Updated all submodules

aristoteleo · Aug 22, 2024 · 25bf43f · 25bf43f
1 parent 508dc2d
commit 25bf43f
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Showing 4 changed files with 67 additions and 3 deletions.
diff --git a/docs/docs/tutorials/notebooks b/docs/docs/tutorials/notebooks
diff --git a/docs/spateo-tutorials b/docs/spateo-tutorials
diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks
diff --git a/spateo/alignment/utils.py b/spateo/alignment/utils.py
@@ -334,6 +334,11 @@ def solve_RT_by_correspondence(
         return R, t
 
 
+##############
+# Simulation #
+##############
+
+
 def split_slice(
     adata,
     spatial_key,
@@ -350,3 +355,62 @@ def split_slice(
         sorted_adata.obs["slice"] = slice_id
         split_adata.append(sorted_adata)
     return split_adata[:split_num]
+
+
+def tps_deformation(
+    adata,
+    spatial_key,
+    key_added,
+    grid_num=2,
+    tps_noise_scale=25,
+    add_corner_points=True,
+    alpha=0.1,
+    inplace=True,
+):
+    from tps import ThinPlateSpline
+
+    spatial = adata.obsm[spatial_key]
+    # get min max
+    x_min, x_max = np.min(spatial[:, 0]), np.max(spatial[:, 0])
+    y_min, y_max = np.min(spatial[:, 1]), np.max(spatial[:, 1])
+
+    # define the length of grid
+    grid_size_x = (x_max - x_min) / grid_num
+    grid_size_y = (y_max - y_min) / grid_num
+    # generate the grid
+    x_grid = np.linspace(x_min, x_max, grid_num + 1)[:-1] + grid_size_x / 2
+    y_grid = np.linspace(y_min, y_max, grid_num + 1)[:-1] + grid_size_y / 2
+    xx, yy = np.meshgrid(x_grid, y_grid)
+    # generate control points
+    src_points = []
+    dst_points = []
+    for i in range(xx.shape[0]):
+        for j in range(xx.shape[1]):
+            x_center, y_center = xx[i, j], yy[i, j]
+            x = x_center
+            y = y_center
+            src_points.append(np.column_stack([x, y]))
+            dst_points.append(
+                src_points[-1] + np.random.normal(scale=(grid_size_x + grid_size_y) * tps_noise_scale / 2, size=(1, 2))
+            )
+    src_points = np.concatenate(src_points, axis=0)
+    dst_points = np.concatenate(dst_points, axis=0)
+    if add_corner_points:
+        src_points = np.concatenate(
+            [np.array([[x_min, y_min], [x_min, y_max], [x_max, y_max], [x_max, y_min]]), src_points], 0
+        )
+        dst_points = np.concatenate(
+            [np.array([[x_min, y_min], [x_min, y_max], [x_max, y_max], [x_max, y_min]]), dst_points], 0
+        )
+    # calculate the TPS deformation
+    tps = ThinPlateSpline(alpha=alpha)  # Regularization
+    tps.fit(src_points, dst_points)
+    # perform tps deformation
+    tps_spatial = tps.transform(spatial)
+    if inplace:
+        adata.obsm[key_added] = tps_spatial
+        return lambda x: tps.transform(x)
+    else:
+        adata_tps = adata.copy()
+        adata_tps.obsm[key_added] = tps_spatial
+        return adata_tps, lambda x: tps.transform(x)
+8 −3		3_alignment/3D reconstruction with pairwise alignment.ipynb
+8 −0		3_alignment/Alignment between images.ipynb
+66 −54		3_alignment/Basic usage of Spateo alignment for 2D slices.ipynb
+7 −0		3_alignment/Global refinement by considering multiple slices.ipynb
+8 −0		3_alignment/Incorporate label consistency prior.ipynb
+7 −0		3_alignment/Incorporating mesh information to improve 3D reconstruction.ipynb
+7 −0		3_alignment/Integrate multimodalities data for alignment.ipynb
+419 −207		3_alignment/Nonrigid alignment of Spateo for 2D slices.ipynb
+4 −5		3_alignment/Using GPU SVI Sparse calculation for efficiency and scalibity.ipynb
+12 −29		6_cci.md
+0 −0		6_cci/1_cell-cell_communication_LR_coexpression_analysis.ipynb
+0 −1,125		6_cci/2_cell-cell_interaction_effects_modeling.ipynb
+1,258 −0		6_cci/2_cell-cell_interaction_effects_modeling_inference.ipynb
+1,466 −0		6_cci/2_cell-cell_interaction_effects_modeling_selecting_target_genes.ipynb
+0 −2,285		6_cci/Spateo_figure_6.ipynb
+0 −3,779		6_cci/Spateo_figure_S5.ipynb
+0 −1,274		6_cci/Spateo_figure_S6.ipynb