From a1514c51624863b1d8f6d04b4248bd6269c14923 Mon Sep 17 00:00:00 2001 From: Winklmayr Date: Mon, 20 Jan 2025 17:15:10 +0100 Subject: [PATCH] adapt filenames in data-loader to new dataset structure --- src/bio_image_datasets/arctique_dataset.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/bio_image_datasets/arctique_dataset.py b/src/bio_image_datasets/arctique_dataset.py index d2026f6..a880480 100644 --- a/src/bio_image_datasets/arctique_dataset.py +++ b/src/bio_image_datasets/arctique_dataset.py @@ -21,8 +21,8 @@ class ArctiqueDataset(Dataset): def __init__(self, local_path): """ Initializes the ArctiqueDataset with the given local path. - The three PanNuke dataset is located on the /fast file system on the MDC cluster under the path - '/fast/AG_Kainmueller/synth_unc_models/data/v_review_sample1500_NOISY'. + The dataset is located on the /fast file system on the MDC cluster under the path + '/fast/AG_Kainmueller/data/patho_foundation_model_bench_data/arctique_dataset/arctique'. Args: local_path (str): Path to the directory containing the files. """ @@ -30,9 +30,9 @@ def __init__(self, local_path): print("LOCAL PATH", local_path) - self.images_folder = os.path.join(local_path, f'train/images/') - self.semantic_masks_folder = os.path.join(local_path, f'train/masks/semantic_noise_0') - self.instance_masks_folder = os.path.join(local_path, f'train/masks/instance_noise_0') + self.images_folder = os.path.join(local_path, f'images/') + self.semantic_masks_folder = os.path.join(local_path, f'masks/semantic') + self.instance_masks_folder = os.path.join(local_path, f'masks/instance') self.sample_IDs = [int(name.split("_")[1].split(".")[0]) for name in os.listdir(self.images_folder)]