From b3139a67af47b0c14ec2c6ee67d40f98cb9b7542 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Thu, 29 Aug 2024 15:44:37 +0100
Subject: [PATCH] dropping the return of plotting outputs as not needed now we
use workflow manager
---
ews/coordinator/processor_epidemiology.py | 31 +++--------------------
1 file changed, 3 insertions(+), 28 deletions(-)
diff --git a/ews/coordinator/processor_epidemiology.py b/ews/coordinator/processor_epidemiology.py
index 0a2aa23..15cf9c8 100644
--- a/ews/coordinator/processor_epidemiology.py
+++ b/ews/coordinator/processor_epidemiology.py
@@ -553,26 +553,6 @@ class ProcessorEpidemiology(ProcessorBase):
logger.debug('Saving tif output as png for easier viewing')
plotRaster.save_raster_as_png(outfile)
- # comparison figure
-
- # TODO: make this plot configurable? with function or args?
- #logger.info('Plotting epi output alongside contributing components')
- # figure_func = getattr(EpiAnalysis,'plot_compare_host_env_dep_infection')
- logger.info('Plotting composite image of epi formulations')
- figure_func = getattr(EpiAnalysis, 'plot_compare_epi_cases')
-
- # isolate the config for this function, in case of modifications
- config_epi_for_comparison = config.copy()
-
- fig,axes,cases = figure_func(
- config_epi_for_comparison,
- start_str = start_string,
- end_str = end_string)
-
- SaveFileName = f"{case_specific_path}/EPI_{config_filename}_comparison"
-
- fig.savefig(SaveFileName+'.png',dpi=300)
-
# slice the epi results into before forecast and in forecast
for epiconf in config['Epi']:
@@ -633,8 +613,8 @@ class ProcessorEpidemiology(ProcessorBase):
return proc_out
- def process_EWS_plotting_epi(self, jobPath,config) -> [str]:
- '''Returns a list of output files for transfer.'''
+
+ def process_EWS_plotting_epi(self, job_path, config):
logger.info('started process_EWS_plotting_epi()')
@@ -676,7 +656,7 @@ class ProcessorEpidemiology(ProcessorBase):
# TODO: handle multiple diseases and regions in Processor as a loop, or in the config
deposition_disease_name = [disease_latin_name_dict[disease]+'_DEPOSITION' for disease in diseases][0]
- ews_plot_dir = f"{jobPath}/plotting/"
+ ews_plot_dir = f"{job_path}/plotting/"
Path(ews_plot_dir).mkdir(parents=True, exist_ok=True)
@@ -758,11 +738,6 @@ class ProcessorEpidemiology(ProcessorBase):
logger.error('EWS-Plotting did not produce any output')
raise RuntimeError
- # provide to list for transfer
- ews_plotting_outputs: [str] = [item for ews_plotting_output in ews_plotting_output_globs for item in glob(ews_plotting_output)]
-
- return ews_plotting_outputs
-
if __name__ == '__main__':
processor = ProcessorEpidemiology()
--
GitLab