Viewing the GBCD with GMT

[J B]

Hello,

I am interested in using GMT to reconstruct the grain boundary character distribution (GBCD) data that can be output by DREAM.3D. Is anyone was aware of who has done this or what groups are doing this? I can't find any documentation on how to use GMT to plot a GBCD.

Thanks!

[Michael Jackson]

There is a script floating around the DREAM.3D sources that depends on GMT version 5. The folks at CMU use it to plot their GBCD results. 

Script it here:

https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/Draw_stereograms-gmt-v5.1.sh

Instructions are here

https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/UsingGMT.md

At one point I was able to get this to run on windows using MSys. I have a special setup bash alias on OS X to get things moving. I have never tried it on LINUX. In theory it should work.

Mike Jackson

--
You received this message because you are subscribed to the Google Groups "dream3d-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dream3d-user...@googlegroups.com.
To post to this group, send email to dream3...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/fbfb16da-a59d-4bfe-b72e-0a191efe5d9f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Mingyan Wang]

Hi Mike, 

This thread definitely helped me with viewing GBCD results on GMT. Thank you!

However, the results can only be viewed as a discrete plot instead of a continuous plot. According to "Draw_stereograms_gmt-v5.1.sh" line 70, I'm missing a script called "bc". But I couldn't find this in GMT or ImageMagick or GhostScript folder. Could you help me out with where "bc" is located and what it is doing?

Thanks,

Mingyan

[Michael Jackson]

I have no idea what it does. On macOS it is located in /usr/bin/bc and I
bet the same location on Linux. If you are on Windows then I am not sure
where/how to get it. sorry.


--
Mike Jackson [mike.j...@bluequartz.net]

Mingyan Wang wrote:
> Hi Mike,
>
> This thread definitely helped me with viewing GBCD results on GMT. Thank
> you!
> However, the results can only be viewed as a discrete plot instead of a
> continuous plot. According to "Draw_stereograms_gmt-v5.1.sh" line 70,
> I'm missing a script called "bc". But I couldn't find this in GMT or
> ImageMagick or GhostScript folder. Could you help me out with where "bc"
> is located and what it is doing?
>
> Thanks,
> Mingyan
>
> On Friday, 18 September 2015 01:53:25 UTC+2, Michael Jackson wrote:
>
> There is a script floating around the DREAM.3D sources that depends
> on GMT version 5. The folks at CMU use it to plot their GBCD results.
>
> Script it here:
> https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/Draw_stereograms-gmt-v5.1.sh
> <https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/Draw_stereograms-gmt-v5.1.sh>
>
> Instructions are here

> https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/UsingGMT.md <https://github.com/dream3d/DREAM3D/blob/develop/Tools/GMT/UsingGMT.md>

>
> At one point I was able to get this to run on windows using MSys. I
> have a special setup bash alias on OS X to get things moving. I have
> never tried it on LINUX. In theory it should work.
>
> Mike Jackson
>
>

> On Sep 17, 2015, at 7:46 PM, J B <johnm...@gmail.com <javascript:>>

> wrote:
>
>> Hello,
>>
>> I am interested in using GMT to reconstruct the grain boundary
>> character distribution (GBCD) data that can be output by DREAM.3D.
>> Is anyone was aware of who has done this or what groups are doing
>> this? I can't find any documentation on how to use GMT to plot a GBCD.
>>
>> Thanks!
>>
>> --
>> You received this message because you are subscribed to the Google
>> Groups "dream3d-users" group.
>> To unsubscribe from this group and stop receiving emails from it,

>> send an email to dream3d-user...@googlegroups.com <javascript:>.

>> To post to this group, send email to dream3...@googlegroups.com

>> <javascript:>.

>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dream3d-users/fbfb16da-a59d-4bfe-b72e-0a191efe5d9f%40googlegroups.com

>> <https://groups.google.com/d/msgid/dream3d-users/fbfb16da-a59d-4bfe-b72e-0a191efe5d9f%40googlegroups.com?utm_medium=email&utm_source=footer>.

>> For more options, visit https://groups.google.com/d/optout

>> <https://groups.google.com/d/optout>.

>
> --
> You received this message because you are subscribed to the Google
> Groups "dream3d-users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to dream3d-user...@googlegroups.com

> <mailto:dream3d-user...@googlegroups.com>.

> To post to this group, send email to dream3...@googlegroups.com

> <mailto:dream3...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/dream3d-users/7139f5c6-3041-4eaa-b583-114df85d70e1%40googlegroups.com
> <https://groups.google.com/d/msgid/dream3d-users/7139f5c6-3041-4eaa-b583-114df85d70e1%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Mingyan Wang]

Hi Mike,

Aha, I see where the problem is. I'll try to run the script on Linux.

Thank you,

Mingyan

> <mailto:dream3d-users+unsub...@googlegroups.com>.

[Che C]

Hi Mike,

I am attempting to use the DrawStereograms.sh to plot a pole figure (.dat file acquired from Dream.3D). However, I am getting a strange error involving

nearneighbor: Warning: No valid values in grid [filenameTempPDFnn.grd]

As well as some other references to this grd file, which never existed.

The program then "finishes", generating a skeleton for a pole figure, with no colors filled in.

Do you have any idea what might be happening? 

Thanks,

Che

[Ryan DeMott]

Hello,

I've been working on using GMT to plot GBCD follwoing the instructions here: https://github.com/BlueQuartzSoftware/DREAM3D/blob/develop/Tools/GMT/UsingGMT.md as mentioned earlier in this thread, but I'm having trouble getting it working. I got everything isntalled correctly I believe, but when I try to confirm that all of the executables are in the path, it seems the "convert" file is not where it should be. The instructions say you should see the following outputs:

$ which gmt
/c/Applications/gmt5/bin/gmt
$ which convert
/c/Applications/gs/gs9.10/bin/convert
$ which gswin32c
/c/Applications/ImageMagick-6.8.8-4/gswin32c

But what I get is:

$ which gmt

/c/programs/gmt5/bin/gmt

$ which gswin32c

/c/programs/gs9.27/bin/gswin32c

$ which convert

/c/WINDOWS/system32/convert

I'm a bit confused about the instructions because I'm pretty sure that "gswin32c" should be in the ghost script directory and "convert" should be in the ImageMagick directory but they're switched in the outputs in the instructions. I've gone searching in the ImageMagick directory for anything called "convert" but can't seem to find anything. The only thing in the ghostscript directory is gswin32c.

 I've never really run programs in command line before so I'm not too sure what I'm doing. Any help would be appreciated.

Ryan DeMott 

[Michael Jackson]

Ryan,

   It has been a *very* long time since I have run the GMT scripts. You are correct that the tools should be in the GMT and GS directories. NOTHING should be in the /c/WINDOWS directory. You may have to adjust your PATH so that it looks in the GMT and GS directories *before* any other directory.

 

--

Mike Jackson

--

You received this message because you are subscribed to the Google Groups "dream3d-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dream3d-user...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/5c2cb843-0963-4331-afb4-8f0a1de2f162%40googlegroups.com.

[Ryan DeMott]

Mike,

I got it working. It seems that new versions of ImageMagick don't have the convert utility, so when you install ImageMagick, you have to select the option to install legacy utilities.

Ryan

To unsubscribe from this group and stop receiving emails from it, send an email to dream3...@googlegroups.com.

[Michael Jackson]

Good to know. It has been on my list of things to do to figure out how to integrate pole figure codes that are more inline with what is seen in the literature.

To unsubscribe from this group and stop receiving emails from it, send an email to dream3d-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/e789cc4f-00b9-4305-8263-e48d9c4dfcdf%40googlegroups.com.