test.py

from __future__ import print_function
from __future__ import division
import torch
import onnxruntime
import numpy as np
import pandas as pd
import torchvision
from torchvision import transforms
import matplotlib.pyplot as plt
from sklearn.metrics import precision_recall_fscore_support, accuracy_score, confusion_matrix, ConfusionMatrixDisplay
import seaborn as sn
import random
import time
import json
from PIL import Image
from PIL import ImageFile
from pathlib import Path
import argparse
print("PyTorch Version: ",torch.__version__)
print("Torchvision Version: ",torchvision.__version__)

parser = argparse.ArgumentParser('arguments for testing the model')

parser.add_argument('--ts_empty_folder', type=str, default="/data/taulukot/solukuvat/empty/test/",
                    help='path to test data')
parser.add_argument('--ts_ok_folder', type=str, default="/data/taulukot/solukuvat/ok/test/",
                    help='path to test data')
parser.add_argument('--results_folder', type=str, default="./results/aug_28022024/",
                    help='Folder for saving results')
parser.add_argument('--model_path', type=str, default="/koodit/table_segmentation/empty_cell_detection/train/models/aug_b32_lr0001_28022024.onnx",
                    help='path to load model file from')
parser.add_argument('--batch_size', type=int, default=16,
                    help='batch_size')
parser.add_argument('--num_classes', type=int, default=2,
                    help='number of classes for classification')
parser.add_argument('--name', type=str, default='empty_cell_augment_28022024',
                    help='name given to result files')

start = time.time()

# nohup python test.py > logs/aug_test_28022024.txt 2>&1 &
# echo $! > output/save_pid.txt

torch.manual_seed(67)
random.seed(67)

args = parser.parse_args()

ImageFile.LOAD_TRUNCATED_IMAGES = True
Image.MAX_IMAGE_PIXELS = None

# https://pytorch.org/tutorials/beginner/finetuning_torchvision_models_tutorial.html


def get_data():
    empty_path = Path(args.ts_empty_folder)
    ok_path = Path(args.ts_ok_folder)

    empty_files = list(empty_path.glob('*.jpg'))
    ok_files = list(ok_path.glob('*.jpg'))

    empty_labels = np.zeros(len(empty_files))
    ok_labels = np.ones(len(ok_files))

    #ts_data_files = ts_data_files[:20]
    #ts_data_labels = ts_data_labels[:20]
    #ts_ok_files = ts_ok_files[:20]
    #ts_ok_labels = ts_ok_labels[:20]

    ts_files = empty_files + ok_files
    ts_labels = np.concatenate((empty_labels, ok_labels))

    print('Test data with empty cells: ', len(empty_files))
    print('Test data without empty cells: ', len(ok_files))

    return ts_files, ts_labels


def initialize_model():
    model = onnxruntime.InferenceSession(args.model_path)
    input_size = 224
    return model, input_size

# Function for getting precision, recall and F-score metrics
def get_precision_recall(y_true, y_pred):
    precision_recall_fscore = precision_recall_fscore_support(y_true, y_pred, average=None)

    prec_0 = precision_recall_fscore[0][0]
    rec_0 = precision_recall_fscore[1][0]
    F_0 = precision_recall_fscore[2][0]

    prec_1 = precision_recall_fscore[0][1]
    rec_1 = precision_recall_fscore[1][1]
    F_1 = precision_recall_fscore[2][1]

    print('\nPrecision for ok: %.2f'%prec_1)
    print('Recall for ok: %.2f'%rec_1)
    print('F-score for ok: %.2f'%F_1)

    print('Precision for empty: %.2f'%prec_0 )
    print('Recall for empty: %.2f'%rec_0)
    print('F-score for empty: %.2f'%F_0)


def createConfusionMatrix(y_true, y_pred):
    classes = np.array(['empty', 'ok'])

    # Build confusion matrix
    cf_matrix = confusion_matrix(y_true, y_pred)
    print(cf_matrix)
    df_cm = pd.DataFrame(cf_matrix, index=classes,
                         columns=classes)
    plt.figure(figsize=(12, 7))    
    return sn.heatmap(df_cm, annot=True).get_figure()

def save_preds(y_true, y_pred, paths):
    # Identifies images that were not classified correctly
    incorrect_indices = np.where(y_true != y_pred)
    incorrectly_predicted_images = paths[incorrect_indices]
    correct_labels = y_true[incorrect_indices].astype(str)
    incorrect_preds = dict(zip(incorrectly_predicted_images, correct_labels))

    print(f'{len(incorrect_preds)} incorrect predictions')

    # Save file names and labels of incorrectly classified images
    with open(args.results_folder + args.name + '_incorrect_preds', "w") as fp:
        json.dump(incorrect_preds, fp)

# Initialize the model for this run
model, input_size = initialize_model()

# Print the model we just instantiated
#print(model_ft)

data_transforms = transforms.Compose([
        transforms.Resize((input_size, input_size)),
        transforms.ToTensor()
    ])

print("Initializing Datasets and Dataloaders...")

ts_files, ts_labels = get_data()

# Function for getting model predictions on test data
def test_model(model, ts_files, ts_labels):
    since = time.time()
    label_preds = []
    true_labels = []
    paths = []
    n = len(ts_files)
    # Iterate over data
    for i in range(n):
        print(f'{i}/{n}')
        image = Image.open(ts_files[i])
        label = ts_labels[i]
        image = data_transforms(image.convert("RGB")).unsqueeze(0)
        # Transform tensor to numpy array
        img = image.detach().cpu().numpy()
        input = {model.get_inputs()[0].name: img}
        # Run model prediction
        output = model.run(None, input)
        # Get predicted class
        pred = np.argmax(output[0], 1)
        pred_class = pred.item()
        label_preds.append(pred_class)
        true_labels.append(label)
        paths.append(str(ts_files[i]))

    time_elapsed = time.time() - since
    print('Testing complete in {:.0f}m {:.0f}s'.format(time_elapsed // 60, time_elapsed % 60))

    return np.array(label_preds), np.array(true_labels), np.array(paths)

ts_labels = np.array(ts_labels)

# Test model
y_pred, y_true, paths = test_model(model, ts_files, ts_labels)
# Saves information of incorrect predictions
save_preds(y_true, y_pred, paths)
# Calculates and prints precision, recall and F-score metrics
get_precision_recall(y_true, y_pred)

# Save confusion matrix to Tensorboard
#cm = createConfusionMatrix(y_true, y_pred)
#writer.add_figure("Confusion matrix", cm)
# Create and save confusion matrix of the predictions and true labels
conf_matrix = ConfusionMatrixDisplay.from_predictions(y_true, y_pred, normalize='true', display_labels=np.array(['empty', 'ok']))
plt.savefig(args.results_folder + args.name + '_conf_matrix.jpg', bbox_inches='tight')

end = time.time()
time_in_mins = (end - start) / 60
print('Time: %.2f minutes' % time_in_mins)