.ply file input

[Kosnicki]

Hi there, I am just starting to use PlantCV and am going through the tutorials and documentation. The imaging files that come off our instrumentation is in a .ply file format (3D scans). I noticed that the inputs in your tutorials are typically in .png, .jpeg, etc. formats. Is there a way I can use PlantCV with my file types or is there some sort of conversion step I need to implement before doing so?

[HaleySchuhl]

Hello @Kosnicki ,

Thanks for asking! We currently don't have any support for .ply file 3D scans, but it's certainly something that we could have discussed in the past. I'd be very interested in hearing more about the types of data you have and traits you wish to extract. It would be interesting but not sure what it would take to do it.

[Kosnicki]

Hello Haley, Thank you for your reply. We currently are just looking at standard measurements like biomass, max height, average height, NDVI, PSRI, NPCI, etc. Do you know if there would be a way that we could convert files from the ply format to a 2D format to then use in PlantCV? The ply files does contain RGB values. Best, Kassi

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On Mon, Dec 5, 2022 at 10:53 AM Haley Schuhl ***@***.***> wrote: Hello @Kosnicki <https://github.com/Kosnicki> , Thanks for asking! We currently don't have any support for .ply file 3D scans, but it's certainly something that we could have discussed in the past. I'd be very interested in hearing more about the types of data you have and traits you wish to extract. — Reply to this email directly, view it on GitHub <#986 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVCTLGQEPLUKUGJRD4S4ETWLYMYNANCNFSM6AAAAAASSJUQTQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[HaleySchuhl]

None that I'm personally familiar with, but this post seems to mention some open source tools that might do the type of conversion you're talking about. https://stackoverflow.com/questions/51350493/convertion-of-ply-format-to-pcd-format

Do you also have NIR values for the scans? We have functionality that combines RGB + NIR to calculate NDVI with image fusion in the v4.x branch (https://plantcv.readthedocs.io/en/4.x/image_fusion/).

[Kosnicki]

Thanks, Haley! Yes, we also have the NIR values in addition to the RGB values. My thought is that I somehow extract this information and put it into a format which plantcv can use as input. Thanks for your help. Best, Kassi

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On Mon, Dec 5, 2022 at 11:40 AM Haley Schuhl ***@***.***> wrote: None that I'm personally familiar with, but this post seems to mention some open source tools that might do the type of conversion you're talking about. https://stackoverflow.com/questions/51350493/convertion-of-ply-format-to-pcd-format Do you also have NIR values for the scans? We have functionality that combines RGB + NIR to calculate NDVI with image fusion in the v4.x branch ( https://plantcv.readthedocs.io/en/4.x/image_fusion/). — Reply to this email directly, view it on GitHub <#986 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVCTLD35VDU3P3TCWE2OATWLYSJPANCNFSM6AAAAAASSJUQTQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Kosnicki]

So, am I correct in that PlantCV with take the converted pcd file as an input?

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On Mon, Dec 5, 2022 at 11:40 AM Haley Schuhl ***@***.***> wrote: None that I'm personally familiar with, but this post seems to mention some open source tools that might do the type of conversion you're talking about. https://stackoverflow.com/questions/51350493/convertion-of-ply-format-to-pcd-format Do you also have NIR values for the scans? We have functionality that combines RGB + NIR to calculate NDVI with image fusion in the v4.x branch ( https://plantcv.readthedocs.io/en/4.x/image_fusion/). — Reply to this email directly, view it on GitHub <#986 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVCTLD35VDU3P3TCWE2OATWLYSJPANCNFSM6AAAAAASSJUQTQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[HaleySchuhl]

As far as I know, you'd be the first user to try that format as well! The back end of readimage is cv2.imread so if they support that file extension then we should be able to read it in with mode="native".

[Kosnicki]

Hi Haley, I am working to get my files in the pcd format and test in PlantCV. I'm wondering how PlantCV takes NIR and NDVI inputs. That information is contained in our PLY files and I am trying to maintain that information when converting to pcd. How does PlantCV take in this information? Is it within one file or do you have to upload additional files respective to addition scalar fields (NIR, NDVI, etc)?

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On Mon, Dec 5, 2022 at 12:03 PM Haley Schuhl ***@***.***> wrote: As far as I know, you'd be the first user to try that format as well! The back end of readimage is cv2.imread so if they support that file extension then we should be able to read it in with mode="native". — Reply to this email directly, view it on GitHub <#986 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVCTLEPHLAEQA2RVLRN3TTWLYVAFANCNFSM6AAAAAASSJUQTQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[HaleySchuhl]

Hello, we usually see NIR images show up as grayscale .png files. In the case of dual or multi-plant workflows, we do support configurations that allow >1 image per workflow with "coprocessing" or with the pcv.get_nir function which assumes the NIR & RGB image will be in the same directory with the same pattern of filename. The only example we have of combining these two image types to calculate NDVI is on the v4.x branch (https://plantcv.readthedocs.io/en/4.x/image_fusion/).

@nfahlgren are you aware of any open source Python packages out there that handle .PLY file data?