app.py

import os 
os.system('pip install detectron2 -f https://dl.fbaipublicfiles.com/detectron2/wheels/cu102/torch1.9/index.html')
os.system('pip install torch==1.9.0 torchvision==0.10.0')

import gradio as gr
# check pytorch installation: 
import torch, torchvision
print(torch.__version__, torch.cuda.is_available())
assert torch.__version__.startswith("1.9")   # please manually install torch 1.9 if Colab changes its default version
import detectron2
from detectron2.utils.logger import setup_logger
import numpy as np
import os, json, random
from detectron2 import model_zoo
from detectron2.engine import DefaultPredictor
from detectron2.config import get_cfg
from PIL import Image
from pathlib import Path
from matplotlib import pyplot as plt


cfg = get_cfg()
cfg.MODEL.DEVICE='cpu'
cfg.INPUT.MASK_FORMAT='bitmask'
cfg.MODEL.ROI_HEADS.NUM_CLASSES = 3 
cfg.TEST.DETECTIONS_PER_IMAGE = 1000
cfg.merge_from_file(model_zoo.get_config_file("COCO-InstanceSegmentation/mask_rcnn_R_50_FPN_3x.yaml"))
cfg.MODEL.ROI_HEADS.SCORE_THRESH_TEST = 0.5  # set threshold for this model
cfg.MODEL.WEIGHTS = "model_final.pth"

predictor = DefaultPredictor(cfg)


def inference(img):
    class_names = ['0','1','2'] #['astro', 'cort', 'sh-sy5y']
    im = np.asarray(Image.open(img).convert('RGB'))
    outputs = predictor(im)
    pred_classes = outputs['instances'].pred_classes.cpu().numpy().tolist()
    take = outputs['instances'].scores >= 0.5 #Threshold
    pred_masks = outputs['instances'].pred_masks[take].cpu().numpy()
    pred_class = max(set(pred_classes), key=pred_classes.count)

    mask = np.stack(pred_masks)
    mask = np.any(mask == 1, axis=0)

    p = plt.imshow(im,cmap='gray')
    p = plt.imshow(mask, alpha=0.4)
    p = plt.xticks(fontsize=8)
    p = plt.yticks(fontsize=8)
    p = plt.title("cell type: " + class_names[pred_class])

    return plt




title = "Sartorius Cell Instance Segmentation"
description = "Sartorius Cell Instance Segmentation Demo: Current Kaggle competition - kaggle.com/c/sartorius-cell-instance-segmentation"
article = "<p style='text-align: center'><a href='https://ai.facebook.com/blog/-detectron2-a-pytorch-based-modular-object-detection-library-/' target='_blank'>Detectron2: A PyTorch-based modular object detection library</a> | <a href='https://github.com/facebookresearch/detectron2' target='_blank'>Github Repo</a></p>"
examples = [['0030fd0e6378.png']]  
gr.Interface(inference, inputs=gr.inputs.Image(type="filepath"), outputs=gr.outputs.Image('plot')  ,enable_queue=True, title=title,
    description=description,
    article=article,
    examples=examples).launch(debug=False)