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Convert NRRD format to image





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The NRRD (Nearly Raw Raster Data) file is a nearly raw raster data file.

It was developed to support scientific visualization and image processing applications.



Tested in Anaconda and Python 3.7

import os.path as path
import sys
sys.path.insert(0, path.abspath('../'))
import nrrd_handler
import urllib.request
import matplotlib.pyplot as plt
file_path = 'CT-chest.nrrd'
 
if not path.exists(file_path):
    urllib.request.urlretrieve("http://www.slicer.org/w/img_auth.php/3/31/CT-chest.nrrd", file_path)
 
nH = nrrd_handler.NrrdHandler(file_path)
 
img_pynrrd = nH.read_by_pynrrd()
img_sitk = nH.read_by_sitk()
 
plt.imshow(img_pynrrd[:,:,0])
plt.show()
 
plt.imshow(img_sitk[0])
plt.show()
 


read-nrrd2img - GitHub



Downloading and Viewing the CT-chest.nrrd File



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Tested in Anaconda and Python 3.7

import numpy as np
import nrrd
import cv2
 
filename = "Guenette_FN_CISS_Subject_09.nrrd"
filedata, fileheader = nrrd.read(filename)
print("fileheader", fileheader)
print("filedata", filedata.shape)
 
for i in range(filedata.shape[2]):
    _slice = filedata[:,:,i]
    print(type(_slice))
    print(_slice.shape)
    slice = (_slice.astype(np.float64)-_slice.min()) / (_slice.max()-_slice.min())
    slice = slice.astype('float32')
    cv2.imshow("raw image", slice)
    cv2.waitKey(30)
    cv2.imwrite("slice_" + str(i).zfill(3)+ ".jpg", slice*255, [cv2.IMWRITE_JPEG_QUALITY, 100])
    '''
    cv2.imwrite("slice_" + str(i).zfill(3)+ ".png", slice*255)
    '''
cv2.destroyAllWindows
 


simple_nrrd_reader - GitHub



Viewing and saving images from the Guenette_FN_CISS_Subject_09.nrrd file



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Distribution of software for the processing and analysis of scientific images

The toolkit for scientific image processing and analysis

Fiji distribution of ImageJ












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