def _get_parameter_files():
"""
Extracts the available parameter files from the param sub folder
"""
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]
join = os.path.join
pdir = join(exedir, "param")
if os.path.exists(pdir):
p_files = glob.glob(join(pdir, "*.dat"))
pset = []
for f in p_files:
p = os.path.basename(f).split(".")[0]
pset.append(p)
return pset
else:
errmsg = (
"The model parameter directory param is missing. "
"It must be in the same directory as the program "
"executable"
)
error(errmsg, title="Error starting the program", buttons=["OK"])
sys.exit(-1)
def _get_parameter_files():
"""
Extracts the available parameter files from the param sub folder
"""
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]
join = os.path.join
pdir = join(exedir, 'param')
if os.path.exists(pdir):
p_files = glob.glob(join(pdir, '*.dat'))
pset = []
for f in p_files:
p = os.path.basename(f).split('.')[0]
pset.append(p)
return pset
else:
print "Not finding the parameter directory", pdir
errmsg = 'The model parameter directory param is missing. '\
'It must be in the same directory as the program '\
'executable'
error(errmsg, title='Error starting the program',
buttons=['OK'])
sys.exit(-1)
def add_current_state_to_database(self):
mdv = self.main_window
# file name may contain unicode characters
data_id = mdv.annotations_view.annotations_container.name
if data_id is '':
data_id = 'anonymous_annotations'
elif type(data_id) is unicode:
u_data_id = unicodedata.normalize('NFKD', data_id)
data_id = u_data_id.encode('ascii','ignore')
try:
self.database.store_result(
data_id,
mdv.annotations_view.annotations_container,
mdv.model,
mdv.log_likelihood
)
except PyannoValueError as e:
logger.info(e)
errmsg = e.args[0]
error('Error: ' + errmsg)
if self.db_window_open:
self.database_window.db_updated = True
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_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 _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 _action_failure(self, err):
self._action_finally()
if isinstance(err, PyannoValueError):
errmsg = err.args[0]
if 'Annotations' in errmsg:
# raised when annotations are incompatible with the model
error('Error: ' + errmsg)
else:
# re-raise exception if it has not been handled
raise err
def _check_for_subjects_surfaces_fired(self):
project_surface_directory=self.project_surface_directory
subject_id=self.subject_id
os.environ['SUBJECTS_DIR']=self.project_surface_directory
if os.path.isfile(os.path.join(project_surface_directory,subject_id,
'mri','aparc+aseg.mgz')):
self.subjects_existence=True
message(message='Subject %s was successfully found at %s.'%(subject_id,os.path.join(project_surface_directory,subject_id)),title='Subject successfully found', buttons=['OK'])
else:
self.subjects_existence=False
error(message='Subject %s was not found at %s. Please check your subject directory and subject id'%(subject_id,os.path.join(project_surface_directory,subject_id)), title='Subject not found', buttons=['OK'])
def _action_failure(self, err):
self._action_finally()
if isinstance(err, PyannoValueError):
errmsg = err.args[0]
if 'Annotations' in errmsg:
# raised when annotations are incompatible with the model
error('Error: ' + errmsg)
else:
# re-raise exception if it has not been handled
raise err
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_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 _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 _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 _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 _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 _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 _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 run_model(self, modeldata):
self.simulation = True
self.md = modeldata
self.c_stock = numpy.empty(shape=(0, 10), dtype=numpy.float32)
self.c_change = numpy.empty(shape=(0, 10), dtype=numpy.float32)
self.co2_yield = numpy.empty(shape=(0, 3), dtype=numpy.float32)
self.timemap = defaultdict(list)
self.area_timemap = defaultdict(list)
samplesize = self.md.sample_size
msg = "Simulating %d samples for %d timesteps" % (
samplesize, self.md.simulation_length)
progress = ProgressDialog(title="Simulation",
message=msg,
max=samplesize,
show_time=True,
can_cancel=True)
progress.open()
timesteps = self.md.simulation_length
self.timestep_length = self.md.timestep_length
self.ml_run = True
self.infall = {}
self.initial_mode = self.md.initial_mode
if self.initial_mode == 'steady state':
self.initial_def = self.md.steady_state
else:
self.initial_def = self.md.initial_litter
timemsg = None
for j in range(samplesize):
(cont, skip) = progress.update(j)
if not cont or skip:
break
self.draw = True
self.curr_yr_ind = 0
self.curr_month_ind = 0
for k in range(timesteps):
self._predict_timestep(j, k)
self.ml_run = False
self._fill_moment_results()
progress.update(samplesize)
if timemsg is not None:
error(timemsg, title='Error handling timesteps', buttons=['OK'])
return self.c_stock, self.c_change, self.co2_yield
def run_model(self, modeldata):
self.simulation = True
self.md = modeldata
self.c_stock = numpy.empty(shape=(0,10), dtype=numpy.float32)
self.c_change = numpy.empty(shape=(0,10), dtype=numpy.float32)
self.co2_yield = numpy.empty(shape=(0,3), dtype=numpy.float32)
self.timemap = defaultdict(list)
self.area_timemap = defaultdict(list)
samplesize = self.md.sample_size
msg = "Simulating %d samples for %d timesteps" % (samplesize,
self.md.simulation_length)
progress = ProgressDialog(title="Simulation", message=msg,
max=samplesize, show_time=True,
can_cancel=True)
progress.open()
timesteps = self.md.simulation_length
self.timestep_length = self.md.timestep_length
self.ml_run = True
self.infall = {}
self.initial_mode = self.md.initial_mode
if self.initial_mode=='steady state':
self.initial_def = self.md.steady_state
else:
self.initial_def = self.md.initial_litter
timemsg = None
for j in range(samplesize):
(cont, skip) = progress.update(j)
if not cont or skip:
break
self.draw = True
self.curr_yr_ind = 0
self.curr_month_ind = 0
for k in range(timesteps):
self._predict_timestep(j, k)
self.ml_run = False
self._fill_moment_results()
progress.update(samplesize)
if timemsg is not None:
error(timemsg, title='Error handling timesteps',
buttons=['OK'])
return self.c_stock, self.c_change, self.co2_yield
def add_current_state_to_database(self):
mdv = self.main_window
# file name may contain unicode characters
data_id = mdv.annotations_view.annotations_container.name
if data_id is '':
data_id = 'anonymous_annotations'
elif type(data_id) is unicode:
u_data_id = unicodedata.normalize('NFKD', data_id)
data_id = u_data_id.encode('ascii', 'ignore')
try:
self.database.store_result(
data_id, mdv.annotations_view.annotations_container, mdv.model,
mdv.log_likelihood)
except PyannoValueError as e:
logger.info(e)
errmsg = e.args[0]
error('Error: ' + errmsg)
if self.db_window_open:
self.database_window.db_updated = True
def set_scales(self, xscale, yscale):
"""Detect if the x-axis scale was changed and let the plotter know
"""
if not self.plot:
return
try:
xs = self.plot.format_scale('x', xscale)
self.xscale = xscale
self.plot.set_xscale(xs)
except:
self.xscale = '1.0'
error('Invalid X scale request')
try:
ys = self.plot.format_scale('y', yscale)
self.yscale = yscale
self.plot.set_yscale(ys)
except:
self.yscale = '1.0'
error('Invalid Y scale request')
self.plot.change_plot()
return
def set_scales(self, xscale, yscale):
"""Detect if the x-axis scale was changed and let the plotter know
"""
if not self.plot:
return
try:
xs = self.plot.format_scale('x', xscale)
self.xscale = xscale
self.plot.set_xscale(xs)
except:
self.xscale = '1.0'
error('Invalid X scale request')
try:
ys = self.plot.format_scale('y', yscale)
self.yscale = yscale
self.plot.set_yscale(ys)
except:
self.yscale = '1.0'
error('Invalid Y scale request')
self.plot.change_plot()
return
def error_dialog(message):
error(message)
raise InaivuError(message)
