In [5]:

    

%matplotlib inline

import numpy as np # linear algebra
import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)
import dicom
import os
import scipy.ndimage
import matplotlib.pyplot as plt

from skimage import measure, morphology
from mpl_toolkits.mplot3d.art3d import Poly3DCollection

# Some constants 
INPUT_FOLDER = "/Volumes/homes/users/anthony.reina/dicom" \
               "/Lung CT/stage1/00cba091fa4ad62cc3200a657aeb957e/"
patients = os.listdir(INPUT_FOLDER)
patients.sort()


    

In [10]:

    

# Load the scans in given folder path
def load_scan(path):
    slices = [dicom.read_file(path + s) for s in os.listdir(path)]
    slices.sort(key = lambda x: float(x.ImagePositionPatient[2]))
    try:
        slice_thickness = np.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])
    except:
        slice_thickness = np.abs(slices[0].SliceLocation - slices[1].SliceLocation)
        
    for s in slices:
        s.SliceThickness = slice_thickness
        
    return slices


    

In [11]:

    

def get_pixels_hu(slices):
    image = np.stack([s.pixel_array for s in slices])
    # Convert to int16 (from sometimes int16), 
    # should be possible as values should always be low enough (<32k)
    image = image.astype(np.int16)

    # Set outside-of-scan pixels to 0
    # The intercept is usually -1024, so air is approximately 0
    image[image == -2000] = 0
    
    # Convert to Hounsfield units (HU)
    for slice_number in range(len(slices)):
        
        intercept = slices[slice_number].RescaleIntercept
        slope = slices[slice_number].RescaleSlope
        
        if slope != 1:
            image[slice_number] = slope * image[slice_number].astype(np.float64)
            image[slice_number] = image[slice_number].astype(np.int16)
            
        image[slice_number] += np.int16(intercept)
    
    return np.array(image, dtype=np.int16)


    

In [16]:

    

first_patient = load_scan(INPUT_FOLDER)


    

In [18]:

    




    

    
Out[18]:





(0008, 0005) Specific Character Set              CS: 'ISO_IR 100'
(0008, 0016) SOP Class UID                       UI: CT Image Storage
(0008, 0018) SOP Instance UID                    UI: 1.2.840.113654.2.55.247817952625791837963403492891187883824
(0008, 0060) Modality                            CS: 'CT'
(0008, 103e) Series Description                  LO: 'Axial'
(0010, 0010) Patient's Name                      PN: '00cba091fa4ad62cc3200a657aeb957e'
(0010, 0020) Patient ID                          LO: '00cba091fa4ad62cc3200a657aeb957e'
(0010, 0030) Patient's Birth Date                DA: '19000101'
(0018, 0050) Slice Thickness                     DS: '2.5'
(0018, 0060) KVP                                 DS: ''
(0020, 000d) Study Instance UID                  UI: 2.25.86208730140539712382771890501772734277950692397709007305473
(0020, 000e) Series Instance UID                 UI: 2.25.11575877329635228925808596800269974740893519451784626046614
(0020, 0011) Series Number                       IS: '3'
(0020, 0012) Acquisition Number                  IS: '1'
(0020, 0013) Instance Number                     IS: '134'
(0020, 0020) Patient Orientation                 CS: ''
(0020, 0032) Image Position (Patient)            DS: ['-145.500000', '-158.199997', '-356.200012']
(0020, 0037) Image Orientation (Patient)         DS: ['1.000000', '0.000000', '0.000000', '0.000000', '1.000000', '0.000000']
(0020, 0052) Frame of Reference UID              UI: 2.25.83033509634441686385652073462983801840121916678417719669650
(0020, 1040) Position Reference Indicator        LO: 'SN'
(0020, 1041) Slice Location                      DS: '-356.200012'
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 512
(0028, 0011) Columns                             US: 512
(0028, 0030) Pixel Spacing                       DS: ['0.597656', '0.597656']
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 16
(0028, 0102) High Bit                            US: 15
(0028, 0103) Pixel Representation                US: 1
(0028, 0120) Pixel Padding Value                 US: 63536
(0028, 1050) Window Center                       DS: '40'
(0028, 1051) Window Width                        DS: '400'
(0028, 1052) Rescale Intercept                   DS: '-1024'
(0028, 1053) Rescale Slope                       DS: '1'
(7fe0, 0010) Pixel Data                          OW: Array of 524288 bytes

In [15]:

    

INPUT_FOLDER


    

    
Out[15]:





'/Volumes/homes/users/anthony.reina/dicom/Lung CT/stage1/00cba091fa4ad62cc3200a657aeb957e/'

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