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Commit bb8897a1 authored by roelo008's avatar roelo008
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Lots of new stuff and housekeeping

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do_design.py deleted 100644 → 0
View file @ 7e36f4fd
""""
ideeen over data management voor DOREN project
class: EVA
init: alle eva headers
att: requirement 1
att: requirement 2
att: processing log
att: nr of plots
method: rename cols
method: enforce requirement(req_x)
method: enforce requirements(**reqs)
method: add col
method: print processing log
method: generate table of species inventories
method: print EVA to file(txt, csv, shp, pkl)
method: add raster covariable(cov_name)
"""
eva = do.Eva()
eva.basic_prep()
eva.add_col()
eva.apply_requirements(eva.req1, eva.req2, eva.req4)
eva.add_cov("soil")
eva.add_cov("temp")
eva.add_cov("precip")
eva.add_ndep("POSCH")
eva.to_file('shp')
eva.to_file('csv')
eva.print_log()
species = eva.yield_species()
species.to_file('shp')
species.to_file('csv')
doren_main.py
View file @ bb8897a1
from utils import doren_classes as dc
doren = dc.Doren(header_src=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\EVA\EVA_Doren_header.csv',
sp_src=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\EVA\EVA_Doren_species.csv',
verbose=True)
doren.initiate(sample=False)
sp_src=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\EVA\EVA_Doren_species.csv')
doren.initiate()
doren.apply_requirements('req1', 'req2', 'req3', 'req4', 'req8', 'req9', 'req10',
aoi_src=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\geodata\eva_aoi_fin_3035.shp',
dem_src=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\covariables\DEM\DTM_3035.tif')
doren.add_posch(posch_src_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\POSCH_dep\v2')
doren.add_covar(covar_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\covariables\soil\b_processed',
covar_src='WRBLEV1_laea.tif', covar_name='soil_type', nominal=True)
doren.add_covar(covar_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\covariables\DEM',
covar_src='DTM_3035.tif', covar_name='elevation')
doren.add_covar(covar_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\b_geodata\eur_cntrs_3035',
covar_src='esri_eur_cntrs_3035.shp', covar_name='country', raster=False, column='CNTRYNAME')
covar_src='esri_eur_cntrs_3035.shp', covar_name='country', raster=False, column='CNTRYNAME',
keep_all=True)
doren.add_yearly_covar(covar_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\covariables\EObs\2_compiled',
covar_src_basename="EObs_v200e_rr_5yrmean", covar_name='5_yearly_precip')
doren.add_yearly_covar(covar_dir=r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\a_brondata\covariables\EObs\2_compiled',
covar_src_basename="EObs_v200e_tg_5yrmean", covar_name='5_yearly_temp')
doren.filter_by_buffer(species_name='Calluna vulgaris', buffer_size=50000)
doren.write_stuff('buffer_png')
doren.write_stuff('headers_PG')
doren.select_plts_w_species(species_name='Empetrum nigrum')
doren.filter_by_buffer_around_positive_plots(buffer_size=100000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG', covars=True)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Empetrum nigrum", buffer_size=10000)
doren.write_stuff('NDep_PG', covars=True)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Empetrum nigrum", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff('NDep_PG', covars=True)
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Empetrum nigrum", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff('NDep_PG', covars=True)
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Empetrum nigrum", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff('NDep_PG', covars=True)
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calluna vulgaris", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calluna vulgaris", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calluna vulgaris", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calluna vulgaris", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calluna vulgaris", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Anemone nemorosa", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Anemone nemorosa", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Anemone nemorosa", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Anemone nemorosa", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Anemone nemorosa", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Briza media", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Briza media", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Briza media", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Briza media", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Briza media", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Vaccinium oxycoccos", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Vaccinium oxycoccos", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Vaccinium oxycoccos", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Vaccinium oxycoccos", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Vaccinium oxycoccos", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Drosera rotundifolia", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Drosera rotundifolia", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Drosera rotundifolia", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Drosera rotundifolia", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Drosera rotundifolia", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Puccinellia fasciculata", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Puccinellia fasciculata", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Puccinellia fasciculata", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Puccinellia fasciculata", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Puccinellia fasciculata", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Centaurium pulchellum", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Centaurium pulchellum", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Centaurium pulchellum", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Centaurium pulchellum", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Centaurium pulchellum", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calamagrostis epigejos", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calamagrostis epigejos", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calamagrostis epigejos", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calamagrostis epigejos", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Calamagrostis epigejos", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name='Rumex acetosa', buffer_size=25000)
doren.write_stuff('buffer_png')
doren.write_stuff('headers_PG')
doren.filter_by_buffer(species_name="Gentiana cruciata", buffer_size=5000)
doren.write_stuff('species_PG')
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Gentiana cruciata", buffer_size=10000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Gentiana cruciata", buffer_size=25000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Gentiana cruciata", buffer_size=50000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.filter_by_buffer(species_name="Gentiana cruciata", buffer_size=100000)
doren.write_stuff('NDep_PG')
doren.write_stuff("buffer_png")
doren.write_stuff('species_list')
doren.write_stuff('report')
utils/doren.py
View file @ bb8897a1
......@@ -45,19 +45,6 @@ def eva_colnames_new():
'latitude', 'location_uncertainty_m', 'dataset']
def eva_colnames_drop():
"""
:return: list of improved colnames from EVA database which can be dropped
"""
return ['slope_deg', 'cover_total_perc', 'cover_tree_layer_perc',
'cover_shrub_layer_perc', 'cover_herb_layer_perc', 'cover_moss_layer_perc', 'cover_lichen_layer_perc',
'cover_algae_layer_perc', 'cover_litter_layer_perc', 'cover_open_water_perc', 'cover_bare_rock_perc',
'height_highest_trees_m', 'height_lowest_trees_m', 'height_highest_shrubs_m', 'height_lowest_shrubs_m',
'avg_height_high_herbs_cm', 'avg_height_lowest_herbs_cm', 'maximum_height_herbs_cm',
'maximum_height_cryptogams_mm', 'mosses_identified_bool', 'lichens_identified_bool', 'remarks',
'locality', 'dataset', 'name_association', 'name_alliance']
def get_aoi(*src):
"""
Read an aoi shapefile from source, return as single ply after dissolving. If no arguments provided, return whole
......
utils/doren_classes.py
View file @ bb8897a1
This diff is collapsed.
utils/doren_outputs.py 0 → 100644
View file @ bb8897a1
"""
Class containing several output methods for DOREN objects
"""
import doren_classes as dc
\ No newline at end of file
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