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.Image(shape=(112, 112)) o = gr.Image() examples = [["img1.jpg"], ["img2.jpg"]] title = None #"Left Ventricle Segmentation" description = "This semantic segmentation model identifies the left ventricle in echocardiogram images." # 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()