CamiTK 5.0.2

This is the release notes for CamiTK 5.0.2

CamiTK 5.0.2 comes with

• a brand new web site (click here for all the details)
• 13 new features: viewer extension framework, slice arbitrary orientation, mesh projection, and more… (click here for all the details)
• 10 code quality and devops improvements: updated dependencies and toolchain, improved continuous integration, multi-architecture support, improved quality, and more… (click here for all the details)
• and over 11 bug fixed

Thanks to all the direct contributors (committers and issue submitters) and to everyone who gave this project financial, moral or any other kind of support!

CamiTK 5.0 teaser

New website

generated thanks to Hugo docsy theme

New viewer extension framework

it's easier to create new viewers (example: the bitmap viewer)

New viewer extension framework

it's easier to create new viewers (example: a 2D+3D mixed viewer)

New viewer extension framework

it's easier to customize CamiTK-imp

Arbitrary orientation in 3D volume

Volume slice are not limited anymore to axial, coronal and sagittal views

Mesh projection in images

Mesh contours can now be "projected" in slices

Improved Image Look Up Table

Now works for all voxel types, improved graphics and customizable number of histogram bins

Improved volume rendering

Now works for all voxel types, simplified GUI, some default color map are provided

Improved action state machine

Can now start without the command line, improved XML log rendering in browser, some bug fixes

Improved action family reorganization

Menus therefore offers a more coherent UI

Improved action viewer

More compact GUI to display description, targets and parameters of an action

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CamiTK 5.0 stats

• 483 commits
• 1375 files changed, 253797 insertions(+), 30288 deletions(-)
• 83 merge requests
• from 5 contributors (commiters) and more (bug reports)

What OpenHub says about CamiTK

This is an independent review of our code base (click on the links for more information)

New website

This new CamiTK website was completely rewritten from scratch using a static generator:

• its structure is modern, reactive and comprehensive: it is organized in 7 clear sections (about, community, support, news & release, download, documentation and API documentation)
• it has an improved presentation of what is CamiTK, explaining the end-user application and framework separately
• it contains all the documentation previously available in the so-called “wiki” part and all the API documentation
• the documentation is now fully structured with sections, step-by-steps and a logical learning progression
• a search box is available on the top right to search an information on the entire website including all the documentation (just type in something and press enter). Note that it is using a local search engine.
• it is a static web site generated thanks to the Docsy theme of Hugo
• it is written in MarkDown
• all the website source is available on the corresponding gitlab project and open to contributors

The Docsy Hugo theme allows us to focus on then content, not on reinventing a website infrastructure from scratch. That’s really similar to the way the CamiTK team feel about prototyping software! But it also deliver the source to anyone who would like to contribute without needing any specific language knowledge (if you don’t know MarkDown, don’t worry, it is self explanatory).

For instance: you see something that you can improve in this page: just click on Edit this page in the top right corner, edit the source, commit and that’s it your contribution will appear here in the next hourly update…

New features

Viewer extension framework

The main new feature of CamiTK 5 is the viewer extension. Viewers are now first class extension in CamiTK.

For users:

• in CamiTK-imp the central viewer can be customized at any time. CamiTK-imp will remember the user preferences.
• a new Bitmap viewer is available in CamiTK-imp that improve 2D images visualization (3D rotations are blocked and image is flipped automatically)

For developers:

• all viewers previously available in CamiTK core are now available as extensions. A new CamiTK extension can easily include a new instance of an existing viewer extension class or use a default instance.
• you can now develop new viewers quickly and efficiently. All new viewer extensions will be automatically integrated and available in applications (e.g. CamiTK-imp) as are new action and component extensions.
• you can now very easily integrate existing viewer into a new viewer (e.g. a new 3D + bitmap viewer for instance)

As this changes the viewer management API, we encourage you to check the detailed migration guide (but don’t worry the API did not change that much)

BitmapViewer::BitmapViewer(QString name) : InteractiveViewer(name, InteractiveViewer::SLICE_VIEWER) {
    // 2D images need x right, y up, z front
    getRendererWidget()->setCameraOrientation(RendererWidget::RIGHT_DOWN);
    // no decoration and grey background
    getRendererWidget()->toggleOrientationDecorations(false);
    getRendererWidget()->setGradientBackground(false);
    getRendererWidget()->setBackgroundColor(0.8, 0.8, 0.8);
    // parallel projection
    getRendererWidget()->getActiveCamera()->ParallelProjectionOn();

    // can only display 2D bitmap = SingleImageComponent
    setComponents(QStringList() << "SingleImageComponent");

    setDescription("BitmapViewer is a simple 2D image viewer");

    ...
}

(more details in merge request !147 issue #98 , merge request !145 issue #100 issue #102 , merge request !144 issue #94 , merge request !141 issue #92 issue #92 issue #93 issue #32 , merge request !137 , merge request !132 , merge request !124)

Arbitrary orientation in 3D volume

This features allows the user to create a slice in a 3D image of an arbitrary orientation. With this feature, the visualization of a 3D image is not limited anymore to orthogonal axial, coronal and sagittal slices.

The GUI allows the user to interact with the arbitrary orientation by modifying any of the degrees of freedom (3 rotations, one translation) in order to position the arbitrary slice anywhere in the volume.

The GUI also allows the user to visualized the arbitrary slice in 3D only, in the medical image viewer or in the dedicated arbitrary slice viewer. Check the new “View → Arbitrary Slice” action!

(more details in merge request !136 issue #61)

Mesh projection

This new action adds the visualization of the contour of a mesh onto a 3D image. This action creates mesh contour in the direction of the axial, coronal, sagittal and arbitrary slices and “project” them in the 3D and 2D viewers.

This action takes into account the frame framework of the slice and mesh.

To try it open the sinus test data (image and mesh), right-click on the mesh in the explorer and choose “View → Mesh Projection”.

(more details in merge request !170)

…and 10 other new features

CamiTK 5.0 also

• improves Lookup Table (more details in merge request !166 issue #116)
• improves Volume Rendering (more details in merge request !166 issue #116)
• improves action state machine (start with no param + XML log rendering + can be opened in browser) (more details in merge request !165 issue #114 , merge request !163 issue #113 , merge request !159 issue #57)
• has more coherent UI (actions and menu reorganization) (more details in merge request !166 issue #116)
• replaces copyright text by a more discrete watermark (more details in merge request !168 issue #118)
• has more compact action viewer GUI (the description, targets and parameters of an action are now displayed as tabs)
• removes console on windows version of all GUI CamiTK application (camitk-imp, camitk-actionstatemachine, camitk-wizard) (more details in merge request !157 issue #83)
• simplifies DICOM opening GUI (automatic select when unique series) (more details in merge request !127 issue #56, merge request !128)
• improves ICP algorithm GUI (more details in merge request !125)
• adds tutorial to demonstrates calling actions from another action (more details in merge request !117)

Code quality and devops improvements

Updated dependencies

Most of CamiTK 5.0 dependencies were updated:

• Win7 → Win10
• CMake 3.2 → 3.13 (min, 3.17 supported)
• Qt 5.3 → 5.11 (min, 5.15 supported)
• VTK 6 → VTK 7.1 (min, VTK 8 supported)
• ITK 4.12 (min, ITK 4.13 supported)
• gdcm 2.8 (min, 3.0 supported)

Check the full support policy documentation for more information.

(more details in merge request !179 issue #117 , merge request !147 , merge request !119 , merge request !155 issue #108 , merge request !135 , merge request !134 , merge request !133 , merge request !120 , merge request !107)

Updated toolchain

CamiTK is now compatible to C++14 and C++17 standards. Three compilers were tested successfully :

• gcc 8 and 9
• clang 11
• MSVC++ 14.26

(more details in merge request !181)

Improved Continuous integration

Our gitlab continuous integration was also largely improved

• All continuous integration is now using docker images (even on Windows 10/11!). This facilitates deployment and reuse as well as allow any developer to reproduce the same continuous integration system. You can download the windows docker image in our gitlab container repository
• failed test are reran during the same pipeline to avoid false positive
• and much more…

(more details in merge request !164 issue #115 , merge request !150 issue #97 , merge request !149 , merge request !146 , merge request !109 , merge request !105 , merge request !104 issue #80 , merge request !103 issue #79 , merge request !100)

• cQ and devops improvement: CI for debian packaging (more details in merge request !180 , merge request !174 , merge request !171 , merge request !152 , merge request !151 , merge request !99 , merge request !98)

Multi-arch support

On Linux, we added multi-arch support. This means means that if you are not using Debian or Ubuntu, there is a great chance that you will be able to build and install CamiTK easily. This also means that processors other than x86-4 (aka amd64 x64 or Intel 64) can also be used if the dependencies are available.

(more details in merge request !183 issue #125 , merge request !172 issue #123 , merge request !156 issue #109)

Improved code quality

CamiTK Community Edition source code quality for also improved thanks to static analysis and various code cleaning, mainly:

• Compilation with three different compilers and -Wall (all warnings flag)
• clang-tidy
• cppcheck
• clazy

(more details in merge request !181 , merge request !130 , merge request !129)

Other quality improvements

We also took care of other various things in order to improve the quality of the code base

• rewritten outdated API documentation (more details in merge request !161 issue #110)
• updated qtpropertybrowser code (more details in merge request !160 issue #99)
• improved CMake macro documentation (more details in merge request !111)
• improved wizard generated Q_PLUGIN_METADATA merge request !101 (more details in issue #76)
• improved config test (more details in merge request !96)

Bug Fixed

We also fixed bugs reported by developers or users

• Fixed “Action Viewer popup selector not working” (more details in merge request !173 and issue #124)
• Fixed “CMake error when trying to install a CEP dependent on another CEP” (more details in merge request !167 issue #119)
• Fixed “Camitk-imp crash when using Application Close on a component” (more details in merge request !158 issue #111)
• Fixed “Invisible VTK 3D widget” (more details in merge request !153 issue #105)
• Fixed “Bug when there is no plugin to open directory data” (more details in merge request !131)
• Fixed “DLL import missing 3 core classes” (more details in merge request !122 issue #88)
• Fixed “Bug on CEP library install” (more details in merge request !121 issue #87)
• Fixed “Add/remove component child in explorer” (more details in merge request !115 issue #84)
• Fixed “Double property limited to int range” (more details in merge request !114 issue #86)
• Fixed “Manual threshold filter parameter” (more details in merge request !110 issue #62)
• and some others (for instance more details in merge request !183 merge request !182 merge request !97)

Full list of merge requests

72 merged requests between 15 July 2018 and 04 May 2021

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