Pydicom: how to convert dicom to jpeg

[wanghaisheng]

what i want is to get a jpeg file for each dcm file ?is there any best practices of pydicom ,i find nothing looking over documentation

[scaramallion]

Not tested, but you should be able to use pillow and numpy:

from PIL.Image import fromarray

ds = read_file('file-in.dcm')
im = fromarray(ds.pixel_array)
im.save('file-out.jpg')

You will likely have to do some work to ensure you have the image data in a suitable format prior to saving.

[mrbean-bremen]

I think this can be closed as answered.

[tedivm]

This doesn't work for me, so I'm guessing it doesn't work for others. I'm including some code that converts a dicom file into a png for the next person who ends up here via google :-)

import numpy as np
import png
import pydicom

ds = pydicom.dcmread(path)

shape = ds.pixel_array.shape

# Convert to float to avoid overflow or underflow losses.
image_2d = ds.pixel_array.astype(float)

# Rescaling grey scale between 0-255
image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0

# Convert to uint
image_2d_scaled = np.uint8(image_2d_scaled)

# Write the PNG file
with open(destination, 'wb') as png_file:
    w = png.Writer(shape[1], shape[0], greyscale=True)
    w.write(png_file, image_2d_scaled)

[wanghaisheng]

@tedivm wonderful

[gitkwr]

Thanks @tedivm. Wrapped your code into a function for convenient copy-paste

import numpy as np
import png, os, pydicom

source_folder = r'path\to\source'
output_folder = r'path\to\output\folder'


def dicom2png(source_folder, output_folder):
    list_of_files = os.listdir(source_folder)
    for file in list_of_files:
        try:
            ds = pydicom.dcmread(os.path.join(source_folder,file))
            shape = ds.pixel_array.shape

            # Convert to float to avoid overflow or underflow losses.
            image_2d = ds.pixel_array.astype(float)

            # Rescaling grey scale between 0-255
            image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0

            # Convert to uint
            image_2d_scaled = np.uint8(image_2d_scaled)

            # Write the PNG file
            with open(os.path.join(output_folder,file)+'.png' , 'wb') as png_file:
                w = png.Writer(shape[1], shape[0], greyscale=True)
                w.write(png_file, image_2d_scaled)
        except:
            print('Could not convert: ', file)


dicom2png(source_folder, output_folder)

[tedivm]

@rohit-patel - you forgot to import os ;-)

[samra-irshad]

This doesn't work for me, so I'm guessing it doesn't work for others. I'm including some code that converts a dicom file into a png for the next person who ends up here via google :-)

import numpy as np
import png
import pydicom

ds = pydicom.dcmread(path)

shape = ds.pixel_array.shape

# Convert to float to avoid overflow or underflow losses.
image_2d = ds.pixel_array.astype(float)

# Rescaling grey scale between 0-255
image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0

# Convert to uint
image_2d_scaled = np.uint8(image_2d_scaled)

# Write the PNG file
with open(destination, 'wb') as png_file:
    w = png.Writer(shape[1], shape[0], greyscale=True)
    w.write(png_file, image_2d_scaled)

Only solution that worked for my problem, thank you!

[kyshel]

This doesn't work for me, so I'm guessing it doesn't work for others. I'm including some code that converts a dicom file into a png for the next person who ends up here via google :-)

import numpy as np
import png
import pydicom

ds = pydicom.dcmread(path)

shape = ds.pixel_array.shape

# Convert to float to avoid overflow or underflow losses.
image_2d = ds.pixel_array.astype(float)

# Rescaling grey scale between 0-255
image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0

# Convert to uint
image_2d_scaled = np.uint8(image_2d_scaled)

# Write the PNG file
with open(destination, 'wb') as png_file:
    w = png.Writer(shape[1], shape[0], greyscale=True)
    w.write(png_file, image_2d_scaled)

@tedivm
got an error， maybe it can be optimized?

Traceback (most recent call last):
  File "D:/ml/untitled/dcm2png.py", line 81, in <module>
    dcm2png(file,'png2\\'+file+'.png')
  File "D:/ml/untitled/dcm2png.py", line 16, in dcm2png
    shape = ds.pixel_array.shape
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 778, in __getattr__
    return object.__getattribute__(self, name)
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 1615, in pixel_array
    self.convert_pixel_data()
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 1324, in convert_pixel_data
    self._convert_pixel_data_without_handler()
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 1434, in _convert_pixel_data_without_handler
    raise last_exception
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 1414, in _convert_pixel_data_without_handler
    self._do_pixel_data_conversion(handler)
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\dataset.py", line 1441, in _do_pixel_data_conversion
    arr = handler.get_pixeldata(self)
  File "D:\ProgramData\Anaconda3\envs\py36\lib\site-packages\pydicom\pixel_data_handlers\numpy_handler.py", line 263, in get_pixeldata
    "Unable to convert the pixel data: one of Pixel Data, Float "
AttributeError: Unable to convert the pixel data: one of Pixel Data, Float Pixel Data or Double Float Pixel Data must be present in the dataset