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adding basic queries
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@Robbie1977
Robbie1977 committed Sep 5, 2024
1 parent 49c1b3c commit bc83611
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Showing 3 changed files with 163 additions and 1 deletion.
3 changes: 3 additions & 0 deletions src/vfb_connect/cross_server_tools.py
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Expand Up @@ -862,6 +862,9 @@ def xref_2_vfb_id(self, acc=None, db='', id_type='', reverse_return=False, retur
if return_just_ids and not reverse_return:
id_list = []
for id in acc:
if id not in result.keys():
print(f"No match found for {id}")
continue
id_list.append(result[id][0]['vfb_id']) # This takes the first match only
if len(result[id]) > 1:
print(f"Multiple matches found for {id}: {result[id]}")
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13 changes: 13 additions & 0 deletions src/vfb_connect/schema/test/vfb_term_test.py
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Expand Up @@ -502,5 +502,18 @@ def test_vfbterm_xref(self):
print(self.vfb.xref_2_vfb_id(term.xref_id, return_just_ids=True, verbose=True))
self.assertEqual(self.vfb.xref_2_vfb_id(term.xref_id, return_just_ids=True)[0], term.id)

def test_load_synapes(self):
term = self.vfb.term('VFB_jrchk6dr')
print("got term ", term)
term.load_skeleton(template='JRC2018Unisex')
con = term.load_skeleton_synaptic_connections().to_dict('records')
print(con[0])
self.assertGreater(len(con),10)
term = self.vfb.term('VFB_00102gjr')
print("got term ", term)
con = term.load_skeleton_synaptic_connections().to_dict('records')
print(con[0])
self.assertGreater(len(con),10)

if __name__ == "__main__":
unittest.main()
148 changes: 147 additions & 1 deletion src/vfb_connect/schema/vfb_term.py
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Expand Up @@ -12,6 +12,9 @@

import webbrowser

NEUPRINT_TOKEN = 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6InZmYndvcmtzaG9wLm5ldXJvZmx5MjAyMEBnbWFpbC5jb20iLCJsZXZlbCI6Im5vYXV0aCIsImltYWdlLXVybCI6Imh0dHBzOi8vbGg2Lmdvb2dsZXVzZXJjb250ZW50LmNvbS8tWXFDN21NRXd3TlEvQUFBQUFBQUFBQUkvQUFBQUFBQUFBQUEvQU1adXVjbU5zaXhXZDRhM0VyTTQ0ODBMa2IzNDdvUlpfUS9zOTYtYy9waG90by5qcGc_c3o9NTA_c3o9NTAiLCJleHAiOjE3OTQwOTE4ODd9.ceg4mrj2o-aOhK0NHNGmBacg8R34PBPoLBwhCo4uOCQ'
CATMAID_TOKEN = None

neuron_containing_anatomy_tags = [
"Painted_domain",
"Synaptic_neuropil_domain",
Expand Down Expand Up @@ -2684,18 +2687,161 @@ def load_volume(self, template=None, verbose=False, query_by_label=True, force_r
self._volume.label = self.name
self._volume.id = self.id

def _extract_url_parameter(self, url, parameter='dataset', verbose=False):
"""
Extract the value of a query parameter from a URL.
"""
from urllib.parse import urlparse, parse_qs
# Parse the URL
parsed_url = urlparse(url)
print("Parsed URL: ", parsed_url) if verbose else None
# Extract the query parameters as a dictionary
query_params = parse_qs(parsed_url.query)
print("Query Params: ", query_params) if verbose else None
# Get the value of the 'dataset' parameter
param_value = query_params.get(parameter)
print("Param Value: ", param_value) if verbose else None
# Return the first value if the parameter exists
if param_value:
print(f"Found {parameter} parameter {param_value} of type {type(param_value)}") if verbose else None
if isinstance(param_value, list):
print("Returning first value: ", param_value[0]) if verbose else None
return param_value[0]
if isinstance(param_value, str):
print("Returning value: ", param_value) if verbose else None
return param_value
return None

def load_skeleton_synaptic_connections(self, template=None, verbose=False):
"""
Load the synaptic connections for the neuron's skeleton.
"""
import flybrains
import navis
from navis import transforms
template = self.get_default_template(template=template)
if not self._skeleton or self._skeleton_template != template:
print(f"No skeleton loaded yet for {self.name} so loading...") if verbose else None
template = self.get_default_template(template=template)
self.load_skeleton(template=template, verbose=verbose)
if self._skeleton:
print(f"Loading synaptic connections for {self.name}...") if verbose else None
xref = self.xref
if 'catmaid' in self.xref_url:
print("Loading synaptic connections from CATMAID...") if verbose else None
skid = int(self.xref_id.split(':')[-1])
db = self.xref_id.split(':')[0]
print("CATMAID skeleton ID: ", skid) if verbose else None
server = "https://" + self.xref_url.split('://')[-1].split('/')[0]
print("CATMAID Server: ", server) if verbose else None
pid = self._extract_url_parameter(self.xref_url, parameter='pid', verbose=verbose)
import pymaid
catmaid = pymaid.connect_catmaid(server=server, project_id=pid, api_token=CATMAID_TOKEN, max_threads=10)
connectors = pymaid.get_connectors([skid],remote_instance=catmaid)
print("Connectors: ", connectors) if verbose else None
# Check available transforms
available_transforms = transforms.registry.summary()
print("Available transforms: ", available_transforms) if verbose else None
target = None
source = None
name = db.split('_')[-1].upper()
if not 'L1EM' in name:
if name in available_transforms.source.to_list():
source = name
if name.lower() in available_transforms.source.to_list():
source = name.lower()
if self.vfb.lookup_name(self._skeleton_template) in available_transforms.target.to_list():
target = self._skeleton_template
if not target or not source:
print("falling back to manual transforms...") if verbose else None
if 'fafb' in name.lower():
source = 'FAFB'
target = 'JRC2018U'
JRC2018U = flybrains.JRC2018U
FAFB14 = flybrains.FAFB
elif 'fanc' in name.lower():
source = 'FANC'
target = 'JRC2018U'
FANC = flybrains.FANC
JRC2018U = flybrains.JRC2018U
else:
print("No transform available for ", db)
print("Transforming from ", source, " to ", target) if verbose else None
aligned_connectors = navis.xform_brain(connectors, source=source, target=target)
else:
aligned_connectors = connectors
print("FULL FEATURE NOT YET IMPLEMENTED")
return aligned_connectors

if 'neuprint' in self.xref_url:
print("Loading synaptic connections from neuprint...") if verbose else None
from navis.interfaces.neuprint import fetch_synapses, Client


bodyId = int(self.xref_id.split(':')[-1])
db = self.xref_id.split(':')[0]
print("Neuprint bodyId: ", bodyId) if verbose else None
server = self.xref_url.split('://')[-1].split('/')[0]
print("Neuprint Server: ", server) if verbose else None
ds = self._extract_url_parameter(self.xref_url, parameter='dataset', verbose=verbose)
print("Neuprint Dataset: ", ds) if verbose else None
client = Client(server=server, dataset=ds, token=NEUPRINT_TOKEN)
connectors = fetch_synapses(bodyId, client=client)
print("Connectors: ", connectors) if verbose else None
# Check available transforms
available_transforms = transforms.registry.summary()
print("Available transforms: ", available_transforms) if verbose else None
target = None
source = None
if '%3A' in ds:
ds = ds.replace('%3A', ':')
name = ds.split(':')[0].upper()
if name in available_transforms.source.to_list():
source = name
if name.lower() in available_transforms.source.to_list():
source = name.lower()
if self.vfb.lookup_name(self._skeleton_template) in available_transforms.target.to_list():
target = self._skeleton_template
if not target or not source:
print("falling back to manual transforms...") if verbose else None
if 'manc' in name.lower():
source = 'MANC'
target = 'JRCVNC2018U'
elif 'hemibrain' in name.lower():
source = 'hemibrain'
target = 'JRC2018U'
elif 'optic-lobe' in name.lower():
source = 'JRCFIB2022Mraw'
target = 'JRC2018U'
else:
print("No transform available for ", ds)
print("Transforming from ", source, " to ", target) if verbose else None
aligned_connectors = navis.xform_brain(connectors, source=source, target=target)

print("Aligned Connectors before: ", aligned_connectors) if verbose else None
if len(aligned_connectors) > 0:
# Adding 'connector_id' from index if not already present
if 'connector_id' not in aligned_connectors.columns:
aligned_connectors['connector_id'] = aligned_connectors.index

# Convert 'bodyId' to 'id' using vfb.xref_2_vfb_id method
acc = aligned_connectors.bodyId.to_list()
print("Body IDs: ", acc) if verbose else None
print(f"type(acc): {type(acc)}") if verbose else None
print(f"acc[0]: {type(acc[0])}") if verbose else None
print("DB: ", db) if verbose else None
vfb_ids = self.vfb.xref_2_vfb_id(acc=acc, db=db, return_just_ids=True, verbose=verbose)
print("VFB IDs: ", vfb_ids) if verbose else None
if 'id' not in aligned_connectors.columns and vfb_ids:
print("Adding 'id' column to aligned_connectors") if verbose else None
aligned_connectors['id'] = vfb_ids
print("Aligned Connectors after: ", aligned_connectors) if verbose else None
print("FULL FEATURE NOT YET IMPLEMENTED")
return aligned_connectors
self._skeleton._set_connectors(aligned_connectors)
print("Connectors set for ", self.name) if verbose else None
print(self._skeleton.connectors) if verbose else None
return

# TODO: Load synaptic connections
# see https://github.com/navis-org/navis/blob/1eead062710af6adabc9e9c40196ad7be029cb52/navis/interfaces/neuprint.py#L491
print("FEATURE NOT YET IMPLEMENTED")
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