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Is there a software package that when I have my printer connected directly to my PC via USB could record and export hot end temperature data overtime?

Ideally this data would be recorded in a way that I could export it and manipulate it in the likes of Excel.

E.g. I see Pronterface has a temperature graph but it doesn't seem possible to export this. I know Simplify3D has a temperature plot in the machine control panel, anyone know if you can export from this?

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I don't know if using OctoPrint is an option. If so, there is a plugin that claims to do exactly this. And you could probably find a few more if you looked for them. Note that I have no first hand experience with this plugin, but I can vouch for OctoPrint being convenient and by default it shows a temperature graph.

It might even be relatively easy to write your own plugin to accomplish this. This will mostly depend on your comfort with coding in Python/JavaScript.

As a sidenote: if your printer is connected directly to your computer via USB, chances are pretty high it is a simple serial connection. Having multiple programs use this connection at once is not possible as far as I know.

This implies that you will not be able to have your current software send it G-code lines while having another one recording the temperature values sent back from the printer.

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