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Merged
guillaumevernieres merged 1 commit into from
Mar 24, 2025
Merged

Add more LETKF model space plots and EVA plots for LETKF diags #511

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2 changes: 2 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,9 @@ plot_parametric_b: "OFF"
plot_background: "OFF"
plot_increment: "ON"
plot_analysis: "OFF"
plot_letkf_ensemble: "OFF"
eva_plots: "ON"
eva_letkf_plots: "OFF"
qos: "batch"
hpc: "hercules"
eva_module: "EVA/orion"
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84 changes: 80 additions & 4 deletions applications/cycle_diagnostics/vrfy_script.py
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Expand Up @@ -68,7 +68,8 @@

# for eva
diagdir = os.path.join(comout, 'diags')
HOMEgdas = os.getenv('HOMEgdas')
letkfdiagdir = os.path.join(comout, 'letkf', 'diags')
HOMEgdasmv = os.getenv('HOMEgdasmv')

# Get flags from environment variables (set in the bash driver)
plot_ensemble_b = os.getenv('PLOT_ENSEMBLE_B', 'OFF').upper() == 'ON'
Expand All @@ -78,6 +79,7 @@
plot_increment = os.getenv('PLOT_INCREMENT', 'OFF').upper() == 'ON'
plot_analysis = os.getenv('PLOT_ANALYSIS', 'OFF').upper() == 'ON'
eva_plots = os.getenv('EVA_PLOTS', 'OFF').upper() == 'ON'
eva_letkf_plots = os.getenv('EVA_LETKF_PLOTS', 'OFF').upper() == 'ON'

# output directory
vrfyout = os.getenv('VRFYOUT', './vrfyout')
Expand Down Expand Up @@ -257,7 +259,54 @@
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
colormap='nipy_spectral',
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_bkg_mean'))] # ocean mean ensemble background
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_bkg_mean')), # ocean mean ensemble background
plotConfig(grid_file=grid_file,
data_file=os.path.join(comout, 'letkf', f'enkfgdas.ice.t{cyc}z.ensmean_post.nc'),
variables_horiz={'aice_h': [0.0, 1.0]},
colormap='jet',
projs=['North', 'South', 'Global'],
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_ana_mean')), # sea ice mean ensemble analysis
plotConfig(grid_file=grid_file,
layer_file=layer_file,
data_file=os.path.join(comout, 'letkf', f'enkfgdas.ocean.t{cyc}z.ensmean_post.nc'),
lats=np.arange(-60, 60, 10),
lons=np.arange(-280, 80, 30),
variables_zonal={'Temp': [-1.8, 34.0],
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
variables_meridional={'Temp': [-1.8, 34.0],
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
variables_horiz={'ave_ssh': [-1.8, 1.3],
'Temp': [-1.8, 34.0],
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
colormap='nipy_spectral',
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_ana_mean')), # ocean mean ensemble analysis
plotConfig(grid_file=grid_file,
layer_file=layer_file,
data_file=os.path.join(comout, 'letkf', f'enkfgdas.ocean.t{cyc}z.ensmean_incr.nc'),
lats=np.arange(-60, 60, 10),
lons=np.arange(-280, 80, 30),
variables_zonal={'Temp': [-0.5, 0.5],
'Salt': [-0.1, 0.1]},
variables_horiz={'Temp': [-0.5, 0.5],
'Salt': [-0.1, 0.1],
'ave_ssh': [-0.1, 0.1]},
variables_meridional={'Temp': [-0.5, 0.5],
'Salt': [-0.1, 0.1]},
colormap='seismic',
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_incr_mean')), # ocean mean LETKF increment
plotConfig(grid_file=grid_file,
data_file=os.path.join(comout, 'letkf', f'enkfgdas.ice.t{cyc}z.ensmean_incr.nc'),
lats=np.arange(-60, 60, 10),
variables_horiz={'aice_h': [-0.2, 0.2]},
colormap='seismic',
projs=['North', 'South'],
vrfyout=os.path.join(vrfyout, 'vrfy', 'letkf_incr_mean'))] # sea ice mean LETKF increment
configs.extend(config_letkf)

# Background plotting configuration
Expand Down Expand Up @@ -356,8 +405,8 @@ def plot_marine_vrfy(config):

# Run EVA
if eva_plots:
evadir = os.path.join(HOMEgdas)
marinetemplate = os.path.join(evadir, 'marine_gdas_plots.yaml')
evadir = os.path.join(HOMEgdasmv)
marinetemplate = os.path.join(evadir, 'configs', 'marine_gdas_plots.yaml')
varyaml = os.path.join(comout, 'yaml', 'var.yaml')

# it would be better to refrence the dirs explicitly with the comout path
Expand All @@ -381,6 +430,33 @@ def plot_marine_vrfy(config):
print('running eva on', infile)
subprocess.run(['eva', infile], check=True)

# Run EVA on LETKF diags
if eva_letkf_plots:
evadir = os.path.join(HOMEgdasmv)
marinetemplate = os.path.join(evadir, 'configs', 'marine_letkf_gdas_plots.yaml')
letkfyaml = os.path.join(comout, 'letkf', 'letkf.yaml')

# it would be better to refrence the dirs explicitly with the comout path
# but eva doesn't allow for specifying output directories
os.chdir(os.path.join(vrfyout, 'vrfy'))
if not os.path.exists('preevayamls_letkf'):
os.makedirs('preevayamls_letkf')
if not os.path.exists('evayamls_letkf'):
os.makedirs('evayamls_letkf')

gen_eva_obs_yaml.gen_eva_obs_yaml(letkfyaml, marinetemplate, 'preevayamls_letkf')

files = os.listdir('preevayamls_letkf')
for file in files:
infile = os.path.join('preevayamls_letkf', file)
marine_eva_post.marine_eva_post(infile, 'evayamls_letkf', letkfdiagdir)

files = os.listdir('evayamls_letkf')
for file in files:
infile = os.path.join('evayamls_letkf', file)
print('running eva on', infile)
subprocess.run(['eva', infile], check=True)

#######################################
# calculate diag statistics
#######################################
Expand Down
222 changes: 222 additions & 0 deletions configs/marine_letkf_gdas_plots.yaml
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@@ -0,0 +1,222 @@
# template YAML file to create EVA YAML files
# based on obs spaces listed in JEDI YAML files
datasets:
- name: experiment
type: IodaObsSpace
filenames:
- @FILENAME@
@CHANNELSKEY@
groups:
- name: ObsValue
variables: &variables @VARIABLES@
- name: ObsError
- name: ombg
- name: oman
- name: hofx_y_mean_xb0
- name: EffectiveQC0
- name: MetaData
- name: PreQC
transforms:

# bkg
- transform: arithmetic
new name: experiment::bkg::${variable}
equals: experiment::ObsValue::${variable}-experiment::ombg::${variable}
for:
variable: *variables

# Generate omb that passed QC for JEDI
- transform: accept where
new name: experiment::OmBQC::${variable}
starting field: experiment::ombg::${variable}
where:
- experiment::EffectiveQC0::${variable} == 0
for:
variable: *variables

# Generate oma that passed QC for JEDI
- transform: accept where
new name: experiment::OmAQC::${variable}
starting field: experiment::oman::${variable}
where:
- experiment::EffectiveQC0::${variable} == 0
for:
variable: *variables

# Generate oma that passed QC for JEDI
- transform: accept where
new name: experiment::hofxQC::${variable}
starting field: experiment::hofx_y_mean_xb0::${variable}
where:
- experiment::EffectiveQC0::${variable} == 0
for:
variable: *variables





graphics:

plotting_backend: Emcpy
figure_list:

# ---------- Map Plots ----------
# Map plot of OmBQC
# --------

- batch figure:
variables: *variables
@CHANNELSKEY@
dynamic options:
- type: vminvmaxcmap
data variable: experiment::OmBQC::${variable}
figure:
layout: [1,1]
figure size: [20,10]
title: 'Ensemble mean OmB post QC | @NAME@ @CYCLE@ | ${variable_title}'
output name: map_plots_letkf/@NAME@/${variable}/@CHANNELVAR@/@NAME@_${variable}@CHANNELVAR@OmBQC.png
tight_layout: true
plots:
- mapping:
projection: plcarr
domain: global
add_map_features: ['coastline']
add_grid:
add_colorbar:
label: '${variable}'
layers:
- type: MapScatter
longitude:
variable: experiment::MetaData::longitude
latitude:
variable: experiment::MetaData::latitude
data:
variable: experiment::OmBQC::${variable}
@CHANNELKEY@
markersize: 0.01
label: '$(variable)'
colorbar: true
# below may need to be edited/removed
cmap: 'seismic'
vmin: ${dynamic_vmin}
vmax: ${dynamic_vmax}


# Histogram plots
# ---------------

# OmA pre and post QC
- batch figure:
variables: *variables
figure:
layout: [1,1]
title: 'Ensemble mean OmA pre- and post QC | @NAME@ | ${variable_title}'
output name: histograms_letkf/@NAME@/${variable}/oma_pre_post_qc_${variable}.png
plots:
- add_xlabel: 'Observation minus anl pre- and post-QC'
add_ylabel: 'Count'
add_legend:
loc: 'upper left'
statistics:
fields:
- field_name: experiment::OmAQC::${variable}
xloc: 0.5
yloc: -0.10
kwargs:
fontsize: 6
statistics_variables:
- n
- min
- mean
- max
- std
layers:
- type: Histogram
data:
variable: experiment::OmAQC::${variable}
color: 'blue'
label: 'OmA (post QC)'
bins: 100
alpha: 0.5
- type: Histogram
data:
variable: experiment::oman::${variable}
color: 'red'
label: 'OmA (pre QC)'
bins: 100
alpha: 0.5

# diff between OmA and OmB
- batch figure:
variables: *variables
figure:
layout: [1,1]
title: 'Ensemble mean OmA and OmB, post-QC | @NAME@ | ${variable_title}'
output name: histograms_letkf/@NAME@/${variable}/oma_omb_histogram_${variable}.png
plots:
- add_xlabel: 'OmA and OmB post-QC'
add_ylabel: 'Count'
add_legend:
loc: 'upper left'
statistics:
fields:
- field_name: experiment::OmAQC::${variable}
xloc: 0.5
yloc: -0.10
kwargs:
fontsize: 6
statistics_variables:
- n
- min
- mean
- max
- std
layers:
- type: Histogram
data:
variable: experiment::OmAQC::${variable}
color: 'blue'
label: 'OmA (post QC)'
bins: 100
alpha: 0.5
- type: Histogram
data:
variable: experiment::OmBQC::${variable}
color: 'red'
label: 'OmB (post QC)'
bins: 100
alpha: 0.5

- batch figure:
variables: *variables
@CHANNELSKEY@
figure:
layout: [1,1]
title: 'Observations vs. ensemble mean JEDI h(x) | @NAME@ @CYCLE@ | ${variable_title}'
output name: observation_scatter_plots_letkf/jedi_hofx_vs_obs_@CYCLE@_@NAME@_${variable}@CHANNELVAR@.png
plots:
- add_xlabel: 'Observation Value'
add_ylabel: 'JEDI h(x)'
add_grid:
add_legend:
loc: 'upper left'
layers:
- type: Scatter
x:
variable: experiment::ObsValue::${variable}
y:
variable: experiment::hofx_y_mean_xb0::${variable}
@CHANNELKEY@
markersize: 1
color: 'black'
label: 'JEDI h(x) versus obs (all obs)'
- type: Scatter
x:
variable: experiment::ObsValue::${variable}
y:
variable: experiment::hofxQC::${variable}
@CHANNELKEY@
markersize: 1
color: 'red'
label: 'JEDI h(x) versus obs (passed QC in JEDI)'
2 changes: 2 additions & 0 deletions configs/vrfy_config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,9 @@ plot_parametric_b: "OFF"
plot_background: "OFF"
plot_increment: "ON"
plot_analysis: "OFF"
plot_letkf_ensemble: "OFF"
eva_plots: "ON"
eva_letkf_plots: "OFF"
qos: "batch"
hpc: "hercules"
eva_module: "EVA/orion"
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