{"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":"import numpy as np\nimport copy\nimport matplotlib.pyplot as plt\nimport h5py\nimport scipy\nfrom PIL import Image\nfrom scipy import ndimage\nimport pydicom\nimport pylibjpeg\n\n\n%matplotlib inline\n%load_ext autoreload\n%autoreload 2\n","metadata":{"execution":{"iopub.status.busy":"2023-07-21T05:56:43.396657Z","iopub.execute_input":"2023-07-21T05:56:43.397197Z","iopub.status.idle":"2023-07-21T05:56:43.446009Z","shell.execute_reply.started":"2023-07-21T05:56:43.397154Z","shell.execute_reply":"2023-07-21T05:56:43.444812Z"}}},{"cell_type":"code","source":"def dicom_to_png(input_path, output_path):\n    ds = pydicom.dcmread(input_path)\n    dicom_array = ds.pixel_array\n    dicom_array = ((dicom_array - dicom_array.min()) / (dicom_array.ptp()) * 255).astype(np.uint8)\n    image = Image.fromarray(dicom_array)\n    image.save(output_path)\n\n# Load the CSV data\ntrain_df = pd.read_csv('/kaggle/input/osic-pulmonary-fibrosis-progression/train.csv')\ntest_df = pd.read_csv('/kaggle/input/osic-pulmonary-fibrosis-progression/test.csv')\n\n# Convert all DICOM files to PNG files in the training and testing folders\noutput_dir = '/kaggle/working'\nfor dataset_type in ['train', 'test']:\n    input_dir = f'/kaggle/input/osic-pulmonary-fibrosis-progression/{dataset_type}'\n    for patient_dir in os.listdir(input_dir):\n        for dicom_file in os.listdir(os.path.join(input_dir, patient_dir)):\n            input_path = os.path.join(input_dir, patient_dir, dicom_file)\n            output_path = os.path.join(output_dir, dataset_type, patient_dir, dicom_file.replace('.dcm', '.png'))\n            os.makedirs(os.path.dirname(output_path), exist_ok=True)\n            dicom_to_png(input_path, output_path)","metadata":{"execution":{"iopub.status.busy":"2023-07-21T06:09:34.205013Z","iopub.execute_input":"2023-07-21T06:09:34.205468Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]}]}