ucl-eo / workshop2022 Goto Github PK

• decide visualisation scheme by Monday
• QA for MODIS LAI time series plotting
• Aspatial data explorer
• Spatial VI (link with DigitalAfrica team?)
• Instruct GEE account approval with @MarcYin

Priorities:

• legend/palette issue
• apply-mask as default
• axis labels (year, lai, precp, && their units) for TS figures
• upload mofa csv file(s) to GitHub
• add scatterplots as subplots: mofa yield vs precp
• displaying district/county names on click

Targets set on 11-Mar-2022:

• generate histogram per QA level
• generate IO webpage
• Tidy up, fix all bugs
• change rain m to mm
• add 1-to-1 line for scatterplot

Additional feature only if have time:

• all districts, instead of northern (in progress)
• some demo of toolboxes : e.g. upload own vector / raster
• user-defined AOI
• drawing tools: TBD: remove?
• on-click: per-pixel TS explorer
• graph of ALL properties of pixel, on click
• yield estimate to be related: e.g average yield over the masked area
• add scatterplots as subplots: mofa yield vs empirical yield; and show stats of graph

Show how you can manually tune th emodel to match observations

Tasks

• 2000-2021 Ensemble Generation
• pixel-by-pixel DA
• Fewer parameters ensemble generation

Keynote Content

• Crop Model principles
• WOFOST introduction
• WOFOST implementation and ensemble generation
• Multi-years Yield Map
• In season simulation

WE need a URL for each field folder photos

@MarcYin

Each talk or interactive thing to have its own section with

• A link to the material (github)
• A list of issues (on github)
• A link to binder (if needed)
  Need to check the syntax of the link to Binder

• Model runs need reduced parameter sets
• AMAX scalar anchored using AMAXTB_200
• Plot some parameter trajectories in max_LAI space and/or length of season space
• Ensure same wofost model is run in here & jasmin

@jgomezdans @MarcYin

When do you assume harvesting is? I can see field notes mention ‘ready for harvesting’ but don’t seem to say when that was. Surely we should constraint or at least check that we have that right.

The autofit doesn’t seem to be working – is that broken ATM?

Im playing with Fengs maize mapper, and it would be really useful if GS 1 and 2 were indicated on the plots … I can see you can read off when 1, 2.0 GS is, but that’s quite hard to do. Esp since 1 isnt shown directly. Feng - Can you pls show GS 1 and GS 2 as vertical lines in both the modelling plots and the data plots?

Also, once you go into LAI movie mode, there doesn’t seem a way to switch back to showing yield map without reloading, which is clunky. Is that fixable?

Also, whilst there is ‘help’ for the terms used on the sliders, there is no help for the quantities plotted … also, no units given for these (that could be in the help). It is hard to work out what you are seeing.

Also, I cant see the measured yield data anywhere in the plots - where is that?

Need a link from the DEA practical

• What do you have to do to double yield?
• What do you hav to do to do a short vs long season simulation?
• Fit the model to the observations

https://docs.github.com/en/pages/quickstart

• @NPounder to produce a meteo file with seasonal foracasts until 1st-2nd week Sept 2021 over study area (~lat=9.5, lon=-0.5)
• @jgomezdans to run an ensemble (parameters+meteo) over growing season 2021
• Have a notebook that plots the meteo data and allows selection of a field to do assimilation until mid Sept and forecast end of season

• Only single location as limited time etc.

• international flights between London and Accra
• domestic flights between Accra and Tamale
• Tamale hotel, Mar 20-23 Can @asarefi please confirm if Tamale hotel can be booked and invoiced by GSSTI?
• Accra hotel, Mar 19
• Accra hotel, Mar 23-26
• need passport info from @jgomezdans @profLewis @MarcYin to book tickets: passport number, expiry date, date of birth, mobile number, and ID email address.
• Risk assessment
• travel insurance
• book in-person visa appointments

Qingling and Kofi has updated the draft invitation. Any final proof @profLewis ?
https://liveuclac-my.sharepoint.com/:w:/r/personal/ucfaqqw_ucl_ac_uk/_layouts/15/Doc.aspx?sourcedoc=%7B6D15C7A1-C4FF-4E2B-A8A1-C1D6120642DC%7D&file=Stakeholder-invitation-letter-draft.docx&action=default&mobileredirect=true

• Model exploration with parameters ("sliders")
• Automatically fit the LAI ("DA button")
• Plot yield distribution for all fields w/boxplots
• Per pixel LAI exploration
  • Show yield
  • Show parameter spatial distribution

Framework of presentation: [By Friday morning]

1. Basic concept of monitoring vegetation with remote sensing
   1.1 plant canopy scale visualisation
   1.2 leaf level with prospect
   1.B NDVI to LAI and why not
2. Archetypes over the US and some validation
3. Modelling and application
4. How to Ghana fields and issues
5. Results and validation against the ground measurements
6. Emphasis the importance of sentinel 2 and planet on monitoring smallholder farming and why we do the archetypes

Ive tried to run Fengs script standalone, with an environment from the yml file.

I get the error below. So, you need the retry package, which Ive put in the environment file. And will retry....

Platform not recognized, using system temp directory for PCSE settings.
Platform not recognized, using system temp directory for PCSE settings.
Building PCSE demo database at: /var/folders/qk/t8kmgc253rg566r5qy3wrq9w0000gn/T/.pcse/pcse.db ... OK

ModuleNotFoundError Traceback (most recent call last)
File ~/Documents/GitHub/Workshop2022/notebooks/create_map.py:21, in
19 from map_utils import get_lai_gif, get_pixel, get_field_bounds, da_pix, get_lai_color_bar
20 from map_utils import debounce
---> 21 from wofost_utils import create_ensemble, wofost_parameter_sweep_func, get_era5_gee
22 from wofost_utils import ensemble_assimilation
24 from ipywidgets import Image as ImageWidget

File ~/Documents/GitHub/Workshop2022/notebooks/./python/wofost_utils.py:35, in
33 import pip
34 import shutil
---> 35 from retry import retry
37 try:
38 ee.Initialize(opt_url="https://earthengine-highvolume.googleapis.com/")

ModuleNotFoundError: No module named 'retry'

• 1. Planet LAI 01-Satellite_data.ipynb
• 2. GEE backend NDVI/LAI 01B_NDVI_LAI.ipynb [End of Monday]
• 3. Require WOFOST ensemble over the field measurement sites from @jgomezdans and @Ma-hy [End of Monday]
• 4. Integrate WOFOST slider into GEE backend LAI [End of Wednsday]

@MarcYin can you put some instructions on the readme for a local install for users

That might be
get miniconda (point them at site)
cd $DISTO
conda env create -f environment.yml -n uclnceo
postBuild

or whatever

• Contact HangHui re MCMC
• Need to get some form of within-season forecast example from Hongyuan/Nicola

Talk contents

• DA concepts (just an outline, mostly pictures)
  • Drivers/States/Parameters and models
  • Model & observation uncertainties (examples)
• Assimilation: blending models & observations. Mostly pictures and no maths
  • Correct the model trajectory/state: filters
  • Pros/cons
  • Variational methods: Parameter estimation
  • Pros/cons
  • Ensemble methods
• Example of system working with the crop model
  • Ensemble generation (parameters, possibly weather)
  • Linking model predictions with observed LAI
  • Yield prediction
  • Model parameter interpretation
• DA and within-season forecasting introduction @Ma-hy to provide some slides