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Author Topic: Voxel image stack and then what?  (Read 39892 times)
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blob
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« on: December 19, 2011, 10:08:25 PM »

OK so there is now a voxel bitmap stack export facility in the latest M3D beta (thanks Jesse) which makes it much easier to produce such stacks than using the animation tool but how do we go on from there to 3D meshes?

As most will probably already know since it has been mentioned a few times, it is possible to use the ImageJ 3D viewer plugin for that purpose and this is probably the easiest/most straightforward way to do it.

I've now also found this interesting MVE-2 modular program http://herakles.zcu.cz/research/projects/11/index.php which can also produce 3D meshes out of bitmap stacks by chaining appropriate modules.

Example: VolumeImageLoader -> Mv2Array2RegGrid -> MarchingCube or MarchingTetrahedra5 or MarchingTetrahedra6 -> ObjSaver

Meshes produced with the marching tetrahedra modules will absolutely need to be post-processed in Meshlab using the the reorient faces coherently filter and remeshing/simplification/smoothing is also likely necessary for any meshes produced by MVE-2 which could be done in Meshlab, Meshman or OpenFlipper using appropriate operators.

Please post if you know of other software for bitmap stack to mesh conversion as well as mesh simplification/smoothing, etc...

Cheers.
« Last Edit: December 19, 2011, 10:15:03 PM by blob » Logged
huminado
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« Reply #1 on: December 21, 2011, 04:06:44 AM »

Thanks for this post!

Example: VolumeImageLoader -> Mv2Array2RegGrid -> MarchingCube or MarchingTetrahedra5 or MarchingTetrahedra6 -> ObjSaver

I think you meant:

Example: VolumeImageLoader -> MveArray2RegGrid -> MarchingCube or MarchingTetrahedra5 or MarchingTetrahedra6 -> ObjSaver

at least I couldn't find Mv2Array2RegGrid.  [I'm having trouble with the MveArray2RegGrid module "GridND do not contain point attributes with name Values."]
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blob
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« Reply #2 on: December 21, 2011, 05:32:36 AM »

Thanks for this post!

Example: VolumeImageLoader -> Mv2Array2RegGrid -> MarchingCube or MarchingTetrahedra5 or MarchingTetrahedra6 -> ObjSaver

I think you meant:

Example: VolumeImageLoader -> MveArray2RegGrid -> MarchingCube or MarchingTetrahedra5 or MarchingTetrahedra6 -> ObjSaver

at least I couldn't find Mv2Array2RegGrid.  [I'm having trouble with the MveArray2RegGrid module "GridND do not contain point attributes with name Values."]

Yeah it's indeed MveArray2RegGrid, sorry about the typo.

And AttrName in MveArray2RegGrid and PointAttributeName in the isosurface extractor modules setups (MarchingCube, MarchingTetras) must match otherwise you get the error you get. Sorry about forgetting to mention this as well.

I can tell you it took me more than a bit of time of fiddling to figure all that out.  Hopefully you're getting there faster than I did.  

afro
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huminado
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« Reply #3 on: December 21, 2011, 08:24:58 AM »

All very new to me.  I tried Fiji instead (based on ImageJ) - I think it might have everything I need.  Import the image stack, then save-as and wavefront is right there in the list (instead of messing with the viewer).  Great tools to know about all of them.
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DarkBeam
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« Reply #4 on: December 21, 2011, 10:32:22 AM »

I asked Aexion's help, and he wrote this article; http://www.incendia.net/wiki/index.php/Raw_Voxel_Data_Export

The second part can be applied to Mandelbulb's voxels I hope? smiley
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blob
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« Reply #5 on: December 21, 2011, 10:46:23 AM »

The second part can be applied to Mandelbulb's voxels I hope? smiley
Even if 3DCoat can import a stack of bitmap, it currently costs from $99 to $249 depending on the version. sad

Considering that, I'll have to pass on even trying it.
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Theli
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« Reply #6 on: December 21, 2011, 01:15:25 PM »

There's a trail version of 3D coat available. Unfortunately it cannot import a model from bitmaps. It only takes a format called "RAW". I assume it includes all slices in a single file.
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bib
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« Reply #7 on: December 22, 2011, 01:27:07 AM »

There's a trail version of 3D coat available. Unfortunately it cannot import a model from bitmaps. It only takes a format called "RAW". I assume it includes all slices in a single file.

I struggle to get something. I used Fiji to export as RAW then tried to import into 3DCoat, without success.

I might have access to a 3D printer and they ask me for a STL or DXF format. In Fiji I found a way to see the object in 3D (plugins/3D viewer) and in that plugin I can export as DXF or STL, but it says that there is no mesh to export sad

All very new to me.  I tried Fiji instead (based on ImageJ) - I think it might have everything I need.  Import the image stack, then save-as and wavefront is right there in the list (instead of messing with the viewer).  Great tools to know about all of them.

If I use the export to Wavefront OBJ, the file is too small to be true: 108 bytes whereas my bitmap stack is 119MB big in total. Trying to import into 3DCoat gives nothing obviously.

Any tips please?


* fiji.png (141.78 KB, 528x573 - viewed 1058 times.)
« Last Edit: December 22, 2011, 01:40:19 AM by bib » Logged

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huminado
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« Reply #8 on: December 22, 2011, 04:57:28 AM »

Fiji seems to take a random amount of time to actually write the file (or maybe it's a bug).  I sometimes had to close the app and still watch the file folder before the file had a non-zero size, and even then, some of the obj's didn't work, and I did the whole process over.
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bib
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« Reply #9 on: December 22, 2011, 10:02:05 AM »

Yes Fiji seems quite buggy. It uses an enormous amount of RAM, as you said the time taken to export is random and the file stays empty, and when trying to close the program it makes the PC swap like crazy...

Any other solutions?
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visual.bermarte
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« Reply #10 on: December 22, 2011, 10:38:46 AM »

I see a lot of holes in the structure; try to reduce iterations number, maybe?
Plus a lot of ram is needed (together with a 64 bit OS).
To build a pile of 2000 pngs (2000x2000 px.)  with 1:1 ratio (full scale and maximum quality) one should run imageJ (64 bit ver.) with something like 16 gigas on board..otherwise one should decrease the scale and quality.

this one was produced using 1000 pngs with a scale around 2:1 without 64 bit (cinema 4d was used).
Volume rendering with Blender is nice 2 [but there's no mesh] (;
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blob
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« Reply #11 on: December 22, 2011, 10:50:57 AM »

All the meshes I have produced with ImageJ are full of holes though this can possibly be fixed in Meshlab which has a filter for closing holes in meshes, haven't tried it though so can't say whether it works well or at all.

Unfortunately mesh generation from stack is extremely memory demanding whatever the application it seems as MVE-2 I have linked in my initial post also chokes for lack of memory if the stack exceeds a certain size. A 2003 stack is OK but a 4003 will fail.
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blob
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« Reply #12 on: December 22, 2011, 11:30:57 AM »

Here is a raw obj mesh loaded in Sculptris that was generated from a 2003 stack in MVE-2 using the marching cubes operator.


* bulbmesh.jpg (61.04 KB, 579x549 - viewed 1064 times.)
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bib
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« Reply #13 on: December 22, 2011, 11:55:20 AM »

Here is a raw obj mesh loaded in Sculptris that was generated from a 2003 stack in MVE-2 using the marching cubes operator.

I tried MVE-2 but could not make it work (various error messages, something to do with the Save object that should have an output) Do you have a screenshot of the "process" please? My stack is 500x500x500. Is that too big? I have 8GB of RAM.
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Between order and disorder reigns a delicious moment. (Paul ValÚry)
blob
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« Reply #14 on: December 22, 2011, 12:54:09 PM »

I tried MVE-2 but could not make it work (various error messages, something to do with the Save object that should have an output) Do you have a screenshot of the "process" please? My stack is 500x500x500. Is that too big? I have 8GB of RAM.
Here is a screenie as well as a test project file using marching tetrahedra5 (which you'll obviously need to edit as far as input goes).

I don't know if your stack is too big, if it chokes for lack of memory it should tell you with an error message, as it's a 32bit app I don't think it will be able to use 8GB but only 2 or perhaps 3 I guess, you've got to try.


* MVE-2.png (22.55 KB, 687x398 - viewed 999 times.)
* test2.zip (0.9 KB - downloaded 271 times.)
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