def _modelrun_event_fired(self):
# set the parameter set to use
fn = os.path.split(sys.executable)
if fn[1].lower().startswith('python'):
exedir = os.path.abspath(os.path.split(sys.argv[0])[0])
else:
exedir = fn[0]
pdir = os.path.join(exedir, 'param')
parfile = os.path.join(pdir, '%s.dat' % self.parameter_set)
if self.initial_mode=='zero' and self.litter_mode=='zero':
errmsg = ("Both soil carbon input and initial state may not be "
"zero simultaneously.")
error(errmsg, title='Invalid model parameters', buttons=['OK'])
return
if self.climate_mode=='yearly' and not self.yearly_climate:
errmsg = ("Climate mode may not be 'yearly' if there are no "
"yearly climate entries in the data file.")
error(errmsg, title='Invalid model parameters', buttons=['OK'])
return
if self.leaching>0:
errmsg = ("Leaching parameter may not be larger than 0.")
error(errmsg, title='Invalid model parameters', buttons=['OK'])
return
if self.climate_mode=='monthly' and not self.monthly_climate:
errmsg = ("Climate mode may not be 'monthly' if there are no "
"monthly climate entries in the data file.")
error(errmsg, title='Invalid model parameters', buttons=['OK'])
return
yassorunner = ModelRunner(parfile)
if not yassorunner.is_usable_parameter_file():
errmsg = ("The selected parameter file has wrong number of columns "
"and cannot be used.")
error(errmsg, title='Invalid model parameters', buttons=['OK'])
return
self.yassorunner = yassorunner
if self.initial_mode=='steady state':
steady_state = self.yassorunner.compute_steady_state(self)
self._set_steady_state(steady_state)
self._init_results()
self.c_stock, self.c_change, self.co2_yield = \
self.yassorunner.run_model(self)
self._create_co2_plot()
self._chart_type_changed()
def _modelrun_event_fired(self):
# set the parameter set to use
fn = os.path.split(sys.executable)
if fn[1].lower().startswith("python"):
exedir = os.path.abspath(os.path.split(sys.argv[0])[0])
else:
exedir = fn[0]
pdir = os.path.join(exedir, "param")
parfile = os.path.join(pdir, "%s.dat" % self.parameter_set)
self.yassorunner = ModelRunner(parfile)
if self.initial_mode == "steady state":
steady_state = self.yassorunner.compute_steady_state(self)
self._set_steady_state(steady_state)
self._init_results()
self.c_stock, self.c_change, self.co2_yield = self.yassorunner.run_model(self)
self._create_co2_plot()
self._chart_type_changed()
class Yasso(HasTraits):
"""
The Yasso model
"""
# Parameters
p_sets = _get_parameter_files()
parameter_set = Enum(p_sets)
leaching = Float(default_value=0.0)
# Initial condition
initial_mode = Enum(["non zero", "zero", "steady state"])
initial_litter = List(trait=LitterComponent)
steady_state = List(trait=LitterComponent)
# Litter input at each timestep in the simulation
litter_mode = Enum(["yearly", "constant yearly", "monthly"])
constant_litter = List(trait=LitterComponent)
monthly_litter = List(trait=TimedLitterComponent)
yearly_litter = List(trait=TimedLitterComponent)
woody_size_limit = Float(default_value=3.0)
area_change = List(trait=AreaChange)
# Climate definition for the simulation
climate_mode = Enum(["yearly", "constant yearly", "monthly"])
constant_climate = YearlyClimate()
monthly_climate = List(
trait=MonthlyClimate,
value=[
MonthlyClimate(month=1),
MonthlyClimate(month=2),
MonthlyClimate(month=3),
MonthlyClimate(month=4),
MonthlyClimate(month=5),
MonthlyClimate(month=6),
MonthlyClimate(month=7),
MonthlyClimate(month=8),
MonthlyClimate(month=9),
MonthlyClimate(month=10),
MonthlyClimate(month=11),
MonthlyClimate(month=12),
],
)
yearly_climate = List(trait=YearlyClimate)
# All data as text
all_data = Str()
data_file = Str()
# How the model will be run
sample_size = Int()
duration_unit = Enum(["year", "month"])
timestep_length = Range(low=1)
simulation_length = Range(low=1)
result_type = Enum(["C stock", "C change", "CO2 production"])
presentation_type = Enum(["chart", "array"])
chart_type = Enum(["common scale", "autofit"])
# Buttons
new_data_file_event = Button("New...")
open_data_file_event = Button("Open...")
save_data_file_event = Button("Save")
save_as_file_event = Button("Save as...")
modelrun_event = Button("Run model")
save_result_event = Button("Save raw results...")
save_moment_event = Button("Save moment results...")
# and the results stored
# Individual model calls
# iteration,time, total, woody, acid, water, ethanol, non_soluble, humus
c_stock = Array(dtype=float32, shape=(None, 10))
# iteration,time, total, woody, acid, water, ethanol, non_soluble, humus
c_change = Array(dtype=float32, shape=(None, 10))
# time, iteration, CO2 production
co2_yield = Array(dtype=float32, shape=(None, 3))
# time, mean, mode, var, skewness, kurtosis, 95% conf-, 95% conf+
stock_tom = Array(dtype=float32, shape=(None, 8))
stock_woody = Array(dtype=float32, shape=(None, 8))
stock_non_woody = Array(dtype=float32, shape=(None, 8))
stock_acid = Array(dtype=float32, shape=(None, 8))
stock_water = Array(dtype=float32, shape=(None, 8))
stock_ethanol = Array(dtype=float32, shape=(None, 8))
stock_non_soluble = Array(dtype=float32, shape=(None, 8))
stock_humus = Array(dtype=float32, shape=(None, 8))
change_tom = Array(dtype=float32, shape=(None, 8))
change_woody = Array(dtype=float32, shape=(None, 8))
change_non_woody = Array(dtype=float32, shape=(None, 8))
change_acid = Array(dtype=float32, shape=(None, 8))
change_water = Array(dtype=float32, shape=(None, 8))
change_ethanol = Array(dtype=float32, shape=(None, 8))
change_non_soluble = Array(dtype=float32, shape=(None, 8))
change_humus = Array(dtype=float32, shape=(None, 8))
co2 = Array(dtype=float32, shape=(None, 8))
# plot variables
stock_plots = Instance(GridContainer)
change_plots = Instance(GridContainer)
co2_plot = Instance(GridContainer)
p_timestep = Array()
ps_tom = Array()
ps_woody = Array()
ps_non_woody = Array()
ps_acid = Array()
ps_water = Array()
ps_ethanol = Array()
ps_non_soluble = Array()
ps_humus = Array()
pc_tom = Array()
pc_non_woody = Array()
pc_acid = Array()
pc_water = Array()
pc_ethanol = Array()
pc_non_soluble = Array()
pc_humus = Array()
#############################################################
# UI view
#############################################################
view = View(
VGroup(
HGroup(
Item("new_data_file_event", show_label=False),
Item("open_data_file_event", show_label=False),
Item("save_data_file_event", show_label=False),
Item("save_as_file_event", show_label=False),
Item("data_file", style="readonly", show_label=False),
),
HGroup(
Item(
"all_data",
show_label=False,
editor=CodeEditor(),
has_focus=True,
# width=300, height=400,
)
),
label="All data",
),
VGroup(
HGroup(
Item("parameter_set", width=-145, help=PARAMETER_SET_HELP),
Item("leaching", width=-45, label="Litter bag adjustment parameter", help=LEACHING_HELP),
show_border=True,
),
VGroup(
HGroup(
Item(
name="initial_mode",
style="custom",
label="Initial state:",
emphasized=True,
help=INITIAL_STATE_HELP,
)
),
Item(
"initial_litter",
visible_when='initial_mode=="non zero"',
show_label=False,
editor=litter_te,
width=790,
height=75,
),
),
VGroup(
HGroup(
Item(
"litter_mode",
style="custom",
label="Soil carbon input:",
emphasized=True,
help=SOIL_CARBON_INPUT_HELP,
)
),
HGroup(
Item(
"constant_litter",
visible_when='litter_mode=="constant yearly"',
show_label=False,
editor=litter_te,
full_size=False,
springy=False,
width=-790,
height=-75,
),
Item(
"monthly_litter",
visible_when='litter_mode=="monthly"',
show_label=False,
editor=timed_litter_te,
full_size=False,
springy=False,
width=-790,
height=-75,
),
Item(
"yearly_litter",
visible_when='litter_mode=="yearly"',
show_label=False,
editor=timed_litter_te,
full_size=False,
springy=False,
width=-790,
height=-75,
),
),
HGroup(
Item(
"area_change",
visible_when='litter_mode=="yearly" or ' 'litter_mode=="monthly"',
show_label=False,
editor=change_te,
full_size=False,
springy=False,
width=-150,
height=-75,
),
spring,
),
),
VGroup(
HGroup(Item("climate_mode", style="custom", label="Climate:", emphasized=True, help=CLIMATE_HELP)),
HGroup(
Item(
"monthly_climate",
show_label=False,
visible_when='climate_mode=="monthly"',
editor=monthly_climate_te,
width=200,
height=75,
),
Item(
"yearly_climate",
show_label=False,
visible_when='climate_mode=="yearly"',
editor=yearly_climate_te,
width=200,
height=75,
),
VGroup(
Item("object.constant_climate.mean_temperature", style="readonly"),
Item("object.constant_climate.annual_rainfall", style="readonly"),
Item("object.constant_climate.variation_amplitude", style="readonly"),
show_border=True,
visible_when='climate_mode=="constant yearly"',
),
),
),
label="Data to use",
),
VGroup(
Group(
HGroup(
Item("sample_size", width=-45, help=SAMPLE_SIZE_HELP),
Item("simulation_length", width=-45, label="Number of timesteps", help=SIMULATION_LENGTH_HELP),
Item("timestep_length", width=-45, help=TIMESTEP_LENGTH_HELP),
Item("duration_unit", style="custom", show_label=False),
),
HGroup(
Item("woody_size_limit", width=-45, help=WOODY_SIZE_LIMIT_HELP),
Item("modelrun_event", show_label=False),
),
show_border=True,
),
HGroup(
Item("result_type", style="custom", label="Show", emphasized=True, help=SHOW_HELP),
Item("save_result_event", show_label=False),
Item("save_moment_event", show_label=False),
),
HGroup(
Item("presentation_type", style="custom", label="As", emphasized=True, help=AS_HELP),
Item("chart_type", style="custom", label="Chart type", visible_when='presentation_type=="chart"'),
),
HGroup(
Item(
"c_stock",
visible_when='result_type=="C stock" and \
presentation_type=="array"',
show_label=False,
editor=c_stock_te,
width=600,
),
Item(
"c_change",
visible_when='result_type=="C change" and \
presentation_type=="array"',
show_label=False,
editor=c_stock_te,
),
Item(
"co2_yield",
visible_when='result_type=="CO2 production" ' 'and presentation_type=="array"',
show_label=False,
editor=co2_yield_te,
),
Item(
"stock_plots",
editor=ComponentEditor(),
show_label=False,
width=600,
height=600,
visible_when='result_type=="C stock" and \
presentation_type=="chart"',
),
Item(
"change_plots",
editor=ComponentEditor(),
show_label=False,
width=600,
height=600,
visible_when='result_type=="C change" and \
presentation_type=="chart"',
),
Item(
"co2_plot",
editor=ComponentEditor(),
show_label=False,
width=600,
height=600,
# springy=False, full_size=False, resizable=False,
visible_when='result_type=="CO2 production" and \
presentation_type=="chart"',
),
),
label="Model run",
),
VGroup(Label(label="Yasso07 soil carbon model", emphasized=True), Label(label=APP_INFO), label="About"),
title="Yasso 07",
id="simosol.yasso07",
dock="horizontal",
resizable=True,
width=800,
height=600,
scrollable=True,
buttons=NoButtons,
menubar=MenuBar(Menu(CloseAction, name="File"), Menu(UndoAction, RedoAction, RevertAction, name="Edit")),
help=False,
)
###############################################################################
# Initialisation
###############################################################################
def __init__(self):
self.sample_size = 10
self.simulation_length = 10
fn = os.path.split(sys.executable)
if fn[1].lower().startswith("python"):
exedir = os.path.abspath(os.path.split(sys.argv[0])[0])
self.data_file = self._get_data_file_path(exedir)
else:
self.data_file = self._get_data_file_path(fn[0])
try:
f = open(self.data_file)
self._load_all_data(f)
f.close()
except:
self.all_data = DATA_STRING
self.data_file = ""
def _get_data_file_path(self, exedir):
join = os.path.join
self.state_file = join(exedir, "yasso.state")
if os.path.exists(self.state_file):
f = open(self.state_file)
datafile = f.read()
if len(datafile) > 0 and datafile[-1] == "\n":
datafile = datafile[:-1]
f.close()
if not os.path.exists(datafile):
os.remove(self.state_file)
datafile = join(exedir, "demo_data.txt")
else:
datafile = join(exedir, "demo_data.txt")
return datafile
def _write_state(self, filename):
f = open(self.state_file, "w")
f.write(filename)
f.close()
###############################################################################
# Event handlers
###############################################################################
#########################
# for plot data
#########################
def _create_stock_plots(self, common_scale=False):
max = None
min = 0
stom, max, min = self._create_plot(max, min, self.stock_tom, "Total organic matter")
swoody, max, min = self._create_plot(max, min, self.stock_woody, "Woody matter")
snonwoody, max, min = self._create_plot(max, min, self.stock_non_woody, "Non-woody matter")
sa, max, min = self._create_plot(max, min, self.stock_acid, "Acid soluble")
sw, max, min = self._create_plot(max, min, self.stock_water, "Water soluble")
se, max, min = self._create_plot(max, min, self.stock_ethanol, "Ethanol soluble")
sn, max, min = self._create_plot(max, min, self.stock_non_soluble, "Non soluble")
sh, max, min = self._create_plot(max, min, self.stock_humus, "Humus")
if common_scale:
for pl in (stom, swoody, snonwoody, sa, sw, se, sn, sh):
pl.value_range.set_bounds(min, max)
container = GridContainer(stom, swoody, snonwoody, sa, sw, se, sn, sh)
container.shape = (3, 3)
container.spacing = (-8, -8)
self.stock_plots = container
def _create_change_plots(self, common_scale=False):
max = None
min = 0
ctom, max, min = self._create_plot(max, min, self.change_tom, "Total organic matter")
cwoody, max, min = self._create_plot(max, min, self.change_woody, "Woody matter")
cnonwoody, max, min = self._create_plot(max, min, self.change_non_woody, "Non-woody matter")
ca, max, min = self._create_plot(max, min, self.change_acid, "Acid soluble")
cw, max, min = self._create_plot(max, min, self.change_water, "Water soluble")
ce, max, min = self._create_plot(max, min, self.change_ethanol, "Ethanol soluble")
cn, max, min = self._create_plot(max, min, self.change_non_soluble, "Non soluble")
ch, max, min = self._create_plot(max, min, self.change_humus, "Humus")
if common_scale:
for pl in (ctom, cwoody, cnonwoody, ca, cw, ce, cn, ch):
pl.value_range.set_bounds(min, max)
container = GridContainer(ctom, cwoody, cnonwoody, ca, cw, ce, cn, ch)
container.shape = (3, 3)
container.spacing = (-15, -15)
self.change_plots = container
def _create_co2_plot(self):
max = None
min = 0
co2, max, min = self._create_plot(max, min, self.co2, "CO2 production (in carbon)")
container = GridContainer(co2, Plot(), Plot(), Plot())
container.shape = (2, 2)
self.co2_plot = container
def _create_plot(self, max, min, dataobj, title):
x = dataobj[:, 0]
y = dataobj[:, 1]
if y.max() > max:
max = y.max()
if y.min() < min:
min = y.min()
if self.sample_size > 1:
y2 = dataobj[:, 6]
y3 = dataobj[:, 7]
if y3.max() > max:
max = y3.max()
if y2.min() < min:
min = y2.min()
plotdata = ArrayPlotData(x=x, y=y, y2=y2, y3=y3)
else:
plotdata = ArrayPlotData(x=x, y=y)
plot = Plot(plotdata)
plot.plot(("x", "y"), type="line", color="blue")
if self.sample_size > 1:
plot.plot(("x", "y2"), type="line", color="red")
plot.plot(("x", "y3"), type="line", color="red")
# plot.padding_right = 45
# plot.padding_left = 25
# plot.padding_top = 25
# plot.padding_bottom = 25
plot.title = title
plot.title_font = "Arial 10"
return plot, max, min
########################
# for running the model
########################
def _modelrun_event_fired(self):
# set the parameter set to use
fn = os.path.split(sys.executable)
if fn[1].lower().startswith("python"):
exedir = os.path.abspath(os.path.split(sys.argv[0])[0])
else:
exedir = fn[0]
pdir = os.path.join(exedir, "param")
parfile = os.path.join(pdir, "%s.dat" % self.parameter_set)
self.yassorunner = ModelRunner(parfile)
if self.initial_mode == "steady state":
steady_state = self.yassorunner.compute_steady_state(self)
self._set_steady_state(steady_state)
self._init_results()
self.c_stock, self.c_change, self.co2_yield = self.yassorunner.run_model(self)
self._create_co2_plot()
self._chart_type_changed()
########################
# for chart type
########################
def _chart_type_changed(self):
if self.chart_type == "autofit":
self._create_stock_plots()
self._create_change_plots()
elif self.chart_type == "common scale":
self._create_stock_plots(common_scale=True)
self._create_change_plots(common_scale=True)
########################
# for buttons
########################
def _new_data_file_event_fired(self):
filename = save_file()
if filename != "":
try:
self._reset_data()
f = open(filename, "w")
f.close()
self.data_file = filename
self._write_state(filename)
self.all_data = DATA_STRING
except:
pass
def _open_data_file_event_fired(self):
filename = open_file()
if filename != "":
try:
f = open(filename)
self.data_file = filename
self._write_state(filename)
self._load_all_data(f)
f.close()
except:
pass
def _save_data_file_event_fired(self):
if self.data_file == "":
filename = save_file()
if filename == "":
return
self.data_file = filename
self._write_state(filename)
self._save_all_data()
def _save_as_file_event_fired(self):
filename = save_file()
if filename == "":
return
self.data_file = filename
self._write_state(filename)
self._save_all_data()
def _load_all_data(self, datafile):
"""
Loads all data from a single file. Data in sections defined by [name],
data in whitespace delimited rows
"""
self._reset_data()
sectionp = re.compile("\[([\w+\s*]+)\]")
datap = re.compile("[+-Ee\d+\.\d*\s*]+")
active = None
data = defaultdict(list)
alldata = ""
linecount = 0
for line in datafile:
linecount += 1
alldata += line
m = re.match(sectionp, line)
if m is not None:
active = m.group(1)
d = re.match(datap, line)
if d is not None:
try:
vals = [float(val) for val in d.group(0).split()]
data[active].append(vals)
except ValueError:
errmsg = (
"There's an error on line %s\n %s"
"for section %s\n"
"Values must be space separated and . is the decimal"
" separator" % (linecount, d.group(0), active)
)
error(errmsg, title="Error saving data", buttons=["OK"])
self.all_data = alldata
for section, vallist in data.items():
if section == "Initial state":
self._set_initial_state(vallist)
elif section == "Constant soil carbon input":
self._set_constant_litter(vallist)
elif section == "Monthly soil carbon input":
self._set_monthly_litter(vallist)
elif section == "Yearly soil carbon input":
self._set_yearly_litter(vallist)
elif section == "Relative area change":
self._set_area_change(vallist)
elif section == "Constant climate":
self._set_constant_climate(vallist)
elif section == "Monthly climate":
self._set_monthly_climate(vallist)
elif section == "Yearly climate":
self._set_yearly_climate(vallist)
def _save_all_data(self):
f = open(self.data_file, "w")
f.write(self.all_data)
f.close()
f = open(self.data_file)
self._load_all_data(f)
f.close()
def _reset_data(self):
"""
Empties all input data structures
"""
self.initial_litter = []
self.steady_state = []
self.constant_litter = []
self.monthly_litter = []
self.yearly_litter = []
self.area_change = []
self.constant_climate.mean_temperature = 0
self.constant_climate.annual_rainfall = 0
self.constant_climate.variation_amplitude = 0
self.yearly_climate = []
self.monthly_climate = []
def _set_initial_state(self, data):
errmsg = (
"Soil carbon components should contain: \n"
" mass, mass std, acid, acid std, water, water std,\n"
" ethanol, ethanol std, non soluble, non soluble std,"
"\n humus, humus std, size class"
)
for vals in data:
ok, obj = self._load_litter_object(vals, errmsg)
if not ok:
break
self.initial_litter.append(obj)
def _set_steady_state(self, data):
errmsg = (
"Soil carbon components should contain: \n"
" mass, mass std, acid, acid std, water, water std,\n"
" ethanol, ethanol std, non soluble, non soluble std,"
"\n humus, humus std, size class"
)
self.steady_state = []
for vals in data:
ok, obj = self._load_litter_object(vals, errmsg)
if not ok:
break
self.steady_state.append(obj)
def _set_constant_litter(self, data):
errmsg = (
"Soil carbon components should contain: \n"
" mass, mass std, acid, acid std, water, water std,\n"
" ethanol, ethanol std, non soluble, non soluble std,"
"\n humus, humus std, size class"
)
for vals in data:
ok, obj = self._load_litter_object(vals, errmsg)
if not ok:
break
self.constant_litter.append(obj)
def _set_monthly_litter(self, data):
errmsg = (
"timed soil carbon components should contain: \n"
" timestep, mass, mass std, acid, acid std, water, "
"water std,\n"
" ethanol, ethanol std, non soluble, non soluble std,"
"\n humus, humus std, size class"
)
for vals in data:
ok, obj = self._load_litter_object(vals, errmsg, True)
if not ok:
break
self.monthly_litter.append(obj)
def _set_yearly_litter(self, data):
errmsg = (
"timed soil carbon components should contain: \n"
" timestep, mass, mass std, acid, acid std, water, "
"water std,\n"
" ethanol, ethanol std, non soluble, non soluble std,"
"\n humus, humus std, size class"
)
for vals in data:
ok, obj = self._load_litter_object(vals, errmsg, True)
if not ok:
break
self.yearly_litter.append(obj)
def _set_area_change(self, data):
errmsg = "Area change should contain:\n timestep, relative area change"
for vals in data:
if len(vals) == 2:
obj = AreaChange(timestep=int(vals[0]), rel_change=vals[1])
self.area_change.append(obj)
elif vals != []:
errmsg = errmsg + "\n%s data values found, 2 needed" % (len(data))
error(errmsg, title="error reading data", buttons=["OK"])
break
def _set_yearly_climate(self, data):
errmsg = (
"Yearly climate should contain: timestep, mean temperature,\n"
"annual rainfall and temperature variation amplitude"
)
for vals in data:
if len(vals) == 4:
obj = YearlyClimate(
timestep=int(vals[0]),
mean_temperature=vals[1],
annual_rainfall=vals[2],
variation_amplitude=vals[3],
)
self.yearly_climate.append(obj)
elif vals != []:
errmsg = errmsg + "\n%s data values found, 4 needed" % (len(data))
error(errmsg, title="error reading data", buttons=["OK"])
break
def _set_constant_climate(self, data):
errmsg = (
"Constant climate should contain: mean temperature,\n" "annual rainfall and temperature variation amplitude"
)
if len(data[0]) == 3:
self.constant_climate.mean_temperature = data[0][0]
self.constant_climate.annual_rainfall = data[0][1]
self.constant_climate.variation_amplitude = data[0][2]
elif data[0] != []:
errmsg = errmsg + "\n%s data values found, 3 needed" % (len(data))
error(errmsg, title="error reading data", buttons=["OK"])
def _set_monthly_climate(self, data):
errmsg = "Monthly climate data should contain: month,\n" "temperature and rainfall"
for vals in data:
if len(vals) == 3:
obj = MonthlyClimate(month=int(vals[0]), temperature=vals[1], rainfall=vals[2])
self.monthly_climate.append(obj)
elif vals != []:
errmsg = errmsg + "\n%s data values found, 3 needed" % (len(data))
error(errmsg, title="Error reading data", buttons=["OK"])
break
def _load_litter_object(self, data, errmsg, hastime=False):
obj = None
loaded = True
if hastime:
if len(data) == 14:
obj = TimedLitterComponent(
timestep=int(data[0]),
mass=data[1],
mass_std=data[2],
acid=data[3],
acid_std=data[4],
water=data[5],
water_std=data[6],
ethanol=data[7],
ethanol_std=data[8],
non_soluble=data[9],
non_soluble_std=data[10],
humus=data[11],
humus_std=data[12],
size_class=data[13],
)
elif data != []:
errmsg = errmsg + "\n%s data values found, 14 needed" % (len(data))
error(errmsg, title="Error reading data", buttons=["OK"])
loaded = False
elif data == []:
loaded = False
else:
if len(data) == 13:
obj = LitterComponent(
mass=data[0],
mass_std=data[1],
acid=data[2],
acid_std=data[3],
water=data[4],
water_std=data[5],
ethanol=data[6],
ethanol_std=data[7],
non_soluble=data[8],
non_soluble_std=data[9],
humus=data[10],
humus_std=data[11],
size_class=data[12],
)
elif data != []:
errmsg = errmsg + "\n%s data values found, 13 needed" % (len(data))
error(errmsg, title="Error reading data", buttons=["OK"])
loaded = False
elif data == []:
loaded = False
return loaded, obj
def _save_moment_event_fired(self):
filename = save_file()
if filename != "":
f = open(filename, "w")
if self.result_type == "C stock":
comps = (
("tom", self.stock_tom),
("woody", self.stock_woody),
("non-woody", self.stock_non_woody),
("acid", self.stock_acid),
("water", self.stock_water),
("ethanol", self.stock_ethanol),
("non-soluble", self.stock_non_soluble),
("humus", self.stock_humus),
)
elif self.result_type == "C change":
comps = (
("tom", self.change_tom),
("woody", self.change_woody),
("non-woody", self.change_non_woody),
("acid", self.change_acid),
("water", self.change_water),
("ethanol", self.change_ethanol),
("non-soluble", self.change_non_soluble),
("humus", self.change_humus),
)
elif self.result_type == "CO2 production":
comps = (("CO2", self.co2),)
header = (
"# component, time step, mean, mode, var, skewness, "
"kurtosis, 95% confidence lower limit, 95% upper limit"
)
header = self._make_result_header(header)
f.write(header + "\n")
for comp, res in comps:
for row in res:
resrow = ""
for num in row:
resrow = " ".join([resrow, str(num)])
resrow = " ".join((comp, resrow))
f.write(resrow + "\n")
f.close()
def _save_result_event_fired(self):
filename = save_file()
if filename != "":
f = open(filename, "w")
if self.result_type == "C stock":
res = self.c_stock
header = (
"# sample, time step, total om, woody om, non-woody om," " acid, water, ethanol, non-soluble, humus"
)
elif self.result_type == "C change":
res = self.c_change
header = (
"# sample, time step, total om, woody om, non-woody om," " acid, water, ethanol, non soluble, humus"
)
elif self.result_type == "CO2 production":
res = self.co2_yield
header = "# sample, time step, CO2 production (in carbon)"
header = self._make_result_header(header)
f.write(header + "\n")
for row in res:
resrow = ""
for num in row:
resrow = " ".join([resrow, str(num)])
f.write(resrow + "\n")
f.close()
def _make_result_header(self, header):
"""Adds metadata about the results into the header"""
hstr = "#########################################################\n"
hstr += "# " + self.result_type + "\n"
hstr += "#########################################################\n"
hstr += "# Datafile used: " + self.data_file + "\n"
hstr += "# Settings:\n"
hstr += "# initial state: " + self.initial_mode + "\n"
hstr += "# soil carbon input: " + self.litter_mode + "\n"
hstr += "# climate: " + self.climate_mode + "\n"
hstr += "# sample size: " + str(self.sample_size) + "\n"
hstr += "".join(["# timestep length: ", str(self.timestep_length), " (", self.duration_unit, ")\n"])
hstr += "# woody litter size limit: " + str(self.woody_size_limit) + "\n"
hstr += "#\n"
return hstr + header
def _init_results(self):
"""
model results: stock & change
sample, timestep, tom, woody, non-woody, acid, water, ethanol,
non soluble humus
model results: CO2
sample, timestep, CO2 production
summary results
common format: time, mean, mode, var, skewness, kurtosis,
95% confidence-, 95% confidence+
"""
self.c_stock = empty(dtype=float32, shape=(0, 10))
self.c_change = empty(dtype=float32, shape=(0, 10))
self.co2_yield = empty(dtype=float32, shape=(0, 3))
self.stock_tom = empty(dtype=float32, shape=(0, 8))
self.stock_woody = empty(dtype=float32, shape=(0, 8))
self.stock_non_woody = empty(dtype=float32, shape=(0, 8))
self.stock_acid = empty(dtype=float32, shape=(0, 8))
self.stock_water = empty(dtype=float32, shape=(0, 8))
self.stock_ethanol = empty(dtype=float32, shape=(0, 8))
self.stock_non_soluble = empty(dtype=float32, shape=(0, 8))
self.stock_humus = empty(dtype=float32, shape=(0, 8))
self.change_tom = empty(dtype=float32, shape=(0, 8))
self.change_woody = empty(dtype=float32, shape=(0, 8))
self.change_non_woody = empty(dtype=float32, shape=(0, 8))
self.change_acid = empty(dtype=float32, shape=(0, 8))
self.change_water = empty(dtype=float32, shape=(0, 8))
self.change_ethanol = empty(dtype=float32, shape=(0, 8))
self.change_non_soluble = empty(dtype=float32, shape=(0, 8))
self.change_humus = empty(dtype=float32, shape=(0, 8))
self.co2 = empty(dtype=float32, shape=(0, 8))
