SURE-tools 2.1.37__py3-none-any.whl → 2.1.38__py3-none-any.whl

SURE/perturb/perturb.py

@@ -1,5 +1,6 @@
 import re
 import numpy as np
+from numba import njit
 from itertools import chain
 from joblib import Parallel, delayed
 from typing import Literal
@@ -27,6 +28,20 @@ class LabelMatrix:
             
     def inverse_transform(self, matrix):
         return matrix_to_labels(matrix=matrix, unique_labels=self.labels_)
+
+class DoseMatrix:
+    def __init__(self):
+        self.labels_ = None 
+        
+    def fit_transform(self, labels, label_dose, control_label=None):
+        mat, self.labels_ = dose_to_matrix(labels, label_dose)
+        
+        if control_label is not None:
+            idx = np.where(self.labels_==control_label)[0]
+            mat = np.delete(mat, idx, axis=1)
+            self.labels_ = np.delete(self.labels_, idx)
+            
+        return mat 
         
 def label_to_matrix(labels, sep_pattern=r'[;_\-\s]'):
     """
@@ -91,3 +106,45 @@ def parallel_label_to_matrix(labels, sep_pattern=r'[;_\-\s]', n_jobs=4):
 def matrix_to_labels(matrix, unique_labels):
     return [';'.join([unique_labels[i] for i in np.where(row)[0]]) 
             for row in matrix]
+
+
+
+
+
+
+
+@njit(parallel=True)
+def _numba_fill_matrix(dose_matrix, label_indices, label_doses):
+    """Numba 加速的矩阵填充函数"""
+    for i in range(len(label_indices)):
+        for j, dose in zip(label_indices[i], label_doses[i]):
+            dose_matrix[i, j] = dose
+
+def dose_to_matrix(labels, label_dose, all_labels=None):
+    """
+    使用 Numba 的终极加速版本（需预先安装 numba）
+    """
+    if all_labels is None:
+        all_labels = sorted(set().union(*labels))
+    
+    label_to_idx = {label: idx for idx, label in enumerate(all_labels)}
+    n_samples = len(labels)
+    n_labels = len(all_labels)
+    dose_matrix = np.zeros((n_samples, n_labels), dtype=np.float64)
+    
+    # 预处理为 Numba 兼容格式
+    label_indices = []
+    label_doses = []
+    for sample_labels in labels:
+        indices = []
+        doses = []
+        if sample_labels:
+            for label in sample_labels:
+                indices.append(label_to_idx[label])
+                doses.append(label_dose[label])
+        label_indices.append(np.array(indices, dtype=np.int64))
+        label_doses.append(np.array(doses, dtype=np.float64))
+    
+    # 调用 Numba 加速函数
+    _numba_fill_matrix(dose_matrix, label_indices, label_doses)
+    return dose_matrix,all_labels

{sure_tools-2.1.37.dist-info → sure_tools-2.1.38.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.37
+Version: 2.1.38
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.37.dist-info → sure_tools-2.1.38.dist-info}/RECORD

@@ -12,14 +12,14 @@ SURE/flow/__init__.py,sha256=rsAjYsh1xVIrxBCuwOE0Q_6N5th1wBgjJceV0ABPG3c,183
 SURE/flow/flow_stats.py,sha256=cBBsPEDpWNMpbzlyQ3f0385RSrX6_5RCH2caOyi4ihM,9908
 SURE/flow/plot_quiver.py,sha256=UbmuScUcgbQHeMmjKmgqxjrIjHhiHx0VWct16UMMwuE,8110
 SURE/perturb/__init__.py,sha256=ouxShhbxZM4r5Gf7GmKiutrsmtyq7QL8rHjhgF0BU08,32
-SURE/perturb/perturb.py,sha256=uUFUNJzIzvjA_2rN8801Le-i3oS7vOEvFav1w_lSFSE,3544
+SURE/perturb/perturb.py,sha256=vuE5apV2tRgW6aVaPmGlVeEObNiig_punQET13QSUms,5304
 SURE/utils/__init__.py,sha256=QJUOfrXzdWSmoM0P3LH8oKEHttzCWqpDy2UF0F0dtN4,673
 SURE/utils/custom_mlp.py,sha256=rHnx9jEef02zfCUdbYVCmbuHcDdIBmRgt__wpdpZvYg,8104
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.37.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.37.dist-info/METADATA,sha256=9OEHt9VYrCralJ-l5Ssbk8lAie-8BGHRvwNNpUUqG_E,2651
-sure_tools-2.1.37.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.37.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.37.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.37.dist-info/RECORD,,
+sure_tools-2.1.38.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.38.dist-info/METADATA,sha256=sC9emzBRwPVin5Lmmb2a8EgDKZ0_orNky12KqISuzCM,2651
+sure_tools-2.1.38.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.38.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.38.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.38.dist-info/RECORD,,