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| import os | |
| import slideio | |
| from PIL import Image | |
| ####################Convert SVS files to JPEG files#################### | |
| # Set the path to the svs files | |
| svs_path = "/Users/josedelgado/Downloads/" | |
| # Set the path to the output directory | |
| output_path = "/Users/josedelgado/Documents/GitHub/microbiology/Images" | |
| # Set the size of the representative image | |
| size = (224, 224) | |
| # Loop through the svs files | |
| for root, dirs, files in os.walk(svs_path): | |
| for filename in files: | |
| if filename.endswith(".svs"): | |
| print("processing " + os.path.join(root, filename) ) | |
| # Open the svs file | |
| slide = slideio.open_slide(os.path.join(root, filename)) | |
| # Get the number of scenes in the slide | |
| num_scenes = slide.num_scenes | |
| for i in range(num_scenes): | |
| # Get the scene | |
| scene = slide.get_scene(i) | |
| # Check if the scene is not None | |
| if scene is not None: | |
| # Get the metadata of the scene | |
| metadata_str = scene.get_raw_metadata() | |
| print(metadata_str) | |
| # Loop through the channels | |
| for j in range(scene.num_channels): | |
| # Read the channel datay | |
| channel_data = scene.read_block(channel_indices=[j], size=(8000,0)) | |
| # Convert the channel data to a PIL image | |
| image = Image.fromarray(channel_data) | |
| # Set the output filename | |
| output_filename = os.path.splitext(filename)[0] + f"_scene_{i}_channel_{j}.jpeg" | |
| # Set the output directory | |
| output_dir = os.path.join(output_path, os.path.relpath(root, svs_path)) | |
| # Create the output directory if it doesn't exist | |
| if not os.path.exists(output_dir): | |
| os.makedirs(output_dir) | |
| # Save the image in the ImageNet file folder format | |
| output_file = os.path.join(output_dir, output_filename) | |
| image.save(output_file) | |
| else: | |
| print(f"Scene {i} is None for file {filename}") |