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Add option for processing local files and add API functions for vensim
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@nanglo123
nanglo123 committed Jan 24, 2024
1 parent 7e2dd13 commit 71d0fc5
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Showing 3 changed files with 160 additions and 139 deletions.
Empty file added mira/sources/system_dynamics/__init__.py
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229 changes: 90 additions & 139 deletions mira/sources/vensim.py → ...urces/system_dynamics/parse_pysd_model.py
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Original file line number Diff line number Diff line change
@@ -1,21 +1,7 @@
"""This module implements parsing Vensim models by Ventana Systems denoted by the .mdl file
and turning them into MIRA template models.
The documentation for vensim models is defined here:
https://www.vensim.com/documentation/sample_models.html
SIR mdl file example here: https://www.vensim.com/documentation/sample_models.html
"""

__all__ = ["template_model_from_mdl_file_url"]

import pandas as pd
import pysd
from pysd.translators.vensim.vensim_file import VensimFile
import requests
import sympy
import re
import tempfile


from mira.metamodel import *
from mira.metamodel.utils import safe_parse_expr
Expand All @@ -26,106 +12,37 @@
get_sympy,
)


NEW_CONTROL_DELIMETER = (
" ******************************************************** .Control "
"********************************************************"
)
CONTROL_VARIABLE_NAMES = {"FINALTIME", "INITIALTIME", "SAVEPER", "TIMESTEP"}
UTF_ENCODING = "{UTF-8} "


def state_to_concept(state) -> Concept:
"""
Create a MIRA Concept from a state
Parameters
----------
state : pd.Series
The series that contains state data
Returns
-------
:
The MIRA concept created from the state
"""
name = state["Py Name"]
description = state["Comment"]
unit_dict = {
"expression": state["Units"].replace(" ", "")
if state["Units"]
else None
}
unit_expr = get_sympy(unit_dict, UNIT_SYMBOLS)
units_obj = Unit(expression=unit_expr) if unit_expr else None

return Concept(name=name, units=units_obj, description=description)


def process_expression_text(expr_text, symbols):
"""
Create a sympy expression from a string expression using the supplied mapping of symbols
Parameters
----------
expr_text : str
The string expression
symbols : dict[str,sympy.Symbol]
A mapping of string symbol to a symbol in sympy
Returns
-------
: sympy.Expr
The sympy expression
"""
# strip leading and trailing white spaces
# remove spaces between operators and operands
# replace space between two words that makeup a variable name with "_"'
expr_text = (
expr_text.strip()
.replace(" * ", "*")
.replace(" - ", "-")
.replace(" / ", "/")
.replace(" + ", "+")
.replace("^", "**")
.replace(" ", "_")
.replace('"', "")
.lower()
)

sympy_expr = safe_parse_expr(expr_text, symbols)
return sympy_expr


def template_model_from_mdl_file_url(url) -> TemplateModel:
"""
Return a template model from a Vensim file
def template_model_from_pysd_model(
pysd_model, model_text=None
) -> TemplateModel:
"""Given a model and its accompanying model text, parse the arguments to extract information
to create an equivalent MIRA template model.
Parameters
----------
url : str
The url to the mdl file
pysd_model : Model
The pysd model object
model_text : str
The plain-text information representing the model structure. Used for extracting
expressions.
Returns
-------
:
A MIRA Template Model
MIRA template model
"""
data = requests.get(url).content
temp_file = tempfile.NamedTemporaryFile(
mode="w+b", suffix=".mdl", delete=False
)

with temp_file as file:
file.write(data)

utf_encoding = "{UTF-8} "

vensim_file = VensimFile(temp_file.name)
model_split_text = vensim_file.model_text.split("|")
model = pysd.read_vensim(temp_file.name)
model_doc_df = model.doc
state_initial_values = model.run().iloc[0]
model_split_text = model_text.split("|")
model_doc_df = pysd_model.doc
state_initial_values = pysd_model.run().iloc[0]

# Mapping of variable name in vensim model to variable python-equivalent name
old_name_new_pyname_map = dict(
Expand All @@ -142,6 +59,13 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
)
)

new_symbols = dict(
zip(
model_doc_df["Real Name"],
list(map(lambda x: sympy.Symbol(x), model_doc_df["Py Name"])),
)
)

# Mapping of name to string expression
new_var_expression_map = {}

Expand All @@ -152,8 +76,8 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
continue

# first entry usually has encoding type
if utf_encoding in text:
text = text.replace(utf_encoding, "")
if UTF_ENCODING in text:
text = text.replace(UTF_ENCODING, "")

var_declaration = text.split("~")[0].split("=")
old_var_name = var_declaration[0].strip()
Expand Down Expand Up @@ -182,8 +106,12 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
state_rate_map[state_name] = {"inputs": [], "outputs": []}
state_expr_text = new_var_expression_map[state_name]
state_arg_text = re.search("INTEG+ \( (.*),", state_expr_text).group(1)
state_arg_sympy = process_expression_text(state_arg_text, symbols)

# maybe use mapping of real name to symbol of py name and don't have to call
# process_expression_text
# state_arg_sympy = process_expression_text(state_arg_text, symbols)

state_arg_sympy = safe_parse_expr(state_arg_text, new_symbols)
# map of states to rate laws that affect the state
state_sympy_map[state_name] = state_arg_sympy

Expand Down Expand Up @@ -225,6 +153,7 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
mira_initials[initial.concept.name] = initial

# process parameters
test_units = []
mira_parameters = {}
for name, expression in new_var_expression_map.items():
if expression.replace(".", "").replace(" ", "").isdecimal():
Expand All @@ -239,6 +168,7 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
"description": model_parameter_info["Comment"].values[0],
"units": {"expression": unit_text},
}
test_units.append((name, unit_text))
else:
parameter = {
"id": name,
Expand All @@ -247,31 +177,6 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
}
mira_parameters[name] = parameter_to_mira(parameter)

# add initials as parameters
# for name, param_val in state_initial_values.items():
# py_name = old_name_new_pyname_map.get(name)
# if py_name in concepts:
# param_name = str(mira_initials[py_name].expression)
# param_description = "Total {} count at timestep 0".format(py_name)
#
# if concepts[py_name].units:
# unit_text = str(concepts[py_name].units.expression).replace(
# " ", ""
# )
# parameter = {
# "id": param_name,
# "value": param_val,
# "description": param_description,
# "units": {"expression": unit_text},
# }
# else:
# parameter = {
# "id": param_name,
# "value": param_val,
# "description": param_description,
# }
# mira_parameters[param_name] = parameter_to_mira(parameter)

# construct transitions mapping that determine inputs and outputs states to a rate-law
transition_map = {}
auxiliaries = model_doc_df[model_doc_df["Type"] == "Auxiliary"]
Expand Down Expand Up @@ -348,13 +253,8 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
)
)

static_states = all_states - used_states
for state in static_states:
concepts = concepts[state].copy(deep=True)
templates.append(StaticConcept(subject=concepts))

tm_description = model_split_text[0].split("~")[1]
anns = Annotations(descriptin=tm_description)
anns = Annotations(description=tm_description)

return TemplateModel(
templates=templates,
Expand All @@ -364,11 +264,62 @@ def template_model_from_mdl_file_url(url) -> TemplateModel:
)


if __name__ == "__main__":
VENSIM_SIR_URL = (
"https://raw.githubusercontent.com/SDXorg/test-models/master/samples/SIR/SIR"
".mdl"
def state_to_concept(state) -> Concept:
"""Create a MIRA Concept from a state
Parameters
----------
state : pd.Series
The series that contains state data
Returns
-------
:
The MIRA concept created from the state
"""
name = state["Py Name"]
description = state["Comment"]
unit_dict = {
"expression": state["Units"].replace(" ", "")
if state["Units"]
else None
}
unit_expr = get_sympy(unit_dict, UNIT_SYMBOLS)
units_obj = Unit(expression=unit_expr) if unit_expr else None

return Concept(name=name, units=units_obj, description=description)


def process_expression_text(expr_text, symbols):
"""Create a sympy expression from a string expression using the supplied mapping of symbols
Parameters
----------
expr_text : str
The string expression
symbols : dict[str,sympy.Symbol]
A mapping of string symbol to a symbol in sympy
Returns
-------
: sympy.Expr
The sympy expression
"""
# strip leading and trailing white spaces
# remove spaces between operators and operands
# replace space between two words that makeup a variable name with "_"'
expr_text = (
expr_text.strip()
.replace(" * ", "*")
.replace(" - ", "-")
.replace(" / ", "/")
.replace(" + ", "+")
.replace("^", "**")
.replace(" ", "_")
.replace('"', "")
.lower()
)
vensim_tm_sir = template_model_from_mdl_file_url(VENSIM_SIR_URL)

print()
sympy_expr = safe_parse_expr(expr_text, symbols)
return sympy_expr
70 changes: 70 additions & 0 deletions mira/sources/system_dynamics/vensim.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
"""This module implements parsing Vensim models by Ventana Systems denoted by the .mdl file
and turning them into MIRA template models.
The documentation for vensim models is defined here:
https://www.vensim.com/documentation/sample_models.html
SIR mdl file example here: https://www.vensim.com/documentation/sample_models.html
"""

__all__ = ["template_model_from_mdl_file", "template_model_from_mdl_url"]

import tempfile

import pysd
from pysd.translators.vensim.vensim_file import VensimFile
import requests

from mira.metamodel import TemplateModel
from mira.sources.system_dynamics.parse_pysd_model import (
template_model_from_pysd_model,
)


def template_model_from_mdl_file(fname) -> TemplateModel:
"""Return a template model from a local Vensim file
Parameters
----------
fname : str
The path to the local Vensim file
Returns
-------
:
A MIRA template model
"""
pysd_model = pysd.read_vensim(fname)
vensim_file = VensimFile(fname)
return template_model_from_pysd_model(pysd_model, vensim_file.model_text)


def template_model_from_mdl_url(url) -> TemplateModel:
"""Return a template model from a Vensim file provided by an url
Parameters
----------
url : str
The url to the mdl file
Returns
-------
:
A MIRA Template Model
"""
data = requests.get(url).content
temp_file = tempfile.NamedTemporaryFile(
mode="w+b", suffix=".mdl", delete=False
)

with temp_file as file:
file.write(data)

pysd_model = pysd.read_vensim(temp_file.name)
vensim_file = VensimFile(temp_file.name)

return template_model_from_pysd_model(pysd_model, vensim_file.model_text)


if __name__ == "__main__":
template_model_from_mdl_url("https://raw.githubusercontent.com/SDXorg/test-models/master/samples/SIR/SIR.mdl")

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