Dear Andras,
I installed the JupyterKernel but I receive error output as below:
Then I launched jupyter through anaconda. it looks like as below:
I have 4.9 nighly version of slicer which I dont see here.
Please guide.
Thank you
Regards,
Saima Safdar
I’ve improved module documentation - see https://github.com/Slicer/SlicerJupyter/blob/master/README.md
If the instructions are still not clear enough then let us know.
I only see a small part of the error message. Could you please copy-paste the content of the error box? Could you please also copy the Slicer application log (menu: Help / Report a bug)?
Yes Please see the errors below:
Traceback (most recent call last):
File "D:\anaconda\lib\site-packages\tornado\web.py", line 1543, in _execute
result = yield result
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1099, in run
value = future.result()
File "D:\anaconda\lib\site-packages\tornado\concurrent.py", line 260, in result
raise_exc_info(self._exc_info)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1107, in run
yielded = self.gen.throw(*exc_info)
File "D:\anaconda\lib\site-packages\notebook\services\sessions\handlers.py", line 73, in post
type=mtype))
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1099, in run
value = future.result()
File "D:\anaconda\lib\site-packages\tornado\concurrent.py", line 260, in result
raise_exc_info(self._exc_info)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1107, in run
yielded = self.gen.throw(*exc_info)
File "D:\anaconda\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 79, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1099, in run
value = future.result()
File "D:\anaconda\lib\site-packages\tornado\concurrent.py", line 260, in result
raise_exc_info(self._exc_info)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1107, in run
yielded = self.gen.throw(*exc_info)
File "D:\anaconda\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 92, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 1099, in run
value = future.result()
File "D:\anaconda\lib\site-packages\tornado\concurrent.py", line 260, in result
raise_exc_info(self._exc_info)
File "D:\anaconda\lib\site-packages\tornado\gen.py", line 315, in wrapper
yielded = next(result)
File "D:\anaconda\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 148, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "D:\anaconda\lib\site-packages\jupyter_client\multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "D:\anaconda\lib\site-packages\jupyter_client\manager.py", line 259, in start_kernel
**kw)
File "D:\anaconda\lib\site-packages\jupyter_client\manager.py", line 204, in _launch_kernel
return launch_kernel(kernel_cmd, **kw)
File "D:\anaconda\lib\site-packages\jupyter_client\launcher.py", line 128, in launch_kernel
proc = Popen(cmd, **kwargs)
File "D:\anaconda\lib\subprocess.py", line 394, in __init__
errread, errwrite)
File "D:\anaconda\lib\subprocess.py", line 644, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
The setup for JupyterKernel
Log from slicer warning message:
Kernelspec install error output:
[InstallKernelSpec] Removing existing kernelspec in C:\\Users\\22374464\\AppData\\Roaming\\jupyter\\kernels\\slicer-4.9
[InstallKernelSpec] Installed kernelspec slicer-4.9 in C:\\Users\\22374464\\AppData\\Roaming\\jupyter\\kernels\\slicer-4.9
Is this build version? It is high probability that I have got similar error. I have a built version of Slicer and then need to build SlicerJupiter. Then I copied the files:
cp -r /home/broncho/SlicerExtensions/SlicerJupyter-build/inner-build/lib/Slicer-4.9 /home/software/medical/slicer4.9/Slicer-SuperBuild-Release/Slicer-build/share/
cp -r /home/broncho/SlicerExtensions/SlicerJupyter-build/lib/Slicer-4.9 /home/software/medical/slicer4.9/Slicer-SuperBuild-Release/Slicer-build/lib/
Didn’t working without copied libraries from inner-build.
Then in Slicer I have selected Jupyter directiory(virtual environment).
This information may be useful.
no its not build version
@saima Can you copy here the contents of the file C:\Users\22374464\AppData\Roaming\jupyter\kernels\slicer-4.9\kernel.json?
Please see the contents of file kernel.json
{
"display_name": "Slicer 4.9",
"language" : "python",
"argv": [
"C:/Program Files/Slicer 4.9.0-2018-08-17/bin/../Slicer.exe",
"--no-splash",
"--python-code",
"connection_file=r'{connection_file}'; print('Jupyter connection file: ['+connection_file+']'); slicer.modules.jupyterkernel.startKernel(connection_file);slicer.util.mainWindow().showMinimized()"
]
}
Does Slicer start if you type this on the command-line?
C:/Program Files/Slicer 4.9.0-2018-08-17/bin/../Slicer.exe
Could you please also try with the latest nightly build (that you’ve downloaded just now)? Install SlicerJupyter extension, install the kernel, restart Jupyter, create a new notebook with Slicer-4.9 kernel.
Dear Andras,
The file slicer.exe is at location: D:\Slicer4.9\Slicer 4.9.0-2018-08-17
Its not at C:/Program Files/Slicer 4.9.0-2018-08-17/bin/…/Slicer.exe.
Should I change the script manually? or should I reinstall in C drive
Yes I tried with the latest nightly build.
Yes, changing the path in kernel.json file should fix the issue.
Did you move Slicer manually from C:\Program Files\... to D:\Slicer4.9\...?
no I didnt I installed on D drive.
Yes its connected now.
Why the path was not correct?
Thank you so much Andras
Dear Andras can I have code completion in this.
I’ve checked the implementation and kernel.json was only updated once, when a specific Slicer version was installed the first time. You’ve installed first on the C drive and then when you uninstalled and reinstalled it on D drive, the program path in the kernel file still pointed to the deleted installation.
I’ve pushed a fix - now kernel.json is updated whenever the kernel is installed. So, the error should not occur anymore for SlicerJupyter versions that you download tomorrow or later.
Yes I followed the steps you mentioned. Kernel is running but I dont get the auto complete. I changed the path manually. Should I install again the slicer and the extensions.
Yes, you will need to update to get new fixes/features.
To make sure that your kernel is using the latest Slicer version, please enter the following into a cell in your Jupyter notebook, run it, and let us know what version do you get:
print slicer.app.applicationVersionIts 4.9.0-2018-08-17
That version did not contain auto-complete yet. You need to install latest nightly version and reinstall the extension and kernel as described above.
Hi everyone.
I am trying to prepare the environment for my friend but when running the jupyter kernel Slicer exit abnormally. I followed instruction from github.
I downloaded stable Slicer then installed SlicerJupyter(it didn’t appear in modules then manually copy libs). What am I doing wrong?
Greetings.