3D_tissue_visualization/5. Cell instance visualization.py at main · hwanglab/3D_tissue_visualization · GitHub

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# %% Import modules
import sys
sys.path.append('/home/choiyoonho/Documents/HT/3D tissue visualization/')  # <- Working directory where the Utils.py is located.
from Utils import *


# %% Load data
root = '/home/choiyoonho/Documents/HT/HE/Final_data/cropped'
bf_paths = natsort.natsorted(glob(root+'/BF/*'))
ht_paths = natsort.natsorted(glob(root+'/HT/*'))
he_paths = natsort.natsorted(glob(root+'/HE/*'))
jsons = natsort.natsorted((glob('/home/choiyoonho/Documents/HT/HE/Final_data/cropped/Cell_instance/json/*')))

bf_paths = pop_insert(bf_paths, 0, 2)
ht_paths = pop_insert(ht_paths, 0, 2)

type_info = {
    "0" : ["No-label", [0  ,   0,   0]],
    "1" : ["Neoplastic", [255,   0, 0]],
    "2" : ["Inflamatory", [0,   0, 255]],
    "3" : ["Connective", [0  , 255,   0]],
    "4" : ["Necrosis", [255, 0,   0]],
    "5" : ["No-label", [255,   0,   0]]
}

# plt.figure(figsize=(8, 12))
for i, [he_path, ht_path, json_path] in enumerate(zip(he_paths, ht_paths, jsons)):
    he = cv2.imread(he_path)
    he = cv2.cvtColor(he, cv2.COLOR_BGR2RGB)
    ht, _ = load_hdf5_with_attributes(ht_path)  # HT scale

    plt.subplot(5, 3, i * 3 + 1)
    plt.imshow(he)
    plt.title('HE #{}'.format(i+1))
    plt.axis('off')

    plt.subplot(5, 3, i * 3 + 2)
    bbox_list, centroid_list, contour_list, type_list = read_json(json_path)
    coords_xmin, coords_ymin, coords_xmax, coords_ymax = 0, 0, he.shape[1], he.shape[0]
    info_dict = get_info_dict(contour_list, coords_xmin, coords_ymin, coords_xmax, coords_ymax)
    overlaid_output = visualize_instances_dict(he, info_dict, type_colour=type_info)
    # cv2.imwrite(os.path.join(save_fig, 'HE_' + str(i + 1) + '_seg.png'), overlaid_output)
    plt.imshow(overlaid_output)
    plt.axis('off')
    plt.title('Segmentation Overlay - #{}'.format(i+1))
    #
    plt.subplot(5, 3, i * 3 + 3)
    temp_ht = (ht[:,:,0]-ht[:,:,0].min())/ht[:,:,0].max()
    plt.imshow(temp_ht*255, cmap='gray')
    plt.title('HT #{}'.format(i+1))
    plt.axis('off')

plt.suptitle('Serial section images for z axis')
plt.tight_layout()

save_fig= os.path.join('/home/choiyoonho/Documents/HT/HE/Final_data/cropped', 'figs')
plt.savefig(os.path.join(save_fig, 'HE_seg_HT.png'))