app.py

"""
<script src="https://cdn.jsdelivr.net/npm/[email protected]/release/current/standard/papaya.min.js"></script>
<link href="https://cdn.jsdelivr.net/npm/[email protected]/release/current/standard/papaya.min.css" rel="stylesheet">
<div class="papaya" data-params="params"></div>

TODO:
https://www.gradio.app/guides/custom-components-in-five-minutes
https://github.com/gradio-app/gradio/issues/6821

"""


import os
import gradio as gr

import numpy as np
import PIL
import SimpleITK as sitk

THIS_DIR = os.path.dirname(os.path.abspath(__file__))
example_image_path = os.path.join(THIS_DIR,'files','promis12-test-Case00.nii.gz') # from promise12
example_mask_path = os.path.join(THIS_DIR,'files','promis12-test-Case00-mask.nii.gz') # from promise12

mydict = {}

def load_data(input1,input2):
    global mydict
    mydict['image_path'] = input1.name
    mydict['mask_path'] = input2.name
    img = sitk.GetArrayFromImage(sitk.ReadImage(mydict['image_path']))
    mask = sitk.GetArrayFromImage(sitk.ReadImage(mydict['mask_path']))
    minval,maxval = np.min(img),np.max(img)
    img = ((img-minval)/(maxval-minval)).clip(0,1)*255
    mydict['img'] = img.astype(np.uint8)
    mydict['mask'] = mask.astype(np.uint8)
    return f"Image and mask files uploaded, move the above slider to trigger rendering of below component."

def render(x, state):
    if len(mydict)==4:
        if x > mydict['img'].shape[0]-1:
            x = mydict['img'].shape[0]-1
        if x < 0:
            x = 0
        image = mydict['img'][x,:,:]
        mask = mydict['mask'][x,:,:]
        value = (image,[(mask,"prostate")])
        zmin, zmax = 0,mydict['img'].shape[0]-1
    else:
        image = np.zeros(10,10)
        zmin, zmax = None, None
        value = (image,[])

    return value,f'z-value: {x}, (zmin: {zmin}, zmax: {zmax})'

with gr.Blocks() as demo:
    with gr.Column():
        gr.Markdown(
        """
        # bare-bones nifti image and mask viewer with Gradio 
        """)
    with gr.Row():
        image_file = gr.File(label="upload image nifti file here")
        mask_file = gr.File(label="upload mask nifti file here")
    
    with gr.Column():
        btn = gr.Button("upload")
        slider = gr.Slider(0, 20, step=1)
        state = gr.State(value=0)
        out = gr.Textbox(label='text-comment')
    with gr.Row():
        myimage = gr.AnnotatedImage(height=512)
    gr.Examples(
        [[example_image_path,example_mask_path]],
        [image_file, mask_file],
    )
    btn.click(fn=load_data, 
        inputs=[image_file,mask_file], outputs=out,
    )
    slider.change(
        render,
        inputs=[slider, state],
        outputs=[myimage,out],
        api_name="hohoho"
    )

if __name__ == "__main__":
    demo.launch()