write a tif file

assia855 · April 19, 2022, 9:57am

Hello, I’m trying to save my processed data in tif format using this code, but all what I got is a black image. any suggestion to solve this error. thanks in advance.

`
writer = sitk.ImageFileWriter()

writer.SetFileName(‘opened_otsu’+ ‘tif’)
writer.Execute(opened)
`

dchen · April 19, 2022, 1:03pm

Are you sure it’s totally black? It could be that the pixels are just all very low intensity. I’d suggest getting a histogram of the image and looking at the values in that. Or load view it in Fiji/ImageJ and window and level the image.

assia855 · April 19, 2022, 1:32pm

You’re right that it wasn’t completely white, it’s just that it has a very low intensity, but I also changed the extension to nrrd with tif I couldn’t have the same view as I had with myshow3d plot. Any idea please on how can I visualize it on Fiji with tuf format.

dchen · April 19, 2022, 1:44pm

I just used SimpleITK’s Show function, and if you have Fiji/ImageJ installed in a known location, SimpleITK will find it. For example:

sitk.Show(opened)

assia855 · April 19, 2022, 1:45pm

Thank you, but I would like to save it as well in tif format.

dchen · April 19, 2022, 1:47pm

In my case, I just wrote myself a little ‘show’ python script. Then any file on the command line is read by SimpleITK and sent to Fiji.

github.com

dave3d/SimpleITKUtilities/blob/main/show.py

#! /usr/bin/env python


#  A simple script that uses SimpleITK's Show function to display images
#  in Fiji/ImageJ, be default.
#
import sys
import SimpleITK as sitk

for x in sys.argv[1:]:
  print(x)
  img = sitk.ReadImage(x)
  sitk.Show(img)

assia855 · April 19, 2022, 2:02pm

Thanks. I will give it a try