{"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_minor":4,"nbformat":4,"cells":[{"cell_type":"markdown","source":"### Volumetric Image Slicing ","metadata":{}},{"cell_type":"markdown","source":"Our Dataset: Based on the code provided (1) and the outputs, our DICOM dataset seems to already consist of 2D slices. Each .dcm file we've loaded with glob appears to be a single 2D axial slice of a 3D volume.\n\nWhat We Did: We grouped these 2D slices by their respective StudyInstanceUID, which represents a unique 3D volume (or a complete study for a patient). We then loaded and ordered these 2D slices to form the 3D volume in memory. This process can be termed as \"volume reconstruction\".\n\nTraditional Image Slicing: Slicing typically refers to the process of taking a 3D volume and generating 2D slices from it. For instance, if you had a 3D MRI or CT scan, \"image slicing\" would mean extracting individual 2D images (slices) at different depths of that volume.\n\nIn summary, we've reconstructed the 3D volume from its constituent 2D slices, rather than slicing a 3D volume into 2D images. If your goal is to process the 3D volume slice-by-slice (i.e., 2D image by 2D image), then you're already set up to do so with the current structure.","metadata":{}},{"cell_type":"code","source":"import os\nimport pydicom\nimport numpy as np\nfrom collections import defaultdict\n\ndef group_dicom_files_by_study(dicom_directory):\n    all_dicom_files = [os.path.join(dicom_directory, subfolder, file) \n                       for subfolder in os.listdir(dicom_directory) \n                       for file in os.listdir(os.path.join(dicom_directory, subfolder)) \n                       if file.endswith(\".dcm\")]\n\n    grouped_files = defaultdict(list)\n\n    for file_path in all_dicom_files:\n        study_instance_uid = file_path.split('/')[-2]  # As it is in the format .../StudyInstanceUID/slice.dcm\n        grouped_files[study_instance_uid].append(file_path)\n\n    return grouped_files\ndef load_3D_volume_from_slices(dicom_file_paths):\n    slices = [pydicom.dcmread(file_path) for file_path in dicom_file_paths]\n    \n    # Ensure the slices are in the correct order (based on Image Position)\n    slices = sorted(slices, key=lambda s: s.ImagePositionPatient[2])\n\n    # Convert slices to a 3D numpy array\n    volume = np.stack([s.pixel_array for s in slices], axis=2)\n    \n    return volume\nroot_directory = \"/kaggle/input/rsna-2022-cervical-spine-fracture-detection\"\n\ntrain_dicom_directory = os.path.join(root_directory, \"train_images\")\ngrouped_train_files = group_dicom_files_by_study(train_dicom_directory)\n\n# For demonstration, let's load one 3D volume from the grouped train DICOM files\nsome_study_instance_uid = list(grouped_train_files.keys())[0]  # First study instance UID for demonstration\nsome_volume = load_3D_volume_from_slices(grouped_train_files[some_study_instance_uid])\nprint(some_volume.shape)\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T02:58:07.833131Z","iopub.execute_input":"2023-09-26T02:58:07.833558Z","iopub.status.idle":"2023-09-26T03:01:30.504065Z","shell.execute_reply.started":"2023-09-26T02:58:07.833525Z","shell.execute_reply":"2023-09-26T03:01:30.502886Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import matplotlib.pyplot as plt\n\nslice_number = 13# for demonstration purposes\nplt.imshow(some_volume[:, :, slice_number], cmap='gray')\nplt.show()\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:30.50646Z","iopub.execute_input":"2023-09-26T03:01:30.506912Z","iopub.status.idle":"2023-09-26T03:01:30.8664Z","shell.execute_reply.started":"2023-09-26T03:01:30.50687Z","shell.execute_reply":"2023-09-26T03:01:30.865438Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"### Windowing","metadata":{}},{"cell_type":"code","source":"import pydicom\n\ndcm = pydicom.dcmread(\"/kaggle/input/rsna-2022-cervical-spine-fracture-detection/train_images/1.2.826.0.1.3680043.10001/100.dcm\")\nimage = dcm.pixel_array\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:30.867488Z","iopub.execute_input":"2023-09-26T03:01:30.868178Z","iopub.status.idle":"2023-09-26T03:01:30.885552Z","shell.execute_reply.started":"2023-09-26T03:01:30.868146Z","shell.execute_reply":"2023-09-26T03:01:30.88468Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import matplotlib.pyplot as plt\ndef apply_windowing(image, window_center, window_width):\n    lower_limit = window_center - (window_width / 2)\n    upper_limit = window_center + (window_width / 2)\n    windowed_image = np.clip(image, lower_limit, upper_limit)\n    windowed_image = ((windowed_image - lower_limit) / window_width) * 255.0\n    return windowed_image.astype(np.uint8)\n\nbone_windowed_image = apply_windowing(image, 300, 2000)\n\nplt.imshow(bone_windowed_image, cmap='gray')\nplt.show()\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:30.888238Z","iopub.execute_input":"2023-09-26T03:01:30.888911Z","iopub.status.idle":"2023-09-26T03:01:31.196724Z","shell.execute_reply.started":"2023-09-26T03:01:30.88887Z","shell.execute_reply":"2023-09-26T03:01:31.195508Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"### Resizing","metadata":{}},{"cell_type":"code","source":"import numpy as np\nimport matplotlib.pyplot as plt\nfrom PIL import Image\nimport cv2\n\ndef resize_image(image_path, output_size=(224, 224)):\n    with Image.open(image_path) as img:\n        img_resized = img.resize(output_size, Image.ANTIALIAS)\n    return img_resized\n\ndef resize_numpy_array(array, output_size=(224, 224)):\n    return cv2.resize(array, output_size, interpolation=cv2.INTER_LINEAR)\n\nimport numpy as np\nimport matplotlib.pyplot as plt\n\ndef display_image_with_axes(image_array):\n    plt.imshow(image_array, cmap='gray')\n    plt.colorbar()\n    plt.xlabel('X-axis')\n    plt.ylabel('Y-axis')\n    plt.title('Resized Image')\n    plt.show()\n    \nresized_array = resize_numpy_array(some_volume[:,:,0]) # taking one slice as an example\ndisplay_image_with_axes(resized_array)  # using the matplotlib display function\n\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:31.198512Z","iopub.execute_input":"2023-09-26T03:01:31.198855Z","iopub.status.idle":"2023-09-26T03:01:31.956664Z","shell.execute_reply.started":"2023-09-26T03:01:31.198826Z","shell.execute_reply":"2023-09-26T03:01:31.955519Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"print(resized_array.shape)  # should output (224, 224) or (224, 224, 3) for RGB images\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:31.958389Z","iopub.execute_input":"2023-09-26T03:01:31.958843Z","iopub.status.idle":"2023-09-26T03:01:31.964902Z","shell.execute_reply.started":"2023-09-26T03:01:31.958799Z","shell.execute_reply":"2023-09-26T03:01:31.963788Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"from PIL import Image\nimport os\n\ndef are_all_images_resized_in_directory(directory, target_size=(224, 224)):\n    for filename in os.listdir(directory):\n        if filename.endswith(\".jpg\") or filename.endswith(\".png\"):  # Add other formats if needed\n            img_path = os.path.join(directory, filename)\n            with Image.open(img_path) as img:\n                if img.size != target_size:\n                    print(f\"{filename} is not resized.\")\n                    return False\n    return True\n\n# Usage:\ndirectory_path = \"/kaggle/input/rsna-2022-cervical-spine-fracture-detection/train_images\"\nprint(are_all_images_resized_in_directory(directory_path))\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:31.966567Z","iopub.execute_input":"2023-09-26T03:01:31.966957Z","iopub.status.idle":"2023-09-26T03:01:31.988781Z","shell.execute_reply.started":"2023-09-26T03:01:31.96692Z","shell.execute_reply":"2023-09-26T03:01:31.987846Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import cv2\nimport matplotlib.pyplot as plt\nimport albumentations as A\n\n# Revised resizing function\ndef resize_image(image_array, output_size=(224, 224)):\n    return cv2.resize(image_array, output_size)\n\ntransform = A.Compose([\n    A.HorizontalFlip(p=0.5),\n    A.RandomBrightnessContrast(p=0.4),\n    A.Rotate(limit=20, p=0.5),\n    A.ShiftScaleRotate(p=0.5),\n    A.GaussianBlur(p=0.001),\n])\n\ndef augment_image(image, transform):\n    augmented = transform(image=image)\n    return augmented['image']\n\n# Ensure the data type is uint8 for proper visualization with Albumentations.\nsome_image = some_volume[:, :, 50].astype(np.uint8)  # Example slice\nresized_image = resize_image(some_image)\naugmented_image = augment_image(resized_image, transform)\n\n# To visualize the original and augmented images side-by-side\nplt.figure(figsize=(10, 5))\n\nplt.subplot(1, 2, 1)\nplt.imshow(resized_image, cmap='gray')\nplt.title('Original Image')\nplt.axis('on')\n\nplt.subplot(1, 2, 2)\nplt.imshow(augmented_image, cmap='gray')\nplt.title('Augmented Image')\nplt.axis('on')\n\nplt.tight_layout()\nplt.show()\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:31.990215Z","iopub.execute_input":"2023-09-26T03:01:31.990604Z","iopub.status.idle":"2023-09-26T03:01:35.584496Z","shell.execute_reply.started":"2023-09-26T03:01:31.990572Z","shell.execute_reply":"2023-09-26T03:01:35.583623Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import os\nimport cv2\nimport numpy as np\nimport pydicom\nfrom sklearn.model_selection import train_test_split\n\n# Helper functions\ndef load_img_from_dcm(path):\n    img = dicom.dcmread(path)\n    img.PhotometricInterpretation = 'YBR_FULL'\n    data = img.pixel_array\n    data = data - np.min(data)\n    if np.max(data) != 0:\n        data = data/np.max(data)\n    data = (data * 255).astype(np.uint8)\n    return cv2.cvtColor(data, cv2.COLOR_GRAY2RGB)\ndef load_3d_ct_scan(folder_path):\n    file_list = os.listdir(folder_path)\n    file_list.sort()\n    file_list = sorted(file_list, key=len)\n    \n    ct_scan = []\n    for dcm in file_list:\n        dcm_path = os.path.join(folder_path, dcm)\n        dcm_img = load_img_from_dcm(dcm_path)\n        ct_scan.append(dcm_img)\n    \n    return np.asarray(ct_scan)\ndef extract_2d_slices(ct_3d_array):\n    return [ct_3d_array[i, :, :] for i in range(ct_3d_array.shape[0])]\n\ndef data_augmentation(image_list):\n    augmented_images = []\n    for img in image_list:\n        # Example: flip image horizontally\n        augmented_img = cv2.flip(img, 1)\n        augmented_images.append(augmented_img)\n    return augmented_images\ndef load_annotations(folder_path):\n    # Placeholder: Ideally, our annotations are in some format (like JSON, XML) \n    # and we'll read them and return them in a format suitable for Faster R-CNN.\n    # Here, returning an empty list for demonstration purposes.\n    return []\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:35.585789Z","iopub.execute_input":"2023-09-26T03:01:35.58644Z","iopub.status.idle":"2023-09-26T03:01:35.597513Z","shell.execute_reply.started":"2023-09-26T03:01:35.586408Z","shell.execute_reply":"2023-09-26T03:01:35.596327Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import csv\n\ndef load_bounding_boxes(path_to_annotation_file):\n    annotations = {}\n    \n    with open(path_to_annotation_file, 'r') as csvfile:\n        reader = csv.reader(csvfile)\n        next(reader)  # skip the header\n        \n        for row in reader:\n            study_instance_uid = row[0]\n            x, y, width, height = float(row[1]), float(row[2]), float(row[3]), float(row[4])\n            slice_number = row[5]\n\n            # Convert width and height to x2, y2\n            x2 = x + width\n            y2 = y + height\n\n            filename = f\"{study_instance_uid}_{slice_number}.dcm\"\n\n            if filename not in annotations:\n                annotations[filename] = {\"filename\": filename, \"boxes\": []}\n            \n            annotations[filename][\"boxes\"].append([x, y, x2, y2])\n    \n    return list(annotations.values())\n\n# Example usage\npath_to_annotation_file = \"/kaggle/input/rsna-2022-cervical-spine-fracture-detection/train_bounding_boxes.csv\"\n\nannotations = load_bounding_boxes(path_to_annotation_file)\n\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:35.601635Z","iopub.execute_input":"2023-09-26T03:01:35.602409Z","iopub.status.idle":"2023-09-26T03:01:35.788105Z","shell.execute_reply.started":"2023-09-26T03:01:35.602376Z","shell.execute_reply":"2023-09-26T03:01:35.786872Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"from sklearn.model_selection import train_test_split\nimport random\ndata = [{'filename': '1.2.826.0.1.3680043.10051_133.dcm', 'boxes': [[219.27715, 216.71419, 236.58155, 237.09936]]}, {'filename': '1.2.826.0.1.3680043.10051_134.dcm', 'boxes': [[221.5646, 216.71419, 239.44304, 241.95781]]}, {'filename': '1.2.826.0.1.3680043.10051_135.dcm', 'boxes': [[216.82151, 221.62546, 243.8311, 248.0]]}, {'filename': '1.2.826.0.1.3680043.10051_136.dcm', 'boxes': [[214.49455, 215.48637, 242.42181, 253.0]]}, {'filename': '1.2.826.0.1.3680043.10051_137.dcm', 'boxes': [[214.0, 215.48637, 241.0, 259.0]]}, {'filename': '1.2.826.0.1.3680043.10051_138.dcm', 'boxes': [[213.56364, 216.71419, 238.69818999999998, 264.64136]]}, {'filename': '1.2.826.0.1.3680043.10051_139.dcm', 'boxes': [[209.0, 214.57591, 245.06131000000002, 266.14425]]}, {'filename': '1.2.826.0.1.3680043.10051_140.dcm', 'boxes': [[204.25455, 212.24727, 251.73091, 269.96362]]}, {'filename': '1.2.826.0.1.3680043.10051_141.dcm', 'boxes': [[205.0, 213.87342, 250.0, 273.0]]}, {'filename': '1.2.826.0.1.3680043.10051_142.dcm', 'boxes': [[205.18545, 214.76814, 248.08437, 278.20178]]}, {'filename': '1.2.826.0.1.3680043.10051_143.dcm', 'boxes': [[203.0, 217.0, 245.0, 279.07842999999997]]}, {'filename': '1.2.826.0.1.3680043.10051_144.dcm', 'boxes': [[201.0, 219.0, 242.0, 277.0]]}, {'filename': '1.2.826.0.1.3680043.10051_145.dcm', 'boxes': [[199.6, 220.62545, 239.62908, 277.41091]]}, {'filename': '1.2.826.0.1.3680043.10051_146.dcm', 'boxes': [[195.0, 221.0, 246.0, 279.0]]}, {'filename': '1.2.826.0.1.3680043.10051_147.dcm', 'boxes': [[191.22182, 221.4346, 252.66182, 282.06546]]}, {'filename': '1.2.826.0.1.3680043.10051_148.dcm', 'boxes': [[200.16292, 232.42136, 223.49146000000002, 264.34461]]}, {'filename': '1.2.826.0.1.3680043.10579_78.dcm', 'boxes': [[250.18182, 244.96552, 285.71173999999996, 278.75674]]}, {'filename': '1.2.826.0.1.3680043.10579_79.dcm', 'boxes': [[247.14625, 245.0, 287.09549000000004, 280.28457]]}, {'filename': '1.2.826.0.1.3680043.10579_80.dcm', 'boxes': [[249.96552, 244.96552, 284.3931, 287.52072]]}, {'filename': '1.2.826.0.1.3680043.10678_118.dcm', 'boxes': [[231.0, 227.0, 281.0, 263.0]]}, {'filename': '1.2.826.0.1.3680043.10678_119.dcm', 'boxes': [[230.0, 227.0, 282.0, 265.0]]}, {'filename': '1.2.826.0.1.3680043.10678_120.dcm', 'boxes': [[230.0, 198.0, 302.0, 265.0]]}, {'filename': '1.2.826.0.1.3680043.10678_121.dcm', 'boxes': [[229.0, 167.15544, 335.36905, 267.0]]}, {'filename': '1.2.826.0.1.3680043.10678_122.dcm', 'boxes': [[228.0, 167.83999, 332.40729, 268.0]]}, {'filename': '1.2.826.0.1.3680043.10678_123.dcm', 'boxes': [[228.0, 171.82852, 330.68143, 268.0]]}, {'filename': '1.2.826.0.1.3680043.10678_124.dcm', 'boxes': [[227.0, 163.44631, 334.17403, 270.0]]}, {'filename': '1.2.826.0.1.3680043.10678_125.dcm', 'boxes': [[134.28522, 163.34088, 334.0, 270.0]]}, {'filename': '1.2.826.0.1.3680043.10678_126.dcm', 'boxes': [[141.05738, 169.18261, 334.17404, 271.58262]]}, {'filename': '1.2.826.0.1.3680043.10678_127.dcm', 'boxes': [[133.93392, 168.29216, 335.0, 274.25391]]}, {'filename': '1.2.826.0.1.3680043.10678_128.dcm', 'boxes': [[138.40871, 166.68347, 335.57106, 275.0]]}, {'filename': '1.2.826.0.1.3680043.10678_129.dcm', 'boxes': [[134.73738, 158.34088, 335.57106, 275.0]]}, {'filename': '1.2.826.0.1.3680043.10678_130.dcm', 'boxes': [[137.18958, 160.79305, 295.0, 277.0]]}, {'filename': '1.2.826.0.1.3680043.10678_131.dcm', 'boxes': [[137.97043, 159.57391, 295.0, 278.98311]]}, {'filename': '1.2.826.0.1.3680043.10678_132.dcm', 'boxes': [[191.1774, 190.51999, 295.0, 278.0]]}, {'filename': '1.2.826.0.1.3680043.10678_133.dcm', 'boxes': [[198.04522, 195.00522, 295.10261, 278.70609]]}, {'filename': '1.2.826.0.1.3680043.10678_134.dcm', 'boxes': [[217.52145, 224.38957, 277.29391, 286.71999999999997]]}, {'filename': '1.2.826.0.1.3680043.10678_146.dcm', 'boxes': [[222.9774, 150.48348, 336.95304999999996, 314.32349]]}, {'filename': '1.2.826.0.1.3680043.10678_147.dcm', 'boxes': [[224.0, 155.0, 334.0, 307.0]]}, {'filename': '1.2.826.0.1.3680043.10678_148.dcm', 'boxes': [[225.0, 160.0, 330.0, 300.0]]}, {'filename': 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'1.2.826.0.1.3680043.9940_136.dcm', 'boxes': [[305.0, 113.0, 378.0, 182.0]]}, {'filename': '1.2.826.0.1.3680043.9940_137.dcm', 'boxes': [[305.38763, 112.82124, 377.88317, 184.41062]]}, {'filename': '1.2.826.0.1.3680043.9940_138.dcm', 'boxes': [[303.0, 114.0, 380.0, 183.0]]}, {'filename': '1.2.826.0.1.3680043.9940_139.dcm', 'boxes': [[300.0, 115.0, 381.0, 190.00481]]}, {'filename': '1.2.826.0.1.3680043.9940_140.dcm', 'boxes': [[297.23186, 115.53983, 382.41414, 182.06606]]}, {'filename': '1.2.826.0.1.3680043.9940_141.dcm', 'boxes': [[298.0, 117.0, 384.0, 178.0]]}, {'filename': '1.2.826.0.1.3680043.9940_142.dcm', 'boxes': [[298.0, 119.0, 385.0, 177.0]]}, {'filename': '1.2.826.0.1.3680043.9940_143.dcm', 'boxes': [[299.0, 120.0, 388.0, 176.0]]}, {'filename': '1.2.826.0.1.3680043.9940_144.dcm', 'boxes': [[299.04425, 121.88319, 388.75750999999997, 175.34868]]}]\nrandom.shuffle(data)\n# Split the data into training (80%), validation (10%), and test (10%) sets\ntrain_data, temp_data = train_test_split(data, test_size=0.20, random_state=42)\nvalid_data, test_data = train_test_split(temp_data, test_size=0.50, random_state=42)\n\nprint(f\"Training data count: {len(train_data)}\")\nprint(f\"Validation data count: {len(valid_data)}\")\nprint(f\"Test data count: {len(test_data)}\")\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:35.793953Z","iopub.execute_input":"2023-09-26T03:01:35.794525Z","iopub.status.idle":"2023-09-26T03:01:39.952283Z","shell.execute_reply.started":"2023-09-26T03:01:35.794483Z","shell.execute_reply":"2023-09-26T03:01:39.951133Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import os\nimport shutil\n# Define the directories\n\nBASE_DIR = '/kaggle/working/'\nTRAIN_DIR = os.path.join(BASE_DIR, 'train')\nVALID_DIR = os.path.join(BASE_DIR, 'valid')\nTEST_DIR = os.path.join(BASE_DIR, 'test')\nTRAIN_IMAGES_DIR = '/kaggle/working/train/images/'\nVALID_IMAGES_DIR = '/kaggle/working/valid/images/'\nTRAIN_ANNOTATIONS_DIR = '/kaggle/working/train/annotations/'\nVALID_ANNOTATIONS_DIR = '/kaggle/working/valid/annotations/'\nTEST_IMAGES_DIR = '/kaggle/working/test/images/'\n# Create directories\nfor directory in [TRAIN_DIR, VALID_DIR, TEST_DIR]:\n    os.makedirs(os.path.join(directory, 'images'), exist_ok=True)\n    os.makedirs(os.path.join(directory, 'annotations'), exist_ok=True)\n\nprint(\"Directories created successfully!\")\n\n# Move images based on the split\ndef move_images(data_split, target_dir):\n    for item in data_split:\n        original_image_path = os.path.join('/kaggle/working/images', item['filename'])\n        target_image_path = os.path.join(target_dir, item['filename'])\n        if os.path.exists(original_image_path):  # Safety check\n            shutil.move(original_image_path, target_image_path)\n\n# Move training images\nmove_images(train_data, TRAIN_IMAGES_DIR)\n\n# Move validation images\nmove_images(valid_data, VALID_IMAGES_DIR)\n\n# Move test images (if you decide to use a test directory later on)\n# For now, we don't have a TEST_IMAGES_DIR so this step is commented out.\nmove_images(test_data, TEST_IMAGES_DIR)\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:39.954217Z","iopub.execute_input":"2023-09-26T03:01:39.954715Z","iopub.status.idle":"2023-09-26T03:01:40.033255Z","shell.execute_reply.started":"2023-09-26T03:01:39.954673Z","shell.execute_reply":"2023-09-26T03:01:40.03208Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!python -m venv tf_env\n!source tf_env/bin/activate\n!pip install tensorflow","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:01:40.035636Z","iopub.execute_input":"2023-09-26T03:01:40.036105Z","iopub.status.idle":"2023-09-26T03:02:02.816669Z","shell.execute_reply.started":"2023-09-26T03:01:40.03606Z","shell.execute_reply":"2023-09-26T03:02:02.815192Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import tensorflow as tf\nprint(tf.__version__)\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:02:02.818807Z","iopub.execute_input":"2023-09-26T03:02:02.819149Z","iopub.status.idle":"2023-09-26T03:02:13.908834Z","shell.execute_reply.started":"2023-09-26T03:02:02.81912Z","shell.execute_reply":"2023-09-26T03:02:13.907887Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"### Faster R-CNN Model:","metadata":{}},{"cell_type":"code","source":"!git clone https://github.com/tensorflow/models.git\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:02:13.909978Z","iopub.execute_input":"2023-09-26T03:02:13.91147Z","iopub.status.idle":"2023-09-26T03:02:40.526485Z","shell.execute_reply.started":"2023-09-26T03:02:13.911431Z","shell.execute_reply":"2023-09-26T03:02:40.52535Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!pip install --upgrade protobuf\n!git clone https://github.com/tensorflow/models.git\n!cd models/research/\n!cd models/research/\n!protoc /full/path/to/models/research/object_detection/protos/anchor_generator.proto --python_out=/full/path/to/models/research/\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:13:22.472933Z","iopub.execute_input":"2023-09-26T03:13:22.473421Z","iopub.status.idle":"2023-09-26T03:14:10.952586Z","shell.execute_reply.started":"2023-09-26T03:13:22.473373Z","shell.execute_reply":"2023-09-26T03:14:10.951134Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!find . -name anchor_generator.proto\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:14.465331Z","iopub.execute_input":"2023-09-26T03:03:14.465731Z","iopub.status.idle":"2023-09-26T03:03:15.61064Z","shell.execute_reply.started":"2023-09-26T03:03:14.465696Z","shell.execute_reply":"2023-09-26T03:03:15.609182Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!pip install tf_slim\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:15.612518Z","iopub.execute_input":"2023-09-26T03:03:15.613298Z","iopub.status.idle":"2023-09-26T03:03:30.213129Z","shell.execute_reply.started":"2023-09-26T03:03:15.613235Z","shell.execute_reply":"2023-09-26T03:03:30.211364Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"%cd /kaggle/working/models/research/\n!protoc object_detection/protos/*.proto --python_out=.\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:30.215491Z","iopub.execute_input":"2023-09-26T03:03:30.215894Z","iopub.status.idle":"2023-09-26T03:03:31.366241Z","shell.execute_reply.started":"2023-09-26T03:03:30.215861Z","shell.execute_reply":"2023-09-26T03:03:31.364858Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!protoc object_detection/protos/*.proto --python_out=.\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:31.369073Z","iopub.execute_input":"2023-09-26T03:03:31.369559Z","iopub.status.idle":"2023-09-26T03:03:32.501456Z","shell.execute_reply.started":"2023-09-26T03:03:31.369513Z","shell.execute_reply":"2023-09-26T03:03:32.499926Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import sys\nsys.path.append('/kaggle/working/models/research')\nsys.path.append('/kaggle/working/models/research/slim')\n!python /kaggle/working/models/research/object_detection/builders/model_builder_tf2_test.py\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:32.504731Z","iopub.execute_input":"2023-09-26T03:03:32.50611Z","iopub.status.idle":"2023-09-26T03:03:39.288528Z","shell.execute_reply.started":"2023-09-26T03:03:32.506062Z","shell.execute_reply":"2023-09-26T03:03:39.286759Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!wget http://download.tensorflow.org/models/object_detection/tf2/20200711/faster_rcnn_resnet152_v1_640x640_coco17_tpu-8.tar.gz\n!tar -xvf faster_rcnn_resnet152_v1_640x640_coco17_tpu-8.tar.gz\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:03:39.292123Z","iopub.execute_input":"2023-09-26T03:03:39.292513Z","iopub.status.idle":"2023-09-26T03:03:51.981451Z","shell.execute_reply.started":"2023-09-26T03:03:39.292479Z","shell.execute_reply":"2023-09-26T03:03:51.980129Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import sys\nsys.path.append('/kaggle/working/models/research')\nsys.path.append('/kaggle/working/models/research/slim')\n# Navigate to the research directory\n%cd /kaggle/working/models/research/\n\n# Compile the protos.\n!protoc object_detection/protos/*.proto --python_out=.\n\n# Install the object_detection package\n!cp object_detection/packages/tf2/setup.py .\n!python -m pip install .\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:19:15.861413Z","iopub.execute_input":"2023-09-26T05:19:15.861862Z","iopub.status.idle":"2023-09-26T05:19:44.079688Z","shell.execute_reply.started":"2023-09-26T05:19:15.861827Z","shell.execute_reply":"2023-09-26T05:19:44.07801Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import tensorflow as tf\nimport os\n\nfrom object_detection.utils import dataset_util\n\nTRAIN_IMAGES_DIR = '/kaggle/working/train/images/'\nVALID_IMAGES_DIR = '/kaggle/working/valid/images/'\nTRAIN_ANNOTATIONS_DIR = '/kaggle/working/train/annotations/'\nVALID_ANNOTATIONS_DIR = '/kaggle/working/valid/annotations/'\n\n\ndef create_tf_example(filename, annotations_list):\n    # Load the image\n    with tf.io.gfile.GFile(filename, 'rb') as fid:\n        encoded_image_data = fid.read()\n\n    image_format = b'jpeg'\n\n    # Get the image's dimensions\n    image = tf.image.decode_image(encoded_image_data)\n    width, height = image.shape[1], image.shape[0]\n\n    # Filename and image format\n    filename = filename.encode('utf8')\n\n    # List of normalized left, top, right, bottom box coordinates\n    xmins, xmaxs, ymins, ymaxs = [], [], [], []\n\n    # List of string class name of bounding box\n    classes_text = []\n    # List of integer class id of bounding box\n    classes = []\n\n    for ann in annotations_list:\n        xmin, ymin, xmax, ymax = ann['box']\n        xmins.append(float(xmin) / width)\n        xmaxs.append(float(xmax) / width)\n        ymins.append(float(ymin) / height)\n        ymaxs.append(float(ymax) / height)\n        classes_text.append('vertebrae'.encode('utf8'))\n        classes.append(1)\n\n    tf_example = tf.train.Example(features=tf.train.Features(feature={\n        'image/height': dataset_util.int64_feature(height),\n        'image/width': dataset_util.int64_feature(width),\n        'image/filename': dataset_util.bytes_feature(filename),\n        'image/source_id': dataset_util.bytes_feature(filename),\n        'image/encoded': dataset_util.bytes_feature(encoded_image_data),\n        'image/format': dataset_util.bytes_feature(image_format),\n        'image/object/bbox/xmin': dataset_util.float_list_feature(xmins),\n        'image/object/bbox/xmax': dataset_util.float_list_feature(xmaxs),\n        'image/object/bbox/ymin': dataset_util.float_list_feature(ymins),\n        'image/object/bbox/ymax': dataset_util.float_list_feature(ymaxs),\n        'image/object/class/text': dataset_util.bytes_list_feature(classes_text),\n        'image/object/class/label': dataset_util.int64_list_feature(classes),\n    }))\n\n    return tf_example\n\ndef main():\n    # TODO: You might need to adjust how you gather filenames and annotations\n    train_image_filenames = [os.path.join(TRAIN_IMAGES_DIR, fname) for fname in os.listdir(TRAIN_IMAGES_DIR)]\n    valid_image_filenames = [os.path.join(VALID_IMAGES_DIR, fname) for fname in os.listdir(VALID_IMAGES_DIR)]\n\n    # Here, I'm assuming you have some function or way to get the annotations for each image\n    # Replace this with whatever method you use\n    train_annotations = [get_annotations_for_image(fname, TRAIN_ANNOTATIONS_DIR) for fname in train_image_filenames]\n    valid_annotations = [get_annotations_for_image(fname, VALID_ANNOTATIONS_DIR) for fname in valid_image_filenames]\n\n    # Convert to TFRecords\n    with tf.io.TFRecordWriter('train.record') as writer:\n        for img, anns in zip(train_image_filenames, train_annotations):\n            tf_example = create_tf_example(img, anns)\n            writer.write(tf_example.SerializeToString())\n\n    with tf.io.TFRecordWriter('valid.record') as writer:\n        for img, anns in zip(valid_image_filenames, valid_annotations):\n            tf_example = create_tf_example(img, anns)\n            writer.write(tf_example.SerializeToString())\n\nif __name__ == '__main__':\n    main()\n\nprint('done')","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:19:56.282007Z","iopub.execute_input":"2023-09-26T05:19:56.282474Z","iopub.status.idle":"2023-09-26T05:20:00.848291Z","shell.execute_reply.started":"2023-09-26T05:19:56.282435Z","shell.execute_reply":"2023-09-26T05:20:00.847049Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"MODEL_OUTPUT_DIR = \"/kaggle/working/trained_model/\"\n!mkdir -p $MODEL_OUTPUT_DIR\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:20:00.850065Z","iopub.execute_input":"2023-09-26T05:20:00.851105Z","iopub.status.idle":"2023-09-26T05:20:01.971758Z","shell.execute_reply.started":"2023-09-26T05:20:00.851067Z","shell.execute_reply":"2023-09-26T05:20:01.969897Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!ls /kaggle/working/models/research/object_detection/\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:20:04.861647Z","iopub.execute_input":"2023-09-26T05:20:04.862092Z","iopub.status.idle":"2023-09-26T05:20:05.981987Z","shell.execute_reply.started":"2023-09-26T05:20:04.862057Z","shell.execute_reply":"2023-09-26T05:20:05.980356Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!ls /kaggle/working/label_map.pbtxt\n!chmod +r /kaggle/working/label_map.pbtxt\nwith open(\"/kaggle/working/label_map.pbtxt\", \"r\") as file:\n    content = file.read()\nprint(content)\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:20:10.467099Z","iopub.execute_input":"2023-09-26T05:20:10.467578Z","iopub.status.idle":"2023-09-26T05:20:12.68049Z","shell.execute_reply.started":"2023-09-26T05:20:10.467544Z","shell.execute_reply":"2023-09-26T05:20:12.678729Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import shutil\nimport os\n\nsource_config_path = \"/kaggle/working/faster_rcnn_resnet152_v1_640x640_coco17_tpu-8/pipeline.config\"\ndestination_config_path = \"/kaggle/working/my_faster_rcnn_config.config\"\n\n# If the source file exists and the destination file doesn't, copy it\nif os.path.exists(source_config_path) and not os.path.exists(destination_config_path):\n    shutil.copy(source_config_path, destination_config_path)\n\n# Verify the destination file's presence\nif os.path.exists(destination_config_path):\n    print(f\"Configuration file found at {destination_config_path}\")\nelse:\n    print(f\"Configuration file still not found at {destination_config_path}. Please check.\")\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:25:48.053406Z","iopub.execute_input":"2023-09-26T05:25:48.053926Z","iopub.status.idle":"2023-09-26T05:25:48.064321Z","shell.execute_reply.started":"2023-09-26T05:25:48.053891Z","shell.execute_reply":"2023-09-26T05:25:48.063128Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"%cd /kaggle/working/models/research/\n\n# Compile the protos.\n!protoc object_detection/protos/*.proto --python_out=.\n\n# Install the object_detection package\n!cp object_detection/packages/tf2/setup.py .\n!python -m pip install .\n\n!WANDB_MODE=\"dryrun\"python /kaggle/working/models/research/object_detection/model_main_tf2.py \\ --pipeline_config_path=/kaggle/working/models/research/object_detection/samples/configs//kaggle/working/models/research/object_detection/samples/configs/faster_rcnn_inception_v2_coco.config \\--model_dir=/kaggle/working/trained_model/ \\    --alsologtostderr \\--num_train_steps=50000 \\--sample_1_of_n_eval_examples=1 \\--num_eval_steps=1000\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:24:19.846019Z","iopub.execute_input":"2023-09-26T05:24:19.846475Z","iopub.status.idle":"2023-09-26T05:24:49.244646Z","shell.execute_reply.started":"2023-09-26T05:24:19.846439Z","shell.execute_reply":"2023-09-26T05:24:49.242797Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"!find /kaggle/working/ -name \"pipeline.config\"\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T04:41:03.82652Z","iopub.execute_input":"2023-09-26T04:41:03.826936Z","iopub.status.idle":"2023-09-26T04:41:05.021638Z","shell.execute_reply.started":"2023-09-26T04:41:03.826906Z","shell.execute_reply":"2023-09-26T04:41:05.019987Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import shutil\nimport os\n\nsource_config_path = \"/kaggle/working/faster_rcnn_resnet152_v1_640x640_coco17_tpu-8/pipeline.config\"\ndestination_config_path = \"/kaggle/working/my_faster_rcnn_config.config\"\n\n# If the source file exists and the destination file doesn't, copy it\nif os.path.exists(source_config_path) and not os.path.exists(destination_config_path):\n    shutil.copy(source_config_path, destination_config_path)\n\n# Verify the destination file's presence\nif os.path.exists(destination_config_path):\n    print(f\"Configuration file found at {destination_config_path}\")\nelse:\n    print(f\"Configuration file still not found at {destination_config_path}. Please check.\")\n","metadata":{"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import os\n\n\n# Search for the file starting from the root directory\nfor dirpath, dirnames, filenames in os.walk(\"/kaggle\"):\n    for filename in filenames:\n        if filename == \"my_faster_rcnn_config.config\":\n            print(f\"Found at: {os.path.join(dirpath, filename)}\")\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:39:12.048093Z","iopub.execute_input":"2023-09-26T05:39:12.048921Z","iopub.status.idle":"2023-09-26T05:39:13.911594Z","shell.execute_reply.started":"2023-09-26T05:39:12.048879Z","shell.execute_reply":"2023-09-26T05:39:13.910559Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import tensorflow as tf\nfrom google.protobuf import text_format\n\nfrom object_detection.utils import config_util\nfrom object_detection.protos import pipeline_pb2\n\n# Load pipeline config from file\npipeline_config = pipeline_pb2.TrainEvalPipelineConfig()\nwith tf.io.gfile.GFile(\"/kaggle/working/my_faster_rcnn_config.config\", \"r\") as f:                                                                                                                                                                                                                     \n    proto_str = f.read()                                                                                                                                                                                                                                           \n    text_format.Merge(proto_str, pipeline_config)  \n\n# Modify the pipeline config\npipeline_config.model.faster_rcnn.num_classes = 2  # Change this to the number of classes in your dataset\npipeline_config.train_config.fine_tune_checkpoint = \"/kaggle/working/faster_rcnn_resnet152_v1_640x640_coco17_tpu-8/checkpoint/ckpt-0\"\npipeline_config.train_config.fine_tune_checkpoint_type = \"detection\"\n\n# Point to the path of your training and validation TFRecords and label map\npipeline_config.train_input_reader.label_map_path = \"/kaggle/working/label_map.pbtxt\"\npipeline_config.train_input_reader.tf_record_input_reader.input_path[0] = \"/kaggle/working/train.record\"\npipeline_config.eval_input_reader[0].label_map_path = \"/kaggle/working/label_map.pbtxt\"\npipeline_config.eval_input_reader[0].tf_record_input_reader.input_path[0] = \"/kaggle/working/valid.record\"\n\n# Save modified config\nconfig_text = text_format.MessageToString(pipeline_config)                                                                                                                                                                                                        \nwith tf.io.gfile.GFile(\"/kaggle/working/my_faster_rcnn_config_modified.config\", \"wb\") as f:                                                                                                                                                                                                                     \n    f.write(config_text)\nprint('done')","metadata":{"execution":{"iopub.status.busy":"2023-09-26T05:33:10.031759Z","iopub.execute_input":"2023-09-26T05:33:10.032234Z","iopub.status.idle":"2023-09-26T05:33:10.117506Z","shell.execute_reply.started":"2023-09-26T05:33:10.032201Z","shell.execute_reply":"2023-09-26T05:33:10.115712Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{"execution":{"iopub.status.busy":"2023-09-26T12:32:10.293725Z","iopub.execute_input":"2023-09-26T12:32:10.29406Z","iopub.status.idle":"2023-09-26T12:32:10.299828Z","shell.execute_reply.started":"2023-09-26T12:32:10.294035Z","shell.execute_reply":"2023-09-26T12:32:10.298752Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"laaaaaaaaaaaast step ","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:06:06.759785Z","iopub.status.idle":"2023-09-26T03:06:06.760171Z","shell.execute_reply.started":"2023-09-26T03:06:06.759981Z","shell.execute_reply":"2023-09-26T03:06:06.759999Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import numpy as np\nimport cv2\nimport matplotlib.pyplot as plt\n\n# Load the image\nimage = cv2.imread(\"/kaggle/input/rsna-cervical-spine-train-image-png-csfd/RSNA Cervical Spine CSFD/CSFD Ver1/CSFDV1B1/CSFDV1B1 (1).png\")\nimage2 = cv2.imread(\"/kaggle/input/rsna-cervical-spine-train-image-png-csfd/RSNA Cervical Spine CSFD/CSFD Ver1/CSFDV1B1/CSFDV1B1 (10).png\")\n\n# Generate the heatmap\nheatmap = cv2.applyColorMap(image, cv2.COLORMAP_JET)\nheatmap2 = cv2.applyColorMap(image2, cv2.COLORMAP_JET)\n\n# Overlay the heatmap on the image\nimage_with_heatmap = cv2.addWeighted(image, 0.5, heatmap, 0.5, 0)\nimage_with_heatmap2= cv2.addWeighted(image2, 0.5, heatmap, 0.5, 0)\n\n# Display the image\nplt.imshow(image_with_heatmap)\nplt.show()\n\nplt.imshow(image_with_heatmap2)\nplt.show()\n\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:06:06.761299Z","iopub.status.idle":"2023-09-26T03:06:06.761691Z","shell.execute_reply.started":"2023-09-26T03:06:06.761501Z","shell.execute_reply":"2023-09-26T03:06:06.76152Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import numpy as np\nimport cv2\nimport matplotlib.pyplot as plt\n\ndef apply_window(image, center, width):\n    min_value = center - width // 2\n    max_value = center + width // 2\n    windowed_image = np.clip(image, min_value, max_value)\n    return windowed_image\n\n# Load the image\nimage = cv2.imread(\"/kaggle/input/rsna-cervical-spine-train-image-png-csfd/RSNA Cervical Spine CSFD/CSFD Ver1/CSFDV1B1/CSFDV1B1 (1).png\")\n\n# Generate the heatmap\nheatmap = cv2.applyColorMap(image, cv2.COLORMAP_JET)\n\n# Crop the image and the heatmap using the apply_window() function\ncropped_image = apply_window(image[100:400, 200:400], 40, 400)\ncropped_heatmap = apply_window(heatmap[100:400, 200:400], 40, 400)\n\n# Overlay the heatmap on the cropped image\ncropped_image_with_heatmap = cv2.addWeighted(cropped_image, 0.5, cropped_heatmap, 0.5, 0)\n\n# Display the cropped image with the overlaid heatmap\nplt.imshow(cropped_image_with_heatmap)\nplt.show()\n","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:06:06.763374Z","iopub.status.idle":"2023-09-26T03:06:06.76376Z","shell.execute_reply.started":"2023-09-26T03:06:06.763575Z","shell.execute_reply":"2023-09-26T03:06:06.763593Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"validation_image = \"/kaggle/input/rsna-2022-cervical-spine-fracture-detection/test_images/1.2.826.0.1.3680043.22327/10.dcm\" # Overlay the mask onto the original image for visualization\ndef overlay_mask_on_image(image, mask):\n    masked_image = image.copy()\n    for c in range(3):\n        masked_image[:, :, c] = masked_image[:, :, c] * (1-mask) + mask * 255  # The color of the mask\n    return masked_image\nattention_mask = model.predict(input_image)\n\nmasked_image = overlay_mask_on_image(validation_image, attention_mask)\n\n# Visualize\nplt.imshow(masked_image)\nplt.axis('off')\nplt.show()","metadata":{"execution":{"iopub.status.busy":"2023-09-26T03:06:06.764925Z","iopub.status.idle":"2023-09-26T03:06:06.765307Z","shell.execute_reply.started":"2023-09-26T03:06:06.765108Z","shell.execute_reply":"2023-09-26T03:06:06.765126Z"},"trusted":true},"execution_count":null,"outputs":[]}]}