Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-15 Thread Miguel Eduardo Delgado Burbano
Dear Antonio,

Thank you very much for your functions. All of them work very well. I
realized that a simple modification of the function read.landmarks from the
nat package allows load into the R console Avizo Landmarks in ascii format
but not semilandmark curves. Again thanks for your kind help.

All best,

Miguel


El lun., 15 de abr. de 2019 5:46 p. m., Antonio Profico <
antonio.prof...@uniroma1.it> escribió:

> Hi Miguel,
>
> thanks for sending me the example files. You can use the existing
> functions embedded in Arothron:
>
> library(Arothron)
> land.set<-"landmarksfromAvizo"
> set<-read.amira.set(land.set,"auto") #this is an array
> bspline<-"bsplinefromAvizo"
> set_2<-read.amira.set(bspline,"auto") #this is an array
> LineSet<-"linesetfromAvizo"
> curve_temp<-read.path.amira(LineSet) #this is a data.frame
> curve<-as.matrix(curve_temp)
>
> library(Morpho)
> #sample evenly spaced points (10 in this case) along "curve"
> ev.sp.points<-equidistantCurve(curve,10)
>
> Best,
>
> Antonio
>
> Il giorno lun 15 apr 2019 alle ore 01:35 Antonio Profico <
> antonio.prof...@uniroma1.it> ha scritto:
>
>> Hi Miguel,
>>
>> please send me the two files from Avizo (.ladmarkAscii) and B-splines
>> (.am).
>> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
>> files from Avizo?
>>
>> I'll add these two functions in Arothron and before to submit the new
>> release to the CRAN I'll send them to you.
>>
>> Best,
>>
>> Antonio
>>
>> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
>> mdelgadoburb...@gmail.com> ha scritto:
>>
>>> Dear All,
>>>
>>> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from
>>> Avizo (Standard Edition 7.1.0). I have used previously the Arothron and Nat
>>> packages to load landmarks derived from Amira into the R console. Now
>>> using the Avizo files such packages do not seem to work. Somebody has a
>>> script to read Avizo files in R or know a way to succesfully load such
>>> files into the R console? Thanks for any suggestion
>>>
>>> All best,
>>>
>>> Miguel
>>>
>>> --
>>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>> ---
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>>> an email to morphmet+unsubscr...@morphometrics.org.
>>>
>>
>>
>> --
>> __
>>
>> Antonio Profico
>> PhD
>> Department of Environmental Biology – Dipartimento di Biologia Ambientale
>> SAPIENZA Università di Roma
>>
>> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
>> Subscription: https://groups.google.com/forum/#!forum/microwear/join
>>
>> Arothron mailing list: https://groups.google.com/forum/#!forum/arothron
>> 
>> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>>
>> Lab.  06 4991 2690
>> Mob. 3293440766
>>
>
>
> --
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
> Subscription: https://groups.google.com/forum/#!forum/microwear/join
>
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> 
> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>
> Lab.  06 4991 2690
> Mob. 3293440766
>

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Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-15 Thread Antonio Profico
Hi Miguel,

thanks for sending me the example files. You can use the existing functions
embedded in Arothron:

library(Arothron)
land.set<-"landmarksfromAvizo"
set<-read.amira.set(land.set,"auto") #this is an array
bspline<-"bsplinefromAvizo"
set_2<-read.amira.set(bspline,"auto") #this is an array
LineSet<-"linesetfromAvizo"
curve_temp<-read.path.amira(LineSet) #this is a data.frame
curve<-as.matrix(curve_temp)

library(Morpho)
#sample evenly spaced points (10 in this case) along "curve"
ev.sp.points<-equidistantCurve(curve,10)

Best,

Antonio

Il giorno lun 15 apr 2019 alle ore 01:35 Antonio Profico <
antonio.prof...@uniroma1.it> ha scritto:

> Hi Miguel,
>
> please send me the two files from Avizo (.ladmarkAscii) and B-splines
> (.am).
> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
> files from Avizo?
>
> I'll add these two functions in Arothron and before to submit the new
> release to the CRAN I'll send them to you.
>
> Best,
>
> Antonio
>
> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
> mdelgadoburb...@gmail.com> ha scritto:
>
>> Dear All,
>>
>> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from
>> Avizo (Standard Edition 7.1.0). I have used previously the Arothron and Nat
>> packages to load landmarks derived from Amira into the R console. Now
>> using the Avizo files such packages do not seem to work. Somebody has a
>> script to read Avizo files in R or know a way to succesfully load such
>> files into the R console? Thanks for any suggestion
>>
>> All best,
>>
>> Miguel
>>
>> --
>> 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.
>>
>
>
> --
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
> Subscription: https://groups.google.com/forum/#!forum/microwear/join
>
> Arothron mailing list: https://groups.google.com/forum/#!forum/arothron
> 
> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>
> Lab.  06 4991 2690
> Mob. 3293440766
>


-- 
__

Antonio Profico
PhD
Department of Environmental Biology – Dipartimento di Biologia Ambientale
SAPIENZA Università di Roma

MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
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Lab.  06 4991 2690
Mob. 3293440766

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Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-14 Thread Miguel Eduardo Delgado Burbano
Dear Murat and Antonio,

Thanks for your fast response. Of course Murat here I attach the
corresponding files (they derived from Avizo not from Amira)

Antonio yes I tried to use the Arothron function read.amira.set () but the
following error appeared: argument "nland" is missing, with no default.

Here I attach three files one is Landmarks_LLM1_landmarksAscii (landmarks
from a human lower molar) and one B-spline in Avizo binary (*.am) format
and the same file in Avizo ascii (*.am) format
(zan0084_manleft_mirrored_01_curve_LM1.am and
zan0084_manleft_mirrored_01_curveascii_LM1.am)

Thanks for your help

All best,


El lun., 15 de abr. de 2019 8:15 a. m., Murat Maga  escribió:

> Dear Antonio and Miguel,
>
>
>
> Would it be possible to share those files with me as well? I would like to
> implement a way to import Amira landmark files into our SlicerMorph
> package, but we don’t have any to play with.
>
>
>
> Best,
>
> M
>
>
>
>
>
> *From:* Antonio Profico 
> *Sent:* Sunday, April 14, 2019 4:35 PM
> *To:* Miguel Eduardo Delgado Burbano 
> *Cc:* MORPHMET ;
> morphmet-requ...@morphometrics.org
> *Subject:* Re: [MORPHMET] Script to read Avizo landmarks and B-splines
>
>
>
> Hi Miguel,
>
>
>
> please send me the two files from Avizo (.ladmarkAscii) and B-splines
> (.am).
>
> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
> files from Avizo?
>
>
>
> I'll add these two functions in Arothron and before to submit the new
> release to the CRAN I'll send them to you.
>
>
>
> Best,
>
>
> Antonio
>
>
>
> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
> mdelgadoburb...@gmail.com> ha scritto:
>
> Dear All,
>
>
>
> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo
> (Standard Edition 7.1.0). I have used previously the Arothron and Nat
> packages to load landmarks derived from Amira into the R console. Now
> using the Avizo files such packages do not seem to work. Somebody has a
> script to read Avizo files in R or know a way to succesfully load such
> files into the R console? Thanks for any suggestion
>
>
>
> All best,
>
>
>
> Miguel
>
> --
> 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.
>
>
>
>
> --
>
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
>
> Subscription: https://groups.google.com/forum/#!forum/microwear/join
>
>
>
> Arothron mailing list: https://groups.google.com/forum/#!forum/arothron
> <https://groups.google.com/forum/#!forum/microwear>
>
> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>
>
> Lab.  06 4991 2690
> Mob. 3293440766
>
> --
> 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
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# Avizo 3D ASCII 2.0


define Markers 11

Parameters {
Color "1.0.9",
NumSets 1,
ContentType "LandmarkSet"
}

Markers { float[3] Coordinates } @1

# Data section follows
@1
1.069824981689453e+002 3.230857086181641e+001 7.741726684570313e+001 
1.067253570556641e+002 3.117101860046387e+001 7.906603240966797e+001 
1.071337509155273e+002 3.062068939208984e+001 8.174322509765625e+001 
1.044278793334961e+002 3.029200363159180e+001 8.385526275634766e+001 
1.035018234252930e+002 3.330528259277344e+001 8.359550476074219e+001 
1.009194259643555e+002 3.421195983886719e+001 8.097939300537109e+001 
1.022753219604492e+002 3.590150451660156e+001 7.821498870849609e+001 
1.029237899780273e+002 3.457044982910156e+001 7.538016510009766e+001 
1.053571166992188e+002 3.398883819580078e+001 7.497612762451172e+001 
1.059745407104492e+002 3.266828918457031e+001 7.570597839355469e+001 
1.031460418701172e+002 3.211197662353516e+001 7.892

Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-14 Thread Antonio Profico
Hi Miguel,

please send me the two files from Avizo (.ladmarkAscii) and B-splines (.am).
Are you sure that read.amira.set() doesn't work with the .landmarkAscii
files from Avizo?

I'll add these two functions in Arothron and before to submit the new
release to the CRAN I'll send them to you.

Best,

Antonio

Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
mdelgadoburb...@gmail.com> ha scritto:

> Dear All,
>
> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo
> (Standard Edition 7.1.0). I have used previously the Arothron and Nat
> packages to load landmarks derived from Amira into the R console. Now
> using the Avizo files such packages do not seem to work. Somebody has a
> script to read Avizo files in R or know a way to succesfully load such
> files into the R console? Thanks for any suggestion
>
> All best,
>
> Miguel
>
> --
> 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.
>


-- 
__

Antonio Profico
PhD
Department of Environmental Biology – Dipartimento di Biologia Ambientale
SAPIENZA Università di Roma

MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
Subscription: https://groups.google.com/forum/#!forum/microwear/join

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Lab.  06 4991 2690
Mob. 3293440766

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