SURE-tools 2.1.1__py3-none-any.whl → 2.1.3__py3-none-any.whl

SURE/PerturbFlow.py

@@ -702,11 +702,11 @@ class PerturbFlow(nn.Module):
         cb = tensor_to_numpy(cb)
         return cb
 
-    def _get_cell_embedding(self, xs):           
+    def _get_basis_embedding(self, xs):           
         zns, _ = self.encoder_zn(xs)
         return zns 
     
-    def get_cell_embedding(self, 
+    def get_basis_embedding(self, 
                              xs, 
                              batch_size: int = 1024):
         """

SURE/flow/__init__.py

@@ -1 +1,2 @@
-from .plot_quiver import plot_quiver
+from .plot_quiver import plot_quiver
+from .flow_stats import calculate_direction_stats,calculate_movement_stats,calculate_movement_energy,calculate_movement_divergence

SURE/flow/flow_stats.py

@@ -0,0 +1,78 @@
+import numpy as np
+from scipy.spatial.distance import pdist, squareform
+
+def calculate_movement_stats(vectors):
+    """
+    计算移动矢量的基本统计量
+    """
+    # 计算每个矢量的模长（移动距离）
+    distances = np.linalg.norm(vectors, axis=1)
+    
+    stats = {
+        'total_movement': np.sum(distances),
+        'mean_distance': np.mean(distances),
+        'median_distance': np.median(distances),
+        'std_distance': np.std(distances),
+        'max_distance': np.max(distances),
+        'min_distance': np.min(distances),
+        'total_points': len(vectors)
+    }
+    
+    return stats, distances
+
+def calculate_direction_stats(vectors):
+    """
+    计算移动方向的一致性
+    """
+    # 单位向量
+    unit_vectors = vectors / np.linalg.norm(vectors, axis=1, keepdims=True)
+    
+    # 平均方向向量
+    mean_direction = np.mean(unit_vectors, axis=0)
+    mean_direction_norm = np.linalg.norm(mean_direction)
+    
+    # 方向一致性（0-1，1表示完全一致）
+    direction_consistency = mean_direction_norm
+    
+    return {
+        'direction_consistency': direction_consistency,
+        'mean_direction': mean_direction,
+        'direction_variance': 1 - direction_consistency  # 方向分散度
+    }
+
+def calculate_movement_energy(vectors, masses=None):
+    """
+    计算移动的能量（假设每个点有质量）
+    """
+    if masses is None:
+        masses = np.ones(len(vectors))  # 默认单位质量
+    
+    # 动能 = 0.5 * mass * velocity^2
+    speeds_squared = np.sum(vectors**2, axis=1)
+    kinetic_energy = 0.5 * masses * speeds_squared
+    
+    return {
+        'total_energy': np.sum(kinetic_energy),
+        'mean_energy': np.mean(kinetic_energy),
+        'energy_std': np.std(kinetic_energy)
+    }
+
+def calculate_movement_divergence(positions, vectors):
+    """
+    计算移动的散度（衡量扩张/收缩）
+    """
+    
+    # 计算移动前后的位置
+    new_positions = positions + vectors
+    
+    # 计算位置变化的协方差
+    orig_cov = np.cov(positions.T)
+    new_cov = np.cov(new_positions.T)
+    
+    # 体积变化（行列式比值）
+    volume_ratio = np.linalg.det(new_cov) / np.linalg.det(orig_cov)
+    
+    return {
+        'volume_expansion': volume_ratio,  # >1扩张, <1收缩
+        'expansion_factor': volume_ratio**(1/positions.shape[1])
+    }

{sure_tools-2.1.1.dist-info → sure_tools-2.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.1
+Version: 2.1.3
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.1.dist-info → sure_tools-2.1.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=RQoIhYQJdQpHdY_sMeDuqurbwvm6IX1XH7SVWG6SmS0,51658
+SURE/PerturbFlow.py,sha256=1vnReRD16B5Yq2Qb9d_9-znuGyWBq6pa5iKfKhaxzK4,51660
 SURE/SURE.py,sha256=_ZOymj24DLQju0Lb90lKspHPmqIUDDzjIEr9t4qgqCI,48364
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=xV10iBbh69g4mjBMb1cQxjuHe8e3Aq7pDzkZmx5G754,260
@@ -9,16 +9,17 @@ SURE/atac/__init__.py,sha256=3smP8IKHfwNCd1G_sZH3pKHXuLkLpFuLtjUTUSy7_As,34
 SURE/atac/utils.py,sha256=m4NYwpy9O5T1pXTzgCOCcmlwrC6GTi-cQ5sm2wZu2O8,4354
 SURE/codebook/__init__.py,sha256=2T5gjp8JIaBayrXAnOJYSebQHsWprOs87difpR1OPNw,243
 SURE/codebook/codebook.py,sha256=ZlN6gRX9Gj2D2u3P5KeOsbZri0MoMAiJo9lNeL-MK-I,17117
-SURE/flow/__init__.py,sha256=uiF9eyo6sz5qw7fRFiKipaXHboAakeIqVWo8yjkq0B0,36
+SURE/flow/__init__.py,sha256=eIcHeeISEOXEB0zRW-uiRlDz5IEUbA7rZZ1htUxhLVU,167
+SURE/flow/flow_stats.py,sha256=wpIxmOpYPU7YcgxqXKS8EDmnZ3oGh-YdBjiBiEmHcoU,2360
 SURE/flow/plot_quiver.py,sha256=spcPC0BDpvC-FBk9XIu6rcJI64bS-U-IVmmKLYHHXgs,1865
 SURE/flow/quiver.py,sha256=_euFqSaRrDoZ_oOabOx20LOoUTJ__XPhLW-vzLNQfAo,1859
 SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
 SURE/utils/custom_mlp.py,sha256=07TYX1HgxfEjb_3i5MpiZfNhOhx3dKntuwGkrpteWiM,7036
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.1.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.1.dist-info/METADATA,sha256=ET1LmoMzkRak6WiRpuGf2dcoY7cLgGoZtNmMkcqi6DU,2650
-sure_tools-2.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.1.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.1.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.1.dist-info/RECORD,,
+sure_tools-2.1.3.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.3.dist-info/METADATA,sha256=FTE9yLoT-6l4LETpjpjlnzA201z3vflub-zDxo_VH_o,2650
+sure_tools-2.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.3.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.3.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.3.dist-info/RECORD,,