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
An indirect proof for this would be to verify that what you call
"approximation error" gives CS values always slightly larger than 1 and
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
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
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.
> 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?
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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
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