python - Create pydicom file from numpy array

Question

I'm trying to create a new dicom image from a standard-sized (512 x 512 or 256 x 256) numpy array.

import dicom, dicom.UID
from dicom.dataset import Dataset, FileDataset

def write_dicom(pixel_array,filename):
    
    file_meta = Dataset()
    ds = FileDataset(filename, {},file_meta = file_meta,preamble=""*128)
    ds.PixelData = pixel_array.tostring()
    ds.save_as(filename)
    return

if __name__ == "__main__":
    import numpy as np
    pixel_array = np.tile(np.arange(256).reshape(16,16), (16,16)) * 4
    write_dicom(pixel_array,'pretty.dcm')

Answer 1

2020 update :)

None of these answers worked for me. This is what I ended up with to save a valid monochrome 16bpp MR slice which is correctly displayed at least in Slicer, Radiant and MicroDicom:

import pydicom
from pydicom.dataset import Dataset, FileDataset
from pydicom.uid import ExplicitVRLittleEndian
import pydicom._storage_sopclass_uids

image2d = image2d.astype(np.uint16)

print("Setting file meta information...")
# Populate required values for file meta information

meta = pydicom.Dataset()
meta.MediaStorageSOPClassUID = pydicom._storage_sopclass_uids.MRImageStorage
meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian  

ds = Dataset()
ds.file_meta = meta

ds.is_little_endian = True
ds.is_implicit_VR = False

ds.SOPClassUID = pydicom._storage_sopclass_uids.MRImageStorage
ds.PatientName = "Test^Firstname"
ds.PatientID = "123456"

ds.Modality = "MR"
ds.SeriesInstanceUID = pydicom.uid.generate_uid()
ds.StudyInstanceUID = pydicom.uid.generate_uid()
ds.FrameOfReferenceUID = pydicom.uid.generate_uid()

ds.BitsStored = 16
ds.BitsAllocated = 16
ds.SamplesPerPixel = 1
ds.HighBit = 15

ds.ImagesInAcquisition = "1"

ds.Rows = image2d.shape[0]
ds.Columns = image2d.shape[1]
ds.InstanceNumber = 1

ds.ImagePositionPatient = r"01"
ds.ImageOrientationPatient = r"1-1"
ds.ImageType = r"ORIGINALPRIMARYAXIAL"

ds.RescaleIntercept = "0"
ds.RescaleSlope = "1"
ds.PixelSpacing = r"11"
ds.PhotometricInterpretation = "MONOCHROME2"
ds.PixelRepresentation = 1

pydicom.dataset.validate_file_meta(ds.file_meta, enforce_standard=True)

print("Setting pixel data...")
ds.PixelData = image2d.tobytes()

ds.save_as(r"out.dcm")

Note the following:

• Going through FileDataset constructor as PyDicom docs suggest was failing to create a valid header for me
• validate_file_meta will create some missing elements in header for you (version)
• You need to specify endianness and explicit/implicit VR twice :/
• This method will allow you to create a valid volume as well as long as you update ImagePositionPatient and InstanceNumber for each slice accordingly
• Make sure your numpy array is cast to data format that has same number of bits as your BitsStored