Dear Joanna,
this is something you can easily check: compare a PCA, shape distances and
also centroid size from TPSRelw with those from MorphoJ after redoing the
GPA: are they different?
If they are, I'd worry. But, unless there's a mistake, I'd say they will be
virtually identical.

Cheers

Andrea

On 22 June 2017 at 12:18, Joanna Lenarczyk <j.kowal...@botany.pl> wrote:

> Hello All,
> I was thinking about using TpsRelw to slide semilandmarks before analysing
> the aligned specimens data in MorphoJ, but does it really make sense to
> double the alignment?
> Even if I have the file after TpsRelw, where landmarks and semilandmarks
> are treated differently, im MorphoJ I make the alignment - Procrustes fit
> again, in which the semilandmarks are treated as landmarks,  they are
> computed as landmarks. So, do I lose the information on the placement of
> semilandmarks or not in MorphoJ?
> Best,
> Joanna
>
> 2017-06-22 11:18 GMT+02:00 Paolo Piras <paolopir...@gmail.com>:
>
>> Hi folks/Andrea,
>>
>> just to underline this:
>>
>> Andrea,when you say
>>
>> "an 'apparent size variable' which is a series of numbers virtually
>> equal to 1 (differences will be approximation errors)."
>> I think that MorphoJ "reads" the actual CS values from the aligned
>> coordinates saved by TPSrelw that, as you say, have lost their original
>> size. However, small deviations from 1 are not due to approximation error
>> as I *suspect* that the "aligned coordinates" saved by TPSrelw are those
>> projected on the tangent plane (by an orthogonal [more commonly used] or
>> stereographic projection) and for this reason they have necesarily a CS
>> larger than 1 that is the radius of the hyperspherical Kendall's Shape
>> Space. In order to reach the tangent plane from the sphere one necessarily
>> must go beyond its radius (that geometrically *IS* the size of a
>> configuration lying on that space) and the CS will be inevitably larger
>> than 1.
>> An indirect proof for this would be to verify that what you call
>> "approximation error" gives CS values always slightly larger than 1 and
>> never smaller.
>> So I think there is no error in having, for those data, CS
>> slightly different (=larger) from 1 as they MUST have CS larger than 1 by
>> construction.
>> However,I'm not sure at 100% if TPSrelw works as I hypothesized here..
>> Playing a bit with TPSrelw could unveil this.
>> All the best
>> Paolo
>>
>>
>> 2017-06-22 11:00 GMT+02:00 andrea cardini <alcard...@gmail.com>:
>>
>>> Hi Pere,
>>> there's plenty of work arounds this. I agree with Carmelo that the nts
>>> format may be easier to edit manually, so that you can put back the
>>> necessary labels.
>>>
>>> HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those data.
>>> As most of the time you may want to analyse both size and shape, instead of
>>> importing in MorphoJ the aligned specimens from the TPSRelw slid
>>> configurations, I'd suggest to save the SCALED ALIGNED SPECIMENS in
>>> TPSRelw. Jim added this option for this purpose: this way you get the
>>> aligned specimens rescaled to the original centroid size. Therefore, when
>>> you import them in MorphoJ and redo the Procrustes fit, you will get both
>>> the aligned specimens as well as their size.
>>> In contrast, if you import the aligned data (not rescaled), size won't
>>> be there but you may be easily tricked and think it is there, because
>>> MorphoJ requires that you redo the Procrustes fit and then you'll get an
>>> 'apparent size variable' which is a series of numbers virtually equal to 1
>>> (differences will be approximation errors).
>>> Use the scaled aligned and you won't have this issue.
>>>
>>> Cheers
>>>
>>> Andrea
>>>
>>> On 22/06/17 10:07, Pere Ibáñez wrote:
>>>
>>>> Hello All,
>>>>
>>>> I am using TPSRelW to slide semilandmarks. Once I have the consensus, I
>>>> use Save aligned to export the aligned coordinates (including slid
>>>> semilandmarks) as a tps file, that I want to import into MorphoJ.
>>>>
>>>> The problem is that the file that is exported has the IDs of the
>>>> specimens empty, with no information. And MorphoJ doesn't import it without
>>>> that information, so I have to type it one by one on the tps file. Does
>>>> anyone know how to export that tps file from TPSRelW without losing the ID?
>>>>
>>>> Thanks!
>>>>
>>>> --
>>>> MORPHMET may be accessed via its webpage at
>>>> http://www.morphometrics.org
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>>>
>>> --
>>>
>>> Dr. Andrea Cardini
>>> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
>>> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
>>> tel. 0039 059 2058472 <059%20205%208472>
>>>
>>> Adjunct Associate Professor, School of Anatomy, Physiology and Human
>>> Biology, The University of Western Australia, 35 Stirling Highway, Crawley
>>> WA 6009, Australia
>>>
>>> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
>>> WEBPAGE: https://sites.google.com/site/alcardini/home/main
>>>
>>> FREE Yellow BOOK on Geometric Morphometrics:
>>> http://www.italian-journal-of-mammalogy.it/public/journals/3
>>> /issue_241_complete_100.pdf
>>>
>>> ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.or
>>> g/en/index.php/GFN/page/calculators/
>>>
>>> --
>>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>> --- You received this message because you are subscribed to the Google
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>>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
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>
>
>
> --
> Joanna Lenarczyk
>
> Zakład Fykologii
> Instytut Botaniki im. W. Szafera Polskiej Akademii Nauk
> ul. Lubicz 46, 31-512 Kraków
> tel. 12 42 41 876
>
> Department of Phycology
> W. Szafer Institute of Botany, Polish Academy of Sciences
> Lubicz 46, PL-31-512 Cracow
> phone +48 12 42 41 876
>
> e-mail: j.lenarc...@botany.pl
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
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>



-- 

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human
Biology, The University of Western Australia, 35 Stirling Highway, Crawley
WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

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