def trajBuilder(new_sol):
stories = ordonnancement(new_sol); res = {}
for plate in stories:
res.update({plate : {}})
for well in stories[plate]:
print plate, well
ensembleTraj = fHacktrack2.ensTraj()
res[plate].update({well:ensembleTraj})
# print ensembleTraj.numMitoses
# print ensembleTraj.lstTraj
num = 0; l=[0]
beginningFrames=[0,128,129,75]
for index in stories[plate][well]:
print "INDEX ", index
solC = stories[plate][well][index]
if type(solC.truth)==str:
l.append(index+1)
continue
singlets = solC.singlets
nextSinglets = solC.nextSinglets
result =filter(lambda x: x[1]==1, zip(solC.hypotheses, solC.truth))
for hyp in result:
s, t = hyp[0]; source = [] ; target = [];
if type(s)==np.int32 and s!=-1:
source.append(filter(lambda x: x.label == s, singlets)[0])
elif type(s)==tuple:
for c in s:
source.append(filter(lambda x: x.label == c, singlets)[0])
if type(t)==np.int32 and t!=-1:
target.append(filter(lambda x: x.label == t, nextSinglets)[0])
elif type(t)==tuple:
for c in t:
target.append(filter(lambda x: x.label == c, nextSinglets)[0])
incoming = len(source) ; outcoming= len(target)
mit = (outcoming>1)
# if mit: pdb.set_trace()
num+=1
if incoming == 0:
# print "APPEAR"
for c in target:
newTraj= fHacktrack2.trajectoire(num, c.center[0], c.center[1], index+1, c.label)
newTraj.longueurs=[index+1]
newTraj.fractions=[1]
ensembleTraj.add(newTraj)
num+=1
continue
elif outcoming ==0:
# print "DISAPPEAR"
if index in l:
#pdb.set_trace()#en fait ce sont au moins les trajectoires qui commencent en 0 et finissent en 0 ie les apparitions disparitions en 0
for c in source:
newTraj = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
newTraj.longueurs = [index]
newTraj.fractions=[1]
ensembleTraj.add(newTraj)
num+=1
continue
elif incoming == 1:
# print "FROM ONE"
c = source[0]
incomingTraj = ensembleTraj.findLabelFrame(c.label, index)
if outcoming <= len(incomingTraj):
first = True; ll=[]; lf=[]
# for traj in incomingTraj:
# ll.extend(traj.longueurs)
# lf.extend(traj.fractions)
# if ll==[] and index>0:
# pdb.set_trace()
for traj in incomingTraj:
try:
t = target.pop()
except IndexError:
continue
else:
traj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
# traj.longueurs = ll; traj.fractions = lf
if first: numC = traj.numCellule
if mit:
# print "ajout mitose"
traj.mitose=1; traj.numCellule = numC; first = False
#traj.ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
else:
i = 0; first = True; ll=[]; lf=[]
# for traj in incomingTraj:
# ll.extend(traj.longueurs)
# lf.extend(traj.fractions)
# if ll==[] and index>0:
# pdb.set_trace()
for t in target:
try:
incomingTraj[i].ajoutPoint(t.center[0], t.center[1], index+1, t.label)
# incomingTraj[i].longueurs = ll; incomingTraj[i].fractions = lf
if first: numC = incomingTraj[i].numCellule
if mit:
# print "ajout mitose"
incomingTraj[i].mitose=1; incomingTraj[i].numCellule = numC; first = False
#incomingTraj[i].ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
i+=1
except IndexError:
if not mit:
#ici on n'y arrive a t=0 quand aucune trajectoire n'est initialise
if index not in beginningFrames: pdb.set_trace()
num+=1
newTraj = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
newTraj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
newTraj.longueurs=[index]; newTraj.fractions = [1]
if first:
numC = num
if mit:
newTraj = fHacktrack2.trajectoire(numC, c.center[0], c.center[1], index, c.label)
newTraj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
newTraj.longueurs = incomingTraj[0].longueurs if incomingTraj !=[] else [index]
newTraj.fractions = incomingTraj[0].fractions if incomingTraj !=[] else [1]
#pdb.set_trace()
# print "ajout mitose"
newTraj.mitose=1
first = False
#newTraj.ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
#pdb.set_trace()
ensembleTraj.add(newTraj)
elif incoming >1:
if outcoming>1:
raise
# print "FROM MORE THAN ONE"
t = target[0]; tt=None
if index not in beginningFrames:
tt=[]; ll=[]; lf=[]
for c in source:
incomingTraj = ensembleTraj.findLabelFrame(c.label, index)
tt.append(incomingTraj[0])
k=0
for lon in incomingTraj[0].longueurs:
ll.append(lon)
lf.append(incomingTraj[0].fractions[k]/float(incoming))
k+=1
# if ll==[] and index>0:
# pdb.set_trace()
i=0
for c in source:
try:
trajC = tt[i]
trajC.longueurs = ll; trajC.fractions = lf
# pdb.set_trace()
except:
#on tombe ici a t=0 mais est-ce qu'on y tombe apres ?
if index not in beginningFrames: pdb.set_trace()
num+=1
trajC = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
trajC.longueurs=[index for bb in range(incoming)]; trajC.fractions = [1/float(incoming) for bb in range(incoming)]
ensembleTraj.add(trajC)
finally:
trajC.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
i+=1
#incomingTraj[0].ajoutMomentInteressant(c.center[0], c.center[1], index)
return res
def lireDot(nomDot):
fDot = open(nomDot, "r")
mesLignes=fDot.readlines()
fDot.close()
del mesLignes[0:3]
mesLignes.reverse()
continuer = True
ensembleTraj = fHacktrack2.ensTraj()
print ensembleTraj.numMitoses
print ensembleTraj.lstTraj
trajCourante = fHacktrack2.trajectoire(0,0,0,0,0)
frameSuivante =-1
idSuivante =-1
while continuer:
ligneCourante=mesLignes.pop()
if ("#AAAAAA" in ligneCourante):
continuer = False
continue
decomp = ligneCourante.split(" ")
decomp[0]=decomp[0][1:-1]
frameCourante = int(decomp[0].split("_")[0])
idCourante = int(decomp[0].split("_")[1])
decomp[2]=decomp[2][1:-1]
# if idCourante==105 and frameCourante ==1:
# pdb.set_trace()
if (int(frameCourante) != int(frameSuivante) or int(idCourante) != int(idSuivante)):
if frameSuivante!=-1 and idSuivante!=-1:
trajCourante.ajoutPoint(0,0, frameSuivante, idSuivante)
trajectoires = ensembleTraj.trouver(trajCourante.numCellule)
lstPointsTotale = []
for trajec in trajectoires.lstTraj:
for element in trajec.lstPoints.keys():
#print element
lstPointsTotale.append(element)
#if lstPointsTotale <> []: print lstPointsTotale
if (frameCourante, idCourante) in lstPointsTotale or (frameCourante, idCourante) in trajCourante.lstPoints.keys():
#print "mitose", frameCourante, idCourante
trajCourante.mitose = 1
ensembleTraj.numMitoses +=1
if (frameCourante, idCourante) in trajCourante.lstPoints.keys():
trajCourante.ajoutPoint(0, 0, frameCourante, idCourante)
ensembleTraj.ajouter(trajCourante)
num = trajCourante.numCellule
# print num
trajCourante.supp()
trajCourante = fHacktrack2.trajectoire(num, 0,0, frameCourante, idCourante)
trajCourante.mitose = 1
else:
# print "nouvelle trajectoire", frameCourante, idCourante
ensembleTraj.ajouter(trajCourante)
num = trajCourante.numCellule+1
trajCourante.supp()
trajCourante = fHacktrack2.trajectoire(num, 0,0, frameCourante, idCourante)
# print trajCourante.lstPoints
else:
# print "ajout point"
trajCourante.ajoutPoint(0, 0, frameCourante, idCourante)
# print trajCourante.lstPoints
frameSuivante = int(decomp[2].split("_")[0])
idSuivante = int(decomp[2].split("_")[1])
ensembleTraj.ajouter(trajCourante)
return ensembleTraj
def trajBuilder(new_sol, training=False):
stories = tracking.ordonnancement(new_sol); res = {}
global movie_length
for plate in stories:
res.update({plate : {}})
movie_length.update({plate : {}})
for well in stories[plate]:
print plate, well
ensembleTraj = fHacktrack2.ensTraj()
res[plate].update({well:ensembleTraj})
movie_length[plate].update({well : max(stories[plate][well].keys())+1})
# print ensembleTraj.numMitoses
# print ensembleTraj.lstTraj
num = 0; l=[0]; mergeList=-1; trajC=None
for index in stories[plate][well]:
print " INDEX ", index,
solC = stories[plate][well][index]
if type(solC.truth)==str:
l.append(index+1)
continue
singlets = solC.singlets
nextSinglets = solC.nextSinglets
result =filter(lambda x: x[1]==1, zip(solC.hypotheses, solC.truth))
for hyp in result:
#print hyp
#if index==86: pdb.set_trace()
s, t = hyp[0]; source = [] ; target = [];
if type(s) in [np.int32, np.uint16] and s!=-1:
source.append(filter(lambda x: x.label == s, singlets)[0])
elif type(s)==tuple:
for c in s:
source.append(filter(lambda x: x.label == c, singlets)[0])
if type(t) in [np.int32, np.uint16] and t!=-1:
target.append(filter(lambda x: x.label == t, nextSinglets)[0])
elif type(t)==tuple:
for c in t:
target.append(filter(lambda x: x.label == c, nextSinglets)[0])
incoming = len(source) ; outcoming= len(target)
mit = (outcoming>1)
# if mit: pdb.set_trace()
num+=1
if incoming == 0:
# print "APPEAR"
for c in target:
newTraj= fHacktrack2.trajectoire(num, c.center[0], c.center[1], index+1, c.label)
newTraj.longueurs=[index+1]
newTraj.fractions=[1]
ensembleTraj.add(newTraj)
num+=1
continue
elif outcoming ==0:
# print "DISAPPEAR"
if index in l:
#pdb.set_trace()#en fait ce sont au moins les trajectoires qui commencent en 0 et finissent en 0 ie les apparitions disparitions en 0
for c in source:
newTraj = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
newTraj.longueurs = [index]
newTraj.fractions=[1]
ensembleTraj.add(newTraj)
num+=1
continue
elif incoming == 1:
# print "FROM ONE"
c = source[0]
incomingTraj = ensembleTraj.findLabelFrame(c.label, index)
if outcoming <= len(incomingTraj):
first = True; ll=[]; lf=[]
# for traj in incomingTraj:
# ll.extend(traj.longueurs)
# lf.extend(traj.fractions)
# if ll==[] and index>0:
# pdb.set_trace()
for traj in incomingTraj:
try:
t = target.pop()
except IndexError:
continue
else:
traj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
# traj.longueurs = ll; traj.fractions = lf
if first: numC = traj.numCellule
if mit:
# print "ajout mitose"
traj.split(index); traj.numCellule = numC; first = False
#traj.ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
else:
i = 0; first = True; ll=[]; lf=[]
# for traj in incomingTraj:
# ll.extend(traj.longueurs)
# lf.extend(traj.fractions)
# if ll==[] and index>0:
# pdb.set_trace()
for t in target:
try:
incomingTraj[i].ajoutPoint(t.center[0], t.center[1], index+1, t.label)
# incomingTraj[i].longueurs = ll; incomingTraj[i].fractions = lf
if first:
numC = incomingTraj[i].numCellule
trajC = incomingTraj[i]
mergeList = incomingTraj[i].fusion
if mit:
# print "ajout mitose"
incomingTraj[i].split(index); incomingTraj[i].numCellule = numC; first = False
#incomingTraj[i].ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
i+=1
except IndexError:
if not mit:
#ici on y arrive a t=0 quand aucune trajectoire n'est initialise ou cas de split a quatre sorti du TS
if index>0 and training==False: pdb.set_trace()
num+=1
newTraj = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
newTraj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
newTraj.longueurs=[index]; newTraj.fractions = [1]
if first:
numC = num
if index>0 and training==False:
print hyp
pdb.set_trace()
if mit:
#ici, quand j'ai une mitose je copie toute la trajectoire precedente dans la nouvelle OU PAS ?
newTraj = fHacktrack2.trajectoire(numC, c.center[0], c.center[1], index, c.label)
newTraj.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
newTraj.longueurs = incomingTraj[0].longueurs if incomingTraj !=[] else [index]
newTraj.fractions = incomingTraj[0].fractions if incomingTraj !=[] else [1]
#print id(trajC), numC, hyp, mergeList
#pdb.set_trace()
newTraj.fusion=list(mergeList) if type(mergeList)==list else mergeList
#pdb.set_trace()
# print "ajout mitose"
newTraj.split(index)
first = False
#newTraj.ajoutMomentInteressant(c.center[0], c.center[1], index)
ensembleTraj.numMitoses+=1
#pdb.set_trace()
ensembleTraj.add(newTraj)
elif incoming >1:
if outcoming>1:
raise
# print "FROM MORE THAN ONE"
t = target[0]; tt=None
if index>0:
tt=[]; ll=[]; lf=[]
for c in source:
incomingTraj = ensembleTraj.findLabelFrame(c.label, index)
try:
tt.append(incomingTraj[0])
except IndexError:
pass
else:
k=0
for lon in incomingTraj[0].longueurs:
ll.append(lon)
lf.append(incomingTraj[0].fractions[k]/float(incoming))
k+=1
# if ll==[] and index>0:
# pdb.set_trace()
i=0
for c in source:
try:
trajC = tt[i]
trajC.longueurs = ll; trajC.fractions = lf
# pdb.set_trace()
except:
#on tombe ici a t=0 mais est-ce qu'on y tombe apres ? oui si on calcule les trajectoires du training
#set pcq il y a des evenements elimines par defaut (mvt a quatre)
if index>0 and training==False: pdb.set_trace()
num+=1
trajC = fHacktrack2.trajectoire(num, c.center[0], c.center[1], index, c.label)
trajC.longueurs=[index for bb in range(incoming)]; trajC.fractions = [1/float(incoming) for bb in range(incoming)]
ensembleTraj.add(trajC)
finally:
trajC.ajoutPoint(t.center[0], t.center[1], index+1, t.label)
#print id(trajC), trajC.numCellule, trajC.fusion
#pdb.set_trace()
trajC.merge(index)
i+=1
#incomingTraj[0].ajoutMomentInteressant(c.center[0], c.center[1], index)
return res