commands.txt

#Download remote sensing and survey data for site and year
Rscript acquire_all_data.R -s RMNP -d C:/Users/tonyt/Documents/Research/final_data -y 2020
Rscript acquire_all_data.R -s NIWO -d C:/Users/tonyt/Documents/Research/final_data -y 2020
Rscript acquire_all_data.R -s HARV -d C:/Users/tonyt/Documents/Research/final_data -y 2019


#Create 16 channel PCA images for HS scenes using CHM as a filter for canopy pixels
python site_pca.py RMNP C:/Users/tonyt/Documents/Research/final_data
python site_pca.py NIWO C:/Users/tonyt/Documents/Research/final_data
python site_pca.py HARV C:/Users/tonyt/Documents/Research/final_data

#Filter and annotate data
python annotation.py NIWO C:\Users\tonyt\Documents\Research\final_data EPSG:32613 filtering -a
python annotation.py NIWO C:\Users\tonyt\Documents\Research\final_data EPSG:32613 snapping -a
python annotation.py NIWO C:\Users\tonyt\Documents\Research\final_data EPSG:32613 scholl -a

python annotation.py HARV C:\Users\tonyt\Documents\Research\final_data EPSG:32618 filtering -a
python annotation.py HARV C:\Users\tonyt\Documents\Research\final_data EPSG:32618 snapping -a
python annotation.py HARV C:\Users\tonyt\Documents\Research\final_data EPSG:32618 scholl -a

python annotation.py RMNP C:\Users\tonyt\Documents\Research\final_data EPSG:32613 filtering -a
python annotation.py RMNP C:\Users\tonyt\Documents\Research\final_data EPSG:32613 snapping -a
python annotation.py RMNP C:\Users\tonyt\Documents\Research\final_data EPSG:32613 scholl -a

#Run experiments:
python experiment_runner.py /home/tony/thesis/lidar_hs_unsup_dl_model/experiment_logs/ experiment_set_1_results.csv /home/tony/thesis/lidar_hs_unsup_dl_model/final_data/ experiments_set_1.csv