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Chris,

Step1: Do you have cmake installed? If not, then I recommend using
homebrew for these things on Mac. Macports or maybe fink might do the
trick, but we might have to ask a support person for other steps.

The rest of the process should be simple:

1. tar xvzf cleaver-v*.tar.gz
2. cd src
3. mkdir build
4. cd build
5. cmake ..
6. make

And it should happily compile. At which point, cleaver will be stored
in build/bin. However, I can predict a couple of problems if you're
using OSX 10.9 (Mavericks). The first is that the current OSX
compiler will complain. If you have a newer version of g++ installed,
then I recommend using that. For example, i have g++-4.8 installed
(also with homebrew). I fix this manually (there are other fancy ways
in cmake, but the following usually works):

cmake -DCMAKE_CXX_COMPILER=g++-4.8 ..

Which is basically forcing cmake to use a different compiler (assuming
you have that compiler installed).

I do currently have cleaver running on my mac, so if you need to me
elaborate on any steps let me know.

Regards,
Josh


On Thu, Apr 10, 2014 at 12:14 PM, Gloschat, Christopher
<cgloschat@wustl.edu> wrote:
> Hey Josh,
>
> I just started using MeshLab for a different project I'm working on that
> uses 3D models. Just to make sure I'm understanding correctly, I would
> output a *.nrrd from Seg3D, use Cleaver to turn the *.nrrd into a mesh,
> load that into MeshLab, and export it as an *.stl? That sounds doable. I
> just checked on installing Cleaver on my Mac. I don't have a ton of
> experience with CMake, honestly I've only attempted to use it once and with
> minimal amounts of success. Any chance someone over there could walk me
> through the process?
>
> Best,
>
> Christopher Gloschat
> PhD Candidate
> Department of Biomedical Engineering
> Washington University in St. Louis
>
> On Apr 10, 2014, at 10:26 AM, Joshua Levine <jlevine@sci.utah.edu> wrote:
>
>> OK. I don't personally have time to do so, but writing a (basic) stl
>> output module for Cleaver would not be a huge time investment for a
>> developer. I don't believe any new data would need to be computed;
>> it's just writing the current data to a file differently.
>>
>> If it's a one-off type thing, meshlab would be my recommendation to
>> Chris. There's a high likelihood it's more robust than us scraping
>> something together on short notice. Since I don't use stl frequently,
>> I'm not entirely well-versed any quirks in meshlab's interpretation of
>> the format. If Chris needs assistance using meshlab in the meantime
>> I'm willing to help.
>>
>> If there's general use for this, maybe it should go on a feature
>> request? (printing 3d images sounds cool...) While meshlab has a
>> reasonable input format (nrrd), the output mesh formats are still a
>> little raw so entertaining suggestions might make sense.
>>
>> Josh
>>
>> On Thu, Apr 10, 2014 at 11:08 AM, Elizabeth Jurrus <liz@sci.utah.edu>
>> wrote:
>>> Hi Josh,
>>>
>>> The stl files are for input to a 3d printer. I've cc'd Chris to see if
>>> there's another format he'd want to try. Otherwise, it doesn't sound too
>>> hard to add meshlab to the data processing pipeline.
>>>
>>> - liz
>>>
>>>
>>>
>>> On 04/09/2014 03:53 PM, Joshua Levine wrote:
>>>>
>>>> Hi Liz,
>>>>
>>>> At the moment, ply. It's not hard to convert using MeshLab, for example
>>>> (open, save as).
>>>>
>>>> Are stl files of general use to you? A lot of the meshing community
>>>> prefers indexed formats (ply, obj, etc.) because they are more compressed
>>>> and preserve mesh topology. Going to stl is a one way street---it can be
>>>> tricky to do stl->ply.
>>>>
>>>> Josh
>>>>
>>>>> On Apr 9, 2014, at 3:09 PM, Elizabeth Jurrus <liz@sci.utah.edu> wrote:
>>>>>
>>>>> Hi guys...
>>>>>
>>>>> Can Cleaver output surface meshes in the STL file format?
>>>>>
>>>>> - liz
>>>
>>>
>

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• [Cleaver] STL format, Elizabeth Jurrus, 04/09/2014
  • Re: [Cleaver] STL format, Joshua Levine, 04/09/2014
    • Re: [Cleaver] STL format, Elizabeth Jurrus, 04/10/2014
      • Re: [Cleaver] STL format, Joshua Levine, 04/10/2014
        • Message not available
          • Re: [Cleaver] STL format, Joshua Levine, 04/10/2014

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