run-gradio.py

import os, os.path
from os.path import splitext
import numpy as np
import sys
import matplotlib.pyplot as plt
import torch
import torchvision
import wget 

destination_folder = "output"
destination_for_weights = "weights"

if os.path.exists(destination_for_weights):
    print("The weights are at", destination_for_weights)
else:
    print("Creating folder at ", destination_for_weights, " to store weights")
    os.mkdir(destination_for_weights)
    
segmentationWeightsURL = 'https://github.com/douyang/EchoNetDynamic/releases/download/v1.0.0/deeplabv3_resnet50_random.pt'

if not os.path.exists(os.path.join(destination_for_weights, os.path.basename(segmentationWeightsURL))):
    print("Downloading Segmentation Weights, ", segmentationWeightsURL," to ",os.path.join(destination_for_weights, os.path.basename(segmentationWeightsURL)))
    filename = wget.download(segmentationWeightsURL, out = destination_for_weights)
else:
    print("Segmentation Weights already present")

torch.cuda.empty_cache()

def collate_fn(x):
    x, f = zip(*x)
    i = list(map(lambda t: t.shape[1], x))
    x = torch.as_tensor(np.swapaxes(np.concatenate(x, 1), 0, 1))
    return x, f, i

model = torchvision.models.segmentation.deeplabv3_resnet50(pretrained=False, aux_loss=False)
model.classifier[-1] = torch.nn.Conv2d(model.classifier[-1].in_channels, 1, kernel_size=model.classifier[-1].kernel_size)

print("loading weights from ", os.path.join(destination_for_weights, "deeplabv3_resnet50_random"))

if torch.cuda.is_available():
    print("cuda is available, original weights")
    device = torch.device("cuda")
    model = torch.nn.DataParallel(model)
    model.to(device)
    checkpoint = torch.load(os.path.join(destination_for_weights, os.path.basename(segmentationWeightsURL)))
    model.load_state_dict(checkpoint['state_dict'])
else:
    print("cuda is not available, cpu weights")
    device = torch.device("cpu")
    checkpoint = torch.load(os.path.join(destination_for_weights, os.path.basename(segmentationWeightsURL)), map_location = "cpu")
    state_dict_cpu = {k[7:]: v for (k, v) in checkpoint['state_dict'].items()}
    model.load_state_dict(state_dict_cpu)

model.eval()

def segment(inp):
    x = inp.transpose([2, 0, 1])  #  channels-first
    x = np.expand_dims(x, axis=0)  # adding a batch dimension    
    
    mean = x.mean(axis=(0, 2, 3))
    std = x.std(axis=(0, 2, 3))
    x = x - mean.reshape(1, 3, 1, 1)
    x = x / std.reshape(1, 3, 1, 1)
    
    with torch.no_grad():
        x = torch.from_numpy(x).type('torch.FloatTensor').to(device)
        output = model(x)    
    
    y = output['out'].numpy()
    y = y.squeeze()
    
    out = y>0    
    
    mask = inp.copy()
    mask[out] = np.array([0, 0, 255])
    
    return mask

import gradio as gr

i = gr.inputs.Image(shape=(112, 112))
o = gr.outputs.Image()

examples = [["img1.jpg"], ["img2.jpg"]]
title = "Left Ventricle Segmentation"
description = "This semantic segmentation model identifies the left ventricle in echocardiogram videos. Accurate evaluation of the motion and size of the left ventricle is crucial for the assessment of cardiac function and ejection fraction. In this interface, the user inputs apical-4-chamber images from echocardiography videos and the model will output a prediction of the localization of the left ventricle in blue. This model was trained on the publicly released EchoNet-Dynamic dataset of 10k echocardiogram videos with 20k expert annotations of the left ventricle and published as part of ‘Video-based AI for beat-to-beat assessment of cardiac function’ by Ouyang et al. in Nature, 2020."
thumbnail = "https://raw.githubusercontent.com/gradio-app/hub-echonet/master/thumbnail.png"

gr.Interface(segment, i, o, examples=examples, allow_flagging=False, analytics_enabled=False,
	title=title, description=description, thumbnail=thumbnail).launch()