Re: size will be missing Re: [MORPHMET] Save aligned in TPSRelW

[alcardini]

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  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 :
>
>> 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 :
>>
>>> 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
 ---
 You received this message because you are subscribed to the Google
 Groups "MORPHMET" group.
 To unsubscribe from this group and stop receiving emails from it, send
 an email to morphmet+unsubscr...@morphometrics.org >>> morphmet+unsubscr...@morphometrics.org>.

>>>
>>> --
>>>
>>> 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 Stir

Re: size will be missing Re: [MORPHMET] Save aligned in TPSRelW

[Joanna Lenarczyk]

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 :

> 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 :
>
>> 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
>>> ---
>>> You received this message because you are subscribed to the Google
>>> Groups "MORPHMET" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to morphmet+unsubscr...@morphometrics.org >> morphmet+unsubscr...@morphometrics.org>.
>>>
>>
>> --
>>
>> 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.or
>> g/en/index.php/GFN/page/calculators/
>>
>> --
>> MORPHMET may be accessed via its webpage at http://w

Re: size will be missing Re: [MORPHMET] Save aligned in TPSRelW

[andrea cardini]

The point is simple: the variables called centroid size and log centroid 
size in MorphoJ won't be the real size of the original structures if 
they're imported without rescaling them.
They are, in my experience, about 1 and, regardless of the reason (which 
I find less important), they're wrong. Of course, if one does not do 
anything with size, shape data will be fine. I would not risk to be 
misled, nevertheless. In fact, I might have happened to review one or 
two papers when someone was testing allometry or something else 
involving size, when size was about 1 for all specimens.


Cheers

Andrea

On 22/06/17 11:18, Paolo Piras wrote:

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 >:


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
---
You received this message because you are subscribed to the
Google Groups "MORPHMET" group.
To unsubscribe from this group and stop receiving emails from
it, send an email to morphmet+unsubscr...@morphometrics.org

>.


-- 


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 
WEBPAG

Re: size will be missing Re: [MORPHMET] Save aligned in TPSRelW

[Paolo Piras]

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 :

> 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
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org > morphmet+unsubscr...@morphometrics.org>.
>>
>
> --
>
> 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.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
> Groups "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>
>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
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to morphmet+unsubscr...@morphometrics.org.