bug in training: tomo_idx

[fm m]

Dear Emmanuel,

 I really enjoy your great job DeepFinder. However, I got a bug in training my data. After annotated my tomogram, then when I run training, a bug said that:

tomoID = int(objelist[index]["tomo_idx"]... Not NoneType.

I checked the xml file after annotated tomogram, there was no "tomo_idx" the the file!!!

I also tried with Chlamydomonas tomogram, and it returned the same problem.

What could be the reasons? How can I solve this problem?

Thanks!

Ming

[Emmanuel Moebel]

Dear Magda,

Sorry for my late response. I have looked into it - indeed, there is a bug, or rather the user experience has not been taken into account correctly. I'll work on it as soon as possible, normally it should be solved in the course of next week.

In the meantime, there is a "quick and dirty" workaround, which involves editing the xml files in a text editor. You can add the "tomo_idx" attribute manually, by using the find-and-replace function of your text editor, with find="<object  " and replace="<object tomo_idx="0" ". I understand this is rather fastidious, and hopefully I can provide you with a better solution ASAP.

Furthermore, there will soon be a Napari plugin that will replace the current graphical user interface. We are currently running the last tests before official release.

Best regards,

Emmanuel Moebel

Le jeu. 27 oct. 2022 à 07:07, Magda Zaoralová <magda.z...@gmail.com> a écrit :

Hi Ming and Emmanuel,

I've got the same issue. Have you, by any chance, found out a solution, please?

Thank you!

Magda

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[Hong ZHAN]

Bonjour Emmanuel,

I did bypass the error using your method to add the tomo_idx.

I left another message in the group and I think Scipion has similar issue but I think I can also do the same trick.

Bien cordialement,

Hong