Java Error when doing non-rigid EC clem alignement

Hello there,

I just freshly installed icy on ubuntu distribution.
I completely new to Icy and EC clem. I followed the videos on the ec clem website but when i am reaching the non rigid alignement, i get a error code when trying to update I get this error code:

java.lang.UnsatisfiedLinkError: ‘long vtk.vtkPoints.VTKInit()’
at vtk.vtkPoints.VTKInit(Native Method)
at vtk.vtkObjectBase.(vtkObjectBase.java:43)
at vtk.vtkObject.(vtkObject.java:94)
at vtk.vtkPoints.(vtkPoints.java:182)
at plugins.perrine.easyclemv0.NonRigidTranformationVTK.createvtkpoints(NonRigidTranformationVTK.java:620)
at plugins.perrine.easyclemv0.NonRigidTranformationVTK.run(NonRigidTranformationVTK.java:85)
at plugins.perrine.easyclemv0.GuiCLEMButtons$1$2.run(GuiCLEMButtons.java:155)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)

I get also this error message when opening the software:
nullStartupMacro.txt (No Such File or Directory)

I guess the two message could be link and may be related to a problem during installation of the software ?
Thanks for your help

Dear Clement Chambaud,

I am inviting @PerrineGilloteaux, one of the developer of ec-CLEM to join this thread, as she might have some helpful insights on this.

And I would like to be sure I understood what you did so far because it could come from several things:

  1. You installed Icy (version 2.0.3.0 I guess?) on Ubuntu (20.04?)
  2. You started Icy. Did you start Icy from its folder ? the download notes says the following: “Icy now includes the VTK binaries (with java binding), be sure to start Icy from its folder so VTK library can load correctly.
    Still you may experience incompatibilities depending your Linux distribution (we tested only for Ubuntu and Mint), in this case you may need to install (or compile) the dedicated VTK package (version 6.3 currently) with java wrapper for your distribution and move the library files (.so) into the lib/linux64/vtk folder of Icy.
  3. You installed the ec-CLEM plugin. Did you install it from the search bar of the Icy software or by copying the .jar in the plugin folder?
  4. You managed to follow& reproduce the first videos from the plugin description page, I mean the introduction to Icy and the rigid registration.
  5. When trying the non-rigid registration, you observe the error code “java.lang.UnsatisfiedLinkError:…”.
  6. On top of this you have a second error message when opening Icy.

Did I summarize what you did correctly?

Best regards,
Marion

1 Like

Hi, waiting for confirmation from Clement, but it looks ideed as the vtk library not loaded problem (as pointed out from the download notes link sent by Marion, Clement could you confirm? Can you send the console output when you launch ICY?
Best regards,
Perrine

Hello,

The thing is I am also new to ubuntu so I did not know if I installed properly Icy.

To answer you question:

  1. You installed Icy (version 2.0.3.0 I guess?) on Ubuntu (20.04?)
    Yes, this is my icy version that I download directly from the website. I have obtained a folder “Icy_all_2.0.3.0” that I unzipped in my documents. Then, I made the Icy.jar file executable from the file properties to be able to launch it. My ubuntu version is 18.04
  2. You started Icy. Did you start Icy from its folder ? the download notes says the following: “ Icy now includes the VTK binaries (with java binding), be sure to start Icy from its folder so VTK library can load correctly.
    Still you may experience incompatibilities depending your Linux distribution (we tested only for Ubuntu and Mint), in this case you may need to install (or compile) the dedicated VTK package (version 6.3 currently) with java wrapper for your distribution and move the library files (.so) into the lib/linux64/vtk folder of Icy.

    I guess yes, because as I mentionned before, I unzipped the folder and made Icy.jar executable and launch from this
  3. You installed the ec-CLEM plugin. Did you install it from the search bar of the Icy software or by copying the .jar in the plugin folder?
    I installed it from the search bar
  4. You managed to follow& reproduce the first videos from the plugin description page, I mean the introduction to Icy and the rigid registration.
    Yes, I was able to place a few points a get an overlay with some imprecisions in the corners due to TEM deformation
  5. When trying the non-rigid registration, you observe the error code “java.lang.UnsatisfiedLinkError:…”.
    Yes. From what I understand in the video, I let my images open and changed the transformation mode to “non ridid”, ticked the box to show grid deformation, run the plugin and click on “update transformation” and at this time the error message appears
  6. On top of this you have a second error message when opening Icy.
    Yes, It is apparently an ImageJ windows that pop and say this message when opening icy

Here is the output console. Yes apparently it cannot run the VTK library

OpenJDK Runtime Environment 11.0.7+10-post-Ubuntu-2ubuntu218.04 (64 bit)
Running on Linux 4.15.0-1087-oem (amd64)
Number of processors : 64
System total memory : 97.6 GB
System available memory : 54.4 GB
Max java memory : 24.4 GB
Image cache initialized (reserved memory = 9531 MB, disk cache location = /tmp)

java.lang.UnsatisfiedLinkError: no vtkalglib in java.library.path: [/usr/local/IMOD/lib, ., /usr/java/packages/lib, /usr/lib/x86_64-linux-gnu/jni, /lib/x86_64-linux-gnu, /usr/lib/x86_64-linux-gnu, /usr/lib/jni, /lib, /usr/lib, /home/ameliebernard/lib/unix64, /tmp/lib, /lib64, /lib/x86_64, /usr/lib64, /usr/lib/x86_64]

Cannot load VTK library…

Icy Version 2.0.3.0 started !

2 Likes

Hi Clement,

We have a FAQ entry about VTK library loading troubleshoot :

You can also have a look into this (old) post here :
https://groups.google.com/d/msg/icy-software/juhGZJFeshE/gZRP3gOxXHYJ

and looking at others replies too.
Hope that will help you in resolving your issue !

– Stephane

1 Like

Hello,

Apparently my problem is now solved. I did not managed to do the manipulation proposed above because I am quite new to ubuntu and using this kind of things.

What I did:

  • Install the latest Java version
  • Download and unzipp the latest vtk version (but not really installing I guess)
3 Likes

Hi Clement,

I am glad it now works :smiley: Thank you for sharing what you did.

Best regards,
Marion

1 Like