Merge branch 'yifan'

Author: YifanLu2000

docs/technicals/spatial_transcriptomics_alignment.md

@@ -1,4 +1,26 @@
 # Spatial transcriptomics alignment
 
-This section describes the technical details behind Spateo's spatial transcriptomics alignment pipeline.
+This section describes the technical details behind Spateo's spatial transcriptomics alignment pipeline. 
+
+## Background
+
+The sequential slicing and subsequent spatial transcriptomic profiling at the whole embryo level offer us an unprecedented opportunity to reconstruct the molecular hologram of the entire 3D embryo structure. However, conventional sectioning and downstream library preparation can rotate, transform, deform, and introduce missing regions in each profiled tissue section. In addition, with advancements in technology, spatial transcriptomics techniques with single-cell and even subcellular resolution are gradually emerging, and a single slice often contains hundreds of thousands of cells. Therefore, it is in general necessary to develop scalable and robust algorithms to reconstruct 3D structures to recover the relative spatial locations of single cells across different slices while allowing local distortion within the same slice. 
+
+
+## Methodology
+Consider a series of spatially-resolved transcriptomics samples, such as consecutive tissue sections from the same embryo, denote as $\mathcal{D} = \{\mathcal{S}^i\}_{i=1}^k$, where $\mathcal{S}^i=$ is the $i$-th section
+
+
+### Problem formulation
+
+### Generative process
+
+### Transformation model
+
+### Define prior distributions
+
+### Variational Bayesian Inference
+
+## Function Design
+
 

spateo/align.py

@@ -3,6 +3,7 @@
     BA_transform_and_assignment,
     Mesh_correction,
     align_preprocess,
+    calc_distance,
     calc_exp_dissimilarity,
     generate_label_transfer_dict,
     generate_label_transfer_prior,

spateo/alignment/__init__.py

@@ -2,6 +2,7 @@
 from .methods import (
     Mesh_correction,
     align_preprocess,
+    calc_distance,
     calc_exp_dissimilarity,
     generate_label_transfer_dict,
 )

spateo/alignment/methods/__init__.py

@@ -23,6 +23,7 @@
     _power,
     _prod,
     _unsqueeze,
+    calc_distance,
     check_backend,
     check_exp,
     con_K,

spateo/alignment/methods/backend.py

@@ -528,7 +528,7 @@ def diag(self, a, k=0):
         """
         raise NotImplementedError()
 
-    def unique(self, a, return_inverse=False):
+    def unique(self, a, return_index=False, return_inverse=False):
         r"""
         Finds unique elements of given tensor.
 
@@ -1058,8 +1058,8 @@ def data(self, a, type_as=None):
         else:
             return np.asarray(a, dtype=type_as.dtype)
 
-    def unique(self, a, return_inverse=False, axis=None):
-        return np.unique(a, return_inverse=return_inverse, axis=axis)
+    def unique(self, a, return_index, return_inverse=False, axis=None):
+        return np.unique(a, return_index=return_index, return_inverse=return_inverse, axis=axis)
 
     def unsqueeze(self, a, axis=-1):
         return np.expand_dims(a, axis)
@@ -1325,8 +1325,27 @@ def data(self, a, type_as=None):
         else:
             return torch.as_tensor(a, dtype=type_as.dtype, device=type_as.device)
 
-    def unique(self, a, return_inverse=False, axis=None):
-        return torch.unique(a, return_inverse=return_inverse, dim=axis)
+    def unique(self, a, return_index=False, return_inverse=False, axis=None):
+        unique_values, inverse_indices = torch.unique(a, sorted=False, return_inverse=True, dim=axis)
+
+        result = [unique_values]
+
+        if return_index:
+            x_sort, idx_sorted = torch.sort(inverse_indices)
+            return_index = idx_sorted[
+                torch.hstack(
+                    [
+                        torch.where((x_sort[1:] - x_sort[:-1]) != 0)[0],
+                        torch.tensor([len(inverse_indices) - 1], device=x_sort.device),
+                    ]
+                )
+            ]
+            result.append(return_index)
+
+        if return_inverse:
+            result.append(inverse_indices)
+
+        return tuple(result) if len(result) > 1 else result[0]
 
     def unsqueeze(self, a, axis=-1):
         return torch.unsqueeze(a, axis)

spateo/alignment/methods/morpho_class.py

@@ -244,7 +244,6 @@ def run(
         Returns:
             np.ndarray: The final cell-cell assignment matrix.
         """
-        # print(f'summin: {self.nx.sum(self.exp_layers_A[0], axis=1, keepdims=True).min()}')
         if self.nn_init:
             self._coarse_rigid_alignment()
 
@@ -560,7 +559,6 @@ def _guidance_pair_preprocess(
         self.X_AI = self.nx.from_numpy(self.guidance_pair[1], type_as=self.type_as)
         self.V_AI = self.nx.zeros(self.X_AI.shape, type_as=self.type_as)
         self.R_AI = self.nx.zeros(self.X_AI.shape, type_as=self.type_as)
-        # print(self.V_AI)
 
         if self.normalize_c:
             # Normalize the guidance pairs
@@ -789,7 +787,6 @@ def _init_probability_parameters(
                     Y=exp_B[sub_sample_B],
                     metric=d_s,
                 )
-                # print(exp_A[sub_sample_A])
                 min_exp_dist = self.nx.min(exp_dist, 1)
                 self.probability_parameters[i] = self.nx.maximum(
                     min_exp_dist[self.nx.argsort(min_exp_dist)[int(sub_sample_A.shape[0] * 0.05)]] / 5,
@@ -821,13 +818,16 @@ def _construct_kernel(
             NotImplementedError: If the specified kernel type is not implemented.
         """
 
-        unique_spatial_coords = _unique(self.nx, self.coordsA, 0)
+        # unique_spatial_coords = _unique(self.nx, self.coordsA, 0)
+        unique_spatial_coords, unique_idx = self.nx.unique(self.coordsA, return_index=True, axis=0)
         inducing_variables_idx = (
             np.random.choice(unique_spatial_coords.shape[0], inducing_variables_num, replace=False)
             if unique_spatial_coords.shape[0] > inducing_variables_num
             else np.arange(unique_spatial_coords.shape[0])
         )
-        self.inducing_variables = unique_spatial_coords[inducing_variables_idx, :]
+        inducing_variables_idx = unique_idx[inducing_variables_idx]
+        self.inducing_variables = self.coordsA[inducing_variables_idx, :]
+        # self.inducing_variables = unique_spatial_coords[inducing_variables_idx, :]
         # (self.inducing_variables, _) = sample(
         #     X=unique_spatial_coords, n_sampling=inducing_variables_num, sampling_method=sampling_method
         # )
@@ -839,6 +839,14 @@ def _construct_kernel(
                 if self.guidance_effect in ["nonrigid", "both"]
                 else None
             )
+        elif self.kernel_type == "geodist":
+            pass
+            # TODO: finish this
+            # if self.graph is None:
+            #     self.graph = _construct_graph(self.coordsA, self.knn)
+            #     self.GammaSparse = con_K_graph(self.graph, inducing_variables_idx, inducing_variables_idx, beta=self.kernel_bandwidth)
+            #     self.U = con_K_graph(self.graph, np.arange(self.NA), inducing_variables_idx, beta=self.kernel_bandwidth)
+
         else:
             raise NotImplementedError(f"Kernel type '{self.kernel_type}' is not implemented.")
 
@@ -1097,7 +1105,6 @@ def _update_assignment_P(
                 exp_layer_dist = calc_distance(
                     self.exp_layers_A, exp_layer_B_chunk, self.dissimilarity, self.label_transfer
                 )
-
                 P, K_NA_spatial_chunk, K_NA_sigma2_chunk, sigma2_related_chunk = get_P_core(
                     spatial_dist=spatial_dist, exp_dist=exp_layer_dist, **common_kwargs
                 )
@@ -1120,7 +1127,6 @@ def _update_assignment_P(
                 Y=self.coordsB[self.batch_idx, :] if self.SVI_mode else self.coordsB,
                 metric="euc",
             )  # NA x batch_size (SVI_mode) / NA x NB (not SVI_mode)
-            # print(self.pre_compute_dist)
             if self.pre_compute_dist:
                 exp_layer_dist = (
                     [exp_layer_d[:, self.batch_idx] for exp_layer_d in self.exp_layer_dist]
@@ -1163,7 +1169,6 @@ def _update_assignment_P(
             self.K_NA_sigma2 = self.K_NA_sigma2.to_dense()
 
         self.sigma2_related = sigma2_related / (self.Dim * self.Sp_sigma2)
-        # print(self.sigma2_related)
 
     def _update_gamma(
         self,
@@ -1282,7 +1287,6 @@ def _update_rigid(
             if self.SVI_mode
             else _dot(self.nx)(self.K_NB, self.coordsB)[None, :],
         )
-        # print(self.Sp)
         # solve rotation using SVD formula
         mu_XB, mu_XA, mu_Vn = PXB, PXA, PVA
         mu_X_deno, mu_Vn_deno = _copy(self.nx, self.Sp), _copy(self.nx, self.Sp)
@@ -1462,11 +1466,11 @@ def _wrap_output(
 
         if not (self.vecfld_key_added is None):
             norm_dict = {
-                "mean_transformed": self.nx.to_numpy(self.normalize_means[1]),
-                "mean_fixed": self.nx.to_numpy(self.normalize_means[0]),
+                "mean_transformed": self.nx.to_numpy(self.normalize_means[0]),
+                "mean_fixed": self.nx.to_numpy(self.normalize_means[1]),
                 "scale": self.nx.to_numpy(self.normalize_scales[1]),
-                "scale_transformed": self.nx.to_numpy(self.normalize_scales[1]),
-                "scale_fixed": self.nx.to_numpy(self.normalize_scales[0]),
+                "scale_transformed": self.nx.to_numpy(self.normalize_scales[0]),
+                "scale_fixed": self.nx.to_numpy(self.normalize_scales[1]),
             }
 
             self.vecfld = {
@@ -1488,4 +1492,5 @@ def _wrap_output(
                 "NA": self.NA,
                 "sigma2_variance": self.nx.to_numpy(self.sigma2_variance),
                 "method": "Spateo",
+                "norm_dict": norm_dict,
             }

spateo/alignment/methods/morpho_mesh_correction.py

@@ -31,7 +31,7 @@
 try:
     from .libfastpd import fastpd
 except ImportError:
-    print("fastpd is not installed. Please compile the fastpd library.")
+    print("fastpd is not installed. If you need mesh correction, please compile the fastpd library.")
 
 
 # TODO: add str as the input type for the models