Example
========

Walkthrough for an example case on Linux system:
The example directory includes randomly drawn polygons (example_parcels.shp) and Sentinel2 tiles over Finland (Fin_s2.shp, derived from http://ftpearth.bu.edu/public/emelaas/sentinel2_tiles_world/).
The data in cropyield/example/cropyield_data is only intended for testing purposes.

| According to chapter **Preparation**:

1. Download conda : ``wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh``
2. Install above downloaded
3. Create conda environment with required packages: ``conda env create --file environment.yml``
4. Activate above created environment: ``conda activate cropyield``

| According to chapter **Usage**:

5. Clone the repository: ``git clone https://github.com/myliheik/cropyield.git``
6. Switch into repository directory : ``cd cropyield``
7. Switch to example directory: ``cd example/cropyield_data``
8. Get the data with: ``wget https://a3s.fi/Sentinel2testCase.tar.zst``, and unpack with ``tar -I zstd -xvf Sentinel2testCase.tar.zst``, then switch back to example directory by typing ``cd ..`` twice.
9. Split test-shapefile based on S2 tiles (here only Finland): ``python ../python/splitshp_mp.py ./Sentinel2testCase/example_parcels.shp ./Sentinel2testCase/Fin_s2.shp ../cropyield_shp``
10. Start the process (for the example use the start file within example directory) ``bash start.sh``
11. Check the result files in ./cropyield_results

Resulting files:
-----------------

* Step 9 should create files within cropyield_shp: All tiles here have overlap with the example_parcels file: 34VEN,34VFN,34VFP,35VLH,35VLJ.

* Step 10 should create 2 files in cropyield_results (plus some resampled shapefiles in cropyield_data):
    * array_34VFN_20200626_B04.csv with PlotID as first row following all pixelvalues within each polygon, and
    * meta_34VFN_20200626_B04.csv with PlotID,year,DOY,tilefilename,missionID,count for each polygon.

-> if those files exist and are non empty, everything is fine. If not check the error messages and that all inputs are available.