sandbox.py

import h5py
from openslide import OpenSlide
import matplotlib.pyplot as plt
import numpy as np
# open in read mode
file_path = "FEATURES_DIRECTORY/h5_files/TUPAC-TR-016.h5"
file_path = "results/patches/TUPAC-TR-016.h5"
wsl_path = "data/TUPAC-TR-016.svs"


# Open the slide
slide = OpenSlide(wsl_path)
level = 1
# Get the dimensions of the slide
dimensions = slide.dimensions
print(f"Slide dimensions: {dimensions}")

level_dimensions = slide.level_dimensions[level]
print(f"Level {level} dimensions: {level_dimensions}")
patch_size = 256
with h5py.File(file_path, "r") as f:
    # List all groups
    print("Keys:", list(f.keys()))
    # Access a dataset
    data = f["coords"]
    #data = f["features"]
    print(data.shape, data.dtype)
    print(data[:10])
    n_subplots = 4
    n_rows = int(np.sqrt(n_subplots))
    n_cols = int(np.sqrt(n_subplots))
    fig, ax = plt.subplots(n_rows, n_cols, figsize=(10, 10))
    plot_count = 0
    for i, coord in enumerate(data):
        if i < 4:
            continue
        if plot_count >= n_subplots:
            break
        patch_image = slide.read_region(coord, level, (patch_size, patch_size))
        ax[plot_count//n_cols, plot_count%n_cols].imshow(patch_image)
        ax[plot_count//n_cols, plot_count%n_cols].set_xticks([])
        ax[plot_count//n_cols, plot_count%n_cols].set_yticks([])
        plot_count+=1
    plt.savefig("results/patches/TUPAC-TR-016_patches_samples.png")
    plt.show()