SURE-tools 2.2.12__tar.gz → 2.2.15__tar.gz

{sure_tools-2.2.12 → sure_tools-2.2.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.12
+Version: 2.2.15
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.12 → sure_tools-2.2.15}/SURE/DensityFlow.py

@@ -696,7 +696,7 @@ class DensityFlow(nn.Module):
         """
         Return the mean part of metacell codebook
         """
-        cb = self._get_metacell_coordinates()
+        cb = self._get_codebook()
         cb = tensor_to_numpy(cb)
         return cb
 
@@ -842,47 +842,42 @@ class DensityFlow(nn.Module):
         
         return counts, zs
     
-    def _cell_response(self, xs, factor_idx, perturb):
+    def _cell_response(self, zs, perturb_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
-        zns,_ = self._get_basal_embedding(xs)   
+        #zns,_ = self._get_basal_embedding(xs)   
+        zns = zs
         if perturb.ndim==2:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb])
+            ms = self.cell_factor_effect[perturb_idx]([zns, perturb])
         else:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb.reshape(-1,1)])
+            ms = self.cell_factor_effect[perturb_idx]([zns, perturb.reshape(-1,1)])
             
         return ms 
 
     def get_cell_response(self, 
-                             xs, 
-                             factor_idx,
-                             perturb,
+                             zs, 
+                             perturb_idx,
+                             perturb_us,
                              batch_size: int = 1024):
         """
         Return cells' changes in the latent space induced by specific perturbation of a factor
 
         """
-        xs = self.preprocess(xs)
-        xs = convert_to_tensor(xs, device=self.get_device())
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        dataset = CustomDataset2(xs,ps)
+        #xs = self.preprocess(xs)
+        zs = convert_to_tensor(zs, device=self.get_device())
+        ps = convert_to_tensor(perturb_us, device=self.get_device())
+        dataset = CustomDataset2(zs,ps)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
 
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for X_batch, P_batch, _ in dataloader:
-                zns = self._cell_response(X_batch, factor_idx, P_batch)
+            for Z_batch, P_batch, _ in dataloader:
+                zns = self._cell_response(Z_batch, perturb_idx, P_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 
         Z = np.concatenate(Z)
         return Z
     
-    def get_metacell_response(self, factor_idx, perturb):
-        zs = self._get_codebook()
-        ps = convert_to_tensor(perturb, device=self.get_device())         
-        ms = self.cell_factor_effect[factor_idx]([zs,ps])
-        return tensor_to_numpy(ms)
-    
     def _get_expression_response(self, delta_zs):
         return self.decoder_concentrate(delta_zs)
     

{sure_tools-2.2.12 → sure_tools-2.2.15}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.12
+Version: 2.2.15
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.12 → sure_tools-2.2.15}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.2.12',
+    version='2.2.15',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",