imatge-upc/AI4Agriculture-grape-detection

Object Detection and Weakly SupervisedSemantic Segmentation for Grape Detection

By Pau Márquez Julbe

This project contains the source code to train, evaluate and analyse the object detection and semantic segmentation algorithms built during the final thesis of my bachelor's degree on Data Science and Engineering at UPC. This project has been carried out within the AI4Agriculture pilot.

The models are embedded in a class that normalizes methods to both evaluate and train. The base interface is in src/dl_template.py and both models inherit and implement its functions in train_faster.py and train_unet.py. Both are implemented using PyTorch.

In order to train the models, the train_unet.sh or train_faster.sh can be called. They load the main not default options. The options are contained in the folder options but can be listed by running python3 train_unet.py --help.

In order to use them for evaluation, a dot access dictionary (such as DotMap) has to indicate the options of the model. They can be stored in a JSON options file (or just load it as a dictionary). The following implementation shows how to run it:

# In case we are not in the root folder, append the path
import sys
sys.path.append("..")

from train_unet import UNetHandler
from train_faster import FasterHandler

import os
import json
from dotmap import DotMap

def get_options(checkpoint_dir):
    checkpoint_name = 'model.pt'
    opt_dir = os.path.join(checkpoint_dir, 'opt.json')
    weights_dir = os.path.join(checkpoint_dir, checkpoint_name)

    with open(opt_dir, 'r') as fd:
        opt = json.load(fd)
    
    opt = DotMap({
        # If we are using the Faster R-CNN, the default parameter of trainable_backbone_layers is None
        # but DotMap returns DotMap objects for non initialized entries
        "trainable_backbone_layers": None,
        **{k: '.' + v if type(v) == str and v[:2] == './' else v for k, v in opt.items()},
        
        # Overwrite
        "box_nms_thresh": 0.4, # Set the nms threshold for the Faster R-CNN as you wish
        "purpose": "val", # [val|train] -> val does not shuffle the data loader
        "phase": "val", # [train|val|test|all]
        "log_dash": False, # if True, WANDB is used (only for training)
        "device": "cuda", # set to either cuda or cpu
        "step_batch_size": 1, # Batch loader will load a batch of one element (easier to analyse)
        "checkpoint": weights_dir # add checkpoint to be loaded
    })
    return opt
    
CHECKPOINT_DIR = "../checkpoints_dir/"

opt = get_options(CHECKPOINT_DIR)

model_handler = UNetHandler(opt).init_train() # same with FasterHandler
model_handler.model.eval()

def inference_generator(model_handler, split="train"):
    if split == "train":
        loader = model_handler.train_loader
    elif split == "val":
        loader = model_handler.val_loaders[0][1]
    else:
        raise ValueError("Wrong split assigned")
    for data_d, target_d in model_handler.custom_collate(loader):
        data = model_handler.transform_data(data_d)
        with torch.no_grad():
            res = model_handler.forward(model_handler.model, data)[0]
        yield res

If we are not importing the model from the root folder of the project, we will need to append the relative rute to the roots. In this example we are adding ".." before relative paths.

Note that UNet runs a forward for each patch (slice of an image), so they have to be merged. A function that handles this functionality is contained in notebooks/utils.py. To run it:

from notebooks.utils import get_unet_masks

# Get test loader if desired
test_loader = model_handler.get_data_loader(model_handler.opt, 'test')
# Create generator
unet_masks_generator = get_unet_masks(model_handler, loader = test_loader)
# Get
first_image_inference = next(unet_masks_generator)

mask_with_crf = first_image_inference["crf_mask_0,5"].toarray()
mask_raw = first_image_inference["unet_mask_0,9"].toarray()

raw_full_image = first_image_inference["full_image"]

The models weights and options are contained in this drive folder. You should download them and specify the folders that contain the data in the get_options function.

If we wanted to train one of the models, we would load the model handler as above or use the options parser, as in train_faster.py and train_unet.py. After it is loaded, we would just run the following command:

model_handler.train()

Data

This project handles two datasets: a novel dataset from the AI4Agriculture project (which is still not public) and the WGISD dataset. To use this dataset, set the dataset options to WGISD and fill the other options listed in options/base_options.py.

Models

Object Detection

The object detection neural network implemented in this project is the Faster R-CNN from torchvision.

Weakly Supervised Semantic Segmentation

The implementation of a Weakly Supervised Semantic Segmentation with bounding boxes has been built. It implements the algorithm described in this paper. The implementation is strongly based on the project boxes_tightness_prior, but we have wrapped the constraints and the loss functions into a single module. The losses are included in the src/losses folder and the input parameters are explained by running the help command stated above.

The semantic segmentation neural network is a Residual U-Net. Also extracted from the boxes_tightness_prior project.

Analysis

Notebooks show some of the analysis performed during the project, even though memory issues did not let us upload the whole analysis (images were too big).

Visualization

The code uses wanddb to log and visualize results. It is necessary to set up a wanddb account. Then, create a project called AI4Agriculture in the wandb web site. Now, you have to get an API KEY at: https://wandb.ai/authorize

Now, create a JSON file with your API KEY at the base folder of this repository:

$python

>>> keys = {}
>>> keys['wandb_key']='YOUR KEY'
>>> with open('keys.json', 'wb') as fh: json.dump(keys,fh)
>>>quit()

Make sure no one can read this file:

$chmod 600 keys.json

Edit src/dl_template.py and put your wandb user name in the entity field:

        self.wandb_run = wandb.init(name=self.run_name, project="AI4Agriculture", entity='YOUR_WANDB_USERNAME', config=self.opt)

Aknowledgements

A big thanks to LIVIA to make the code used in their paper Bounding boxes for weakly supervised segmentation: Global constraints get close to full supervision open source.