def layer0(mySet):
myClassTypes = GA.queryByMetaAnnotation('classType')
classTypeGroups = {}
for annotation in myClassTypes:
globals()['{}'.format(annotation)] = []
classTypeGroups[annotation] = []
classTypeGroups['Unclassified'] = []
for neuron in mySet:
thisNeuron = False
for annotation in neuron.annotations:
if annotation in myClassTypes: #and annotation != "Visual_Interneuron" and annotation != "secondary_auditory_interneurons": #(annotation == "Descending Neuron" or annotation == "Ascending Neuron" or annotation == "Visual"):
globals()['{}'.format(annotation)].append(neuron.skeletonID)
classTypeGroups[annotation].append(neuron)
thisNeuron = True
if thisNeuron is False:
classTypeGroups['Unclassified'].append(neuron)
return classTypeGroups
def layer1(mySet=None, classTypeGroups=None):
myCommissures = GA.queryByMetaAnnotation('commissure')
myCommissures.append('unilateral')
print(myCommissures)
finalCommissures = {}
comClass = {}
for annotation in myCommissures:
globals()['{}'.format(annotation)] = []
finalCommissures[annotation] = []
if mySet is not None:
for neuron in mySet:
for annotation in neuron.annotations:
if annotation in myCommissures:
globals()['{}'.format(annotation)].append(
neuron.skeletonID)
finalCommissures[annotation].append(neuron.skeletonID)
if classTypeGroups is not None:
for aClass in classTypeGroups:
comClass[aClass] = {}
for neuron in classTypeGroups[aClass]:
if neuron.commissure not in comClass[aClass]:
comClass[aClass][neuron.commissure] = [neuron]
else:
comClass[aClass][neuron.commissure].append(neuron)
#for annotation in neuron.annotations:
#if annotation in myCommissures:
# if annotation not in comClass[aClass]:
# comClass[aClass][annotation] = [neuron]
# else:
# comClass[aClass][annotation].append(neuron)
if bool(comClass) is False:
return finalCommissures
else:
return comClass
def layer2(args):
myRinds = GA.queryByMetaAnnotation('cellBodyRind')
if type(args) is CS.GFIN_set:
mySet = args
finalRinds = {}
for annotation in myRinds:
globals()['{}'.format(annotation)] = []
finalRinds[annotation] = []
for neuron in mySet:
for annotation in neuron.annotations:
if annotation in myRinds:
globals()['{}'.format(annotation)].append(
neuron.skeletonID)
finalRinds[annotation].append(neuron.skeletonID)
else:
CBR = {}
comsAndClasses = args
classList = list(comsAndClasses.keys())
for aClass in classList:
CBR[aClass] = {}
for aCom in comsAndClasses[aClass]:
CBR[aClass][aCom] = {}
for neuron in comsAndClasses[aClass][aCom]:
for annotation in neuron.annotations:
if annotation in myRinds:
if annotation not in CBR[aClass][aCom]:
CBR[aClass][aCom][annotation] = [neuron]
else:
CBR[aClass][aCom][annotation].append(neuron)
if neuron.cellBodyRind is None:
if 'CBnotInBrain' not in CBR[aClass][aCom]:
CBR[aClass][aCom]['CBnotInBrain'] = [neuron]
else:
CBR[aClass][aCom]['CBnotInBrain'].append(neuron)
return CBR
def builder(SKID=None):
if SKID is None:
# sets list of all skeleton IDs
mySkels = GetAnnotationsRemoveExtraneousInfo.getListOfSkID_int()
# creates dictionary with keys as str(skel IDs) and values as number of synapses with GF1
myGF1Connectivity = GetGF1Connectivity.removeExtra()
myGF2Connectivity = GetGF1Connectivity.removeExtra(
skeleton_id='291870')
# creates empty list to be filled with all instances
myNeurons = []
# creates list of of all instances while setting each instance's name and skeletonID to be an element from
# mySkls
for i in mySkels:
x = GFinputNeuron(i)
myNeurons.append(x)
else:
SKID = int(SKID)
myNeurons = []
x = GFinputNeuron(SKID)
myNeurons.append(x)
myGF1Connectivity = []
myGF2Connectivity = []
# creates dictionary with key-value pairs of str(skelID) and list of str(annotations)
myAnnotations = GetListOfSkIDAndAnnotations.getMyAnnotations()
# creates a dictionary with key-value pairs of int(skelID) and and str(neuron name)
myNames = GetAnnotationsRemoveExtraneousInfo.getLookUpTableSkID_Name()
myCommissures = GetAnnotationsRemoveExtraneousInfo.queryByMetaAnnotation(
'commissure')
myClassTypes = GetAnnotationsRemoveExtraneousInfo.queryByMetaAnnotation(
'classType')
# converts skeletonID attribute to string for use as dictionary key then adds all available synapses from
# dictionary of synapses and all available annotations from dictionary of annotations
for elem in myNeurons:
y = elem.skeletonID
z = str(y)
if z in myGF1Connectivity:
elem.GF1synapseCount = myGF1Connectivity[z]
else:
elem.GF1synapseCount = 0
if z in myGF2Connectivity:
elem.GF2synapseCount = myGF2Connectivity[z]
else:
elem.GF2synapseCount = 0
if z in myAnnotations:
elem.annotations = myAnnotations[z]
p = elem.annotations
for abc in p:
if (
'Unclassified' in abc or 'LC4' in abc or 'LPLC2' in abc or 'JONeuron' in abc or 'GCI' in abc
or 'putative DN' in abc) and 'synaptic' not in abc and 'andGFN' not in \
abc and 'HK' not in abc and 'Exploration' not in abc and 'type 37' not in abc and 'type 38' \
not in abc and 'type 44' not in abc and 'type 48' not in abc and 'miscellaneous' not in abc \
and "Ascending" not in abc and "Descending" not in abc and "shared" not in abc:
elem.classification = abc
if 'RIGHT' in abc or 'LEFT' in abc or 'midLine' in abc:
if elem.hemisphere is None:
elem.hemisphere = abc
elem.somaSide = abc
if "JON" in abc and "synaptic" not in abc:
elem.classification = abc
if elem.commissure is None:
if abc in myCommissures:
elem.commissure = abc
if elem.classType is None:
if abc in myClassTypes:
elem.classType = abc
if elem.cellBodyRind is None:
if 'CBR' in abc and len(abc) == 4:
elem.cellBodyRind = abc
if "JONeuron" in elem.annotations:
elem.identification = 'JONeuron'
if elem.hemisphere is None:
elem.hemisphere = "RIGHT HEMISPHERE"
elem.somaSide = "RIGHT HEMISPHERE"
if elem.commissure is None and 'Bilateral' not in elem.annotations:
elem.commissure = 'unilateral'
if y in myNames:
elem.neuronName = myNames[y]
return myNeurons
import CustomNeuronClassSet as CS
import jsonNeurons as JN
import exportToCSV as E2C
import GetAnnotationsRemoveExtraneousInfo as GA
#commissure = 9809716
mySet = CS.builder()
myClassTypes = GA.queryByMetaAnnotation('classType')
for annotation in myClassTypes:
globals()['{}'.format(annotation)] = []
myCommissures = GA.queryByMetaAnnotation('commissure')
finalCommissures = {}
for annotation in myCommissures:
globals()['{}'.format(annotation)] = []
finalCommissures[annotation] = []
#layer0 set the class types(e.g. visual, secondary_auditory, etc...)
def layer0(mySet):
myClassTypes = GA.queryByMetaAnnotation('classType')
classTypeGroups = {}
for annotation in myClassTypes:
globals()['{}'.format(annotation)] = []
classTypeGroups[annotation] = []
classTypeGroups['Unclassified'] = []
for neuron in mySet:
thisNeuron = False
for annotation in neuron.annotations: