pdxnet-image-analysis-aacr2022/plot_annotation_masks.py at main · TheJacksonLaboratory/pdxnet-image-analysis-aacr2022 · GitHub

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# conda activate /Users/whitebr/opt/anaconda3/envs/histoqc-new

from hne_image_utils.mask_utils import create_tissue_resident_annotation_polygons, plot_polygons
import pandas as pd
import matplotlib.pyplot as plt


all_imgs = ['10256', '10415', '10416', '10779', '11155', '11170', '11547', '12459', '7705', '8197', '8202', '8500', '8501', '9155', '9296', '9468', '9894']
# all_imgs = ['10256']
all_imgs = ['11170']


pdmr_img_dict = {}
for img_name in all_imgs:
    print(img_name)

    image_wsi_file = '/Users/whitebr/work/jax/pdxnet/svs/pdmr/' + img_name + '.svs'
    annotation_geojson_file = '/Users/whitebr/Box/Brian files/' + img_name + '.geojson'
    annotation_geojson_file = '/Users/whitebr/Library/CloudStorage/Box-Box/Brian files/' + img_name + '.geojson'
    tissue_mask_file = '/Users/whitebr/work/jax/HistoQC/old-histoqcs/histoqc_output_pdmr_v2.1-no-blur-no-fat/' + img_name + '.svs/' + img_name + '.svs_mask_use.png'

    annos = create_tissue_resident_annotation_polygons(image_wsi_file, annotation_geojson_file, tissue_mask_file)
    plot_polygons(annos)
    plt.savefig("regional-annos-" + img_name + ".png", bbox_inches="tight")
    plt.savefig("regional-annos-" + img_name + ".pdf", bbox_inches="tight")

    plot_polygons(annos, show_legend = False)
    plt.savefig("regional-annos-" + img_name + "-no-legend.png", bbox_inches="tight")
    plt.savefig("regional-annos-" + img_name + "-no-legend.pdf", bbox_inches="tight")