def execute_controlfile(self, name):
""" Execute controlfile or agenda on workspace.
This method looks recursively for a controlfile with the given name in the current
directory and the arts include path. If such a file has been found it will be parsed
and executed on the workspace.
Args:
name(str): Name of the controlfile
Raises:
Exception: If parsing of the controlfile fails.
Returns:
The controlfile as parsed Agenda object.
"""
if not name in imports:
agenda = Agenda.parse(name)
imports[name] = agenda
else:
agenda = imports[name]
self.execute_agenda(agenda)
return agenda
def execute_controlfile(self, name):
""" Execute a given controlfile on the workspace.
This method looks recursively for a controlfile with the given name in the current
directory and the arts include path. If such a file has been found it will be parsed
and executed on the workspace.
Args:
name(str): Name of the controlfile
Raises:
Exception: If parsing of the controlfile fails.
"""
if not name in imports:
imports[name] = Agenda.parse(name)
include_path_push(os.getcwd())
data_path_push(os.getcwd())
imports[name].execute(self)
include_path_pop()
data_path_pop()
def value(self):
""" Return the value of the variable in a given workspace.
By default this function will check the value in the workspace associated
with the variable of in the workspace object provided as argument to the function
call. If the variable has an associated workspace the workspace provided as
argument will be ignored.
Returns:
The value of the workspace variable represented by an object of the corresponding
python types.
Raises:
Exception: If the type of the workspace variable is not supported by the
interface.
"""
if (self.ws):
ws = self.ws
if not ws:
raise ValueError("WorkspaceVariable object need Workspace to determine value.")
v = arts_api.get_variable_value(ws.ptr, self.ws_id, self.group_id)
if not v.initialized:
raise Exception("WorkspaceVariable " + self.name + " is uninitialized.")
# TODO: Use group attribute here istead of lookup in group_names.
# TODO: Move this to VariableValueStruct class
if group_names[self.group_id] == "Index":
return c.cast(v.ptr, c.POINTER(c.c_long))[0]
if group_names[self.group_id] == "Numeric":
return c.cast(v.ptr, c.POINTER(c.c_double))[0]
if group_names[self.group_id] == "String":
return (c.cast(v.ptr, c.c_char_p)).value.decode("utf8")
if group_names[self.group_id] == "ArrayOfIndex":
return [c.cast(v.ptr, c.POINTER(c.c_long))[i] for i in range(v.dimensions[0])]
if group_names[self.group_id] == "Sparse":
m = v.dimensions[0]
n = v.dimensions[1]
nnz = v.dimensions[2]
data = np.ctypeslib.as_array(c.cast(v.ptr, c.POINTER(c.c_double)), (nnz,))
row_indices = np.ctypeslib.as_array(v.inner_ptr, (nnz,))
col_starts = np.ctypeslib.as_array(v.outer_ptr, (m + 1,))
return sp.sparse.csr_matrix((data, row_indices, col_starts), shape=(m,n))
if group_names[self.group_id] == "Agenda":
return Agenda(v.ptr)
try:
self.update()
a = np.asarray(self)
return a
except:
raise Exception("Type of workspace variable is not supported by the interface.")
def __init__(self, agenda):
""" Create include from argument.
Args:
agenda (str, Agenda): Argument to the INCLUDE statement. This can
either be a string or an Agenda object.
"""
if type(agenda) == str:
if not agenda in imports:
self.agenda = Agenda.parse(agenda)
imports[agenda] = self.agenda
else:
self.agenda = imports[agenda]
elif type(agenda) == Agenda:
self.agenda = agenda
else:
raise Exception("agenda argument must be either a controlfile"
" name or a typhon.arts.workspace.agenda.Agenda object.")
def arts_agenda(func):
"""
Parse python method as ARTS agenda
This decorator can be used to define ARTS agendas using python function syntax.
The function should have one arguments which is assumed to be a Workspace instance.
All expressions inside the function must be calls to ARTS WSMs. The result is an
Agenda object that can be used to copied into a named ARTS agenda
Example:
>>> @arts_agenda
>>> def inversion_iterate_agenda(ws):
>>> ws.x2artsStandard()
>>> ws.atmfields_checkedCalc()
>>> ws.atmgeom_checkedCalc()
>>> ws.yCalc()
>>> ws.VectorAddVector(ws.yf, ws.y, ws.y_baseline)
>>> ws.jacobianAdjustAfterIteration()
>>>
>>> ws.Copy(ws.inversion_iterate_agenda, inversion_iterate_agenda)
"""
source = getsource(func)
source = unindent(source)
ast = parse(source)
func_ast = ast.body[0]
if not type(func_ast) == FunctionDef:
raise Exception("ARTS agenda definition can only decorate function definiitons.")
args = func_ast.args.args
try:
arg_name = func_ast.args.args[0].arg
except:
raise Exception("Agenda definition needs workspace arguments.")
ws = Workspace(0)
context = copy(func.__globals__)
context.update({arg_name : ws})
# Add resolved non-local variables from closure.
nls, _, _, _ = getclosurevars(func)
context.update(nls)
#
# Helper functions
#
callback_body = []
def callback_make_fun(body):
"""
Helper function that creates a wrapper function around
python code to be executed withing an ARTS agenda.
"""
m = Module(body)
def callback(ptr):
try:
context[arg_name].ptr = ptr
eval(compile(m , "<unknown>", 'exec'), context)
except Exception as e:
logger.error(r"Exception in Python callback:\n", e)
context[arg_name].ptr = None
callback_body = []
return callback
def eval_argument(expr):
"""
Evaluate argument of workspace method call.
"""
if not hasattr(expr, "lineno"):
setattr(expr, "lineno", 0)
return eval(compile(Expression(expr), "<unknown>", 'eval'), context)
# Create agenda
a_ptr = arts_api.create_agenda(func.__name__.encode())
agenda = Agenda(a_ptr)
illegal_statement_exception = Exception(
"Agenda definitions may only contain calls to WSMs of the"
"workspace argument " + arg_name + " or INCLUDE statements.")
#
# Here the body of the function definition is traversed. Cases
# that are treated specieal are INCLUDE statements and calls
# of workspace methods. Remaining statements are accumulated
# in callback_body and then added to the agenda as a single callback.
#
for e in func_ast.body:
if not isinstance(e, Expr):
callback_body += [e]
continue
else:
call = e.value
if not isinstance(call, Call):
callback_body += [e]
continue
# Include statement
if type(call.func) == Name:
if not call.func.id == "INCLUDE":
callback_body += [e]
else:
args = []
for a in call.args:
args.append(eval_argument(a))
include = Include(*args)
if len(callback_body) > 0:
agenda.add_callback(callback_make_fun(callback_body))
callback_body = []
arts_api.agenda_append(agenda.ptr, include.agenda.ptr)
else:
att = call.func.value
if not att.id == arg_name:
callback_body += [e]
continue
# Extract method name.
name = call.func.attr
# m is not a workspace method
if not name in workspace_methods:
callback_body += [e]
continue
# m is a workspace method.
m = workspace_methods[name]
args = [ws, m]
for a in call.args:
# Handle starred expression
if type(a) == Starred:
bs = eval_argument(a.value)
for b in bs:
args.append(b)
continue
args.append(eval_argument(a))
# Extract keyword arguments
kwargs = dict()
for k in call.keywords:
kwargs[k.arg] = eval(
compile(Expression(k.value), "<unknown>", 'eval'),
context)
# Add function to agenda
if len(callback_body) > 0:
agenda.add_callback(callback_make_fun(callback_body))
callback_body = []
agenda.add_method(*args, **kwargs)
# Check if there's callback code left to add to the agenda.
if len(callback_body) > 0:
agenda.add_callback(callback_make_fun(callback_body))
callback_body = []
return agenda
def value(self):
""" Return the value of the variable in a given workspace.
By default this function will check the value in the workspace associated
with the variable of in the workspace object provided as argument to the
function call. If the variable has an associated workspace the workspace
provided as argument will be ignored.
Returns:
The value of the workspace variable represented by an object of
the corresponding python types.
Raises:
Exception: If the type of the workspace variable is not supported
by the interface.
"""
if (self.ws):
ws = self.ws
if not ws:
raise ValueError("WorkspaceVariable object need Workspace to determine value.")
v = arts_api.get_variable_value(ws.ptr, self.ws_id, self.group_id)
if not v.initialized:
raise Exception("WorkspaceVariable " + self.name + " is uninitialized.")
if self.group == "Index":
return c.cast(v.ptr, c.POINTER(c.c_long))[0]
elif self.group == "Numeric":
return c.cast(v.ptr, c.POINTER(c.c_double))[0]
elif self.group == "String":
return (c.cast(v.ptr, c.c_char_p)).value.decode("utf8")
elif self.group == "ArrayOfIndex":
return [c.cast(v.ptr, c.POINTER(c.c_long))[i]
for i in range(v.dimensions[0])]
elif self.group == "Sparse":
m = v.dimensions[0]
n = v.dimensions[1]
nnz = v.dimensions[2]
if nnz == 0:
return sp.sparse.csr_matrix(0)
else:
data = np.ctypeslib.as_array(c.cast(v.ptr,
c.POINTER(c.c_double)),
(nnz,))
row_indices = np.ctypeslib.as_array(v.inner_ptr, (nnz,))
col_starts = np.ctypeslib.as_array(v.outer_ptr, (m + 1,))
return sp.sparse.csr_matrix((data, row_indices, col_starts),
shape=(m,n))
elif self.group == "Agenda":
return Agenda(v.ptr)
elif self.ndim:
shape = []
size = 1
for i in range(self.ndim):
shape.append(v.dimensions[i])
size *= v.dimensions[i]
if size > 0:
self.__array_interface__ = {"shape" : tuple(shape),
"typestr" : "|f8",
"data" : (v.ptr, False),
"version" : 3}
return np.asarray(self)
else:
return np.zeros(shape)
else:
try:
return self.to_typhon()
except:
raise Exception("Type of workspace variable is not supported "
+ " by the interface.")
def arts_agenda(func):
"""
Parse python method as ARTS agenda
This decorator can be used to define ARTS agendas using python function syntax.
The function should have one arguments which is assumed to be a Workspace instance.
All expressions inside the function must be calls to ARTS WSMs. The result is an
Agenda object that can be used to copied into a named ARTS agenda
Example:
>>> @arts_agenda
>>> def inversion_iterate_agenda(ws):
>>> ws.x2artsStandard()
>>> ws.atmfields_checkedCalc()
>>> ws.atmgeom_checkedCalc()
>>> ws.yCalc()
>>> ws.VectorAddVector(ws.yf, ws.y, ws.y_baseline)
>>> ws.jacobianAdjustAfterIteration()
>>>
>>> ws.Copy(ws.inversion_iterate_agenda, inversion_iterate_agenda)
"""
source = getsource(func)
ast = parse(source)
func_ast = ast.body[0]
if not type(func_ast) == FunctionDef:
raise Exception(
"ARTS agenda definition can only decorate function definiitons.")
args = func_ast.args.args
try:
arg_name = func_ast.args.args[0].arg
except:
raise Exception("Agenda definition needs workspace arguments.")
ws = Workspace()
context = func.__globals__
context[arg_name] == ws
# Create agenda
a_ptr = arts_api.create_agenda(func.__name__.encode())
agenda = Agenda(a_ptr)
for e in func_ast.body:
if not type(e.value) == Call:
raise Exception("Agendas may only contain call expressions.")
# Extract workspace object.
try:
call = e.value
att = call.func.value
if not att.id == arg_name:
raise (Exception(
"Agenda definition may only contain call to WSMs of the " +
"workspace argument " + arg_name + "."))
except:
raise (Exception(
"Agenda definition may only contain call to WSMs of the " +
"workspace argument " + arg_name + "."))
# Extract method name.
try:
name = call.func.attr
m = workspace_methods[name]
if not type(m) == WorkspaceMethod:
raise Exception(name + " is not a known WSM.")
except:
raise Exception(name + " is not a known WSM.")
# Extract positional arguments
args = [ws, m]
for a in call.args:
args.append(
eval(compile(Expression(a), "<unknown>", 'eval'), context))
# Extract keyword arguments
kwargs = dict()
for k in call.keywords:
kwargs[k.arg] = eval(
compile(Expression(k.value), "<unknown>", 'eval'), context)
# Add function to agenda
agenda.add_method(*args, **kwargs)
return agenda
def arts_agenda(func):
"""
Parse python method as ARTS agenda
This decorator can be used to define ARTS agendas using python function syntax.
The function should have one arguments which is assumed to be a Workspace instance.
All expressions inside the function must be calls to ARTS WSMs. The result is an
Agenda object that can be used to copied into a named ARTS agenda
Example:
>>> @arts_agenda
>>> def inversion_iterate_agenda(ws):
>>> ws.x2artsStandard()
>>> ws.atmfields_checkedCalc()
>>> ws.atmgeom_checkedCalc()
>>> ws.yCalc()
>>> ws.VectorAddVector(ws.yf, ws.y, ws.y_baseline)
>>> ws.jacobianAdjustAfterIteration()
>>>
>>> ws.Copy(ws.inversion_iterate_agenda, inversion_iterate_agenda)
"""
source = getsource(func)
source = unindent(source)
ast = parse(source)
func_ast = ast.body[0]
if not type(func_ast) == FunctionDef:
raise Exception(
"ARTS agenda definition can only decorate function definiitons.")
args = func_ast.args.args
try:
arg_name = func_ast.args.args[0].arg
except:
raise Exception("Agenda definition needs workspace arguments.")
ws = Workspace()
context = copy(func.__globals__)
context.update({arg_name: ws})
# Add resolved non-local variables from closure.
nls, _, _, _ = getclosurevars(func)
context.update(nls)
def eval_argument(expr):
if not hasattr(expr, "lineno"):
setattr(expr, "lineno", 0)
return eval(compile(Expression(expr), "<unknown>", 'eval'), context)
# Create agenda
a_ptr = arts_api.create_agenda(func.__name__.encode())
agenda = Agenda(a_ptr)
illegal_statement_exception = Exception(
"Agenda definitions may only contain calls to WSMs of the"
"workspace argument " + arg_name + " or INCLUDE statements.")
for e in func_ast.body:
try:
call = e.value
except:
raise Exception("Agendas may only contain call expressions.")
# Include statement
if type(call.func) == Name:
if not call.func.id == "INCLUDE":
raise illegal_statement_exception
else:
args = []
for a in call.args:
args.append(eval_argument(a))
include = Include(*args)
arts_api.agenda_append(agenda.ptr, include.agenda.ptr)
else:
att = call.func.value
if not att.id == arg_name:
raise illegal_statement_exception
# Extract method name.
try:
name = call.func.attr
m = workspace_methods[name]
if not type(m) == WorkspaceMethod:
raise Exception(name + " is not a known WSM.")
except:
raise Exception(name + " is not a known WSM.")
# Extract positional arguments
args = [ws, m]
for a in call.args:
# Handle starred expression
if type(a) == Starred:
bs = eval_argument(a.value)
for b in bs:
args.append(b)
continue
args.append(eval_argument(a))
# Extract keyword arguments
kwargs = dict()
for k in call.keywords:
kwargs[k.arg] = eval(
compile(Expression(k.value), "<unknown>", 'eval'), context)
# Add function to agenda
agenda.add_method(*args, **kwargs)
return agenda