Daniel Wamsley image issue

[danwam]

`The original photo had a white label in it, so I blacked that out to see if it helped. The jupyter notebook was done on the image with the blacked out label.

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Daniel Wamsley image 162-2.zip

[HaleySchuhl]

Hi @danwam ,

Thanks for opening an issue and providing all the info needed for us to help! The error you were getting while trying to extract the relative leaf angle (during the pcv.morphology.segment_insertion_angle step) seems to be from a small leaf that wasn't getting joined up with the rest of the plant, AND a typo on my part. I've updated your workflow (attached here) and it should now work on your original image, regardless of blacking out the label or not. The changes I made to improve the workflow are the following:

• Increase the size parameter in the pcv.fill step. We need to remove anything not connected to the plant, so I increased the size until most white speckles got filled in.

• Update the ROI. We want to keep everything that is partially overlapping with our rectangular region of interest (ROI), so we can clean the image better by using an ROI that only keeps the plant. I chose a much smaller ROI since I don't want to partially overlap with the wilted leaf on the bottom right of your plant or the label.

• Update the skeleton parameter in the pcv.morphology.segment_insertion_angle step. We should input the pruned skeleton image, stored in the variable named pruned rather than inputting the original skeleton image. This was a typo and should have always said skeleton=pruned in this step.

• Update the very last cell, where data is getting stored out. We haven't updated this notebook since it was first written, and there's updates we've made to PlantCV functions that mean we now need to save data out with fmt='%s' instead of fmt='%10.5f' .

maize_morphology_updated.ipynb.zip

[danwam]

I am struggling to open the ipynb file on my laptop once I unzip it, so I can view it. Any suggestions?