def buildFromSkidList(myList):
# sets list of all skeleton IDs
mySkels = myList
# creates dictionary with keys as str(skel IDs) and values as number of synapses with DNright
# myDNrightConnectivity = GetDNrightConnectivity.removeExtra(myList)
# creates dictionary with key-value pairs of str(skelID) and list of str(annotations)
myAnnotations = GetAnnotationsByID.getMyAnnotations(myList)
# creates a dictionary with key-value pairs of int(skelID) and and str(neuron name)
myNames = GetAnnotationsByID.getLookUpTableSkID_Name()
# 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 myList:
x = DNinputNeuron(i)
myNeurons.append(x)
# 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 myDNrightConnectivity:
# elem.DNrightsynapseCount = myDNrightConnectivity[z]
if z in myAnnotations:
elem.annotations = myAnnotations[z]
p = elem.annotations
if y in myNames:
elem.neuronName = myNames[y]
return myNeurons
def getNeuronName(self):
y = elem.skeletonID
z = str(y)
myNames = GetAnnotationsByID.getLookUpTableSkID_Name()
if y in myNames:
self.neuronName = myNames[y]
else:
myOtherNames = GetAnnotationsByID.getLookUpTableSkID_Name('CardLab-collaborating')
self.neuronName = myOtherNames[y]
return self.neuronName
def buildSingleCell(SKID):
aCell = DNinputNeuron(SKID)
# sets annotations based on SKID
aCell.annotations = GetAnnotationsByID.setAnnotationLookUpTable(SKID)
aCell.neuronName = GetAnnotationsByID.getName(SKID)
aCell.DNrightsynapseCount = 0
return aCell
def builder(DNSKID, SKID=None):
if SKID is None:
# creates dictionary with keys as str(skel IDs) and values as number of synapses with DNright
myDNrightConnectivity = GetDNrightConnectivity.removeExtra(DNSKID)
# sets string list of all skeleton IDs
mySkels = GetDNrightConnectivity.getMySkids(DNSKID, myDNrightConnectivity)
mySkelIDs = []
for i in mySkels:
mySkelIDs.append(int(i))
# 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 mySkelIDs:
x = DNinputNeuron(i)
myNeurons.append(x)
else:
SKID = int(SKID)
myNeurons = []
x = DNinputNeuron(SKID)
myNeurons.append(x)
myDNrightConnectivity = []
# creates dictionary with key-value pairs of str(skelID) and list of str(annotations)
myAnnotations = GetAnnotationsByID.getMyAnnotations(mySkels)
# creates a dictionary with key-value pairs of int(skelID) and and str(neuron name)
myNames = GetAnnotationsByID.getLookUpTableSkID_Name()
# 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 myDNrightConnectivity:
elem.DNrightsynapseCount = myDNrightConnectivity[z]
else:
elem.DNrightsynapseCount = 0
if z in myAnnotations:
elem.annotations = myAnnotations[z]
p = elem.annotations
for abc in p:
if (
'putative' in abc or 'Unclassified' in abc or 'JO' in abc or 'B1' in abc or 'GCI' in abc or
'Halted' in abc or 'Neuron Fragment' in abc or 'DN' in abc) and 'synaptic' not in abc and \
'input to' not in abc and 'DN106 input neuron' not in abc:
elem.classification = abc
# if ('type 37' in abc or 'type 38' in abc or 'type 44' in abc or 'JO' in abc:
# elem.classification = 'JO'
if elem.classification is None:
elem.classification = "Other"
if "Descending" in abc or 'Ascending' in abc:
if 'Unclassified' in elem.classification and 'type' not in elem.classification:
elem.classification = "Unclassified {} DN input neuron".format(abc)
if 'RIGHT' in abc or 'LEFT' in abc:
if elem.hemisphere is None:
elem.hemisphere = abc
if 'Bilateral' in abc:
elem.hemisphere = abc
if elem.hemisphere is None:
elem.hemisphere = "RIGHT HEMISPHERE"
if y in myNames:
elem.neuronName = myNames[y]
return myNeurons
def builder(SKID):
mySet = DNIN_set(np.array(MyCustomDNNeuronClass.builder(SKID)))
mySet.myDN = GetAnnotationsByID.getDNType(SKID)
mySet.myDNskid = SKID
return mySet