Add output_tile_size parameter to BaseWsiDataset (#193)

- Parameter was accidently removed

dlup/data/dataset.py

@@ -203,6 +203,7 @@ def __init__(
         crop: bool = False,
         mask: MaskTypes | None = None,
         mask_threshold: float | None = 0.0,
+        output_tile_size: tuple[int, int] | None = None,
         annotations: list[_AnnotationTypes] | _AnnotationTypes | None = None,
         labels: list[tuple[str, _LabelTypes]] | None = None,
         backend: ImageBackend = ImageBackend.PYVIPS,
@@ -224,6 +225,9 @@ def __init__(
             Threshold to check against. The foreground percentage should be strictly larger than threshold.
             If None anything is foreground. If 1, the region must be completely foreground.
             Other values are in between, for instance if 0.5, the region must be at least 50% foreground.
+        output_tile_size: tuple[int, int], optional
+            If this value is set, this value will be used as the tile size of the output tiles. If this value
+            is different from the underlying grid, this tile will be extracted around the center of the region.
         annotations :
             Annotation classes.
         labels : list
@@ -242,6 +246,8 @@ def __init__(
         self._crop = crop
         self.regions = regions
 
+        self._output_tile_size = output_tile_size
+
         self.annotations = annotations
         self.labels = labels
         self._backend = backend
@@ -307,6 +313,14 @@ def __getitem__(self, index: Union[int, slice]) -> Union[TileSample, Sequence[Ti
         region_view = slide_image.get_scaled_view(scaling)
         region_view.boundary_mode = BoundaryMode.crop if self.crop else BoundaryMode.zero
 
+        if self._output_tile_size is not None:
+            # If we have an output tile_size, we extract a region around the center of the given region.
+            output_tile_x, output_tile_y = self._output_tile_size
+            coordinates_x = x + w / 2 - output_tile_x / 2
+            coordinates_y = y + h / 2 - output_tile_y / 2
+            coordinates = (coordinates_x, coordinates_y)
+            region_size = self._output_tile_size
+
         region = region_view.read_region(coordinates, region_size)
 
         sample: TileSample = {
@@ -380,6 +394,7 @@ def __init__(
         crop: bool = False,
         mask: MaskTypes | None = None,
         mask_threshold: float | None = 0.0,
+        output_tile_size: tuple[int, int] | None = None,
         annotations: _AnnotationTypes | None = None,
         labels: list[tuple[str, _LabelTypes]] | None = None,
         transform: Callable[[RegionFromWsiDatasetSample], RegionFromWsiDatasetSample] | None = None,
@@ -400,6 +415,7 @@ def __init__(
             crop,
             mask=mask,
             mask_threshold=mask_threshold,
+            output_tile_size=output_tile_size,
             annotations=annotations,
             labels=labels,
             backend=backend,
@@ -418,6 +434,7 @@ def from_standard_tiling(
         mpp: float | None,
         tile_size: tuple[int, int],
         tile_overlap: tuple[int, int],
+        output_tile_size: tuple[int, int] | None = None,
         tile_mode: TilingMode = TilingMode.overflow,
         grid_order: GridOrder = GridOrder.C,
         crop: bool = False,
@@ -442,6 +459,9 @@ def from_standard_tiling(
             Tuple of integers that represent the pixel size of output tiles
         tile_overlap :
             Tuple of integers that represents the overlap of tiles in the x and y direction
+        output_tile_size: tuple[int, int], optional
+            If this value is set, this value will be used as the tile size of the output tiles. If this value
+            is different from the underlying grid, this tile will be extracted around the center of the region.
         tile_mode :
             "skip" or "overflow". see `dlup.tiling.TilingMode` for more information
         grid_order : GridOrder
@@ -523,6 +543,7 @@ def from_standard_tiling(
             crop=crop,
             mask=mask,
             mask_threshold=mask_threshold,
+            output_tile_size=output_tile_size,
             annotations=annotations,
             labels=labels,
             transform=transform,