cellfinder 1.3.2__py3-none-any.whl → 1.4.0__py3-none-any.whl

cellfinder/core/detect/filters/plane/tile_walker.py

@@ -1,8 +1,8 @@
 import math
-from typing import Generator, Tuple
+from typing import Tuple
 
-import numpy as np
-from numba import njit
+import torch
+import torch.nn.functional as F
 
 
 class TileWalker:
@@ -15,74 +15,140 @@ class TileWalker:
     The mean and standard deviation of this tile is calculated, and
     the threshold set at 1 + mean + (2 * stddev).
 
-    Attributes
+    Parameters
     ----------
-    bright_tiles_mask :
-        An boolean array whose entries correspond to whether each tile is
-        bright (1) or dark (0). The values are set in
-        self.mark_bright_tiles().
+    plane_shape : tuple(int, int)
+        Height/width of the planes.
+    soma_diameter : float
+        Diameter of the soma in voxels.
     """
 
-    def __init__(self, img: np.ndarray, soma_diameter: int) -> None:
-        self.img = img
-        self.img_width, self.img_height = img.shape
-        self.tile_width = soma_diameter * 2
-        self.tile_height = soma_diameter * 2
+    def __init__(
+        self, plane_shape: Tuple[int, int], soma_diameter: int
+    ) -> None:
 
-        n_tiles_width = math.ceil(self.img_width / self.tile_width)
-        n_tiles_height = math.ceil(self.img_height / self.tile_height)
-        self.bright_tiles_mask = np.zeros(
-            (n_tiles_width, n_tiles_height), dtype=bool
-        )
+        self.img_height, self.img_width = plane_shape
+        self.tile_height = soma_diameter * 2
+        self.tile_width = soma_diameter * 2
 
-        corner_tile = img[0 : self.tile_width, 0 : self.tile_height]
-        corner_intensity = np.mean(corner_tile)
-        corner_sd = np.std(corner_tile)
-        # add 1 to ensure not 0, as disables
-        self.out_of_brain_threshold = (corner_intensity + (2 * corner_sd)) + 1
+        self.n_tiles_height = math.ceil(self.img_height / self.tile_height)
+        self.n_tiles_width = math.ceil(self.img_width / self.tile_width)
 
-    def _get_tiles(self) -> Generator[Tuple[int, int, np.ndarray], None, None]:
+    def get_bright_tiles(self, planes: torch.Tensor) -> torch.Tensor:
         """
-        Generator that yields tiles of the 2D image.
+        Takes a 3d z-stack. For each z it computes the mean/std of the corner
+        tile and uses that to get a in/out of brain threshold for each z.
 
-        Notes
-        -----
-        The final tile in each dimension can have a smaller size than the
-        rest of the tiles if the tile shape does not exactly divide the
-        image shape.
-        """
-        for y in range(
-            0, self.img_height - self.tile_height, self.tile_height
-        ):
-            for x in range(
-                0, self.img_width - self.tile_width, self.tile_width
-            ):
-                tile = self.img[
-                    x : x + self.tile_width, y : y + self.tile_height
-                ]
-                yield x, y, tile
-
-    def mark_bright_tiles(self) -> None:
-        """
-        Loop through tiles, and if the average value of a tile is
-        greater than the intensity threshold mark the tile as bright
-        in self.bright_tiles_mask.
+        Parameters
+        ----------
+        planes : torch.Tensor
+            3d z-stack.
+
+        Returns
+        -------
+        out_of_brain_thresholds : torch.Tensor
+            3d z-stack whose planar shape is the number of tiles in a plane.
+            The returned data will be on the same torch device as the input
+            planes.
         """
-        threshold = self.out_of_brain_threshold
-        if threshold == 0:
-            return
+        return _get_bright_tiles(
+            planes,
+            self.n_tiles_height,
+            self.n_tiles_width,
+            self.tile_height,
+            self.tile_width,
+        )
 
-        for x, y, tile in self._get_tiles():
-            if not is_low_average(tile, threshold):
-                mask_x = x // self.tile_width
-                mask_y = y // self.tile_height
-                self.bright_tiles_mask[mask_x, mask_y] = True
+    def get_tiled_buffer(self, depth: int, device: str):
+        return torch.zeros(
+            (depth, self.n_tiles_height, self.n_tiles_width),
+            dtype=torch.bool,
+            device=device,
+        )
 
 
-@njit
-def is_low_average(tile: np.ndarray, threshold: float) -> bool:
+@torch.jit.script
+def _get_out_of_brain_threshold(
+    planes: torch.Tensor, tile_height: int, tile_width: int
+) -> torch.Tensor:
     """
-    Return `True` if the average value of *tile* is below *threshold*.
+    Takes a 3d z-stack. For each z it computes the mean/std of the corner tile
+    and uses that to get a in/out of brain threshold for each z-stack.
+
+    Parameters
+    ----------
+    planes :
+        3d z-stack.
+    tile_height :
+        Height of each tile.
+    tile_width :
+        Width of each tile.
+
+    Returns
+    -------
+    out_of_brain_thresholds :
+        1d z-stack.
+    """
+    # get corner tile
+    corner_tiles = planes[:, 0:tile_height, 0:tile_width]
+    # convert from ZYX -> ZK, where K is the elements in the corner tile
+    corner_tiles = corner_tiles.reshape((planes.shape[0], -1))
+
+    # need to operate in float64, in case the values are large
+    corner64 = corner_tiles.type(torch.float64)
+    corner_intensity = torch.mean(corner64, dim=1).type(planes.dtype)
+    # for parity with past when we used np.std, which defaults to ddof=0
+    corner_sd = torch.std(corner64, dim=1, correction=0).type(planes.dtype)
+    # add 1 to ensure not 0, as disables
+    out_of_brain_thresholds = corner_intensity + 2 * corner_sd + 1
+
+    return out_of_brain_thresholds
+
+
+@torch.jit.script
+def _get_bright_tiles(
+    planes: torch.Tensor,
+    n_tiles_height: int,
+    n_tiles_width: int,
+    tile_height: int,
+    tile_width: int,
+) -> torch.Tensor:
     """
-    avg = np.mean(tile)
-    return avg < threshold
+    Loop through the tiles of the plane for each plane. And if the average
+    value of a tile is greater than the intensity threshold of that plain,
+    mark the tile as bright.
+    """
+    bright_tiles_mask = torch.zeros(
+        (planes.shape[0], n_tiles_height, n_tiles_width),
+        dtype=torch.bool,
+        device=planes.device,
+    )
+    # if we don't have enough size for a single tile, it's all outside
+    if planes.shape[1] < tile_height or planes.shape[2] < tile_width:
+        return bright_tiles_mask
+
+    # for each plane, the threshold
+    out_of_brain_thresholds = _get_out_of_brain_threshold(
+        planes, tile_height, tile_width
+    )
+    # thresholds Z -> ZYX shape
+    thresholds = out_of_brain_thresholds.view(-1, 1, 1)
+
+    # ZYX -> ZCYX required for function (C=1)
+    planes = planes.unsqueeze(1)
+    # get the average of each tile
+    tile_avg = F.avg_pool2d(
+        planes,
+        (tile_height, tile_width),
+        ceil_mode=False,  # default is False, but to make sure
+    )
+    # go back from ZCYX -> ZYX
+    tile_avg = tile_avg[:, 0, :, :]
+
+    bright = tile_avg >= thresholds
+    # tile_avg and bright may be smaller than bright_tiles_mask because
+    # avg_pool2d first subtracts the kernel size before computing # tiles.
+    # So contain view to that size
+    bright_tiles_mask[:, : bright.shape[1], : bright.shape[2]][bright] = True
+
+    return bright_tiles_mask