OpenCFU
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qgeissmann
Linux: Command line doesn't function
Running Kubuntu 16.10
I installed OpenCFU and used it's GUI a few times on some test images. Everything worked fine, played with all the settings, and successfully outputted the results to CSVs.
However, when I try to use the terminal (since I want to do batch analyses over 100> plates in the future), I get the the following error:
daniel@Celebrate:~$ opencfu -i /home/daniel/Documents/Gdrive/LabWork/Viability/OpenCFU/20161117_160653.jpg -m auto -d bil -t 3 -r 1 -G 3 ERROR setting-up the INPUT file"/home/daniel/Documents/Gdrive/LabWork/Viability/OpenCFU/20161117_160653.jpg".
Any idea how I may debug this?
Thanks, it's a really cool piece of software.
EDIT: I got it to work by moving the images to my home folder. Weird. Leaving this up, though this work around is sufficient for me.
Thanks for reporting that @danieljnilson! I will try to reproduce/debug that later this week. Could you upload your image, in case it is specific to it ? Cheers,
Here's the image. I re-created the error this morning. Again, the terminal approach works only when the image is placed in the home folder.
Cheers
do you mean if works as expected if you run cd before? E.g.:
$ cd /home/daniel/Documents/Gdrive/LabWork/Viability/OpenCFU
$ opencfu -i 20161117_160653.jpg -m auto -d bil -t 3 -r 1 -G 3
No; it does not work if I cd into the image directory first. Only if the image is in the home directory does the CLI function.
However on a fresh Ubuntu 16.04 VM, the OpenCFU CLI doesn't seem to care where the image is as long I either cd into the directory or I call the file with its full address (such as in my OP). Weird. I presume this might be a compiling derived issue? I don't know enough about compiling to determine what's different between my Kubuntu 16.10 and the Ubuntu 16.04 VM. This may be a niche issue. If you want any system information from me, I'd be happy to provide it but I don't consider it a OpenCFU issue at this point and my VM is a functional&stable work around.
Get into the github account.. cloned it. autoreconfig -i get all the depependencies.... libs... and dev versions. ./configure, make, install... your done!. hint, try to get libs now, dont compile libs. bye.
