wip

nnunetv2/preprocessing/resampling/default_resampling.py

@@ -124,7 +124,7 @@ def resample_data_or_seg_to_shape(data: Union[torch.Tensor, np.ndarray],
 
 def resample_data_or_seg(data: np.ndarray, new_shape: Union[Tuple[float, ...], List[float], np.ndarray],
                          is_seg: bool = False, axis: Union[None, int] = None, order: int = 3,
-                         do_separate_z: bool = False, order_z: int = 0):
+                         do_separate_z: bool = False, order_z: int = 0, dtype_out = None):
     """
     separate_z=True will resample with order 0 along z
     :param data:
@@ -145,9 +145,11 @@ def resample_data_or_seg(data: np.ndarray, new_shape: Union[Tuple[float, ...], L
     else:
         resize_fn = resize
         kwargs = {'mode': 'edge', 'anti_aliasing': False}
-    dtype_data = data.dtype
     shape = np.array(data[0].shape)
     new_shape = np.array(new_shape)
+    if dtype_out is None:
+        dtype_out = data.dtype
+    reshaped_final = np.zeros((data.shape[0], *new_shape), dtype=dtype_out)
     if np.any(shape != new_shape):
         data = data.astype(float)
         if do_separate_z:
@@ -161,22 +163,20 @@ def resample_data_or_seg(data: np.ndarray, new_shape: Union[Tuple[float, ...], L
             else:
                 new_shape_2d = new_shape[:-1]
 
-            reshaped_final_data = []
             for c in range(data.shape[0]):
-                reshaped_data = []
+                reshaped_here = np.zeros((data.shape[1], *new_shape_2d))
                 for slice_id in range(shape[axis]):
                     if axis == 0:
-                        reshaped_data.append(resize_fn(data[c, slice_id], new_shape_2d, order, **kwargs))
+                        reshaped_here[slice_id] = resize_fn(data[c, slice_id], new_shape_2d, order, **kwargs)
                     elif axis == 1:
-                        reshaped_data.append(resize_fn(data[c, :, slice_id], new_shape_2d, order, **kwargs))
+                        reshaped_here[slice_id] = resize_fn(data[c, :, slice_id], new_shape_2d, order, **kwargs)
                     else:
-                        reshaped_data.append(resize_fn(data[c, :, :, slice_id], new_shape_2d, order, **kwargs))
-                reshaped_data = np.stack(reshaped_data, axis)
+                        reshaped_here[slice_id] = resize_fn(data[c, :, :, slice_id], new_shape_2d, order, **kwargs)
                 if shape[axis] != new_shape[axis]:
 
                     # The following few lines are blatantly copied and modified from sklearn's resize()
                     rows, cols, dim = new_shape[0], new_shape[1], new_shape[2]
-                    orig_rows, orig_cols, orig_dim = reshaped_data.shape
+                    orig_rows, orig_cols, orig_dim = reshaped_here.shape
 
                     row_scale = float(orig_rows) / rows
                     col_scale = float(orig_cols) / cols
@@ -189,28 +189,20 @@ def resample_data_or_seg(data: np.ndarray, new_shape: Union[Tuple[float, ...], L
 
                     coord_map = np.array([map_rows, map_cols, map_dims])
                     if not is_seg or order_z == 0:
-                        reshaped_final_data.append(map_coordinates(reshaped_data, coord_map, order=order_z,
-                                                                   mode='nearest')[None])
+                        reshaped_final[c] = map_coordinates(reshaped_here, coord_map, order=order_z, mode='nearest')[None]
                     else:
-                        unique_labels = np.sort(pd.unique(reshaped_data.ravel()))  # np.unique(reshaped_data)
-                        reshaped = np.zeros(new_shape, dtype=dtype_data)
-
+                        unique_labels = np.sort(pd.unique(reshaped_here.ravel()))  # np.unique(reshaped_data)
                         for i, cl in enumerate(unique_labels):
-                            reshaped_multihot = np.round(
-                                map_coordinates((reshaped_data == cl).astype(float), coord_map, order=order_z,
-                                                mode='nearest'))
-                            reshaped[reshaped_multihot > 0.5] = cl
-                        reshaped_final_data.append(reshaped[None])
+                            reshaped_final[c][np.round(
+                                map_coordinates((reshaped_here == cl).astype(float), coord_map, order=order_z,
+                                                mode='nearest')) > 0.5] = cl
                 else:
-                    reshaped_final_data.append(reshaped_data[None])
-            reshaped_final_data = np.vstack(reshaped_final_data)
+                    reshaped_final[c] = reshaped_here
         else:
             # print("no separate z, order", order)
-            reshaped = []
             for c in range(data.shape[0]):
-                reshaped.append(resize_fn(data[c], new_shape, order, **kwargs)[None])
-            reshaped_final_data = np.vstack(reshaped)
-        return reshaped_final_data.astype(dtype_data)
+                reshaped_final[c] = resize_fn(data[c], new_shape, order, **kwargs)
+        return reshaped_final
     else:
         # print("no resampling necessary")
         return data