Conversions

Convert DICOM to JPG, PNG

Converts a single dicom file to an 8 bit format

#Code modified from Ian Pan https://storage.googleapis.com/kaggle-forum-message-attachments/1010629/17014/convert_to_jpeg_for_kaggle.py

def convert_ct_dicom_to_8bit(dicom_file, windows = [[350,40],[1500,-500],[120,70]], imsize=(256.,256.), should_remove_padding = True):
    '''
    Given a DICOM file, window specifications, and image size, return the
    image as a Numpy array scaled to [0,255] of the specified size.

    Parameters
    ----------
    dicom_file: str
        filename that ends in .dcm
    windows: list of lists of ints
        list of window width and window level values
    imsize: tuplet of float
        desired output image size
    should_remove_padding: bool
        if True will remove extra rows/columns of zeroes around the image
    '''
    array = apply_slope_intercept(dicom_file)

    if should_remove_padding:
        array = remove_padding(array)

    #different width, level for each RGB channel
    image = apply_windows(array, windows)
    #resize
    image = resize(image, imsize)

    return image

Save as jpg or png

    image = convert_ct_dicom_to_8bit(dicom_file, windows = [[350,40],[1500,-500],[120,70]], imsize=(256.,256.), should_remove_padding = True)
    im = Image.fromarray(image)
    im.save(dicom_file[-4:] + '.jpg')
    #or
    im.save(dicom_file[-4:] + '.png')

Supporting functions

import pandas as pd
import numpy as np
import pydicom
from scipy.ndimage.interpolation import zoom

#Applies slope and intercept from DICOM tags
def apply_slope_intercept(dicom_file):
    array = dicom_file.pixel_array.copy()
    try:
        slope = float(dicom_file.RescaleSlope)
        intercept = float(dicom_file.RescaleIntercept)
    except Exception:
        slope = 1
        intercept = 0
    if slope != 1 or intercept != 0:
        array = array * slope
        array = array + intercept
    return array

#Removes zeroes around image
def remove_padding(array):
    array = array.copy()
    nonzeros = np.nonzero(array)
    x1 = np.min(nonzeros[0]) ; x2 = np.max(nonzeros[0])
    y1 = np.min(nonzeros[1]) ; y2 = np.max(nonzeros[1])
    return array[x1:x2,y1:y2]

#Apply different W/L settings to different channels to take advantage of RGB structure
def apply_windows(array, windows):
    layers = []
    for values in windows:
        if len(value) >= 2:
            ww = values[0]
            wl = values[1]
            layers.append(np.expand_dims(window(array, WL=wl, WW=ww), axis=3))
    if len(layers) == 0:
        return np.expand_dims(window(array, WL=350, WW=40), axis=3)
    else:
        return np.concatenate(layers, axis=3)

#Resize
def resize(image, imsize):
    rat = max(imsize) / np.max(image.shape[1:])
    return zoom(image, [1.,rat,rat,1.], prefilter=False, order=1)

Common window width and window level for CT exams

Target	WW	WL
brain	80	40
subdural	215	75
stroke_1	8	32
stroke_2	40	40
temporal_bone	2800	600
neck_soft_tissue	375	40
lung	1500	-500
emphysema	800	-800
mediastinum	400	40
pulmonary_embolism	700	100
abdomen	350	40
liver	120	70
kidney	700	50
bone	2500	480

Convert JPG, PNG to DICOM

Converts a single jpg or png file to dicom format

import os
import subprocess
import tempfile
import uuid
from PIL import Image
from pydicom.uid import generate_uid


def from_jpeg(jpeg_fp, dicom_tags={}):
    """Converts JPEG to DICOM as secondary capture, with minimal DICOM tags.
    If JPEG mode is RGBA or CMYK, we must first convert to RGB since these photometric
    interpretations have been retired in the DICOM standard:
    http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.3.html.
    Returns: path to DICOM tempfile
    """
    # If JPEG is RGBA/CMYK mode, convert to RGB mode first.
    im = Image.open(jpeg_fp)
    if im.mode in ("RGBA", "CMYK"):
        im2 = im.convert("RGB")
        im2.save(jpeg_fp)
        im2.close()
    im.close()

    dicom_fp = os.path.join(tempfile.gettempdir(), f"{str(uuid.uuid4())}.dcm")
    try:
        cmd = ["img2dcm", jpeg_fp, dicom_fp]
        for key, value in dicom_tags.items():
            cmd.extend(["-k", f"{key}={value}"])
        subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
    except Exception:
        return None
    return dicom_fp


def from_png(png_fp, dicom_tags={}):
    """Converts PNG to DICOM as secondary capture, with minimal DICOM tags.
    Returns: path to DICOM tempfile
    """
    jpeg_fp = os.path.join(tempfile.gettempdir(), f"{str(uuid.uuid4())}.jpg")
    try:
        cmd = ["convert", png_fp, jpeg_fp]
        subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
    except Exception:
        return None
    return from_jpeg(jpeg_fp, dicom_tags=dicom_tags)

Convert CT nifti to DICOM

Use the convert_ct function in common_utils to convert nifti files to DICOM for upload to MD.ai. You'll need to choose your input and output directories. Optionally, you can change the plane or default window/level settings. You'll also need a sample dicom which you can download from sample image

results = mdai.common_utils.convert_ct(
    input_dir=None,
    output_dir=None,
    input_ext=".nii.gz",
    plane="axial",
    sample_dicom_fp=os.path.join(os.path.dirname(""), "./sample_dicom.dcm"),
    window_center=40,
    window_width=350,
)

This function will write the converted DICOM files to the output directory and will give each image from a nifti file the same Study and Series UIDs. Use the CLI tool to upload the newly created DICOM images into your project

Convert DICOM to nifti

Use the dicom2nifiti library from icometrix

!pip install dicom2nifti

import dicom2nifti
dicom2nifti.convert_directory(dicom_directory, output_folder, compression=True, reorient=True)

This will convert the dicom files from the dicom_directory to the output_folder.

Convert Freeform Annotations to DICOM SEG

Instructions can be found here.

Support functions

Read DICOM UIDs and tags from your original files

Use this code on your original data to create a dataframe of DICOM tags. These are sample tags, you can add or remove values, as needed.

from pathlib import Path
import pydicom

images_path = Path('MY_PATH')
filenames = list(images_path.glob('**/*.dcm'))
info = []

for f in filenames:
    d = pydicom.dcmread(str(f),stop_before_pixels=True)
    info.append({'fn':str(f), 
        'StudyInstanceUID':d.StudyInstanceUID,
        'SeriesInstanceUID':d.SeriesInstanceUID, 
        'SOPInstanceUID':d.SOPInstanceUID, 
        'description':d.SeriesDescription if 'SeriesDescription' in d else "", 
        'name':d.SequenceName if 'SequenceName' in d else "",
        'Modality':d.Modality if 'Modality' in d else "",
        'ContrastAgent':d.ContrastBolusAgent if 'ContrastBolusAgent' in d else "",
        'ScanOptions':d.ScanOptions if 'ScanOptions' in d else "",
        'WW':d.WindowWidth if 'WindowWidth' in d else "",
        'WC':d.WindowCenter if 'WindowCenter' in d else "",
        'ImageType' :d.ImageType if 'ImageType' in d else "",
        'PixelSpacing' :d.PixelSpacing if 'PixelSpacing' in d else "",
        'SliceThickness':d.SliceThickness if 'SliceThickness' in d else "",
        'PhotometricInterpretation':d.PhotometricInterpretation if 'PhotometricInterpretation' in d else ""
                  })
df = pd.DataFrame(info)