When generating the mouse flatmap with SCKAN neuron knowledge, mapmaker crashes with a KeyError message. The error can be found below. The files that produce this message are at the head of the keerans_changes branch, also found on the commit a36841b. The commit of files that will reproduce this issue has been tagged with v2.1.
the command line used to run mapmaker was:
python runmaker.py --source ../flatmap-sources/new-mouse/manifest.json --output ../flatmaps --verbose --background-tiles --debug --log log-files/LOG_410 --authoring
the error produced is:
Traceback (most recent call last): File "/home/keeran/flatmap-maker/mapmaker/__main__.py", line 100, in main mapmaker.make() File "/home/keeran/flatmap-maker/mapmaker/maker.py", line 260, in make self.__flatmap.close() File "/home/keeran/flatmap-maker/mapmaker/flatmap/__init__.py", line 159, in close self.__resolve_connectivity() File "/home/keeran/flatmap-maker/mapmaker/flatmap/__init__.py", line 334, in __resolve_connectivity self.__map_properties.generate_connectivity(self.__feature_map) File "/home/keeran/flatmap-maker/mapmaker/properties/__init__.py", line 133, in generate_connectivity self.__pathways.generate_connectivity(self.__networks.values()) File "/home/keeran/flatmap-maker/mapmaker/properties/pathways.py", line 681, in generate_connectivity self.__route_network_connectivity(network) File "/home/keeran/flatmap-maker/mapmaker/properties/pathways.py", line 617, in __route_network_connectivity route_graphs[path.id] = network.route_graph_from_path(path) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 671, in route_graph_from_path return self.__route_graph_from_connectivity(path) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 1112, in __route_graph_from_connectivity terminal_graphs[terminal_node] = self.__terminal_graph(G, terminal_node, seen_terminals) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 938, in __terminal_graph walk_paths_from_node(start_node, start_dict) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 929, in walk_paths_from_node if 'upstream' in terminal_network.nodes[last_feature]: File "/home/keeran/.cache/pypoetry/virtualenvs/mapmaker-NDtPvMnW-py3.8/lib/python3.8/site-packages/networkx/classes/reportviews.py", line 194, in __getitem__ return self._nodes[n] KeyError: 'spinal_10-1'
note that this error only comes when the ApiNATOMY/SCKAN models have been added to the manifest. without this knowledge, the map does generate, but with plenty of error messages.
When generating the mouse flatmap with SCKAN neuron knowledge, mapmaker crashes with a KeyError message. The error can be found below. The files that produce this message are at the head of the
keerans_changesbranch, also found on the commit a36841b. The commit of files that will reproduce this issue has been tagged withv2.1.the command line used to run mapmaker was:
python runmaker.py --source ../flatmap-sources/new-mouse/manifest.json --output ../flatmaps --verbose --background-tiles --debug --log log-files/LOG_410 --authoringthe error produced is:
Traceback (most recent call last): File "/home/keeran/flatmap-maker/mapmaker/__main__.py", line 100, in main mapmaker.make() File "/home/keeran/flatmap-maker/mapmaker/maker.py", line 260, in make self.__flatmap.close() File "/home/keeran/flatmap-maker/mapmaker/flatmap/__init__.py", line 159, in close self.__resolve_connectivity() File "/home/keeran/flatmap-maker/mapmaker/flatmap/__init__.py", line 334, in __resolve_connectivity self.__map_properties.generate_connectivity(self.__feature_map) File "/home/keeran/flatmap-maker/mapmaker/properties/__init__.py", line 133, in generate_connectivity self.__pathways.generate_connectivity(self.__networks.values()) File "/home/keeran/flatmap-maker/mapmaker/properties/pathways.py", line 681, in generate_connectivity self.__route_network_connectivity(network) File "/home/keeran/flatmap-maker/mapmaker/properties/pathways.py", line 617, in __route_network_connectivity route_graphs[path.id] = network.route_graph_from_path(path) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 671, in route_graph_from_path return self.__route_graph_from_connectivity(path) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 1112, in __route_graph_from_connectivity terminal_graphs[terminal_node] = self.__terminal_graph(G, terminal_node, seen_terminals) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 938, in __terminal_graph walk_paths_from_node(start_node, start_dict) File "/home/keeran/flatmap-maker/mapmaker/routing/__init__.py", line 929, in walk_paths_from_node if 'upstream' in terminal_network.nodes[last_feature]: File "/home/keeran/.cache/pypoetry/virtualenvs/mapmaker-NDtPvMnW-py3.8/lib/python3.8/site-packages/networkx/classes/reportviews.py", line 194, in __getitem__ return self._nodes[n] KeyError: 'spinal_10-1'note that this error only comes when the ApiNATOMY/SCKAN models have been added to the manifest. without this knowledge, the map does generate, but with plenty of error messages.