handle negative eigenvalues

Kapoorlabs-CAPED · Dec 4, 2023 · 1387287 · 1387287
1 parent 7d3d748
commit 1387287
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/src/napatrackmater/Trackmate.py b/src/napatrackmater/Trackmate.py
@@ -14,7 +14,7 @@
 from pathlib import Path
 import concurrent
 from .clustering import Clustering
-
+from lightning import Trainer
 
 class TrackMate:
     def __init__(
@@ -59,7 +59,7 @@ def __init__(
         self.center = center
         self.compute_with_autoencoder = compute_with_autoencoder
         self.latent_features = latent_features
-
+        self.pretrainer = Trainer(accelerator=self.accelerator, devices=self.devices)
         if image is not None:
             self.image = image.astype(np.uint8)
         else:
@@ -1705,6 +1705,7 @@ def _compute_latent_space(self):
                 self.progress_bar.show()
 
             cluster_eval = Clustering(
+                self.pretrainer,
                 self.accelerator,
                 self.devices,
                 self.seg_image[int(time_key), :],
@@ -1767,6 +1768,7 @@ def _assign_cluster_class(self):
                 self.progress_bar.show()
 
             cluster_eval = Clustering(
+                self.pretrainer,
                 self.accelerator,
                 self.devices,
                 self.seg_image[int(time_key), :],

diff --git a/src/napatrackmater/clustering.py b/src/napatrackmater/clustering.py
@@ -44,6 +44,7 @@ def __getitem__(self, idx):
 class Clustering:
     def __init__(
         self,
+        pretrainer: Trainer,
         accelerator: str,
         devices: List[int],
         label_image: np.ndarray,
@@ -59,7 +60,8 @@ def __init__(
         center=True,
         compute_with_autoencoder=True,
     ):
-
+
+        self.pretrainer = pretrainer
         self.accelerator = accelerator
         self.devices = devices
         self.label_image = label_image
@@ -174,7 +176,6 @@ def _latent_computer(self, i, dim):
     def _create_cluster_labels(self):
 
         ndim = len(self.label_image.shape)
-        self.pretrainer = Trainer(accelerator=self.accelerator, devices=self.devices)
         if ndim == 2:
 
             labels, centroids, clouds, marching_cube_points = _label_cluster(