pythonimagemedicalsimpleitkmedical-imaging

SimpleITK cannot show image

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!

Solution

  • 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?