Thermal Workflow HDF5

[msulieman7]

Hello,
I've been running into some issues with the Thermal Workflow script. First things first I found a discrepancy within the script that I was wondering you guys can clarify for me. Within the documentation you guys go over how to insert a CSV file under CSV mode, however if you scroll all the way down to the full script you guys switch the mode to FLIR mode. Is there a reason why you guys do this? Second when I try to run the script on either FLIR/CSV mode it always returns an error. I will attach a couple of images of the errors that im getting. I should mention I am running this on a Linux system

[nfahlgren]

Hi @msulieman7,

It looks like the complete workflow at the bottom of the documentation page is incorrect. The input mode should be set to "csv" for FLIR thermal data.

I am not as sure about the error. It sort of looks like a generic type error that suggests to me that there might be something a little different about your input CSV file than ours. Would it be possible to post an example CSV file so I can compare?

Thanks!

[msulieman7]

Noah, Thanks for the clarification, and sure I will attach a picture of my data in a formatted CSV file. Is there a specific way that the file is supposed to be formatted? Thanks!

…

On Wed, Aug 5, 2020 at 11:00 AM Noah Fahlgren ***@***.***> wrote: Hi @msulieman7 <https://github.com/msulieman7>, It looks like the complete workflow at the bottom of the documentation page is incorrect. The input mode should be set to "csv" for FLIR thermal data. I am not as sure about the error. It sort of looks like a generic type error that suggests to me that there might be something a little different about your input CSV file than ours. Would it be possible to post an example CSV file so I can compare? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#603 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AP7JQ3YNYZV7LNBXPBI4WY3R7F63DANCNFSM4PVUJXOQ> .

[nfahlgren]

Hi @msulieman7,

It looks like the picture did not attach (or at least GitHub did not bring the attachment over), mind dropping it into a comment here?

We do not have a specific format for the file in mind but the code could potentially be more restrictive than we intended. It looks like our files are comma-delimited without quotes and are in scientific notation:

3.409797e+01,3.409173e+01,...
3.410420e+01,3.409797e+01,...
...

It looks like our FLIR camera outputs the files with Windows line returns in CRLF format, so I suspect that the CSV reader we use can handle both CRLF and LF.

[msulieman7]

My apologies I had sent the picture through email, but with that being said I think the reason why it isnt working is because I have the CSV file saved as a text CSV file. Also, does the data have to be in scientific notation? I am using a FLIR 2.5 Camera module which saves the file as a HDF5 file and i'd have to open that file, save it as a text file and then convert it to a CSV file. This is what im working with so I really appreciate your help! Thanks

[nfahlgren]

I think the CSV reader should be able to handle numeric data in a variety of formats.

We are currently using a CSV reader specifically, so it is expecting a CSV plain text file and we have specified that the cells are separated by commas (I know sometimes CSV files use semi-colons, so that would not currently work).

We could add an HDF5 mode to plantcv.readimage potentially. I think that would be relatively straightforward.

[msulieman7]

If thats the case that would be a tremendous help! Using PlantCV with the Thermal Workscript would be a big plus to my Senior Design Project! Thanks again!

[nfahlgren]

Thanks @msulieman7, sounds good! I cannot find any sample HDF5 data from FLIR online, we would need an example in order to build the method.

[msulieman7]

ok so heres the problem I cant attach a HDF5 file through GitHub. Ive been using HDFView to be able to read the file. Is there an email that I can send you a sample of my HDF5 file?

[nfahlgren]

For sure, my address is nfahlgren@danforthcenter.org