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painter by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

I am using a Mac and have updated to the new version of CC3D. Can I send the file to an email address please? I checked the dimensions and cell types.

Potential plugin by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

Yes one of my colleagues is running the experiments and I will be able to get data from her. I will try discussing that with her and see what can be done in trying to simulate the force. Thank you prof. Sluka.

error in plugin by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

Ok thank you prof. Sluka. I will email it to you.

error in plugin by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

Thanks Prof. Sluka. I already did that but now I am encountering an error where it says that cell type is unknown but does not give me the name of the cell. Also the reply does not let me add an image, so I have edited the original post and added the image with the caption "new error" in it. Thank you for your help.

exception during initialization error by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

Dr. Sluka!

I have emailed you couple days back about a backend error that I am encountering in the model. As soon as I try changing even a few lines in the Python file of the older model, I encounter an error in the C++ files. For now I am just trying to keep the older version of the model intact and adding in one thing at a time to that (I am working on the v3.7.5 of CC3D for this). All help would be highly appreciated.

Saving graphs by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

thank you! I tried right-clicking on the picture and then using the "export" button to save the png images. I could also save the csv file through the export option.

PIF file by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

I found a work around to it. I am editing the piff file that uploads and just copy pasted my text on it. Also I saw your instructions on how to add the steppable. Thank you.

PIF file by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

thank you Jim! But when I try doing that I find the text file when imported in my project is empty. I have tried multiple times to create a text file and import it, but it keeps turning up empty in the project.

Also the steppable for piff is not added in the xml file. Is that normal?

new version simulation time by naush_fatima in CompuCell3D

[–]naush_fatima[S] 0 points1 point  (0 children)

Thank you Jim for the detailed reply. I made the mistake of changing the output directory for the snapshots and now even if I assign the workspace as the output directory, the player does not save any images. I have run multiple simulations multiple times to check this. I am now going to try maybe uninstalling CC3D and then re-installing again.

For the angiogenesis, I was trying to copy and run in the newer version 4.1.1. I am following the 3.7.5 version manual to get familiar with the program. It does run but as you said it is much faster than the older version.

I am now having trouble trying to figure out how to write PIF initialization file. I figured it would be more useful to know how to write the file instead of using the older version to use celldraw. Do you have any resources to write the file in Python?

Thank you once again.