Merge pull request #329 from ttngu207/datajoint_pipeline

update: more robust check for subjects in a given block
SainsburyWellcomeCentre · Feb 7, 2024 · a6725ad · a6725ad
2 parents e9c4eab + d2a51e7
commit a6725ad
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Showing 4 changed files with 18 additions and 8 deletions.
diff --git a/aeon/dj_pipeline/analysis/block_analysis.py b/aeon/dj_pipeline/analysis/block_analysis.py
@@ -156,9 +156,20 @@ def make(self, key):
             )
 
         # Subject data
-        subject_names = set(
-            (tracking.SLEAPTracking.PoseIdentity & key & chunk_restriction).fetch("identity_name")
-        )
+        # Get all unique subjects that visited the environment over the entire exp;
+        # For each subject, see 'type' of visit most recent to start of block
+        # If "Exit", this animal was not in the block.
+        subject_visits_df = fetch_stream(
+            acquisition.Environment.SubjectVisits
+            & key
+            & f'chunk_start <= "{chunk_keys[-1]["chunk_start"]}"'
+        )[:block_start]
+        subject_visits_df = subject_visits_df[subject_visits_df.region == "Environment"]
+        subject_names = []
+        for subject_name in set(subject_visits_df.id):
+            _df = subject_visits_df[subject_visits_df.id == subject_name]
+            if _df.type[-1] != "Exit":
+                subject_names.append(subject_name)
         for subject_name in subject_names:
             # positions - query for CameraTop, identity_name matches subject_name,
             pos_query = (

diff --git a/...s/notebooks/social01_block_analysis.ipynb → ...s/social_experiments_block_analysis.ipynb b/...s/notebooks/social01_block_analysis.ipynb → ...s/social_experiments_block_analysis.ipynb
@@ -14,8 +14,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## Create VirtualModule to access `aeon_test_analysis` schema\n",
-    "Currently, the analysis is on `aeon_test_`, will move to `aeon_` soon (once ready for production)"
+    "## Create VirtualModule to access `aeon_block_analysis` schema"
    ],
    "metadata": {
     "collapsed": false,
@@ -29,7 +28,7 @@
    "execution_count": null,
    "outputs": [],
    "source": [
-    "analysis_vm = dj.create_virtual_module('aeon_test_analysis', 'aeon_test_analysis')"
+    "analysis_vm = dj.create_virtual_module('aeon_block_analysis', 'aeon_block_analysis')"
    ],
    "metadata": {
     "collapsed": false,

diff --git a/aeon/dj_pipeline/webapps/sciviz/specsheet.yaml b/aeon/dj_pipeline/webapps/sciviz/specsheet.yaml
@@ -686,7 +686,7 @@ SciViz:
               dj_query: >
                 def dj_query(aeon_archived_exp02_acquisition):
                     acquisition = aeon_archived_exp02_acquisition
-                    return {'query': aeon_acquisition.Experiment(), 'fetch_args': ['experiment_name']}
+                    return {'query': acquisition.Experiment(), 'fetch_args': ['experiment_name']}
             camera_dropdown:
               x: 0
               y: 1

diff --git a/aeon/schema/social.py b/aeon/schema/social.py
@@ -50,7 +50,7 @@
 
 # SubjectVisits
 subject_visits_b = lambda pattern: {
-    "SubjectVisits": reader.Csv(f"{pattern}_SubjectVisit_*", ["id", "type", "region"])
+    "SubjectVisits": reader.Csv(f"{pattern}_SubjectVisits_*", ["id", "type", "region"])
 }
 
 # SubjectWeight