Geometric Morphometry Preparation Guide
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ScribdTranslationsGeometric Morphometry Preparation Guide
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ScribdTranslationsSteps for preparing the material for geometric morphometry, using the programs
tpsDig, Morpheus et al and tpsUtil.
1–Open the tpsDig program
2–Click on File > Input source > choose the figure of interest
3–Mark the desired number of landmarks with the "Digitize landmarks" tool.
(points)
4–Mark with the 'Outline object' tool the starting point of the scanning of
figure, taking care to always choose the same starting point in all figures
5–Right-click on the figure and select 'Save as XY coords'
6–Click on File > Save data as > save the file with the .tps extension
7–Repeat steps 2 to 6 always saving in the same file, selecting the option
Append Commented [-1]: Do this up to this point including the data in
file.
8–Open the Morpheus et al. program and type in the 'Command' space the following
commands: Commented [-2]: From here on only when the file is
complete.
set efa nharmonics X (where X is the number of harmonics that will be used in the analysis)
set efa location off
set efa orientation off
. set efa startingpt off
set efa scale off
. set fullprecision on
9–Click on File > Import > TPSLINE and select the [Link] saved in step 6
10– Type in the Command line 'super bookstein 1 2' (to overlap the two landmarks)
11–Click on Curves > Elliptic Fourier Analysis > EFA
12–Click on Curves > Elliptic Fourier Analysis > Save > Coefficients
13–Save with the .nts extension
14–Open the tpsUtil
15– Select in 'Operation' – Split NTS File
16– Select the file to be transformed into 'Input' and the location and name of the new one
file in 'Output'
17–Click on Setup
19–Click on Create
Import the file XXXX_mod.nts to Excel, creating an XXXX_mod.xls
Remove the first four columns from XXXX_mod.xls
Open the file XXXX_mod.xls in Fitopac and save as XXXX_coef.fpm
Open the file XXXX_coef.fpm in Fitopac and perform PCA, with the centered options.
selected covariance (click to sort).
In the next window, select lambda eigenvectors and lambda root eigenvectors
Record
A file XXXX_coef_PCA_Cov_mc_AutovetoresLambda.fpm will be created.
Open this file in Fitopac and save it with the .nts and .xls extensions
At the end of this step, the files that should be present in the folder are:
. [Link] (with all the population data)
. [Link] (file with the EFA coefficients)
. XXXX_mod.nts (previous file modified after passing through tpsUtil)
. XXXX_coef.fpm
. XXXX_coef_PCA_Cov_mc_AutovetoresLambda.fpm
. XXXX_coef_PCA_Cov_mc_AutovetoresLambda.nts
. XXXX_coef_PCA_Cov_mc_AutovetoresLambda.xls
The last three files are the result of the PCA analysis in fitopac
From this point, you must open the file XXXX_mod.xls and calculate the average,
average but o deviation standard (first line do file
XXXX_coef_PCA_Cov_mc_EigenvectorsLambda.xls), mean plus two times the standard deviation
mean, mean minus the standard deviation and mean minus two times the standard deviation.
Create a spreadsheet in the file XXXX_mod.xls to paste the results of this calculation.
(special color, values).
Import this spreadsheet into Fitopac, making a transposition.
Save this file as a .nts file
Open the [Link] and use the split NTS file tool with the file saved in the step
previous
Save the file with the name [Link]
Open the NTSYSpc
Select the Fourier plot tool
- In the coefficients file line, select the file [Link]
In the harmonics line, enter the number of harmonics used
Click on Compute to perform the contour reconstruction.