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DICOM2JPEGFrame.py
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DICOM2JPEGFrame.py
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#coding:utf-8
import pydicom
import matplotlib.pyplot as plt
from PIL import Image, ImageOps
from io import BytesIO
import sys
import gdcm
import time
import numpy as np
from highdicom.io import ImageFileReader
def window_image(img, window_center, window_width, intercept, slope , ds):
img = (img * slope + intercept) # 灰度值轉化為CT輻射強度,轉化後的結果其實可以理解為"醫用像素值"
img_min = window_center - window_width // 2 # "-"後面的先計算
img_max = window_center + window_width // 2
# 下面其實是一個濾波器,過濾掉噪音
img[img < img_min] = img_min
img[img > img_max] = img_max
if hasattr(ds, 'PhotometricInterpretation'):
if ds.PhotometricInterpretation == 'MONOCHROME1':
print('monochrome1')
img = img.astype(float)
img = 255 - img
pass
pass
return img
pass
# 這裡img是一個二維矩陣
def get_first_of_dicom_field_as_int(x):
# get x[0] as in int is x is a 'pydicom.multival.MultiValue', otherwise get int(x)
if type(x) == pydicom.multival.MultiValue: # 如果有很多个值
return int(x[0])
else:
return int(x)
pass
def get_windowing(data):
# 下面是獲取dicom各個參數
dicom_fields = [data[('0028', '1050')].value, # window center
data[('0028', '1051')].value, # window width
data[('0028', '1052')].value, # intercept
data[('0028', '1053')].value] # slope
# 上面(0028,1053)在dicom中稱為tag
return [get_first_of_dicom_field_as_int(x) for x in dicom_fields]
pass
#https://github.com/pydicom/pydicom/pull/534
def DICOM2JPEGFrame(filename, frameNumber=0):
# This is only used to find the position of the Pixel Data element
ds = pydicom.filereader.dcmread(filename, stop_before_pixels=True)
saveFilename = filename.replace('.dcm', '')
saveFilename = f'{saveFilename}.{str(frameNumber)}.jpg'
with ImageFileReader(filename) as image:
frame = image.read_frame(frameNumber)
#handle the dicom that have window center and window width
if hasattr(ds , 'WindowCenter') and hasattr(ds , 'WindowWidth'):
window_center, window_width, intercept, slope = get_windowing(ds)
img = window_image(frame, window_center, window_width, intercept, slope , ds)
try:
plt.imsave(saveFilename , img, cmap='gray')
return True
except Exception as err:
print(err)
return False
pass
pass
try:
#Handle YBR
if hasattr(ds, 'PhotometricInterpretation'):
if 'YBR' in ds.PhotometricInterpretation:
frameRaw = image.read_frame_raw(frameNumber)
imageFrameRaw = Image.open(BytesIO(frameRaw))
imageFrameRaw.save(saveFilename)
return True
pass
pass
Image.fromarray(frame).save(saveFilename)
return True
except Exception as err:
print(err)
return False
pass
pass
pass
if __name__ == '__main__':
filename = sys.argv[1]
imageFormat = "jpg"
frameNumber = 1
try:
frameNumber = int(sys.argv[2])
except:
frameNumber = 1
pass
status = DICOM2JPEGFrame(filename, frameNumber-1)
pass
sys.modules[__name__] = DICOM2JPEGFrame