Re: [mitk-users] Startup error: ctkPluginException on first run
Hi,
I am not sure what you tried already, but more information would
certainly help here. If you can reproduce a state where you know that
starting your application will show the described errors, have a look at
the output of those two commands before you actually start your app:
/lib64/ld-linux-x86-64.so.2 --list
/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_blueberry_core_expressions.so
ldd -r
/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_blueberry_core_expressions.so
Then start your app and afterwards run the commands again. Is the output
any different?
Best,
Sascha
On 7/19/19 8:09 PM, Nil Goyette wrote:
>
> Hi all,
>
> We can't release our application because of this problem so I tested
> more. Here's some facts about the problem:
>
> * Mitk Workbench doesn't have the problem. It happens only on Linux
> on each new releases (commit + make package), even if they are all
> based on MITK 2018.04.2. I do not use the "build tree", I use
> "make package".
> * --Blueberry.clean and deleting ~/.local/share/Imeka produce almost
> the same error.
> * The paths are right. imagenavigator.so is where the app thinks it is.
> * It's clearly related to plugins.db located in
> ~/.local/share/Imeka. The first (and only) crash is creating this
> file. The next run is doubling its size, to a working condition. A
> working build simply creates the file and continue running the
> application.
> * There's no problem on the computer where the package was created.
> Even when I delete plugins.db. And even when I delete all
> dependencies: Qt, MITK build and our app build. It seems to be
> incompatible between 16.04 and 18.04 builds but I'm not sure about
> that yet. Overall, this makes the bug really hard to test.
>
> Knowing that the Mitk Workbench is fine and that you added "a few Qt
> dependencies" to fix it, can I have more details about what you did?
> How did you know which dependencies to add? I can't really add the
> imagenavigator plugin "more" than it's already added? How am I
> supposed to add them? Moreover, is there a way to have a stacktrace?
> It's only complaining about imagenavigator.so but I know that it
> exists at the right place! I must be doing something in my app that
> MITK Workbench isn't doing and I need to know who the culprint is.
>
> Nil Goyette
>
> Le 2019-06-21 à 04:47, Dinkelacker, Stefan a écrit :
>>
>> Hi,
>>
>>
>>
>> we had several of these issues and shortly before the last release.
>> One had to open the Workbench three times before it continuously
>> worked afterwards. Most of the issues were Qt related and we could
>> fix it by adding a few Qt dependencies to our scripts that are
>> actually meant to be dynamically loaded during runtime. We also
>> noticed that these issues only occurred when starting MITK out of the
>> build tree but the installers just worked fine as all binaries are at
>> a single place.
>>
>>
>>
>> AFAIK we still didn’t find the actual cause for the Poco-issue but it
>> never happened in installers. Do you build installers for your
>> clients or are they using build-tree versions of MITK?
>>
>>
>>
>> I also see that you use the releases/2018-04 branch instead of the
>> latest stable tag v2018.04.2. Just a small warning that it may fail
>> from time to time, even though it should be much more stable than the
>> master branch, though.
>>
>>
>>
>> Stefan
>>
>>
>>
>> *From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
>> *Sent:* Thursday, June 20, 2019 3:41 PM
>> *To:* mitk-users@lists.sourceforge.net
>> *Subject:* [mitk-users] Startup error: ctkPluginException on first run
>>
>>
>>
>> Hi all,
>>
>> I upgraded to MITK 2018.04, built linux installers and my users see
>> this error on the first time they open the application.
>>
>> 0.393! WARNING: Startup error: ctkPluginException: The plugin
>> "/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so"
>> could not be loaded: Cannot load library
>> /home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so:
>> (/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_blueberry_core_expressions.so:
>> undefined symbol:
>> _ZN5berry14ElementHandler6CreateEPNS_19ExpressionConverterEPN4Poco3XML7ElementE)
>>
>> It opens without any problem when they try again. It's happen *only
>> the first time*. It seems you can't mix MITK 2016.11 and MITK
>> 2018.04. We tried deleting the temp folder ~/.local/share/Imeka, or
>> using --Blueberry.clean, but it gives almost the same error as before.
>>
>> 0.437! WARNING: Failed to install plugin
>> QUrl("file:///home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so"
>> )
>> : ctkPluginException: Failed to install plugin
>>
Re: [mitk-users] Startup error: ctkPluginException on first run
Hi all,
We can't release our application because of this problem so I tested
more. Here's some facts about the problem:
* Mitk Workbench doesn't have the problem. It happens only on Linux on
each new releases (commit + make package), even if they are all
based on MITK 2018.04.2. I do not use the "build tree", I use "make
package".
* --Blueberry.clean and deleting ~/.local/share/Imeka produce almost
the same error.
* The paths are right. imagenavigator.so is where the app thinks it is.
* It's clearly related to plugins.db located in ~/.local/share/Imeka.
The first (and only) crash is creating this file. The next run is
doubling its size, to a working condition. A working build simply
creates the file and continue running the application.
* There's no problem on the computer where the package was created.
Even when I delete plugins.db. And even when I delete all
dependencies: Qt, MITK build and our app build. It seems to be
incompatible between 16.04 and 18.04 builds but I'm not sure about
that yet. Overall, this makes the bug really hard to test.
Knowing that the Mitk Workbench is fine and that you added "a few Qt
dependencies" to fix it, can I have more details about what you did? How
did you know which dependencies to add? I can't really add the
imagenavigator plugin "more" than it's already added? How am I supposed
to add them? Moreover, is there a way to have a stacktrace? It's only
complaining about imagenavigator.so but I know that it exists at the
right place! I must be doing something in my app that MITK Workbench
isn't doing and I need to know who the culprint is.
Nil Goyette
Le 2019-06-21 à 04:47, Dinkelacker, Stefan a écrit :
Hi,
we had several of these issues and shortly before the last release.
One had to open the Workbench three times before it continuously
worked afterwards. Most of the issues were Qt related and we could fix
it by adding a few Qt dependencies to our scripts that are actually
meant to be dynamically loaded during runtime. We also noticed that
these issues only occurred when starting MITK out of the build tree
but the installers just worked fine as all binaries are at a single
place.
AFAIK we still didn’t find the actual cause for the Poco-issue but it
never happened in installers. Do you build installers for your clients
or are they using build-tree versions of MITK?
I also see that you use the releases/2018-04 branch instead of the
latest stable tag v2018.04.2. Just a small warning that it may fail
from time to time, even though it should be much more stable than the
master branch, though.
Stefan
*From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
*Sent:* Thursday, June 20, 2019 3:41 PM
*To:* mitk-users@lists.sourceforge.net
*Subject:* [mitk-users] Startup error: ctkPluginException on first run
Hi all,
I upgraded to MITK 2018.04, built linux installers and my users see
this error on the first time they open the application.
0.393! WARNING: Startup error: ctkPluginException: The plugin
"/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so"
could not be loaded: Cannot load library
/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so:
(/home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_blueberry_core_expressions.so:
undefined symbol:
_ZN5berry14ElementHandler6CreateEPNS_19ExpressionConverterEPN4Poco3XML7ElementE)
It opens without any problem when they try again. It's happen *only
the first time*. It seems you can't mix MITK 2016.11 and MITK 2018.04.
We tried deleting the temp folder ~/.local/share/Imeka, or using
--Blueberry.clean, but it gives almost the same error as before.
0.437! WARNING: Failed to install plugin
QUrl("file:///home/fmorency/softwares/MITK-v2018.04.2-54-gca0a3e57c1-linux-x86_64/bin/plugins/liborg_mitk_gui_qt_imagenavigator.so"
)
: ctkPluginException: Failed to install plugin
Caused by: ctkPluginException: The plugin ... *REST IS IDENTICAL*
I guess that renaming the project, from "Imeka" to anything else,
would solve this problem, but we don't really want to change our
company name! Is there a way to avoid this? Asking our users to open
the application twice seems unprofessional.
Nil Goyette
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[mitk-users] how to create wavefront obj file from (dicom) image slices
Dear all,
I am trying to figure out the best way to convert a number of image slices to one volumetric image and export it
to an .obj file.
On the one side, my question is general... having a list, containing a number of "mitk::Image::Pointer"s.. what is the proper way (or "a" proper way)
of converting those to a volumetric image and consequently to a wavefront obj file?
For now, I am trying to do this with DICOM images ... for that, I just took your "Step 1" tutorial project and extended it by a header and a source file, which I have appended to this mail
in case you want to take a look at the code.
I also changed the main function a bit. A file containing just the new stuff is appended as well.
The problem is again: having extracted the images, how can I do the conversion to one 3D image?
I saw an example here:
>>> https://itk.org/Doxygen/html/Examples_2IO_2DicomSeriesReadImageWrite2_8cxx-example.html
in which they use the itk::ImageSeriesReader.
As you can see in my code, I am using the procedure of creating a DICOMFileReaderSelector and letting him "choose" the best reader
(I read a lot through the code and saw, that this is apparently the way of loading DICOM images).
Given the configuration files, an mitkDICOMITKSeriesGDCMReader is chosen (not surprisingly, of course), but its GetOutput() method apparently
can only return one of the images.
In the itk example above however, the image writer is given the whole output of the series reader (" writer->SetInput( reader->GetOutput() ); ").
Is this itk example only possible with the itk:ImageSeriesReader?
I tried to use mitk classes etc., also because it is quite convenient for dicom files and for example all the code in the itk example finding the dicom files in the directory
is not really necessary, which makes it a bit easier.
Or should I just take the example as is, without mitk classes/functions ...?
(Though I have to say that, reading through all the code I just can't imagine that there is not a possibility within mitk, I just suppose I haven't found it by now).
I have tried, read and played around a lot by now, without a lot of success, so I would really appreciate if I could get some help on this topic.
I thank you very much in advance and wish you a great weekend.
Kind regards,
Ivaylo Angelov
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