[MORPHMET] Complaints about 'geomorph' R package

[Mauro Cavalcanti]

Dear members of the R geomorph Development Team,

As you surely know, I am a big fan of the 'geomorph' R package, which I
have been using since its inception (as part of a larger personal move to
do every possible analysis, morphometric or not, using R). Several times, I
have provided tentative bug reports and humble suggestions for improvements
(that sometimes have been incorporated into new releases of the package).

But with due respect, today I have a few severe complaints, that I am
posting here because they may have been of concern for other
morphometricians working with the geomorph package.

My first -- and biggest -- complaint concern the way landmark coordinates
captured by the 'digitize2d' routine are  stored in the latest version of
geomorph. There seems to have been some change in the code (undocumented as
far as I could see) which altered the scaling of the coordinates -- as a
result, I lost weeks of work on a file with more than 70 fish specimens
because when I opened the file in geomorph 2.17 to re-start digitizing the
remaining specimens (after having digitized about 50 in geomorph 2.15), all
coordinates were unexpectedly changed and the file became even unreadable
by Jim Rohlf's tps programs (but before this change in geomorph I could
have the tps programs read files digitized in geomorph without trouble).

Well, at first I solved this by simply downgrading my version of geomorph,
returning to the old 2.15 version and everything worked fine. Since I use
RStudio, i just had to remember to unckeck geomorph in the list of packages
to be updated.

But today, to my dismay and further annoyance, when I upgraded several
packages in my R installation -- even unckecking as usual the geomorphy
entry -- I got a strange error message which turned geomorph (whatever the
installed version) useless! Here it is:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
  there is no package called 'Biostrings'
ERROR: lazy loading failed for package 'geomorph'
* removing 'C:/Program Files/R/R-3.1.3/library/geomorph'


The geomorph package depends on other two packages, 'ape' and 'rgl', but
none of them have been upgraded recently and both load fine and without any
error messages, therefore I suppose the above error is generated by
geomorph itself.

Right, the error message about a missing package may be a minor (and easily
fixed) issue. But so is not the changes done to the digitize2d function,
which lead to data loss and waste of time and resources! Even if there are
some good reason (as surely does!) for changing the scaling of landmark
coordinates, such change should no tbe done without at least providing
users with the option of using the previous mode of operation of the
routine. Besides, such change should be carefully documented (and I could
not fund any mention to it in the "NEWS" file of the latest versions of
geomorph).

I hope you understand my reasons for complaining, and I look forward to
obtaining directions on how to get out of this mess (currently, I cannot
even use geomorph, whatever the version, because as a a result of the
"misisng package" error, the entire package was automatically wiped out of
my R installation...)

Life is short (so we need R)!

With best regards,

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

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[MORPHMET] Yet another sequel to complaints about 'geomorph' R package

[Mauro Cavalcanti]

Dear members of the geomorph R package Development Team,

I at least have been able to track down the "missing library" error when
attempting to install even previous versions of geopmorph.

It turns out that geomorph depends upon a package called 'phangorn' --
which has just been updated to make use of "Biostrings". At least one other
R package (phytools) is also dependent upon phangorn Iand therefore upon
Biostrings too).

The fact that the Biostrings package has not been installed as a depedency
of the latest phangorn is due to the fact that the Bioconductor Project
(and associated packages) is not on CRAN. A big mess, indeed...

Hope this helps!

It seems that these complaints about geomorph are turning to become a
series with many sequels as "Star Wars"...

May the Force Be With You! ;-)

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

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[MORPHMET] A sequel to complaints about 'geomorph' R package

[Mauro Cavalcanti]

Dear members of the geomorph R package Development Team,

After posting my complaints about the current problems in the geomorph R
package I have just stumbled upon, I have been able to at least find a
workaround to the annoying message about the missing "Biostrings" package.

I found out that "Biostrings" is part of the huge "Bioconductor" project
which aims to develop a large set of tools for bioinformatics. Following
the directions here (
https://bioconductor.org/packages/release/bioc/html/Biostrings.html) I have
been able to install the required library (plus several other packages of
ehich Biostrings depends) and afterwards could re-install version 2.15 of
geomorph. Now everything works as before!

But this is a makeshift solution. I have no idea why even previous versions
of geomorph are now requiring "Biostrings" (which are part of Bioconductor,
that I have never had in my R installation). Furthermore, the problem with
the scaling of landmark coordinates in the current version of geomorph
still stands and should be properly treated by offering an option to keep
the 'old' mode in the digitize2d function.

Hope this helps.

With best regards,

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

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Re: [MORPHMET] Information on 3d portable scanner

[Thomas O'Mahoney]

Both Artec scanners and LMI's HDI series scanners are more than good enough
for scanning materials for morphometrics. I have used both on several
projects, and know lots of groups with either that are happy with their
choice. As Dennis says, the LMI series works very well with a turntable.
You can also use a turntable for Artecs-I believe Marcus Bastir has had
some success with this.
Blue light scanners, you are not going to manage colour texture
unfortunately-I have used them out in Kenya with relatively harsh light
conditions and they're pretty bomb proof. The texture capture for the
Artecs is beautiful, but post processing takes a lot longer.
Basically you pay your money and take your choice.
Best,
Tom O'Mahoney
University of Manchester

On 16 December 2015 at 01:26, Helmi Hadi  wrote:

> Dear all,
>
> I too would like to know what are good 3D scanners. I have seen people use
> Microsoft Kinect for 3D scanning an object. Here is a video of it.
>
> https://www.youtube.com/watch?v=rQPTxiK-Crw
>
> I think that 3D scanners will come down in price eventually. The Kinect is
> cheaper than commercial scanners though it is slightly of lower resolution.
>
> I noticed the Creaform  (
> http://www.creaform3d.com/en/metrology-solutions/handheld-portable-3d-scanner-goscan-3d)
> and the Artek 3D scanner  (
> http://www.artec3d.com/hardware/artec-spider#specifications) are almost
> similar in technology and resolution. Maybe it is better to get whichever
> is cheaper.
>
>
> Kind regards,
> Helmi
>
> School of Health Sciences, Universiti Sains Malaysia,
> 16150 Kubang Kerian, Kelantan, MALAYSIA
> Tel: +609 7677834; Fax:+609 7677515
>
>
>
>
> -Original Message-
> From: morphmet [mailto:dsl...@morphometrics.org]
> Sent: 16 December 2015 03:24
> To: Anna Loy ; Dennis E. Slice 
> Cc: morphmet@morphometrics.org
> Subject: Re: [MORPHMET] Information on 3d portable scanner
>
> Replying to the list...
>
> Hi, Anna! No, I am not familiar with that. For the grant that secured the
> HDI, we also included the purchase of the similar Artec hand scanner
> (
> http://landing.artec3d.com/?keyword=artec%20scanner=CNHLk8TL3skCFUQ2gQod2YQMTQ
> )
> for archaeological field work, but did not get enough money for both.
> For our lab, the table-top seemed the best choice. I have used (well,
> minions, you know...) the Artec hand scanner some years ago and it was a
> bit flaky, but worked. I understand now that folks are using it quite
> successfully. I wish we had one. I might can refer you to someone if no one
> on the list has info.
>
> -ds
>
> On 12/15/15 2:12 PM, Anna Loy wrote:
> > Thank you Dennis!
> >
> > Do you have any info regarding the portables CREAFORM?
> >
> > Best
> >
> > Anna
> > 
> > Anna Loy
> > Dip. Bioscienze e Territorio
> > Università del Molise
> > Contrada Fonte Lappone
> > I-86090 Pesche (IS), Italy
> > Tel. 0874 404100
> > Cell. 3316265137
> > mail: a@unimol.it 
> >
> >
> >
> >
> > Il giorno 15/dic/2015, alle ore 19:31, Dennis E. Slice
> > > ha scritto:
> >
> >> We have the HDI 109 scanner with automatic turntable. My minions tell
> >> me it is quite easy to use with ridiculous resolution (I no longer
> >> get to play with the toys. This is probably for the best.). Part of
> >> the proposal for this was to digitize mouse skulls, so we opted for
> >> higher resolution without color.
> >>
> >> We were recently asked to scan a human skull at full resolution. The
> >> resulting file was 10s of gigabytes. I believe bear skulls would be a
> >> challenge because of both physical and digital size. I suspect
> >> resolution is controllable. One student is currently looking at
> >> morphometrics-appropriate decimation algorithms.
> >>
> >> Attached are pics of a macaque we scanned rendering only the vertices.
> >> The skull is about 100cm.
> >>
> >> Morpheus can't handle the full-res scan. Rendering done in Meshlab.
> >> full resolution: 3.4 million vertices (only vertices shown)6.8
> >> million faces
> >>
> >> Morpheus
> >> Pic 1) 500k vertices, 1000k faces
> >> Pic 2) 50k vertices, 100k faces
> >>
> >> -ds
> >>
> >> On 12/13/15 2:54 PM, ANNA LOY wrote:
> >>> Hello everyone
> >>>
> >>> Do any of you have experience with portable 3d scanner (no
> >>> structured
> >>> light) like
> >>>
> >>> *CREAFORM HANDY SCAN700 AMETEK
> >>> *http://www.creaform3d.com/en/metrology-solutions/portable-3d-scanne
> >>> r-handyscan-3d
> >>>
> >>> *GOSCAN 3D CREAFORM*video demo
> >>> https://www.youtube.com/watch?v=4IY1IN8swEc 2pounds no structured
> >>> light (no laser) molto veloce, res fino a 0.1 mm.
> >>>
> >>>
> >>> They seems very fast and easy to use
> >>>
> >>> Also which are differences with portable structured light 3d
> >>> scanners like *HDI 120 Blue-Light Scanner
> >>> *?
> >>>
> >>> I should scan