[question] How to delete all the label indices and label map?

[xiuliren]

I ingested some label indices that are not correct. Creating a new repo and reingest the supervoxels will take a long time. Is that possible to delete all the label indices and label map?

[xiuliren]

I found a related function here, but it only delete some bodies rather than all of them.

neuclease/neuclease/dvid/labelmap/_labelindex.py

Line 209 in 22c3c5d

def delete_labelindices(server, uuid, instance, bodies, *, session=None):

[xiuliren]

according to the comments, I can post an empty label index to delete all of them?

label_index = dvid.LabelIndex()
label_indices = dvid.LabelIndices()
label_indices.indices.extend([label_index])
dvid.post_labelindices(server, uuid, "labels", label_indices)

I just tested this code, this do not work, and I got errors like this:

  File "/mnt/home/jwu/anaconda3/envs/wasp/lib/python3.7/site-packages/requests/models.p[0/801]
e 941, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: http://dvid_server:8000/api/node/941057b7c3fe4318815e6e9f1f6140a4/labels/indices?u=jwu&app=neuclea
se

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "delete_label_indices.py", line 12, in <module>
    dvid.post_labelindices(server, target_uuid, "labels", label_indices)
  File "/mnt/home/jwu/anaconda3/envs/wasp/lib/python3.7/site-packages/neuclease/dvid/_dvid.py"
, line 142, in wrapper
    raise new_ex from ex
requests.exceptions.HTTPError: Error accessing POST http://dvid_server:800
0/api/node/941057b7c3fe4318815e6e9f1f6140a4/labels/indices?u=jwu&app=neuclease
400 Client Error: Bad Request for url: dvid_server:8000/api/node/94
1057b7c3fe4318815e6e9f1f6140a4/labels/indices?u=jwu&app=neuclease
index 0 had label 0, which is a reserved label (/api/node/941057b7c3fe4318815e6e9f1f6140a4/lab
els/indices).

[stuarteberg]

according to the comments, I can post an empty label index to delete all of them?

No, you can only delete indices for an explicitly provided list of bodies, as is done in delete_labelindices().

As far as I can tell, the REST API doesn't offer a way to delete all label indices for the whole instance.

You might want to open a new issue on the dvid repository to request that feature.

[xiuliren]

I just found a related issue in dvid repo:
janelia-flyem/dvid#341

[xiuliren]

@stuarteberg I am trying to use the delete_labelindices, but just found that this is added recently and is not in the conda environment. Could you please help to update the conda environment?

[xiuliren]

I manually added this function to my local nuclease code and works for now. This is pretty hacky though.

[stuarteberg]

This ought to work:

conda install -c flyem-forge 'neuclease>=0.4.post429'

[xiuliren]

thank you!