{"cells":[{"metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true},"cell_type":"code","source":"import numpy as np # linear algebra\nimport pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)\n\n\n","execution_count":null,"outputs":[]},{"metadata":{"_uuid":"d629ff2d2480ee46fbb7e2d37f6b5fab8052498a","_cell_guid":"79c7e3d0-c299-4dcb-8224-4455121ee9b0","trusted":true},"cell_type":"code","source":"import pydicom\nimport os\nimport matplotlib.pyplot as plt","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"from glob import glob","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"patient=\"../input/osic-pulmonary-fibrosis-progression/train/ID00007637202177411956430/\"","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"scans=glob(patient+\"/*.dcm\")","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def load(path):\n    scans=os.listdir(path)\n    slices=[]\n    for s in scans:\n        with pydicom.dcmread(path+\"/\"+s) as f:\n            slices.append(f)\n    slices.sort(key = lambda x: int(x.InstanceNumber))\n    \n    return slices\n","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"p=load(patient)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"def getImage(scans):\n    image = np.stack([s.pixel_array for s in scans])\n    image = image.astype(np.int16)\n    \n    image[image<=-1000] = 0\n    \n    return np.array(image, dtype=np.int16)\nimgs= getImage(p)","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"fig, ax = plt.subplots(1, 2, figsize=(10, 10))\nax[0].set_title(\"original\")\nax[0].imshow(p[25].pixel_array)\nax[1].set_title(\"HU image\")\nax[1].imshow(imgs[25])\n","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"","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}