def get_3d_data_hu(path): # get data in Hunsfield Units
slices = [dicom.read_file(path + '/' + s) for s in os.listdir(path)]
#slices.sort(key=lambda x: int(x.InstanceNumber)) # was x.InstanceNumber
#slices.sort(key = lambda x: int(x.ImagePositionPatient[2])) # from v8 - BUGGY
slices.sort(key = lambda x: float(x.ImagePositionPatient[2])) # from 22.02
image = np.stack([s.pixel_array for s in slices])
image = image.astype(np.int16) # ensure int16 (it may be here uint16 for some images )
image[image == -2000] = 0 #correcting cyindrical bound entrioes to 0
# Convert to Hounsfield units (HU)
# The intercept is usually -1024
for slice_number in range(len(slices)): # from v 8
intercept = slices[slice_number].RescaleIntercept
slope = slices[slice_number].RescaleSlope
if slope != 1: # added 16 Jan 2016, evening
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)
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