OD Calibration NaN problem

I’ve encountered a problem in retrieving my OD calibration file

I write the line:

py calibration/calibrate.py -a -n lyoOD820 -f fitOD -t linear -p od_90, od_135

And I get an output with lists of lists for each holder and seemingly each arrangement of the vials during the calibration. But no graph. At the end of the output there is an error message: ‘ValueError: array must not contain infs or NaNs’. Looking at the numbers in the lists I noticed an odd pattern. I’ve attached a screenshot here. I’ve circled in red an empty list within the list of lists that moves position with each subsquent list. First it’s in the second position, next in the third, and so on. I don’t know if it’s an issue with the optics of a particular holder, or possibly an individual vial as it went around. In the first list of lists, it’s in the 2nd position which if it corresponds to vial 1 then that would have been one of my blank media vials. I’m thinking this empty list is the problem and creating a NaN situation.

Hi Adam,

Based on your screenshot, it looks like a single measurement from every vial was somehow missed. The outer list is the data per vial, the middle list is the data for a given position, and the innermost list are replicates of that position. So when a data point is collected, it is put into the list in the appropriate position based on where the vials are located. Since the missing lists are offset by 1 for each vial, this means that 1 location or data collection didn’t get recorded. Did you happen to hit the back button or use the continue function? And did you run this from the touchscreen or from the computer application?

Please do a quick test - run a calibration without actually moving vials around, just keep hitting next, let the eVOLVER collect data, hit the arrow, etc. and then save that resulting calibration. Don’t hit back / leave the calibration and continue. Do this with the computer based application - not the touchscreen. If this calibration with dummy data looks good (i.e., no missing data points), I imagine it’s an issue with the back/continue functions which we can look into. The app shouldn’t have allowed an incomplete data set to be saved to the eVOLVER, but maybe if you hit back or left the calibration mid cal and hit continue it caused a data point to be lost.


1 Like

Ok thank you Zack. It’s definitely possible. I’ll give that all a try. I was using the touchscreen.