Skip to content

get stress table output from OVERVIEW.OUT #47

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 7 commits into
base: main
Choose a base branch
from
Open

get stress table output from OVERVIEW.OUT #47

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9c2211a
get stress table output from OVERVIEW.OUT. Now only run 1 is handled.
jeevakir Dec 9, 2024
5b34558
Update run.py
jeevakir Dec 12, 2024
2bf12d4
Fixed ecotype lines in Maize
daquinterop Dec 20, 2024
c8e937e
get stress table output from OVERVIEW.OUT. Now only run 1 is handled.
jeevakir Dec 9, 2024
94f29e9
Update run.py
jeevakir Dec 12, 2024
21a3b1b
couple changes to tests and output read functions
daquinterop Dec 20, 2024
2a2a968
fixed conflicts
daquinterop Dec 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
117 changes: 81 additions & 36 deletions DSSATTools/run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,12 @@
from DSSATTools.base.sections import TabularSubsection

OS = platform.system().lower()
OUTPUTS = ['PlantGro', "Weather", "SoilWat", "SoilOrg", "SoilNi"]
OUTPUTS = ['PlantGro', "Weather", "SoilWat", "SoilOrg", "SoilNi",
"OVERVIEW", "Summary"]
OUTPUT_MAP = {
"PlantGro": "GROUT", "SoilWat": "WAOUT", "SoilOrg": "CAOUT",
"Weather": "GROUT", "SoilNi": "NIOUT"
"Weather": "GROUT", "SoilNi": "NIOUT", "OVERVIEW": "OVVEW",
"Summary": "SUMRY"
}
SOIL_LAYER_OUTPUTS = ["SoilNi"]

Expand Down Expand Up @@ -229,8 +231,6 @@ def run(self,
wth_path = os.path.join(self._RUN_PATH, 'Weather')
weather.write(wth_path, management=management)



with open(os.path.join(self._RUN_PATH, CONFILE), 'w') as f:
f.write(f'WED {wth_path}\n')
if crop._CODE in ["WH", "BA"]:
Expand Down Expand Up @@ -264,48 +264,93 @@ def run(self,
var for var in OUTPUTS
if management.simulation_controls.get(OUTPUT_MAP.get(var)) in ("Y", None)
]

# There's not overview file for perenial forages
if crop.crop_name in PERENIAL_FORAGES:
self.OUTPUT_LIST.remove("OVERVIEW")

# Check for man.simulation_controls["WATER"]
if management.simulation_controls["WATER"] == "N":
self.OUTPUT_LIST = list(filter(lambda x: x != "SoilWat", self.OUTPUT_LIST))

for file in self.OUTPUT_LIST:
assert f'{file}.OUT' in OUTPUT_FILES, \
f'{file}.OUT does not exist in {self._RUN_PATH}'
table_start = -1
init_lines = []
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'r', encoding='cp437') as f:
while True:
table_start += 1
init_lines.append(f.readline())
if '@' in init_lines[-1][:10]:
break

try:
df = pd.read_csv(
os.path.join(self._RUN_PATH, f'{file}.OUT'),
skiprows=table_start, sep=' ', skipinitialspace=True
)
df = df.dropna(how="all", axis=1)

except UnicodeDecodeError:
if "OVERVIEW" in file:
self.stress_table = self._get_overview_stress()
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'),
'r', encoding='cp437') as f:
self._output[file] = f.readlines()
else:
table_start = -1
init_lines = []
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'r', encoding='cp437') as f:
lines = f.readlines()
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'w', encoding='utf-8') as f:
f.writelines(lines[table_start:])
df = pd.read_csv(
os.path.join(self._RUN_PATH, f'{file}.OUT'),
skiprows=0, sep=' ', skipinitialspace=True
)
if all(('@YEAR' in df.columns, 'DOY' in df.columns)):
df['DOY'] = df.DOY.astype(int).map(lambda x: f'{x:03d}')
df['@YEAR'] = df['@YEAR'].astype(str)
df.index = pd.to_datetime(
(df['@YEAR'] + df['DOY']),
format='%Y%j'
)
self._output[file] = df
while True:
table_start += 1
init_lines.append(f.readline())
if '@' in init_lines[-1][:10]:
break

try:
df = pd.read_csv(
os.path.join(self._RUN_PATH, f'{file}.OUT'),
skiprows=table_start, sep=' ', skipinitialspace=True
)
df = df.dropna(how="all", axis=1)

except UnicodeDecodeError:
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'r', encoding='cp437') as f:
lines = f.readlines()
with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'w', encoding='utf-8') as f:
f.writelines(lines[table_start:])
df = pd.read_csv(
os.path.join(self._RUN_PATH, f'{file}.OUT'),
skiprows=0, sep=' ', skipinitialspace=True
)
if all(('@YEAR' in df.columns, 'DOY' in df.columns)):
df['DOY'] = df.DOY.astype(int).map(lambda x: f'{x:03d}')
df['@YEAR'] = df['@YEAR'].astype(str)
df.index = pd.to_datetime(
(df['@YEAR'] + df['DOY']),
format='%Y%j'
)
self._output[file] = df

return

def _get_overview_stress(self):
table_start = -1
init_lines=[]
with open(os.path.join(self._RUN_PATH, 'OVERVIEW.OUT'), 'r', encoding='cp437') as f:
while True:
table_start += 1
search_term="DATE"
data = []
init_lines.append(f.readline())
if search_term in init_lines[-1][:12]:
header = ['DATE', 'CROP AGE', 'GROWTH STAGE', 'BIOMASS', 'LEAF LAI', \
'LEAF NUM', 'N_KG', 'N_PERCENT', 'STRESS H2O', 'STRESS Nitr', \
'STRESS Phos1', 'STRESS Phos2', 'RSTG']
break
# Skip the underline or separator line
f.readline()
for line in f:
if re.match(r'^\s*$', line): # Check for an empty line
break
else:
data.append(line.strip())
widths = [7, 5, 11, 8, 7, 6, 5, 5, 6, 6, 6, 6, 6]
df_data=[]
for line in data:
columns = []
start = 0
for width in widths:
columns.append(line[start:start + width].strip()) # Extract and strip
start += width
df_data.append(columns)
df = pd.DataFrame(df_data, columns=header).dropna(how="all", axis=1)
return df


def close(self):
'''
Expand Down
6 changes: 3 additions & 3 deletions DSSATTools/static/Genotype/MZCER048.ECO
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ IB0002 GENERIC MIDWEST2 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.5 0.85
IB0003 GENERIC MIDWEST3 8.0 34.0 34.0 12.5 4.0 6.0 170. 2.0 0.85
IB0004 +5% RUE MIDWEST1 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.4 0.85
DFAULT DEFAULT 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.2 0.85
IB0011 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.0 0.85 #Good KE 24 May 2024
IB0012 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.0 0.85 #Good KE 24 May 2024
IB0013 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 2.0 6.0 100. 7.0 0.85 #Good KE 24 May 2024
IB0011 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.0 0.85
IB0012 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 4.0 6.0 170. 4.0 0.85
IB0013 GENERIC MIDWEST1 8.0 34.0 34.0 12.5 2.0 6.0 100. 7.0 0.85


3 changes: 3 additions & 0 deletions tests/test_run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -786,12 +786,15 @@ def test_outputs():
man = Management(
planting_date=DATES[10],
)
man.simulation_controls["OVVEW"] = "N"
man.simulation_controls["SUMRY"] = "N"

dssat = DSSAT()
dssat.setup(cwd=os.path.join(TMP, 'test_mz'))
dssat.run(
soil=soil, weather=wth, crop=crop, management=man,
)

outputs = ['PlantGro', "Weather", "SoilWat", "SoilOrg"]
assert all(map(lambda x: x in outputs, dssat.output))

Expand Down