diff --git a/ews/coordinator/processor_epidemiology.py b/ews/coordinator/processor_epidemiology.py index b9380fdcc946bcd699487978fab8643c4c8100cc..3be407f887cfa0f483014a216ef550d448ae1707 100644 --- a/ews/coordinator/processor_epidemiology.py +++ b/ews/coordinator/processor_epidemiology.py @@ -582,35 +582,16 @@ class ProcessorEpidemiology(ProcessorBase): for epiconf in config_epi['Epi']: - outfile = epiconf["infectionRasterFileName"]+'_progression.csv' + unit_description = '' + if epiconf.get('rescale_output_by_host_raster',False) is True: + unit_description = '_per_ha_wheat' + outfile = f"{epiconf['infectionRasterFileName']}{unit_description}_progression.csv" # load the full epi results df_full = read_csv(outfile,header=[0],index_col=[0,1]) column_date_fmt = f"{config_epi['StartTimeShort']}_%Y%m%d%H%M" df_full_dates = to_datetime(df_full.columns.astype('str'),format=column_date_fmt) - unit_description = '' - - # convert units from ha_infected/ha_cell to ha_infected/ha_wheat - - if epiconf['rescale_output_by_host_raster'] is True: - - unit_description = '_per_ha_wheat' - - model_colns = df_full.columns - - df_full = self.get_model_divided_by_host_fraction( - df_full, - config_epi['Host']['HostCSV'], - model_colns = model_colns) - - # save to csv - outfile_hawheat = f"{epiconf['infectionRasterFileName']}{unit_description}_progression.csv" - df_full.to_csv(outfile_hawheat,header=True,index=True) - - outfile_hawheat_final = f"{epiconf['infectionRasterFileName']}{unit_description}.csv" - df_full.iloc[:,-1].to_csv(outfile_hawheat_final,header=True,index=True) - # determine date to cut with # plus 1 minute so midnight is associated with preceding day date_to_cut = datetime.datetime.strptime(config_epi['StartString']+'0001','%Y%m%d%H%M')