Re: [mitk-users] Nifti2
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? ___ mitk-users mailing list mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users
Re: [mitk-users] building and setting up an own project with the plugin generator
Hello,
thank you for the quick answer.
I was trying to thoroughly understand the proper structure of an MITK project while building a small application, which is why I am asking questions that may seem
very basic. I looked throughthe example module and also played around with the cmd app, but I still have a question regarding the example module in contrast with
the tutorial steps.
I wanted to build a small application based on QT, much like the step1 - step8 programs in the tutorial.
Clearly, the structure of those is different than the one of the example module and, obviously, the one presented in the
module - creation - tutorial on your website
(there you propose the directory structure including autoload, cmdapps, ... and certain properties of the cmake files).
My question is, whether, in case of implementing a qt - based application, it is recommended to not use the module structure
(e.g. whether the tutorial is also a proposal of how to structure qt - based applications).
Or does it still make sense to create a module and, instead of the folder "cmd apps", maybe create an "application" folder
containing the UI - files (headers, source files and so on)?
Thank you very much in advance!
Kind regards
Ivaylo Angelov
Gesendet: Dienstag, 02. Juli 2019 um 14:27 Uhr
Von: "Dinkelacker, Stefan"
An: "Ivaylo Angelov" , "mitk-users@lists.sourceforge.net"
Betreff: RE: [mitk-users] building and setting up an own project with the plugin generator
We recommend to use the MITK-ProjectTemplate approach to develop in or with MITK: https://github.com/MITK/MITK-ProjectTemplate (see README for instructions, very easy when you already built MITK).
It already has an example command line app in Modules/ExampleModule/cmdapps that is switched on by default. You could start by editing ExampleCmdApp.cpp. Loading and saving/converting files is as easy as the following example pseudo code:
input = mitk::IOUtils::Load(“input.nrrd”);
mitk::IOUtils::Save(input, “output.nifti”);
Feel free to explore the files of the MITK-ProjectTemplate as they tend to include lots of code documentation to showcase basic MITK development.
From: Ivaylo Angelov [mailto:ivaylo_ange...@gmx.de]
Sent: Tuesday, July 2, 2019 12:42 PM
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] building and setting up an own project with the plugin generator
Dear All,
after following the developer tutorial as well as the first-steps-projects I wanted to start working on my own project.
I wanted to start by creating a small application, which for now, is supposed to read in nrrd images and with the help of
certain libraries, for example vtk, transform them to other image formats.
I guessed that building a new project with the plugin - generator, as you are showing on your web page, is a proper
start to that (is that already a wrong assumption, for a project like this, should I proceed differently?).
What I did is to follow the plugin-generator tutorial and create my project ("Angelov_Project") within a folder that i specified with the out-dir flag.
I created a new build directory ("Angelov_Project_bin") for all the binaries... what I did afterwards is to build the project using cmake.
I let all the preselected flags as-is and generated the project.
I chose my project folder ("Angelov_Project") as my source directory and "Angelov_Project_bin" as my build directory.
In the following I tried to build it within Visual Studio, which quickly results in the following errors:
MSB6006, "cmd.exe" exited with code 1 MITK Microsoft.CppCommon.targets line 209
MSB6006, "cmd.exe" exited with code 1 Angelov_Project_configure Microsoft.CppCommon.targets line 209
I guess I am not understanding the whole build process correctly, I also guess that I should have, again (like in the tutorial), selected the MITK directory (where I checked out the suitable version
as described in the tutorial) as the source directory and my project as an external directory, but I though it should be possible in another way,
also because I don't want to build all the other stuff every time I start a project.
Afterwards I saw the possibility of setting the EXTERNAL_MITK_DIR" flag, which, I thought, would solve the problem.
This time, already the configuration with cmake fails, because there is no MITKconfig.cmake file inside the directory
There only is a "MITKConfig.cmake.in", as I saw after looking inside.
It looks like there is something I don't understand on starting my project and the involved build process, therefore I would
appreciate if you could help me with that issue.
I am looking forward to hearing from you soon.
Kind regards
Ivaylo Angelov
___
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mitk-users@lists.sourceforge.net
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Re: [mitk-users] building and setting up an own project with the plugin generator
We recommend to use the MITK-ProjectTemplate approach to develop in or with
MITK: https://github.com/MITK/MITK-ProjectTemplate (see README for
instructions, very easy when you already built MITK).
It already has an example command line app in Modules/ExampleModule/cmdapps
that is switched on by default. You could start by editing ExampleCmdApp.cpp.
Loading and saving/converting files is as easy as the following example pseudo
code:
input = mitk::IOUtils::Load(“input.nrrd”);
mitk::IOUtils::Save(input, “output.nifti”);
Feel free to explore the files of the MITK-ProjectTemplate as they tend to
include lots of code documentation to showcase basic MITK development.
From: Ivaylo Angelov [mailto:ivaylo_ange...@gmx.de]
Sent: Tuesday, July 2, 2019 12:42 PM
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] building and setting up an own project with the plugin
generator
Dear All,
after following the developer tutorial as well as the first-steps-projects I
wanted to start working on my own project.
I wanted to start by creating a small application, which for now, is supposed
to read in nrrd images and with the help of
certain libraries, for example vtk, transform them to other image formats.
I guessed that building a new project with the plugin - generator, as you are
showing on your web page, is a proper
start to that (is that already a wrong assumption, for a project like this,
should I proceed differently?).
What I did is to follow the plugin-generator tutorial and create my project
("Angelov_Project") within a folder that i specified with the out-dir flag.
I created a new build directory ("Angelov_Project_bin") for all the binaries...
what I did afterwards is to build the project using cmake.
I let all the preselected flags as-is and generated the project.
I chose my project folder ("Angelov_Project") as my source directory and
"Angelov_Project_bin" as my build directory.
In the following I tried to build it within Visual Studio, which quickly
results in the following errors:
MSB6006, "cmd.exe" exited with code 1 MITK Microsoft.CppCommon.targets line
209
MSB6006, "cmd.exe" exited with code 1 Angelov_Project_configure
Microsoft.CppCommon.targets line 209
I guess I am not understanding the whole build process correctly, I also guess
that I should have, again (like in the tutorial), selected the MITK directory
(where I checked out the suitable version
as described in the tutorial) as the source directory and my project as an
external directory, but I though it should be possible in another way,
also because I don't want to build all the other stuff every time I start a
project.
Afterwards I saw the possibility of setting the EXTERNAL_MITK_DIR" flag, which,
I thought, would solve the problem.
This time, already the configuration with cmake fails, because there is no
MITKconfig.cmake file inside the directory
There only is a "MITKConfig.cmake.in", as I saw after looking inside.
It looks like there is something I don't understand on starting my project and
the involved build process, therefore I would
appreciate if you could help me with that issue.
I am looking forward to hearing from you soon.
Kind regards
Ivaylo Angelov
___
mitk-users mailing list
mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users
[mitk-users] building and setting up an own project with the plugin generator
Dear All,
after following the developer tutorial as well as the first-steps-projects I wanted to start working on my own project.
I wanted to start by creating a small application, which for now, is supposed to read in nrrd images and with the help of
certain libraries, for example vtk, transform them to other image formats.
I guessed that building a new project with the plugin - generator, as you are showing on your web page, is a proper
start to that (is that already a wrong assumption, for a project like this, should I proceed differently?).
What I did is to follow the plugin-generator tutorial and create my project ("Angelov_Project") within a folder that i specified with the out-dir flag.
I created a new build directory ("Angelov_Project_bin") for all the binaries... what I did afterwards is to build the project using cmake.
I let all the preselected flags as-is and generated the project.
I chose my project folder ("Angelov_Project") as my source directory and "Angelov_Project_bin" as my build directory.
In the following I tried to build it within Visual Studio, which quickly results in the following errors:
MSB6006, "cmd.exe" exited with code 1 MITK Microsoft.CppCommon.targets line 209
MSB6006, "cmd.exe" exited with code 1 Angelov_Project_configure Microsoft.CppCommon.targets line 209
I guess I am not understanding the whole build process correctly, I also guess that I should have, again (like in the tutorial), selected the MITK directory (where I checked out the suitable version
as described in the tutorial) as the source directory and my project as an external directory, but I though it should be possible in another way,
also because I don't want to build all the other stuff every time I start a project.
Afterwards I saw the possibility of setting the EXTERNAL_MITK_DIR" flag, which, I thought, would solve the problem.
This time, already the configuration with cmake fails, because there is no MITKconfig.cmake file inside the directory
There only is a "MITKConfig.cmake.in", as I saw after looking inside.
It looks like there is something I don't understand on starting my project and the involved build process, therefore I would
appreciate if you could help me with that issue.
I am looking forward to hearing from you soon.
Kind regards
Ivaylo Angelov
___
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mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users
