patchcommander rework (#69)

When sampling with more complex patch configurations, patches along the border of the image were not always sampled correctly. For example, with center=True, patches with the center outside the image were not sampled, ignoring the patches from the bottom row of the image. Additionally, with overlap, additional patches around the borders of the images still contained tissue. For example  in the case of a config with half overlapping slides, the patch half a patch size to the upper left of the (0, 0) coordinate was not sampled , while the bottom quarter of this patch still contained the image. These issues are fixed in this PR. For potential required lookup for the visual validation plots for this PR, check intermediate commit 7910ed8/

wholeslidedata/buffer/patchcommander.py

@@ -7,16 +7,16 @@
 import numpy as np
 
 from wholeslidedata.image.wholeslideimage import WholeSlideImage
-
+from wholeslidedata.samplers.utils import crop_data
 
 @dataclass
 class PatchConfiguration:
     patch_shape: tuple = (512, 512, 3)
     spacings: tuple = (0.5,)
     overlap: tuple = (0, 0)
-    offset: tuple = (0, 0)
+    offset: tuple = (0, 0) # This currently has to be provided already scaled
     center: bool = False
-
+    write_shape: tuple = None # This can be used when you crop off (overlapping) borders of the patches, only patches with mask in the inner part will be sampled
 
 class PatchCommander(Commander):
     def __init__(
@@ -81,20 +81,41 @@ def create_message(self) -> dict:
 
 class SlidingPatchCommander(PatchCommander):
     def get_patch_messages(self):
-        messages = []
-        step_row = int(self._patch_configuration.patch_shape[0] * self._ratio) - int(
-            self._patch_configuration.overlap[0] * self._ratio
-        )
-        step_col = int(self._patch_configuration.patch_shape[1] * self._ratio) - int(
-            self._patch_configuration.overlap[1] * self._ratio
-        )
+        step_shape = (int(self._patch_configuration.patch_shape[0]) - int(self._patch_configuration.overlap[0]), int(self._patch_configuration.patch_shape[1]) - int(self._patch_configuration.overlap[1]))
+        step_shape_scaled = (step_shape[0] * self._ratio, step_shape[1] * self._ratio)
+        # TODO: # offset has/had to be provided already scaled, I think this should be changed though
+        # offset_scaled = (self._patch_configuration.offset[0] * self._ratio, self._patch_configuration.offset[1] * self._ratio) 
+        # offset_scaled = tuple(o%ss for o, ss in zip(offset_scaled, step_shape_scaled))
+        offset_scaled = (self._patch_configuration.offset[0], self._patch_configuration.offset[1]) 
+        offset_scaled = tuple(o%ss for o, ss in zip(offset_scaled, step_shape_scaled))
+        patch_shape_scaled = (self._patch_configuration.patch_shape[0] * self._ratio, self._patch_configuration.patch_shape[1] * self._ratio, self._patch_configuration.patch_shape[2])
+
+        if self._patch_configuration.center:
+            first_coord = [
+                offset_scaled[0] - ((offset_scaled[0] + patch_shape_scaled[0] // 2) // step_shape_scaled[0] - (1 if (offset_scaled[0] + patch_shape_scaled[0] // 2) % step_shape_scaled[0] == 0 else 0)) * step_shape_scaled[0],
+                offset_scaled[1] - ((offset_scaled[1] + patch_shape_scaled[1] // 2) // step_shape_scaled[1] - (1 if (offset_scaled[1] + patch_shape_scaled[1] // 2) % step_shape_scaled[1] == 0 else 0)) * step_shape_scaled[1]
+            ]
+        else:
+            first_coord = [
+                offset_scaled[0] - ((offset_scaled[0] + patch_shape_scaled[0]) // step_shape_scaled[0] - (1 if (offset_scaled[0] + patch_shape_scaled[0]) % step_shape_scaled[0] == 0 else 0)) * step_shape_scaled[0],
+                offset_scaled[1] - ((offset_scaled[1] + patch_shape_scaled[1]) // step_shape_scaled[1] - (1 if (offset_scaled[1] + patch_shape_scaled[1]) % step_shape_scaled[1] == 0 else 0)) * step_shape_scaled[1]
+            ]
 
+        max_i = int(self._x_dims + offset_scaled[0] + patch_shape_scaled[0] // 2) if self._patch_configuration.center else int(self._x_dims + offset_scaled[0])
+        max_j = int(self._y_dims + offset_scaled[1] + patch_shape_scaled[0] // 2) if self._patch_configuration.center else int(self._y_dims + offset_scaled[1])
+        max_i = max_i if not self._patch_configuration.center else max_i + patch_shape_scaled[0] // 2
+        max_j = max_j if not self._patch_configuration.center else max_j + patch_shape_scaled[1] // 2
+
+        range_i = list(range(first_coord[0], max_i, step_shape_scaled[0]))
+        range_j = list(range(first_coord[1], max_j, step_shape_scaled[1]))
+
         wsm = None
         if self._mask_path is not None:
             wsm = WholeSlideImage(self._mask_path, backend=self._backend, auto_resample=True)
 
-        for row in range(self._patch_configuration.offset[1], self._y_dims, step_row):
-            for col in range(self._patch_configuration.offset[0], self._x_dims, step_col):
+        messages = []
+        for row in range_j:
+            for col in range_i:
                 if wsm is not None:
                     mask_patch = wsm.get_patch(
                         x=col,
@@ -106,6 +127,8 @@ def get_patch_messages(self):
                         relative=self._level_0_spacing,
                     )
 
+                    if self._patch_configuration.write_shape is not None:
+                        mask_patch = crop_data(mask_patch, self._patch_configuration.write_shape)
                     if np.all(mask_patch == 0):
                         continue