Merge remote-tracking branch 'upstream' into nearest_node

navis-org · Oct 27, 2023 · c6219f9 · c6219f9
2 parents f1f45b8 + 2a452c3
commit c6219f9
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diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -48,6 +48,19 @@ Functions related to searching for neurons and fetching their 3D skeletons:
     pymaid.get_skeleton_change
     pymaid.get_skeleton_ids
 
+
+Neuron labels
+^^^^^^^^^^^^^
+
+.. autosummary::
+    :toctree: generated/
+
+    pymaid.neuron_label.NeuronLabeller
+    pymaid.neuron_label.SkeletonId
+    pymaid.neuron_label.NeuronName
+    pymaid.neuron_label.Annotations
+    pymaid.neuron_label.ThinNeuron
+
 Annotations
 -----------
 Functions to fetch annotations:

diff --git a/docs/source/whats_new.rst b/docs/source/whats_new.rst
@@ -10,6 +10,10 @@ What's new?
    * - Version
      - Date
      -
+   * - Next
+     - n/a
+     - - :class:`pymaid.neuron_label.NeuronLabeller` added for labelling neurons
+         like in the CATMAID frontend.
    * - 2.4.0
      - 27/05/23
      - - :func:`pymaid.get_annotation_graph` deprecated in favour of the new

diff --git a/pymaid/fetch/annotations.py b/pymaid/fetch/annotations.py
@@ -82,6 +82,19 @@ def filter_by_query(
     return filt
 
 
+@cache.wipe_and_retry
+def get_annotation_table(remote_instance=None):
+
+    remote_instance = utils._eval_remote_instance(remote_instance)
+
+    logger.debug("Retrieving list of annotations...")
+
+    remote_annotation_list_url = remote_instance._get_annotation_list()
+    an_list = remote_instance.fetch(remote_annotation_list_url)
+
+    return pd.DataFrame.from_records(an_list["annotations"])
+
+
 @cache.wipe_and_retry
 def get_annotation_id(
     annotations, allow_partial=False, raise_not_found=True, remote_instance=None
@@ -106,6 +119,7 @@ def get_annotation_id(
                         ``{'annotation_name': 'annotation_id', ...}``
 
     """
+    an_list = get_annotation_table()
     remote_instance = utils._eval_remote_instance(remote_instance)
 
     logger.debug("Retrieving list of annotations...")