From b20136759696207a848fb385d7ce5541b1925ab1 Mon Sep 17 00:00:00 2001 From: laynholt Date: Thu, 8 May 2025 10:06:57 +0000 Subject: [PATCH] Fixed bugs that prevented the project from running. Mediar Former values for the F1 metric were achieved. --- core/data/transforms/cell_aware.py | 4 ++-- core/segmentator.py | 10 +++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/core/data/transforms/cell_aware.py b/core/data/transforms/cell_aware.py index b582346..21c606e 100644 --- a/core/data/transforms/cell_aware.py +++ b/core/data/transforms/cell_aware.py @@ -5,12 +5,12 @@ from typing import Dict, Sequence, Tuple, Union from skimage.segmentation import find_boundaries from monai.transforms import RandScaleIntensity, Compose, MapTransform # type: ignore -import logging +from core.logger import get_logger __all__ = ["BoundaryExclusion", "IntensityDiversification"] -logger = logging.getLogger("cell_aware") +logger = get_logger("cell_aware") class BoundaryExclusion(MapTransform): diff --git a/core/segmentator.py b/core/segmentator.py index 7b07172..e76c7d2 100644 --- a/core/segmentator.py +++ b/core/segmentator.py @@ -1270,20 +1270,20 @@ class CellSegmentator: # Use provided start_index when metadata missing base_name = f"prediction_{start_index:04d}" + # Save mask TIFF (16-bit) + mask_filename = f"{base_name}_mask.tif" + mask_path = os.path.join(masks_dir, mask_filename) + tiff.imwrite(mask_path, pred_array.astype(np.uint16), compression="zlib") + # Now pred_array shape is (C, H, W) num_channels = pred_array.shape[0] for channel_idx in range(num_channels): channel_mask = pred_array[channel_idx] # File names - mask_filename = f"{base_name}_ch{channel_idx:01d}.tif" plot_filename = f"{base_name}_ch{channel_idx:01d}.png" - mask_path = os.path.join(masks_dir, mask_filename) plot_path = os.path.join(plots_dir, plot_filename) - # Save mask TIFF (16-bit) - tiff.imwrite(mask_path, channel_mask.astype(np.uint16), compression="zlib") - # Extract corresponding true mask channel if exists true_mask = None if mask_array is not None and mask_array.ndim == 3: