Cleaver2 v2.4

Cleaver is a multimaterial metrahedral meshing library and application developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute. Visit https://www.sci.utah.edu/cibc-software/cleaver.html for more information.

This release contains bug fixes such as: the Constant/Adaptive toggle for the element sizing method parameter, blending function sigma usage and error handing, and preserved spacing for segmentations and indicator functions. The release also contains uniform parameter names between the command line interface and the GUI with tool tips to help the user become familiar with the parameters and an upgrade to ITK 4.13.1 and Qt5.12.

Cleaver2 Release 2.3.1

Version 2.3.1 Release Notes

Bug Fixes:

• Fixed bug causing some 2-material interfaces to project incorrectly when rotating an edge.
• Fixed bug causing flat tets around axis-aligned 2-material interfaces.
• Fixed command line parameter parsing for ‘scaling’.
• Fixed unassigned fields variable when using a segmentation image.
• Fixed UI bug where max dihedral displayed was actually the min dihedral.
• Fixed broken build script for unit tests.
• Fixed ITK based SaveNRRDFile using wrong dimensions and sampling on save.
• Fixed CLI help text for background mesh mode.
• Fixed CLI bug where regular meshes were being labeled as adaptive.
• Fixed output of background mesh to respect verbose option.
• Fixed unnecessary warning of segmentation file use on multiple file input.

Other improvements:

• Decoupled CLI and GUI builds. Now each can be built without the other.
• Removed dependency on ITK. Cleaver can now build against included Teem lib for NRRD file support.
• Improved type safety for some key cleaver types.
• Various code readability improvements.
• Loosened tight-coupling of main Cleaver implementation class.
• Refactored several core Cleaver algorithm components into their own classes.
• Added debug dump file with json serialization of degenerate sets.
• Added fallback for triplepoint computation to use face centroid as position when input fields are numerically unstable.

Cleaver2 Release Candidate 2.3

Version 2.3 Release Notes

Bug Fixes:

• Fixed command line parameter parsing for ‘scaling’.
• Fixed unassigned fields variable when using a segmentation image.
• Fixed UI bug where max dihedral displayed was actually the min dihedral.
• Fixed broken build script for unit tests.
• Fixed ITK based SaveNRRDFile using wrong dimensions and sampling on save.
• Fixed CLI help text for background mesh mode.
• Fixed CLI bug where regular meshes were being labeled as adaptive.
• Fixed output of background mesh to respect verbose option.
• Fixed unnecessary warning of segmentation file use on multiple file input.

Other improvements:

• Decoupled CLI and GUI builds. Now each can be built without the other.
• Removed dependency on ITK. Cleaver can now build against included Teem lib for NRRD file support.
• Improved type safety for some key cleaver types.
• Various code readability improvements.
• Loosened tight-coupling of main Cleaver implementation class.
• Refactored several core Cleaver algorithm components into their own classes.
• Added debug dump file with json serialization of degenerate sets.
• Added fallback for triplepoint computation to use face centroid as position when input fields are numerically unstable.

Cleaver2 Stable Release

This is the latest stable release of Cleaver2.

OSX
Double Click the mountable DMG Cleaver_2.*_osx.dmg
Read the LICENSE.txt and be sure you comply with the license agreement.
Drag Cleaver2 to the Applications shortcut.
Double Click Cleaver2 in Applications or run from the command line: /Applications/Cleaver2.app/Contents/MasOS/cleaver-gui.
You may have to Accept that you are running a program downloaded from the internet.
If the program still doesn't load, open "Settings-->Security" and push "Open Anyway" for Cleaver2.

Windows
Double Click the setup file Cleaver_2.*_win64.exe
You may have to accept that you are opening an unsigned program, such as:
"More Options-->Run Anyway".
Follow the step by step install instructions.
Cleaver2 Should run after installation.

Linux
Please follow build instructions on main page to build from source.

NOTES
Load your image files or test files given in examples.zip.
Run Sizing Field, Generate Mesh, and set visual options as desired.

Version 2.2 Release Notes

- Improved rendering using Qt5 interface with GLSL shaders. - No more confusion between cleaver widget and sizing field widget "Adaptive vs. Constant" - Material Cell vs. Face locks work correctly. - ITK used for NRRD input/output. - Segmentation Label maps supported by default (dialog checkbox for indicator files in Volume Import) - Blending function sigma available in Volume import dialog. - Threaded runs for sizing field and meshing. Program still interactive during steps. - Progress indicator and status bar message updates on the bottom of the app. - Only 1 volume, 1 sizing field, and 1 mesh can be loaded at a time (old data overwritten) for memory management. - Dialog asks to save new sizing fields/meshes on new imports or program exit. - Data manager view on/off in menu added. - Program actions disabled during thread runs, re-enabled as pipeline completed.

Cleaver 2.2 Stable Release

This is the latest stable release of Cleaver2.

OSX
Double Click the mountable DMG Cleaver_2.*_osx.dmg
Read the LICENSE.txt and be sure you comply with the license agreement.
Drag Cleaver2 to the Applications shortcut.
Double Click Cleaver2 in Applications or run from the command line: /Applications/Cleaver2.app/Contents/MasOS/cleaver-gui.
You may have to Accept that you are running a program downloaded from the internet.
If the program still doesn't load, open "Settings-->Security" and push "Open Anyway" for Cleaver2.

Windows
Double Click the setup file Cleaver_2.*_win64.exe
You may have to accept that you are opening an unsigned program, such as:
"More Options-->Run Anyway".
Follow the step by step install instructions.
Cleaver2 Should run after installation.

Linux
Please follow build instructions on main page to build from source.

NOTES
Load your image files or test files given in examples.zip.
Run Sizing Field, Generate Mesh, and set visual options as desired.

Version 2.2 Release Notes

- Improved rendering using Qt5 interface with GLSL shaders. - No more confusion between cleaver widget and sizing field widget "Adaptive vs. Constant" - Material Cell vs. Face locks work correctly. - ITK used for NRRD input/output. - Segmentation Label maps supported by default (dialog checkbox for indicator files in Volume Import) - Blending function sigma available in Volume import dialog. - Threaded runs for sizing field and meshing. Program still interactive during steps. - Progress indicator and status bar message updates on the bottom of the app. - Only 1 volume, 1 sizing field, and 1 mesh can be loaded at a time (old data overwritten) for memory management. - Dialog asks to save new sizing fields/meshes on new imports or program exit. - Data manager view on/off in menu added. - Program actions disabled during thread runs, re-enabled as pipeline completed.

Cleaver2.2 Release Candidate 1

This is the latest test release of Cleaver2.

OSX
Double Click the mountable DMG Cleaver_2.*_osx.dmg
Read the LICENSE.txt and be sure you comply with the license agreement.
Drag Cleaver2 to the Applications shortcut.
Double Click Cleaver2 in Applications or run from the command line: /Applications/Cleaver2.app/Contents/MasOS/cleaver-gui.
You may have to Accept that you are running a program downloaded from the internet.
If the program still doesn't load, open "Settings-->Security" and push "Open Anyway" for Cleaver2.

Windows
Double Click the setup file Cleaver_2.*_win64.exe
You may have to accept that you are opening an unsigned program, such as:
"More Options-->Run Anyway".
Follow the step by step install instructions.
Cleaver2 Should run after installation.

Linux
Please follow build instructions on main page to build from source.

NOTES
Load your image files or test files given in examples.zip.
Run Sizing Field, Generate Mesh, and set visual options as desired.

Cleaver2 Command Line Interface and Graphical User Interface

This is the latest stable release of Cleaver2.

OSX
Double Click the mountable DMG Cleaver_2.*_osx.dmg
Read the LICENSE.txt and be sure you comply with the license agreement.
Drag Cleaver2 to the Applications shortcut.
Double Click Cleaver2 in Applications or run from the command line: /Applications/Cleaver2.app/Contents/MasOS/cleaver-gui.
You may have to Accept that you are running a program downloaded from the internet.
If the program still doesn't load, open "Settings-->Security" and push "Open Anyway" for Cleaver2.

• For Segmentation Tools:
  • Download SCIRun_4.7.2_osx_binaries.tar.gz included in this Release.
  • Extract to a location without spaces.
  • Python should be included in your OSX distribution.

Windows
Double Click the setup file Cleaver_2.*_win32.exe
You may have to accept that you are opening an unsigned program, such as:
"More Options-->Run Anyway".
Follow the step by step install instructions.
Cleaver2 Should run after installation.

• For Segmentation Tools:
  • Download SCIRun4 for Windows (https://www.sci.utah.edu/download/scirun).
  • Install to a location without spaces.
  • Install python2.7+ (www.python.org) to a location with no spaces. Be sure to add Python to PATH in the install options.

Linux
Extract the Linux tarball tar -xf Cleaver_2.*_Linux.tar.gz
Read the LICENSE.txt and be sure you comply with the license agreement.
Double Click Cleaver2 or run from the command line: ./cleaver-gui.

• For Segmentation Tools:
  • Download SCIRun4 source (https://www.sci.utah.edu/download/scirun) and build. (build.sh)
  • Python should be included in your Linux distribution.
• NOTE : This binary was built on 64 bit OpenSuse 13.1. You may have to build your own binary if this one doesn't work for you.

NOTES
Load your image files or test files given in examples.zip.
Run Sizing Field, Generate Mesh, and set visual options as desired.
In order for segmentation tools to work, you must have the following:

• SCIRun4 Installed on your machine. You will need to set the location of SCIRun4 once during GUI Runtime for segmentation tools to function. The command line tool needs the location set explicitly every run.
• Python2.7+ Installed on your machine. You will need to set the location of Python once during GUI Runtime for segmentation tools to function. The command line tool needs the location set explicitly every run.
• Cleaver2 MUST be installed in a location with NO SPACES in the path. (Including the Python and SCIRun4 paths) Due to cross-platform differences and system calls to python and other executables, spaces in the path cause problems. This is expected to be taken care of in the future.
• If you set the wrong paths for SCIRun4 or Python, you can edit the .path file in your Cleaver2 path (or OSX Cleaver2.app/Contents/MacOS/).

Cleaver2.1 Test Release

Please test the examples on both the GUI and CLI. See usage on the main page. Segmentation file may not work with OSX and Linux (binaries link with dynamic libs I was unable to include in time).

NOTE: In order to use segmentation tools, you must install python 2.7+

Cleaver 2

Initial release of Cleaver 2 for the IBBM workshop.