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| import gradio as gr | |
| import openslide | |
| from PIL import Image, ImageDraw | |
| from xml.etree import ElementTree as ET | |
| # accept slide thumbnail, x, y and annotation | |
| def get_mask_from_xml(xml_path, image_size, image_shrinking_factor): | |
| tree = ET.parse(xml_path) | |
| root = tree.getroot() | |
| image = Image.new("L", image_size, "white") | |
| draw = ImageDraw.Draw(image) | |
| draw.fill = True | |
| label2grayscale_color = {"bg": 0, "tissue": 1, "tisuue": 1} | |
| for i in root[0]: | |
| annotation_type = i.attrib["Type"] | |
| annotation_label = i.attrib["PartOfGroup"] | |
| # there is roi rectangle | |
| if annotation_type not in ["Spline", "Polygon", "Rectangle"]: | |
| print(f"Annotation type must be either Spline, Rectangle or Polygon but found: {annotation_type}") | |
| continue | |
| if annotation_label not in label2grayscale_color: | |
| print(f"Annotation label must be either tissue or bg but found: {annotation_label}") | |
| continue | |
| coordinates = [(i.attrib["X"], i.attrib["Y"]) for i in i[0]] | |
| coordinates = [(str2float(x), str2float(y)) for x, y in coordinates] | |
| coordinates = [(x*image_shrinking_factor, y*image_shrinking_factor) for x, y in coordinates] | |
| if annotation_type in ["Spline", "Polygon"]: | |
| draw.polygon(coordinates, fill=label2grayscale_color[annotation_label]) | |
| elif annotation_type == "Rectangle": | |
| # ^ | |
| # | point 1 is bigger than point 3 | |
| # | 0 1 | |
| # | 3 2 | |
| # |-------> | |
| draw.rectangle([coordinates[3], coordinates[1]], fill=label2grayscale_color[annotation_label]) | |
| # if annotation_type == "Spline": | |
| # draw.line(coordinates, fill=label2grayscale_color[annotation_label], width=1) | |
| # elif annotation_type == "Polygon": | |
| # draw.polygon(coordinates, fill=label2grayscale_color[annotation_label]) | |
| return image | |
| # output as png or npy | |
| def process(x, y, annotation_size, annotation): | |
| image_shrinking_factor = annotation_size / min(x, y) | |
| # get thumbnail | |
| image = get_mask_from_xml(annotation, (annotation_size, annotation_size), image_shrinking_factor) | |
| image.save("mask.png") | |
| return "mask.png" | |
| demo = gr.Interface( | |
| fn=process, | |
| inputs=[ | |
| # gr.File(label="Slide thumbnail", type="file", accept=".png"), | |
| gr.Number(label="X", value=10_000), | |
| gr.Number(label="Y", value=10_000), | |
| gr.Number(label="Thumbnail size", value=500), | |
| gr.File(label="ASAP Annotation", file_types=[".xml"]), | |
| ], | |
| outputs="image", | |
| title="Reverse Text", | |
| description="Reverses the text entered by the user", | |
| ) | |
| demo.launch() | |