDurationSpeed(event=event,
animal=animalObject)
#print('duration, speed: ', results)
animalData[file][n][rfid]['DurationSpeed'].append(results)
animalData[file][n][rfid]['speed'].append(results[1])
n += 1
connection.close()
with open("durationSpeedData_{}.json".format(eventToTest), 'w') as jFile:
json.dump(animalData, jFile, indent=3)
print("json file created for all data")
