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| 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 = "Example: Echocardiogram Segmentation" #"Left Ventricle Segmentation" | |
| description = "This semantic segmentation model identifies the left ventricle in echocardiogram images. Read more at the links below." | |
| # 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" | |
| article = "<div style='text-align: center;'><a href='https://pubmed.ncbi.nlm.nih.gov/31993508/' target='_blank'>Deep learning interpretation of echocardiograms</a><center><img src='https://visitor-badge.glitch.me/badge?page_id=example_space_cvpr' alt='visitor badge'></center></div>" | |
| gr.Interface(segment, i, o, examples=examples, allow_flagging=False, analytics_enabled=False, | |
| title=title, description=description, thumbnail=thumbnail,article=article).launch(enable_queue=True) | |