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I have below code. print(image.GetDimension()) works and prints the output (512, 512, 17). But sitk.Show(image) doesn't work.

My Code

import SimpleITK as sitk

path = "C:/Users/myUserName/Desktop/0001.DCM"
image = sitk.ReadImage(path)

print(image.GetDimension())
sitk.Show(image)

My error message is:

RuntimeError: Exception thrown in SimpleITK Show: D:\a\1\sitk\Code\IO\src\sitkImageViewer.cxx:562:
sitk::ERROR: Error in administrating child process: [Access is denied].
Command line: 'C:\Users\myUserName\Fiji.app' 'C:\\Users\\myUserName\\AppData\\Local\\Temp\\TempFile-21536-2.mha'

How can I fix that? I have unzipped ImageJ and put the Fiji.app folder at C:\Users\myUserName\Fiji.app. The DICOM image 0001.DCM has no problem as I can view it via some online DICOM viewer. I am using Windows 10, and run my Python code in Spyder. Thanks in advance!

H42
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  • What happens when you paste the command line into a shell prompt to try and run it by hand? – Dave Chen Oct 21 '21 at 14:42
  • Thanks for your reply. In Windows' cmd, I tried to run `> python` to enter the python environment, and then run the first line `import SimpleITK as sitk`, then I got the error message `C:\Users\myUserName\anaconda3\lib\site-packages\numpy\__init__.py:143: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service`. And then I typed `exit()` to exit . – H42 Oct 22 '21 at 07:30
  • I also tried to run `> python myPythonCode.py` in cmd directly, and then I have the same error message `C:\Users\myUserName\anaconda3\lib\site-packages\numpy\__init__.py:143`... blahblahblah. Any ideas? – H42 Oct 22 '21 at 07:30
  • the mkl-service package isn't installed in your anaconda environment. you can install it like this: conda install -c conda-forge mkl-service – Dave Chen Oct 22 '21 at 13:56
  • @DaveChen Thanks for your reply. I just tried to do it in cmd, and installed mkl-service as you advised. But the error message is still the same. – H42 Oct 23 '21 at 08:37

1 Answers1

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Try setting the SITK_SHOW_COMMAND to point directly to the ImageJ executable. For your installation of Fiji, the environment variable should be set to C:\Users\myUserName\Fiji.app\ImageJ-win64.exe.

OK, here's my slightly modified version of your script:

import SimpleITK as sitk

#path = "C:/Users/myUserName/Desktop/0001.DCM"
path = "C:\SimpleITK-build\SimpleITK-build\ExternalData\Testing\Data\Input\DicomSeries\Image0075.dcm"
image = sitk.ReadImage(path)

print(image.GetDimension())
sitk.Show(image, debugOn=True)

The only difference is that I added the debugOn flag to the call to Show.

And here's my output:

Debug: In D:\bld\libsimpleitk_1627514864077\work\Code\IO\src\sitkImageViewer.cxx, line 495: ExecuteCommand: 'C:/Users/dchen/Fiji.app/ImageJ-win64.exe' '-eval' 'open("C:\\Users\\dchen\\AppData\\Local\\Temp\\TempFile-10808-0.mha"); rename("C:\\Users\\dchen\\AppData\\Local\\Temp\\TempFile-10808-0.mha");'


Debug: In D:\bld\libsimpleitk_1627514864077\work\Code\IO\src\sitkImageViewer.cxx, line 576: Done.  Deleting process.

And you can see exactly the command that SimpleITK is executing to invoke Fiji. In particular, the program being launched is 'C:/Users/dchen/Fiji.app/ImageJ-win64.exe'.

If you turn on the debugOn flag, what does SimpleITK output?

Dave Chen
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    Thanks for your reply. I've tried to do `$SITK_SHOW_COMMAND = "C:\Users\myUserName\Fiji.app\ImageJ-win64.exe"` in my PowerShell, and confirmed that the variable is set using `Get-Variable -Name SITK_SHOW_COMMAND`. I can also confirm that the file `C:\Users\myUserName\Fiji.app\ImageJ-win64.exe` exists. But I still have the same error when running the Python code. – H42 Oct 22 '21 at 07:22
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    I tried `setx SITK_SHOW_COMMAND "C:\Users\myUserName\Fiji.app\ImageJ-win64.exe"` in cmd instead, and it works!. Now the ImageJ pop up and the problem it solved. I have no idea why `$SITK_SHOW_COMMAND = ` in PowerShell doesn't work but `setx` in cmd works. But the problem is now anyway solved. Thanks!! – H42 Oct 23 '21 at 21:44