Merge pull request #295 from CAVEconnectome/skeleton_dev

SkeletonClient.get_skeleton() 'dict' output format now offers numpy a…

caveclient/skeletonservice.py

@@ -585,7 +585,20 @@ def get_skeleton(
             return sk_json
         if endpoint_format == "flatdict":
             assert self._server_version >= Version("0.6.0")
-            return SkeletonClient.decompressBytesToDict(response.content)
+            sk_json = SkeletonClient.decompressBytesToDict(response.content)
+            if "edges" in sk_json.keys():
+                sk_json["edges"] = np.array(sk_json["edges"])
+            if "mesh_to_skel_map" in sk_json.keys():
+                sk_json["mesh_to_skel_map"] = np.array(sk_json["mesh_to_skel_map"])
+            if "vertices" in sk_json.keys():
+                sk_json["vertices"] = np.array(sk_json["vertices"])
+            if "lvl2_ids" in sk_json.keys():
+                sk_json["lvl2_ids"] = np.array(sk_json["lvl2_ids"])
+            if "radius" in sk_json.keys():
+                sk_json["radius"] = np.array(sk_json["radius"])
+            if "compartment" in sk_json.keys():
+                sk_json["compartment"] = np.array(sk_json["compartment"])
+            return sk_json
         if endpoint_format == "swccompressed":
             file_content = SkeletonClient.decompressBytesToString(response.content)
 

pyproject.toml

@@ -56,7 +56,14 @@ docs = [
     "pymdown-extensions",
 ]
 lint = ["ruff"]
-test = ["pytest", "pytest-cov", "pytest-env", "pytest-mock", "responses"]
+test = [
+    "deepdiff>=8.1.1",
+    "pytest",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-mock",
+    "responses",
+]
 
 [tool.bumpversion]
 allow_dirty = false

tests/test_skeletons.py

@@ -1,3 +1,7 @@
+import copy
+
+import deepdiff
+import numpy as np
 import responses
 from packaging.version import Version
 
@@ -184,8 +188,8 @@ def test_get_skeleton(self, myclient, mocker):
             },
             "edges": [
                 [
-                0,
-                1
+                1,
+                0
                 ],
             ],
             "mesh_to_skel_map": [
@@ -195,25 +199,32 @@ def test_get_skeleton(self, myclient, mocker):
             "root": 0,
             "vertices": [
                 [
-                971832,
-                842176,
-                906480
+                1054848., 827272., 601920.
                 ],
                 [
-                972568,
-                842920,
-                905920
+                1054856., 827192., 601920.
                 ],
             ],
             "compartment": [
                 3,
                 3
             ],
             "radius": [
-                237.11754897434668,
-                237.11754897434668
+                203.6853403, 203.6853403
+            ],
+            'lvl2_ids': [
+                173056326983745934, 173126695727923522
             ]
         }
+
+        sk_result = copy.deepcopy(sk)
+        sk_result["edges"] = np.array(sk_result["edges"])
+        sk_result["mesh_to_skel_map"] = np.array(sk_result["mesh_to_skel_map"])
+        sk_result["vertices"] = np.array(sk_result["vertices"])
+        sk_result["lvl2_ids"] = np.array(sk_result["lvl2_ids"])
+        sk_result["radius"] = np.array(sk_result["radius"])
+        sk_result["compartment"] = np.array(sk_result["compartment"])
+
         dict_bytes = SkeletonClient.compressDictToBytes(sk)
         responses.add(responses.GET, url=metadata_url, body=dict_bytes, status=200)
 
@@ -223,4 +234,4 @@ def test_get_skeleton(self, myclient, mocker):
         )
 
         result = myclient.skeleton.get_skeleton(0, None, 4, "dict")
-        assert result == sk
+        assert not deepdiff.DeepDiff(result, sk_result)