SURE-tools 2.1.13__tar.gz → 2.1.15__tar.gz

{sure_tools-2.1.13 → sure_tools-2.1.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.13
+Version: 2.1.15
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.13 → sure_tools-2.1.15}/SURE/PerturbFlow.py

@@ -835,6 +835,44 @@ class PerturbFlow(nn.Module):
         R = np.concatenate(R)
         return R
     
+    def _count(self,concentrate):
+        if self.loss_func == 'bernoulli':
+            counts = self.sigmoid(concentrate)
+        else:
+            counts = concentrate.exp()
+        return counts
+    
+    def _count_sample(self,concentrate):
+        if self.loss_func == 'bernoulli':
+            logits = concentrate
+            counts = dist.Bernoulli(logits=logits).to_event(1).sample()
+        else:
+            counts = self._count(concentrate=concentrate)
+            counts = dist.Poisson(rate=counts).to_event(1).sample()
+        return counts
+    
+    def get_counts(self, zs, 
+                        batch_size: int = 1024, 
+                        use_sampler: bool = False):
+
+        zs = convert_to_tensor(zs, device=self.get_device())
+        dataset = CustomDataset(zs)
+        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
+        
+        E = []
+        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
+            for Z_batch, _ in dataloader:
+                concentrate = self._expression(Z_batch)
+                if use_sampler:
+                    counts = self._count_sample(concentrate)
+                else:
+                    counts = self._count(concentrate)
+                E.append(tensor_to_numpy(counts))
+                pbar.update(1)
+        
+        E = np.concatenate(E)
+        return E
+    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

{sure_tools-2.1.13 → sure_tools-2.1.15}/SURE/SURE.py

@@ -233,7 +233,7 @@ class SURE(nn.Module):
 
         if self.cell_factor_size>0:
             self.cell_factor_effect = MLP(
-                [self.z_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.z_dim],
+                [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
                 activation=activate_fct,
                 output_activation=None,
                 post_layer_fct=post_layer_fct,

{sure_tools-2.1.13 → sure_tools-2.1.15}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.13
+Version: 2.1.15
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.13 → sure_tools-2.1.15}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.13',
+    version='2.1.15',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",