def process(file):
print("**********************")
print(file)
print("**********************")
connection = sqlite3.connect(file)
animalPool = AnimalPool()
animalPool.loadAnimals(connection)
# show the mask of animals at frame 300
animalPool.showMask(300)
def process(file, dataframe, expListToCheck, expListToCheckForPause,
expListToCheckForRfid):
print(file)
#open the database file
connection = sqlite3.connect(file)
c = connection.cursor()
pool = AnimalPool()
pool.loadAnimals(connection)
if len(pool.animalDictionnary.keys()) > 1:
print('More than one animal in this experiment. Please check.')
expListToCheck.append(file)
elif len(pool.animalDictionnary.keys()) == 1:
query = "SELECT PAUSED FROM FRAME WHERE PAUSED = '1'"
c.execute(query)
rows = c.fetchall()
print('existing paused frames: ', rows)
if len(rows) == 0:
# get the RFID of the tracked animal in the database
rfidDatabase = pool.animalDictionnary[1].RFID
print('RFID database: ', rfidDatabase)
#attribute the corresponding frame number to be changed
count = 0
for rfidTable in dataframe['RFID']:
#print('RFID table: ', rfidTable)
if rfidTable in rfidDatabase:
print('RFID: ', rfidTable, rfidDatabase)
frameToPause = dataframe[dataframe['RFID'] ==
rfidTable]['paused_frame'].item()
print('paused frame: ', frameToPause)
count = 1
if count == 0:
print('This RFID is not referenced in the table.')
print(file, rfidDatabase)
expListToCheckForRfid.append(file)
else:
#modify the PAUSED status in the database for the corresponding framenumber
query = "UPDATE FRAME SET PAUSED = '1' WHERE FRAMENUMBER = {}".format(
frameToPause)
c.execute(query)
else:
print('Paused frames already exist; please check')
expListToCheckForPause.append(file)
connection.commit()
c.close()
connection.close()
def set_genotype(files):
if files is None:
print("No files selected (aborting)")
return
for file in files:
print("\n\nFile: ", file)
print("-" * 80)
if not os.path.exists(file):
print(" ! File does not exist... (skipping)")
continue
with mute_prints():
connection = sqlite3.connect(file)
pool = AnimalPool()
pool.loadAnimals(connection)
print(
f"Setting genotype of {len(pool.getAnimalList())} mice, press [Enter] to keep existing one):"
)
for animal in sorted(pool.getAnimalList(), key=lambda a: a.name):
genotype = input(
f" * {animal.name}_{animal.RFID} [{animal.genotype}]: ")
genotype = genotype.strip()
if len(genotype) > 0:
print(
f" - setting {animal.name}_{animal.RFID} to '{genotype}'"
)
animal.setGenotype(genotype)
else:
print(f" - keeping genotype {animal.genotype}")
print("Genotype saved in database.")
print("-" * 120)
if __name__ == '__main__':
#ask the user for database to process
files = getFilesToProcess()
for file in files:
# connect to database
connection = sqlite3.connect(file)
# create an animalPool, which basically contains your animals
animalPool = AnimalPool()
# load infos about the animals
animalPool.loadAnimals(connection)
# load all detection (positions) of all animals for the first hour
animalPool.loadDetection(start=0, end=oneHour)
eventTimeLine = EventTimeLine(connection,
"Oral-genital Contact",
idA=1,
idB=2,
minFrame=0,
maxFrame=oneHour)
print("Event list for label ", eventTimeLine.eventNameWithId)
print("for animal 1:", animalPool.getAnimalDictionnary()[1].RFID)
print("for animal 2:", animalPool.getAnimalDictionnary()[2].RFID)
print("Number of events:", len(eventTimeLine.getEventList()))