Merge pull request #165 from softmatterlab/jp/magik-update

Update graph generators

Author: BenjaminMidtvedt

deeptrack/models/gnns/graphs.py

@@ -16,6 +16,7 @@ def GetEdge(
     end: int,
     radius: int,
     parenthood: pd.DataFrame,
+    columns = [],
     **kwargs,
 ):
     """
@@ -79,7 +80,7 @@ def GetEdge(
         edges.append(combdf)
     # Concatenate the dataframes in a single
     # dataframe for the whole set of edges
-    edgedf = pd.concat(edges)
+    edgedf = pd.concat(edges) if len(edges) > 0 else pd.DataFrame(columns=columns)
 
     # Merge columns contaning the labels into a single column
     # of numpy arrays, i.e., label = [label_x, label_y]
@@ -120,6 +121,7 @@ def EdgeExtractor(nodesdf, nofframes=3, **kwargs):
     """
     # Create a copy of the dataframe to avoid overwriting
     df = nodesdf.copy()
+    columns = df.columns
 
     edgedfs = []
     sets = np.unique(df["set"])
@@ -140,7 +142,7 @@ def EdgeExtractor(nodesdf, nofframes=3, **kwargs):
             window = [elem for elem in window if elem <= df_set["frame"].max()]
 
             # Compute the edges for each frames window
-            edgedf = GetEdge(df_set, start=window[0], end=window[-1], **kwargs)
+            edgedf = GetEdge(df_set, start=window[0], end=window[-1], columns=columns, **kwargs)
             edgedf["set"] = setid
             edgedfs.append(edgedf)
 

deeptrack/test/test_generators.py

@@ -8,8 +8,9 @@
 from .. import generators
 from ..optics import Fluorescence
 from ..scatterers import PointParticle
+from ..models import gnns
 import numpy as np
-
+import pandas as pd
 
 class TestGenerators(unittest.TestCase):
     def test_Generator(self):
@@ -154,7 +155,37 @@ def get_particle_position(result):
         #             a = generator[idx]
 
         #         [self.assertLess(d[-1], 8) for d in generator.data]
+    
 
+    def test_GraphGenerator(self):
+        frame = np.arange(10)
+        centroid = np.random.normal(0.5, 0.1, (10, 2))
+
+        df = pd.DataFrame(
+            {
+                'frame': frame, 
+                'centroid-0': centroid[:, 0], 
+                'centroid-1': centroid[:, 1], 
+                'label': 0, 
+                'set': 0, 
+                'solution': 0.0
+            }
+        )
+        # remove consecutive frames
+        df = df[~df["frame"].isin([3, 4, 5])]
+
+        generator = gnns.generators.GraphGenerator(
+	        nodesdf=df, 
+	        properties=["centroid"], 
+	        min_data_size=8,
+	        max_data_size=9,
+	        batch_size=8,
+	        feature_function=gnns.augmentations.GetGlobalFeature,
+	        radius=0.2,
+            nofframes=3,
+            output_type="edges"
+        )
+        self.assertIsInstance(generator, gnns.generators.ContinuousGraphGenerator)
 
 if __name__ == "__main__":
     unittest.main()