RE: [MORPHMET] placePatch in Morpho (R)

2016-03-10 Thread Murat Maga 
Yes, copy all your meshes to a folder, and pass the path to it to placePatch. I 
thought I used binary stls as well, but I might be mistaken.
Make sure the Z dimname (or sample name) in the p.k.n array matches the 
filenames (minus .ply) since I think I that’s what it uses to match the LM 
array to the mesh.

M



From: morphmet@morphometrics.org [mailto:morphmet@morphometrics.org] On Behalf 
Of Pere Ibáñez
Sent: Thursday, March 10, 2016 7:38 AM
To: MORPHMET 
Subject: [MORPHMET] placePatch in Morpho (R)

I am using the function placePatch in Morpho: placePatch(atlas, dat.array, 
path, prefix = NULL, fileext = ".ply", ray = TRUE, inflate = NULL, tol = 
inflate, relax.patch = TRUE, keep.fix = NULL, rhotol = NULL, silent = FALSE, 
mc.cores = 1). I already created the atlas using createAtlas, and I checked 
using plotAtlas and it looks fine.

In placePatch, in path, I am supposed to specify the directory where the 
surface meshes of the sample are stored. Does this mean that I have to specify 
the folder where all the 3D images are? In that case, must they be in a 
specific format? Ascii PLY maybe?

I tried specifying the folder where my images are, but it didn't work (I 
obtained a pxkxn array with only missing values -NAs-). May this occur because 
my images are Binary PLY?

Thanks in advance!

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[MORPHMET] placePatch in Morpho (R)

2016-03-10 Thread Pere Ibáñez 
I am using the function placePatch in Morpho: placePatch(atlas, dat.array, 
path, prefix = NULL, fileext = ".ply", ray = TRUE, inflate = NULL, tol = 
inflate, relax.patch = TRUE, keep.fix = NULL, rhotol = NULL, silent = 
FALSE, mc.cores = 1). I already created the atlas using createAtlas, and I 
checked using plotAtlas and it looks fine.

In placePatch, in path, I am supposed to specify the directory where the 
surface meshes of the sample are stored. Does this mean that I have to 
specify the folder where all the 3D images are? In that case, must they be 
in a specific format? Ascii PLY maybe?

I tried specifying the folder where my images are, but it didn't work (I 
obtained a pxkxn array with only missing values -NAs-). May this occur 
because my images are Binary PLY?

Thanks in advance!

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Re: [MORPHMET] Crowdsourced GM Bibliography

2016-03-10 Thread Mauro Cavalcanti 
Dear Robert & ALL,

I have, for some years already, keeping lists of GM bibliographies
(selected groups of organisms), as part of the MorphoLib project (
http://morpholib.netai.net). All references are ket in downloadable files
in BiBTeX format and seachable interfaces are provided (automatically
generated from the bibliography files using the Jabref manager).

Hope this helps.

Best regards,

2016-03-09 12:57 GMT-03:00 Robert Z. Selden, Jr. :

> In an attempt to centralize the large wealth (and breadth) of knowledge
> generated through studies of geometric morphometrics, I thought that we
> might all collaborate on a working bibliography. And since geometric
> morphometrics is comprised of a fairly tight-knit international community, 
> *why
> not* make this a crowdsourced project?
>
>
>
> Since the great majority of practitioners are familiar–at least
> peripherally–with scripting, the bibliography is maintained in BibTeX, and
> can be edited in Overleaf. Additionally, using the field “annote,” the
> abstracts for each paper can be included. Further still, the BibTeX text in
> the GMBib.bib file can be cut, then pasted into a text file, where it can
> be imported to a number of reference and .pdf managers.
>
>
>
> I do ask that if you add a citation, you follow the current (BibTeX)
> format, and also place each new reference in alphabetical order (let
> Overleaf refresh after each entry to ensure there are no errors). This will
> help us to ensure that we are not duplicating citations that have already
> been added. Additionally, if you have more information (abstract, DOI,
> etc.) for a reference in the bibliography that is currently posted, please
> add that information.
>
>
>
> The goal of this endeavor is to maintain an active (and accurate) list of
> publications related to geometric morphometrics that can be used in
> classrooms, laboratories, and–yes–your own personal reference manager, and
> to have it maintained by the community of practitioners. So please add your
> new publications as soon as they’re available!
>
>
>
> To begin adding references to the current bibliography, click here
> .
>
>
>
> To generate a searchable .pdf of the current bibliography, simply click on
> the PDF tab at the top of the screen in Overleaf. Feel free to share the *Read
> and Edit* link (
> https://wordpress.com/page/crhrarchaeology.wordpress.com/89371) with
> colleagues and co-workers.
>
>
>
> Any and all users can add new references and edit existing references
> using this link
> .
>
>
>
> If you run into any issues, or just have questions, please forward those
> along.
>
>
>
> I’ve also added a link to my blog (
> https://crhrarchaeology.wordpress.com/morphometrics/gm-bibliography-project/)
> where this same text is posted (archaeologists are nothing if not
> redundant). Many thanks in advance for your contributions—I think that this
> can be a great resource.
>
>
>
> Best,
>
> Zac
>
>
>
>
>
>
>
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>



-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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