SURE-tools 2.1.44__tar.gz → 2.1.46__tar.gz

{sure_tools-2.1.44 → sure_tools-2.1.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.44
+Version: 2.1.46
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.44 → sure_tools-2.1.46}/SURE/PerturbFlow.py

@@ -189,29 +189,10 @@ class PerturbFlow(nn.Module):
                 use_cuda=self.use_cuda,
             )
 
-        #self.encoder_zn = MLP(
-        #    [self.input_size] + hidden_sizes + [[latent_dim, latent_dim]],
-        #    activation=activate_fct,
-        #    output_activation=[None, Exp],
-        #    post_layer_fct=post_layer_fct,
-        #    post_act_fct=post_act_fct,
-        #    allow_broadcast=self.allow_broadcast,
-        #    use_cuda=self.use_cuda,
-        #)
-        
-        self.encoder_zn_loc = MLP(
-            [self.input_size] + hidden_sizes + [self.input_size * latent_dim],
-            activation=activate_fct,
-            output_activation=None,
-            post_layer_fct=post_layer_fct,
-            post_act_fct=post_act_fct,
-            allow_broadcast=self.allow_broadcast,
-            use_cuda=self.use_cuda,
-        )
-        self.encoder_zn_scale = MLP(
-            [self.input_size] + hidden_sizes + [latent_dim],
+        self.encoder_zn = MLP(
+            [self.input_size] + hidden_sizes + [[latent_dim, latent_dim]],
             activation=activate_fct,
-            output_activation=Exp,
+            output_activation=[None, Exp],
             post_layer_fct=post_layer_fct,
             post_act_fct=post_act_fct,
             allow_broadcast=self.allow_broadcast,
@@ -397,11 +378,7 @@ class PerturbFlow(nn.Module):
 
     def guide1(self, xs):
         with pyro.plate('data'):
-            batch_size = xs.shape[0]
-            #zn_loc, zn_scale = self.encoder_zn(xs)
-            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-            zn_loc = zn_loc_3d.sum(dim=1)
+            zn_loc, zn_scale = self.encoder_zn(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -489,11 +466,7 @@ class PerturbFlow(nn.Module):
 
     def guide2(self, xs, us=None):
         with pyro.plate('data'):
-            batch_size = xs.shape[0]
-            #zn_loc, zn_scale = self.encoder_zn(xs)
-            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-            zn_loc = zn_loc_3d.sum(dim=1)
+            zn_loc, zn_scale = self.encoder_zn(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -588,11 +561,7 @@ class PerturbFlow(nn.Module):
     def guide3(self, xs, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                batch_size = xs.shape[0]
-                #zn_loc, zn_scale = self.encoder_zn(xs)
-                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-                zn_loc = zn_loc_3d.sum(dim=1)
+                zn_loc, zn_scale = self.encoder_zn(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def model4(self, xs, us, ys, embeds=None):
@@ -694,11 +663,7 @@ class PerturbFlow(nn.Module):
     def guide4(self, xs, us, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                batch_size = xs.shape[0]
-                #zn_loc, zn_scale = self.encoder_zn(xs)
-                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-                zn_loc = zn_loc_3d.sum(dim=1)
+                zn_loc, zn_scale = self.encoder_zn(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def _total_effects(self, zns, us):
@@ -727,11 +692,7 @@ class PerturbFlow(nn.Module):
         return cb
 
     def _get_basal_embedding(self, xs):           
-        #zns, _ = self.encoder_zn(xs)
-        batch_size = xs.shape[0]
-        zns = self.encoder_zn_loc(xs)
-        zns_3d = zns.view(batch_size, self.input_size, self.latent_dim)
-        zns = zns_3d.sum(dim=1)
+        zns, _ = self.encoder_zn(xs)
         return zns 
     
     def get_basal_embedding(self, 

{sure_tools-2.1.44 → sure_tools-2.1.46}/SURE/flow/flow_stats.py

@@ -1,4 +1,5 @@
 import numpy as np
+from scipy.interpolate import griddata
 from scipy.spatial.distance import pdist, squareform
 from sklearn.decomposition import PCA
 from scipy.stats import pearsonr
@@ -16,6 +17,30 @@ class VectorFieldEval:
         
     def momentum_flow_metric(self, vectors, masses=None):
         return momentum_flow_metric(vectors=vectors, masses=masses)
+    
+    def divergence(self, points, vectors, grid_resolution=30):
+        # 提取坐标和向量分量
+        x_coords = points[:, 0]
+        y_coords = points[:, 1]
+        u_components = vectors[:, 0]  # x方向分量
+        v_components = vectors[:, 1]  # y方向分量
+    
+        # 创建规则网格
+        x_grid = np.linspace(x_coords.min(), x_coords.max(), grid_resolution)
+        y_grid = np.linspace(y_coords.min(), y_coords.max(), grid_resolution)
+        X, Y = np.meshgrid(x_grid, y_grid)
+    
+        # 插值到网格
+        U_grid = griddata((x_coords, y_coords), u_components, (X, Y), method='linear')
+        V_grid = griddata((x_coords, y_coords), v_components, (X, Y), method='linear')
+    
+        # 计算散度
+        dU_dx = np.gradient(U_grid, x_grid, axis=1)
+        dV_dy = np.gradient(V_grid, y_grid, axis=0)
+        divergence = dU_dx + dV_dy
+        divergence[np.isnan(divergence)] = 0
+        
+        return divergence
 
         
 def calculate_movement_stats(vectors):

{sure_tools-2.1.44 → sure_tools-2.1.46}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.44
+Version: 2.1.46
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.44 → sure_tools-2.1.46}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.44',
+    version='2.1.46',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",