{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"name":"python","version":"3.10.13","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"},"kaggle":{"accelerator":"none","dataSources":[{"sourceId":71549,"databundleVersionId":8561470,"sourceType":"competition"},{"sourceId":9155530,"sourceType":"datasetVersion","datasetId":5530837},{"sourceId":87964,"sourceType":"modelInstanceVersion","modelInstanceId":73874,"modelId":98697}],"dockerImageVersionId":30747,"isInternetEnabled":false,"language":"python","sourceType":"notebook","isGpuEnabled":false}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"markdown","source":"Adapted from https://www.kaggle.com/code/itsuki9180/rsna2024-lsdc-submission-baseline and https://www.kaggle.com/code/garykim/glsdc-vit-train\n","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19"}},{"cell_type":"markdown","source":"# Import Libralies","metadata":{}},{"cell_type":"code","source":"import os\nimport gc\nimport sys\nfrom PIL import Image\nimport cv2\nimport math, random\nimport numpy as np\nimport pandas as pd\nimport glob\nfrom tqdm import tqdm\nimport matplotlib.pyplot as plt\nfrom sklearn.model_selection import KFold\nfrom transformers import SwinForImageClassification, SwinConfig, SwinModel, get_cosine_schedule_with_warmup\n\nfrom collections import OrderedDict\n\nimport torch\nimport torch.nn.functional as F\nfrom torch import nn\nfrom torch.utils.data import DataLoader, Dataset\nfrom torch.optim import AdamW\n\nimport timm\nfrom timm.utils import ModelEmaV2\nfrom transformers import get_cosine_schedule_with_warmup\n\nimport albumentations as A\n\nfrom sklearn.model_selection import KFold\n\nimport re\nimport pydicom","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:30.851040Z","iopub.execute_input":"2024-08-12T04:28:30.851351Z","iopub.status.idle":"2024-08-12T04:28:41.424810Z","shell.execute_reply.started":"2024-08-12T04:28:30.851307Z","shell.execute_reply":"2024-08-12T04:28:41.423770Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"rd = '/kaggle/input/rsna-2024-lumbar-spine-degenerative-classification'","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.426530Z","iopub.execute_input":"2024-08-12T04:28:41.427002Z","iopub.status.idle":"2024-08-12T04:28:41.431499Z","shell.execute_reply.started":"2024-08-12T04:28:41.426977Z","shell.execute_reply":"2024-08-12T04:28:41.430429Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Config","metadata":{}},{"cell_type":"code","source":"OUTPUT_DIR = f'/kaggle/input/rsna2024-lsdc-training-baseline/rsna24-results'\ndevice = 'cuda:0' if torch.cuda.is_available() else 'cpu'\nN_WORKERS = os.cpu_count()\nUSE_AMP = True\nSEED = 8620\n\nIMG_SIZE = [512, 512]\nIN_CHANS = 42\nN_LABELS = 25\nN_CLASSES = 3 * N_LABELS\n\nN_FOLDS = 5\n\nMODEL_NAME = \"microsoft/swin-base-patch4-window7-224\"\n\nBATCH_SIZE = 1","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.432698Z","iopub.execute_input":"2024-08-12T04:28:41.433017Z","iopub.status.idle":"2024-08-12T04:28:41.498789Z","shell.execute_reply.started":"2024-08-12T04:28:41.432993Z","shell.execute_reply":"2024-08-12T04:28:41.497880Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"rd = '/kaggle/input/rsna-2024-lumbar-spine-degenerative-classification'\n# /kaggle/input/rsna-v2-results/rsna24-results","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.501333Z","iopub.execute_input":"2024-08-12T04:28:41.501731Z","iopub.status.idle":"2024-08-12T04:28:41.508656Z","shell.execute_reply.started":"2024-08-12T04:28:41.501703Z","shell.execute_reply":"2024-08-12T04:28:41.507808Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"device = torch.device('cuda:0') if torch.cuda.is_available() else torch.device('cpu')\ndevice","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.509666Z","iopub.execute_input":"2024-08-12T04:28:41.510078Z","iopub.status.idle":"2024-08-12T04:28:41.522748Z","shell.execute_reply.started":"2024-08-12T04:28:41.510045Z","shell.execute_reply":"2024-08-12T04:28:41.521878Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"df = pd.read_csv(f'{rd}/test_series_descriptions.csv')\ndf.head()","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.523713Z","iopub.execute_input":"2024-08-12T04:28:41.524006Z","iopub.status.idle":"2024-08-12T04:28:41.555572Z","shell.execute_reply.started":"2024-08-12T04:28:41.523983Z","shell.execute_reply":"2024-08-12T04:28:41.554662Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"study_ids = list(df['study_id'].unique())","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.556823Z","iopub.execute_input":"2024-08-12T04:28:41.557116Z","iopub.status.idle":"2024-08-12T04:28:41.563984Z","shell.execute_reply.started":"2024-08-12T04:28:41.557091Z","shell.execute_reply":"2024-08-12T04:28:41.563009Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"sample_sub = pd.read_csv(f'{rd}/sample_submission.csv')","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.565236Z","iopub.execute_input":"2024-08-12T04:28:41.566053Z","iopub.status.idle":"2024-08-12T04:28:41.578122Z","shell.execute_reply.started":"2024-08-12T04:28:41.566028Z","shell.execute_reply":"2024-08-12T04:28:41.577383Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"LABELS = list(sample_sub.columns[1:])\nLABELS","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.579319Z","iopub.execute_input":"2024-08-12T04:28:41.579710Z","iopub.status.idle":"2024-08-12T04:28:41.587264Z","shell.execute_reply.started":"2024-08-12T04:28:41.579679Z","shell.execute_reply":"2024-08-12T04:28:41.586379Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"CONDITIONS = [\n    'spinal_canal_stenosis', \n    'left_neural_foraminal_narrowing', \n    'right_neural_foraminal_narrowing',\n    'left_subarticular_stenosis',\n    'right_subarticular_stenosis'\n]\n\nLEVELS = [\n    'l1_l2',\n    'l2_l3',\n    'l3_l4',\n    'l4_l5',\n    'l5_s1',\n]","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.590296Z","iopub.execute_input":"2024-08-12T04:28:41.590621Z","iopub.status.idle":"2024-08-12T04:28:41.596523Z","shell.execute_reply.started":"2024-08-12T04:28:41.590597Z","shell.execute_reply":"2024-08-12T04:28:41.595801Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"def atoi(text):\n    return int(text) if text.isdigit() else text\n\ndef natural_keys(text):\n    return [ atoi(c) for c in re.split(r'(\\d+)', text) ]","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.597419Z","iopub.execute_input":"2024-08-12T04:28:41.597681Z","iopub.status.idle":"2024-08-12T04:28:41.607025Z","shell.execute_reply.started":"2024-08-12T04:28:41.597659Z","shell.execute_reply":"2024-08-12T04:28:41.606259Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Define Dataset","metadata":{}},{"cell_type":"code","source":"","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"class RSNA24TestDataset(Dataset):\n    def __init__(self, df, study_ids, phase='test', transform=None):\n        self.df = df\n        self.study_ids = study_ids\n        self.transform = transform\n        self.phase = phase\n    \n    def __len__(self):\n        return len(self.study_ids)\n    \n    def get_img_paths(self, study_id, series_desc):\n        pdf = self.df[self.df['study_id']==study_id]\n        pdf_ = pdf[pdf['series_description']==series_desc]\n        allimgs = []\n        for i, row in pdf_.iterrows():\n            pimgs = glob.glob(f'{rd}/test_images/{study_id}/{row[\"series_id\"]}/*.dcm')\n            pimgs = sorted(pimgs, key=natural_keys)\n            allimgs.extend(pimgs)\n            \n        return allimgs\n    \n    def read_dcm_ret_arr(self, src_path):\n        dicom_data = pydicom.dcmread(src_path)\n        image = dicom_data.pixel_array\n        image = (image - image.min()) / (image.max() - image.min() + 1e-6) * 255\n        img = cv2.resize(image, (IMG_SIZE[0], IMG_SIZE[1]),interpolation=cv2.INTER_CUBIC)\n        assert img.shape==(IMG_SIZE[0], IMG_SIZE[1])\n        return img\n\n    def __getitem__(self, idx):\n        x = np.zeros((IMG_SIZE[0], IMG_SIZE[1], IN_CHANS), dtype=np.uint8)\n        st_id = self.study_ids[idx]        \n        \n        # Sagittal T1\n        allimgs_st1 = self.get_img_paths(st_id, 'Sagittal T1')\n        if len(allimgs_st1)==0:\n            print(st_id, ': Sagittal T1, has no images')\n        \n        else:\n            step = len(allimgs_st1) / 14.0\n            st = len(allimgs_st1)/2.0 - 6.0*step\n            end = len(allimgs_st1)+0.0001\n            for j, i in enumerate(np.arange(st, end, step)):\n                try:\n                    ind2 = max(0, int((i-0.5001).round()))\n                    img = self.read_dcm_ret_arr(allimgs_st1[ind2])\n                    x[..., j] = img.astype(np.uint8)\n                except:\n                    print(f'failed to load on {st_id}, Sagittal T1')\n                    pass\n            \n        # Sagittal T2/STIR\n        allimgs_st2 = self.get_img_paths(st_id, 'Sagittal T2/STIR')\n        if len(allimgs_st2)==0:\n            print(st_id, ': Sagittal T2/STIR, has no images')\n            \n        else:\n            step = len(allimgs_st2) / 14.0\n            st = len(allimgs_st2)/2.0 - 6.0*step\n            end = len(allimgs_st2)+0.0001\n            for j, i in enumerate(np.arange(st, end, step)):\n                try:\n                    ind2 = max(0, int((i-0.5001).round()))\n                    img = self.read_dcm_ret_arr(allimgs_st2[ind2])\n                    x[..., j+14] = img.astype(np.uint8)\n                except:\n                    print(f'failed to load on {st_id}, Sagittal T2/STIR')\n                    pass\n            \n        # Axial T2\n        allimgs_at2 = self.get_img_paths(st_id, 'Axial T2')\n        if len(allimgs_at2)==0:\n            print(st_id, ': Axial T2, has no images')\n            \n        else:\n            step = len(allimgs_at2) / 10.0\n            st = len(allimgs_at2)/2.0 - 4.0*step\n            end = len(allimgs_at2)+0.0001\n\n            for j, i in enumerate(np.arange(st, end, step)):\n                try:\n                    ind2 = max(0, int((i-0.5001).round()))\n                    img = self.read_dcm_ret_arr(allimgs_at2[ind2])\n                    x[..., j+28] = img.astype(np.uint8)\n                except:\n                    print(f'failed to load on {st_id}, Axial T2')\n                    pass  \n            \n            \n        if self.transform is not None:\n            x = self.transform(image=x)['image']\n\n        x = x.transpose(2, 0, 1)\n                \n        return x, str(st_id)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.608229Z","iopub.execute_input":"2024-08-12T04:28:41.608526Z","iopub.status.idle":"2024-08-12T04:28:41.630635Z","shell.execute_reply.started":"2024-08-12T04:28:41.608503Z","shell.execute_reply":"2024-08-12T04:28:41.629761Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"transforms_test = A.Compose([\n    A.Resize(IMG_SIZE[0], IMG_SIZE[1]),\n    A.Normalize(mean=0.5, std=0.5)\n])","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.631730Z","iopub.execute_input":"2024-08-12T04:28:41.632032Z","iopub.status.idle":"2024-08-12T04:28:41.645596Z","shell.execute_reply.started":"2024-08-12T04:28:41.632008Z","shell.execute_reply":"2024-08-12T04:28:41.644732Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"test_ds = RSNA24TestDataset(df, study_ids, transform=transforms_test)\ntest_dl = DataLoader(\n    test_ds, \n    batch_size=1, \n    shuffle=False,\n    num_workers=N_WORKERS,\n    pin_memory=True,\n    drop_last=False\n)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.646433Z","iopub.execute_input":"2024-08-12T04:28:41.646690Z","iopub.status.idle":"2024-08-12T04:28:41.655148Z","shell.execute_reply.started":"2024-08-12T04:28:41.646668Z","shell.execute_reply":"2024-08-12T04:28:41.654307Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Define Model","metadata":{}},{"cell_type":"code","source":"class RSNA24Model(nn.Module):\n    def __init__(self, model_name, in_c=30, n_classes=75, pretrained=True, features_only=False):\n        super().__init__()\n        self.model = timm.create_model(\n                                    model_name,\n                                    pretrained=pretrained, \n                                    features_only=features_only,\n                                    in_chans=in_c,\n                                    num_classes=n_classes,\n                                    global_pool='avg'\n                                    )\n    \n    def forward(self, x):\n        y = self.model(x)\n        return y","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.656191Z","iopub.execute_input":"2024-08-12T04:28:41.656476Z","iopub.status.idle":"2024-08-12T04:28:41.665995Z","shell.execute_reply.started":"2024-08-12T04:28:41.656453Z","shell.execute_reply":"2024-08-12T04:28:41.665158Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Load Models","metadata":{}},{"cell_type":"code","source":"models = []","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.666985Z","iopub.execute_input":"2024-08-12T04:28:41.667231Z","iopub.status.idle":"2024-08-12T04:28:41.682716Z","shell.execute_reply.started":"2024-08-12T04:28:41.667211Z","shell.execute_reply":"2024-08-12T04:28:41.681912Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"CKPT_PATHS = glob.glob('/kaggle/input/swin-transformer-42chans-results/best_wll_model_fold-*.pt')\nCKPT_PATHS = sorted(CKPT_PATHS)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.683823Z","iopub.execute_input":"2024-08-12T04:28:41.684143Z","iopub.status.idle":"2024-08-12T04:28:41.696259Z","shell.execute_reply.started":"2024-08-12T04:28:41.684112Z","shell.execute_reply":"2024-08-12T04:28:41.695497Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"swinConfig = SwinConfig.from_pretrained(\"/kaggle/input/swin-transformer/pytorch/default/1/config.json\")\nswinConfig.num_channels = IN_CHANS\nswinConfig.num_labels = N_CLASSES\nswinConfig.image_size = 512\nswinConfig.patch_size = 4","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.697506Z","iopub.execute_input":"2024-08-12T04:28:41.697891Z","iopub.status.idle":"2024-08-12T04:28:41.721038Z","shell.execute_reply.started":"2024-08-12T04:28:41.697862Z","shell.execute_reply":"2024-08-12T04:28:41.720370Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"\nfor i, cp in enumerate(CKPT_PATHS):\n    print(f'loading {cp}...')\n    model = SwinForImageClassification.from_pretrained(pretrained_model_name_or_path=None,config=swinConfig,state_dict=torch.load(cp),ignore_mismatched_sizes=True)\n    model.eval()\n    model.half()\n    model.to(device)\n    models.append(model)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.721974Z","iopub.execute_input":"2024-08-12T04:28:41.722223Z","iopub.status.idle":"2024-08-12T04:28:41.727292Z","shell.execute_reply.started":"2024-08-12T04:28:41.722202Z","shell.execute_reply":"2024-08-12T04:28:41.726372Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Inference loop","metadata":{}},{"cell_type":"code","source":"autocast = torch.cuda.amp.autocast(enabled=USE_AMP, dtype=torch.half)\ny_preds = []\nrow_names = []\n\nwith tqdm(test_dl, leave=True) as pbar:\n    with torch.no_grad():\n        for idx, (x, si) in enumerate(pbar):\n            x = x.to(device)\n            pred_per_study = np.zeros((25, 3))\n            \n            for cond in CONDITIONS:\n                for level in LEVELS:\n                    row_names.append(si[0] + '_' + cond + '_' + level)\n            \n            with autocast:\n                for m in models:\n                    y = m(x)[0]\n                    for col in range(N_LABELS):\n                        pred = y[:,col*3:col*3+3].T\n                        y_pred = pred.float().softmax(0).cpu().numpy().squeeze(-1)\n                        pred_per_study[col] += y_pred / len(models)\n                y_preds.append(pred_per_study)\n\ny_preds = np.concatenate(y_preds, axis=0)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:41.728402Z","iopub.execute_input":"2024-08-12T04:28:41.728676Z","iopub.status.idle":"2024-08-12T04:28:43.561737Z","shell.execute_reply.started":"2024-08-12T04:28:41.728653Z","shell.execute_reply":"2024-08-12T04:28:43.560752Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Make Submission","metadata":{}},{"cell_type":"code","source":"sub = pd.DataFrame()\nsub['row_id'] = row_names\nsub[LABELS] = y_preds\nsub.head(25)","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:43.564218Z","iopub.execute_input":"2024-08-12T04:28:43.564598Z","iopub.status.idle":"2024-08-12T04:28:43.593862Z","shell.execute_reply.started":"2024-08-12T04:28:43.564564Z","shell.execute_reply":"2024-08-12T04:28:43.592848Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"sub.to_csv('/kaggle/working/submission.csv', index=False)\npd.read_csv('/kaggle/working/submission.csv').head()","metadata":{"execution":{"iopub.status.busy":"2024-08-12T04:28:43.595083Z","iopub.execute_input":"2024-08-12T04:28:43.595429Z","iopub.status.idle":"2024-08-12T04:28:43.614856Z","shell.execute_reply.started":"2024-08-12T04:28:43.595401Z","shell.execute_reply":"2024-08-12T04:28:43.613932Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]}]}