{"cells":[{"metadata":{"trusted":true},"cell_type":"code","source":"!pip install --no-deps '../input/timm-package/timm-0.1.26-py3-none-any.whl' > /dev/null\n!pip install --no-deps '../input/pycocotools/pycocotools-2.0-cp37-cp37m-linux_x86_64.whl' > /dev/null\n!pip install --no-cache-dir --global-option=\"--cpp_ext\" --global-option=\"--cuda_ext\" ../input/nvidiaapex/. > /dev/null","execution_count":null,"outputs":[]},{"metadata":{"_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","trusted":true},"cell_type":"code","source":"import sys\nsys.path.insert(0, \"../input/timm-efficientdet-pytorch\")\nsys.path.insert(0, \"../input/omegaconf\")\nsys.path.insert(0, \"../input/weightedboxesfusion\")\n\nimport re, os\nfrom datetime import datetime\nimport random\nimport time\nimport ensemble_boxes\nimport torch\nimport numpy as np\nimport pandas as pd\nfrom glob import glob\nfrom torch.utils.data import Dataset,DataLoader\nimport albumentations as A\nfrom albumentations.pytorch.transforms import ToTensorV2\nfrom torch.utils.data.sampler import SequentialSampler, RandomSampler\nimport cv2\nimport gc\nfrom apex import amp\nfrom matplotlib import pyplot as plt\nfrom effdet import get_efficientdet_config, EfficientDet, DetBenchEval\nfrom effdet.efficientdet import HeadNet\n\nSEED = 28\n\ndef seed_everything(seed):\n    random.seed(seed)\n    os.environ['PYTHONHASHSEED'] = str(seed)\n    np.random.seed(seed)\n    torch.manual_seed(seed)\n    torch.cuda.manual_seed(seed)\n    torch.backends.cudnn.deterministic = True\n    torch.backends.cudnn.benchmark = True\n\nseed_everything(SEED)","execution_count":null,"outputs":[]},{"metadata":{"_cell_guid":"79c7e3d0-c299-4dcb-8224-4455121ee9b0","_uuid":"d629ff2d2480ee46fbb7e2d37f6b5fab8052498a","trusted":true},"cell_type":"code","source":"DIR_INPUT = '/kaggle/input/global-wheat-detection'\nDIR_TRAIN = f'{DIR_INPUT}/train'\nDIR_TEST = f'{DIR_INPUT}/test'\n\nDIR_WEIGHTS = '/kaggle/input/effdetfold0'\n\nWEIGHTS_FILE = f'{DIR_WEIGHTS}/full-effdet5-cutmix-augmix/best-checkpoint-025epoch.bin'\nN_CLASSES=2\nDEVICE = torch.device('cuda') if torch.cuda.is_available() else torch.device('cpu')","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"test_df = pd.read_csv(f'{DIR_INPUT}/sample_submission.csv')\ntest_df","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"marking = pd.read_csv('../input/global-wheat-detection/train.csv')\n\nbboxs = np.stack(marking['bbox'].apply(lambda x: np.fromstring(x[1:-1], sep=',')))\nfor i, column in enumerate(['x', 'y', 'w', 'h']):\n    marking[column] = bboxs[:,i]\nmarking.drop(columns=['bbox'], inplace=True)\nmarking","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"DATA_ROOT_PATH = '../input/global-wheat-detection/test'\n\nclass DatasetRetriever(Dataset):\n\n    def __init__(self, image_ids, transforms=None):\n        super().__init__()\n        self.image_ids = image_ids\n        self.transforms = transforms\n\n    def __getitem__(self, index: int):\n        image_id = self.image_ids[index]\n        image = cv2.imread(f'{DATA_ROOT_PATH}/{image_id}.jpg', cv2.IMREAD_COLOR)\n        image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB).astype(np.float32)\n        image /= 255.0\n        if self.transforms:\n            sample = {'image': image}\n            sample = self.transforms(**sample)\n            image = sample['image']\n        return image, image_id\n\n    def __len__(self) -> int:\n        return self.image_ids.shape[0]","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def make_predictions(images, score_threshold=0.22):\n    images = torch.stack(images).cuda().float()  \n    predictions = []\n    with torch.no_grad():\n        outputs = model(images, torch.tensor([1]*images.shape[0]).float().cuda())\n        gc.collect()\n        torch.cuda.empty_cache()\n    for i in range(images.shape[0]):\n        boxes = outputs[i].detach().cpu().numpy()[:,:4]    \n        scores = outputs[i].detach().cpu().numpy()[:,4]\n        indexes = np.where(scores > score_threshold)[0]\n        boxes = boxes[indexes]\n        boxes[:, 2] = boxes[:, 2] + boxes[:, 0]\n        boxes[:, 3] = boxes[:, 3] + boxes[:, 1]\n        predictions.append({\n            'boxes': boxes[indexes],\n            'scores': scores[indexes],\n        })\n    return [predictions]\n\ndef run_wbf(predictions, image_index, image_size=512, iou_thr=0.43, skip_box_thr=0.43, weights=None):\n    boxes = [(prediction[image_index]['boxes']/(image_size-1)).tolist() for prediction in predictions]\n    scores = [prediction[image_index]['scores'].tolist() for prediction in predictions]\n    labels = [np.ones(prediction[image_index]['scores'].shape[0]).astype(int).tolist() for prediction in predictions]\n    boxes, scores, labels = ensemble_boxes.ensemble_boxes_wbf.weighted_boxes_fusion(boxes, scores, labels, weights=None, iou_thr=iou_thr, skip_box_thr=skip_box_thr)\n    boxes = boxes*(image_size-1)\n    return boxes, scores, labels","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"# Albumentations\ndef get_train_transforms():\n    return A.Compose(\n        [\n            A.RandomSizedCrop(min_max_height=(800, 800), height=1024, width=1024, p=0.5),\n            A.OneOf([\n                A.HueSaturationValue(hue_shift_limit=0.2, sat_shift_limit= 0.2, \n                                     val_shift_limit=0.2, p=0.9),\n                A.RandomBrightnessContrast(brightness_limit=0.2, \n                                           contrast_limit=0.2, p=0.9),\n            ],p=0.9),\n            A.ToGray(p=0.01),\n            A.HorizontalFlip(p=0.5),\n            A.VerticalFlip(p=0.5),\n            A.Resize(height=512, width=512, p=1),\n            A.Cutout(num_holes=8, max_h_size=64, max_w_size=64, fill_value=0, p=0.5),\n            ToTensorV2(p=1.0),\n        ], \n        p=1.0, \n        bbox_params=A.BboxParams(\n            format='pascal_voc',\n            min_area=0, \n            min_visibility=0,\n            label_fields=['labels']\n        )\n    )\n\ndef get_valid_transforms():\n    return A.Compose([\n        A.Resize(height=512, width=512, p=1.0),\n        ToTensorV2(p=1.0)\n    ], p=1)\n\ndef get_test_transforms():\n    return A.Compose([\n        A.Resize(height=512, width=512, p=1),\n        ToTensorV2(p=1.0)\n    ], p=1)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def load_net_eval(checkpoint_path):\n    config = get_efficientdet_config('tf_efficientdet_d5')\n    net = EfficientDet(config, pretrained_backbone=False)\n\n    config.num_classes = 1\n    config.image_size=512\n    net.class_net = HeadNet(config, num_outputs=config.num_classes, norm_kwargs=dict(eps=.001, momentum=.01))\n\n    checkpoint = torch.load(checkpoint_path, map_location=DEVICE)\n    net.load_state_dict(checkpoint['model_state_dict'])\n\n    del checkpoint\n    gc.collect()\n\n    net = DetBenchEval(net, config)\n    net.eval()\n    return net.cuda()\n\nmodel = load_net_eval(WEIGHTS_FILE)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def collate_fn(batch):\n    return tuple(zip(*batch))\n\ndataset = DatasetRetriever(\n    image_ids=np.array([path.split('/')[-1][:-4] for path in glob(f'{DATA_ROOT_PATH}/*.jpg')]),\n    transforms=get_valid_transforms()\n)\n\n\ntest_data_loader = DataLoader(\n    dataset,\n    batch_size=4,\n    shuffle=False,\n    num_workers=2,\n    drop_last=False,\n    collate_fn=collate_fn\n)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def format_prediction_string(boxes, scores):\n    pred_strings = []\n    for j in zip(scores, boxes):\n        pred_strings.append(\"{0:.4f} {1} {2} {3} {4}\".format(j[0], j[1][0], j[1][1], j[1][2], j[1][3]))\n\n    return \" \".join(pred_strings)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Detection and make Pseudo labels for test dataset","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"detection_threshold = 0.5\nresults = []\ntestdf_psuedo = []\n\nfor images, image_ids in test_data_loader:\n    predictions = make_predictions(images)\n    for i, image in enumerate(images):\n        boxes, scores, labels = run_wbf(predictions, image_index=i)\n        boxes = (boxes*2).round().astype(np.int32).clip(min=0, max=1023)\n        image_id = image_ids[i]\n        \n        boxes = boxes[scores >= detection_threshold].astype(np.int32)\n        scores = scores[scores >= detection_threshold]\n\n        boxes[:, 2] = boxes[:, 2] - boxes[:, 0]\n        boxes[:, 3] = boxes[:, 3] - boxes[:, 1]\n        \n        for box in boxes:\n            #print(box)\n            result = {\n                'image_id': 'nvnn'+image_id,\n                'width': 1024,\n                'height': 1024,\n                'source': 'nvnn',\n                'x': float(box[0]),\n                'y': float(box[1]),\n                'w': float(box[2]),\n                'h': float(box[3])\n            }\n            testdf_psuedo.append(result)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"test_df_pseudo = pd.DataFrame(testdf_psuedo, columns=['image_id', 'width', 'height', 'source', 'x', 'y', 'w', 'h'])\ntest_df_pseudo.head()","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Retrain model with pseudo labels","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"train_df = pd.read_csv(f'{DIR_INPUT}/train.csv')\ntrain_df['x'] = -1\ntrain_df['y'] = -1\ntrain_df['w'] = -1\ntrain_df['h'] = -1\n\ndef expand_bbox(x):\n    r = np.array(re.findall(\"([0-9]+[.]?[0-9]*)\", x))\n    if len(r) == 0:\n        r = [-1, -1, -1, -1]\n    return r\n\ntrain_df[['x', 'y', 'w', 'h']] = np.stack(train_df['bbox'].apply(lambda x: expand_bbox(x)))\ntrain_df.drop(columns=['bbox'], inplace=True)\ntrain_df['x'] = train_df['x'].astype(np.float)\ntrain_df['y'] = train_df['y'].astype(np.float)\ntrain_df['w'] = train_df['w'].astype(np.float)\ntrain_df['h'] = train_df['h'].astype(np.float)\n\ntrain_df.head()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"from effdet import get_efficientdet_config, EfficientDet, DetBenchTrain\nfrom effdet.efficientdet import HeadNet\n\ndef load_net(checkpoint_path):\n    config = get_efficientdet_config('tf_efficientdet_d5')\n    net = EfficientDet(config, pretrained_backbone=False)\n\n    config.num_classes = 1\n    config.image_size=512\n    net.class_net = HeadNet(config, num_outputs=config.num_classes, norm_kwargs=dict(eps=.001, momentum=.01))\n\n    checkpoint = torch.load(checkpoint_path, map_location=DEVICE)\n    net.load_state_dict(checkpoint['model_state_dict'])\n\n    del checkpoint\n    gc.collect()\n\n    net = DetBenchTrain(net, config)\n    return net.cuda()\n\nmodel = load_net(WEIGHTS_FILE)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"image_ids = train_df['image_id'].unique()\nvalid_ids = image_ids[-300:]\ntrain_ids = image_ids[:-300]\n\nvalid_df = train_df[train_df['image_id'].isin(valid_ids)]\n\nframes = [train_df, test_df_pseudo]\n\ntrain_df = pd.concat(frames, ignore_index=True)\ntrain_df.tail()","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Wheat dataset for Training","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"TRAIN_ROOT_PATH = '../input/global-wheat-detection/train'\n\nclass DatasetRetriever(Dataset):\n\n    def __init__(self, marking, image_ids, transforms=None, test=False):\n        super().__init__()\n\n        self.image_ids = image_ids\n        self.marking = marking\n        self.transforms = transforms\n        self.test = test\n\n    def __getitem__(self, index: int):\n        image_id = self.image_ids[index]\n        \n        if self.test or random.random() > 0.5:\n            image, boxes = self.load_image_and_boxes(index)\n        else:\n            image, boxes = self.load_cutmix_image_and_boxes(index)\n\n        # there is only one class\n        labels = torch.ones((boxes.shape[0],), dtype=torch.int64)\n        \n        target = {}\n        target['boxes'] = boxes\n        target['labels'] = labels\n        target['image_id'] = torch.tensor([index])\n\n        if self.transforms:\n            for i in range(10):\n                sample = self.transforms(**{\n                    'image': image,\n                    'bboxes': target['boxes'],\n                    'labels': labels\n                })\n                if len(sample['bboxes']) > 0:\n                    image = sample['image']\n                    target['boxes'] = torch.stack(tuple(map(torch.tensor, zip(*sample['bboxes'])))).permute(1, 0)\n                    target['boxes'][:,[0,1,2,3]] = target['boxes'][:,[1,0,3,2]]  #yxyx: be warning\n                    break\n\n        return image, target, image_id\n\n    def __len__(self) -> int:\n        return self.image_ids.shape[0]\n\n    def load_image_and_boxes(self, index):\n        image_id = self.image_ids[index]\n        if 'nvnn' in image_id:\n            image = cv2.imread(f'{DIR_TEST}/{image_id[4:]}.jpg', cv2.IMREAD_COLOR)\n        else:\n            image = cv2.imread(f'{TRAIN_ROOT_PATH}/{image_id}.jpg', cv2.IMREAD_COLOR)\n\n        image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB).astype(np.float32)\n        image /= 255.0\n        records = self.marking[self.marking['image_id'] == image_id]\n        boxes = records[['x', 'y', 'w', 'h']].values\n        boxes[:, 2] = boxes[:, 0] + boxes[:, 2]\n        boxes[:, 3] = boxes[:, 1] + boxes[:, 3]\n        return image, boxes\n\n    def load_cutmix_image_and_boxes(self, index, imsize=1024):\n        \"\"\" \n        This implementation of cutmix author:  https://www.kaggle.com/nvnnghia \n        Refactoring and adaptation: https://www.kaggle.com/shonenkov\n        \"\"\"\n        w, h = imsize, imsize\n        s = imsize // 2\n    \n        xc, yc = [int(random.uniform(imsize * 0.25, imsize * 0.75)) for _ in range(2)]  # center x, y\n        indexes = [index] + [random.randint(0, self.image_ids.shape[0] - 1) for _ in range(3)]\n\n        result_image = np.full((imsize, imsize, 3), 1, dtype=np.float32)\n        result_boxes = []\n\n        for i, index in enumerate(indexes):\n            image, boxes = self.load_image_and_boxes(index)\n            if i == 0:\n                x1a, y1a, x2a, y2a = max(xc - w, 0), max(yc - h, 0), xc, yc  # xmin, ymin, xmax, ymax (large image)\n                x1b, y1b, x2b, y2b = w - (x2a - x1a), h - (y2a - y1a), w, h  # xmin, ymin, xmax, ymax (small image)\n            elif i == 1:  # top right\n                x1a, y1a, x2a, y2a = xc, max(yc - h, 0), min(xc + w, s * 2), yc\n                x1b, y1b, x2b, y2b = 0, h - (y2a - y1a), min(w, x2a - x1a), h\n            elif i == 2:  # bottom left\n                x1a, y1a, x2a, y2a = max(xc - w, 0), yc, xc, min(s * 2, yc + h)\n                x1b, y1b, x2b, y2b = w - (x2a - x1a), 0, max(xc, w), min(y2a - y1a, h)\n            elif i == 3:  # bottom right\n                x1a, y1a, x2a, y2a = xc, yc, min(xc + w, s * 2), min(s * 2, yc + h)\n                x1b, y1b, x2b, y2b = 0, 0, min(w, x2a - x1a), min(y2a - y1a, h)\n            result_image[y1a:y2a, x1a:x2a] = image[y1b:y2b, x1b:x2b]\n            padw = x1a - x1b\n            padh = y1a - y1b\n\n            boxes[:, 0] += padw\n            boxes[:, 1] += padh\n            boxes[:, 2] += padw\n            boxes[:, 3] += padh\n\n            result_boxes.append(boxes)\n\n        result_boxes = np.concatenate(result_boxes, 0)\n        np.clip(result_boxes[:, 0:], 0, 2 * s, out=result_boxes[:, 0:])\n        result_boxes = result_boxes.astype(np.int32)\n        result_boxes = result_boxes[np.where((result_boxes[:,2]-result_boxes[:,0])*(result_boxes[:,3]-result_boxes[:,1]) > 0)]\n        return result_image, result_boxes","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"class AverageMeter(object):\n    \"\"\"Computes and stores the average and current value\"\"\"\n    def __init__(self):\n        self.reset()\n\n    def reset(self):\n        self.val = 0\n        self.avg = 0\n        self.sum = 0\n        self.count = 0\n\n    def update(self, val, n=1):\n        self.val = val\n        self.sum += val * n\n        self.count += n\n        self.avg = self.sum / self.count\n\ndef collate_fn(batch):\n    return tuple(zip(*batch))\n\ntrain_dataset = DatasetRetriever(\n    image_ids=np.array(list(set(train_df['image_id'].values))).astype('O'),\n    marking=train_df,\n    transforms=get_train_transforms(),\n    test=False,\n)\n\nvalidation_dataset = DatasetRetriever(\n    image_ids=np.array(list(set(train_df['image_id'].values))).astype('O'),\n    marking=train_df,\n    transforms=get_valid_transforms(),\n    test=False,\n)\n\n# split the dataset in train and test set\nindices = torch.randperm(len(train_dataset)).tolist()\ntrain_dataset = torch.utils.data.Subset(train_dataset, indices[:-50])\nvalidation_dataset = torch.utils.data.Subset(validation_dataset, indices[-50:])\n\ndevice = torch.device('cuda') if torch.cuda.is_available() else torch.device('cpu')","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"image, target, image_id = train_dataset[1]\nboxes = target['boxes'].cpu().numpy().astype(np.int32)\n\nnumpy_image = image.permute(1,2,0).cpu().numpy()\n\nfig, ax = plt.subplots(1, 1, figsize=(16, 8))\n\nfor box in boxes:\n    cv2.rectangle(numpy_image, (box[1], box[0]), (box[3],  box[2]), (0, 1, 0), 2)\n    \nax.set_axis_off()\nax.imshow(numpy_image);","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Retrain the EfficientDet","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"import warnings\n\nwarnings.filterwarnings(\"ignore\")\n\nclass Fitter:\n    \n    def __init__(self, model, device, config):\n        self.config = config\n        self.epoch = 0\n\n        self.base_dir = f'./{config.folder}'\n        if not os.path.exists(self.base_dir):\n            os.makedirs(self.base_dir)\n        \n        self.log_path = f'{self.base_dir}/log.txt'\n        self.best_summary_loss = 10**5\n\n        self.model = model\n        self.device = device\n\n        param_optimizer = list(self.model.named_parameters())\n        no_decay = ['bias', 'LayerNorm.bias', 'LayerNorm.weight']\n        optimizer_grouped_parameters = [\n            {'params': [p for n, p in param_optimizer if not any(nd in n for nd in no_decay)], 'weight_decay': 0.001},\n            {'params': [p for n, p in param_optimizer if any(nd in n for nd in no_decay)], 'weight_decay': 0.0}\n        ] \n\n        self.optimizer = torch.optim.AdamW(self.model.parameters(), lr=config.lr)\n        self.scheduler = config.SchedulerClass(self.optimizer, **config.scheduler_params)\n        self.log(f'Fitter prepared. Device is {self.device}')\n\n    def fit(self, train_loader, validation_loader):\n        for e in range(self.config.n_epochs):\n            if self.config.verbose:\n                lr = self.optimizer.param_groups[0]['lr']\n                timestamp = datetime.utcnow().isoformat()\n                self.log(f'\\n{timestamp}\\nLR: {lr}')\n\n            t = time.time()\n            summary_loss = self.train_one_epoch(train_loader)\n\n            self.log(f'[RESULT]: Train. Epoch: {self.epoch}, summary_loss: {summary_loss.avg:.5f}, time: {(time.time() - t):.5f}')\n            self.save(f'{self.base_dir}/last-checkpoint.bin')\n\n            t = time.time()\n            summary_loss = self.validation(validation_loader)\n\n            self.log(f'[RESULT]: Val. Epoch: {self.epoch}, summary_loss: {summary_loss.avg:.5f}, time: {(time.time() - t):.5f}')\n            if summary_loss.avg < self.best_summary_loss:\n                self.best_summary_loss = summary_loss.avg\n                self.model.eval()\n                self.save(f'{self.base_dir}/best-checkpoint-{str(self.epoch).zfill(3)}epoch.bin')\n                for path in sorted(glob(f'{self.base_dir}/best-checkpoint-*epoch.bin'))[:-3]:\n                    os.remove(path)\n\n            if self.config.validation_scheduler:\n                self.scheduler.step(metrics=summary_loss.avg)\n\n            self.epoch += 1\n        return self.model\n\n    def validation(self, val_loader):\n        self.model.eval()\n        summary_loss = AverageMeter()\n        t = time.time()\n        for step, (images, targets, image_ids) in enumerate(val_loader):\n            if self.config.verbose:\n                if step % self.config.verbose_step == 0:\n                    print(\n                        f'Val Step {step}/{len(val_loader)}, ' + \\\n                        f'summary_loss: {summary_loss.avg:.5f}, ' + \\\n                        f'time: {(time.time() - t):.5f}', end='\\r'\n                    )\n            with torch.no_grad():\n                images = torch.stack(images)\n                batch_size = images.shape[0]\n                images = images.to(self.device).float()\n                boxes = [target['boxes'].to(self.device).float() for target in targets]\n                labels = [target['labels'].to(self.device).float() for target in targets]\n\n                loss, _, _ = self.model(images, boxes, labels)\n                summary_loss.update(loss.detach().item(), batch_size)\n\n        return summary_loss\n\n    def train_one_epoch(self, train_loader):\n        self.model.train()\n        summary_loss = AverageMeter()\n        t = time.time()\n        for step, (images, targets, image_ids) in enumerate(train_loader):\n            if self.config.verbose:\n                if step % self.config.verbose_step == 0:\n                    print(\n                        f'Train Step {step}/{len(train_loader)}, ' + \\\n                        f'summary_loss: {summary_loss.avg:.5f}, ' + \\\n                        f'time: {(time.time() - t):.5f}', end='\\r'\n                    )\n            \n            images = torch.stack(images)\n            images = images.to(self.device).float()\n            batch_size = images.shape[0]\n            boxes = [target['boxes'].to(self.device).float() for target in targets]\n            labels = [target['labels'].to(self.device).float() for target in targets]\n\n            self.optimizer.zero_grad()\n            \n            loss, _, _ = self.model(images, boxes, labels)\n            \n            with amp.scale_loss(loss, self.optimizer) as scaled_loss:\n                scaled_loss.backward()\n            \n            # loss.backward()\n            \n            if step % 3 == 0:\n                self.optimizer.step()\n                self.optimizer.zero_grad()\n\n            summary_loss.update(loss.detach().item(), batch_size)\n\n            # self.optimizer.step()\n\n            if self.config.step_scheduler:\n                self.scheduler.step()\n\n        return summary_loss\n    \n    def save(self, path):\n        self.model.eval()\n        torch.save({\n            'model_state_dict': self.model.model.state_dict(),\n            'optimizer_state_dict': self.optimizer.state_dict(),\n            'scheduler_state_dict': self.scheduler.state_dict(),\n            'best_summary_loss': self.best_summary_loss,\n            'epoch': self.epoch,\n        }, path)\n\n    def load(self, path):\n        checkpoint = torch.load(path)\n        self.model.model.load_state_dict(checkpoint['model_state_dict'])\n        self.optimizer.load_state_dict(checkpoint['optimizer_state_dict'])\n        self.scheduler.load_state_dict(checkpoint['scheduler_state_dict'])\n        self.best_summary_loss = checkpoint['best_summary_loss']\n        self.epoch = checkpoint['epoch'] + 1\n        \n    def log(self, message):\n        if self.config.verbose:\n            print(message)\n        with open(self.log_path, 'a+') as logger:\n            logger.write(f'{message}\\n')","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"class TrainGlobalConfig:\n    num_workers = 2\n    batch_size = 4 \n    n_epochs = 10\n    lr = 0.0002\n\n    folder = 'full-effdet5-cutmix-augmix'\n\n    verbose = True\n    verbose_step = 1\n\n    step_scheduler = False  # do scheduler.step after optimizer.step\n    validation_scheduler = True  # do scheduler.step after validation stage loss\n    \n    SchedulerClass = torch.optim.lr_scheduler.ReduceLROnPlateau\n    scheduler_params = dict(\n        mode='min',\n        factor=0.5,\n        patience=1,\n        verbose=False, \n        threshold=0.0001,\n        threshold_mode='abs',\n        cooldown=0, \n        min_lr=1e-8,\n        eps=1e-08\n    )","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def collate_fn(batch):\n    return tuple(zip(*batch))\n\ndef run_training():\n    device = torch.device('cuda:0')\n    model.to(device)\n\n    train_loader = torch.utils.data.DataLoader(\n        train_dataset,\n        batch_size=TrainGlobalConfig.batch_size,\n        sampler=RandomSampler(train_dataset),\n        pin_memory=False,\n        drop_last=True,\n        num_workers=TrainGlobalConfig.num_workers,\n        collate_fn=collate_fn,\n    )\n    val_loader = torch.utils.data.DataLoader(\n        validation_dataset, \n        batch_size=TrainGlobalConfig.batch_size,\n        num_workers=TrainGlobalConfig.num_workers,\n        shuffle=False,\n        sampler=SequentialSampler(validation_dataset),\n        pin_memory=False,\n        collate_fn=collate_fn,\n    )\n\n    fitter = Fitter(model=model, device=device, config=TrainGlobalConfig)\n    return fitter.fit(train_loader, val_loader)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"if len(os.listdir(DIR_TEST)) > 10:\n    model = run_training()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"model.eval()\ntorch.save({\n    'model_state_dict': model.model.state_dict()\n}, '/kaggle/working/pl.bin')","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"## Predictions","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"DATA_ROOT_PATH = '../input/global-wheat-detection/test'\n\nclass DatasetRetriever(Dataset):\n\n    def __init__(self, image_ids, transforms=None):\n        super().__init__()\n        self.image_ids = image_ids\n        self.transforms = transforms\n\n    def __getitem__(self, index: int):\n        image_id = self.image_ids[index]\n        image = cv2.imread(f'{DATA_ROOT_PATH}/{image_id}.jpg', cv2.IMREAD_COLOR)\n        image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB).astype(np.float32)\n        image /= 255.0\n        if self.transforms:\n            sample = {'image': image}\n            sample = self.transforms(**sample)\n            image = sample['image']\n        return image, image_id\n\n    def __len__(self) -> int:\n        return self.image_ids.shape[0]","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"dataset = DatasetRetriever(\n    image_ids=np.array([path.split('/')[-1][:-4] for path in glob(f'{DATA_ROOT_PATH}/*.jpg')]),\n    transforms=get_valid_transforms()\n)\n\n\ndata_loader = DataLoader(\n    dataset,\n    batch_size=4,\n    shuffle=False,\n    num_workers=2,\n    drop_last=False,\n    collate_fn=collate_fn\n)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"class BaseWheatTTA:\n    \"\"\" author: @shonenkov \"\"\"\n    image_size = 512\n\n    def augment(self, image):\n        raise NotImplementedError\n    \n    def batch_augment(self, images):\n        raise NotImplementedError\n    \n    def deaugment_boxes(self, boxes):\n        raise NotImplementedError\n\nclass TTAHorizontalFlip(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n\n    def augment(self, image):\n        return image.flip(1)\n    \n    def batch_augment(self, images):\n        return images.flip(2)\n    \n    def deaugment_boxes(self, boxes):\n        boxes[:, [1,3]] = self.image_size - boxes[:, [3,1]]\n        return boxes\n\nclass TTAVerticalFlip(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n    \n    def augment(self, image):\n        return image.flip(2)\n    \n    def batch_augment(self, images):\n        return images.flip(3)\n    \n    def deaugment_boxes(self, boxes):\n        boxes[:, [0,2]] = self.image_size - boxes[:, [2,0]]\n        return boxes\n    \nclass TTARotate90(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n    \n    def augment(self, image):\n        return torch.rot90(image, 1, (1, 2))\n\n    def batch_augment(self, images):\n        return torch.rot90(images, 1, (2, 3))\n    \n    def deaugment_boxes(self, boxes):\n        res_boxes = boxes.copy()\n        res_boxes[:, [0,2]] = self.image_size - boxes[:, [1,3]]\n        res_boxes[:, [1,3]] = boxes[:, [2,0]]\n        return res_boxes\n    \nclass TTARotate180(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n    \n    def augment(self, image):\n        return torch.rot90(image, 2, (1, 2))\n\n    def batch_augment(self, images):\n        return torch.rot90(images, 2, (2, 3))\n    \n    def deaugment_boxes(self, boxes):\n        boxes[:, [0,1,2,3]] = self.image_size - boxes[:, [2,3,0,1]]\n        return boxes\n    \nclass TTARotate270(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n    \n    def augment(self, image):\n        return torch.rot90(image, 3, (1, 2))\n\n    def batch_augment(self, images):\n        return torch.rot90(images, 3, (2, 3))\n    \n    def deaugment_boxes(self, boxes):\n        res_boxes = boxes.copy()\n        res_boxes[:, [0,2]] = boxes[:, [1,3]]\n        res_boxes[:, [1,3]] = self.image_size - boxes[:, [2,0]]\n        return res_boxes\n    \nclass TTACompose(BaseWheatTTA):\n    \"\"\" author: @shonenkov \"\"\"\n    def __init__(self, transforms):\n        self.transforms = transforms\n        \n    def augment(self, image):\n        for transform in self.transforms:\n            image = transform.augment(image)\n        return image\n    \n    def batch_augment(self, images):\n        for transform in self.transforms:\n            images = transform.batch_augment(images)\n        return images\n    \n    def prepare_boxes(self, boxes):\n        result_boxes = boxes.copy()\n        result_boxes[:,0] = np.min(boxes[:, [0,2]], axis=1)\n        result_boxes[:,2] = np.max(boxes[:, [0,2]], axis=1)\n        result_boxes[:,1] = np.min(boxes[:, [1,3]], axis=1)\n        result_boxes[:,3] = np.max(boxes[:, [1,3]], axis=1)\n        return result_boxes\n    \n    def deaugment_boxes(self, boxes):\n        for transform in self.transforms[::-1]:\n            boxes = transform.deaugment_boxes(boxes)\n        return self.prepare_boxes(boxes)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"from itertools import product\n\ntta_transforms = []\nfor tta_combination in product([TTAHorizontalFlip(), None], \n                               [TTAVerticalFlip(), None],\n                               [TTARotate90(), TTARotate180(), TTARotate270(), None]):\n    tta_transforms.append(TTACompose([tta_transform for tta_transform in tta_combination if tta_transform]))","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def load_net_eval(checkpoint_path):\n    config = get_efficientdet_config('tf_efficientdet_d5')\n    net = EfficientDet(config, pretrained_backbone=False)\n\n    config.num_classes = 1\n    config.image_size=512\n    net.class_net = HeadNet(config, num_outputs=config.num_classes, norm_kwargs=dict(eps=.001, momentum=.01))\n\n    checkpoint = torch.load(checkpoint_path, map_location=DEVICE)\n    net.load_state_dict(checkpoint['model_state_dict'])\n\n    del checkpoint\n    gc.collect()\n\n    net = DetBenchEval(net, config)\n    net.eval()\n    return net.cuda()\n\nmodel = load_net_eval('pl.bin')","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def make_tta_predictions(images, score_threshold=0.25):\n    with torch.no_grad():\n        images = torch.stack(images).float().cuda()\n        predictions = []\n        for tta_transform in tta_transforms:\n            result = []\n            det = model(tta_transform.batch_augment(images.clone()), torch.tensor([1]*images.shape[0]).float().cuda())\n\n            for i in range(images.shape[0]):\n                boxes = det[i].detach().cpu().numpy()[:,:4]    \n                scores = det[i].detach().cpu().numpy()[:,4]\n                indexes = np.where(scores > score_threshold)[0]\n                boxes = boxes[indexes]\n                boxes[:, 2] = boxes[:, 2] + boxes[:, 0]\n                boxes[:, 3] = boxes[:, 3] + boxes[:, 1]\n                boxes = tta_transform.deaugment_boxes(boxes.copy())\n                result.append({\n                    'boxes': boxes,\n                    'scores': scores[indexes],\n                })\n            predictions.append(result)\n    return predictions","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"import matplotlib.pyplot as plt\n\nfor j, (images, image_ids) in enumerate(data_loader):\n    break\n\npredictions = make_tta_predictions(images)\n\ni = 1\nsample = images[i].permute(1,2,0).cpu().numpy()\n\nboxes, scores, labels = run_wbf(predictions, image_index=i)\nboxes = boxes.round().astype(np.int32).clip(min=0, max=511)\n\nfig, ax = plt.subplots(1, 1, figsize=(16, 8))\n\nfor box in boxes:\n    cv2.rectangle(sample, (box[0], box[1]), (box[2], box[3]), (1, 0, 0), 1)\n\nax.set_axis_off()\nax.imshow(sample)\nplt.plot()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"results = []\n\nfor images, image_ids in data_loader:\n    predictions = make_tta_predictions(images)\n    for i, image in enumerate(images):\n        boxes, scores, labels = run_wbf(predictions, image_index=i)\n        boxes = (boxes*2).round().astype(np.int32).clip(min=0, max=1023)\n        image_id = image_ids[i]\n\n        boxes[:, 2] = boxes[:, 2] - boxes[:, 0]\n        boxes[:, 3] = boxes[:, 3] - boxes[:, 1]\n\n        result = {\n            'image_id': image_id,\n            'PredictionString': format_prediction_string(boxes, scores)\n        }\n        results.append(result)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"test_df = pd.DataFrame(results, columns=['image_id', 'PredictionString'])\ntest_df.to_csv('submission.csv', index=False)\ntest_df.head()","execution_count":null,"outputs":[]}],"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat":4,"nbformat_minor":4}