Error in Import_StereoMorph_Curve

[raisalhaq]

When I try to import coordinates from Stereomorph file

import_StereoMorph_curve1('D:/DATA R 4/shapes')

it doesn't work: Error in import_StereoMorph_curve1("D:/DATA R 4/shapes") : Deprecated due to major updates in StereoMorph export file format. You can try the solution by Stas Malavin before this being fixed in Momocs: https://github.com/stas-malavin/Momocs/blob/master/R/importSM.r

I have no idea with ImportSM.r, it takes me too long to understand it I hope to get a simpler code to import coordinates from stereoMorph file?

[vbonhomme]

And by my side it takes me too long to cope with all changes. Try sending me the file exported by stereomorph and I can give it a try (but not before few weeks I guess - MomX will solve many problems like this and I'm on it). Or you'd better use ImageJ for now?

Le lun. 15 juin 2020 à 09:47, raisalhaq notifications@github.com a écrit :

When I try to import coordinates from Stereomorph file

import_StereoMorph_curve1('D:/DATA R 4/shapes')

it doesn't work: Error in import_StereoMorph_curve1("D:/DATA R 4/shapes") : Deprecated due to major updates in StereoMorph export file format. You can try the solution by Stas Malavin before this being fixed in Momocs: https://github.com/stas-malavin/Momocs/blob/master/R/importSM.r

I have no idea with ImportSM.r, it takes me too long to understand it I hope to get a simpler code to import coordinates from stereoMorph file?

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[raisalhaq]

Thank you very much,

I used the stereoMorph for normalization the data, by adding two landmarks may it give better results (referred to; "Identification of inter- and intra-species variation in cereal grains through geometric morphometric analysis, and its resilience under experimental charring

my recent analysis only used Fourier with norm=True, (black silhouette image directly turn into an outline in Momocs), and it works for further analysis such as PCA, LDA etc.

The questions:

1. It's enough if I only to use eFourier with norm=True, (without adding landmark)? and it would be accepted for publication purposes?

2. I never try image J, it's also capable of giving the landmark, for normalization, as well as stereoMorph?

3. If there is another way for normalization data before eFourier, please let me now. I will try it

I'm still working on stereoMorph, I will send the file when it was done. its really need time to draw the outline manually

Thank you Rayz

[vbonhomme]

Le lun. 15 juin 2020 à 11:07, raisalhaq notifications@github.com a écrit :

Thank you very much,

I used the stereoMorph for normalization the data, by adding two landmarks may it give better results (referred to; "Identification of inter- and intra-species variation in cereal grains through geometric morphometric analysis, and its resilience under experimental charring

my recent analysis only used Fourier with norm=True, (black silhouette image directly turn into an outline in Momocs), and it works for further analysis such as PCA, LDA etc.

The questions:

1.

It's enough if I only to use eFourier with norm=True, (without adding landmark)? and it would be accepted for publication purposes?

depends on the shape. on cereals or anything ± ellipsoid and with bilateral symmetry I'm tempted to say no (see ?efourier # Details)

1. 2.

I never try image J, it's also capable of giving the landmark, for normalization, as well as stereoMorph?

yes in a much easier way (two points, File > export as xy)

1. 2.

If there is another way for normalization data before eFourier, please let me now. I will try it

procrustes, in some cases, would be a way but two landmarks are safer

1.

I'm still working on stereoMorph, I will send the file when it was done. its really need time to draw the outline manually

Thank you Rayz

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[raisalhaq]

Thank you, your advises are really helps I will try my best

[raisalhaq]

Dear vincent Bonhomme,

I have tried to use ImageJ for outline extraction, and it works as well as using silhouette images. Unfortunately, The outlines and Landmarks files are saved separated in ImageJ.

I have no idea, how to add coupe of landmarks and align with the outlines for normalization before
e-Fourier.

If you have an advice for this case, it would really help and solve my problems

Samples and results of ImageJ as attached TRIAL_IMAGEJ.zip

Thank you Rayz

[vbonhomme]

There is a tie_jpg_txt that does the job

Le lun. 15 juin 2020 13:32, raisalhaq notifications@github.com a écrit :

Dear vincent Bonhomme,

I have tried to use ImageJ for outline extraction, and it works as well as using silhouette images. Unfortunately, The outlines and Landmarks files are saved separated in ImageJ.

I have no idea, how to add coupe of landmarks and align with the outlines for normalization before e-Fourier.

If you have an advice for this case, it would really help and solve my problems

Samples and results of ImageJ as attached TRIAL_IMAGEJ.zip https://github.com/MomX/Momocs/files/4779816/TRIAL_IMAGEJ.zip

Thank you Rayz

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[raisalhaq]

Thank you so much it works, so happy with that