Problem with c3d from Motive

[Yoann]

Salut Arnaud,

J'essaye de lire les c3d créé par Motive avec BTK 0.3.0. Je suis capable de le lire mais tout de suite après la commande "btkReadAcquisition", j'ai le message suivant:

Warning: Essai_001.c3d - The number of blocks to be read in the parameter section is different than the number of blocks read. The value kept is the number of blocks read.

Finalement, j'utilise le même traitment qui fonctionnait avant pour recréer un nouveau c3d avec "btkWriteAcquisition" à partir des données obtenus. Le c3d se créé mais je ne suis pas capable de le lire:

No IO found, the file is not supported or valid or the file suffix is misspelled (Some IO use it to verify they can read the file)

Pourrais tu m'aider SVP?

Merci.

Yoann

[Arnaud Barré]

Can you send me a C3D file generated by Motive?

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[Yoann Dessery]

Voilà!

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

[Arnaud Barré]

I also should have asked you the C3D file generated by BTK :-)

On my side, I have just tried with Matlab and Mokka and the regenerated file was correctly loaded.

acq = btkReadAcquisition('../../Essai_001.c3d’);
btkWriteAcquisition(acq,'../../Essai_001_saved_bis.c3d');
acq2 = btkReadAcquisition('../../Essai_001_saved_bis.c3d’);

What are the Matlab commands that you used?

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> <Essai_001.c3d>

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[Yoann Dessery]

C’est étrange!

Voici le fichier créé.

[Arnaud Barré]

All the bytes in your file are set to 0x00. This already happened to me once. To fix the problem. I restarted Matlab (or the computer) and I have no more this problem after that. I have to dig more in the Windows API to better understand this issue. Let me know if this does not solve the problem.

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> <Essai_001_traite.c3d>

>
>
>
>> On 21 Sep 2016, at 18:25, Arnaud Barré <arnaud...@gmail.com> wrote:
>>
>> I also should have asked you the C3D file generated by BTK :-)
>>
>> On my side, I have just tried with Matlab and Mokka and the regenerated file was correctly loaded.
>>
>> acq = btkReadAcquisition('../../Essai_001.c3d’);
>> btkWriteAcquisition(acq,'../../Essai_001_saved_bis.c3d');
>> acq2 = btkReadAcquisition('../../Essai_001_saved_bis.c3d’);
>>
>> What are the Matlab commands that you used?
>>
>>> On Sep 21, 2016, at 12:16 PM, Yoann Dessery <ydes...@gmail.com> wrote:
>>>
>>> Voilà!
>>>

>>> Yoann Dessery, PhD
>>> Kneemo Researcher in Peacocks Medical Group Ltd.
>>>
>>>
>>>

[Yoann Dessery]

J’ai redémarré l’ordi et j’ai toujours les mêmes messages dès que j’ouvre le fichier c3d et après que je l’ai transformé.

[Arnaud Barré]

Can you answer these questions?
- What is your OS, its architecture,
- your Matlab version (architecture also),
- Which file did you download on the website of BTK?
- Is it the first you use BTK on this computer?

[Yoann Dessery]

Can you answer these questions?
- What is your OS, its architecture,

Windows XP (sur une machine virtuelle VM Ware fusion pour Mac)

 
- your Matlab version (architecture also), 

Matlab 2011a

- Which file did you download on the website of BTK?

Yes, long time ago

- Is it the first you use BTK on this computer?

Non, je l’utilise depuis 4 ans maintenant

As tu besoin de plus d’informations?

[Arnaud Barré]

Can you do the following steps:
- Verify that Windows XP is up to date.
- Restart MacOS
- Download the latest version of BTK for Matlab [1]
- Launch VMware
- Test the version of BTK
- Save one file in the Windows file system
- Save one file in the MacOS file system

Can you also try with Mokka (under MacOS and Windows) if this does not work with Matlab.

[1] https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/b-tk/btk-0.3.0_WinXP_MatlabR2008b_32bit.zip

[Yoann Dessery]

J’ai fait tout ce qui était inscrit et la conclusion est que Mokka (mac et windows) n’a aucun problème à lire le fichier c3d de base mais ne peut pas lire celui que je créé par la suite.

J’ai toujours les mêmes messages d’erreurs dans matlab également (voir capture d’écran).

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

[Yoann Dessery]

D’ailleurs je confirme que c’est avec les nouveaux fichiers c3d car je viens d’essayer un de mes anciens et cela fonctionne parfaitement!

[Yoann Dessery]

C’est encore moi! je viens de remarquer que Mokka a des problèmes avec les blocs aussi (sur mac et windows) —> voir image jointe

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

[Yoann Dessery]

Pour essayer de comprendre, j’ai essayé de comparer un c3d fonctionnant (à droite sur l’image jointe) et un ne fonctionnant pas (à gauche sur l’image jointe). il est possible de voir que le problème vient surement du nombre de frames.

à droite: 800 frames allant de 1 à 800

à gauche: 647 frames allant de 1 à 646 —> ce qui fait 646 frames donc problème

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

[Arnaud Barré]

The warnings are not important. They are only here to inform you that the structure of the C3D file is not perfect, but this is not critical. Because this already confused some users in the past, it was decided to hide these warnings by default in OpenMA.

Regarding the number of frames, the difference is because Motive sets the first frame to 0, but this not possible. The C3D format starts to 1 or greater. I modified your file manually with a hex editor to set the first frame to 1. Can you try on your side to rewrite the attached file and see if this works?

[Yoann Dessery]

J’ai essayé un basic Read-Write-Read et toujours pareil (voir image jointe).

Par contre, j’ai essayé un open-export-open avec Mokka et le fichier de base ‘Essai_001.c3d’ et je n’ai pas de problème.

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

On 22 Sep 2016, at 01:42, Arnaud Barré <arnaud...@gmail.com> wrote:

The warnings are not important. They are only here to inform you that the structure of the C3D file is not perfect, but this is not critical. Because this already confused some users in the past, it was decided to hide these warnings by default in OpenMA.

Regarding the number of frames, the difference is because Motive sets the first frame to 0, but this not possible. The C3D format starts to 1 or greater. I modified your file manually with a hex editor to set the first frame to 1. Can you try on your side to rewrite the attached file and see if this works?

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<Essai_001_modified.c3d>

On Sep 21, 2016, at 6:17 PM, Yoann Dessery <ydes...@gmail.com> wrote:

Pour essayer de comprendre, j’ai essayé de comparer un c3d fonctionnant (à droite sur l’image jointe) et un ne fonctionnant pas (à gauche sur l’image jointe). il est possible de voir que le problème vient surement du nombre de frames.
à droite: 800 frames allant de 1 à 800
à gauche: 647 frames allant de 1 à 646 —> ce qui fait 646 frames donc problème

Yoann Dessery, PhD
Kneemo Researcher in Peacocks Medical Group Ltd.

<Comparaison files.tiff>

[Yoann Dessery]

C’est vraiment un problème avec Matlab 2011 et Windows XP car je viens d’essayer avec mon ordi du boulot où j’ai Matlab 2015b avec Windows 8 et cela fonctionne bien avec le fichier de base.

Yoann Dessery, PhD

Kneemo Researcher in Peacocks Medical Group Ltd.

On 22 Sep 2016, at 01:42, Arnaud Barré <arnaud...@gmail.com> wrote:

The warnings are not important. They are only here to inform you that the structure of the C3D file is not perfect, but this is not critical. Because this already confused some users in the past, it was decided to hide these warnings by default in OpenMA.

Regarding the number of frames, the difference is because Motive sets the first frame to 0, but this not possible. The C3D format starts to 1 or greater. I modified your file manually with a hex editor to set the first frame to 1. Can you try on your side to rewrite the attached file and see if this works?

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<Essai_001_modified.c3d>

On Sep 21, 2016, at 6:17 PM, Yoann Dessery <ydes...@gmail.com> wrote:

Pour essayer de comprendre, j’ai essayé de comparer un c3d fonctionnant (à droite sur l’image jointe) et un ne fonctionnant pas (à gauche sur l’image jointe). il est possible de voir que le problème vient surement du nombre de frames.
à droite: 800 frames allant de 1 à 800
à gauche: 647 frames allant de 1 à 646 —> ce qui fait 646 frames donc problème

Yoann Dessery, PhD
Kneemo Researcher in Peacocks Medical Group Ltd.

<Comparaison files.tiff>

[Edmund Cramp]

I see a couple of potential issues with the Essai_001.C3D file - the first frame number is "0" but that's not a valid frame number for point data - this file should start at Frame 1 and end with Frame 648.  In addition, although there is no ANALOG data in the file, there's also no ANALOG group, so any attempt to read the ANALOG group to discover if the file contains analog data i.e. the value of the ANALOG:USED parameter, will fail.  Both of these errors could easily be fixed with a couple of quick edits but may point to issues with the software that created the file.

One oddity is that the subjects direction of progression in the file is in the Z axis which is not normal but is allowed. 

Edmund Cramp

[Yoann Dessery]

Thank you for the information!

 

Both of these errors could easily be fixed with a couple of quick edits but may point to issues with the software that created the file.

How can I edit the file to open it with btk?

 

Do you know why can I open it with a newer version of Matlab and Windows while not with Matlab2011 and XP?

 

Thank you.

 

Yoann Dessery

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