partner_treenode_id in catmaid_get_connector_table() is own skid

[mmc46]

partner_treenode_id in catmaid_get_connector_table() is the treenode id of the own skid, not the partner neuron, as the name suggests.

test_table = catmaid_get_connector_table(skids = 38885, direction = "outgoing")

str(test_table)
'data.frame':	2090 obs. of  10 variables:
 $ connector_id       : int  10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 ...
 $ skid               : int  38885 38885 38885 38885 38885 38885 38885 38885 38885 38885 ...
 $ x                  : num  391093 391093 391093 391093 391093 ...
 $ y                  : num  126860 126860 126860 126860 126860 ...
 $ z                  : num  176800 176800 176800 176800 176800 ...
 $ confidence         : int  5 5 5 5 5 5 5 5 5 5 ...
 $ user_id            : int  117 117 117 117 117 117 117 117 117 117 ...
 $ partner_treenode_id: int  10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 ...
 $ last_modified      : chr  "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" ...
 $ partner_skid       : int  8414264 9040302 1765477 3969059 3968536 6151467 3967642 3967814 1703725 8618038 ...

node_detail = catmaid_get_treenodes_detail(unique(test_table$partner_treenode_id))
str(node_detail)
'data.frame':	308 obs. of  10 variables:
 $ treenode_id : int  10161599 3201630 6286558 10613576 10613581 6281239 10641290 6291076 3203539 374997 ...
 $ parent_id   : int  10161616 3201613 6286557 6286558 10613576 6281238 6280932 6291072 6281180 374998 ...
 $ x           : num  390993 390742 342614 342700 343110 ...
 $ y           : num  126726 127087 152881 153034 153534 ...
 $ z           : num  176840 177440 190240 190440 190680 ...
 $ confidence  : int  5 5 5 5 5 5 5 5 5 5 ...
 $ radius      : num  -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
 $ skid        : int  38885 38885 38885 38885 38885 38885 38885 38885 38885 38885 ...
 $ edition_time: num  1.49e+09 1.46e+09 1.48e+09 1.49e+09 1.49e+09 ...
 $ user_id     : int  117 61 94 117 117 94 61 94 61 11 ...

unique(node_detail$skid)
[1] 38885

[jefferis]

Thanks. Can you check what happens when your looking in the other direction?

…

Sent from my iPhone

On 8 Apr 2019, at 17:57, Marta Costa ***@***.***> wrote: partner_treenode_id in catmaid_get_connector_table() is the treenode id of the own skid, not the partner neuron, as the name suggests. test_table = catmaid_get_connector_table(skids = 38885, direction = "outgoing") str(test_table) 'data.frame': 2090 obs. of 10 variables: $ connector_id : int 10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 10161597 ... $ skid : int 38885 38885 38885 38885 38885 38885 38885 38885 38885 38885 ... $ x : num 391093 391093 391093 391093 391093 ... $ y : num 126860 126860 126860 126860 126860 ... $ z : num 176800 176800 176800 176800 176800 ... $ confidence : int 5 5 5 5 5 5 5 5 5 5 ... $ user_id : int 117 117 117 117 117 117 117 117 117 117 ... $ partner_treenode_id: int 10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 10161599 ... $ last_modified : chr "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" "2017-03-27T11:47:20.733479+00:00" ... $ partner_skid : int 8414264 9040302 1765477 3969059 3968536 6151467 3967642 3967814 1703725 8618038 ... node_detail = catmaid_get_treenodes_detail(unique(test_table$partner_treenode_id)) str(node_detail) 'data.frame': 308 obs. of 10 variables: $ treenode_id : int 10161599 3201630 6286558 10613576 10613581 6281239 10641290 6291076 3203539 374997 ... $ parent_id : int 10161616 3201613 6286557 6286558 10613576 6281238 6280932 6291072 6281180 374998 ... $ x : num 390993 390742 342614 342700 343110 ... $ y : num 126726 127087 152881 153034 153534 ... $ z : num 176840 177440 190240 190440 190680 ... $ confidence : int 5 5 5 5 5 5 5 5 5 5 ... $ radius : num -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ... $ skid : int 38885 38885 38885 38885 38885 38885 38885 38885 38885 38885 ... $ edition_time: num 1.49e+09 1.46e+09 1.48e+09 1.49e+09 1.49e+09 ... $ user_id : int 117 61 94 117 117 94 61 94 61 11 ... unique(node_detail$skid) [1] 38885``` — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[mmc46]

Incoming?

test_table_inc = catmaid_get_connector_table(skids = 38885, direction = "incoming")
node_detail_inc = catmaid_get_treenodes_detail(unique(test_table_inc$partner_treenode_id))
unique(node_detail_inc$skid)
[1] 38885

[jefferis]

Thanks for confirming that the tree node ids always relate to the query skeleton not to the postsynaptic side of the connector. This was a misreading of the catmaid docs at:

https://github.com/catmaid/CATMAID/blob/fecb9430c106ecd3a9975df7c195847938491799/django/applications/catmaid/control/connector.py#L386-L396.

I guess I will have to change the column name from partner_treenode_id to treenode_id and clarify docs.