Adding new Feature/pavd

[drnimbusrain]

Some cleaning and testing needed, but eventually this draft PR will close #66 and add the ability of canopy-app to read 3D inputs of observed GEDI Plant Area Volume Density (PAVD) profiles for a user-set range of latitude and longitude bounds. Previously canopy-app could only be driven by prescribed plant shape distribution functions.

Note: The PAVD input data example file is based on preliminary GEDI gridded/raster data provided from Scott Goetz and Pat Burns of NAU. The following is needed to move this PR forward:

• Use the updated version of their gridded PAVD dataset on the NAU HPC Portal
• Verification and comparisons of PAVD highest height bins against updated 1 km GEDI FCH (also used in canopy dataset blended with Potapov FCH for gap filling and in high latitudes) from NAU HPC Portal. May need to establish an altitude cutoff threshold for real vs negligible PAVD.
• Integrated PAVD (i.e., PAI) comparison against updated, gridded 1 km VIIRS PAI is needed to validate spatial distribution and column values.

[drnimbusrain]

@angehung5 Thanks for the updated daily LAI in SE files. Can you remove the 'time' column from all updated txt files? canopy-app doesn't use the timestamp in txt files currently, and you can see the CI fails when trying to run .txt files.

Also, can you update these .NC files here at the feature/pavd branch for new PAVD product too?

[drnimbusrain]

@angehung5 I changed the methods of how I am using the PAVD. Given its uncertainty, and relatively coarse vertical resolution from NAU (5 m), I think one way we can use it more consistently for now is to identify the observed PAVD height of maximum vegetation, and still apply the distributions from Massman (i.e., the standard deviations above/below the maximum) based on input vegetation type.

Below is my single point test for the updated Lang FCH dataset and PAVD point profile example you provided:

Foliage Distribution Based Height Maximum

PAVD Based Vegetation Height Maximum

You can see that even though we are limiting the PAVD application for now, it works much better, and the novel aspect is we are using the observed GEDI PAVD height of maximum foliage density to constrain the shape functions that are still applied. I would need to briefly test the gridded impacts with new Lang FCH as well, but what do you think?

[drnimbusrain]

@angehung5 If you could provide a review of this as well, when you have the time. If OK, do you think we should add a sensitivity test to your paper for using the observed PAVD max from GEDI as well? You can see that it has an affect on the wind speed profile compared to default profile from Massman. Thanks!

[drnimbusrain]

@angehung5 If you could provide a review of this as well, when you have the time. If OK, do you think we should add a sensitivity test to your paper for using the observed PAVD max from GEDI as well? You can see that it has an affect on the wind speed profile compared to default profile from Massman. Thanks!

@angehung5 Can you please give this a review ASAP?

[angehung5]

I changed the description of pavd_opt in README since single point text files are available now.

[angehung5]

@drnimbusrain A quick comparison of Massman shape function and GEDI PAVD. Seems the wind reduction based on PAVD is generally lower compared with Massman. The foliage vertical distribution is different as well, especially at Lower Teakettle, probably because PAVD values are actually averages over certain area (0.01 degree resol) and maybe affected by surrounding vegetations. It should also be noted that the vertical resolution of PAVD profile is much coarser.

[drnimbusrain]

@drnimbusrain A quick comparison of Massman shape function and GEDI PAVD. Seems the wind reduction based on PAVD is generally lower compared with Massman. The foliage vertical distribution is different as well, especially at Lower Teakettle, probably because PAVD values are actually averages over certain area (0.01 degree resol) and maybe affected by surrounding vegetations. It should also be noted that the vertical resolution of PAVD profile is much coarser.

Thank you @angehung5 for doing the review and test!

First, to clarify, I am only using the height of PAVD maximum from GEDI, and not the actual entire PAVD profile. So, the GEDI PAVD is used to only set the height of maximum foliage density and uses the vegtype set standard deviations above and below the maximum based on Massman, so it really is a hybrid approach right now. With the major issues of the gridded PAVD observations (coarse vertical res, inconsistencies with FCH we have right now from NAU, with no response back from them whatsoever, this is the best we have right now. Either way, using Massman, or hybrid PAVD/Massman approach has uncertainty in where the peak foliage density is set, but seems Massman approach is better right now.

Thus, can you also plot the foliage profiles for the different methods for each site to see how they vary? I wonder how you are setting the PAVD for these plots.

[angehung5]

The shapes at Chestnut and GOA look ok, although the height of maximum density is lower than Massman. Willow Creek and Lower Teakettle have the same issue that the maximum height of PAVD is comparable to the canopy height but PAVD values peak near the surface and are relatively low near the canopy top.

PAVD at Lower Teakettle for example, FH=32m

lat,lon,lev01,pavd01,lev02,pavd02,lev03,pavd03,lev04,pavd04,lev05,pavd05,lev06,pavd06,lev07,pavd07,lev08,pavd08,lev09,pavd09,lev10,pavd10,lev11,pavd11,lev12,pavd12,lev13,pavd13,lev14,pavd14
37.00,240.99,2.50,0.0682,7.50,0.0632,12.50,0.0449,17.50,0.0274,22.50,0.0210,27.50,0.0166,32.50,0.0120,37.50,0.0076,42.50,0.0043,47.50,0.0020,52.50,0.0007,57.50,0.0002,62.50,0.0000,67.50,0.0000

Agreed gridding should be the main reason here. Since the maximum heights of PAVD are reasonable (consistent with canopy height), satellite does see the forests. However, the surrounding shorter vegetations introduce a much lower height of maximum PAVD, which we can see at Lower Teakettle.