From 3401fea59760d434aa17d60ae81e8dceb3df1620 Mon Sep 17 00:00:00 2001 From: Jonas Teuwen Date: Thu, 12 Oct 2023 13:32:20 +0200 Subject: [PATCH] Adapt to upstream dlup --- ahcore/callbacks.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/ahcore/callbacks.py b/ahcore/callbacks.py index c90c6cb..e053488 100644 --- a/ahcore/callbacks.py +++ b/ahcore/callbacks.py @@ -21,8 +21,8 @@ from dlup import SlideImage from dlup._image import Resampling from dlup.annotations import WsiAnnotations -from dlup.data.dataset import ConcatDataset, TiledROIsSlideImageDataset -from dlup.data.transforms import RenameLabels, convert_annotations +from dlup.data.dataset import ConcatDataset, TiledWsiDataset +from dlup.data.transforms import convert_annotations, rename_labels from dlup.tiling import Grid, GridOrder, TilingMode from dlup.writers import TiffCompression, TifffileImageWriter from pytorch_lightning.callbacks import Callback @@ -119,8 +119,9 @@ def _generate_regions(self) -> list[tuple[int, int]]: """ regions = [] for coordinates in self._grid: - if self._mask is None or self._is_masked((coordinates[0], coordinates[1])): - regions.append(coordinates) + _coordinates = (coordinates[0], coordinates[1]) + if self._mask is None or self._is_masked(_coordinates): + regions.append(_coordinates) return regions def _is_masked(self, coordinates: tuple[int, int]) -> bool: @@ -201,9 +202,7 @@ def _get_annotation_data( raise ValueError("Index map is not provided.") _annotations = self._annotations.read_region(coordinates, self._scaling, self._region_size) - _annotations = RenameLabels(remap_labels=self._data_description.remap_labels)({"annotations": _annotations})[ - "annotations" - ] + _annotations = rename_labels(_annotations, remap_labels=self._data_description.remap_labels) points, boxes, region, roi = convert_annotations( _annotations, @@ -361,7 +360,7 @@ def _batch_end( f"TrainerFn {trainer.state.fn} is not supported for {self.__class__.__name__}." ) - current_dataset: TiledROIsSlideImageDataset + current_dataset: TiledWsiDataset current_dataset, _ = total_dataset.index_to_dataset(self._dataset_index) # type: ignore slide_image = current_dataset.slide_image