def compFeatures(data, length, who, ctrlStatus, percentile, *args):
how_many=5
outputFolder='../prediction/annotations'
plwList=defaultdict(int)
whoList={}
extractors=[]
for feature_name in args:
extractor = cellExtractor(feature_name)
extractors.append(extractor)
bestMovies = extractor.dataToBestMovies(data, length, who, ctrlStatus, percentile, how_many=how_many)
#plwList.extend(bestMovies.keys())
whoList[feature_name]=bestMovies
for el in bestMovies:
plwList[el]+=len(bestMovies[el])
plwList={el:plwList[el] for el in filter(lambda x: np.all([x in whoList[feature_name] for feature_name in args]), plwList.keys())}
sort= sorted(plwList, key=operator.itemgetter(1))
chosen=sort[-how_many:]
num=1
for el in chosen:
plate, well=el
filename = "PL{}___P{}___T00000.xml".format(plate, well)
file_ = open(os.path.join(outputFolder, filename), 'w')
file_.write(initXml())
for i,feature_name in enumerate(args):
resultCour = whoList[feature_name][el]
print len(resultCour)#donc attention ici on n'a que les index des trajectoires dans le fichier coord
file_.write(extractors[i].wellToXml(length,who, plate, well, resultCour, outputFolder, num)) # _writeXml(plate, well, resultCour, num))
num+=1
file_.write(finirXml())
file_.close()
return chosen
def writeTracks(self):
'''
To produce annotated tracklets, either all tracklets (option all_=True) or only those used for feature extraction (option all=False)
'''
intensity_qc_dict = self._getIntensityQC()
if 'tracking_annotations' not in os.listdir(self.settings.outputFolder):
os.mkdir(os.path.join(self.settings.outputFolder, 'tracking_annotations'))
if 'annotations' not in os.listdir(os.path.join(self.settings.outputFolder, 'tracking_annotations')):
os.mkdir(os.path.join(os.path.join(self.settings.outputFolder, 'tracking_annotations', 'annotations')))
if self.settings.all_trajectory_xml:
well_files = filter(lambda x: self.settings.traj_filename.split('{}')[0] in x, os.listdir(os.path.join(self.settings.outputFolder, self.plate)))
else:
well_files = filter(lambda x: self.settings.feature_filename.split('{}')[0] in x, os.listdir(os.path.join(self.settings.outputFolder, self.plate)))
for file_ in well_files:
well_num=int(file_.split('_')[2][1:])
well = '{:>05}_01'.format(well_num)
nomFichier = "PL"+self.plate+"___P"+well+"___T00001.xml"
nomFichier = os.path.join(self.settings.outputFolder,'tracking_annotations', 'annotations', nomFichier)
if self.settings.all_trajectory_xml:
f=open(os.path.join(self.settings.outputFolder, self.plate, file_), 'r')
d=pickle.load(f); f.close()
ensTraj = d['tracklets dictionary'][self.plate][well]
_ = sortiesAll(nomFichier, ensTraj)
else:
f=open(os.path.join(self.settings.outputFolder, self.plate, file_), 'r')
_,coord,_=pickle.load(f); f.close()
compteur =1
fichierX = open(nomFichier, "w")
fichierX.write(initXml())
if intensity_qc_dict is not None and well_num in intensity_qc_dict:
frames_to_skip = intensity_qc_dict[well_num]
else:
frames_to_skip=None
for lstPoints in coord:
frameL=lstPoints[0]; X=lstPoints[1]; Y=lstPoints[2]
d={(frameL[k]+len(np.where(frames_to_skip<=frameL[k])[0]),0):(X[k], Y[k]) for k in range(len(frameL))}
txt, coord = ecrireXml(compteur,d, True)
fichierX.write(txt)
compteur+=1
if compteur>1600:
break
fichierX.write(finirXml())
fichierX.close()
print 'finally ', compteur, 'trajectories'
return
def findingSharpMovements(setting_file='bgeig/settings/settings_bgeig.py', measure='turningangle',
speed_filter=10, nocontact=True):
settings=Settings(setting_file, globals())
f=open(settings.dict_corresp_nuclei_cyto)
dict_corresp=pickle.load(f); f.close()
plates=os.listdir(settings.dataFolder)
sharp={}; contact={}
for plate in plates:
print '-----', plate, '<br>'
wells=['{:>05}_01'.format(k) for k in range(21, 25)]
sharp[plate]={}; contact[plate]={}
for well in wells:
print well, '<br>'
sharp[plate][well]=defaultdict(list)
contact[plate][well]=defaultdict(list)
contact_count=0; not_contact=0
f=open(os.path.join(settings.outputFolder, plate, settings.feature_filename.format(well)))
_, coord, hist, id_list=pickle.load(f); f.close()
nomFichier = "PL"+plate+"___P"+well+"___T00001.xml"
nomFichier = os.path.join(settings.outputFolder,'sharp_mov', 'annotations', nomFichier)
compteur =1
fichierX = open(nomFichier, "w")
fichierX.write(initXml())
for i,el in enumerate(hist[measure]):
if np.any(np.array(el)>0.70):
wh_=np.where((np.array(el)>0.70)&(np.array(hist['displacements'][i][:-1])>speed_filter))[0]
if wh_.shape[0]==0:
continue
d={}
id_=id_list[i]
currcoord=np.array(zip(*coord[i]))
sharp[plate][well][id_].append(currcoord[0][0][0])
assert(len(el)==len(currcoord)-2)
for index in range(len(el)):
el=currcoord[index]
im, cell_id=el[0]
corresp_cytoplasm = dict_corresp[plate][well][im][cell_id]
if Counter(dict_corresp[plate][well][im].values())[corresp_cytoplasm]>1:
contact[plate][well][id_].append(im)
if index in wh_:
sharp[plate][well][id_].append(im)
if nocontact:
try:
previous_im, previous_id = currcoord[index-1][0]
except IndexError:
previous_im=im
previous_id=cell_id
try:
next_im, next_id = currcoord[index+1][0]
except IndexError:
next_im=im
next_id=cell_id
previous_cytoplasm = dict_corresp[plate][well][previous_im][previous_id]
next_cytoplasm=dict_corresp[plate][well][next_im][next_id]
test = Counter(dict_corresp[plate][well][im].values())[corresp_cytoplasm]==1\
and Counter(dict_corresp[plate][well][previous_im].values())[previous_cytoplasm]==1\
and Counter(dict_corresp[plate][well][next_im].values())[next_cytoplasm]==1
else:
test=True
if test:
d[tuple(el[0])]=(el[1], el[2])
not_contact+=1
else:
contact_count+=1
txt, _ = ecrireXml(compteur,d, True)
fichierX.write(txt)
compteur+=1
fichierX.write(finirXml())
fichierX.close()
print 'Cells with sharp movements + contact', contact_count#, '<br>'
print 'Cells with sharp movements + alone', not_contact#, '<br>'
#So if I'm looking for the track ids that contain at least one sharp movement
#I should be able to find it in the dictionary sharp which is saved in projects/Geiger/results/dict_nuclei_sharpmov_10pixelmin.pkl
return sharp, contact