Kaggle competition: Global Wheat Detection
<SOS> metric: custom metric Kaggle data source: global-wheat-detection<import_modules>
!pip install --no-deps '.. /input/timm-package/timm-0.1.26-py3-none-any.whl' > /dev/null
!pip install --no-deps '.. /input/pycocotools/pycocotools-2.0-cp37-cp37m-linux_x86_64.whl' > /dev/null
xgb.__version__<import_modules>
marking = pd.read_csv('.. /input/global-wheat-detection/train.csv')
 bboxs = np.stack(marking['bbox'].apply(lambda x: np.fromstring(x[1:-1], sep=',')))
 for i, column in enumerate(['x', 'y', 'w', 'h']):
marking[column] = bboxs[:,i]
marking.drop(columns=['bbox'], inplace=True )
import numpy as np
import pandas as pd
import zipfile
from sklearn.model_selection import train_test_split, KFold
from sklearn.metrics import log_loss, roc_auc_score
from sklearn.linear_model import LogisticRegression
import gc
import os 
<load_from_csv>
skf = StratifiedKFold(n_splits=5, shuffle=True, random_state=42)
 df_folds = marking[['image_id']].copy()
df_folds.loc[:, 'bbox_count'] = 1
df_folds = df_folds.groupby('image_id' ).count()
df_folds.loc[:, 'source'] = marking[['image_id', 'source']].groupby('image_id' ).min() ['source']
df_folds.loc[:, 'stratify_group'] = np.char.add(
 df_folds['source'].values.astype(str),
df_folds['bbox_count'].apply(lambda x: f'_{x // 15}' ).values.astype(str)
)
 df_folds.loc[:, 'fold'] = 0
for fold_number,(train_index, val_index)in enumerate(skf.split(X=df_folds.index, y=df_folds['stratify_group'])) :
df_folds.loc[df_folds.iloc[val_index].index, 'fold'] = fold_number
sample_submission = pd.read_csv('/kaggle/input/dogs-vs-cats-redux-kernels-edition/sample_submission.csv')
 sample_submission.tail()<define_variables>
TRAIN_ROOT_PATH = '.. /input/global-wheat-detection/train'
def collate_fn(batch):
return tuple(zip(*batch))
class DatasetRetriever(Dataset):
def __init__(self, marking, image_ids, transforms=None, test=False):
super().__init__()
self.image_ids = image_ids
self.marking = marking
self.transforms = transforms
self.test = test
def __getitem__(self, index: int):
image_id = self.image_ids[index]
image, boxes = self.load_image_and_boxes(index)
 labels = torch.ones(( boxes.shape[0],), dtype=torch.int64)
 target = {}
target['boxes'] = boxes
target['labels'] = labels
target['image_id'] = torch.tensor([index])
 if self.transforms:
for i in range(10):
sample = self.transforms(**{
'image': image,
'bboxes': target['boxes'],
'labels': labels
})
 if len(sample['bboxes'])> 0:
image = sample['image']
target['boxes'] = torch.stack(tuple(map(torch.tensor, zip(*sample['bboxes'])))).permute(1, 0)
 break
return image, target, image_id
def __len__(self)-> int:
return self.image_ids.shape[0]
def load_image_and_boxes(self, index):
image_id = self.image_ids[index]
image = cv2.imread(f'{TRAIN_ROOT_PATH}/{image_id}.jpg', cv2.IMREAD_COLOR)
 image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB ).astype(np.float32)
 image /= 255.0
records = self.marking[self.marking['image_id'] == image_id]
boxes = records[['x', 'y', 'w', 'h']].values
boxes[:, 2] = boxes[:, 0] + boxes[:, 2]
boxes[:, 3] = boxes[:, 1] + boxes[:, 3]
return image, boxes
TRAIN_FOLDER = '.. /input/cats-and-dogs-embedded-data/train/train/'
TEST_FOLDER = '.. /input/cats-and-dogs-embedded-data/test/test/'
IMG_SIZE = 224<load_pretrained>
def load_net(checkpoint_path):
config = get_efficientdet_config('tf_efficientdet_d5')
 net = EfficientDet(config, pretrained_backbone=False)
 config.num_classes = 1
config.image_size = 512
net.class_net = HeadNet(config, num_outputs=config.num_classes, norm_kwargs=dict(eps=.001, momentum=.01))
checkpoint = torch.load(checkpoint_path)
 net.load_state_dict(checkpoint, strict=False)
 del checkpoint
gc.collect()
net = DetBenchEval(net, config)
 net.eval() ;
return net.cuda()
models = [
load_net('.. /input/wheat-effdet5-fold0-best-checkpoint/fold0-best-all-states.bin'),
load_net('.. /input/wheat-effdet5-fold0-best-checkpoint/fold0-best-all-states.bin'),
load_net('.. /input/wheat-effdet5-fold0-best-checkpoint/fold0-best-all-states.bin'),
load_net('.. /input/wheat-effdet5-fold0-best-checkpoint/fold0-best-all-states.bin'),
load_net('.. /input/wheat-effdet5-fold0-best-checkpoint/fold0-best-all-states.bin')
 ]
train_image_list = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_1/train_image_list.npy')
 test_image_list = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_1/test_image_list.npy' )<define_variables>
%%time
all_predictions = []
for fold_number in range(5):
validation_dataset = DatasetRetriever(
 image_ids=df_folds[df_folds['fold'] == fold_number].index.values,
marking=marking,
transforms=get_valid_transforms() ,
test=True, 
)
 validation_loader = DataLoader(
 validation_dataset,
batch_size=4,
shuffle=False,
num_workers=2,
drop_last=False,
collate_fn=collate_fn 
)
 for images, targets, image_ids in tqdm(validation_loader, total=len(validation_loader)) :
with torch.no_grad() :
images = torch.stack(images)
 images = images.cuda().float()
det = models[fold_number](images, torch.tensor([1]*images.shape[0] ).float().cuda())
 for i in range(images.shape[0]):
boxes = det[i].detach().cpu().numpy() [:,:4]
scores = det[i].detach().cpu().numpy() [:,4]
boxes[:, 2] = boxes[:, 2] + boxes[:, 0]
boxes[:, 3] = boxes[:, 3] + boxes[:, 1]
all_predictions.append({
'pred_boxes':(boxes*2 ).clip(min=0, max=1023 ).astype(int),
'scores': scores,
'gt_boxes':(targets[i]['boxes'].cpu().numpy() *2 ).clip(min=0, max=1023 ).astype(int),
'image_id': image_ids[i],
} )
ids = [int(x.split('.')[0])for x in test_image_list]
ids[:20]<load_pretrained>
@jit(nopython=True)
 def calculate_iou(gt, pr, form='pascal_voc')-> float:

 if form == 'coco':
gt = gt.copy()
pr = pr.copy()
gt[2] = gt[0] + gt[2]
gt[3] = gt[1] + gt[3]
pr[2] = pr[0] + pr[2]
pr[3] = pr[1] + pr[3]
dx = min(gt[2], pr[2])- max(gt[0], pr[0])+ 1
if dx < 0:
return 0.0
dy = min(gt[3], pr[3])- max(gt[1], pr[1])+ 1
if dy < 0:
return 0.0
overlap_area = dx * dy
union_area =(
(gt[2] - gt[0] + 1)*(gt[3] - gt[1] + 1)+ 
(pr[2] - pr[0] + 1)*(pr[3] - pr[1] + 1)-
overlap_area 
)
 return overlap_area / union_area
@jit(nopython=True)
 def find_best_match(gts, pred, pred_idx, threshold = 0.5, form = 'pascal_voc', ious=None)-> int:

 best_match_iou = -np.inf
best_match_idx = -1
for gt_idx in range(len(gts)) :
if gts[gt_idx][0] < 0:
continue
iou = -1 if ious is None else ious[gt_idx][pred_idx]
if iou < 0:
iou = calculate_iou(gts[gt_idx], pred, form=form)
 if ious is not None:
ious[gt_idx][pred_idx] = iou
if iou < threshold:
continue
if iou > best_match_iou:
best_match_iou = iou
best_match_idx = gt_idx
return best_match_idx
@jit(nopython=True)
 def calculate_precision(gts, preds, threshold = 0.5, form = 'coco', ious=None)-> float:

 n = len(preds)
 tp = 0
fp = 0
for pred_idx in range(n):
best_match_gt_idx = find_best_match(gts, preds[pred_idx], pred_idx,
threshold=threshold, form=form, ious=ious)
 if best_match_gt_idx >= 0:
tp += 1
gts[best_match_gt_idx] = -1
else:
fp += 1
fn =(gts.sum(axis=1)> 0 ).sum()
return tp /(tp + fp + fn)
 @jit(nopython=True)
 def calculate_image_precision(gts, preds, thresholds =(0.5,), form = 'coco')-> float:

 n_threshold = len(thresholds)
 image_precision = 0.0
ious = np.ones(( len(gts), len(preds)))* -1
for threshold in thresholds:
precision_at_threshold = calculate_precision(gts.copy() , preds, threshold=threshold,
form=form, ious=ious)
 image_precision += precision_at_threshold / n_threshold
return image_precision
def show_result(sample_id, preds, gt_boxes):
sample = cv2.imread(f'{TRAIN_ROOT_PATH}/{sample_id}.jpg', cv2.IMREAD_COLOR)
 sample = cv2.cvtColor(sample, cv2.COLOR_BGR2RGB)
 fig, ax = plt.subplots(1, 1, figsize=(16, 8))
for pred_box in preds:
cv2.rectangle(
 sample, 
(pred_box[0], pred_box[1]), 
(pred_box[2], pred_box[3]), 
(220, 0, 0), 2 
)
 for gt_box in gt_boxes:
cv2.rectangle(
 sample, 
(gt_box[0], gt_box[1]), 
(gt_box[2], gt_box[3]), 
(0, 0, 220), 2 
)
 ax.set_axis_off()
ax.imshow(sample)
 ax.set_title("RED: Predicted | BLUE - Ground-truth")
 iou_thresholds = numba.typed.List()
for x in [0.5, 0.55, 0.6, 0.65, 0.7, 0.75]:
iou_thresholds.append(x )
target = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_1/target.npy' )<load_pretrained>
def calculate_final_score(all_predictions, score_threshold):
final_scores = []
for i in range(len(all_predictions)) :
gt_boxes = all_predictions[i]['gt_boxes'].copy()
pred_boxes = all_predictions[i]['pred_boxes'].copy()
scores = all_predictions[i]['scores'].copy()
image_id = all_predictions[i]['image_id']
indexes = np.where(scores>score_threshold)
 pred_boxes = pred_boxes[indexes]
scores = scores[indexes]
image_precision = calculate_image_precision(gt_boxes, pred_boxes,thresholds=iou_thresholds,form='pascal_voc')
 final_scores.append(image_precision)
 return np.mean(final_scores )
train_EB7_ns = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_4/cats_and_dogs_4/train_EB7_ns.npy')
 test_EB7_ns = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_4/cats_and_dogs_4/test_EB7_ns.npy')
 train_EB4_ns = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_4/cats_and_dogs_4/train_EB4_ns.npy')
 test_EB4_ns = np.load('.. /input/cats-and-dogs-embedded-data/cats_and_dogs_4/cats_and_dogs_4/test_EB4_ns.npy' )<split>
%%time
best_final_score, best_score_threshold = 0, 0
for score_threshold in tqdm(np.arange(0, 1, 0.01), total=np.arange(0, 1, 0.01 ).shape[0]):
final_score = calculate_final_score(all_predictions, score_threshold)
 if final_score > best_final_score:
best_final_score = final_score
best_score_threshold = score_threshold
X_train, X_val, y_train, y_val = train_test_split(train_EB7_ns, target, test_size=0.1, random_state=42 )<compute_train_metric>
print('-'*30)
 print(f'[Best Score Threshold]: {best_score_threshold}')
 print(f'[OOF Score]: {best_final_score:.4f}')
 print('-'*30 )
lr = LogisticRegression(C=0.026, max_iter=10000)
 lr.fit(X_train, y_train)
 val_preds_EB7_lr = lr.predict_proba(X_val)[:,1]
test_preds_EB7_lr = lr.predict_proba(test_EB7_ns)[:,1]
print(roc_auc_score(y_val, val_preds_EB7_lr))
print(log_loss(y_val, val_preds_EB7_lr))<train_model>
i = 0
gt_boxes = all_predictions[i]['gt_boxes'].copy()
pred_boxes = all_predictions[i]['pred_boxes'].copy()
scores = all_predictions[i]['scores'].copy()
image_id = all_predictions[i]['image_id']
indexes = np.where(scores>best_score_threshold)
 pred_boxes = pred_boxes[indexes]
scores = scores[indexes]
show_result(image_id, pred_boxes, gt_boxes )
<drop_column><EOS> 
DATA_ROOT_PATH = '.. /input/global-wheat-detection/test'
class TestDatasetRetriever(Dataset):
def __init__(self, image_ids, transforms=None):
super().__init__()
self.image_ids = image_ids
self.transforms = transforms
def __getitem__(self, index: int):
image_id = self.image_ids[index]
image = cv2.imread(f'{DATA_ROOT_PATH}/{image_id}.jpg', cv2.IMREAD_COLOR)
 image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB ).astype(np.float32)
 image /= 255.0
if self.transforms:
sample = {'image': image}
sample = self.transforms(**sample)
 image = sample['image']
return image, image_id
def __len__(self)-> int:
return self.image_ids.shape[0]
def get_valid_transforms() :
return A.Compose(
 [
A.Resize(height=512, width=512, p=1.0),
ToTensorV2(p=1.0),
],
p=1.0, 
)
 dataset = TestDatasetRetriever(
 image_ids=np.array([path.split('/')[-1][:-4] for path in glob(f'{DATA_ROOT_PATH}/*.jpg')]),
transforms=get_valid_transforms() 
)
 def collate_fn(batch):
return tuple(zip(*batch))
data_loader = DataLoader(
 dataset,
batch_size=2,
shuffle=False,
num_workers=4,
drop_last=False,
collate_fn=collate_fn 
)
 def make_predictions(images, score_threshold=0.1):
images = torch.stack(images ).cuda().float()
predictions = []
for net in models:
with torch.no_grad() :
det = net(images, torch.tensor([1]*images.shape[0] ).float().cuda())
 result = []
for i in range(images.shape[0]):
boxes = det[i].detach().cpu().numpy() [:,:4]
scores = det[i].detach().cpu().numpy() [:,4]
indexes = np.where(scores > score_threshold)[0]
boxes = boxes[indexes]
boxes[:, 2] = boxes[:, 2] + boxes[:, 0]
boxes[:, 3] = boxes[:, 3] + boxes[:, 1]
result.append({
'boxes': boxes[indexes],
'scores': scores[indexes],
})
 predictions.append(result)
 return predictions
def run_wbf(predictions, image_index, image_size=512, iou_thr=0.55, skip_box_thr=best_score_threshold, weights=None):
boxes = [(prediction[image_index]['boxes']/(image_size-1)).tolist() for prediction in predictions]
scores = [prediction[image_index]['scores'].tolist() for prediction in predictions]
labels = [np.ones(prediction[image_index]['scores'].shape[0] ).tolist() for prediction in predictions]
boxes, scores, labels = weighted_boxes_fusion(boxes, scores, labels, weights=None, iou_thr=iou_thr, skip_box_thr=skip_box_thr)
 boxes = boxes*(image_size-1)
 return boxes, scores, labels
def format_prediction_string(boxes, scores):
pred_strings = []
for j in zip(scores, boxes):
pred_strings.append("{0:.4f} {1} {2} {3} {4}".format(j[0], j[1][0], j[1][1], j[1][2], j[1][3]))
return " ".join(pred_strings)
 results = []
for images, image_ids in data_loader:
predictions = make_predictions(images)
 for i, image in enumerate(images):
boxes, scores, labels = run_wbf(predictions, image_index=i)
 boxes =(boxes*2 ).astype(np.int32 ).clip(min=0, max=1023)
 image_id = image_ids[i]
boxes[:, 2] = boxes[:, 2] - boxes[:, 0]
boxes[:, 3] = boxes[:, 3] - boxes[:, 1]
result = {
'image_id': image_id,
'PredictionString': format_prediction_string(boxes, scores)
 }
results.append(result)
 test_df = pd.DataFrame(results, columns=['image_id', 'PredictionString'])
 test_df.to_csv('submission.csv', index=False )