SURE-tools 2.4.35__tar.gz → 2.4.39__tar.gz

{sure_tools-2.4.35 → sure_tools-2.4.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.4.35
+Version: 2.4.39
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.4.35 → sure_tools-2.4.39}/SURE/DensityFlow.py

@@ -758,6 +758,28 @@ class DensityFlow(nn.Module):
         cb = self._get_codebook()
         cb = tensor_to_numpy(cb)
         return cb
+    
+    def _get_complete_embedding(self, xs, us):
+        basal,_ = self._get_basal_embedding(xs)
+        dzs = self._total_effects(basal, us)
+        return basal + dzs 
+    
+    def get_complete_embedding(self, xs, us, batch_size:int=1024):
+        xs = self.preprocess(xs)
+        xs = convert_to_tensor(xs, device=self.get_device())
+        us = convert_to_tensor(us, device=self.get_device())
+        dataset = CustomDataset2(xs, us)
+        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
+
+        Z = []
+        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
+            for X_batch, U_batch, _ in dataloader:
+                zns = self._get_complete_embedding(X_batch, U_batch)
+                Z.append(tensor_to_numpy(zns))
+                pbar.update(1)
+
+        Z = np.concatenate(Z)
+        return Z
 
     def _get_basal_embedding(self, xs):           
         loc, scale = self.encoder_zn(xs)
@@ -1142,7 +1164,7 @@ class DensityFlow(nn.Module):
                 pbar.set_postfix({'loss': str_loss})
                 pbar.update(1)
                 
-    '''@classmethod
+    @classmethod
     def save_model(cls, model, file_path, compression=False):
         """Save the model to the specified file path."""
         file_path = os.path.abspath(file_path)
@@ -1169,10 +1191,17 @@ class DensityFlow(nn.Module):
         else:
             with open(file_path, 'rb') as pickle_file:
                 model = pickle.load(pickle_file)
+                
+        print(f"🧬 DensityFlow Initialized:")
+        print(f"   - Latent Dimension: {model.latent_dim}")
+        print(f"   - Gene Dimension: {model.input_size}")
+        print(f"   - Hidden Dimensions: {model.hidden_layers}")
+        print(f"   - Device: {model.get_device()}")
+        print(f"   - Parameters: {sum(p.numel() for p in model.parameters()):,}")
         
-        return model'''
+        return model
         
-    def save(self, path):
+'''    def save(self, path):
         """Save model checkpoint"""
         torch.save({
             'model_state_dict': self.state_dict(),
@@ -1209,7 +1238,7 @@ class DensityFlow(nn.Module):
         checkpoint = torch.load(model_path, map_location=model.get_device())
         model.load_state_dict(checkpoint['model_state_dict'])
         
-        return model
+        return model'''
 
         
 EXAMPLE_RUN = (

{sure_tools-2.4.35 → sure_tools-2.4.39}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.4.35
+Version: 2.4.39
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.4.35 → sure_tools-2.4.39}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.4.35',
+    version='2.4.39',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",