app.py

import spaces
import gradio as gr
from util import imread, imsave, copy_skimage_data
import torch
from PIL import Image, ImageDraw
import numpy as np
from os.path import join


def torch_compile(*args, **kwargs):
    def decorator(func):
        return func

    return decorator


torch.compile = torch_compile  # temporary workaround

default_model = 'ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c'
default_score_thresh = .9
default_nms_thresh = np.round(np.pi / 10, 4)
default_samples = 128
default_order = 5

examples_dir = 'examples'
copy_skimage_data(examples_dir)
examples = [
    [join(examples_dir, 'bbbc039_test_00014.png'), 'ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c', False, default_score_thresh, False,
     default_nms_thresh, True, 64, True],
    [join(examples_dir, 'coins.png'), 'ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c', False, default_score_thresh, False,
     default_nms_thresh, True, 64, True],
    [join(examples_dir, 'cell.png'), 'ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c', False, default_score_thresh, False,
     default_nms_thresh, True, 64, True],
]


@spaces.GPU
def predict(
        filename, model=None,
        enable_score_threshold=False, score_threshold=.9,
        enable_nms_threshold=False, nms_threshold=0.3141592653589793,
        enable_samples=False, samples=128,
        use_label_channels=False,
        enable_order=False, order=5,
        device=None,
):
    from cpn import CpnInterface
    from prep import multi_norm
    from celldetection import label_cmap, to_h5, data, __version__

    global default_model
    assert isinstance(filename, str)

    if device is None:
        if torch.cuda.device_count():
            device = 'cuda'
        else:
            device = 'cpu'

    meta = dict(
        cd_version=__version__,
        filename=str(filename),
        model=model,
        device=device,
        use_label_channels=use_label_channels,
        enable_score_threshold=enable_score_threshold,
        score_threshold=float(score_threshold),
        enable_order=enable_order,
        order=order,
        enable_nms_threshold=enable_nms_threshold,
        nms_threshold=float(nms_threshold),
    )
    print(meta, flush=True)

    raw = img = imread(filename)
    print('Image:', img.dtype, img.shape, (img.min(), img.max()), flush=True)
    if model is None or len(str(model)) <= 0:
        model = default_model

    img = multi_norm(img, 'cstm-mix')  # TODO

    kw = {}
    if enable_score_threshold:
        kw['score_thresh'] = score_threshold
    if enable_nms_threshold:
        kw['nms_thresh'] = nms_threshold
    if enable_order:
        kw['order'] = order
    if enable_samples:
        kw['samples'] = samples
    m = CpnInterface(model.strip(), device=device, **kw)
    y = m(img, reduce_labels=not use_label_channels)

    dst_h5 = '.'.join(filename.split('.')[:-1]) + '.h5'
    to_h5(
        dst_h5, inputs=img, **y,
        attributes=dict(inputs=meta)
    )

    labels = y['labels']
    vis_labels = label_cmap(labels)

    dst_csv = '.'.join(filename.split('.')[:-1]) + '.csv'
    data.labels2property_table(
        labels,
        "label", "area", "feret_diameter_max", "bbox", "centroid", "convex_area",
        "eccentricity", "equivalent_diameter",
        "extent", "filled_area", "major_axis_length",
        "minor_axis_length", "orientation", "perimeter",
        "solidity", "mean_intensity", "max_intensity", "min_intensity",
        intensity_image=raw
    ).to_csv(dst_csv)

    return vis_labels, img, dst_h5, dst_csv


with gr.Blocks(title='Cell Segmentation with Contour Proposal Networks') as app:
    with gr.Row():
        gr.Markdown("<center><strong><font size='7'>"
                    "Cell Segmentation with Contour Proposal Networks 🤗</font></strong></center>")

    with gr.Row():
        with gr.Column():
            img = gr.components.Image(label="Upload Input Image", type="filepath", interactive=True,
                                      value=examples[0][0])
        with gr.Column():
            model_name = gr.components.Textbox(label='Model Name', value=default_model, max_lines=1)
            with gr.Row():
                score_thresh_ck = gr.components.Checkbox(label="Use custom Score Threshold", value=False)
                score_thresh = gr.components.Slider(minimum=0, maximum=1, label="Score Threshold",
                                                    value=default_score_thresh)
            with gr.Row():
                nms_thresh_ck = gr.components.Checkbox(label="Use custom NMS Threshold", value=False)
                nms_thresh = gr.components.Slider(minimum=0, maximum=1, label="NMS Threshold", value=default_nms_thresh)
            # with gr.Row():
            #     # The range of this would need to be model dependent
            #     order_ck = gr.components.Checkbox(label="Use custom Order", value=False)
            #     order = gr.components.Slider(minimum=0, maximum=1, label="Order", value=default_order)
            with gr.Row():
                samples_ck = gr.components.Checkbox(label="Use custom Sample Points", value=False)
                samples = gr.components.Slider(minimum=8, maximum=256, label="Sample Points", value=default_samples)
            with gr.Row():
                channels = gr.components.Checkbox(label="Allow overlapping objects", value=True)
            with gr.Row():
                clr = gr.Button('Reset')
                btn = gr.Button('Run')
    with gr.Row():
        with gr.Column():
            out_img = gr.Image(label="Processed Image")
        with gr.Column():
            out_vis = gr.Image(label="Label Image (random colors, transparent overlap)")
    with gr.Row():
        out_h5 = gr.File(label="Download Results as HDF5 File")
        out_csv = gr.File(label="Download Properties as CSV File")

    with gr.Row():
        gr.Examples(
            fn=predict,
            examples=examples,
            inputs=[img, model_name, score_thresh_ck, score_thresh, nms_thresh_ck, nms_thresh, samples_ck, samples,
                    channels],
            outputs=[out_vis, out_img, out_h5, out_csv],
            cache_examples=True,
            batch=False
        )

    btn.click(
        predict,
        inputs=[img, model_name, score_thresh_ck, score_thresh, nms_thresh_ck, nms_thresh, samples_ck, samples,
                channels],
        outputs=[out_vis, out_img, out_h5, out_csv]
    )
    clr.click(
        lambda: (
        None, default_score_thresh, default_nms_thresh, False, False, None, None, None, False, default_samples),
        inputs=[],
        outputs=[img, score_thresh, nms_thresh, score_thresh_ck, nms_thresh_ck, out_img, out_h5, out_vis, samples_ck,
                 samples]
    )

    with gr.Row():
        gr.Markdown("<center><font size='3'>"
                    "<a href='https://github.com/FZJ-INM1-BDA/celldetection'>Visit us on GitHub</a></font></center>")
app.launch()