def getLookUpTable():
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
#object_ids = [134]
#created_by = [134]
#annotated_with = [863792]
headers = config.CatmaidApiTokenAuth(token)
allAnnotations = requests.get(
'https://neuropil.janelia.org/tracing/fafb/v14-seg-li-190805.0/{}/annotations/'
.format(project_id),
auth=auth)
someData = json.loads(allAnnotations.content.decode('utf-8'))
#print(someData)
AnnotationLookUpTable = {}
AnnotationLookUpTable = someData["annotations"]
myLookUpTable = {}
for d in AnnotationLookUpTable:
myLookUpTable[d['id']] = d['name']
return myLookUpTable
def correctAnnotations(self):
mySet = NeuronObjectData.removeSomaless(self)
rightHem = []
leftHem = []
for item in mySet:
if item.soma[0] < 500000:
rightHem.append(item.skeletonID + 1)
elif item.soma[0] > 550000:
leftHem.append(item.skeletonID + 1)
responseOne = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/remove'
.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={
'entity_ids': rightHem,
'annotation_ids': [1223085]
})
responseOne = json.loads(responseOne.content)
print(responseOne)
responseTwo = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14-seg-li-190805.0/{}/annotations/remove'
.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={
'entity_ids': leftHem,
'annotation_ids': [1167304]
})
responseTwo = json.loads(responseTwo.content)
print(responseTwo)
return
def GetAnnotations():
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
object_ids = [134]
created_by = [134]
annotated_with = [863792]
headers = config.CatmaidApiTokenAuth(token)
#print(str(headers))
payload = {
#'skeleton_ids': [
0
#],
#'type': "",
#'name': "",
#"id": 0
#'annotated_with': '8863792'
}
response = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/query-targets'
.format(project_id),
auth=auth,
data={'annotated_with': 863792})
return response
def getLookUpTable():
import requests
import json
import itertools
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
object_ids = [134]
created_by = [134]
annotated_with = [863792]
headers = config.CatmaidApiTokenAuth(token)
allAnnotations = requests.get(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/'.format(
project_id),
auth=auth)
someData = json.loads(allAnnotations.content)
#print(someData)
AnnotationLookUpTable = {}
AnnotationLookUpTable = someData["annotations"]
myLookUpTable = {}
for d in AnnotationLookUpTable:
myLookUpTable[d['id']] = d['name']
return myLookUpTable
def addAnnotation(self, newAnnotation, addToSkeletons=True, metaAnnotations=None):
"""
:param newAnnotation: array of string - to be added to catmaid annotation of neurons (if looking for bulk annotations: set from GFIN objects
:param addToSkeletons: default is true - if false, will create annotation and annotate it with a meta_annotation
:param metaAnnotations: default is none - should be array[string] if desired
:return: print out: success or error (with error message), annotations added (name and id), neuron ids, and list of any new annotations
"""
if addToSkeletons is True:
mySkids = []
for item in self:
mySkids.append(item.skeletonID)
response = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/add'.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={'skeleton_ids': mySkids, 'annotations': newAnnotation}
)
else:
response = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/add'.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={'annotations': newAnnotation, 'meta_annotations': metaAnnotations}
)
myResults = json.loads(response.content)
print(myResults)
return
def setAnnotationLookUpTable(SKIDS):
response = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/forskeletons'
.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={'skeleton_ids[0]': SKIDS})
myData = json.loads(response.content)
myAnnotations = myData['annotations']
a = []
for i in myAnnotations:
a.append(myAnnotations[i])
return a
def addAnnotation(neuron, newAnnotation, addToSkeletons=True):
if addToSkeletons is True:
mySkids = [neuron]
response = requests.post(
'https://neuropil.janelia.org/tracing/fafb/v14-seg-li-190805.0/{}/annotations/add'
.format(project_id),
auth=config.CatmaidApiTokenAuth(token),
data={
'skeleton_ids': mySkids,
'annotations': newAnnotation
})
myResults = json.loads(response.content)
print(myResults)
return
import config
import json
import requests
import itertools
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
#dn_autoseg_exploration
#annotation = 217283624
#descending neuron
#annotation = 2998068
#Putative_Ascending
#annotation = 217284386
#Ascending Neuron
#annotation = 3552044
#Old GetLookUpTable
# coding: utf-8
# returns dictionary containing a lookup table with int(annotation id) as key and annotation string/name as value
def getLookUpTable():
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
#object_ids = [134]
'''
Emily Tenshaw & Jason Polsky
CAT-Card
Updated 12/1/2020
Pulls annotation data for GF Input neurons
Unsure why needed - mostly written by Jason
'''
import config
import requests
import json
import GetAnnotationsRemoveExtraneousInfo as GARI
token = config.token
auth = config.CatmaidApiTokenAuth(token)
project_id = config.project_id
object_ids = [134]
created_by = [134]
annotated_with = [863792]
headers = config.CatmaidApiTokenAuth(token)
# returns dictionary containing a lookup table with int(annotation id) as key and annotation string/name as value
def getLookUpTable():
allAnnotations = requests.get(
'https://neuropil.janelia.org/tracing/fafb/v14/{}/annotations/'.format(
project_id),
auth=auth)