def processAll():
#choose the sqlite files to process
files = getFilesToProcess()
#choose the file containing the frame numbers that should be paused
refFile = getCsvFileToProcess()
#open the file containing the frame number that should be set on pause.
df = pd.read_csv(refFile, sep=';')
expListToCheck = []
expListToCheckForPause = []
expListToCheckForRfid = []
chronoFullBatch = Chronometer("Full batch")
if (files != None):
for file in files:
print("Processing file", file)
process(file, df, expListToCheck, expListToCheckForPause,
expListToCheckForRfid)
chronoFullBatch.printTimeInS()
print('Experiment files to be checked for multiple animals: ')
print(expListToCheck)
print('Experiment files to be checked for paused frames: ')
print(expListToCheckForPause)
print('Experiment files to be checked for RFID: ')
print(expListToCheckForRfid)
print("*** ALL JOBS DONE ***")
def processAll():
files = getFilesToProcess()
chronoFullBatch = Chronometer("Full batch")
if (files != None):
for file in files:
print("Processing file", file)
process(file)
chronoFullBatch.printTimeInS()
print("*** ALL JOBS DONE ***")
def processAll():
files = getFilesToProcess()
chronoFullBatch = Chronometer("Full batch")
if (files != None):
for file in files:
try:
print("Processing file", file)
process(file)
except FileProcessException:
print("STOP PROCESSING FILE " + file, file=sys.stderr)
chronoFullBatch.printTimeInS()
print("*** ALL JOBS DONE ***")
data.append( row[0] )
return data
if __name__ == '__main__':
print("Code launched.")
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()
files = getFilesToProcess()
chronoFullBatch = Chronometer("Full batch" )
if ( files != None ):
for file in files:
try:
print ( "Processing file" , file )
process( file )
except FileProcessException:
print ( "STOP PROCESSING FILE " + file , file=sys.stderr )
flushEventTimeLineCache()
chronoFullBatch.printTimeInS()
def process( shiftData = True ):
# shiftdata to see all animal's activity timeline on y axis
print("Code launched.")
saveFile = "figTimeLineActivity"
#Choose the files to process
files = getFilesToProcess()
tmin, tmax, text_file = getMinTMaxTAndFileNameInput()
for file in files:
print(file)
expName = file[-22:-7]
print( expName )
connection = sqlite3.connect( file )
pool = AnimalPool( )
pool.loadAnimals( connection )
pool.loadDetection( start = tmin, end = tmax, lightLoad=True)
#Load the timeline of the nest4 event over all individuals
print( "Loading all nest4 for file " + file )
nest4TimeLine = {}
nest4TimeLine["all"] = EventTimeLine( connection, "Nest4_", minFrame=tmin, maxFrame=tmax )
#Load the timeline of the nest3 event over all individuals
print( "Loading all nest3 for file " + file )
nest3TimeLine = {}
nest3TimeLine["all"] = EventTimeLine( connection, "Nest3_", minFrame=tmin, maxFrame=tmax )
print("loading night events for file " + file)
nightTimeLine = EventTimeLine( connection, "night" , minFrame=tmin, maxFrame=tmax )
''' build the plot '''
#ymax=200
ymax = 40
ymin=-30
fig, ax = plt.subplots( 1,1 , figsize=(8, 2 ) )
ax = plt.gca() # get current axis
ax.set_xlabel("time")
ax.set_xlim([0, tmax])
ax.set_ylim([ymin, ymax])
#set x axis
formatter = matplotlib.ticker.FuncFormatter( frameToTimeTicker )
ax.xaxis.set_major_formatter(formatter)
ax.tick_params(labelsize=6 )
ax.xaxis.set_major_locator(ticker.MultipleLocator( 30 * 60 * 60 * 12 ))
ax.xaxis.set_minor_locator(ticker.MultipleLocator( 30 * 60 * 60 ))
#draw the rectangles for the nights
for nightEvent in nightTimeLine.getEventList():
ax.axvspan( nightEvent.startFrame, nightEvent.endFrame, alpha=0.1, color='black')
ax.text( nightEvent.startFrame+(nightEvent.endFrame-nightEvent.startFrame)/2 , 0.90*ymax , "dark phase" ,fontsize=6, ha='center')
#plot the distance traveled per timeBin min time bin
timeBin = 1
dt = {}
totalDistance = {}
i=0
for animal in pool.animalDictionnary.keys():
print ( pool.animalDictionnary[animal].RFID )
dist = pool.animalDictionnary[animal].getDistancePerBin(binFrameSize = timeBin*oneMinute, maxFrame = tmax )
if shiftData:
for i2 in range( len(dist) ):
dist[i2]= dist[i2]/100
if shiftData:
for i2 in range( len(dist) ): # shift data in y
dist[i2]= dist[i2]+i*40
dt[animal] = dist
'''
for x in pool.animalDictionnary[animal].getDistancePerBin(binFrameSize = timeBin*oneMinute, maxFrame = tmax )
dist.append( x )
'''
#dt[animal] = [x/100 for x in pool.animalDictionnary[animal].getDistancePerBin(binFrameSize = timeBin*oneMinute, maxFrame = tmax )]
totalDistance[animal] = pool.animalDictionnary[animal].getDistance(tmin=tmin, tmax=tmax)
i+=1 # shift data
nTimeBins = len(dt[1])
print(nTimeBins)
abs = [10*oneMinute]
for t in range(1, nTimeBins):
x = abs[t-1] + timeBin*oneMinute
abs.append(x)
#print(abs)
print(len(abs))
text_file.write( "{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format( "file", "rfid", "genotype", "user1", "tmin", "tmax", "totalDistance" ) )
for animal in pool.animalDictionnary.keys():
#print(dt[animal])
ax.plot( abs, dt[animal], color = getAnimalColor(animal), linewidth=0.6 )
#prepare data to be written in a txt file, with tab separating columns
line =""
line+= str ( file )+ "\t"
line+= str ( pool.animalDictionnary[animal].RFID )+ "\t"
line+= str ( pool.animalDictionnary[animal].genotype )+ "\t"
line+= str ( pool.animalDictionnary[animal].user1 )+ "\t"
line+= str ( tmin )+ "\t"
line+= str ( tmax )+ "\t"
line+= str ( totalDistance[animal]/100 )+ "\t"
for val in dt[animal]:
line+= str( val )+ "\t"
text_file.write( line )
text_file.write( "\n" )
#Print the name and genotype of the animals on the graph, with the corresponding colors and the total distance traveled over the experiment
legendHeight = 0.6*ymax
for animal in pool.animalDictionnary.keys():
print ( pool.animalDictionnary[animal].RFID )
ax.text(30*60*60, legendHeight, "{} {} ({} m)".format(pool.animalDictionnary[animal].RFID[5:], pool.animalDictionnary[animal].genotype, round(totalDistance[animal]/100)), color=getAnimalColor(animal), fontsize=5 )
legendHeight += 12
yLabels=[]
line = -20
yTickList = []
addThickness=0
fig.suptitle("Activity time line {}".format( expName ))
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
#draw the nest4 time line
yLabels.append("nest4")
lineData = []
for eventList in nest4TimeLine["all"].eventList:
lineData.append( ( eventList.startFrame-addThickness , eventList.duration()+addThickness ))
ax.broken_barh( lineData , ( line-4, 4 ), facecolors = "black" )
yTickList.append(line)
line+=10
#draw the nest3 time line
yLabels.append("nest3")
addThickness=0
lineData = []
for eventList in nest3TimeLine["all"].eventList:
lineData.append( ( eventList.startFrame-addThickness , eventList.duration()+addThickness ))
ax.broken_barh( lineData , ( line-4, 4 ), facecolors = "black" )
yTickList.append(line)
line+=10
#draw the y axis
yLab=[0, 40, 80, 120, 160, 200]
#yLab=[0, 40]
for i in yLab:
yTickList.append(i)
yLabels.append(i)
ax.set_yticks( yTickList )
ax.set_yticklabels( yLabels )
plt.tight_layout()
print ("Saving figure...")
fig.savefig( "FigActivityTimeLine_{}.pdf".format( expName ) ,dpi=100)
plt.close( fig )
text_file.close()
