fixing issue if node-ids are not continguous

bmtk/simulator/bionet/bionetwork.py

@@ -133,7 +133,7 @@ def local_gids(self):
         return list(self._rank_node_gids.keys())
 
     def add_nodes(self, node_population):
-        self._gid_pool.add_pool(node_population.name, node_population.n_nodes())
+        self._gid_pool.add_pool(node_population.name, node_population.node_ids)
         super(BioNetwork, self).add_nodes(node_population)
 
     def get_virtual_cells(self, population, node_id, spike_trains, spikes_generator=None, sim=None):

bmtk/simulator/bionet/gids.py

@@ -14,14 +14,17 @@ def __init__(self):
         self._offsets = np.array([0], dtype=np.uint64)
         self._offset2pool_map = {}
 
-    def add_pool(self, name, n_nodes):
+    def add_pool(self, name, node_ids):
+        n_nodes = np.max(node_ids) + 1
         offset_index = len(self._offsets)
+
         self._offset2pool_map[offset_index] = name
         self._offsets = np.append(self._offsets, np.array([self._accumulated_offset + n_nodes], dtype=np.uint64))
 
         self._pool_offsets[name] = self._accumulated_offset
         self._accumulated_offset += n_nodes
 
+
     def get_gid(self, name, node_id):
         return int(self._pool_offsets[name] + node_id)
 

bmtk/simulator/core/sonata_reader/network_reader.py

@@ -151,6 +151,10 @@ def get_nodes(self):
                 for node in node_group:
                     yield node_adaptor.get_node(node)
 
+    @property
+    def node_ids(self):
+        return self._node_pop.node_ids
+
 
 class SonataEdges(EdgesReader):
     def __init__(self, edge_population, adaptor):

tests/simulator/bionet/test_gids.py

@@ -1,14 +1,16 @@
 import pytest
+import numpy as np
+
 from .conftest import *
 
 
 @pytest.mark.skipif(not nrn_installed, reason='NEURON is not installed')
 def test_gid_pool():
     gid_map = GidPool()
-    gid_map.add_pool(name='p1', n_nodes=1000)
-    gid_map.add_pool(name='p2', n_nodes=10000)
-    gid_map.add_pool(name='p3', n_nodes=1)
-    gid_map.add_pool(name='p4', n_nodes=500)
+    gid_map.add_pool(name='p1', node_ids=list(range(1000)))
+    gid_map.add_pool(name='p2', node_ids=list(range(10000)))
+    gid_map.add_pool(name='p3', node_ids=[0])
+    gid_map.add_pool(name='p4', node_ids=np.arange(500, dtype=int))
 
     assert(gid_map.get_gid(name='p1', node_id=0) == 0)
     assert(gid_map.get_pool_id(0) == (0, 'p1'))