app.py

import os
import sys
import json
import uuid
import shutil
import tempfile
import pydicom
import datetime
from datetime import timezone
import pandas as pd
import SimpleITK as sitk
from huggingface_hub import snapshot_download

import gradio as gr
from gradio_pdf import PDF

HF_ACCESS_TOKEN = os.environ.get("HF_ACCESS_TOKEN")
USERNAME = os.environ.get("USERNAME")
PASSWORD = os.environ.get("PASSWORD")

dlqlf_model_folder = snapshot_download(repo_id="cvib/dlqlf-model",repo_type='model',token=HF_ACCESS_TOKEN)
# we are pulling report_utils from cvib/dlqlf-model
sys.path.append(os.path.join(dlqlf_model_folder,"report"))
from report_utils import NiftiVisualizer

mlqlf_repo_folder = snapshot_download(repo_id="cvib/mlqlf-model",repo_type='model',token=HF_ACCESS_TOKEN)
sys.path.append(os.path.join(mlqlf_repo_folder,"lungseg","src"))
sys.path.append(os.path.join(mlqlf_repo_folder,"mlqlf","src"))

from lungqia import compute_lungqia_wrapper
from foobar import transform_lungqia_to_mlqlf

def imread(file_list):
    reader = sitk.ImageSeriesReader()
    reader.SetFileNames(file_list)
    img_obj = reader.Execute()
    return img_obj

def main_func(input_file_list):
    with tempfile.TemporaryDirectory() as tempdir:

        print('start time:',datetime.datetime.now(timezone.utc).strftime('%Y-%m-%d-%H-%M-%S-%Z'))
        image_file = os.path.join(tempdir,f"image.nii.gz")
        first_file = input_file_list[0].name
        file_list = []
        if first_file.endswith(".dcm"):
            for x in input_file_list:
                file_path = x.name
                ds = pydicom.dcmread(file_path,stop_before_pixels=True)
                item = dict(
                    file_path=file_path,
                    instance_number=int(ds.InstanceNumber)
                )
                file_list.append(item)
            file_list = sorted(file_list,key=lambda x:x['instance_number'])
            file_list = [x['file_path'] for x in file_list]
            img_obj = imread(file_list)
        else:
            raise ValueError("only accept .dcm files!")

        sitk.WriteImage(img_obj,image_file)
        seri_file = os.path.join(tempdir,'image.seri')
        with open(seri_file,'w') as f:
            for x in file_list:
                f.write(f"{x}\n")

        work_dir = os.path.join(tempdir,f"work_dir")
        compute_lungqia_wrapper(seri_file,tempdir,lungseg_enable=True,work_dir=work_dir)
        novsl_nifti_file = os.path.join(work_dir,"novsl.nii.gz")
        wlung_nifti_file = os.path.join(work_dir,"wlung.nii.gz")
        lungqia_csv = os.path.join(tempdir,"lungqia_results.csv")

        assert(os.path.exists(novsl_nifti_file))
        assert(os.path.exists(wlung_nifti_file))
        assert(os.path.exists(lungqia_csv))

        transform_lungqia_to_mlqlf(lungqia_csv,novsl_nifti_file,wlung_nifti_file,tempdir)
        mlqlf_csv_file = os.path.join(tempdir,"mlqlf.csv")
        mlqlf_nifti_file = os.path.join(tempdir,"mlqlf.nii.gz")

        assert(os.path.exists(mlqlf_csv_file))
        assert(os.path.exists(mlqlf_nifti_file))

        my_uid = uuid.uuid4().hex
        output_pdf_file = os.path.join('/tmp',f'{my_uid}.pdf')
        output_csv_file = os.path.join('/tmp',f'{my_uid}.csv')

        inst = NiftiVisualizer("NA",image_file,mlqlf_nifti_file,mlqlf_csv_file,tempdir)
        tmp_pdf_file = inst.gen_pdf()
        assert(os.path.exists(tmp_pdf_file))

        output_df = pd.read_csv(mlqlf_csv_file)
        shutil.copy(tmp_pdf_file,output_pdf_file)
        shutil.copy(mlqlf_csv_file,output_csv_file)
        
        print('uid:',os.path.basename(output_csv_file))
        print('end time:',datetime.datetime.now(timezone.utc).strftime('%Y-%m-%d-%H-%M-%S-%Z'))
        return output_pdf_file, output_df, output_pdf_file, output_csv_file

with gr.Blocks() as demo:
    with gr.Column():
        gr.Markdown(
        """
        # demo - MLQLF (aka LDTA)
        + on the left panel, drag dicom files that belong to the same series to below box.
        + wait for files to be uploaded and click the `process` button at the bottom of the left panel.
        + wait for process to be completed to download the pdf/json on the right panel.
        """)
    with gr.Row():
        with gr.Column():
            in_file = gr.File(label="upload dicom files here",file_count='multiple')
            btn = gr.Button("process")
        with gr.Column():
            pdf = PDF(label="Upload a PDF", interactive=True)
            gr_df = gr.Dataframe()
            download_button_pdf = gr.DownloadButton("Download report pdf", visible=True)
            download_button_csv = gr.DownloadButton("Download report csv", visible=True)
    btn.click(fn=main_func, 
        inputs=[in_file],
        outputs=[pdf,gr_df,download_button_pdf,download_button_csv],
    )

if __name__ == "__main__":
    demo.queue().launch(
        server_name="0.0.0.0",
        debug=True,
        show_api=True,
        share=False,
        auth=(USERNAME,PASSWORD),
    )

"""

docker run -it -u $(id -u):$(id -g) -p 7860:7860 \
    -v $PWD:/opt/demo -w /opt/demo --env-file=.env \
    mlqlf-gradio bash

python app.py

"""