ImprovingMeshQualityOfMarchingCubes - Revision history

Cscheid at 20:39, 21 June 2007

2007-06-21T20:39:31Z

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	To compile the basic software, which generates isosurfaces using Macet, you will need [http://teem.sourceforge.net teem] and [http://www.boost.org boost] to be installed. There is a linux makefile and a Visual Studio solution file available. The source is available [http://www.sci.utah.edu/~cscheid/software/macet.tar.gz here (.tar.gz)] or [http://www.sci.utah.edu/~cscheid/software/macet.zip here (.zip)]		To compile the basic software, which generates isosurfaces using Macet, you will need [http://teem.sourceforge.net teem] and [http://www.boost.org boost] to be installed. There is a linux makefile and a Visual Studio solution file available. The source is available [http://www.sci.utah.edu/~cscheid/software/macet.tar.gz here (.tar.gz)] or [http://www.sci.utah.edu/~cscheid/software/macet.zip here (.zip)]

			== Usage ==

			To generate a macet isosurface:

			./macet <nrrd_file> <iso_value> <output_off_file> -isCombined

			To generate a regular Marching Cubes isosurface:

			./macet <nrrd_file> <iso_value> <output_off_file>

Cscheid at 20:32, 21 June 2007

2007-06-21T20:32:24Z

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	to other related isosurface extraction algorithms such as Marching		to other related isosurface extraction algorithms such as Marching
	Tetrahedra, and Marching Octahedra.		Tetrahedra, and Marching Octahedra.

			== Get the software ==

			To compile the basic software, which generates isosurfaces using Macet, you will need [http://teem.sourceforge.net teem] and [http://www.boost.org boost] to be installed. There is a linux makefile and a Visual Studio solution file available. The source is available [http://www.sci.utah.edu/~cscheid/software/macet.tar.gz here (.tar.gz)] or [http://www.sci.utah.edu/~cscheid/software/macet.zip here (.zip)]

Cscheid at 20:02, 21 June 2007

2007-06-21T20:02:52Z

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	~~== The paper ==~~		[[Image:Macet_paper_teaser.png]]

	Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John Schreiner, Claudio Silva. Edge Transformations for Improving Mesh Quality of Marching Cubes. 2007, submitted.		Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John Schreiner, Claudio Silva. Edge Transformations for Improving Mesh Quality of Marching Cubes. 2007, submitted.

Cscheid at 18:06, 21 June 2007

2007-06-21T18:06:30Z

← Older revision		Revision as of 18:06, 21 June 2007
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	Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John Schreiner, Claudio Silva. Edge Transformations for Improving Mesh Quality of Marching Cubes. 2007, submitted.		Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John Schreiner, Claudio Silva. Edge Transformations for Improving Mesh Quality of Marching Cubes. 2007, submitted.

	== ~~Reproducing the results~~ ==		=== Abstract ===

	~~The results in this paper can be completely reproduced using open-source software and publicly available datasets.~~		Marching Cubes is a popular choice for isosurface
			extraction from regular grids due to its simplicity, robustness, and
	~~== Alternative #1: Ubuntu repository ==~~		efficiency. One of the key shortcomings of this approach is the
			quality of the resulting meshes, which tend to have many poorly
	~~If you run Ubuntu Linux~~, ~~you can simply add our APT repository~~		shaped and degenerate triangles.
			This issue is often addressed
	~~deb http://vgc~~.~~sci.utah.edu/ubuntu edgy main~~		through post processing operations such as smoothing. As we
			describe, while these improve the mesh, they do not remove all
	~~and install~~ the ~~package "ectmc" we are currently creating. This will install all~~ the ~~software you need with~~ the ~~right versions~~, ~~so running the experiments will be a matter of downloading the actual vistrail containing the workflows~~ and ~~running it:~~		degeneracies, and incur an increased and unbounded error between the
			resulting mesh and the original isosurface.
	~~# apt-get install ectmc~~		Rather than modifying the resulting mesh, we propose a method
			to modify the grid on which Marching Cubes operates.
	~~Follow [[InstallingVisTrailsOnUbuntu \|~~ these ~~instructions]].~~		This modification greatly increases the quality of the extracted
			isosurface. In our experiments, it did not create a single
	~~== Alternative #2: Downloading~~ and ~~using VisTrails manually ==~~		degenerate triangle, unlike any other method we experimented with.
			Our method essentially eliminates postprocessing related to mesh
	~~You can download all~~ the ~~individual software manually~~.		quality. We show improvements in subsequent mesh processing,
			using the generated surface directly as input to a tetrahedral mesh
	~~=== Our algorithm ===~~		generator.
			The method incurs minimal computational overhead,
	~~[http://www~~.~~sci.utah.edu/~cscheid/software/ectmc/ectmc.zip ZIP File]~~		requiring at most twice the execution time of the original Marching
			Cubes algorithm in our experiments. Most importantly, it can be
	~~[http://www~~.~~sci.utah.edu/~cscheid/software/ectmc/ectmc.tar.gz Gzipped tarball]~~		readily integrated in existing Marching Cubes implementations, and is
			orthogonal to many Marching Cubes enhancements (such as out-of-core
	~~==== Core requirements ====~~		and acceleration methods). The method can also be directly applied
			to other related isosurface extraction algorithms such as Marching
	~~[http://teem.sourceforge.net/ Teem]~~		Tetrahedra, and Marching Octahedra.

	~~[http://www.cs.princeton.edu/gfx/proj/trimesh2/ Trimesh2]~~

	~~[http://www.boost.org/ Boost]~~

	~~[http://vcg.sourceforge.net/tiki-index.php?page=Metro Metro]~~

	~~[http://tetgen.berlios.de/ Tetgen]~~

	~~=== Requirements for running the~~ experiments ~~===~~

	* [http://www.vtk.org VTK] Version 5.0 or higher, with ~~Python bindings~~
	* [http://matplotlib.~~sourceforge.net] Matplotlib~~
	* [http://afront.sourceforge.net] Afront

	~~=== VisTrails packages ===~~

	~~[http://www~~.sci.utah.edu/~cscheid/software/ectmc/macet_packages.tar.gz tarball of all necessary VisTrails packages.]. Extract this file into your .vistrails/userpackages directory. This will allow VisTrails to see the packages with extended functionality. Then, ~~add~~ the ~~following lines~~ to ~~your .vistrails/startup~~.~~py:~~

	~~addPackage('ectmc')~~
	~~addPackage('trimesh2')~~
	~~addPackage('meshutils')~~
	~~addPackage('afront')~~
	~~addPackage('metro')~~
	~~addPackage('teem')~~

	~~If any~~ of the ~~software you installed is not~~ in ~~the PATH for the user that's running VisTrails~~, ~~you~~ can ~~explicitly add the path as an extra parameter to these addPackages. For example:~~

	~~addPackage~~(~~'afront', '/home/user/downloads/afront')~~

	or

	~~addPackage('trimesh2', '/home/user/local/bin'~~)

	~~== Datasets ==~~

	~~The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data~~, ~~so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers~~ and ~~dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].~~

	~~== Vistrail ==~~

	The vistrail you will need to open is available [http://www.sci.utah.edu/~cscheid/software/ectmc/macet.xml here]. Each version shows a different technique. The topmost one is the one we are proposing (MACET).

Cscheid: /* VisTrails packages */

2007-04-18T15:52:57Z

VisTrails packages

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	=== VisTrails packages ===		=== VisTrails packages ===

	~~(TODO: Finish the text)~~ [http://www.sci.utah.edu/~cscheid/software/ectmc/macet_packages.tar.gz tarball of all necessary VisTrails packages.]		[http://www.sci.utah.edu/~cscheid/software/ectmc/macet_packages.tar.gz tarball of all necessary VisTrails packages.]. Extract this file into your .vistrails/userpackages directory. This will allow VisTrails to see the packages with extended functionality. Then, add the following lines to your .vistrails/startup.py:

			addPackage('ectmc')
			addPackage('trimesh2')
			addPackage('meshutils')
			addPackage('afront')
			addPackage('metro')
			addPackage('teem')

			If any of the software you installed is not in the PATH for the user that's running VisTrails, you can explicitly add the path as an extra parameter to these addPackages. For example:

			addPackage('afront', '/home/user/downloads/afront')

			or

			addPackage('trimesh2', '/home/user/local/bin')

	== Datasets ==		== Datasets ==

Cscheid at 15:35, 18 April 2007

2007-04-18T15:35:28Z

← Older revision		Revision as of 15:35, 18 April 2007
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	== Reproducing the results ==		== Reproducing the results ==

	The results in this paper can be completely reproduced using open-source software and publicly available datasets~~. We will soon post here the set of workflows needed to run the experiments directly in VisTrails, along with the necessary software~~.		The results in this paper can be completely reproduced using open-source software and publicly available datasets.

	== Alternative #1: Ubuntu repository ==		== Alternative #1: Ubuntu repository ==

Cscheid at 20:57, 17 April 2007

2007-04-17T20:57:45Z

← Older revision		Revision as of 20:57, 17 April 2007
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	The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].		The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].

	~~You~~ will		== Vistrail ==

			The vistrail you will need to open is available [http://www.sci.utah.edu/~cscheid/software/ectmc/macet.xml here]. Each version shows a different technique. The topmost one is the one we are proposing (MACET).

Cscheid at 16:31, 6 April 2007

2007-04-06T16:31:10Z

← Older revision		Revision as of 16:31, 6 April 2007
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	* [http://matplotlib.sourceforge.net] Matplotlib		* [http://matplotlib.sourceforge.net] Matplotlib
	* [http://afront.sourceforge.net] Afront		* [http://afront.sourceforge.net] Afront

			=== VisTrails packages ===

			(TODO: Finish the text) [http://www.sci.utah.edu/~cscheid/software/ectmc/macet_packages.tar.gz tarball of all necessary VisTrails packages.]

	== Datasets ==		== Datasets ==

	The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].		The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].

			You will

Cscheid at 16:28, 6 April 2007

2007-04-06T16:28:50Z

← Older revision		Revision as of 16:28, 6 April 2007
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	The results in this paper can be completely reproduced using open-source software and publicly available datasets. We will soon post here the set of workflows needed to run the experiments directly in VisTrails, along with the necessary software.		The results in this paper can be completely reproduced using open-source software and publicly available datasets. We will soon post here the set of workflows needed to run the experiments directly in VisTrails, along with the necessary software.

	== ~~Necessary~~ software ==		== Alternative #1: Ubuntu repository ==

			If you run Ubuntu Linux, you can simply add our APT repository

			deb http://vgc.sci.utah.edu/ubuntu edgy main

			and install the package "ectmc" we are currently creating. This will install all the software you need with the right versions, so running the experiments will be a matter of downloading the actual vistrail containing the workflows and running it:

			# apt-get install ectmc

			Follow [[InstallingVisTrailsOnUbuntu \| these instructions]].

			== Alternative #2: Downloading and using VisTrails manually ==

			You can download all the individual software manually.

	=== Our algorithm ===		=== Our algorithm ===
Line 15:		Line 29:
	[http://www.sci.utah.edu/~cscheid/software/ectmc/ectmc.tar.gz Gzipped tarball]		[http://www.sci.utah.edu/~cscheid/software/ectmc/ectmc.tar.gz Gzipped tarball]

	=== ~~Requirements~~ ===		==== Core requirements ====

	[http://teem.sourceforge.net/ Teem]		[http://teem.sourceforge.net/ Teem]
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	[http://tetgen.berlios.de/ Tetgen]		[http://tetgen.berlios.de/ Tetgen]

	== ~~Datasets~~ ==		=== Requirements for running the experiments ===

	~~The datasets we used are all available on~~ the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].

	=~~= Running the Experiments~~ ==

	The easiest way to run the experiments is through VisTrails. We will provide a vistrail with all the necessary workflows (comparisons, mesh quality histograms, distance measures). For that you'll need VisTrails proper and some additional software.

	* [http://www.vtk.org VTK] Version 5.0 or higher, with Python bindings		* [http://www.vtk.org VTK] Version 5.0 or higher, with Python bindings
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	* [http://afront.sourceforge.net] Afront		* [http://afront.sourceforge.net] Afront

	== ~~How not to compile anything~~ ==		== Datasets ==

	~~If you run Ubuntu Linux, you can simply add our APT repository~~		The datasets we used are all available on the [http://www.volvis.org Volvis website]. We use the NRRD toolset to access the data, so you need the NRRD header files to go with the raw volumes. You can get the NRRD headers and dataset we used [http://www.sci.utah.edu/~cscheid/software/ectmc/data here].

	~~deb~~ http://~~vgc~~.~~sci~~.~~utah~~.~~edu/ubuntu edgy main~~

	~~and install~~ the ~~package "ectmc" we are currently creating. This will install all~~ the ~~software~~ you need with the ~~right versions, so running the experiments will be a matter of downloading the actual vistrail containing the workflows and running it:~~

	~~# apt-get install ectmc~~

	~~Follow [[InstallingVisTrailsOnUbuntu \| these instructions]]~~.

	~~== How not to install anything ==~~

	You can ~~burn one of~~ the ~~Live CDs~~ we ~~will provide here, for i386 or amd64~~. ~~Boot into Ubuntu, and double click on the VisTrails icon~~. ~~It will open VisTrails with the right file~~.

Cscheid at 19:47, 5 April 2007

2007-04-05T19:47:23Z

← Older revision		Revision as of 19:47, 5 April 2007
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	and install the package "ectmc" we are currently creating. This will install all the software you need with the right versions, so running the experiments will be a matter of downloading the actual vistrail containing the workflows and running it:		and install the package "ectmc" we are currently creating. This will install all the software you need with the right versions, so running the experiments will be a matter of downloading the actual vistrail containing the workflows and running it:

	# apt-get install ectmc		# apt-get install ectmc

	Follow [[InstallingVisTrailsOnUbuntu \| these instructions]].		Follow [[InstallingVisTrailsOnUbuntu \| these instructions]].