app.py

#!/usr/bin/env python
# coding: utf-8

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import gradio as gr
from fastai.vision.all import *
import skimage

import matplotlib.pyplot as plt
import matplotlib as mpl
from mpl_toolkits.axes_grid1 import make_axes_locatable


def get_files(path):
    folders = path.ls()
    imgs = []
    for f in folders:
        try:
            imgs.append(glob.glob(f'{f}/*camera7*.jpg')[0])
        except:
            continue
    return imgs

def get_mask(filename):
  txt = Path(Path(filename).name).stem
  scene_id = re.findall("\d+", txt)[0]
  db_path = 'celine-3.db'
  conn = sql.connect(db_path)
  c = conn.cursor()

  query = "SELECT trt FROM scenes WHERE scene_id == ?"
  params = [scene_id]
  c.execute(query,params)
  trt = c.fetchall()[0][0]
  
  trt_list = ['PCCCC', 'PCFCF', 'PFEFE', 'PHNHN']
  mask = np.load(glob.glob(f'{path/Path(filename).stem}/*.npy')[0]).squeeze()
  mask = np.where(mask>0.5,1,0)
  mask= mask.astype(np.uint8)
  mask *= [i+1 for i,j in enumerate(trt_list) if j == trt][0]
  return mask



@patch
def __call__(self:DiceLoss, pred, targ):
        targ = self._one_hot(targ, pred.shape[self.axis])
        pred, targ = TensorBase(pred), TensorBase(targ)
        assert pred.shape == targ.shape, 'input and target dimensions differ, DiceLoss expects non one-hot targs'
        pred = self.activation(pred)
        sum_dims = list(range(2, len(pred.shape)))
        inter = torch.sum(pred*targ, dim=sum_dims)
        union = (torch.sum(pred**2+targ, dim=sum_dims) if self.square_in_union
            else torch.sum(pred+targ, dim=sum_dims))
        dice_score = (2. * inter + self.smooth)/(union + self.smooth)

        x = ((1-dice_score).flatten().mean() if self.reduction == "mean" else (1-dice_score).flatten().sum())

        
        return torch.log((torch.exp(x) + torch.exp(-x)) / 2.0)
    
    
class CombinedLoss:
    "Dice and Focal combined"
    def __init__(self, axis=1, smooth=1., alpha=1., reduction=None):
        store_attr()
        self.focal_loss = FocalLossFlat(axis=axis)
        self.dice_loss =  DiceLoss(axis, smooth)
        
    def __call__(self, pred, targ):
        return self.focal_loss(pred, targ) + self.alpha * self.dice_loss(pred, targ)
    
    def decodes(self, x):    return x.argmax(dim=self.axis)
    def activation(self, x): return F.softmax(x, dim=self.axis)



learn = load_learner('resnet50_dice906.pkl')



def predict(img):
    img = PILImage.create(img)
    inp,preds,pred_idx,probs = learn.predict(img,with_input=True)
    
    cm = mpl.cm.rainbow
    bounds = [0,1,2,3,4,5]
    norm = mpl.colors.BoundaryNorm(bounds, cm.N)
    
    fig,axs = plt.subplots(1,1,figsize = (10,10),gridspec_kw={'width_ratios': [1]})
    
    #axs[0].imshow(inp.permute(1,2,0))
    
    axs.imshow(preds,cmap = 'rainbow',vmax = 4)
    divider = make_axes_locatable(axs)
    cax1 = divider.append_axes('right', size = '3%', pad = 0.05)
    cbar = fig.colorbar(mpl.cm.ScalarMappable(norm,cm),ax = axs, cax = cax1, label = "")
    cbar.ax.set_yticklabels(['','BG','Cabage','Kale','Fennel','Bean'], fontsize = 15)
    axs.set_axis_off()
    plt.savefig("image.png", dpi = 100)
    pred = PILImage.create("image.png")
    return np.array(pred)


title = "Multispecies Canopies Segmenter"

description = "A multispecies canopies Segmentation model that will segment your images according to the species your plants belong. It can identify Beans, Cabbages ,Kale & Fennel BG stands for BackGround/"

examples = ['192.168.42.17-00610-AFECF1.jpg',
           "192.168.42.19-00951-AFECF1.jpg",
            "192.168.42.19-01010-AFECF2",
            "Registered_images_190_camera7.jpg"]
interpretation='default'




gr.Interface(fn=predict, inputs="image", outputs="image", title=title,description=description,
             examples=examples).launch(share=True)


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