Re: [mitk-users] 2D FiberBundleMapper

[Nil Goyette]

Hi Peter,

Excellent news! I subscribed to that task. I can cherry-pick your commits
and test if you need it.
It may not be a priority right now for my boss, but I kinda want to do a
2021.02 release :) The 2D fibers mapper is the only missing part.
Thanks.

Le jeu. 28 oct. 2021, à 05 h 47, Neher, Peter 
a écrit :

> Looks like I already started with that before I left in February :)
>
> I can reproduce the bug and I will try to look into it. Here is the
> corresponding task:
>
> https://phabricator.mitk.org/T28772
>
>
>
> Best,
>
> Peter
>
>
> ------
>
> *Von:* Nil Goyette 
> *Gesendet:* Mittwoch, 27. Oktober 2021 17:22
> *An:* Neher, Peter
> *Cc:* mitk-users@lists.sourceforge.net
> *Betreff:* Re: [mitk-users] 2D FiberBundleMapper
>
>
>
> Hi Peter,
>
>
>
> I understand, I had the same kid "problem" last year :)
>
> No, I didn't investigate more. Our program based on MITK is not a priority
> right now and I've put enough time on that bug to be discouraged, so I was
> waiting for an easy answer!
>
> I'll wait and hope that you accidentally reproduce this bug when you
> update your dependencies.
>
> Thanks for the answer.
>
>
>
> Le mar. 26 oct. 2021, à 03 h 32, Neher, Peter 
> a écrit :
>
> Hi Nil,
>
>
>
> sorry for getting back to you on this so late. I was on parental leave
> until yesterday.
>
>
>
> Regarding your problem with VTK9, I unfortunately don't have any
> experience with this yet. I am planning to get on this in the next months,
> since we will have new projects that are going to be based on MITK
> Diffusion. As soon as I have any insights there I can let you know. If you
> already made progress, we are of course happy for contributions! I know,
> this is probably not the answer you hoped for. Sorry about that :)
>
>
>
> Best,
>
> Peter
>
>
> --
>
> *Von:* Nil Goyette 
> *Gesendet:* Dienstag, 28. September 2021 18:48
> *An:* mitk-users@lists.sourceforge.net
> *Betreff:* Re: [mitk-users] 2D FiberBundleMapper
>
>
>
> Hi all,
>
>
>
> Anyone can help me with this problem? If Peter Neher is still around, he's
> the best person to answer this question.
>
>
>
> Nil
>
>
>
>
>
> Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette  a
> écrit :
>
> Hi all,
>
>
>
> I've been trying to port our application to MITK 2021.02. I usually look
> at mitk-diffusion because we both work with the FiberBundle class and this
> helps me a lot! (Thank you Peter). However, I have a problem that I'm
> unable to solve. The 2D FiberBundle doesn't seem to work with vtk9. See
> https://i.imgur.com/d8I2PtP.png
>
>- The crosshair is in the middle of a set of streamlines but we only
>see them in the sagittal view. If I want to see them in the other views, I
>need to place the crosshair at a "random" location. To see them in all
>views, I need to be at a weird location that is not the center of the 
> image.
>- The streamlines are visible only in 3 slices. If I go further than
>that, they simply disappear.
>- But they are completely visible like in the 3D view. I tried
>changing the Fiber2DSliceThickness property. To have an "acceptable"
>result, I need to use a really small number like 0.01. The screenshot above
>is using 0.1. At 0.5, I can see the whole streamlines.
>- It's as if the streamlines are not where we see them. As if they
>were really tiny.
>- Or the shaders are simply broken on vtk9.
>
> I can clearly see that the mapper in mitk-diffusion (latest release using
> VTK 8.1.0) works, so I tried removing our modifications as much as possible
> to be as identical to mitk-diffusion as possible. I'm using the same
> TrackVis loader, FiberBundle, mapper 2D 3D, etc. It didn't change anything.
>
>
>
> At that point, I'm already at several days of debugging, I don't know what
> to try and I would gladly accept any help!
>
>
>
> Nil
>
>

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Re: [mitk-users] 2D FiberBundleMapper

[Nil Goyette]

Hi Peter,

I understand, I had the same kid "problem" last year :)
No, I didn't investigate more. Our program based on MITK is not a priority
right now and I've put enough time on that bug to be discouraged, so I was
waiting for an easy answer!
I'll wait and hope that you accidentally reproduce this bug when you update
your dependencies.
Thanks for the answer.

Le mar. 26 oct. 2021, à 03 h 32, Neher, Peter 
a écrit :

> Hi Nil,
>
>
> sorry for getting back to you on this so late. I was on parental leave
> until yesterday.
>
>
> Regarding your problem with VTK9, I unfortunately don't have any
> experience with this yet. I am planning to get on this in the next months,
> since we will have new projects that are going to be based on MITK
> Diffusion. As soon as I have any insights there I can let you know. If you
> already made progress, we are of course happy for contributions! I know,
> this is probably not the answer you hoped for. Sorry about that :)
>
>
> Best,
>
> Peter
>
>
> --
> *Von:* Nil Goyette 
> *Gesendet:* Dienstag, 28. September 2021 18:48
> *An:* mitk-users@lists.sourceforge.net
> *Betreff:* Re: [mitk-users] 2D FiberBundleMapper
>
> Hi all,
>
> Anyone can help me with this problem? If Peter Neher is still around, he's
> the best person to answer this question.
>
> Nil
>
>
> Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette  a
> écrit :
>
>> Hi all,
>>
>> I've been trying to port our application to MITK 2021.02. I usually look
>> at mitk-diffusion because we both work with the FiberBundle class and this
>> helps me a lot! (Thank you Peter). However, I have a problem that I'm
>> unable to solve. The 2D FiberBundle doesn't seem to work with vtk9. See
>> https://i.imgur.com/d8I2PtP.png
>>
>>- The crosshair is in the middle of a set of streamlines but we only
>>see them in the sagittal view. If I want to see them in the other views, I
>>need to place the crosshair at a "random" location. To see them in all
>>views, I need to be at a weird location that is not the center of the 
>> image.
>>- The streamlines are visible only in 3 slices. If I go further than
>>that, they simply disappear.
>>- But they are completely visible like in the 3D view. I tried
>>changing the Fiber2DSliceThickness property. To have an "acceptable"
>>result, I need to use a really small number like 0.01. The screenshot 
>> above
>>is using 0.1. At 0.5, I can see the whole streamlines.
>>- It's as if the streamlines are not where we see them. As if they
>>were really tiny.
>>- Or the shaders are simply broken on vtk9.
>>
>> I can clearly see that the mapper in mitk-diffusion (latest release using
>> VTK 8.1.0) works, so I tried removing our modifications as much as possible
>> to be as identical to mitk-diffusion as possible. I'm using the same
>> TrackVis loader, FiberBundle, mapper 2D 3D, etc. It didn't change anything.
>>
>> At that point, I'm already at several days of debugging, I don't know
>> what to try and I would gladly accept any help!
>>
>> Nil
>>
>
>
> --
> Nil Goyette
> Développeur principal
> www.imeka.ca
>
> During this time of social distancing, we offer free webinars on subjects
> that matter. <https://www.imeka.ca/webinars/>
>
> CONFIDENTIALITY NOTICE: This message, and any attachments, is intended
> only for the use of the addressee or his authorized representative. It may
> contain information that is privileged, confidential and exempt from
> disclosure under applicable law. If the reader of this message is not the
> intended recipient, or his authorized representative, you are hereby
> notified that any dissemination, distribution or copying of this message
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>
>
> AVIS DE CONFIDENTIALITÉ : Ce message, ainsi que tout fichier qui y est
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Re: [mitk-users] 2D FiberBundleMapper

[Nil Goyette]

Hi all,

Anyone can help me with this problem? If Peter Neher is still around, he's
the best person to answer this question.

Nil


Le jeu. 9 sept. 2021, à 13 h 04, Nil Goyette  a
écrit :

> Hi all,
>
> I've been trying to port our application to MITK 2021.02. I usually look
> at mitk-diffusion because we both work with the FiberBundle class and this
> helps me a lot! (Thank you Peter). However, I have a problem that I'm
> unable to solve. The 2D FiberBundle doesn't seem to work with vtk9. See
> https://i.imgur.com/d8I2PtP.png
>
>- The crosshair is in the middle of a set of streamlines but we only
>see them in the sagittal view. If I want to see them in the other views, I
>need to place the crosshair at a "random" location. To see them in all
>views, I need to be at a weird location that is not the center of the 
> image.
>- The streamlines are visible only in 3 slices. If I go further than
>that, they simply disappear.
>- But they are completely visible like in the 3D view. I tried
>changing the Fiber2DSliceThickness property. To have an "acceptable"
>result, I need to use a really small number like 0.01. The screenshot above
>is using 0.1. At 0.5, I can see the whole streamlines.
>- It's as if the streamlines are not where we see them. As if they
>were really tiny.
>- Or the shaders are simply broken on vtk9.
>
> I can clearly see that the mapper in mitk-diffusion (latest release using
> VTK 8.1.0) works, so I tried removing our modifications as much as possible
> to be as identical to mitk-diffusion as possible. I'm using the same
> TrackVis loader, FiberBundle, mapper 2D 3D, etc. It didn't change anything.
>
> At that point, I'm already at several days of debugging, I don't know what
> to try and I would gladly accept any help!
>
> Nil
>


-- 
Nil Goyette
Développeur principal
www.imeka.ca

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[mitk-users] 2D FiberBundleMapper

[Nil Goyette]

Hi all,

I've been trying to port our application to MITK 2021.02. I usually look at
mitk-diffusion because we both work with the FiberBundle class and this
helps me a lot! (Thank you Peter). However, I have a problem that I'm
unable to solve. The 2D FiberBundle doesn't seem to work with vtk9. See
https://i.imgur.com/d8I2PtP.png

   - The crosshair is in the middle of a set of streamlines but we only see
   them in the sagittal view. If I want to see them in the other views, I need
   to place the crosshair at a "random" location. To see them in all views, I
   need to be at a weird location that is not the center of the image.
   - The streamlines are visible only in 3 slices. If I go further than
   that, they simply disappear.
   - But they are completely visible like in the 3D view. I tried changing
   the Fiber2DSliceThickness property. To have an "acceptable" result, I need
   to use a really small number like 0.01. The screenshot above is using 0.1.
   At 0.5, I can see the whole streamlines.
   - It's as if the streamlines are not where we see them. As if they were
   really tiny.
   - Or the shaders are simply broken on vtk9.

I can clearly see that the mapper in mitk-diffusion (latest release using
VTK 8.1.0) works, so I tried removing our modifications as much as possible
to be as identical to mitk-diffusion as possible. I'm using the same
TrackVis loader, FiberBundle, mapper 2D 3D, etc. It didn't change anything.

At that point, I'm already at several days of debugging, I don't know what
to try and I would gladly accept any help!

Nil

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that matter. 

CONFIDENTIALITY NOTICE: This 
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Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan,

as always, thank you for your answer.

   1. "Spare the last step" Yes, of course, it would fix the recompilation
   problem but not the others (see april 21th message). And as I said it's not
   compatible with our build system. We're preparing the mitk build in our
   cicd and using it to build our own project when we modify it. This is much
   faster than building the whole mitk+imeka project. We could abandon this
   method, but it's not worth it if it only fixes a part of the problem.
   2. Haha, yes, there is some wrong command line usage. I usually use
   cmake-gui so I don't deactivate the testing twice. And I don't specify the
   Qt directory if cmake doesn't ask for it.
   3. Yes, thanks again for the shortcut. It's nice to learn little tricks
   like that.
   4. I totally agree with your last sentence: it should be done in a few
   seconds. This is indeed the expected result.

I tested on a Linux vm with the exact same results (mitk recompilation). I
know that it's not supposed to happen but it's clearly happening and I
still have all the same problems. I would gladly use the extension method
but it's not working as intended. Do you have any other ideas on how to fix
this magical problem? At that point, I'd prefer trying the "mitk as a
library" method again, but it would be nice to have a minimal working
example (applications, modules, plugins, cmakelist). I usually look at
MitkDiffusion for examples but there's no cmake files anymore so it looks
like Peter switched too!

Nil

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Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan,

Sorry for the late reply, I'm not working on this project often. I didn't
record a screencast but I took note of what I did. Maybe you will be able
to spot what I did wrong.

# Install Qt 5.12.10 (QtScript, QtWebEngine, OpenSSL 1.1)
# Install CMake 3.19.7

# Create an empty extension project
mkdir C:\imeka
cd C:\imeka
mkdir C:\imeka\mibrain
mkdir C:\imeka\mibrain\Modules
Add a ModuleList.cmake file with an empty MITK_MODULES list
mkdir C:\imeka\mibrain\Plugins
Add a PluginList.cmake file with an empty MITK_PLUGINS list

# Get MITK
git clone https://phabricator.mitk.org/source/mitk.git
cd mitk
git checkout v2021.02

# Build MITK
cd ..
mkdir mitk_build_5.12
cd C:/Imeka/mitk_build_5.12
cmake -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE:STRING=Release
-DCMAKE_CONFIGURATION_TYPES:STRING="Debug;Release" -DBUILD_TESTING:BOOL=OFF
-DQt5_DIR:PATH=C:/Qt/5.12.10/msvc2017_64/lib/cmake/Qt5
-DBUILD_TESTING:BOOL=0 C:/Imeka/mitk/
Open the solution in Visual Studio and Build. Wait. Visual Studio tells me
that everything has succeeded, nothing has failed.
== Génération : 20 a réussi, 0 a échoué, 0 à jour, 2 a été ignoré
==
At that point, I can open the Workbench - About, and see ITK 4.13.3, VTK
9.0.1, Qt 5.12.10

# Add 2 plugins that we need (skipping this part still lead to a full MITK
recompilation)
cd MITK-build
cmake -DMITK_BUILD_org.mitk.gui.qt.moviemaker:BOOL=ON
-DMITK_BUILD_org.mitk.gui.qt.segmentation:BOOL=ON C:/Imeka/mitk/
Open the solution in Visual Studio and Build. Wait. Visual Studio tells me
that everything has succeeded, nothing has failed.
== Génération : 18 a réussi, 0 a échoué, 2 à jour, 0 a été ignoré
==
I can still open the Workbench and see the About dialog. And I see the 2
added plugins.
A rebuild (just for testing) in Visual Studio is fast, as expected, because
it's doing nothing.

# Add our own projet (MITK extension)
cd ..
cmake -DMITK_EXTENSION_DIRS:PATH="C:/Imeka/mibrain" C:/Imeka/mitk/
Open the solution in Visual Studio and Build. Wait. Visual Studio tells me
that everything has succeeded, nothing has failed.
*But it's a complete MITK build again. *

So, do you see anything obvious?

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Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan,

Still no success. I deleted everything and started from a fresh build.
Adding an "empty" project to  MITK_EXTENSION_DIRS does start a new MITK
build. Removing it does the same thing. Once it's added, I can add modules
and plugins without full compilation though. This being said, I see some
problems with MITK extensions that I want to share with you:

   1. This full recompilation problem is incompatible with our automated
   build system. I understand that it shouldn't happen, but it does happen.
   2. Changing something in the extension (our project) takes much longer
   than usual because Visual Studio now checks the complete MITK project
   instead of our tiny project.
   3. The Solution explorer only contains the MITK projects and
   dependencies.
   4. Visual Studio doesn't seem to understand what's going on. There's no
   help, no intellisense, no nothing.
   5. We must name our plugins "org.mitk.xyz" otherwise cmake tells us that
   it's an invalid symbolic name. We already have our plugin names starting
   with org.imeka because we want to recognize them.
   6. I didn't get further than that but I feel that there will be more
   pain-points. Possibly the branding (name and icon of the final application).

I think it's best if we avoid this extension feature., so I'll ask
something new. *Is there an up-to-date (2021.02) project that uses MITK as
a library OR a minimal working example of such a thing?*
I'm not used to cmake at all. I can modify existing cmake files but
creating new ones for a new project is a big chore. Being able to read and
copy such an exemple will greatly help me and probably some other users too.

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Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan.

I'm currently testing the MITK extension. I created an almost empty project
as you suggested . To be more specific, a "Modules" folder with an
empty MITK_MODULES list, and a "Plugins" with an empty MITK_PLUGINS list.
The simple fact of adding this extension to  MITK_EXTENSION_DIRS starts a
full compilation again. There's no ITK, no dependencies, no nothing!
Reading your last email, you seem to say that this full recompilation is
not normal. Can you please confirm?

Nil

Le ven. 9 avr. 2021, à 04 h 49, Dinkelacker, Stefan <
s.dinkelac...@dkfz-heidelberg.de> a écrit :

> Hi,
>
>
> the project template (or generally speaking an "MITK extension") can be
> built just like plain MITK, there is nothing extra or separate script/code
> paths in our build scripts. That's the cool thing about the project
> template/MITK extensions. It mirrors the MITK directory structure and all
> the magic happens within the MITK build system, not the project template
> build system. It basically works by following path and filename
> conventions. It is virtually like forking the MITK repository and adding
> dependencies, modules, plugins, applications, and build configurations
> right to the MITK repo, but with the advantage that you do not have to
> touch the original repo but have an extra directory/repo for your own stuff
> that is "mounted" into the MITK directory.
>
>
> Notice that the project template is full of examples/demos that you do not
> need for your own stuff. Their purpose is to show how things are supposed
> to be done and that it is just like you would do stuff right in the MITK
> directory. One of the examples is that even the configurations of a few
> MITK-dependencies like ITK can be modified from an extension [1]. And this
> is why MITK was basically rebuilt completely when you added the
> ProjectTemplate itself to MITK_EXTENSION_DIRS since ITK as a core
> dependency needed a rebuild.
>
>
> Since you already have all your stuff and just want to migrate, start with
> an empty directory instead of the project template and just use the project
> template as an example-based manual/inspiration.
>
>
> For example, a minimum start could be to simple create a Modules folder,
> put a ModuleList.cmake in it and reference your first module [2]. That's
> all you need to add a module to MITK. When you then add your root directory
> to MITK_EXTENSION_DIRS (you can also do this in the MITK-build, not only
> in the MITK-superbuild as long as you do not change anything on
> superbuild-level), MITK will look for a Modules/ModuleList.cmake files not
> only in its own root directory but in all extension dirs and handle it just
> like its own Modules/ModuleList.cmake file.
>
>
> Best,
>
> Stefan
>
>
> [1]
> https://github.com/MITK/MITK-ProjectTemplate/blob/master/CMakeExternals/Customization/ITK.cmake
>
> [2] https://github.com/MITK/MITK-ProjectTemplate/tree/master/Modules
>
>
> --
> *Von:* Nil Goyette 
> *Gesendet:* Freitag, 9. April 2021 04:19
> *An:* Dinkelacker, Stefan
> *Cc:* mitk-users@lists.sourceforge.net
> *Betreff:* Re: [mitk-users] PluginGenerator and ProjectTemplate
>
> Hi Stefan,
> I'm still unable to generate the solution, with Qt5.12 or Qt5.15, with or
> without a reference to MitkAppUtil, with or without a
> "find_package(Qt5WebEngine REQUIRED)".. I get the same error as before.
> This being said, I think I need to clarify the framework/library thing
> before we go further. If I understand correctly:
>
>- MITK as a framework. Should use the ProjectTemplate and link to this
>template in the MITK superbuild.
>- MITK as a library.. Use our own cmake and link to MITK build dir.
>
> In our case, we use the standard MITK UI and features, we pick some useful
> MITK plugins and add some of our own. This is a "framework" usage, right? I
> tried the ProjectTemplate approach once and what I really disliked is that
> it recompiled MITK in full when I told cmake the MITK_EXTENSION_DIRS to
> my project. This is not compatible with our build system where we build
> MITK once and use the build artifacts to build our own project fast. Do you
> have a solution for this?
> Nil
>
> Le mer. 7 avr. 2021, à 06 h 59, Dinkelacker, Stefan <
> s.dinkelac...@dkfz-heidelberg.de> a écrit :
>
>> Hi,
>>
>>
>> my first guess is that your executable is infected with this dependency
>> from MitkAppUtil, which has a PUBLIC package dependency to WebEngine.
>> Usually CMake is right in its assumptions regarding find_package(). So a
>> first step would be to do a manual find_package for WebEngine and continue
>> from there. If i

Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan,
I'm still unable to generate the solution, with Qt5.12 or Qt5.15, with or
without a reference to MitkAppUtil, with or without a
"find_package(Qt5WebEngine REQUIRED)".. I get the same error as before.
This being said, I think I need to clarify the framework/library thing
before we go further. If I understand correctly:

   - MITK as a framework. Should use the ProjectTemplate and link to this
   template in the MITK superbuild.
   - MITK as a library.. Use our own cmake and link to MITK build dir.

In our case, we use the standard MITK UI and features, we pick some useful
MITK plugins and add some of our own. This is a "framework" usage, right? I
tried the ProjectTemplate approach once and what I really disliked is that
it recompiled MITK in full when I told cmake the MITK_EXTENSION_DIRS to my
project. This is not compatible with our build system where we build MITK
once and use the build artifacts to build our own project fast. Do you have
a solution for this?
Nil

Le mer. 7 avr. 2021, à 06 h 59, Dinkelacker, Stefan <
s.dinkelac...@dkfz-heidelberg.de> a écrit :

> Hi,
>
>
> my first guess is that your executable is infected with this dependency
> from MitkAppUtil, which has a PUBLIC package dependency to WebEngine.
> Usually CMake is right in its assumptions regarding find_package(). So a
> first step would be to do a manual find_package for WebEngine and continue
> from there. If it still cannot be found, but other components of Qt were
> found, double-check your installation and maybe manually look for the
> Config.cmake file in the lib/cmake subfolder of your Qt installation. Since
> you seem to use MITK as library it is hard to make better guesses at the
> moment. I also did not use Qt 5.15 yet, only 5.12.
>
>
> Best,
>
> Stefan
> --
> *Von:* Nil Goyette 
> *Gesendet:* Dienstag, 6. April 2021 17:21
> *An:* Dinkelacker, Stefan
> *Cc:* mitk-users@lists.sourceforge.net
> *Betreff:* Re: [mitk-users] PluginGenerator and ProjectTemplate
>
> Hi Stefan,
>
> My module wasn't found because I included "MitkTestingHelper" in the wrong
> place. There was no useful error message so I had to guess it.
> But now I have another problem and you may be able to help me. The CMake
> Configure part is ok, but when I click on Generate, I get this error
>
> CMake Error at
> C:/Imeka/mitk/CMake/mitkFunctionCreateBlueBerryApplication.cmake:88
> (add_executable):
> Target "MI-Brain" links to target "Qt5::WebEngine" but the target was not
> found. Perhaps a find_package() call is missing for an IMPORTED target, or
> an ALIAS target is missing?
> Call Stack (most recent call first):
> Apps/MI-Brain/CMakeLists.txt:34 (mitkFunctionCreateBlueBerryApplication)
> which is surprising because I don't use or try to include WebEngine. A git
> grep WebEngine returns nothing. And I know and verified that I installed
> WebEngine along with Qt 5.15.X. Do you know what is causing this?
>
> NIl
>
> Le lun. 5 avr. 2021, à 19 h 19, Dinkelacker, Stefan <
> s.dinkelac...@dkfz-heidelberg.de> a écrit :
>
>> Hi Nil,
>>
>>
>> you do *not* need to use the ProjectTemplate but it is at least the
>> strongly recommended way for new MITK developers to go the framework route
>> with MITK. You can still continue using MITK as plain
>> CMake-based toolkit/library. As written in T27701, we just want to get rid
>> of the ProjectGeneration part, not the PluginGeneration part.
>>
>>
>> We focus on the ProjectTemplate since we recognized that most of the
>> external developers are not primarily developers but scientists and while
>> they usually have at least a basic level of knowledge in C++ to get things
>> done, CMake is already something different. Using the ProjectTemplate
>> basically means using MITK as we do internally (which is a big plus for us
>> regarding support) and that people just need to add modules, plugins, or
>> dependencies to an existing application backed by examples/templates.
>>
>>
>> When a module is suddenly missing it is probably related to a missing
>> implicit dependency that is not there anymore (we revisited the ITK
>> dependencies of all MITK modules in v2021.02 for example). The CMake output
>> / summary should print out why a module is missing.
>>
>>
>> Best,
>>
>> Stefan
>>
>>
>>
>>
>>
>> --
>> *Von:* Nil Goyette 
>> *Gesendet:* Donnerstag, 1. April 2021 21:51
>> *An:* mitk-users@lists.sourceforge.net
>> *Betreff:* [mitk-users] PluginGenerator and ProjectTemplate
>>
>> Hi all,
>>
>> I tried porting my application t

Re: [mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi Stefan,

My module wasn't found because I included "MitkTestingHelper" in the wrong
place. There was no useful error message so I had to guess it.
But now I have another problem and you may be able to help me. The CMake
Configure part is ok, but when I click on Generate, I get this error

CMake Error at
C:/Imeka/mitk/CMake/mitkFunctionCreateBlueBerryApplication.cmake:88
(add_executable):
Target "MI-Brain" links to target "Qt5::WebEngine" but the target was not
found. Perhaps a find_package() call is missing for an IMPORTED target, or
an ALIAS target is missing?
Call Stack (most recent call first):
Apps/MI-Brain/CMakeLists.txt:34 (mitkFunctionCreateBlueBerryApplication)
which is surprising because I don't use or try to include WebEngine. A git
grep WebEngine returns nothing. And I know and verified that I installed
WebEngine along with Qt 5.15.X. Do you know what is causing this?

NIl

Le lun. 5 avr. 2021, à 19 h 19, Dinkelacker, Stefan <
s.dinkelac...@dkfz-heidelberg.de> a écrit :

> Hi Nil,
>
>
> you do *not* need to use the ProjectTemplate but it is at least the
> strongly recommended way for new MITK developers to go the framework route
> with MITK. You can still continue using MITK as plain
> CMake-based toolkit/library. As written in T27701, we just want to get rid
> of the ProjectGeneration part, not the PluginGeneration part.
>
>
> We focus on the ProjectTemplate since we recognized that most of the
> external developers are not primarily developers but scientists and while
> they usually have at least a basic level of knowledge in C++ to get things
> done, CMake is already something different. Using the ProjectTemplate
> basically means using MITK as we do internally (which is a big plus for us
> regarding support) and that people just need to add modules, plugins, or
> dependencies to an existing application backed by examples/templates.
>
>
> When a module is suddenly missing it is probably related to a missing
> implicit dependency that is not there anymore (we revisited the ITK
> dependencies of all MITK modules in v2021.02 for example). The CMake output
> / summary should print out why a module is missing.
>
>
> Best,
>
> Stefan
>
>
>
>
>
> --
> *Von:* Nil Goyette 
> *Gesendet:* Donnerstag, 1. April 2021 21:51
> *An:* mitk-users@lists.sourceforge.net
> *Betreff:* [mitk-users] PluginGenerator and ProjectTemplate
>
> Hi all,
>
> I tried porting my application to 2121.02 and there's plenty of cmake
> errors because one of my modules is suddenly missing. So I tried using the
> good old PluginGenerator, but  I see that there's a problem with it. It's
> not built when I build MITK. It was decided in T27701
> <https://phabricator.mitk.org/T27701> to get rid of it. I learned that
> there's a ProjectTemplate
> <https://phabricator.mitk.org/source/mitk-projecttemplate/>. Is the old
> method (our project linking to MITK_BUILD) not working anymore? Can you
> please confirm that we must now use this ProjectTemplate?
> --
> Nil Goyette
> Développeur principal
> www.imeka.ca
>

-- 
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[mitk-users] PluginGenerator and ProjectTemplate

[Nil Goyette]

Hi all,

I tried porting my application to 2121.02 and there's plenty of cmake
errors because one of my modules is suddenly missing. So I tried using the
good old PluginGenerator, but  I see that there's a problem with it. It's
not built when I build MITK. It was decided in T27701
<https://phabricator.mitk.org/T27701> to get rid of it. I learned that
there's a ProjectTemplate
<https://phabricator.mitk.org/source/mitk-projecttemplate/>. Is the old
method (our project linking to MITK_BUILD) not working anymore? Can you
please confirm that we must now use this ProjectTemplate?
-- 
Nil Goyette
Développeur principal
www.imeka.ca

-- 
During this time of social distancing, we offer free webinars on subjects 
that matter. <https://www.imeka.ca/webinars/>

CONFIDENTIALITY NOTICE: This 
message, and any attachments, is intended only for the use of the addressee 
or his authorized representative. It may contain information that is 
privileged, confidential and exempt from disclosure under applicable law. 
If the reader of this message is not the intended recipient, or his 
authorized representative, you are hereby notified that any dissemination, 
distribution or copying of this message and any attachments is strictly 
prohibited. The integrity of this message cannot be guaranteed on the 
Internet, IMEKA shall not be liable for its content if altered, changed or 
falsified. If you have received this message in error, please contact 
immediately the sender and delete this message and any attachments from 
your system.


AVIS DE CONFIDENTIALITÉ : Ce message, ainsi que tout fichier 
qui y est joint, est destiné exclusivement aux personnes à qui il est 
adressé. Il peut contenir des informations de nature confidentielle qui ne 
doivent être divulguées en vertu des lois applicables. Si vous n'êtes pas 
le destinataire de ce message ou un mandataire autorisé de celui-ci, vous 
êtes avisé par la présente que toute impression, diffusion, distribution ou 
reproduction de ce message et de tout fichier qui y est joint est 
strictement interdite. L'intégrité de ce message n'étant pas assurée sur 
Internet, IMEKA ne peut être tenue responsable de son contenu s'il a été 
altéré, déformé ou falsifié. Si ce message vous a été transmis par erreur, 
veuillez en aviser sans délai l'expéditeur et l'effacer ainsi que tout 
fichier joint sans en conserver de copie.
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[mitk-users] ITK failed 'lrintf'

[Nil Goyette]

Hi all,

I've been trying, without success, to build MITK v2021.02 on Windows 10, VS
2019, CMake 3.19.7, Qt5.12.10.

The error is well-known by ITK
https://github.com/InsightSoftwareConsortium/ITK/issues/1967 and has been
fixed in the last weeks. Has this been fixed in MITK?

Nil Goyette

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[mitk-users] macOS support

[Nil Goyette via mitk-users]

Hi all,

macOS was already a Tier 2 platform in MITK 2018.04, so we've been
wondering what your future plans are about macOS support. With OpenGL
deprecation, adoption of Metal and the move to ARM processors, macOS is now
a really different beast. The nightly documentation says that macOS will
still be a Tier 2 platform, but what about Big Sur?

-- 
Nil
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[mitk-users] Crosshair in screenshots

[Nil Goyette via mitk-users]

Hi all,

Is there a way to remove the crosshair in 2D and the axial, coronal and
sagittal rectangles in 3D? Reading the code, I understand that you remove
some "decorations"

mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart();
renderWindowPart->EnableDecorations(false);
take screenshot
renderWindowPart->EnableDecorations(true);

namely "colored rectangles", "department logo", "menu", "gradient" and
"corner annotation". I thought that "colored rectangles" was what I needed
but they are still visible in the screenshots so it must be something else,
or it's a bug.  I couldn't find anything on your issues list, except for
the logo. Tested on MITK 2018.04 on Windows.

Nil
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[mitk-users] HiDPI retina QPainter

[Nil Goyette]

HI all,

Some users complained that the font size on their too-expensive 
MacBookPro was too small (only in MITK). I have no absolute proof but 
it's probably because they have HiDPI screen. I understand that it's 
possible to increase the size of the font in Preferences - General - 
Theme, but I discovered that I also have a problem when drawing with a 
QPainter! I draw a macOS widget and it's rendered perfectly on a normal 
screen, but not on a HiDPI screen.


I don't know much about this subject, but I think MITK (or us in a 
plugin?) is supposed to activate it or something. For example, afaik, 
the font size is supposed to be scaled automatically, since Qt 5.7 or 
around that. Currently, all the text in MITK is hard to read on macOS 
but is perfect on other OSes. So, do you guys have any experience with 
this? Do you know how I can fix my font size and QPainter problem?


Nil Goyette



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Re: [mitk-users] Startup error: ctkPluginException on first run

[Nil Goyette]

Hi Sascha,

I finally found the problem. I compared MITK Workbench and my app, cmake 
files, cpp, etc. Turns out that those three lines are really important 
on Linux, but not on macOS and Windows. I stupidly removed them when 
porting from the last MITK version.


QStringList preloadLibs;
preloadLibs << "liborg_mitk_gui_qt_ext";
app.setPreloadLibraries(preloadLibs);

Thank you for your support.

Nil

Le 2019-07-22 à 15:54, Nil Goyette a écrit :


Hi Sascha,

I tried on a broken and a good setup (some of my builds work on my 
computer but never on my colleagues'). Sadly, I got exactly the same 
output on both. This doesn't any sense to me.


$ /lib64/ld-linux-x86-64.so.2 --list 
bin/plugins/liborg_blueberry_core_expressions.so
bin/plugins/liborg_blueberry_core_expressions.so: error while loading 
shared libraries: liborg_blueberry_core_runtime.so: cannot open shared 
object file: No such file or directory


$ ldd -r bin/plugins/liborg_blueberry_core_expressions.so
bin/plugins/liborg_blueberry_core_expressions.so: 
/usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.12' not found 
(required by bin/plugins/liborg_blueberry_core_expressions.so)

    linux-vdso.so.1 (0x7ffdbfbf3000)
    libgtk3-nocsd.so.0 => /usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0 
(0x7fe317301000)

    liborg_blueberry_core_runtime.so => not found
    libCTKPluginFramework.so.0.1 => not found
    libCTKCore.so.0.1 => not found
    libmbilog.so => not found
    libPocoXML.so.60 => not found
    libPocoFoundation.so.60 => not found
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
(0x7fe3170e2000)
    libQt5Core.so.5 => /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 
(0x7fe316997000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 
(0x7fe31660e000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 
(0x7fe3163f6000)

    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fe316005000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fe315e01000)
    /lib64/ld-linux-x86-64.so.2 (0x7fe317768000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x7fe315be4000)
    libicui18n.so.60 => /usr/lib/x86_64-linux-gnu/libicui18n.so.60 
(0x7fe315743000)
    libicuuc.so.60 => /usr/lib/x86_64-linux-gnu/libicuuc.so.60 
(0x7fe31538c000)
    libdouble-conversion.so.1 => 
/usr/lib/x86_64-linux-gnu/libdouble-conversion.so.1 (0x7fe31517b000)
    libglib-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0 
(0x7fe314e64000)

    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fe314ac6000)
    libicudata.so.60 => /usr/lib/x86_64-linux-gnu/libicudata.so.60 
(0x7fe312f1d000)
    libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 
(0x7fe312cab000)
undefined symbol: _ZTIN5berry6ObjectE 
(bin/plugins/liborg_blueberry_core_expressions.so)

*... Around 110 lines of **undefined symbol ...
2 lines are somewhat different*
symbol qt_version_tag version Qt_5.12 not defined in file 
libQt5Core.so.5 with link time reference 
(bin/plugins/liborg_blueberry_core_expressions.so)
symbol _ZdlPvm version Qt_5 not defined in file libQt5Core.so.5 with 
link time reference (bin/plugins/liborg_blueberry_core_expressions.so)


Running the same commands while the application is running or after 
the application closes give the same results, except for the .so 
address (0x00...). With all those problems, I wonder how the 
application manages to start! How can an application starts with 
missing libraries and undefined symbols...


Nil

Le 2019-07-19 à 16:06, Sascha Zelzer a écrit :


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. Th

Re: [mitk-users] Startup error: ctkPluginException on first run

[Nil Goyette]

Hi Sascha,

I tried on a broken and a good setup (some of my builds work on my 
computer but never on my colleagues'). Sadly, I got exactly the same 
output on both. This doesn't any sense to me.


$ /lib64/ld-linux-x86-64.so.2 --list 
bin/plugins/liborg_blueberry_core_expressions.so
bin/plugins/liborg_blueberry_core_expressions.so: error while loading 
shared libraries: liborg_blueberry_core_runtime.so: cannot open shared 
object file: No such file or directory


$ ldd -r bin/plugins/liborg_blueberry_core_expressions.so
bin/plugins/liborg_blueberry_core_expressions.so: 
/usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.12' not found 
(required by bin/plugins/liborg_blueberry_core_expressions.so)

    linux-vdso.so.1 (0x7ffdbfbf3000)
    libgtk3-nocsd.so.0 => /usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0 
(0x7fe317301000)

    liborg_blueberry_core_runtime.so => not found
    libCTKPluginFramework.so.0.1 => not found
    libCTKCore.so.0.1 => not found
    libmbilog.so => not found
    libPocoXML.so.60 => not found
    libPocoFoundation.so.60 => not found
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
(0x7fe3170e2000)
    libQt5Core.so.5 => /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 
(0x7fe316997000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 
(0x7fe31660e000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 
(0x7fe3163f6000)

    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fe316005000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fe315e01000)
    /lib64/ld-linux-x86-64.so.2 (0x7fe317768000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x7fe315be4000)
    libicui18n.so.60 => /usr/lib/x86_64-linux-gnu/libicui18n.so.60 
(0x7fe315743000)
    libicuuc.so.60 => /usr/lib/x86_64-linux-gnu/libicuuc.so.60 
(0x7fe31538c000)
    libdouble-conversion.so.1 => 
/usr/lib/x86_64-linux-gnu/libdouble-conversion.so.1 (0x7fe31517b000)
    libglib-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0 
(0x7fe314e64000)

    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fe314ac6000)
    libicudata.so.60 => /usr/lib/x86_64-linux-gnu/libicudata.so.60 
(0x7fe312f1d000)

    libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x7fe312cab000)
undefined symbol: _ZTIN5berry6ObjectE 
(bin/plugins/liborg_blueberry_core_expressions.so)

*... Around 110 lines of **undefined symbol ...
2 lines are somewhat different*
symbol qt_version_tag version Qt_5.12 not defined in file 
libQt5Core.so.5 with link time reference 
(bin/plugins/liborg_blueberry_core_expressions.so)
symbol _ZdlPvm version Qt_5 not defined in file libQt5Core.so.5 with 
link time reference (bin/plugins/liborg_blueberry_core_expressions.so)


Running the same commands while the application is running or after the 
application closes give the same results, except for the .so address 
(0x00...). With all those problems, I wonder how the application manages 
to start! How can an application starts with missing libraries and 
undefined symbols...


Nil

Le 2019-07-19 à 16:06, Sascha Zelzer a écrit :


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

Re: [mitk-users] Startup error: ctkPluginException on first run

[Nil Goyette]

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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Re: [mitk-users] Nifti2

[Nil Goyette]

Hi Peter,

No, I didn't check anything more than NiBabel and MITK. I thought you 
simply needed to fine-tune a reader but it looks more complex! Thank you 
for checking.


Nil Goyette

Le 2019-06-28 à 07:24, Neher, Peter a écrit :


In this case it's rather complicated to use vtk to read nifti2 since 
vtk has no real support for 4D images. Did you check if itk 5 is 
capable of loading nifti2?


Peter


*Von:* Nil Goyette 
*Gesendet:* Donnerstag, 27. Juni 2019 16:30
*An:* Neher, Peter; mitk-users@lists.sourceforge.net
*Betreff:* Re: AW: [mitk-users] Nifti2

Hi Peter,

All kind of images. In fact, I'm not entirelly sure, our users are 
starting to receive some Nifti2 images from their colleagues and it's 
not only related to diffusion. I know they're not using bval/bvec 
loading like we can see in MitkDiffusion. They are loading "normal" 3D 
and 4D images.


Nil

Le 2019-06-27 à 10:22, Neher, Peter a écrit :


Another question regarding your use case. Do you need this feature 
only for diffusion-weighted images or for all kinds of images?


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Re: [mitk-users] Nifti2

[Nil Goyette]

Hi Peter,

All kind of images. In fact, I'm not entirelly sure, our users are 
starting to receive some Nifti2 images from their colleagues and it's 
not only related to diffusion. I know they're not using bval/bvec 
loading like we can see in MitkDiffusion. They are loading "normal" 3D 
and 4D images.


Nil

Le 2019-06-27 à 10:22, Neher, Peter a écrit :


Another question regarding your use case. Do you need this feature 
only for diffusion-weighted images or for all kinds of images?


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[mitk-users] Startup error: ctkPluginException on first run

[Nil Goyette]

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] Not all plugins

[Nil Goyette]

Hi all,

How can I build the plugins I want without using MITK_BUILD_ALL_PLUGINS? 
Our in-house application requires more plugins, such as 
"org.blueberry.core.jobs", "org.mitk.core.jobs", 
"org.mitk.gui.qt.segmentation", etc.


I tried setting some to ":ON" in PluginList.cmake and adding some in 
Workbench/target_libraries.cmake, but visual studio wasn't compiling 
anything more. Maybe I just need to start from a clean build, but the 
question is worth asking anyway.


Nil Goyette



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[mitk-users] Nifti2

[Nil Goyette]

Hi all,

I tried opening a Nifti2 image in MITK 2018.04 and it seems I can't.

3526.53 core.mod.core.ioUtil ERROR: No reader available for 
'C:/Users/Nil/Desktop/nifti2.nii.gz'


I created my images with this python code

import numpy as np
import nibabel as nib

data = np.random.rand(4, 5, 6, 7).astype(np.float64)
affine = np.eye(4)

nib.save(nib.Nifti1Image(data, affine), 'nifti1.nii.gz')
nib.save(nib.Nifti2Image(data, affine), 'nifti2.nii.gz')

I know that VTK supports it since 6.2. Is it supposed to work?

Nil Goyette

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Re: [mitk-users] MITK 2018.04 beta

[Nil Goyette]

Hi Stefan, Matt,

I tested on another vm and on a Mac Mini. You're right, it works perfectly. I 
probably broke something. Shit happens. Thank you for taking the time to test.

Nil

Le 2018-10-17 à 03:36, Dinkelacker, Stefan a écrit :
Hi, I also tested on macOS High Sierra and Mojave now and it works for me. 
Stefan

From: Nil Goyette [mailto:nil.goye...@usherbrooke.ca]
Sent: Dienstag, 16. Oktober 2018 22:24
To: Dinkelacker, Stefan; 
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: AW: MITK 2018.04 beta


Hi Stefan

Thank you for your answer. It's a simple 3D image which I can open on Windows 
and Linux, nothing fancy. As I wrote, the problem is only on macOS [1], the 
other OS are perfectly able to load an image. If someone can actually test on 
macOS, it will confirm that I'm wrong/right.

I tried adding the --BlueBerry.clean flag and I have the same error. The only 
other problem I can think of is that it's a VirtualBox VM. It usually breaks 
the graphic a little, but not the behavior. I'll try finding a real mac to 
test, it may be the cause of the problem.

Nil

[1] 
http://mitk.org/download/releases/MITK-2018.04-beta/MITK-2018.04-beta-mac64.dmg

Le 2018-10-16 à 15:46, Dinkelacker, Stefan a écrit :

Hi Nil,



in the current head of the beta branch, fresh build, I can open each and every 
.nii.gz image in our MITK-Data repository (tested on Windows). Specializations 
like peak images, SH images, or diffusion weighted images are recognized as 
well and I can choose alternative readers for them. Also, all unit tests run 
successfully on Windows, Linux, and macOS.



Best,

Stefan



Von: Nil Goyette <mailto:nil.goye...@usherbrooke.ca>

Gesendet: Dienstag, 16. Oktober 2018 18:49

An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>

Betreff: [mitk-users] MITK 2018.04 beta



Hi all,



Seeing that I couldn't load a nii.gz image in my own app based on the

beta, I tested the official macOS beta release and it actually can't

load nii.gz image. "No reader available for ... .nii.gz" Can someone

please confirm? It's kind of a big deal if true :)



Nil Goyette



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Re: [mitk-users] MITK 2018.04 beta

[Nil Goyette]

Hi Stefan

Thank you for your answer. It's a simple 3D image which I can open on Windows 
and Linux, nothing fancy. As I wrote, the problem is only on macOS [1], the 
other OS are perfectly able to load an image. If someone can actually test on 
macOS, it will confirm that I'm wrong/right.

I tried adding the --BlueBerry.clean flag and I have the same error. The only 
other problem I can think of is that it's a VirtualBox VM. It usually breaks 
the graphic a little, but not the behavior. I'll try finding a real mac to 
test, it may be the cause of the problem.

Nil

[1] 
http://mitk.org/download/releases/MITK-2018.04-beta/MITK-2018.04-beta-mac64.dmg

Le 2018-10-16 à 15:46, Dinkelacker, Stefan a écrit :

Hi Nil,

in the current head of the beta branch, fresh build, I can open each and every 
.nii.gz image in our MITK-Data repository (tested on Windows). Specializations 
like peak images, SH images, or diffusion weighted images are recognized as 
well and I can choose alternative readers for them. Also, all unit tests run 
successfully on Windows, Linux, and macOS.

Best,
Stefan

Von: Nil Goyette <mailto:nil.goye...@usherbrooke.ca>
Gesendet: Dienstag, 16. Oktober 2018 18:49
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] MITK 2018.04 beta

Hi all,

Seeing that I couldn't load a nii.gz image in my own app based on the
beta, I tested the official macOS beta release and it actually can't
load nii.gz image. "No reader available for ... .nii.gz" Can someone
please confirm? It's kind of a big deal if true :)

Nil Goyette

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[mitk-users] MITK 2018.04 beta

[Nil Goyette]

Hi all,

Seeing that I couldn't load a nii.gz image in my own app based on the 
beta, I tested the official macOS beta release and it actually can't 
load nii.gz image. "No reader available for ... .nii.gz" Can someone 
please confirm? It's kind of a big deal if true :)

Nil Goyette

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Re: [mitk-users] OpenMP

[Nil Goyette]

Hi Peter,

Surprisingly I fixed it. In 3 easy steps :) I don't even know if all 
cores are used, but it does compile and start.


*Cherry-pick your 4 commits, fix conflicts*
0e19e394243f  Omp variable int and omp.h includes
82a46f59a410  Replace reduction by critical
3fc94be7814c  Add openmp dependency to AlgotihmsExt and MapperExt
75840ab56a34  Add openmp as external project

*Modify **MITK_OpenMP_Config.cmake**to look like
*

find_package(OpenMP REQUIRED)
if(OpenMP_CXX_FOUND)
    list(APPEND ALL_LIBRARIES ${OpenMP_CXX_LIBRARIES})
endif()

*Fix Classificaton/CLUtilities dependencies* and other simple ***clang * 
compilation errors

*Add "OpenMP|OpenMP_CXX".
*** We don't even use OpemMP there, but we use Eigen which uses OpenMP. 
I'm not sure what's the clean way to handle this. I just know that it 
fixes the problem.


My setup is:

 * macOS 10.13.6, XCode 10.0, Qt 5.11.1
 * brew install libomp cmake
 * cmake -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=OFF
   -DMITK_BUILD_ALL_PLUGINS:BOOL=ON -DMITK_USE_Vigra:BOOL=ON
   -DMITK_USE_MatchPoint:BOOL=ON -DGIT_EXECUTABLE:PATH=/usr/bin/git ..

I will test "port install libomp" and/or "libomp-devel" in the next days 
because I'm not really a homebrew user. I'll keep you updated.


Nil Goyette

Le 2018-10-09 à 13:40, Neher, Peter a écrit :
This is where I'm stuck. Didn't have the time to investigate further 
since I'm out of office for a while.


Peter

Am 09.10.2018 15:42 schrieb Nil Goyette :

Hi Peter,

What do you mean by "unsuccessful until now"? I tested
T25191-v2018.04-beta, cherry-picking your 4 OpenMP commits and it's
still unsuccessful. I have a list of undefined symbols, for example
Undefined symbols for architecture x86_64:
   "___kmpc_critical", referenced from:
   _.omp_outlined..8 in mitkWeightedPointTransform.cpp

Is this where you're stuck at? Or were you successful?

Nil Goyette

Le 2018-10-03 à 09:08, Neher, Peter a écrit :
> Hi Nil,
>
> The trick is that we do not build MITK Diffusion for Mac, which
is admittedly a rather poor solution. Apple Clang does not ship
with openmp anymore. The branch you mentioned was a first try to
fix this following this solution:
https://iscinumpy.gitlab.io/post/omp-on-high-sierra/
> Unfortunately unsuccessful until now. Feel free to check it out
though. Since we don't have a mac developer working with
diffusion, this issue is not well covered on our side.
>
> Peter
>
> -Ursprüngliche Nachricht-
> Von: Nil Goyette 
> Gesendet: Mittwoch, 3. Oktober 2018 14:56
> An: mitk-users@lists.sourceforge.net; Neher, Peter

> Betreff: OpenMP
>
> Hi all, Peter,
>
> I'm trying to build MITK beta on macOS (all tools
installed/upgraded with mac port) and it's failing in the
DiffusionImaging module because of OpenMP.
>
>

.../Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp:21:10:
fatal error: 'omp.h' file not found #include 
>    ^~~
>
> What's the trick? Do you use a special flag? Does the T25420-Omp
[1] branch fix this?
>
> Nil
>
>
> [1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/
>




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Re: [mitk-users] OpenMP

[Nil Goyette]

Hi Peter,

What do you mean by "unsuccessful until now"? I tested 
T25191-v2018.04-beta, cherry-picking your 4 OpenMP commits and it's 
still unsuccessful. I have a list of undefined symbols, for example

Undefined symbols for architecture x86_64:
  "___kmpc_critical", referenced from:
  _.omp_outlined..8 in mitkWeightedPointTransform.cpp

Is this where you're stuck at? Or were you successful?

Nil Goyette

Le 2018-10-03 à 09:08, Neher, Peter a écrit :

Hi Nil,

The trick is that we do not build MITK Diffusion for Mac, which is admittedly a 
rather poor solution. Apple Clang does not ship with openmp anymore. The branch 
you mentioned was a first try to fix this following this solution: 
https://iscinumpy.gitlab.io/post/omp-on-high-sierra/
Unfortunately unsuccessful until now. Feel free to check it out though. Since 
we don't have a mac developer working with diffusion, this issue is not well 
covered on our side.

Peter

-Ursprüngliche Nachricht-----
Von: Nil Goyette 
Gesendet: Mittwoch, 3. Oktober 2018 14:56
An: mitk-users@lists.sourceforge.net; Neher, Peter 
Betreff: OpenMP

Hi all, Peter,

I'm trying to build MITK beta on macOS (all tools installed/upgraded with mac 
port) and it's failing in the DiffusionImaging module because of OpenMP.

.../Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp:21:10:
 fatal error: 'omp.h' file not found #include 
   ^~~

What's the trick? Do you use a special flag? Does the T25420-Omp [1] branch fix 
this?

Nil


[1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/





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[mitk-users] OpenMP

[Nil Goyette]

Hi all, Peter,

I'm trying to build MITK beta on macOS (all tools installed/upgraded 
with mac port) and it's failing in the DiffusionImaging module because 
of OpenMP.


.../Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp:21:10:
 fatal error: 'omp.h' file not found
#include 
 ^~~

What's the trick? Do you use a special flag? Does the T25420-Omp [1] 
branch fix this?


Nil


[1] https://phabricator.mitk.org/source/mitk/browse/T25420-Omp/



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Re: [mitk-users] Warnings treated as errors in tests

[Nil Goyette]

Hi Stefan,

Yeah, of course there's a warning, and I will post it :) However, I was 
surprised that my project compiles in Release and not in Debug. I 
thought that maybe there was a config error in MITK's cmake files. Debug 
and release should both use the same warning flags by default, no?


Sorry, there's a lot of french in the output.
7>-- Début de la génération : Projet : 
ImekaBoundingObjectTestDriver, Configuration : Debug x64 --

7>BoundingObjectTest.cpp
7>c:\program files (x86)\microsoft visual 
studio\2017\community\vc\tools\msvc\14.14.26428\include\xutility(2483): 
error C2220: avertissement considéré comme une erreur - aucun fichier 
'object' généré
7>c:\program files (x86)\microsoft visual 
studio\2017\community\vc\tools\msvc\14.14.26428\include\xutility(2483): 
warning C4996: 'std::copy::_Unchecked_iterators::_Deprecate': Call to 
'std::copy' with parameters that may be unsafe - this call relies on the 
caller to check that the passed values are correct. To disable this 
warning, use -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use 
Visual C++ 'Checked Iterators'
7>c:\program files (x86)\microsoft visual 
studio\2017\community\vc\tools\msvc\14.14.26428\include\xutility(2483): 
note: voir la déclaration de 'std::copy::_Unchecked_iterators::_Deprecate'
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itktransform.hxx(529): note: 
voir la référence à l'instanciation de la fonction modèle '_OutIt 
std::copy(_InIt,_InIt,_OutIt)' en cours de compilation

7>    with
7>    [
7>    _OutIt=double *,
7>    T=double,
7>    _InIt=const double *
7>    ]
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itktransform.hxx(524): note: 
pendant la compilation de la fonction membre '' (classe )
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itkmatrixoffsettransformbase.h(101): 
note: voir la référence à l'instanciation de classe modèle 
'itk::Transform' en cours de compilation

7>    with
7>    [
7>    TParametersValueType=mitk::ScalarType
7>    ]
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itkaffinetransform.h(104): 
note: voir la référence à l'instanciation de classe modèle 
'itk::MatrixOffsetTransformBase' en cours de 
compilation

7>    with
7>    [
7>    TParametersValueType=mitk::ScalarType
7>    ]
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itkscalableaffinetransform.h(38): 
note: voir la référence à l'instanciation de classe modèle 
'itk::AffineTransform' en cours de compilation

7>    with
7>    [
7>    TParametersValueType=mitk::ScalarType
7>    ]
7>d:\imeka\mitk_2018.04\ep\include\itk-4.13\itkaffinegeometryframe.h(112): 
note: voir la référence à l'instanciation de classe modèle 
'itk::ScalableAffineTransform' en cours de compilation

7>    with
7>    [
7>    TScalar=mitk::ScalarType
7>    ]
7>c:\imeka\mitk\mitk2018.04\modules\core\include\mitkaffinetransform3d.h(25): 
note: voir la référence à l'instanciation de classe modèle 
'itk::AffineGeometryFrame' en cours de compilation
7>Génération du projet "ImekaBoundingObjectTestDriver.vcxproj" terminée 
-- ÉCHEC.


Nil Goyette

Le 2018-09-26 à 15:53, Dinkelacker, Stefan a écrit :

Hi, if there's a C2220, there's also at least one warning that triggered the 
error. So it would help to post it, too. :-) Stefan

Von: Nil Goyette 
Gesendet: Dienstag, 25. September 2018 19:18
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Warnings treated as errors in tests

Hi all,

When building my app that uses MITK master on VS2017, I get the "C2220
error" only in Debug and only in a test module. There's no problem in
Release. As you may know, this error means that the "warnings are
treated as errors" and there was at least one warning. To get it to
compile, I must Right click on my module - Properties - C/C++ - General
- Warning level - Consider warnings as errors - No (/WX-).

Since it compiles in Release, I'm not sure what to do. Do you guys know
how to fix this?

Nil



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[mitk-users] master or beta

[Nil Goyette]

Hi all,

I've been working on the MITK 2018.04 version of our application in the 
last month and I think I made a bad decision. I'm using your master 
branch, modifying some small part of your code, pulling each week to get 
the new stuff, etc. Of course, I was bitten by the "floca" "First fix" 
commit. And by a "include omp.h" that doesn't compile on macOS. Etc.


My question is, should I use ONLY the beta (T25191-v2018.04-beta, 
right?) branch? Will this branch become the official release? Or is it 
the master branch?


Nil Goyette



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[mitk-users] Warnings treated as errors in tests

[Nil Goyette]

Hi all,

When building my app that uses MITK master on VS2017, I get the "C2220 
error" only in Debug and only in a test module. There's no problem in 
Release. As you may know, this error means that the "warnings are 
treated as errors" and there was at least one warning. To get it to 
compile, I must Right click on my module - Properties - C/C++ - General 
- Warning level - Consider warnings as errors - No (/WX-).


Since it compiles in Release, I'm not sure what to do. Do you guys know 
how to fix this?


Nil



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Re: [mitk-users] 3D interactor

[Nil Goyette]

Hi Daniel.

Thank you for your answer. I started reading the Gizmo code friday and 
it does most of what I need! The translation is working as intended. I'm 
still working on the scaling and rotation, but overall your code is 
really helpful!


Nil

Le 2018-09-24 à 04:44, Daniel Maleike a écrit :

Hi Nil,

There was a very simple on/off context menu entry implemented for the gizmo 
object but we did not include that in Data Manager in hope of a better UI. If 
you want to try the simple version in your applicaiton, you can have a look at 
a Data Manager modification of mine at

https://github.com/maleike/MITK/commit/e5461f280915eb1291826c2b033ff646f17b3b20#diff-6bc302362095be409143a5f4951eee71

and

https://github.com/maleike/MITK/commit/b67e1d0591d282fd3a32a79283fbed2afdbaaff8#diff-6bc302362095be409143a5f4951eee71

When trying this code you might want to compare the latest branch version of 
QmitkDataManagerView.cpp and the Gizmo module against your version, I might 
have missed a more recent commit.

More importantly (perhaps Stefan was refering to this): the code that 
implements the gizmo deals with exactly what you described: it reacts on 3D 
window interaction, reads perspective information from the VTK camera, inspects 
a selected BaseData object's axes, calculates an axis of movement and then 
moves the object along that axis. You might need to write your own specific 
kind of interaction, but you might find helpful snippets of code in Gizmo.

Kind regards,
Daniel Maleike



Nil Goyette  hat am 19. September 2018 um 19:29 
geschrieben:


Hi Stefan,


I wasn't aware of this module, thanks for telling me. This being said,
if it looks like the images in https://phabricator.mitk.org/T19489, I
can't use it. My users do not like this new way of interacting. I didn't
test it though so I don't know if it behaves like I want it to behave.
Is there a plugin in the workbench where I can use it?


Nil


Le 2018-09-19 à 02:53, Dinkelacker, Stefan a écrit :

Hi Nil,


did you already have a look into the Gizmo module. It contains a
dedicated interactor for moving and rotating objects of all kinds and
also comes with a visual cursor that has handles and control the type
of movement/rotation. It was contributed by Daniel Maleike, who has
more information about it if you have in-depth questions.


Best,

Stefan


*Von:* Nil Goyette 
*Gesendet:* Dienstag, 18. September 2018 17:00
*An:* mitk-users@lists.sourceforge.net
*Betreff:* [mitk-users] 3D interactor

Hi all,

I'm using the AffineImageCropperInteractor class and there's one
behavior I want to change.

   * When I rotate in the 3D view then move an object, it follows the
 slope of the image's slice.
   * When I pass in front of a group of streamlines (list of lines in
 3D, in a polydata), the object flickers because it's moved from
 the background to the streamline, background again to another
 streamline, etc.
   * When I move an object in the 3D view and I traverse an axis'
 border, the object is suddenly huge because it was moved just
 above the border.

Can I make the Interactor "stupid"/unaware of any object? I want it to
act as if there was nothing. In fact, I want it to behave like in the
2D views: simply moving parallel to the cameras. Is there a way to do
this without modifying MITK's code? If not, can you please tell me
what I should try? I already tried modifying
mitk::VtkPropRenderer::PickWorldPoint but I have weird memory crashes
so I prefer asking!

Nil Goyette

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Re: [mitk-users] CTK fails at qRestAPI

[Nil Goyette]

Hi Peter,

I confirm that *-DGIT_EXECUTABLE:PATH=/usr/bin/git* solves this problem. 
Thank you.


Nil

Le 2018-09-20 à 01:59, Neher, Peter a écrit :

I had the same issue on all nightly clients (windows & linux). I had to set the 
git variable for the superbuild manually. But then it was correctly handed down to 
the CTK and qRestApi build. Occurred after we switched from downloading the 
qRestApi tarball to the direct git clone.

Peter

-Ursprüngliche Nachricht-
Von: Dinkelacker, Stefan 
Gesendet: Mittwoch, 19. September 2018 22:35
An: Nil Goyette ; mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] CTK fails at qRestAPI

Hi, we can't reproduce your issue on any of our Linux dart clients. So I just 
can assume that it is a local configuration quirk of your machine. AFAIK CMake 
has a FindGit module, you could try to add a respective find_package() call to 
the CMake script and see if it finds Git. Best, Stefan 

Von: Nil Goyette 
Gesendet: Mittwoch, 19. September 2018 22:04
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] CTK fails at qRestAPI

Hi all,

I'm trying to build a slightly modified version of MITK master and it fails at 
when trying to clone qRestAPI. It fails with Xenial and Bionic but it works on 
Windows. I use Qt 5.11.1 and cmake 3.11.4. I enable Vigra, MatchPoint and 
BuildAllPlugins.

[ 17%] Performing configure step for 'CTK'
loading initial cache file
/home/nil/Imeka/MITK/MITK-build/ep/tmp/CTK-cache-Release.cmake
-- Checking to see if CXX compiler accepts flag -fvisibility=hidden
-- Checking to see if CXX compiler accepts flag -fvisibility=hidden - yes
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep.txt
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep-withext.txt
-- Generated:
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput.txt
-- SuperBuild - First pass
-- SuperBuild - First pass - done
-- SuperBuild - Log4Qt[OPTIONAL]
-- SuperBuild - VTK[OPTIONAL]
-- SuperBuild - PythonQt[OPTIONAL]
-- SuperBuild - ZMQ[OPTIONAL]
-- SuperBuild - QtSOAP[OPTIONAL]
-- SuperBuild - qxmlrpc[OPTIONAL]
-- SuperBuild - OpenIGTLink[OPTIONAL]
-- SuperBuild - ITK[OPTIONAL]
-- SuperBuild - QtTesting[OPTIONAL]
-- SuperBuild - CTK => Requires DCMTK, qRestAPI,
-- SuperBuild -   DCMTK[OK]
-- SuperBuild -   qRestAPI[OK]
CMake Error at
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:2324
(message):
error: could not find git for clone of qRestAPI Call Stack (most recent 
call first):
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:3100
(_ep_add_download_command)
CMakeExternals/qRestAPI.cmake:60 (ExternalProject_Add)
CMake/ctkMacroCheckExternalProjectDependency.cmake:795 (include)
CMake/ctkMacroCheckExternalProjectDependency.cmake:858
(ExternalProject_Include_Dependencies)
CMake/ctkBlockCheckDependencies.cmake:134
(ExternalProject_Include_Dependencies)
CMakeLists.txt:974 (include)

I can't find much on Internet concerning this error. I know 'git' is in my 
PATH. I added my ssh key to ssh-agent and to my github account. I'm not sure 
what else to test. Have you seen this error?

Nil
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[mitk-users] CTK fails at qRestAPI

[Nil Goyette]

Hi all,

I'm trying to build a slightly modified version of MITK master and it 
fails at when trying to clone qRestAPI. It fails with Xenial and Bionic 
but it works on Windows. I use Qt 5.11.1 and cmake 3.11.4. I enable 
Vigra, MatchPoint and BuildAllPlugins.


[ 17%] Performing configure step for 'CTK'
loading initial cache file 
/home/nil/Imeka/MITK/MITK-build/ep/tmp/CTK-cache-Release.cmake

-- Checking to see if CXX compiler accepts flag -fvisibility=hidden
-- Checking to see if CXX compiler accepts flag -fvisibility=hidden - yes
-- Generated: 
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep.txt
-- Generated: 
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput-alldep-withext.txt
-- Generated: 
/home/nil/Imeka/MITK/MITK-build/ep/src/CTK-build/DGraphInput.txt

-- SuperBuild - First pass
-- SuperBuild - First pass - done
-- SuperBuild - Log4Qt[OPTIONAL]
-- SuperBuild - VTK[OPTIONAL]
-- SuperBuild - PythonQt[OPTIONAL]
-- SuperBuild - ZMQ[OPTIONAL]
-- SuperBuild - QtSOAP[OPTIONAL]
-- SuperBuild - qxmlrpc[OPTIONAL]
-- SuperBuild - OpenIGTLink[OPTIONAL]
-- SuperBuild - ITK[OPTIONAL]
-- SuperBuild - QtTesting[OPTIONAL]
-- SuperBuild - CTK => Requires DCMTK, qRestAPI,
-- SuperBuild -   DCMTK[OK]
-- SuperBuild -   qRestAPI[OK]
CMake Error at 
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:2324 
(message):

  error: could not find git for clone of qRestAPI
Call Stack (most recent call first):
/home/nil/tools/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/ExternalProject.cmake:3100 
(_ep_add_download_command)

  CMakeExternals/qRestAPI.cmake:60 (ExternalProject_Add)
  CMake/ctkMacroCheckExternalProjectDependency.cmake:795 (include)
  CMake/ctkMacroCheckExternalProjectDependency.cmake:858 
(ExternalProject_Include_Dependencies)
  CMake/ctkBlockCheckDependencies.cmake:134 
(ExternalProject_Include_Dependencies)

  CMakeLists.txt:974 (include)

I can't find much on Internet concerning this error. I know 'git' is in 
my PATH. I added my ssh key to ssh-agent and to my github account. I'm 
not sure what else to test. Have you seen this error?


Nil



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Re: [mitk-users] 3D interactor

[Nil Goyette]

Hi Stefan,


I wasn't aware of this module, thanks for telling me. This being said, 
if it looks like the images in https://phabricator.mitk.org/T19489, I 
can't use it. My users do not like this new way of interacting. I didn't 
test it though so I don't know if it behaves like I want it to behave. 
Is there a plugin in the workbench where I can use it?



Nil


Le 2018-09-19 à 02:53, Dinkelacker, Stefan a écrit :


Hi Nil,


did you already have a look into the Gizmo module. It contains a 
dedicated interactor for moving and rotating objects of all kinds and 
also comes with a visual cursor that has handles and control the type 
of movement/rotation. It was contributed by Daniel Maleike, who has 
more information about it if you have in-depth questions.



Best,

Stefan


*Von:* Nil Goyette 
*Gesendet:* Dienstag, 18. September 2018 17:00
*An:* mitk-users@lists.sourceforge.net
*Betreff:* [mitk-users] 3D interactor

Hi all,

I'm using the AffineImageCropperInteractor class and there's one 
behavior I want to change.


  * When I rotate in the 3D view then move an object, it follows the
slope of the image's slice.
  * When I pass in front of a group of streamlines (list of lines in
3D, in a polydata), the object flickers because it's moved from
the background to the streamline, background again to another
streamline, etc.
  * When I move an object in the 3D view and I traverse an axis'
border, the object is suddenly huge because it was moved just
above the border.

Can I make the Interactor "stupid"/unaware of any object? I want it to 
act as if there was nothing. In fact, I want it to behave like in the 
2D views: simply moving parallel to the cameras. Is there a way to do 
this without modifying MITK's code? If not, can you please tell me 
what I should try? I already tried modifying 
mitk::VtkPropRenderer::PickWorldPoint but I have weird memory crashes 
so I prefer asking!


Nil Goyette


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[mitk-users] 3D interactor

[Nil Goyette]

Hi all,

I'm using the AffineImageCropperInteractor class and there's one 
behavior I want to change.


 * When I rotate in the 3D view then move an object, it follows the
   slope of the image's slice.
 * When I pass in front of a group of streamlines (list of lines in 3D,
   in a polydata), the object flickers because it's moved from the
   background to the streamline, background again to another
   streamline, etc.
 * When I move an object in the 3D view and I traverse an axis' border,
   the object is suddenly huge because it was moved just above the border.

Can I make the Interactor "stupid"/unaware of any object? I want it to 
act as if there was nothing. In fact, I want it to behave like in the 2D 
views: simply moving parallel to the cameras. Is there a way to do this 
without modifying MITK's code? If not, can you please tell me what I 
should try? I already tried modifying 
mitk::VtkPropRenderer::PickWorldPoint but I have weird memory crashes so 
I prefer asking!


Nil Goyette
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Re: [mitk-users] VS2015 toolchain

[Nil Goyette]

Hi Stefan,

Thank you for you answer. Yes, I tested 2018.04 on VS2015 and VS2017 and 
it does compile and work on both versions. In fact, this is exactly why 
I ask: I would prefer keeping only one version of VS.


I'm aware that there's some problems if we use a unsupported version of 
VS, but isn't it the point of a toolchain? TBH, it's the first time I 
hear about VS toolchains so it's not entirely clear to me what they can 
do. I thought that I could use a single VS version (2017) to build:


 * 2016.11 using VS2015 toolchain
 * 2018.04 using the latest VS2017 toolchain

Are you telling me I can't?

Nil

Le 2018-05-09 à 06:00, Dinkelacker, Stefan a écrit :

Hi,

support for VS2017 was introduced after the 2016.11 release and AFAIR we had to 
upgrade some external dependencies and adapt our code. So this will not work 
out of box with 2016.11. However, we're working with VS 2017 over a year now 
and it works well even with the upgrades of VS 2017, tested up to v15.6. The 
upcoming 2018.04 release will fully support VS 2015 and 2017.

Best,
Stefan

-Original Message-
From: Nil Goyette [mailto:nil.goye...@imeka.ca]
Sent: Dienstag, 8. Mai 2018 18:04
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] VS2015 toolchain

Hi all,

Last year I installed VS2017 to test compiliing MITK 2016.11; it failed
(as it should) and it broke my VS2015 for some reasons. I want to test
again but I don't want the same problem to happen. Did someone test
compiling MITK 2016.11 on VS2017 with the 2015 toolchain? Did it work?
Did you need to change a config/property somewhere?

Nil
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[mitk-users] VS2015 toolchain

[Nil Goyette]

Hi all,

Last year I installed VS2017 to test compiliing MITK 2016.11; it failed 
(as it should) and it broke my VS2015 for some reasons. I want to test 
again but I don't want the same problem to happen. Did someone test 
compiling MITK 2016.11 on VS2017 with the 2015 toolchain? Did it work? 
Did you need to change a config/property somewhere?


Nil


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[mitk-users] Diffusion C++11

[Nil Goyette]

Hi Peter, all,

Just to warn you that the DiffusionImaging module on master can't be 
compiled anymore since about 1 week. All the errors I can see are in

DiffusionImaging\FiberTracking\cmdapps\Fiberfox\FiberfoxOptimization.cpp
and thy are all related to the "new" C++11 random features.

Is it my job to add C++11 in my cmake config or it's your job in the 
cmakelist?


Nil


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Re: [mitk-users] Linux icon

[Nil Goyette]

Hi Sascha,

I'm talking about the icon in the taskbar (vertical in Unity, horizontal 
on most other). When I open the Workbench, I can see the blue "M" icon 
on a white background. When I open my app, it's a default icon choosen 
by the OS. Only on Linux.


Anyway, while writing this message, I searched more and fixed the 
problem :) Turns out that the advisor->SetWindowIcon line was commented 
in my WorkbenchAdvisor, probably by myself months ago, when I realized 
that it was doing "nothing". I was wrong.


Thank you for your time.

Nil

Le 2017-07-05 à 13:41, Sascha Zelzer a écrit :

Hi,

what icon location are we talking about? If it is the icon in the 
window decoration, this is set via some Qt API, if I remember 
correctly, and should work on all three platforms.


If it is about the icon in some desktop environment menu or shortcut, 
there is no "desktop entry file" provided with MITK AFAIK (for 
Windows, there is an embedded .ico file in the executable itself and 
on MacOS there should be a Info.plist file in the application bundle).


- Sascha


On 07/05/2017 05:16 PM, Nil Goyette wrote:

Hi all,

We found that there's no icon in our linux executable. There's one on 
Windows and OS X but on Linux it's a "?" or a black square with a 
"forbidden" red circle. I searched in the cmake file but there's 
strangely not much about icons and there's no ".desktop" file so the 
icon is probably set in Qt somewhere. Do you know who are the usual 
suspects for a missing icon? Where should I check?


Nil


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[mitk-users] Linux icon

[Nil Goyette]

Hi all,

We found that there's no icon in our linux executable. There's one on 
Windows and OS X but on Linux it's a "?" or a black square with a 
"forbidden" red circle. I searched in the cmake file but there's 
strangely not much about icons and there's no ".desktop" file so the 
icon is probably set in Qt somewhere. Do you know who are the usual 
suspects for a missing icon? Where should I check?


Nil


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Re: [mitk-users] Special reinit

[Nil Goyette]

Hi,

I tested PlanePositionManagerService and the results are still wrong. 
The rotation is kept but the offset and bounds are also kept, which lock 
the 2D views on the first loaded object. This seems normal because the 
width and height are saved in the object.


While testing, I found that method: 
mitk::SliceNavigationController::ReorientSlices, taking the plane's 
normal or 2 vectors. If I save the normal before updating the plane, 
update the plane and call ReorientSlices(normal), wouldn't that work? I 
can't test it right now but it looks like it could pay off.


Nil

Le 2017-07-04 à 04:00, Dinkelacker, Stefan a écrit :


Hi,

Maybe the way the Position node stuff of the 3D-interpolation [1] is a 
good hint for that. For each drawn contour it generates a PlanarCircle 
as helper object. When clicking on one of these nodes, the according 
plane is adjusted to be able to continue the contour.


Best,
Stefan

[1] 
https://github.com/MITK/MITK/blob/master/Modules/Segmentation/Interactions/mitkSegTool2D.cpp#L465-L521


*From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
*Sent:* Montag, 3. Juli 2017 17:41
*To:* Dinkelacker, Stefan; mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] Special reinit

Hi Stefan, hi all,

Anyone can help me with this? Here's a better explanation of what I 
need. Lets say:
1) I load a small object, place the scene as I like (zoom, rotate 3D 
and axes, etc.) http://i.imgur.com/MBHAqza.png
2) I load a second object: the reference image. 
http://i.imgur.com/Gy93a3a.png <http://i.imgur.com/Gy93a3a.png> This 
screenshot was taken just before the automatic reinit in 
RenderingManager::InitializeViews (using a breakpoint).


In the last screenshot, my goal would be to leave the planes 
untouched, except for the bounds. I should be able to see the image in 
the sagittal/coronal planes and I should to be able to see the image 
*if* I zoom back. I know it's not currently possible in MITK. I'm 
asking how to do it in the code. I tried some things but it always 
produce horrors like [3] in my previous message. Any ideas how I can 
achieve that?


Nil

Le 2017-06-21 à 09:09, Nil Goyette a écrit :

Hi Stefan,

Thank you for your answer. I'm working in
InitializeViewsByBoundingObjects and InitializeViews, so I'm aware
of this method. If I understand correctly, it returns a geometry
with orthogonal planes (reinited, reseted?). I would gladly use
the offset/bounds of this geometry but I also want to *keep the
rotation* of the planes.

In fact, that's what I tried to do in the snippet below.
timeGeometry IS the result of
ds->ComputeBoundingGeometry3D(ds->GetAll());.

Nil

Le 2017-06-21 à 03:44, Dinkelacker, Stefan a écrit :

Hi,

if you want to recompute the bounding box of the scene, 
mitk::DataStorage has a method for this purpose:

   mitk::TimeGeometry::Pointer geo = 
ds->ComputeBoundingGeometry3D(ds->GetAll());

Best,

Stefan

____

    Von: Nil Goyette<nil.goye...@imeka.ca> <mailto:nil.goye...@imeka.ca>

Gesendet: Dienstag, 20. Juni 2017 17:24

An:mitk-users@lists.sourceforge.net
<mailto:mitk-users@lists.sourceforge.net>

Betreff: [mitk-users] Special reinit

Hi all,

Lets start by saying that I know "Reinit" is not the right choice of

word in this case! A reinit would reset the axis, as it should. Lets

say, for the sake of the discussion, that I want a reinit that simply

update the scene's bounding box, nothing else, like  [1] to [2] (made by

hand, so not exact!):

- No camera modification, so everything is still at the same place

- Keep the axis rotated if they were

- Resize the scene if an object was added/deleted

I tried adding this snippet in RenderingManager::InitializeViews. In

clear english: reuse the old geometry for the current plane, but update

it with the new offset and bounds that we just calculated.

auto newGeo = timeGeometry->GetGeometryForTimeStep(0);

auto oldTimeGeo = nc->GetCreatedWorldGeometry();

auto oldGeo = oldTimeGeo->GetGeometryForTimeStep(0);

oldGeo->GetIndexToWorldTransform()->SetOffset(

newGeo->GetIndexToWorldTransform()->GetOffset());

oldGeo->SetBounds(newGeo->GetBounds());

nc->SendCreatedWorldGeometryUpdate();

nc->SetInputWorldTimeGeometry(oldTimeGeo);

nc->Update();

...

This doesn't work; it throws the planes in strange places [3], probably

because I broke their affine matrix. I tried many things but my biggest

success was to remove the call to SetInputWorldTimeGeometry [4]. I

checked in DisplayInteractor::Rotate to see if there was a way to find

the old rotation app

Re: [mitk-users] Special reinit

[Nil Goyette]

Hi Stefan, hi all,

Anyone can help me with this? Here's a better explanation of what I 
need. Lets say:
1) I load a small object, place the scene as I like (zoom, rotate 3D and 
axes, etc.) http://i.imgur.com/MBHAqza.png
2) I load a second object: the reference image. 
http://i.imgur.com/Gy93a3a.png This screenshot was taken just before the 
automatic reinit in RenderingManager::InitializeViews (using a breakpoint).


In the last screenshot, my goal would be to leave the planes untouched, 
except for the bounds. I should be able to see the image in the 
sagittal/coronal planes and I should to be able to see the image *if* I 
zoom back. I know it's not currently possible in MITK. I'm asking how to 
do it in the code. I tried some things but it always produce horrors 
like [3] in my previous message. Any ideas how I can achieve that?


Nil

Le 2017-06-21 à 09:09, Nil Goyette a écrit :


Hi Stefan,

Thank you for your answer. I'm working in 
InitializeViewsByBoundingObjects and InitializeViews, so I'm aware of 
this method. If I understand correctly, it returns a geometry with 
orthogonal planes (reinited, reseted?). I would gladly use the 
offset/bounds of this geometry but I also want to *keep the rotation* 
of the planes.


In fact, that's what I tried to do in the snippet below. timeGeometry 
IS the result of ds->ComputeBoundingGeometry3D(ds->GetAll());.


Nil

Le 2017-06-21 à 03:44, Dinkelacker, Stefan a écrit :

Hi,

if you want to recompute the bounding box of the scene, mitk::DataStorage has a 
method for this purpose:

   mitk::TimeGeometry::Pointer geo = 
ds->ComputeBoundingGeometry3D(ds->GetAll());

Best,
Stefan
________
Von: Nil Goyette<nil.goye...@imeka.ca>
Gesendet: Dienstag, 20. Juni 2017 17:24
An:mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Special reinit

Hi all,

Lets start by saying that I know "Reinit" is not the right choice of
word in this case! A reinit would reset the axis, as it should. Lets
say, for the sake of the discussion, that I want a reinit that simply
update the scene's bounding box, nothing else, like  [1] to [2] (made by
hand, so not exact!):
- No camera modification, so everything is still at the same place
- Keep the axis rotated if they were
- Resize the scene if an object was added/deleted

I tried adding this snippet in RenderingManager::InitializeViews. In
clear english: reuse the old geometry for the current plane, but update
it with the new offset and bounds that we just calculated.

auto newGeo = timeGeometry->GetGeometryForTimeStep(0);
auto oldTimeGeo = nc->GetCreatedWorldGeometry();
auto oldGeo = oldTimeGeo->GetGeometryForTimeStep(0);

oldGeo->GetIndexToWorldTransform()->SetOffset(
newGeo->GetIndexToWorldTransform()->GetOffset());
oldGeo->SetBounds(newGeo->GetBounds());

nc->SendCreatedWorldGeometryUpdate();

nc->SetInputWorldTimeGeometry(oldTimeGeo);
nc->Update();
...

This doesn't work; it throws the planes in strange places [3], probably
because I broke their affine matrix. I tried many things but my biggest
success was to remove the call to SetInputWorldTimeGeometry [4]. I
checked in DisplayInteractor::Rotate to see if there was a way to find
the old rotation applied to the plane but it doesn't seem to be possible.

Anyway, I'm mostly wondering how YOU, the mitk experts :), would do it.
Thank you for your time.

Nil

[1]http://i.imgur.com/krzBvJV.png
[2]http://i.imgur.com/NWDQQqg.png
[3]http://i.imgur.com/7wwWczy.png
[4]http://i.imgur.com/m9jwrpE.png



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Re: [mitk-users] Segmentation shift

[Nil Goyette]

Hi Stefan,

Ouch, I now have second thoughts on fixing this! No, seriously, I'll try 
it anyway but I do start with a less-than-positive attitude ;) I'm not 
sure it's the same bug though. The visual is different. I can reinit 
then rotate the axis as much as I want and it's ok. If I do a Global 
Reinit though, I do have the bug.


I checked in PaintbrushTool::MouseMoved, there's this snippet which 
surprised me:


Point3D worldCoordinates = positionEvent->GetPositionInWorld();
Point3D indexCoordinates;
m_WorkingSlice->GetGeometry()->WorldToIndex(worldCoordinates, 
indexCoordinates);

MITK_DEBUG << "Mouse at W " << worldCoordinates << std::endl;
MITK_DEBUG << "Mouse at I " << indexCoordinates << std::endl;

*Reinited or not*, the world coordinates are always what I think they 
will be, but the index coordinates look totally random. One of the index 
is ~0.0 because it's a plane but the 2 others... I thought it would be 
the same data as in my status bar "Position: <>; Index: <>" but it's 
not, far from it. Should the indices be the equal? Where are these 
"random" indices coming from?


Nil

Le 2017-06-21 à 03:40, Dinkelacker, Stefan a écrit :

Hi,

this may also have something to do with [1]? Make sure to click on "Show older 
changes" to see all the comments and example images/animations.

Best,
Stefan

[1] https://phabricator.mitk.org/T18776

Von: Nil Goyette <nil.goye...@imeka.ca>
Gesendet: Dienstag, 20. Juni 2017 20:04
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Segmentation shift

Hi all,

My boss asked me to let the users decide if they want to reinit or not.
They will live with the consequence of not being aligned if they don't.
Of course I found this http://i.imgur.com/GKGKwmV.png I know this is a
well-known bug and it has been repaired in
https://phabricator.mitk.org/T22619 but I have a question about this bug.

Does anyone know why there's a shift and/or how it could be repaired? I
mean, without a reinit, of course. I plan to fix it myself and it would
help me if someone gives me some hints. Thank you for your time.

Nil
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Re: [mitk-users] Special reinit

[Nil Goyette]

Hi Stefan,

Thank you for your answer. I'm working in 
InitializeViewsByBoundingObjects and InitializeViews, so I'm aware of 
this method. If I understand correctly, it returns a geometry with 
orthogonal planes (reinited, reseted?). I would gladly use the 
offset/bounds of this geometry but I also want to *keep the rotation* of 
the planes.


In fact, that's what I tried to do in the snippet below. timeGeometry IS 
the result of ds->ComputeBoundingGeometry3D(ds->GetAll());.


Nil

Le 2017-06-21 à 03:44, Dinkelacker, Stefan a écrit :

Hi,

if you want to recompute the bounding box of the scene, mitk::DataStorage has a 
method for this purpose:

   mitk::TimeGeometry::Pointer geo = 
ds->ComputeBoundingGeometry3D(ds->GetAll());

Best,
Stefan
________
Von: Nil Goyette <nil.goye...@imeka.ca>
Gesendet: Dienstag, 20. Juni 2017 17:24
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Special reinit

Hi all,

Lets start by saying that I know "Reinit" is not the right choice of
word in this case! A reinit would reset the axis, as it should. Lets
say, for the sake of the discussion, that I want a reinit that simply
update the scene's bounding box, nothing else, like  [1] to [2] (made by
hand, so not exact!):
- No camera modification, so everything is still at the same place
- Keep the axis rotated if they were
- Resize the scene if an object was added/deleted

I tried adding this snippet in RenderingManager::InitializeViews. In
clear english: reuse the old geometry for the current plane, but update
it with the new offset and bounds that we just calculated.

auto newGeo = timeGeometry->GetGeometryForTimeStep(0);
auto oldTimeGeo = nc->GetCreatedWorldGeometry();
auto oldGeo = oldTimeGeo->GetGeometryForTimeStep(0);

oldGeo->GetIndexToWorldTransform()->SetOffset(
newGeo->GetIndexToWorldTransform()->GetOffset());
oldGeo->SetBounds(newGeo->GetBounds());

nc->SendCreatedWorldGeometryUpdate();

nc->SetInputWorldTimeGeometry(oldTimeGeo);
nc->Update();
...

This doesn't work; it throws the planes in strange places [3], probably
because I broke their affine matrix. I tried many things but my biggest
success was to remove the call to SetInputWorldTimeGeometry [4]. I
checked in DisplayInteractor::Rotate to see if there was a way to find
the old rotation applied to the plane but it doesn't seem to be possible.

Anyway, I'm mostly wondering how YOU, the mitk experts :), would do it.
Thank you for your time.

Nil

[1] http://i.imgur.com/krzBvJV.png
[2] http://i.imgur.com/NWDQQqg.png
[3] http://i.imgur.com/7wwWczy.png
[4] http://i.imgur.com/m9jwrpE.png
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[mitk-users] Segmentation shift

[Nil Goyette]

Hi all,

My boss asked me to let the users decide if they want to reinit or not. 
They will live with the consequence of not being aligned if they don't. 
Of course I found this http://i.imgur.com/GKGKwmV.png I know this is a 
well-known bug and it has been repaired in 
https://phabricator.mitk.org/T22619 but I have a question about this bug.


Does anyone know why there's a shift and/or how it could be repaired? I 
mean, without a reinit, of course. I plan to fix it myself and it would 
help me if someone gives me some hints. Thank you for your time.


Nil


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[mitk-users] Special reinit

[Nil Goyette]

Hi all,

Lets start by saying that I know "Reinit" is not the right choice of 
word in this case! A reinit would reset the axis, as it should. Lets 
say, for the sake of the discussion, that I want a reinit that simply 
update the scene's bounding box, nothing else, like  [1] to [2] (made by 
hand, so not exact!):

- No camera modification, so everything is still at the same place
- Keep the axis rotated if they were
- Resize the scene if an object was added/deleted

I tried adding this snippet in RenderingManager::InitializeViews. In 
clear english: reuse the old geometry for the current plane, but update 
it with the new offset and bounds that we just calculated.


auto newGeo = timeGeometry->GetGeometryForTimeStep(0);
auto oldTimeGeo = nc->GetCreatedWorldGeometry();
auto oldGeo = oldTimeGeo->GetGeometryForTimeStep(0);

oldGeo->GetIndexToWorldTransform()->SetOffset(
  newGeo->GetIndexToWorldTransform()->GetOffset());
oldGeo->SetBounds(newGeo->GetBounds());

nc->SendCreatedWorldGeometryUpdate();

nc->SetInputWorldTimeGeometry(oldTimeGeo);
nc->Update();
...

This doesn't work; it throws the planes in strange places [3], probably 
because I broke their affine matrix. I tried many things but my biggest 
success was to remove the call to SetInputWorldTimeGeometry [4]. I 
checked in DisplayInteractor::Rotate to see if there was a way to find 
the old rotation applied to the plane but it doesn't seem to be possible.


Anyway, I'm mostly wondering how YOU, the mitk experts :), would do it. 
Thank you for your time.


Nil

[1] http://i.imgur.com/krzBvJV.png
[2] http://i.imgur.com/NWDQQqg.png
[3] http://i.imgur.com/7wwWczy.png
[4] http://i.imgur.com/m9jwrpE.png

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Re: [mitk-users] Root properties on MITK scene files

[Nil Goyette]

Hi Frederico,

I'm pretty sure I am that user Stefan is talking about :) It was months 
ago so you can be sceptical about some (or all) of the things I will 
write.  If I remember correctly, the "Persistence Service" is the same 
as a QSettings object but in a non-UI module. This may be practical to 
some users but it was totaly useless to me. There's also the Preferences 
system but it's not what I had in mind because it applies to alll MITK's 
instances instead of only to the current scene.


What I did was to modify the Persistence and SceneSerialization classes 
of MITK to save properties in the scene. It wasn't really complicated 
because these 2 classes almost already do what we want.


Sadly, I couldn't contribute this code to MITK because it's super 
complicated to modify a feature as some users may be using it. I can't 
share the code at the moment because I don't have it with me but I could 
put it on my github account if you like. It was a WIP but it was working 
quite well.


Nil Goyette

Le 2017-06-06 à 12:03, Dinkelacker, Stefan a écrit :


Hi,

see the MITK Persistence Service [1]. I can remember that some users 
had issues with the service, though. Searching a little bit in the 
mailing list archive should shed light on this. I guess it isn’t 
possible with reasonable efforts to implement partial extraction.


Best,
Stefan

[1] 
http://docs.mitk.org/2016.03/PersistenceConceptPage.html#PersistenceMITKService


*From:*Federico Milano [mailto:fmil...@gmail.com]
*Sent:* Dienstag, 6. Juni 2017 17:22
*To:* mitk-users@lists.sourceforge.net
*Subject:* [mitk-users] Root properties on MITK scene files

Hi. I would need to store some data as general properties for the MITK 
scene, I think of those like "root" properties.


What is the best way to do this? Should I create an invisible node 
just to store these properties?


I would also like to retrieve those properties from any .mitk file 
without the need of decompressing the whole file.


What do you think would be the best way to achieve this kind of 
functionality?


Thanks in advance,

Federico

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[mitk-users] LabelSetImage mapper in 3D

[Nil Goyette]

Hi all,

What can I do to see my segmentation in the 3D mapper?

I searched a little and I can see that there's a 
mitkLabelSetImageVtkMapper2D class, without a 3D version, but the same 
can be said about mitkImageVtkMapper2D, yet we can see them in 3D. This 
makes make understand that we don't need a 3D mapper to see something in 
3D. What do we need to do to activate the "replication" of the 2D slices 
into 3D?

Nil Goyette


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[mitk-users] AccessByItk_n

[Nil Goyette]

Hi all,

I have this error: "Prohibited image access: the requested image part is 
already in use and cannot be requested recursively!" and I'm not sure 
what it means. It's caused by the AccessByItk_n in 
mitkCorrectorAlgorithm.cpp in GenerateData().

I did modify the [old] segmentation plugin  so I'm probably to blame 
here. I replaced all mitk::LabelSetImage usages with mitk::Image because 
the plugin can do nothing with them anyway. Everything still works as it 
should except the +/- Correction button.

I tried reducing the number of  smart pointers pointing to 
m_WorkingImage but GenerateData() itself makes it go up by one so I 
don't see how I could make it stay at 1 in my own code. Any ideas what I 
can do to fix this?

Nil

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Re: [mitk-users] MITK 2016.11 released

[Nil Goyette]

Hi MITK team,

Thank you for this release and for your good work. The changes in the 
geometry system are indeed awesome :)


I have one question about vtk. I was surprised to see that vtk *7.0* 
didn't make it into the list of update even if you updated it. So I 
checked VTK.cmake and realized that you are still using the old OpenGL 
backend. If I understand correctly, the OS X bug is directly caused by 
this backend.


1. What are your plans concerning the new backend? Do you plan to use
   it on the next MITK's version?
2. What's the problem with the new backend? I guess that all MITK's
   mappers need to be updated and you didn't have enough time to do it.
   Anything else? I ask because we have our own mappers here and I will
   probably face the same problems :)
3. Totally unrelated and not useful question... Why do you name the
   release 2016.11 when you release it in 2017.02? :D

Again, thank you for your time.

Nil

Le 2017-02-06 à 08:57, Goch, Caspar Jonas a écrit :


Dear MITK users,

we are happy to announce the release of MITK 2016.11!

New supported versions are CMake 3.5 or newer, Qt 5.6 or 5.7.1 
 (version 5.8 is not yet supported).


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[mitk-users] Reinit and orientation

[Nil Goyette]

Hi all,

I was reading the RenderingManager code to understand how one would do a 
Reinit while keeping the image orientation. For example, if the 
patient's nose points to the right, then Reinit would align the image on 
the grid, as it should, but the nose would still points right.

Right now, Reinit is visually removing all transformations, without 
changing any real data. I don't understand how it does though because 
the code is complex and it goes quite deep. There's so much 
initialization code that's it's easy to get lost in it. There's also 
this preserveRoughOrientationInWorldSpace parameter which seems to do 
what I want but is sadly unused.

Can you please help me on this matter?

Nil


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Re: [mitk-users] Force plugin to load

[Nil Goyette]

Hi all,

In fact, I searched in your codebase how to open a view by ID and found 
this snippet:
auto workbench = berry::PlatformUI::GetWorkbench();
auto window = workbench->GetActiveWorkbenchWindow();
berry::IWorkbenchPage::Pointer page = window->GetActivePage();
page->ShowView(viewID);

I had some problem because I was writing the plugin's ID instead of the 
view's, but it's working perfectly now. I wrote this snippet on the last 
line of my WorkbenchWindowAdvisor::PostWindowCreate() and everything 
seems ok.  Of course, it would be better if the plugin loaded without 
forcing it to display but this is by far the best solution I found.

Nil

Le 2016-12-02 à 17:48, Nil Goyette a écrit :
> Hi Stefan, Hi poor Paul Palei,
>
> I found a way to do what I want. Turns out an 'eager' plugin can access
> the good old IDataStorageService, which I can use to add my category
> nodes AND add a listener so I can change the node's parent when they are
> loaded.
>
> Of course it would be better if I could force my plugin to load but it's
> probably a big can of worms. Thank you for your help.
>
> Nil
>
> Le 2016-12-02 à 11:06, Nil Goyette a écrit :
>> Hi,
>>
>> Yes, we are already using this. We have our own app, perspective,
>> preferences, WorkbenchWindowAdvisor, etc. We may not be aware of all the
>> things we can do with these classes though. I think they are mostly used
>> to set up the UI. Do you have a particular idea in mind on how to do
>> what I want?
>>
>> We also use SetCloseable(false); on our plugin. It's never closed...
>> it's just not opened/activated ;) when there's another plugin in front.
>>
>> Nil
>>
>> Le 2016-12-02 à 03:42, Kislinskiy, Stefan a écrit :
>>> Hi,
>>>
>>> with this high amount of customization you may be interested in creating 
>>> your own Workbench-like application were you can set up a default 
>>> perspective any many more things to your needs. This is quite easy to 
>>> achieve. Have a look at [1,2] for an example. It also seems to be possible 
>>> to make a plugin kind of "non-closeable" like the Data Manager.
>>>
>>> Best,
>>> Stefan
>>>
>>> [1] https://github.com/MITK/MITK/tree/v2016.03.0/Applications/Diffusion
>>> [2] 
>>> https://github.com/MITK/MITK/tree/v2016.03.0/Plugins/org.mitk.gui.qt.diffusionimagingapp
>>> 
>>> Von: Nil Goyette <nil.goye...@imeka.ca>
>>> Gesendet: Donnerstag, 1. Dezember 2016 17:01
>>> An: Kislinskiy, Stefan; mitk-users@lists.sourceforge.net
>>> Betreff: Re: AW: [mitk-users] Force plugin to load
>>>
>>> Hi Stefan,
>>>
>>> This is only for non-UI code, right? Setting IO classes, preferences,
>>> node descriptors, etc.?
>>>
>>> I ask because I doubt what I want to do is possible. Maybe you can tell.
>>> At the start of our app, we create 3 category nodes: Anatomies, ROIs and
>>> Tracts. Each time a file is loaded, the plugin places the new node in
>>> the right group, based on a predicate. Of course, without our plugin,
>>> the groups don't exist and the nodes just pile up in the DM.
>>>
>>> If we can 1) access the DM 2) create nodes 3) be warned when there's a
>>> new node (NodeAdded), then it's perfect. We have other problems, but I'm
>>> pretty sure we can fix them if we can fix this :)
>>>
>>> Nil
>>>
>>> Le 2016-11-30 à 18:12, Kislinskiy, Stefan a écrit :
>>>> This may not be the answer you are exactly looking for, but you should 
>>>> consider calling your initialization code from the start method of your 
>>>> plugin activator and set the eager policy. See [1,2] for an example.
>>>>
>>>> Best,
>>>> Stefan
>>>>
>>>> [1] 
>>>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/manifest_headers.cmake#L6
>>>> [2] 
>>>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/src/internal/org_mitk_simulation_Activator.cpp#L85
>>>> 
>>>> Von: Nil Goyette <nil.goye...@imeka.ca>
>>>> Gesendet: Mittwoch, 30. November 2016 21:27
>>>> An: mitk-users@lists.sourceforge.net
>>>> Betreff: [mitk-users] Force plugin to load
>>>>
>>>> Hi all,
>>>>
>>>> I know that we can use Perspective::CreateInitialLayout to ask a plugin
>>&g

Re: [mitk-users] Force plugin to load

[Nil Goyette]

Hi Stefan, Hi poor Paul Palei,

I found a way to do what I want. Turns out an 'eager' plugin can access 
the good old IDataStorageService, which I can use to add my category 
nodes AND add a listener so I can change the node's parent when they are 
loaded.

Of course it would be better if I could force my plugin to load but it's 
probably a big can of worms. Thank you for your help.

Nil

Le 2016-12-02 à 11:06, Nil Goyette a écrit :
> Hi,
>
> Yes, we are already using this. We have our own app, perspective,
> preferences, WorkbenchWindowAdvisor, etc. We may not be aware of all the
> things we can do with these classes though. I think they are mostly used
> to set up the UI. Do you have a particular idea in mind on how to do
> what I want?
>
> We also use SetCloseable(false); on our plugin. It's never closed...
> it's just not opened/activated ;) when there's another plugin in front.
>
> Nil
>
> Le 2016-12-02 à 03:42, Kislinskiy, Stefan a écrit :
>> Hi,
>>
>> with this high amount of customization you may be interested in creating 
>> your own Workbench-like application were you can set up a default 
>> perspective any many more things to your needs. This is quite easy to 
>> achieve. Have a look at [1,2] for an example. It also seems to be possible 
>> to make a plugin kind of "non-closeable" like the Data Manager.
>>
>> Best,
>> Stefan
>>
>> [1] https://github.com/MITK/MITK/tree/v2016.03.0/Applications/Diffusion
>> [2] 
>> https://github.com/MITK/MITK/tree/v2016.03.0/Plugins/org.mitk.gui.qt.diffusionimagingapp
>> 
>> Von: Nil Goyette <nil.goye...@imeka.ca>
>> Gesendet: Donnerstag, 1. Dezember 2016 17:01
>> An: Kislinskiy, Stefan; mitk-users@lists.sourceforge.net
>> Betreff: Re: AW: [mitk-users] Force plugin to load
>>
>> Hi Stefan,
>>
>> This is only for non-UI code, right? Setting IO classes, preferences,
>> node descriptors, etc.?
>>
>> I ask because I doubt what I want to do is possible. Maybe you can tell.
>> At the start of our app, we create 3 category nodes: Anatomies, ROIs and
>> Tracts. Each time a file is loaded, the plugin places the new node in
>> the right group, based on a predicate. Of course, without our plugin,
>> the groups don't exist and the nodes just pile up in the DM.
>>
>> If we can 1) access the DM 2) create nodes 3) be warned when there's a
>> new node (NodeAdded), then it's perfect. We have other problems, but I'm
>> pretty sure we can fix them if we can fix this :)
>>
>> Nil
>>
>> Le 2016-11-30 à 18:12, Kislinskiy, Stefan a écrit :
>>> This may not be the answer you are exactly looking for, but you should 
>>> consider calling your initialization code from the start method of your 
>>> plugin activator and set the eager policy. See [1,2] for an example.
>>>
>>> Best,
>>> Stefan
>>>
>>> [1] 
>>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/manifest_headers.cmake#L6
>>> [2] 
>>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/src/internal/org_mitk_simulation_Activator.cpp#L85
>>> 
>>> Von: Nil Goyette <nil.goye...@imeka.ca>
>>> Gesendet: Mittwoch, 30. November 2016 21:27
>>> An: mitk-users@lists.sourceforge.net
>>> Betreff: [mitk-users] Force plugin to load
>>>
>>> Hi all,
>>>
>>> I know that we can use Perspective::CreateInitialLayout to ask a plugin
>>> to be at a specific posion and to open. This is working in MOST cases
>>> but not all.
>>>
>>> If the user opens another plugin X, stack it on the main plugin, then
>>> close the program, the app will open with plugin X in front of our main
>>> plugin, which will be inactive (You may need to do it many times if you
>>> want to see it. Without --BlueBerry.clean of course). The plugin's
>>> Activator and the view's constructor won't be called.
>>>
>>> Wathever plugins is in front of our plugin, we need to load it anyway
>>> because it loads the AUTOLOAD_WITH modules and the constructor of our
>>> view is doing important stuff. So, is there a way to force a plugin to load?
>>> Thank you for your time :)
>>>
>>> Nil
>>>
>>>
>>> --
>>> ___
>>> mitk-users mailing list
>>> mitk-users@lists.sourceforge.net
>>> https://lists.sourceforg

Re: [mitk-users] Force plugin to load

[Nil Goyette]

Hi,

Yes, we are already using this. We have our own app, perspective, 
preferences, WorkbenchWindowAdvisor, etc. We may not be aware of all the 
things we can do with these classes though. I think they are mostly used 
to set up the UI. Do you have a particular idea in mind on how to do 
what I want?

We also use SetCloseable(false); on our plugin. It's never closed... 
it's just not opened/activated ;) when there's another plugin in front.

Nil

Le 2016-12-02 à 03:42, Kislinskiy, Stefan a écrit :
> Hi,
>
> with this high amount of customization you may be interested in creating your 
> own Workbench-like application were you can set up a default perspective any 
> many more things to your needs. This is quite easy to achieve. Have a look at 
> [1,2] for an example. It also seems to be possible to make a plugin kind of 
> "non-closeable" like the Data Manager.
>
> Best,
> Stefan
>
> [1] https://github.com/MITK/MITK/tree/v2016.03.0/Applications/Diffusion
> [2] 
> https://github.com/MITK/MITK/tree/v2016.03.0/Plugins/org.mitk.gui.qt.diffusionimagingapp
> 
> Von: Nil Goyette <nil.goye...@imeka.ca>
> Gesendet: Donnerstag, 1. Dezember 2016 17:01
> An: Kislinskiy, Stefan; mitk-users@lists.sourceforge.net
> Betreff: Re: AW: [mitk-users] Force plugin to load
>
> Hi Stefan,
>
> This is only for non-UI code, right? Setting IO classes, preferences,
> node descriptors, etc.?
>
> I ask because I doubt what I want to do is possible. Maybe you can tell.
> At the start of our app, we create 3 category nodes: Anatomies, ROIs and
> Tracts. Each time a file is loaded, the plugin places the new node in
> the right group, based on a predicate. Of course, without our plugin,
> the groups don't exist and the nodes just pile up in the DM.
>
> If we can 1) access the DM 2) create nodes 3) be warned when there's a
> new node (NodeAdded), then it's perfect. We have other problems, but I'm
> pretty sure we can fix them if we can fix this :)
>
> Nil
>
> Le 2016-11-30 à 18:12, Kislinskiy, Stefan a écrit :
>> This may not be the answer you are exactly looking for, but you should 
>> consider calling your initialization code from the start method of your 
>> plugin activator and set the eager policy. See [1,2] for an example.
>>
>> Best,
>> Stefan
>>
>> [1] 
>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/manifest_headers.cmake#L6
>> [2] 
>> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.simulation/src/internal/org_mitk_simulation_Activator.cpp#L85
>> 
>> Von: Nil Goyette <nil.goye...@imeka.ca>
>> Gesendet: Mittwoch, 30. November 2016 21:27
>> An: mitk-users@lists.sourceforge.net
>> Betreff: [mitk-users] Force plugin to load
>>
>> Hi all,
>>
>> I know that we can use Perspective::CreateInitialLayout to ask a plugin
>> to be at a specific posion and to open. This is working in MOST cases
>> but not all.
>>
>> If the user opens another plugin X, stack it on the main plugin, then
>> close the program, the app will open with plugin X in front of our main
>> plugin, which will be inactive (You may need to do it many times if you
>> want to see it. Without --BlueBerry.clean of course). The plugin's
>> Activator and the view's constructor won't be called.
>>
>> Wathever plugins is in front of our plugin, we need to load it anyway
>> because it loads the AUTOLOAD_WITH modules and the constructor of our
>> view is doing important stuff. So, is there a way to force a plugin to load?
>> Thank you for your time :)
>>
>> Nil
>>
>>
>> --
>> ___
>> mitk-users mailing list
>> mitk-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mitk-users


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Re: [mitk-users] Scene properties

[Nil Goyette]

Hi Stefan,

Thank you for the information on DataNode. As for the persistence 
system... Oh. Shit. Ok :) This wasn't my understanding at all.
This sentence in the documentation makes people believe something false 
and, if you're right, should be updated to avoid confusion:/

/

"/These properties can be stored inside a MITK scene together with the 
data so that the user loads data and restores the application state at 
once./" 
http://docs.mitk.org/2016.03/PersistenceConceptPage.html#PersistenceMITKService


If I understand you correctly, the persistence system is exacly like 
QSettings but without the need for a Qt dependency. It's not linked at 
all to the saving and loading of a scene, by design.


We need this feature because we want the user to

 * have the same data+views+params when he loads his scene, so he can
   continue his work at the same point
 * be able to send his scene to a colleague and both see the exact same
   thing

so I'll try to code is the next weeks. Would MITK be interested in this 
contribution?


Nil

Le 2016-11-29 à 08:08, Kislinskiy, Stefan a écrit :


Hi Nil,

AFAIK the Persistence Service was intentionally designed to be not 
included in a scene file as it is indeed something similar to 
QSettings. If you want to store settings in your scene file, you can 
do so by using properties.


Note that there are several property lists. The lists you see by 
default in the Properties View are the general DataNODE properties. 
There are also specialized DataNODE properties per render window. 
Properties in these specialized lists are used instead of the general 
ones in the according render window if present. DataNODE properties 
are usually dedicated to the appearance of data. There is also a 
BASEData property list for each data item in your scene. This list is 
dedicated to meta data like the original path of an image, DICOM tags, 
and so on. In the Preferences you can switch on the “Developer Mode” 
for the Properties, which enables you to switch between the lists in 
the view to get an idea of all the lists.


Best,
Stefan

*From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
*Sent:* Montag, 28. November 2016 21:33
*To:* mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] Scene properties

Hi all,

I was testing the persistence system again, but on MITK 2016.03 this 
time. I did fall on all the same traps so this old conversation helped 
me. I have some new questions though.


Right now, the persistence system simply creates PersistentData.xml in 
AppData/.../#_MitkPersistence, with '#' starting at 45 and going up.


  * The first file (45) is never used after. It's never found by MITK.
On the second run, it creates '46' and the data are read on all
the next runs. But the real problem comes next.
  * Why? I don't understand the point of saving a xml file in AppData.
Isn't this a new QSettings? I thought the data was going to be
saved in the scene.

In fact, I searched in your code using 'git grep' and I can't find 
where PersistenceService is used when saving a scene. I can see it is 
used in PersistenceService::Save() and PersistenceService::Load() when 
a filename is passed, but afaik it never happens. GetDataNodes() could 
be called by the scene-saving code but it's not. Knowing all this, I'm 
less surprised that BeforePropertyListReplaced() was never called!


Can someone please confirm that the persistence system is working when 
saving and loading a scene?
And if it does, can you please tell me how!?! Where in 
SceneSerialization does it happens?

Thank you for your time.

Nil

Le 2016-04-06 à 12:22, Nil Goyette a écrit :

Ah, thank you, mitk::PersistenceService::LoadModule() was the missing

piece of information.

The service is not a nullptr anymore and I can get the properties

associated with an ID and they are kept during the lifetime of the

application.

So, I added the call to AddPropertyListReplacedObserver(this) but

BeforePropertyListReplaced() and AfterPropertyListReplaced() are never

called. I thought they would be called when the user saves and load a scene.

Did I miss something?

Le 2016-04-06 05:49, Kolb, Christoph a écrit :

I have just tested the PersistenceService in a Plugin and got the same 
error message:

"The calling module probably misses a US_MODULE_NAME compile definition 
and/or a call to

US_INITIALIZE_MODULE in one of its source files."

It worked after I added a dependency to MitkPersistence and

called mitk::PersistenceService::LoadModule() in the constructor of my 
pluginView. I also needed to

put US_INITIALIZE_MODULE in the source.

Regards

Christoph



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Re: [mitk-users] Scene properties

[Nil Goyette]

Hi all,

I was testing the persistence system again, but on MITK 2016.03 this 
time. I did fall on all the same traps so this old conversation helped 
me. I have some new questions though.


Right now, the persistence system simply creates PersistentData.xml in 
AppData/.../#_MitkPersistence, with '#' starting at 45 and going up.


 * The first file (45) is never used after. It's never found by MITK.
   On the second run, it creates '46' and the data are read on all the
   next runs. But the real problem comes next.
 * Why? I don't understand the point of saving a xml file in AppData.
   Isn't this a new QSettings? I thought the data was going to be saved
   in the scene.

In fact, I searched in your code using 'git grep' and I can't find where 
PersistenceService is used when saving a scene. I can see it is used in 
PersistenceService::Save() and PersistenceService::Load() when a 
filename is passed, but afaik it never happens. GetDataNodes() could be 
called by the scene-saving code but it's not. Knowing all this, I'm less 
surprised that BeforePropertyListReplaced() was never called!


Can someone please confirm that the persistence system is working when 
saving and loading a scene?
And if it does, can you please tell me how!?! Where in 
SceneSerialization does it happens?

Thank you for your time.

Nil

Le 2016-04-06 à 12:22, Nil Goyette a écrit :

Ah, thank you, mitk::PersistenceService::LoadModule() was the missing
piece of information.

The service is not a nullptr anymore and I can get the properties
associated with an ID and they are kept during the lifetime of the
application.

So, I added the call to AddPropertyListReplacedObserver(this) but
BeforePropertyListReplaced() and AfterPropertyListReplaced() are never
called. I thought they would be called when the user saves and load a scene.
Did I miss something?

Le 2016-04-06 05:49, Kolb, Christoph a écrit :

I have just tested the PersistenceService in a Plugin and got the same error 
message:
"The calling module probably misses a US_MODULE_NAME compile definition and/or 
a call to
US_INITIALIZE_MODULE in one of its source files."

It worked after I added a dependency to MitkPersistence and
called mitk::PersistenceService::LoadModule() in the constructor of my 
pluginView. I also needed to
put US_INITIALIZE_MODULE in the source.

Regards
Christoph
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[mitk-users] DM Actions contribution

[Nil Goyette]

Hi all,

I added 2 features in our version of MITK and I wanted to know your opinion.

*Actions in the Data Manager*

Check image [1]. I wanted some of the contextMenuAction to be visible in 
the DM, with the following options:

- Always visible or only on hover?
- Only in context menu, or in DM or both?
- Icon position with an idx system.

Of course I used the existing contextMenuAction class because my new 
version would have been almost identical. I don't feel it's too much of 
a hack but, yes, it's an abuse of the name "contextMenuAction". Anyway, 
I'm quite satisfied with the implementation.


*Drag n' Drop actions*

Some actions are not applied to the current node but on another one. 
Check image [2]. In this example, I Cut a tract with a ROI. Of course, 
this could be done with NodeSelected() + a button in a plugin, or a 
combobox in a plugin or with plenty of ways but we thought that DnD was 
a much better idea. I still use the contextMenuAction for those actions. 
It's currently hardcoded a bit, much more hackish than my previous idea 
and chould be enhanced in many ways but you get the idea.


It has been tested on the major OSes and our users are happy.
So, what do you guys think? Should it be contributed upstream?

Nil

[1] http://imgur.com/VnJBmmb
[2] http://imgur.com/X2g5CYl

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[mitk-users] Segmentation and reinit

[Nil Goyette]

Hi all,

A reinit is forced on the segmented image when we create a new 
segmentation. I think that most (all?) segmentation tools ignore the 
affine. As Andreas wrote on the ML: "The segmentation plugin requires 
the woldgeometry to be aligned to the selected image." Can I know the 
reasons? Did you try a version without reinit, then concluded you needed 
one?

In fact, I commented the code that forces a reinit and tested, using the 
coupled crosshair rotation to fake a big transformation.
The results were horrible :) The colored contour and the mask are bad.
http://imgur.com/fYIw0y0
http://imgur.com/7oxr1VB
http://imgur.com/VDHNd2P
http://imgur.com/5iT4xsb
I guess this is the reason why you force a reinit, but can you give more 
information?
Do you think there would be a way to do it without?
Thanks for your time.

Nil


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[mitk-users] QmitkRenderWindowMenu OS X

[Nil Goyette]

Hi all,

One of my user found another bug on OS X. The 3 buttons in the 4 views 
have a strange behavior. Only on OS X of course. There's no problem when 
the application boots. They are all visible when they should be.

When one of the views is set to fullscreen, so:
- The normal m_FullScreenButton button on all views
- "Big 3D", "Axial plane", "Sagittal plane" or "Coronal plane" actions 
in m_SettingsButton.
we can't see the button anymore. Or they flicker. Or they are always 
visible. Or a random happy mix.

A search on Phabricator returns only results from 2009. Someone saw this 
problem? Has it been solved?

Nil


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[mitk-users] Drag plugin on OX X

[Nil Goyette]

Hi all,

On of my user told me that it was near-impossible to dock a plugin on OS 
X. I tested on OS X 10.11 on our application and on MITK Workbench 
2016.03 and he's right. I couldn't find any bug report on this problem 
on Phabricator so I'm asking here.


Docking left, top, right and down of the stdmultiwidget is "ok" when 
you're in the right zone. That is, in a really specific zone near the 
middle of the render windows. It's not particularly great but it works.


If you're anywhere else though, the shadow of the plugin flickers when 
you move. As if Qt understood only for 1 mouseevent that the position 
was right, but then it's lost and the plugin detaches if you release the 
mouse.


I did succeed one time, moving the mouse really fast and releasing 
randomly, hoping to be in the right millisecond :) It was impossible to 
put a plugin *on* another plugin though (creating tabs).


It's working flawlessly on Windows and Linux, but it's a horror on OS X. 
Someone saw this problem? Has it been solved?


Nil

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[mitk-users] XCode debugging

[Nil Goyette]

Hi all,

Someone knows how to open a MITK project in xcode and run/debug it? Is 
it possible? I tried and I saw a bunch of random errors. Might as well 
ask before losing time on this :)

Nil


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Re: [mitk-users] Vigra and cmake > 3.2.x

[Nil Goyette]

Hi Stefan,

Thank you for your answer. I was probably unclear in my message. I'm not 
asking for a backport and I don't care much for 2015.05 because we are 
on 2016.03 now.

The problem I have is that the build fails in 2016.03+VS2013+Vigra if I 
use anything else than CMake3.2. It does work on OS X though (3.3.2). I 
haven't tested on Linux yet.

Nil

Le 2016-09-29 à 05:08, Kislinskiy, Stefan a écrit :
> Hi Nil, we didn't backport these CMake-related fixes so the maximum 
> compatible CMake version for MITK 2015.05 is 3.2.
>
> Best,
> Stefan
>
> -Original Message-
> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
> Sent: Mittwoch, 28. September 2016 21:40
> To: mitk-users@lists.sourceforge.net
> Subject: [mitk-users] Vigra and cmake > 3.2.x
>
> Hi all.
>
> I tried to compile MITK using CMake 3.3, 3.4, 3.5 and 3.6 (VS2013, Vigra
> enabled) on MITK 2015.05 and it failed each time. I don't remember the exact 
> message and it's not important now because we have 2016.03.
>
> So I tested again with CMake 3.6.2 (VS2013, Vigra enabled) and it fails with 
> this message:
> 20>  CMake Error at CMakeLists.txt:821 (find_package):
> 20>By not providing "FindVigra.cmake" in CMAKE_MODULE_PATH this
> project has
> 20>asked CMake to find a package configuration file provided by
> "Vigra", but
> 20>CMake did not find one.
> 20>
> 20>Could not find a package configuration file provided by "Vigra"
> with any of
> 20>the following names:
> 20>
> 20>  VigraConfig.cmake
> 20>  vigra-config.cmake
> 20>
> 20>Add the installation prefix of "Vigra" to CMAKE_PREFIX_PATH or set
> 20>"Vigra_DIR" to a directory containing one of the above files.  If
> "Vigra"
> 20>provides a separate development package or SDK, be sure it has been
> 20>installed.
> 20>
> 20>
> 20>  -- Configuring incomplete, errors occurred!
>
> The only other version I tested is CMake 3.2.x and it does work.
> Is there a fix for this?
>
> Nil
>
>
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[mitk-users] Vigra and cmake > 3.2.x

[Nil Goyette]

Hi all.

I tried to compile MITK using CMake 3.3, 3.4, 3.5 and 3.6 (VS2013, Vigra 
enabled) on MITK 2015.05 and it failed each time. I don't remember the 
exact message and it's not important now because we have 2016.03.

So I tested again with CMake 3.6.2 (VS2013, Vigra enabled) and it fails 
with this message:
20>  CMake Error at CMakeLists.txt:821 (find_package):
20>By not providing "FindVigra.cmake" in CMAKE_MODULE_PATH this 
project has
20>asked CMake to find a package configuration file provided by 
"Vigra", but
20>CMake did not find one.
20>
20>Could not find a package configuration file provided by "Vigra" 
with any of
20>the following names:
20>
20>  VigraConfig.cmake
20>  vigra-config.cmake
20>
20>Add the installation prefix of "Vigra" to CMAKE_PREFIX_PATH or set
20>"Vigra_DIR" to a directory containing one of the above files.  If 
"Vigra"
20>provides a separate development package or SDK, be sure it has been
20>installed.
20>
20>
20>  -- Configuring incomplete, errors occurred!

The only other version I tested is CMake 3.2.x and it does work.
Is there a fix for this?

Nil


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Re: [mitk-users] Neglected icon attribute in the extension point of the QmitkDataManagerView

[Nil Goyette]

Hi all,

I tested this feature with MITK 2016.03 (I was testing with 2015.05 
before) and I still can't get any context menu icons. I tested with a 
random datamanager icon:
icon=":/org.mitk.gui.qt.datamanager/Refresh_48.png"
just to confirm Sascha'a concern and I can see the damn icon.

Then I tried @zimmerm suggestion (in the linked bug). I changed nothing 
else except:
QIcon icon;
if (QFile::exists(cmIcon))
{
   icon = QIcon(cmIcon);
}
else
{
   icon = berry::AbstractUICTKPlugin::ImageDescriptorFromPlugin(
 (*cmActionsIt)->GetContributor()->GetName(), cmIcon);
}
contextMenuAction = new QAction(icon, cmLabel, parent);

And it actually works. I see my icons now and I still see MITK's (which 
is normal because there's no mitk's plugins using this code). Tested on 
Windows, OS X and linux.

Nil

Le 2016-09-19 à 16:18, Nil Goyette a écrit :
> Hi all,
>
> Can I get an update on this? I lost many hours trying to to load an icon
> for my action and I can't get it to work. There's is still this old task
> https://phabricator.mitk.org/rMITKa5312246035bdf65d22364816b508129ce06c16d
> on this bug.
>
> I couldn't find any plugin in MITK's code that loads an icon for a
> context menu using plugin.xml so I can't copy what you did.
>
> Are Sascha's concerns still valid? It won't work if my plugin
> (resources) are loaded after this line
> contextMenuAction = new QAction( QIcon(cmIcon), cmLabel, parent);
> in QmitkDataManagerView.cpp? Is there a safe place to put my icon?
>
> Nil
>
> Le 2014-12-01 à 13:19, Martin Klemm a écrit :
>> Hi
>>
>> I merged the patch into the master and closed the bug last week. The
>> changes (without the additions of Sascha) are already included in the
>> MITK 2014.10 release.
>>
>> Best
>>
>> Martin
>>
>> On 12/01/2014 12:40 AM, Sascha Zelzer wrote:
>>> I just shortly looked at the patch. It indeed relies on a qrc location.
>>> This will only work if the contributing plug-in is loaded (otherwise,
>>> the Qt resources would not be accessible). The final fix should rely on
>>> the CTK resource system to retrieve the icon (as specified in the
>>> CACHED_RESOURCE_FILES variable) and create a QIcon instance from an
>>> in-memory representation of the icon similar to the code creating the
>>> MITK Workbench toolbar and menu entries showing the view icons.
>>>
>>> Best,
>>> Sascha
>>>
>>> On 11/09/2014 10:27 PM, Rostislav Khlebnikov wrote:
>>>> Hm, setting it to the "qrc" location (i.e. ":/icons/icon.png") seems to
>>>> work.
>>>>
>>>> All best,
>>>>Rostislav.
>>>>
>>>> On 09/11/2014 20:41, Rostislav Khlebnikov wrote:
>>>>> Hi guys,
>>>>>
>>>>> am I missing something? I applied the patch attached to the bug, but the
>>>>> icon is still missing.
>>>>>
>>>>> I added my icon to the CACHED_RESOURCE_FILES in files.cmake for my
>>>>> plugin. The location is, say, "resources/icon.png" and in plugin.xml I 
>>>>> have
>>>>> >>>> icon="resources/icon.png" class="MyAction" />
>>>>>
>>>>> Any ideas on why this might not work?
>>>>>
>>>>> Thanks,
>>>>> Rostislav.
>>>>>
>>>>> On 10/07/2014 10:43, Martin Klemm wrote:
>>>>>> Hi Sascha,
>>>>>>
>>>>>> thanks for the answer and sorry for not writing you for so long. I
>>>>>> opened a bug report http://bugs.mitk.org/show_bug.cgi?id=17907 and
>>>>>> attached the patch file. Is there something else I have to do now? Or
>>>>>> will you do the rest?
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 28.05.2014 18:09, Sascha Zelzer wrote:
>>>>>>> Hi Martin,
>>>>>>>
>>>>>>> I think it just hasn't been done yet. I also don't see a reason for not
>>>>>>> doing it. Would you be up for contributing a patch to enable icons in
>>>>>>> the context menu?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Sascha
>>>>>>>
>>>>>>> On 05/06/2014 10:37 AM, Martin Klemm wrote:
>>>>>>>> Hello,
>>>>>>>&g

Re: [mitk-users] Ignoring unknown target "org_blueberry_core_jobs" for installation

[Nil Goyette]

Hi Stefan,

I hope you didn't loose too much time on this. I found the "problem".
I forgot to check MITK_BUILD_ALL_PLUGINS only on my OS X machine... so 
of course I had a lot of missing plugins only on my OS X machine. Herp derp.
*My bad*

Sorry for this and thank you for your time.

Nil


Le 2016-09-26 à 09:14, Kislinskiy, Stefan a écrit :
> Sorry, I have nothing specific in mind but I know that there were some 
> improvements the last weeks/months specifically regarding MITK and OS X. 
> Let's call it hope. :-)
>
>
> -Original Message-
> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
> Sent: Montag, 26. September 2016 15:02
> To: Kislinskiy, Stefan; mitk-users@lists.sourceforge.net
> Subject: Re: [mitk-users] Ignoring unknown target "org_blueberry_core_jobs" 
> for installation
>
> Hi Stefan,
>
> I'm currently building it. Is there a particular commit that makes you think 
> it might work on OS X? We prefer working from releases/tags + cherry-pick.
>
> Nil
>
> Le 2016-09-26 à 04:05, Kislinskiy, Stefan a écrit :
>> Hi Nil,
>>
>> As I have no experience with OS X, I'll would like to ask you, if you could 
>> please check, if this is still an issue with the current master?
>>
>> Best,
>> Stefan
>>
>> -Original Message-
>> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
>> Sent: Freitag, 23. September 2016 20:03
>> To: mitk-users@lists.sourceforge.net
>> Subject: Re: [mitk-users] Ignoring unknown target
>> "org_blueberry_core_jobs" for installation
>>
>> Hi all,
>>
>> Here's more information if it can help someone helping me.
>>
>> - It works perfectly on linux too.
>> - There's no error message if I use EXCLUDE_PLUGINS instead of PLUGINS (or 
>> if I use neither) but I only see my plugins, not mitk's. On Windows and 
>> Linux, the toolbar is filled, so I guess I see the complete list of plugins.
>>
>> I'm not sure what else to test. Anyone?
>>
>> Nil
>>
>> Le 2016-09-22 à 16:24, Nil Goyette a écrit :
>>> Hi all,
>>>
>>> I finally ported my application to MITK 2016.03 and everything went
>>> well enough. As always, thank you for your good job.
>>>
>>> I do have a problem on OS X when I try to cmake (yes, the verb ^^)
>>> though. I see a serie of warnings:
>>>
>>> CMake warning at ./mitkFunctionInstallAutoLoadModules.cmake:87
>>> (message):
>>>   Ignoring unknown target "org_blueberry_core_jobs" for installation.
>>> Call Stack (most recent call first):
>>> ./mitkFunctionInstallAutoLoadModules.cmake:102
>>> ./mitkFunctionCreateBlueBerryApplication.cmake:188
>>>   Our cmake.
>>>
>>> Idem with org_mitk_gui_qt_common_legacy,
>>> org_mitk_gui_qt_core_application, movie maker, segmentation, etc.
>>>
>>> My application opens with my main plugin but I can't see the other
>>> plugins, like movie maker, segmentation, etc. Do you have any ideas
>>> how I could fix this? Just to be clear, it does work perfectly on Windows.
>>> The warnings and missing plugins is only on OS X.
>>>
>>> Thank you for your time.
>>>
>>> Nil
>> --
>>  ___
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>
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Re: [mitk-users] Ignoring unknown target "org_blueberry_core_jobs" for installation

[Nil Goyette]

Hi Stefan,

I'm currently building it. Is there a particular commit that makes you 
think it might work on OS X? We prefer working from releases/tags + 
cherry-pick.

Nil

Le 2016-09-26 à 04:05, Kislinskiy, Stefan a écrit :
> Hi Nil,
>
> As I have no experience with OS X, I'll would like to ask you, if you could 
> please check, if this is still an issue with the current master?
>
> Best,
> Stefan
>
> -Original Message-
> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
> Sent: Freitag, 23. September 2016 20:03
> To: mitk-users@lists.sourceforge.net
> Subject: Re: [mitk-users] Ignoring unknown target "org_blueberry_core_jobs" 
> for installation
>
> Hi all,
>
> Here's more information if it can help someone helping me.
>
> - It works perfectly on linux too.
> - There's no error message if I use EXCLUDE_PLUGINS instead of PLUGINS (or if 
> I use neither) but I only see my plugins, not mitk's. On Windows and Linux, 
> the toolbar is filled, so I guess I see the complete list of plugins.
>
> I'm not sure what else to test. Anyone?
>
> Nil
>
> Le 2016-09-22 à 16:24, Nil Goyette a écrit :
>> Hi all,
>>
>> I finally ported my application to MITK 2016.03 and everything went
>> well enough. As always, thank you for your good job.
>>
>> I do have a problem on OS X when I try to cmake (yes, the verb ^^)
>> though. I see a serie of warnings:
>>
>> CMake warning at ./mitkFunctionInstallAutoLoadModules.cmake:87
>> (message):
>>  Ignoring unknown target "org_blueberry_core_jobs" for installation.
>> Call Stack (most recent call first):
>> ./mitkFunctionInstallAutoLoadModules.cmake:102
>> ./mitkFunctionCreateBlueBerryApplication.cmake:188
>>  Our cmake.
>>
>> Idem with org_mitk_gui_qt_common_legacy,
>> org_mitk_gui_qt_core_application, movie maker, segmentation, etc.
>>
>> My application opens with my main plugin but I can't see the other
>> plugins, like movie maker, segmentation, etc. Do you have any ideas
>> how I could fix this? Just to be clear, it does work perfectly on Windows.
>> The warnings and missing plugins is only on OS X.
>>
>> Thank you for your time.
>>
>> Nil
> --
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> mitk-users mailing list
> mitk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mitk-users


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Re: [mitk-users] Ignoring unknown target "org_blueberry_core_jobs" for installation

[Nil Goyette]

Hi all,

Here's more information if it can help someone helping me.

- It works perfectly on linux too.
- There's no error message if I use EXCLUDE_PLUGINS instead of PLUGINS 
(or if I use neither) but I only see my plugins, not mitk's. On Windows 
and Linux, the toolbar is filled, so I guess I see the complete list of 
plugins.

I'm not sure what else to test. Anyone?

Nil

Le 2016-09-22 à 16:24, Nil Goyette a écrit :
> Hi all,
>
> I finally ported my application to MITK 2016.03 and everything went well
> enough. As always, thank you for your good job.
>
> I do have a problem on OS X when I try to cmake (yes, the verb ^^)
> though. I see a serie of warnings:
>
> CMake warning at ./mitkFunctionInstallAutoLoadModules.cmake:87
> (message):
> Ignoring unknown target "org_blueberry_core_jobs" for installation.
> Call Stack (most recent call first):
> ./mitkFunctionInstallAutoLoadModules.cmake:102
> ./mitkFunctionCreateBlueBerryApplication.cmake:188
> Our cmake.
>
> Idem with org_mitk_gui_qt_common_legacy,
> org_mitk_gui_qt_core_application, movie maker, segmentation, etc.
>
> My application opens with my main plugin but I can't see the other
> plugins, like movie maker, segmentation, etc. Do you have any ideas how
> I could fix this? Just to be clear, it does work perfectly on Windows.
> The warnings and missing plugins is only on OS X.
>
> Thank you for your time.
>
> Nil

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Re: [mitk-users] Neglected icon attribute in the extension point of the QmitkDataManagerView

[Nil Goyette]

Hi all,

Can I get an update on this? I lost many hours trying to to load an icon 
for my action and I can't get it to work. There's is still this old task 
https://phabricator.mitk.org/rMITKa5312246035bdf65d22364816b508129ce06c16d 
on this bug.

I couldn't find any plugin in MITK's code that loads an icon for a 
context menu using plugin.xml so I can't copy what you did.

Are Sascha's concerns still valid? It won't work if my plugin 
(resources) are loaded after this line
contextMenuAction = new QAction( QIcon(cmIcon), cmLabel, parent);
in QmitkDataManagerView.cpp? Is there a safe place to put my icon?

Nil

Le 2014-12-01 à 13:19, Martin Klemm a écrit :
> Hi
>
> I merged the patch into the master and closed the bug last week. The
> changes (without the additions of Sascha) are already included in the
> MITK 2014.10 release.
>
> Best
>
> Martin
>
> On 12/01/2014 12:40 AM, Sascha Zelzer wrote:
>> I just shortly looked at the patch. It indeed relies on a qrc location.
>> This will only work if the contributing plug-in is loaded (otherwise,
>> the Qt resources would not be accessible). The final fix should rely on
>> the CTK resource system to retrieve the icon (as specified in the
>> CACHED_RESOURCE_FILES variable) and create a QIcon instance from an
>> in-memory representation of the icon similar to the code creating the
>> MITK Workbench toolbar and menu entries showing the view icons.
>>
>> Best,
>> Sascha
>>
>> On 11/09/2014 10:27 PM, Rostislav Khlebnikov wrote:
>>> Hm, setting it to the "qrc" location (i.e. ":/icons/icon.png") seems to
>>> work.
>>>
>>> All best,
>>>   Rostislav.
>>>
>>> On 09/11/2014 20:41, Rostislav Khlebnikov wrote:
 Hi guys,

 am I missing something? I applied the patch attached to the bug, but the
 icon is still missing.

 I added my icon to the CACHED_RESOURCE_FILES in files.cmake for my
 plugin. The location is, say, "resources/icon.png" and in plugin.xml I have
 >>> icon="resources/icon.png" class="MyAction" />

 Any ideas on why this might not work?

 Thanks,
Rostislav.

 On 10/07/2014 10:43, Martin Klemm wrote:
> Hi Sascha,
>
> thanks for the answer and sorry for not writing you for so long. I
> opened a bug report http://bugs.mitk.org/show_bug.cgi?id=17907 and
> attached the patch file. Is there something else I have to do now? Or
> will you do the rest?
>
> Best regards,
>
> Martin
>
>
>
> On 28.05.2014 18:09, Sascha Zelzer wrote:
>> Hi Martin,
>>
>> I think it just hasn't been done yet. I also don't see a reason for not
>> doing it. Would you be up for contributing a patch to enable icons in
>> the context menu?
>>
>> Thanks,
>>
>> Sascha
>>
>> On 05/06/2014 10:37 AM, Martin Klemm wrote:
>>> Hello,
>>>
>>> I was successful in adding a new context menu action to the data manager
>>> menu:
>>>
>>> >> point="org.mitk.gui.qt.datamanager.contextMenuActions">
>>> >> label="Group"
>>> icon="resources/grouping_icon.png" class="GroupAction" />
>>> 
>>>
>>> The action is shown and works as expected, however, the icon is missing.
>>> In QmitkDataManagerView::CreateQtPartControl(QWidget* parent) the
>>> context menu extension service is opened to read the descriptor name,
>>> label, class and icon attribute but is not using the icon to create the
>>> action:
>>>
>>> ...
>>> if((*cmActionsIt)->GetAttribute("nodeDescriptorName",
>>> cmNodeDescriptorName)
>>> && (*cmActionsIt)->GetAttribute("label", cmLabel)
>>> && (*cmActionsIt)->GetAttribute("class", cmClass))
>>>   {
>>> (*cmActionsIt)->GetAttribute("icon", cmIcon);
>>> // create context menu entry here
>>> tmpDescriptor =
>>> QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(QString::fromStdString(cmNodeDescriptorName));
>>>
>>>
>>> contextMenuAction = new QAction( 
>>> QString::fromStdString(cmLabel),
>>> parent);
>>> ...
>>>
>>> Is there a reason why the icon is not used?
>>>
>>> Best regards,
>>>
>>> Martin
>>>
>>> --
>>>
>>> Is your legacy SCM system holding you back? Join Perforce May 7 to
>>> find out:
>>>  3 signs your SCM is hindering your productivity
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[mitk-users] Loading scene event

[Nil Goyette]

Hi All,

I asked some months ago if there was a way (signal/slot, bool somewhere, 
etc.) to know if a scene is loading, or finished loading. Someone told 
me there was no way to know at the moment.

The problem is that, as our application grow bigger and more complex, we 
need to know! I hacked my way around the problem but this is getting 
dirty and I would prefer a good solution.

I'm not a MITK's expert, but I'm starting to know how stuff works and I 
want to code it. Can someone tells me how it *could* be done? A 
signal/slot would be realy cool, but I don't see how this would be 
feasible. Any idea to do it properly? Something that you would want to 
merge. Thank you for your time.

Nil


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[mitk-users] mitkFiberBundleMapper3D

[Nil Goyette]

Hi all,

I don't know if Peter Neher is still the DiffusionImage expert. If it's 
the case, hi Peter.


I found this line
fiberPolyData->GetPointData()->AddArray(fiberBundle->GetFiberColors());
in mitkFiberBundleMapper3D in 2015.05 (still in master) and I think this 
is unfortunate.


It changes the last modified time (MTime) of the polydata, which can 
make some algorithms execute again. For example, lets say you

1) load a FiberBundle
2) build an Octree in NodeAdded (so, before the mapper does anything)
3) call BuildLocator() on it to avoid the automatic call later.
4) The mapper is called, MTime is updated.
5) BuildLocator() will be called/built again when you use the Octree 
because it thinks the object was modified.


You're the expert here, so you may know something I don't, but I'm 
pretty sure a mapper shouldn't modify its mapped object.


I tested removing that line and adding
m_FiberPolyData->GetPointData()->AddArray(GetFiberColors());
in the constructor and in SetFiberPolyData() after the color has been 
set. It seems good to me. Maybe I'm forgetting some edge cases though.


Nil

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Re: [mitk-users] IO module not loaded in package

[Nil Goyette]

Hi Sascha,

Thank you for your answer. You are right. My 'hack' plugin was the only 
plugin depending in MitkCore! As for the other 3 questions, I think I'm 
following the rules. Everything is wqorking as expected, thanks again ;)


Nil


Le 2016-06-20 à 02:03, Sascha Zelzer a écrit :


Hi Nil,


1) As far as I remember, the plug-in order when calling 
mitkFunctionCreateBlueBerryApplication does not matter


2) ctkPluginActivator is the base class for all CTK plugin activators. 
The berry::AbstractUICTKPlugin class derives from it (well, from 
berry::Plugin which in turn implements ctkPluginActivator) and can be 
used in BlueBerry Workbench plug-ins. It is nor required to use it, 
but it provides some convenience methods for easier access to 
preferences, and the plug-in persistend state area for example. Last, 
the berry::IApplication is the main entry point for a complete 
application. It is tied to the org.blueberry.osgi.applications 
extension point. Usually, you would not create your own but rely on 
the one provided by MITK.


3) Q_PLUGIN_METADATA is not used by CTK or BlueBerry but required by 
the Qt plugin system, if I remember correctly. Using the project name 
as the identifier is a good idea to avoid confusion.



Now, the auto-load issue. The general problem is, that the install 
scripts are quite involved because they try to do the "right thing". 
When you install a BlueBerry application via 
mitkFunctionCreateBlueBerryApplication, the CMake macro is able to 
retrieve all transitive plug-in dependencies (also from external 
projects) and install them explicitly.  The auto-load modules (which 
also need to be installed explicitly) are derived from this set of 
plug-ins. When you declare a module in your project to be auto-loaded 
with MitkCore (which belongs to the external MITK project) but none of 
your own plug-ins have a direct dependency on MitkCore, the CMake 
scripts are not able to find your auto-load module and install it 
(they will only "see" the auto-load modules from external projects 
like MITK itself). This is a bug in the system. Your work-around works 
because your dummy-plugin depends on MitkCore and when you install 
your application the scripts see the MitkCore dependency and now also 
has the current list of modules that are to be auto-loaded with it 
(including yours). A better work-around could be to just add the 
MitkCore dependency explicitly to one of your existing plug-ins (even 
if that plug-in already transitively depends on it).


I couldn't think of a quick solution to fix the install scripts in a 
good way yet. One approach could be to expose another CMake macro 
which lets you install auto-load modules explicitly yourself 
(essentially refactoring the mitkFunctionInstallAutoLoadModules macro).



Cheers,

Sascha


On 06/16/2016 07:19 PM, Nil Goyette wrote:


Hi all.

Is there someone who can answer my questions?
My IO module is loading now, but this is such an hack, maybe an 
answer to 2) could help me.

Thank you for your time.

Nil

Le 2016-06-08 à 10:32, Nil Goyette a écrit :


Hi all,

Thank you Pierre-Yves and Stefan. I did find a workaround yesterday. 
It's totally a hack and I don't even understand how it can work. I 
simply added back a plugin that I deleted earlier. The plugin only 
contains its activator, depends on CTK and MitkCore, requires no 
other plugin. It simply does nothing. And yet, my IO module works 
when I use it in my app. It's as if doing something random fixed my 
module.


Here are some questions for you!
1) I know the order of the plugins in Plugins/plugin.xml is 
important, but is it important in Apps/{name}/CMakeList.txt, in the 
list of plugins that we pass to mitkFunctionCreateBlueBerryApplication?
2) What's the differences between ctkPluginActivator, 
berry::AbstractUICTKPlugin and berry::IApplication? When should we 
use them? I discovered that we use them almost randomly. This can't 
be right :/
3) Is the ID important in the activator? "Q_PLUGIN_METADATA(IID 
"org_imeka_app")" Should it be identical to the project's name in 
the plugin's cmakelist? I tested with random names and it seems to work.


Le 2016-06-08 à 03:53, Kislinskiy, Stefan a écrit :


Hi,

I remember a similar question from a coworker. He wasn’t able to 
get his autoload modules loaded from the package he made out of his 
project template based application. He also found a solution to 
this bug if I remember correctly: He added the corresponding bin 
folder of the module in charge to the path, so i. e., when you 
autoload with MitkCore, this would be MITK-build/bin/MitkCore/Release.


Does it help (for now) as workaround?

Best,

Stefan

*From:*Pierre-Yves Menguy [mailto:pierreyves.men...@gmail.com]
*Sent:* Dienstag, 7. Juni 2016 16:11
*To:* Nil Goyette
*Cc:* mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] IO module not loaded in package

Hello,

I had a similar problem when updating from 2014.10 to 201

Re: [mitk-users] IO module not loaded in package

[Nil Goyette]

Hi all,

Thank you Pierre-Yves and Stefan. I did find a workaround yesterday. 
It's totally a hack and I don't even understand how it can work. I 
simply added back a plugin that I deleted earlier. The plugin only 
contains its activator, depends on CTK and MitkCore, requires no other 
plugin. It simply does nothing. And yet, my IO module works when I use 
it in my app. It's as if doing something random fixed my module.


Here are some questions for you!
1) I know the order of the plugins in Plugins/plugin.xml is important, 
but is it important in Apps/{name}/CMakeList.txt, in the list of plugins 
that we pass to mitkFunctionCreateBlueBerryApplication?
2) What's the differences between ctkPluginActivator, 
berry::AbstractUICTKPlugin and berry::IApplication? When should we use 
them? I discovered that we use them almost randomly. This can't be right :/
3) Is the ID important in the activator? "Q_PLUGIN_METADATA(IID 
"org_imeka_app")" Should it be identical to the project's name in the 
plugin's cmakelist? I tested with random names and it seems to work.


Le 2016-06-08 à 03:53, Kislinskiy, Stefan a écrit :


Hi,

I remember a similar question from a coworker. He wasn’t able to get 
his autoload modules loaded from the package he made out of his 
project template based application. He also found a solution to this 
bug if I remember correctly: He added the corresponding bin folder of 
the module in charge to the path, so i. e., when you autoload with 
MitkCore, this would be MITK-build/bin/MitkCore/Release.


Does it help (for now) as workaround?

Best,

Stefan

*From:*Pierre-Yves Menguy [mailto:pierreyves.men...@gmail.com]
*Sent:* Dienstag, 7. Juni 2016 16:11
*To:* Nil Goyette
*Cc:* mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] IO module not loaded in package

Hello,

I had a similar problem when updating from 2014.10 to 2016.03 (big gap).
When looking into it, I noticed my library wasn't packaged, it was 
left out during the process (both NSIS and ZIP).


I couldn't find a fix that involved only changes into my own code, and 
my code was similar to the IOExt/Diffusion module.


As a last chance, I created a MITK fork to include my own IO module 
(and several small changes as image compression during the writing 
process), and the package was able to recognize the module and ship it 
with my own app (which is still in a separate project).


I tried to check out the demo template on Github (commit 1552ddd), and 
it fails to pack with this log :


1>EXEC : warning : target 'MyAwesomeLib.dll' is not absolute...

1>EXEC : warning : target 'MyAwesomeLib.dll' does not exist...

I'm using Windows, compiling under vs2013 x64.

I'm sorry because my solution may not suit your situation, I just 
wanted to add my own insight and maybe get a solution if someone post 
it in this thread.


Pierre-Yves.

On 7 June 2016 at 15:01, Nil Goyette <nil.goye...@imeka.ca 
<mailto:nil.goye...@imeka.ca>> wrote:


Hi all,

On MITK2015.05, I renamed our plugin to respect a .app, .eager and .view
logic, and moved some files. Everything still work perfectly, except
when I try to run the application from a package. My IO module (using
AUTOLOAD_WITH) is not loaded but everything else is perfect.

I get no error message or warning on Windows and Linux, but I get this
on OS X:
Pre-loading library "liborg_mitk_gui_qt_ext" failed: "Cannot load
library liborg_mitk_gui_qt_ext: (dlopen(liborg_mitk_gui_qt_ext.dylib,
5): image not found"

I tried changing the order of the modules and the plugins in their
CMakeList. I tried doing exactly what you do in your IO modules (like
DiffusionIO). I tried many irrelevant things that I won't mention :) I'm
not sure what to test now.

Do you know what could cause this? I would gladly take any hints or
ideas! Because right now my only idea is to revert my huge commit, then
rename one thing at the time, compile, create a package, test, rename
the next thing, ...

Nil


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J-Flow, sFlow a

[mitk-users] IO module not loaded in package

[Nil Goyette]

Hi all,

On MITK2015.05, I renamed our plugin to respect a .app, .eager and .view 
logic, and moved some files. Everything still work perfectly, except 
when I try to run the application from a package. My IO module (using 
AUTOLOAD_WITH) is not loaded but everything else is perfect.

I get no error message or warning on Windows and Linux, but I get this 
on OS X:
Pre-loading library "liborg_mitk_gui_qt_ext" failed: "Cannot load 
library liborg_mitk_gui_qt_ext: (dlopen(liborg_mitk_gui_qt_ext.dylib, 
5): image not found"

I tried changing the order of the modules and the plugins in their 
CMakeList. I tried doing exactly what you do in your IO modules (like 
DiffusionIO). I tried many irrelevant things that I won't mention :) I'm 
not sure what to test now.

Do you know what could cause this? I would gladly take any hints or 
ideas! Because right now my only idea is to revert my huge commit, then 
rename one thing at the time, compile, create a package, test, rename 
the next thing, ...

Nil


--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: [mitk-users] Image Cropper -> AffineImageCropperInteractor

[Nil Goyette]

Hi All,

Stefan, no, I didn't miss that. And as I wrote, the interactor is also 
broken on the MITK Workbench so my code is irrelevant here.

Any news on this? I was going to start coding my own but I prefer asking 
before, in case someone is already working on it.

Nil

Le 2016-04-27 à 11:02, Kislinskiy, Stefan a écrit :
> Maybe you missed the unusual state machine / event config combination of the 
> fixed image cropper?
> https://github.com/MITK/MITK/blob/master/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp#L362-365
>
> Best,
> Stefan
>
> -Original Message-
> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
> Sent: Mittwoch, 27. April 2016 15:27
> To: Kislinskiy, Stefan; Wegner; mitk-users@lists.sourceforge.net
> Subject: Re: AW: [mitk-users] Image Cropper -> AffineImageCropperInteractor
>
> HI Stefan and Ingmar,
>
> "I guess, you're not working with the 2016.03 release / latest master branch?"
> Yes, I was. You made me doubt so I downloaded a fresh 2016.03 installer and 
> tested with several images.
>
> I can see 2 "modes", either
> - the mouse is reversed (go farther to make the BO smaller) but the scaling 
> behavior is correct. The majority of my images have this problem.
> - the mouse is not reversed but the scaling behavior is horrible. As 
> explained in my last message, each ctrl-right-click+move makes the BO smaller 
> in all directions, wherever I go. Here's an image where I can see this:
> https://drive.google.com/file/d/0B6we0HAWUUiEMkx3VS1fb21iVzg/view?usp=sharing
>
> I don't actually use the plugin, I'm just testing the 
> AffineImageCropperInteractor with it because I need it :)
>
> Nil
>
> Le 2016-04-27 à 02:43, Kislinskiy, Stefan a écrit :
>> Hi Nil and Ingmar,
>>
>> as we originally planned to include the new image cropper in the 2016.03 
>> release, we didn't fix the current image cropper (which broke somewhere 
>> since the 2015.05 release) just until quite recently, to have a working 
>> image cropper for the 2016.03 release. For me, it's working fine now. I 
>> guess, you're not working with the 2016.03 release / latest master branch?
>>
>> As Ingmar said, we improved/rewrote the image cropper but unfortunately it 
>> just didn't make it into 2016.03. However, we'll merge the new image cropper 
>> very soon to replace the current one. We'll keep you up-to-date.
>>
>> Best,
>> Stefan
>>
>> 
>> Von: Wegner [iweg...@gmx.de]
>> Gesendet: Dienstag, 26. April 2016 21:09
>> An: Nil Goyette; mitk-users@lists.sourceforge.net
>> Betreff: Re: [mitk-users] Image Cropper ->
>> AffineImageCropperInteractor
>>
>> Hi Nil,
>> I just heard from the users meeting that the mitk team was working for
>> a replacement of that image cropper plugin!
>>
>> For the time being try to pick the corners of the square from the
>> inside and then to move and resize it (right, middle, left mouse
>> button). I remember that when you cross the middle the sizing inverts
>> so a size decrease turned into an increase.
>> Tricky but who would have known that this plugin would be used from so
>> many users!
>>
>> Best,
>> Ingmar
>>
>> Am 26.04.2016 um 17:49 schrieb Nil Goyette:
>>> Hi all,
>>>
>>> I was searching my good old Ctrl-click AffineInteractor and finally
>>> found it in AffineImageCropperInteractor. A free 3D interactor is
>>> really nice, but... it's unusable now :(
>>>
>>> The translation part works perfectly, but the scaling (right mouse
>>> button) is horrible. Each time I right-click+move, the bounding
>>> object gets smaller in all dimensions. So I try to fix the other
>>> dimensions and fall in the same trap! Again and again.
>>>
>>> I tought the bug was in my code but I have the same problem in the
>>> workbench. Try it! It's really hard now to place a BO around the
>>> things you want.
>>>
>>> Nil

--
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Re: [mitk-users] Image Cropper -> AffineImageCropperInteractor

[Nil Goyette]

HI Stefan and Ingmar,

"I guess, you're not working with the 2016.03 release / latest master 
branch?"
Yes, I was. You made me doubt so I downloaded a fresh 2016.03 installer 
and tested with several images.

I can see 2 "modes", either
- the mouse is reversed (go farther to make the BO smaller) but the 
scaling behavior is correct. The majority of my images have this problem.
- the mouse is not reversed but the scaling behavior is horrible. As 
explained in my last message, each ctrl-right-click+move makes the BO 
smaller in all directions, wherever I go. Here's an image where I can 
see this:
https://drive.google.com/file/d/0B6we0HAWUUiEMkx3VS1fb21iVzg/view?usp=sharing

I don't actually use the plugin, I'm just testing the 
AffineImageCropperInteractor with it because I need it :)

Nil

Le 2016-04-27 à 02:43, Kislinskiy, Stefan a écrit :
> Hi Nil and Ingmar,
>
> as we originally planned to include the new image cropper in the 2016.03 
> release, we didn't fix the current image cropper (which broke somewhere since 
> the 2015.05 release) just until quite recently, to have a working image 
> cropper for the 2016.03 release. For me, it's working fine now. I guess, 
> you're not working with the 2016.03 release / latest master branch?
>
> As Ingmar said, we improved/rewrote the image cropper but unfortunately it 
> just didn't make it into 2016.03. However, we'll merge the new image cropper 
> very soon to replace the current one. We'll keep you up-to-date.
>
> Best,
> Stefan
>
> 
> Von: Wegner [iweg...@gmx.de]
> Gesendet: Dienstag, 26. April 2016 21:09
> An: Nil Goyette; mitk-users@lists.sourceforge.net
> Betreff: Re: [mitk-users] Image Cropper -> AffineImageCropperInteractor
>
> Hi Nil,
> I just heard from the users meeting that the mitk team was working for a
> replacement of that image cropper plugin!
>
> For the time being try to pick the corners of the square from the inside
> and then to move and resize it (right, middle, left mouse button). I
> remember that when you cross the middle the sizing inverts so a size
> decrease turned into an increase.
> Tricky but who would have known that this plugin would be used from so
> many users!
>
> Best,
> Ingmar
>
> Am 26.04.2016 um 17:49 schrieb Nil Goyette:
>> Hi all,
>>
>> I was searching my good old Ctrl-click AffineInteractor and finally
>> found it in AffineImageCropperInteractor. A free 3D interactor is really
>> nice, but... it's unusable now :(
>>
>> The translation part works perfectly, but the scaling (right mouse
>> button) is horrible. Each time I right-click+move, the bounding object
>> gets smaller in all dimensions. So I try to fix the other dimensions and
>> fall in the same trap! Again and again.
>>
>> I tought the bug was in my code but I have the same problem in the
>> workbench. Try it! It's really hard now to place a BO around the things
>> you want.
>>
>> Nil
>>
>> --
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>> of
>> your business applications. It resolves application problems quickly and
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[mitk-users] Image Cropper -> AffineImageCropperInteractor

[Nil Goyette]

Hi all,

I was searching my good old Ctrl-click AffineInteractor and finally 
found it in AffineImageCropperInteractor. A free 3D interactor is really 
nice, but... it's unusable now :(

The translation part works perfectly, but the scaling (right mouse 
button) is horrible. Each time I right-click+move, the bounding object 
gets smaller in all dimensions. So I try to fix the other dimensions and 
fall in the same trap! Again and again.

I tought the bug was in my code but I have the same problem in the 
workbench. Try it! It's really hard now to place a BO around the things 
you want.

Nil

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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Re: [mitk-users] Rebuilding on Mac

[Nil Goyette]

Ah, good. It's an easier fix :)
I'll cherry-pick that. Thank you.

Le 2016-04-22 02:12, Kislinskiy, Stefan a écrit :
> Hi,
>
> see http://bugs.mitk.org/show_bug.cgi?id=19686 :-)
>
> Best,
> Stefan
> ____________
> Von: Nil Goyette [nil.goye...@imeka.ca]
> Gesendet: Donnerstag, 21. April 2016 20:47
> An: mitk-users@lists.sourceforge.net
> Betreff: Re: [mitk-users] Rebuilding on Mac
>
> Hi all,
>
> We had a lot of problems building OS X on 2015.05 and it's *much* better 
> right now. Qt5LinguistTools is the only problem now. As you wrote, it's easy 
> to fix, simply change Qt5LinguistTools_DIR in the inner MITK_build dir. It's 
> strange, considering that all other Qt libraries are found, but that's not a 
> big deal at all.
>
> I'm on OS X 10.9 and I installed Qt5.5.1 by the installer found on the Qt 
> website in ~/Qt/*
> Thank you for your good work.
>
> Nil
>
> Le 2016-04-15 06:13, Admin Uniapp a écrit :
> Hi Sascha,
>
> I tried deleting the cache a few times and rebuilding but every time it comes 
> back with the same error. I remember when I installed MITK on linux I had to 
> install qttools5-dev-tools or something similar and add the 
> Qt5LinguistTools_DIR to the cmake file and point it to the right directory 
> installed by qttools5-dev-tools. Is there a similar step for mac? Or this 
> should not be necessary at all?
>
> Many thanks
> Dora
>
> On Wed, Apr 13, 2016 at 9:16 PM, Sascha Zelzer 
> <sascha.zel...@gmail.com<mailto:sascha.zel...@gmail.com>> wrote:
> The linguist tools are a dependency of every CTK plug-in
>
> https://github.com/commontk/CTK/blob/master/CMake/ctkMacroBuildPlugin.cmake#L319
>
> You shouldn't need to add the Qt5*_DIR CMake variables yourself. I'd
> suggest to try removing all of the Qt5*_DIR variables from the CMake
> cache and run configure again (from the MITK build directory, not the
> MITK-superbuild one).
>
> Cheers,
> Sascha
>
> On 04/13/2016 10:08 PM, Kislinskiy, Stefan wrote:
>> That's strange as i'm pretty sure that the linguist tools are not a 
>> dependency of MITK, not even a transitive one. Is it possible that you have 
>> that dependency in your own code/module/plugin/app? Search for "Qt5|" in all 
>> of your CMakeLists.txt files to get an overview of your Qt dependencies. The 
>> MITK Qt 5 dependencies are listed in [1]. A few optional modules have an 
>> additional dependency to Qt5Quick.
>>
>> [1] https://github.com/MITK/MITK/blob/master/CMakeLists.txt#L207
>>
>> Best,
>> Stefan
>>
>> 
>> Von: Admin Uniapp [contactuni...@gmail.com<mailto:contactuni...@gmail.com>]
>> Gesendet: Mittwoch, 13. April 2016 19:55
>> An: MITK
>> Betreff: Re: [mitk-users] Rebuilding on Mac
>>
>> Hi again,
>>
>> I tried to build from the master branch again today, this time at build 
>> time, it complains about not finding "Qt5LinguistTools", so I added 
>> Qt5LinguistTools_DIR to the cmake and pointed it to the right 
>> Qt5LinguistToolsConfig.cmake file but it still complains about not finding 
>> the tool. Am I doing something wrong here?
>>
>> Many thanks
>> Dora
>>
>> On Wed, Apr 13, 2016 at 6:55 PM, Admin Uniapp 
>> <<mailto:contactuni...@gmail.com>contactuni...@gmail.com<mailto:contactuni...@gmail.com><mailto:<mailto:contactuni...@gmail.com>contactuni...@gmail.com<mailto:contactuni...@gmail.com>>>
>>  wrote:
>> Hi again,
>>
>> I tried to build from the master branch again today, this time at build 
>> time, it complains about not finding "Qt5LinguistTools", so I added 
>> Qt5LinguistTools_DIR to the cmake and pointed it to the right 
>> Qt5LinguistToolsConfig.cmake file but it still complains about not finding 
>> the tool. Am I doing something wrong here?
>>
>> Many thanks
>> Dora
>>
>> On Wed, Apr 13, 2016 at 7:45 AM, Kislinskiy, Stefan 
>> <s.kislins...@dkfz-heidelberg.de<mailto:s.kislins...@dkfz-heidelberg.de><mailto:<mailto:s.kislins...@dkfz-heidelberg.de>s.kislins...@dkfz-heidelberg.de<mailto:s.kislins...@dkfz-heidelberg.de>>>
>>  wrote:
>> Hi,
>>
>> after some fixes yesterday, the current development branch is supposed to be 
>> the base for the upcoming release. Just the release branching, version 
>> number update and MITK-ProjectTemplate adaptions are missing. According to 
>> [1] the code is compiling also on OS X. What's the compile errors you have 
>> had?
>>
>> [1] http://goo.gl/pHvIs9
>>
>&

Re: [mitk-users] Rebuilding on Mac

[Nil Goyette]

Hi all,

We had a lot of problems building OS X on 2015.05 and it's *much* better 
right now. Qt5LinguistTools is the only problem now. As you wrote, it's 
easy to fix, simply change Qt5LinguistTools_DIR in the inner MITK_build 
dir. It's strange, considering that all other Qt libraries are found, 
but that's not a big deal at all.


I'm on OS X 10.9 and I installed Qt5.5.1 by the installer found on the 
Qt website in ~/Qt/*

Thank you for your good work.

Nil

Le 2016-04-15 06:13, Admin Uniapp a écrit :

Hi Sascha,

I tried deleting the cache a few times and rebuilding but every time 
it comes back with the same error. I remember when I installed MITK on 
linux I had to install qttools5-dev-tools or something similar and add 
the Qt5LinguistTools_DIR to the cmake file and point it to the right 
directory installed by qttools5-dev-tools. Is there a similar step for 
mac? Or this should not be necessary at all?


Many thanks
Dora

On Wed, Apr 13, 2016 at 9:16 PM, Sascha Zelzer 
> wrote:


The linguist tools are a dependency of every CTK plug-in


https://github.com/commontk/CTK/blob/master/CMake/ctkMacroBuildPlugin.cmake#L319

You shouldn't need to add the Qt5*_DIR CMake variables yourself. I'd
suggest to try removing all of the Qt5*_DIR variables from the CMake
cache and run configure again (from the MITK build directory, not the
MITK-superbuild one).

Cheers,
Sascha

On 04/13/2016 10:08 PM, Kislinskiy, Stefan wrote:
> That's strange as i'm pretty sure that the linguist tools are
not a dependency of MITK, not even a transitive one. Is it
possible that you have that dependency in your own
code/module/plugin/app? Search for "Qt5|" in all of your
CMakeLists.txt files to get an overview of your Qt dependencies.
The MITK Qt 5 dependencies are listed in [1]. A few optional
modules have an additional dependency to Qt5Quick.
>
> [1] https://github.com/MITK/MITK/blob/master/CMakeLists.txt#L207
>
> Best,
> Stefan
>
> 
> Von: Admin Uniapp [contactuni...@gmail.com
]
> Gesendet: Mittwoch, 13. April 2016 19:55
> An: MITK
> Betreff: Re: [mitk-users] Rebuilding on Mac
>
> Hi again,
>
> I tried to build from the master branch again today, this time
at build time, it complains about not finding "Qt5LinguistTools",
so I added Qt5LinguistTools_DIR to the cmake and pointed it to the
right Qt5LinguistToolsConfig.cmake file but it still complains
about not finding the tool. Am I doing something wrong here?
>
> Many thanks
> Dora
>
> On Wed, Apr 13, 2016 at 6:55 PM, Admin Uniapp
>> wrote:
> Hi again,
>
> I tried to build from the master branch again today, this time
at build time, it complains about not finding "Qt5LinguistTools",
so I added Qt5LinguistTools_DIR to the cmake and pointed it to the
right Qt5LinguistToolsConfig.cmake file but it still complains
about not finding the tool. Am I doing something wrong here?
>
> Many thanks
> Dora
>
> On Wed, Apr 13, 2016 at 7:45 AM, Kislinskiy, Stefan
>> wrote:
> Hi,
>
> after some fixes yesterday, the current development branch is
supposed to be the base for the upcoming release. Just the release
branching, version number update and MITK-ProjectTemplate
adaptions are missing. According to [1] the code is compiling also
on OS X. What's the compile errors you have had?
>
> [1] http://goo.gl/pHvIs9
>
> Best,
> Stefan
> 
> Von: Admin Uniapp [contactuni...@gmail.com
>]
> Gesendet: Dienstag, 12. April 2016 18:41
> An: Kislinskiy, Stefan
> Cc: Clarkson, Matt; MITK
> Betreff: Re: [mitk-users] Rebuilding on Mac
>
> Hi everyone,
>
> Following my last month questions and with your help, I did
manage to install MITK 2015.05.2 using Qt4 on a new iMac. However,
a few days ago I updated the OSX El Capitan with a new security
update and had to rebuild my MITK plugins to update few changes I
had in my code. Since, then I have been facing strange problems,
first of all the same MITK code was not building again throwing
errors at:
>
> Modules/MapperExt/src/mitkUnstructuredGridMapper2D.cpp
> Modules/MapperExt/src/vtkMitkOpenGLVolumeTextureMapper3D.cpp
>
> Complaining about using delete[] for arrays in 

Re: [mitk-users] SetDataStorage in QmitkDataManagerView.cpp

[Nil Goyette]

Hi Stefan, Michael,

I don't really have an opinion on the subject at hand because I know 
almost nothing about blueberry.
My suggestion is simply : if you keep the code this way, can you please 
always call SetDataManager()? It will make your code an epsilon less 
complicated and your users' code a lot less complicated.


In all cases, we did it in our in-house version of MITK. It would be 
simpler for us (and maybe for other) if it was already in MITK.


Nil

Le 2016-04-04 05:05, Müller, Michael a écrit :


Hi Nil, Stefan,

Well, I disagree to what you said Stefan and I suppose to leave it how 
it is implemented. We had some hard discussions about how “dynamic” 
the whole DataManager monster should be. The key point is – surprise, 
surprise - that other views may add context menu action to the 
DataManager without any dependency. As a central view within a highly 
dynamic application framework this makes sense.


I agree that there are much lines of BlueBerry code needed making some 
files or sections hard to read. And I agree that the DataManager 
monster class has grown to Godzilla in the meantime. Maybe introducing 
some shortcut code for Blueberry and some refactoring and care for the 
DataManager is the alternative to going back to good old monolithic times.


Bye

Michael

*Von:*Kislinskiy, Stefan [mailto:s.kislins...@dkfz-heidelberg.de]
*Gesendet:* Montag, 4. April 2016 10:34
*An:* Nil Goyette <nil.goye...@imeka.ca>; mitk-users@lists.sourceforge.net
*Betreff:* Re: [mitk-users] SetDataStorage in QmitkDataManagerView.cpp

Hi Nil,

as far as I know, the context menu entries of the Data Manager were 
never fully implemented in BlueBerry. Well, to be honest, they might 
have been implemented since the last BlueBerry update a year ago but 
you probably know more than me when you are fiddling around with them 
at the moment. :-) However, I know that there are (were?) historic, 
ugly, hard-coded workarounds for certain data types in the Data 
Manager, sorry. In the BlueBerry/OSGI/Eclipse world, this is supposed 
to be loosely coupled and dynamic. If it isn’t in MITK (which I 
guess), that would be a nice mini project. You could help us by filing 
a feature request in our bug tracker for your needs/thoughts and 
setting its target milestone to AfterNextRelease, in order to have a 
realistic chance of having these features implemented in the release 
after next.


Best regards,
Stefan

*From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
*Sent:* Freitag, 1. April 2016 17:38
*To:* mitk-users@lists.sourceforge.net 
<mailto:mitk-users@lists.sourceforge.net>

*Subject:* [mitk-users] SetDataStorage in QmitkDataManagerView.cpp

Hi MITK,

I was creating a context menu action and I saw that SetDataStorage was 
never called. I found in QmitkDataManagerView.cpp this snippet:

if(className == "QmitkCreatePolygonModelAction")
{
  contextMenuAction->*SetDataStorage*(this->GetDataStorage());
  if(smoothed == "false")
  {
contextMenuAction->SetSmoothed(false);
  }
  else
  {
contextMenuAction->SetSmoothed(true);
  }
contextMenuAction->SetDecimated(m_SurfaceDecimation);
}
else if(className == "QmitkStatisticsAction")
{
  contextMenuAction->SetFunctionality(this);
}
else if(className == "QmitkCreateSimulationAction")
{
  contextMenuAction->*SetDataStorage*(this->GetDataStorage());
}

I don't understand this decision. Why not simply always set it? I know 
that Smoothed, Decimated and Functionality are hacks useful only to a 
single class, but DataStorage is useful in many cases. Well, I don't 
know for the other programmers out there, but I often need the 
DataStorage in my context menu actions.


Right now, I'm forced to use my plugin's context, getServiceReference, 
IDataStorageService and include a lot of files to get it. This could 
easily be avoided if SetDataStorage was always called. I just tried it 
and it works perfectly. In fact, I don't see how it could break anything.


Nil



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Re: [mitk-users] Scene properties

[Nil Goyette]

Ah, thank you, mitk::PersistenceService::LoadModule() was the missing 
piece of information.

The service is not a nullptr anymore and I can get the properties 
associated with an ID and they are kept during the lifetime of the 
application.

So, I added the call to AddPropertyListReplacedObserver(this) but 
BeforePropertyListReplaced() and AfterPropertyListReplaced() are never 
called. I thought they would be called when the user saves and load a scene.
Did I miss something?

Le 2016-04-06 05:49, Kolb, Christoph a écrit :
> I have just tested the PersistenceService in a Plugin and got the same error 
> message:
> "The calling module probably misses a US_MODULE_NAME compile definition 
> and/or a call to
> US_INITIALIZE_MODULE in one of its source files."
>
> It worked after I added a dependency to MitkPersistence and
> called mitk::PersistenceService::LoadModule() in the constructor of my 
> pluginView. I also needed to
> put US_INITIALIZE_MODULE in the source.
>
> Regards
> Christoph
>
> On Tue, 2016-04-05 at 19:09 +0200, Sascha Zelzer wrote:
>> You could at least put a breakpoint in the activator load() method of
>> the persistence module and another at the line where you try to retrieve
>> the persistence service. Are both breakpoints hit? What is their hit order?
>>
>> Cheers,
>> Sascha
>>
>> On 04/05/2016 10:31 AM, Kislinskiy, Stefan wrote:
>>> Thanks Matt, seems like this feature could be broken and we should 
>>> investigate then. I just
>>> found a bug in our tracker [1] which sounds like it was never completely 
>>> implemented? I'll
>>> check. I would recommend you guys to subscribe to the bug to stay in the 
>>> loop.
>>>
>>> [1] http://bugs.mitk.org/show_bug.cgi?id=18542
>>>
>>> Best regards,
>>> Stefan
>>> 
>>> Von: Clarkson, Matt [m.clark...@ucl.ac.uk]
>>> Gesendet: Dienstag, 5. April 2016 10:02
>>> An: Kislinskiy, Stefan
>>> Cc: MITK
>>> Betreff: Re: [mitk-users] Scene properties
>>>
>>> Hi there,
>>>
>>> This rings a bell in my mind. I believe I found similar things to Nil.
>>>
>>> I had an auto-loaded module, that created a dialog box to set the file name 
>>> of an IGTToolStorage
>>> file, and the port name of the COM port to connect to, for an NDI Tracker. 
>>> I wanted to persist
>>> the settings, so that the user didn't have to keep repeatedly setting the 
>>> filename and port,
>>> which in all likelihood remain fairly constant for each users setup. I 
>>> could not get the
>>> PersistenceService to work, and it performed differently on Linux/Mac to 
>>> Windows. Im basically
>>> using MITK 2015.05.2.
>>>
>>> In the attached file you will see I ended up commenting it out, and 
>>> resorting to QSettings.
>>> So, I would be interested in the outcome of this.
>>> Any ideas what is going on?
>>>
>>> Is it something to do with the fact that its an auto-loaded module, and the 
>>> order of auto-
>>> loading?
>>>
>>> Thanks
>>>
>>> Matt

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Re: [mitk-users] Scene properties

[Nil Goyette]

Hi Stefan,

My class extending mitk::PropertyListReplacedObserver is in a module 
now, but I still can't get it to work. GetPeristenceService() always 
return a nullptr, wathever I try. I tried mimicking OpenCVVideoSupport 
as much as possible, to no avail. Do you have any ideas on what I could 
have done wrong? Thank you for your time.


Nil

Le 2016-03-15 04:40, Kislinskiy, Stefan a écrit :


Hi Nil,

I would recommend to move such code into a module. That’s why it is 
working in Modules/IGTUI/Qmitk and Modules/OpenCVVideoSupport/UI. The 
alternative is to make your plugin context available by providing a 
static access method for the context in your plugin activator. See 
org_mitk_gui_qt_simulation_Activator.h for an example. In 
QmitkSimulationView.cpp right below the includes I wrote a helper 
method to get a service by using this plugin context. You should be 
able to get the persistence service like this without the macros (just 
follow the macros, they are doing nothing special, they are just for 
convenience). I still would recommend the former solution though, as 
it is clean and wouldn’t require any workaround code.


I’ll correct the typo in GetPeristenceService() for the upcoming release.

Best,
Stefan

*From:*Nil Goyette [mailto:nil.goye...@imeka.ca]
*Sent:* Montag, 14. März 2016 21:09
*To:* mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] Scene properties

Hi Stefan,

I tried the persistence service and I got this error each time I use 
GetPeristenceService().


WARNING: In us::GetModuleContext at 
\Modules\CppMicroServices\core\include\usGetModuleContext.h:57 :
Module 'org_imeka_qt_brainanalysis' unknown. The calling module 
probably misses a US_MODULE_NAME compile definition and/or a call to 
US_INITIALIZE_MODULE in one of its source files.


I didn't find such a thing in the QmitkOpenCVVideoControls example so 
I randomly added a US_INITIALIZE_MODULE in my plugin activator and now 
GetPersistenceService() finds its module but returns a nullptr.  I 
can't give you more information than that because PersistenceService.h 
is a macro hell.


Do you know how to make it work?

Nil

Le 2016-03-07 09:35, Nil Goyette a écrit :

Hi Stefan,

/These properties can be stored inside a MITK scene together with
the data so that the user loads data and restores the application
state at once./ - MITK Persistence Service

I can't test it now but this is exactly what I needed. Thank you.

Nil

Le 2016-03-07 01:29, Kislinskiy, Stefan a écrit :

Hi Nil,

please seehttp://docs.mitk.org/2015.05/PersistenceConceptPage.html.

Best,

Stefan



Von: Nil Goyette [nil.goye...@imeka.ca <mailto:nil.goye...@imeka.ca>]

Gesendet: Freitag, 4. März 2016 15:15

An:mitk-users@lists.sourceforge.net
<mailto:mitk-users@lists.sourceforge.net>

Betreff: [mitk-users] Scene properties

Hi all,

Is there a concept of scene property? I have some parameters(widget) in

my plugin, like MinFiberLength, MaxFiberLength, etc. which are not saved

when I save the scene. These parameters don't belong to any node, and

they don't fit as a Preference because the user will probably change

them when loading other data. That leaves me with "scene property", but

I don't think they exist.

My plan is to put the properties in a hidden node, but it does seem like

an hack. It's still the less hackish method I can find without modifying

MITK's code. Is there a right way to do that?

Nil



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[mitk-users] SetDataStorage in QmitkDataManagerView.cpp

[Nil Goyette]

Hi MITK,

I was creating a context menu action and I saw that SetDataStorage was 
never called. I found in QmitkDataManagerView.cpp this snippet:

if(className == "QmitkCreatePolygonModelAction")
{
  contextMenuAction->*SetDataStorage*(this->GetDataStorage());
  if(smoothed == "false")
  {
contextMenuAction->SetSmoothed(false);
  }
  else
  {
contextMenuAction->SetSmoothed(true);
  }
  contextMenuAction->SetDecimated(m_SurfaceDecimation);
}
else if(className == "QmitkStatisticsAction")
{
  contextMenuAction->SetFunctionality(this);
}
else if(className == "QmitkCreateSimulationAction")
{
  contextMenuAction->*SetDataStorage*(this->GetDataStorage());
}

I don't understand this decision. Why not simply always set it? I know 
that Smoothed, Decimated and Functionality are hacks useful only to a 
single class, but DataStorage is useful in many cases. Well, I don't 
know for the other programmers out there, but I often need the 
DataStorage in my context menu actions.


Right now, I'm forced to use my plugin's context, getServiceReference, 
IDataStorageService and include a lot of files to get it. This could 
easily be avoided if SetDataStorage was always called. I just tried it 
and it works perfectly. In fact, I don't see how it could break anything.


Nil
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[mitk-users] Disable context menu action

[Nil Goyette]

Hi all,

is it possible to disable a context menu action? I saw that 
m_ComponentSlider looks disabled when you right click on an image with 
only one component, but it's probably an "inner" behavior, where the 
object itself knows what to do.

I know I can show/hide them with QmitkNodeDescriptorManager and 
QmitkNodeDescriptor, but disabling would be a better UI choice for the 
users. Is it possible? Thank you for your time.

Nil

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Re: [mitk-users] Scene properties

[Nil Goyette]

Hi Stefan,

/These properties can be stored inside a MITK scene together with the 
data so that the user loads data and restores the application state at 
once./ - MITK Persistence Service


I can't test it now but this is exactly what I needed. Thank you.

Nil


Le 2016-03-07 01:29, Kislinskiy, Stefan a écrit :

Hi Nil,

please see http://docs.mitk.org/2015.05/PersistenceConceptPage.html.

Best,
Stefan

Von: Nil Goyette [nil.goye...@imeka.ca]
Gesendet: Freitag, 4. März 2016 15:15
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Scene properties

Hi all,

Is there a concept of scene property? I have some parameters(widget) in
my plugin, like MinFiberLength, MaxFiberLength, etc. which are not saved
when I save the scene. These parameters don't belong to any node, and
they don't fit as a Preference because the user will probably change
them when loading other data. That leaves me with "scene property", but
I don't think they exist.

My plan is to put the properties in a hidden node, but it does seem like
an hack. It's still the less hackish method I can find without modifying
MITK's code. Is there a right way to do that?

Nil
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[mitk-users] Loading scene

[Nil Goyette]

Hi all,

Is there some bool or signal to know if we are currently loading a 
scene? Some kind of warning? It would be nice to have that because I'm 
doing some work in NodeAdded and it's totally useless (and buggy) if 
there's still some data to load. I want to delay the work until the 
scene has finished loading.

Nil

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[mitk-users] Scene properties

[Nil Goyette]

Hi all,

Is there a concept of scene property? I have some parameters(widget) in 
my plugin, like MinFiberLength, MaxFiberLength, etc. which are not saved 
when I save the scene. These parameters don't belong to any node, and 
they don't fit as a Preference because the user will probably change 
them when loading other data. That leaves me with "scene property", but 
I don't think they exist.

My plan is to put the properties in a hidden node, but it does seem like 
an hack. It's still the less hackish method I can find without modifying 
MITK's code. Is there a right way to do that?

Nil

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Re: [mitk-users] aboutAction

[Nil Goyette]

"if you really need a custom About dialog, you would need to change the 
MITK source code directly."
We already have our modified version of MITK so, as you said,  we will 
simply change the About page in the 2015.05.02 version.

Thank you for looking at the problem.

Nil

Le 2015-09-30 09:25, Kislinskiy, Stefan a écrit :
> Hi Nil,
>
> see bug #19340. I added you to Cc for that bug.
>
> Best,
> Stefan
>
> -----Original Message-
> From: Nil Goyette [mailto:nil.goye...@imeka.ca]
> Sent: Freitag, 25. September 2015 19:50
> To: mitk-users@lists.sourceforge.net
> Subject: Re: [mitk-users] aboutAction
>
> Hi all,
>
> I tried again to see my About dialog and found a strange behavior.
> I do see my About dialog if I set this line to true:
> static bool USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS = false;
>
> But the Ctrl-O shortcut stops working because there are 2 registered actions 
> on the same hotkey.
> In fact, the shortcut works as long as I don't click on Open in the menu with 
> a mouse, after I see:
> "QAction::eventFilter: Ambiguous shortcut overload: Ctrl+O"
>
> I don't really want to activate experimental stuff but I need our own About 
> dialog.
> Anyone know how? Thank you.
>
> Nil
>
> Le 2015-09-21 09:39, Nil Goyette a écrit :
>> Hi all,
>>
>> I pulled MITK 2015.05.02 in our modified MITK branch and everything
>> still works except :) the About page. I heard the only necessary
>> change is to write this (and code the AboutHandler class) in the
>> plugin.xml of our plugin:
>> 
>>  > class="AboutHandler"/>
>> 
>>
>> Since it was working before the git pull, can someone confirm that
>> About extension is still working? Thank you.
>>
>> Nil

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Re: [mitk-users] aboutAction

[Nil Goyette]

Hi all,

I tried again to see my About dialog and found a strange behavior.
I do see my About dialog if I set this line to true:
static bool USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS = false;

But the Ctrl-O shortcut stops working because there are 2 registered 
actions on the same hotkey.
In fact, the shortcut works as long as I don't click on Open in the menu 
with a mouse, after I see:
"QAction::eventFilter: Ambiguous shortcut overload: Ctrl+O"

I don't really want to activate experimental stuff but I need our own 
About dialog.
Anyone know how? Thank you.

Nil

Le 2015-09-21 09:39, Nil Goyette a écrit :
> Hi all,
>
> I pulled MITK 2015.05.02 in our modified MITK branch and everything
> still works except :) the About page. I heard the only necessary change
> is to write this (and code the AboutHandler class) in the plugin.xml of
> our plugin:
> 
>  class="AboutHandler"/>
> 
>
> Since it was working before the git pull, can someone confirm that About
> extension is still working? Thank you.
>
> Nil
>
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[mitk-users] aboutAction

[Nil Goyette]

Hi all,

I pulled MITK 2015.05.02 in our modified MITK branch and everything 
still works except :) the About page. I heard the only necessary change 
is to write this (and code the AboutHandler class) in the plugin.xml of 
our plugin:

   


Since it was working before the git pull, can someone confirm that About 
extension is still working? Thank you.

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Re: [mitk-users] DataStorage in module

[Nil Goyette]

Hi Sascha,

Nice, I wasn't aware of the Read(DataStorage) method. It does what I need.
Except I also need the DataStorage in the writer class, which, afaik, 
can't access the DataStorage.

As I don't see any alternative, I'll keep my hack as-is for now. It's a 
singleton in the FiberTracking module. A kind of service I guess :)

I added a comment in bug #17912, so it got a little attention! Thank you 
for your help.

Nil

Le 2015-07-22 02:35, Sascha Zelzer a écrit :
 Hi Nil,

 there is a feature request about moving the IDataStorageService class 
 to a module and make it accessible from a module context (which would 
 publish it as a service for plugins as well) but it didn't get much 
 attention yet: http://bugs.mitk.org/show_bug.cgi?id=17912

 You are talking about an IO module, so assuming you have your own 
 reader for trk files, there is an overload of IFileReader::Read which 
 is passed the data storage instance which is to be filled with the 
 read data. The workbench open file action always calls this method and 
 allows you inspect the current contents.

 If you are not using your own reader, how are you listening to load 
 events of trk files?

 Best,
 Sascha

 On 07/21/2015 08:08 PM, Nil Goyette wrote:
 Hi all,

 I know it's possible to access the DataStorage in a view (with
 GetDataStorage) and in a plugin (with the plugin's context and
 IDataStorageService), but I have a special case where I need the
 DataStorage in a IO module. Before you tell me Don't do that, here's
 my use-case :)

 The user loads a .trk file, which may be linked to a reference image, so
 before loading the trk, we check the DataStorage if such an image exists
 and use its affine transformation if it does. Here I say a .trk file,
 but I will have the same problem with surfaces (some are not in world
 position)

 I currently handle the situation with a ugly hack, but I would be
 interested in a cleaner solution if there's one.
 Thank you.

 Nil

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[mitk-users] DataStorage in module

[Nil Goyette]

Hi all,

I know it's possible to access the DataStorage in a view (with 
GetDataStorage) and in a plugin (with the plugin's context and 
IDataStorageService), but I have a special case where I need the 
DataStorage in a IO module. Before you tell me Don't do that, here's 
my use-case :)

The user loads a .trk file, which may be linked to a reference image, so 
before loading the trk, we check the DataStorage if such an image exists 
and use its affine transformation if it does. Here I say a .trk file, 
but I will have the same problem with surfaces (some are not in world 
position)

I currently handle the situation with a ugly hack, but I would be 
interested in a cleaner solution if there's one.
Thank you.

Nil


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Re: [mitk-users] OS X compilation

[Nil Goyette]

Hi Andreas,

Yes, I do use mac ports.
I wasn't sure what you meant by removing entries in the vigra cmake 
cache, but I tried what you suggested and it works.
Thank you  very much for the test and the fast response.

What I did, described here for other users with the same problem:
1) Get the error described in previous messages
2) Open cmake at \your_build_dir\ep\src\Vigra-build
3) Blank (don't delete) the lines of jpeg, png and tiff (include and 
library)
4) Configure, generate
5) Try to compile mitk again

Nil

Le 2015-07-15 10:34, Fetzer, Andreas a écrit :
 Hi Nil,

 yes this should work, no need to upgrade ;)

 We were able to reproduce your error in the meantime, using the computer
 of one of my colleagues.

 Are you using mac ports?

 In our case the libraries jpeg, png were automatically installed via
 macports (located somewhere /opt/local)
 and these libraries were automatically found by the vigra cmake setup.
 A quick workaround would be to manually remove these entries in the the
 Vigra-build cmake cache.

 We will work on a better fix. The according bug is:
 http://bugs.mitk.org/show_bug.cgi?id=19181

 Hope this helps!

 Andreas

 Am 15/07/15 16:16 schrieb Nil Goyette unter nil.goye...@imeka.ca:

 Hi Andreas,

 I take the CMAKE_CXX_COMPILER value and add -v
 Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
 Target: x86_64-apple-darwin13.4.0
 Thread model: posix

 So I don't have the Tier 1 specs, nor the Tier 2, I have something
 inbetween: OS X 10.9 + clang 6.0.
 Should this work? If not, damn, I guess I'll need to upgrade to 10.10

 Nil

 Le 2015-07-15 02:35, Fetzer, Andreas a écrit :
 Hi Nil,

 what clang version are you working with?

 Our Tier 1 supported Mac OS X platform for the 2015.05 release is OS X
 10.10 using apple-clang 6.0, as you can see here:

 http://docs.mitk.org/2015.05/SupportedPlatformsPage.html

 OS X  10.9 with older clang versions are not fully supported anymore.

 However I still have 10.9 on my laptop, using apple clang 6.0. I tried
 to
 reproduce the build errors but the HDF5/vigra build completed without
 errors.

 My office computer as well as our continuos mac os x dartclient are both
 10.10 systems using the latest apple clang 6.1. On both the build works.

 So I guess this must be related to your compiler version.

 Best,
 Andreas

 Am 14/07/15 19:23 schrieb Nil Goyette unter nil.goye...@imeka.ca:

 Hi all,

 I'm trying to compile MITK 2015.05 on
 OS X 10.9, cmake 2.3, Boost + Vigra + All Apps + All Plugins enabled,
 -std=C++11
 and I get this error

 Linking CXX shared library libvigraimpex.dylib
 Undefined symbols for architecture x86_64:
 _H5P_CLS_DATASET_CREATE_ID_g, referenced from:
 void vigra::HDF5File::write_1u, double,
 vigra::StridedArrayTag(std::__1::basic_stringchar,
 std::__1::char_traitschar, std::__1::allocatorchar ,
 vigra::MultiArrayView1u, double, vigra::StridedArrayTag const, int,
 int, vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
 void vigra::HDF5File::write_1u, int,
 vigra::StridedArrayTag(std::__1::basic_stringchar,
 std::__1::char_traitschar, std::__1::allocatorchar ,
 vigra::MultiArrayView1u, int, vigra::StridedArrayTag const, int,
 int,
 vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
 ld: symbol(s) not found for architecture x86_64
 clang: error: linker command failed with exit code 1 (use -v to see
 invocation)
 make[5]: *** [src/impex/libvigraimpex.5.1.10.0.dylib] Error 1
 make[4]: *** [src/impex/CMakeFiles/vigraimpex.dir/all] Error 2
 make[3]: *** [all] Error 2
 make[2]: *** [ep/src/Vigra-stamp/Vigra-build] Error 2
 make[1]: *** [CMakeFiles/Vigra.dir/all] Error 2
 make: *** [all] Error 2

 I haven't found anything related to this problem on bugzilla or on the
 ML.
 Anyone knows how to fix this?

 Nil

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Re: [mitk-users] OS X compilation

[Nil Goyette]

Hi Andreas,

I take the CMAKE_CXX_COMPILER value and add -v
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

So I don't have the Tier 1 specs, nor the Tier 2, I have something 
inbetween: OS X 10.9 + clang 6.0.
Should this work? If not, damn, I guess I'll need to upgrade to 10.10

Nil

Le 2015-07-15 02:35, Fetzer, Andreas a écrit :
 Hi Nil,

 what clang version are you working with?

 Our Tier 1 supported Mac OS X platform for the 2015.05 release is OS X
 10.10 using apple-clang 6.0, as you can see here:

 http://docs.mitk.org/2015.05/SupportedPlatformsPage.html

 OS X  10.9 with older clang versions are not fully supported anymore.

 However I still have 10.9 on my laptop, using apple clang 6.0. I tried to
 reproduce the build errors but the HDF5/vigra build completed without
 errors.

 My office computer as well as our continuos mac os x dartclient are both
 10.10 systems using the latest apple clang 6.1. On both the build works.

 So I guess this must be related to your compiler version.

 Best,
 Andreas

 Am 14/07/15 19:23 schrieb Nil Goyette unter nil.goye...@imeka.ca:

 Hi all,

 I'm trying to compile MITK 2015.05 on
 OS X 10.9, cmake 2.3, Boost + Vigra + All Apps + All Plugins enabled,
 -std=C++11
 and I get this error

 Linking CXX shared library libvigraimpex.dylib
 Undefined symbols for architecture x86_64:
_H5P_CLS_DATASET_CREATE_ID_g, referenced from:
void vigra::HDF5File::write_1u, double,
 vigra::StridedArrayTag(std::__1::basic_stringchar,
 std::__1::char_traitschar, std::__1::allocatorchar ,
 vigra::MultiArrayView1u, double, vigra::StridedArrayTag const, int,
 int, vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
void vigra::HDF5File::write_1u, int,
 vigra::StridedArrayTag(std::__1::basic_stringchar,
 std::__1::char_traitschar, std::__1::allocatorchar ,
 vigra::MultiArrayView1u, int, vigra::StridedArrayTag const, int, int,
 vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
 ld: symbol(s) not found for architecture x86_64
 clang: error: linker command failed with exit code 1 (use -v to see
 invocation)
 make[5]: *** [src/impex/libvigraimpex.5.1.10.0.dylib] Error 1
 make[4]: *** [src/impex/CMakeFiles/vigraimpex.dir/all] Error 2
 make[3]: *** [all] Error 2
 make[2]: *** [ep/src/Vigra-stamp/Vigra-build] Error 2
 make[1]: *** [CMakeFiles/Vigra.dir/all] Error 2
 make: *** [all] Error 2

 I haven't found anything related to this problem on bugzilla or on the ML.
 Anyone knows how to fix this?

 Nil

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Re: [mitk-users] OS X and Qt5

[Nil Goyette]

Hi Andreas, Hi diffusion guys,

No, I got no error. There are 3 reasons why I think the Diffusion 
modules and plugins are not built.

1) I built MITK on Windows twice using the same configuration, one with 
Qt4 and the other with Qt5.
Then, I open MitkWorkbench.bat. In the Qt5 version, I have all kinds of 
plugins, including FiberProcessing, ODF details, Tensors, etc.
There's nothing related to diffusion in the Qt4 version though.

2) cmake fails because one of our module depends on MitkFiberTracking. 
It passes when I remove this dependency.

3) On the cmakelist.txt of MitkFiberTracking, only Qt5|Core appears, 
without any mention of Qt4|QtCore

In fact, my last message was misleading, I don't need the Diffusion 
application or plugins, I only need to be able to depend on the 
MitkFiberTracking module.

Nil

Le 2015-07-15 02:39, Fetzer, Andreas a écrit :
 Hi Nil,

 are you talking about using the MitkDiffusion module or building the
 MitkDiffusion Application?
 There should not be any hard Qt5 dependency since we still had to provide
 Qt4 compatibility due to
 this OS X Qt5 issue.

 On my machine the diffusion module was build using Qt4. Did you get any
 errors?

 Maybe someone of the diffusion guys can comment on that as well...

 Cheers again ;)
 Andreas

 Am 14/07/15 23:02 schrieb Nil Goyette unter nil.goye...@imeka.ca:

 Hi,

 One last question concerning Qt5 (I hope). In fact, I'm pretty sure I
 know the answer, I just need you to confirm my fear :)

 Is it currently impossible to use MitkDiffusion on OS X?
 If yes, is it because of the Qt5 hard dependency?
 If yes again, why would MItkDiffusion absolutely need Qt5?!?

 Nil

 Le 2015-07-14 08:51, Nil Goyette a écrit :
 Hi Thomas and Andreas,

 Thank you both for your answers, I'll stay on Qt4 for the time being :)

 Qt5 version  5.5
 Ahhh, good to know! You saved me a lot of useless work.

 Nil

 Le 2015-07-14 04:12, Fetzer, Andreas a écrit :
 Hi,

 due to this bug:

 http://bugs.mitk.org/show_bug.cgi?id=18521

 we are currently stuck with qt 4 on Mac OS X.
 We are already working on a solution, but the problem is located
 somewhere
 deep in the QWidgets / Blueberry hierarchy,
 and hence it is not easy to even find out, what is going wrong.

 The build errors that you experienced Nil, are due to the latest Qt 5.5
 version, which was actually released after MITK 2015.05.
 Every Qt5 version  5.5 should work without any problems with VS 2013.

 Best regards,
 Andreas

 Am 14/07/15 00:43 schrieb Fitze Thomas (fitz) unter f...@zhaw.ch:

 Hi Nil,

 I played around with it for a bit and i did manage to compile a
 working
 workbench with qt5.3 under OS X 10.10. However, there seem to be a few
 issues left. For example, the resizing of plugin views will randomly
 (or
 so it seems) stop working. When embedding QML inside of QWidgets with
 the
 workbench, things get messy with GUI elements stopping to work all
 over
 the place - no crashes tho. The standalone QML example (multi view
 widget) seems to work fine.

 Cheers,
 Thomas

 On 13 Jul 2015, at 18:25 , Nil Goyette nil.goye...@imeka.ca wrote:

 Hi all,

 I'm not sure what to think about Qt5 support on OS X because of:
 - Qt 5 is default for Windows and Linux, Qt 4 for Mac OS X
 - http://bugs.mitk.org/show_bug.cgi?id=18856

 Moreover, I tried compiling MITK 2015.05 with VS2013 and it fails in
 CTK.
 CTK/Libs/PluginFramework/ctkPluginArchiveSQL_p.h:68:23 error: no
 template named 'QSharedPointer' ; did you mean 'QSharedDataPointer' ?

 Does MITK2015.05 + OS X + Qt5 currently work? Or are we still stuck
 with
 qt4?

 Thank you for your time.


--
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
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Re: [mitk-users] OS X and Qt5

[Nil Goyette]

Hi Peter,

You're perfectly right, I just checked and I added Qt5|Core myself for 
some reasons. My bad.
Thank you both for your help.

Nil

Le 2015-07-15 10:24, Peter Neher a écrit :
 Hi Nil,

 all diffusion modules are independent of Qt as far as I know. I just
 checked the CmakeLists.txt of the FiberTracking module and there is no
 Qt dependency listed.

 Peter

 On 15.07.2015 15:42, Nil Goyette wrote:
 Hi Andreas, Hi diffusion guys,

 No, I got no error. There are 3 reasons why I think the Diffusion
 modules and plugins are not built.

 1) I built MITK on Windows twice using the same configuration, one with
 Qt4 and the other with Qt5.
 Then, I open MitkWorkbench.bat. In the Qt5 version, I have all kinds of
 plugins, including FiberProcessing, ODF details, Tensors, etc.
 There's nothing related to diffusion in the Qt4 version though.

 2) cmake fails because one of our module depends on MitkFiberTracking.
 It passes when I remove this dependency.

 3) On the cmakelist.txt of MitkFiberTracking, only Qt5|Core appears,
 without any mention of Qt4|QtCore

 In fact, my last message was misleading, I don't need the Diffusion
 application or plugins, I only need to be able to depend on the
 MitkFiberTracking module.

 Nil

 Le 2015-07-15 02:39, Fetzer, Andreas a écrit :
 Hi Nil,

 are you talking about using the MitkDiffusion module or building the
 MitkDiffusion Application?
 There should not be any hard Qt5 dependency since we still had to provide
 Qt4 compatibility due to
 this OS X Qt5 issue.

 On my machine the diffusion module was build using Qt4. Did you get any
 errors?

 Maybe someone of the diffusion guys can comment on that as well...

 Cheers again ;)
 Andreas

 Am 14/07/15 23:02 schrieb Nil Goyette unter nil.goye...@imeka.ca:

 Hi,

 One last question concerning Qt5 (I hope). In fact, I'm pretty sure I
 know the answer, I just need you to confirm my fear :)

 Is it currently impossible to use MitkDiffusion on OS X?
 If yes, is it because of the Qt5 hard dependency?
 If yes again, why would MItkDiffusion absolutely need Qt5?!?

 Nil

 Le 2015-07-14 08:51, Nil Goyette a écrit :
 Hi Thomas and Andreas,

 Thank you both for your answers, I'll stay on Qt4 for the time being :)

 Qt5 version  5.5
 Ahhh, good to know! You saved me a lot of useless work.

 Nil

 Le 2015-07-14 04:12, Fetzer, Andreas a écrit :
 Hi,

 due to this bug:

 http://bugs.mitk.org/show_bug.cgi?id=18521

 we are currently stuck with qt 4 on Mac OS X.
 We are already working on a solution, but the problem is located
 somewhere
 deep in the QWidgets / Blueberry hierarchy,
 and hence it is not easy to even find out, what is going wrong.

 The build errors that you experienced Nil, are due to the latest Qt 5.5
 version, which was actually released after MITK 2015.05.
 Every Qt5 version  5.5 should work without any problems with VS 2013.

 Best regards,
 Andreas

 Am 14/07/15 00:43 schrieb Fitze Thomas (fitz) unter f...@zhaw.ch:

 Hi Nil,

 I played around with it for a bit and i did manage to compile a
 working
 workbench with qt5.3 under OS X 10.10. However, there seem to be a few
 issues left. For example, the resizing of plugin views will randomly
 (or
 so it seems) stop working. When embedding QML inside of QWidgets with
 the
 workbench, things get messy with GUI elements stopping to work all
 over
 the place - no crashes tho. The standalone QML example (multi view
 widget) seems to work fine.

 Cheers,
 Thomas

 On 13 Jul 2015, at 18:25 , Nil Goyette nil.goye...@imeka.ca wrote:

 Hi all,

 I'm not sure what to think about Qt5 support on OS X because of:
 - Qt 5 is default for Windows and Linux, Qt 4 for Mac OS X
 - http://bugs.mitk.org/show_bug.cgi?id=18856

 Moreover, I tried compiling MITK 2015.05 with VS2013 and it fails in
 CTK.
 CTK/Libs/PluginFramework/ctkPluginArchiveSQL_p.h:68:23 error: no
 template named 'QSharedPointer' ; did you mean 'QSharedDataPointer' ?

 Does MITK2015.05 + OS X + Qt5 currently work? Or are we still stuck
 with
 qt4?

 Thank you for your time.


--
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
___
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Re: [mitk-users] OS X and Qt5

[Nil Goyette]

Hi Thomas and Andreas,

Thank you both for your answers, I'll stay on Qt4 for the time being :)

Qt5 version  5.5
Ahhh, good to know! You saved me a lot of useless work.

Nil

Le 2015-07-14 04:12, Fetzer, Andreas a écrit :
 Hi,

 due to this bug:

 http://bugs.mitk.org/show_bug.cgi?id=18521

 we are currently stuck with qt 4 on Mac OS X.
 We are already working on a solution, but the problem is located somewhere
 deep in the QWidgets / Blueberry hierarchy,
 and hence it is not easy to even find out, what is going wrong.

 The build errors that you experienced Nil, are due to the latest Qt 5.5
 version, which was actually released after MITK 2015.05.
 Every Qt5 version  5.5 should work without any problems with VS 2013.

 Best regards,
 Andreas

 Am 14/07/15 00:43 schrieb Fitze Thomas (fitz) unter f...@zhaw.ch:

 Hi Nil,

 I played around with it for a bit and i did manage to compile a working
 workbench with qt5.3 under OS X 10.10. However, there seem to be a few
 issues left. For example, the resizing of plugin views will randomly (or
 so it seems) stop working. When embedding QML inside of QWidgets with the
 workbench, things get messy with GUI elements stopping to work all over
 the place - no crashes tho. The standalone QML example (multi view
 widget) seems to work fine.

 Cheers,
 Thomas

 On 13 Jul 2015, at 18:25 , Nil Goyette nil.goye...@imeka.ca wrote:

 Hi all,

 I'm not sure what to think about Qt5 support on OS X because of:
 - Qt 5 is default for Windows and Linux, Qt 4 for Mac OS X
 - http://bugs.mitk.org/show_bug.cgi?id=18856

 Moreover, I tried compiling MITK 2015.05 with VS2013 and it fails in
 CTK.
 CTK/Libs/PluginFramework/ctkPluginArchiveSQL_p.h:68:23 error: no
 template named 'QSharedPointer' ; did you mean 'QSharedDataPointer' ?

 Does MITK2015.05 + OS X + Qt5 currently work? Or are we still stuck
 with
 qt4?

 Thank you for your time.


 -
 -
 Don't Limit Your Business. Reach for the Cloud.
 GigeNET's Cloud Solutions provide you with the tools and support that
 you need to offload your IT needs and focus on growing your business.
 Configured For All Businesses. Start Your Cloud Today.
 https://www.gigenetcloud.com/
 ___
 mitk-users mailing list
 mitk-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/mitk-users

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 https://lists.sourceforge.net/lists/listinfo/mitk-users


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[mitk-users] OS X compilation

[Nil Goyette]

Hi all,

I'm trying to compile MITK 2015.05 on
OS X 10.9, cmake 2.3, Boost + Vigra + All Apps + All Plugins enabled, 
-std=C++11
and I get this error

Linking CXX shared library libvigraimpex.dylib
Undefined symbols for architecture x86_64:
   _H5P_CLS_DATASET_CREATE_ID_g, referenced from:
   void vigra::HDF5File::write_1u, double, 
vigra::StridedArrayTag(std::__1::basic_stringchar, 
std::__1::char_traitschar, std::__1::allocatorchar , 
vigra::MultiArrayView1u, double, vigra::StridedArrayTag const, int, 
int, vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
   void vigra::HDF5File::write_1u, int, 
vigra::StridedArrayTag(std::__1::basic_stringchar, 
std::__1::char_traitschar, std::__1::allocatorchar , 
vigra::MultiArrayView1u, int, vigra::StridedArrayTag const, int, int, 
vigra::MultiArrayShape1u::type, int) in hdf5_rf_impex.cxx.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see 
invocation)
make[5]: *** [src/impex/libvigraimpex.5.1.10.0.dylib] Error 1
make[4]: *** [src/impex/CMakeFiles/vigraimpex.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [ep/src/Vigra-stamp/Vigra-build] Error 2
make[1]: *** [CMakeFiles/Vigra.dir/all] Error 2
make: *** [all] Error 2

I haven't found anything related to this problem on bugzilla or on the ML.
Anyone knows how to fix this?

Nil

--
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GigeNET's Cloud Solutions provide you with the tools and support that
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Re: [mitk-users] OS X and Qt5

[Nil Goyette]

Hi,

One last question concerning Qt5 (I hope). In fact, I'm pretty sure I 
know the answer, I just need you to confirm my fear :)

Is it currently impossible to use MitkDiffusion on OS X?
If yes, is it because of the Qt5 hard dependency?
If yes again, why would MItkDiffusion absolutely need Qt5?!?

Nil

Le 2015-07-14 08:51, Nil Goyette a écrit :
 Hi Thomas and Andreas,

 Thank you both for your answers, I'll stay on Qt4 for the time being :)

 Qt5 version  5.5
 Ahhh, good to know! You saved me a lot of useless work.

 Nil

 Le 2015-07-14 04:12, Fetzer, Andreas a écrit :
 Hi,

 due to this bug:

 http://bugs.mitk.org/show_bug.cgi?id=18521

 we are currently stuck with qt 4 on Mac OS X.
 We are already working on a solution, but the problem is located somewhere
 deep in the QWidgets / Blueberry hierarchy,
 and hence it is not easy to even find out, what is going wrong.

 The build errors that you experienced Nil, are due to the latest Qt 5.5
 version, which was actually released after MITK 2015.05.
 Every Qt5 version  5.5 should work without any problems with VS 2013.

 Best regards,
 Andreas

 Am 14/07/15 00:43 schrieb Fitze Thomas (fitz) unter f...@zhaw.ch:

 Hi Nil,

 I played around with it for a bit and i did manage to compile a working
 workbench with qt5.3 under OS X 10.10. However, there seem to be a few
 issues left. For example, the resizing of plugin views will randomly (or
 so it seems) stop working. When embedding QML inside of QWidgets with the
 workbench, things get messy with GUI elements stopping to work all over
 the place - no crashes tho. The standalone QML example (multi view
 widget) seems to work fine.

 Cheers,
 Thomas

 On 13 Jul 2015, at 18:25 , Nil Goyette nil.goye...@imeka.ca wrote:

 Hi all,

 I'm not sure what to think about Qt5 support on OS X because of:
 - Qt 5 is default for Windows and Linux, Qt 4 for Mac OS X
 - http://bugs.mitk.org/show_bug.cgi?id=18856

 Moreover, I tried compiling MITK 2015.05 with VS2013 and it fails in
 CTK.
 CTK/Libs/PluginFramework/ctkPluginArchiveSQL_p.h:68:23 error: no
 template named 'QSharedPointer' ; did you mean 'QSharedDataPointer' ?

 Does MITK2015.05 + OS X + Qt5 currently work? Or are we still stuck
 with
 qt4?

 Thank you for your time.


--
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
___
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