From 6476578a438b6514d0c639f788b176b02caee139 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Wed, 14 Sep 2022 14:38:04 +0100
Subject: [PATCH] wiring in the newly separated post_processing module into
coordinator, rather than the plotting module
---
ProcessorDeposition.py | 40 ++++++++++++++++++++--------------------
ProcessorEnvironment.py | 22 +++++++++++-----------
ProcessorEpidemiology.py | 14 +++++++-------
3 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/ProcessorDeposition.py b/ProcessorDeposition.py
index b57ed20..e460cba 100644
--- a/ProcessorDeposition.py
+++ b/ProcessorDeposition.py
@@ -1,19 +1,19 @@
#ProcessorDeposition.py
'''Functions to process the deposition component.'''
-from glob import glob
import logging
-from pathlib import Path
import os
+from glob import glob
+from pathlib import Path
from string import Template
-from plotting.common.plotting_coordinator.ews_depo_disease_plotting_coordinator import EWSPlottingDepoBase
-
from ProcessorUtils import (
- get_only_existing_globs,
- subprocess_and_log,
- add_filters_to_sublogger,
+ get_only_existing_globs,
+ subprocess_and_log,
+ add_filters_to_sublogger,
)
+from ews_postprocessing.deposition.deposition_post_processor import DepositionPostProcessor
+
logger = logging.getLogger('Processor.Deposition')
add_filters_to_sublogger(logger)
@@ -92,23 +92,23 @@ def process_EWS_plotting_dep(jobPath,config):
logger.info(f"Running EWS-Plotting with the following configs:\n{sys_config}\n{name_extraction_config}\n{run_config}\n{run_config_norm}\n{chart_config}")
- depo_plotter = EWSPlottingDepoBase()
- depo_plotter.set_param_config_files(sys_config_file_arg=sys_config,
- depo_name_extraction_config_file_arg=name_extraction_config,
- chart_config_file_arg= chart_config,
- depo_plotting_run_config_file_arg=run_config,
- depo_plotting_normalized_run_config_file_arg=run_config_norm,
- name_file_wildcard_arg=name_file_wildcard,
- wheat_sources_dir_arg=deposition_path,
- output_dir_arg=output_dir,
- issue_date_arg=config['StartString'],
- extraction_file_prefix_arg=extraction_file_prefix)
+ depo_processor = DepositionPostProcessor()
+ depo_processor.set_param_config_files(sys_config_file_arg = sys_config,
+ depo_name_extraction_config_file_arg = name_extraction_config,
+ chart_config_file_arg = chart_config,
+ depo_plotting_run_config_file_arg = run_config,
+ depo_plotting_normalized_run_config_file_arg = run_config_norm,
+ name_file_wildcard_arg = name_file_wildcard,
+ wheat_sources_dir_arg = deposition_path,
+ output_dir_arg = output_dir,
+ issue_date_arg = config['StartString'],
+ extraction_file_prefix_arg = extraction_file_prefix)
# asia/east africa env suit should not perform normalization, false gets passed here for these areas
- depo_plotter.name_extract_params.NORMALIZE = (normalize.upper() == "TRUE")
+ depo_processor.name_extract_params.NORMALIZE = (normalize.upper() == "TRUE")
- depo_plotter.plot_depo()
+ depo_processor.process()
# check the output
EWSPlottingOutputDir = f"{output_dir}/images/"
diff --git a/ProcessorEnvironment.py b/ProcessorEnvironment.py
index caac0bd..be0b5f0 100644
--- a/ProcessorEnvironment.py
+++ b/ProcessorEnvironment.py
@@ -12,8 +12,8 @@ import tarfile
import iris
from iris.cube import CubeList
+from ews_postprocessing.environmental_suitability.env_suit_post_processor import EnvSuitPostProcessor
from plotting.common.utils import EnvSuitDiseaseInfo
-from plotting.common.plotting_coordinator.ews_env_disease_plotting_coordinator import EWSPlottingEnvSuitBase
import EnvSuitPipeline as esp
from ProcessorUtils import (
@@ -151,15 +151,15 @@ def process_EWS_plotting_env2_0(jobPath,config):
logger.info(f"Running EWS-Plotting with the following configs:\n{sys_config}\n{run_config}\n{chart_config}")
- env_suit_plotter = EWSPlottingEnvSuitBase()
- env_suit_plotter.set_param_config_files(sys_params_file_arg=sys_config,
- chart_params_file_arg=chart_config,
- run_params_file_arg=run_config,
- es_output_dir_arg=output_dir,
- issue_date_arg=config['StartString'],
- disease_csv_template_arg=csv_template_dir)
+ env_suit_processor = EnvSuitPostProcessor()
+ env_suit_processor.set_param_config_files(sys_params_file_arg = sys_config,
+ chart_params_file_arg = chart_config,
+ run_params_file_arg = run_config,
+ es_output_dir_arg = output_dir,
+ issue_date_arg = config['StartString'],
+ disease_csv_template_arg = csv_template_dir)
- env_suit_plotter.run_params.FILTER_FOR_COUNTRY = (filter_for_country.upper() == "TRUE")
+ env_suit_processor.run_params.FILTER_FOR_COUNTRY = (filter_for_country.upper() == "TRUE")
# Include further diseases in plotting. In this case the irrigated suitabilite for the rusts.
# TODO: move this part out into a config
@@ -169,9 +169,9 @@ def process_EWS_plotting_env2_0(jobPath,config):
EnvSuitDiseaseInfo("Stripe rust temp-only", "stripe_temponly", config['StartString'], "StripeRust_TempOnly", csv_template_dir)
]
- env_suit_plotter.add_diseases(diseases=extra_diseases)
+ env_suit_processor.add_diseases(diseases=extra_diseases)
- env_suit_plotter.plot_env_suit()
+ env_suit_processor.process()
# check the output
EWSPlottingOutputDir = f"{output_dir}/images/"
diff --git a/ProcessorEpidemiology.py b/ProcessorEpidemiology.py
index 9be9664..f8c9cb5 100644
--- a/ProcessorEpidemiology.py
+++ b/ProcessorEpidemiology.py
@@ -23,7 +23,7 @@ from EpiModel import ( # created by rs481
EpiPrepLoader,
plotRaster
)
-from plotting.common.plotting_coordinator.ews_epi_disease_plotting_coordinator import EWSPlottingEPIBase
+from ews_postprocessing.epi.epi_post_processor import EPIPostPostProcessor
from ProcessorUtils import (
open_and_check_config,
@@ -575,8 +575,8 @@ def process_EWS_plotting_epi(jobPath,config):
logger.info(f"Running EWS-Plotting with the following configs:\n{sys_config}\n{run_config}\n{chart_config}")
- epi_plotter = EWSPlottingEPIBase()
- epi_plotter.set_param_config_files(sys_params_file_arg=sys_config,
+ epi_processor = EPIPostPostProcessor()
+ epi_processor.set_param_config_files(sys_params_file_arg=sys_config,
chart_params_file_arg=chart_config,
run_params_file_arg=run_config,
epi_input_csv_arg=epi_filename+'_seasonsofar.csv',
@@ -587,7 +587,7 @@ def process_EWS_plotting_epi(jobPath,config):
wheat_source_disease_name_arg=deposition_disease_name,
map_title_arg=map_title,
chart_area_prefix=plotting_region_name_lower)
- epi_plotter.plot_epi()
+ epi_processor.process()
# prepare command for seasonplusforecast
@@ -595,8 +595,8 @@ def process_EWS_plotting_epi(jobPath,config):
logger.info(f"Running EWS-Plotting with the following configs:\n{sys_config}\n{run_config}\n{chart_config}")
- epi_plotter_2 = EWSPlottingEPIBase()
- epi_plotter_2.set_param_config_files(sys_params_file_arg=sys_config,
+ epi_processor_2 = EPIPostPostProcessor()
+ epi_processor_2.set_param_config_files(sys_params_file_arg=sys_config,
chart_params_file_arg=chart_config,
run_params_file_arg=run_config,
epi_input_csv_arg=epi_filename+'.csv', # for seasonplusforecast
@@ -608,7 +608,7 @@ def process_EWS_plotting_epi(jobPath,config):
wheat_source_disease_name_arg=deposition_disease_name,
map_title_arg=map_title,
chart_area_prefix=plotting_region_name_lower)
- epi_plotter_2.plot_epi()
+ epi_processor_2.process()
# check the output
EWSPlottingOutputDir = f"{ews_plot_dir}/images/"
--
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