def database(tmp_path):
params = pd.DataFrame()
params["name"] = list("abc")
database = prepare_database(
path=tmp_path / "test.db",
params=params,
dash_options={
"a": 3,
"no_browser": True
},
constraints=[{
"loc": "a",
"type": "increasing"
}],
optimization_status="success",
)
tables = ["params_history", "criterion_history", "timestamps"]
for i in range(10):
params = pd.Series(index=list("abc"), data=i)
critval = i**2
time = datetime(year=2020,
month=4,
day=9,
hour=12,
minute=41,
second=i)
rows = [params, {"value": critval}, {"value": time}]
upd_db.append_rows(database, tables, rows)
sleep(0.1)
return database
def wrapper_log_gradient(*args, **kwargs):
gradient = func(*args, **kwargs)
if database:
data = [dict(zip(names, gradient))]
append_rows(database, ["gradient_history"], data)
return gradient
def wrapper_log_evaluation(params, *args, **kwargs):
criterion_value, comparison_plot_data = func(
params, *args, **kwargs)
if database:
adj_params = params.copy().set_index("name")["value"]
cp_data = {"value": comparison_plot_data["value"].to_numpy()}
crit_val = {"value": criterion_value}
append_rows(database, tables, [adj_params, crit_val, cp_data])
return criterion_value
def database(tmp_path):
params = pd.DataFrame()
params["name"] = list("abc")
database = prepare_database(
path=tmp_path / "test.db",
params=params,
db_options={"a": 3},
optimization_status="success",
)
tables = ["params_history", "criterion_history"]
for i in range(10):
params = pd.Series(index=list("abc"), data=i)
critval = i ** 2
append_rows(database, tables, [params, {"value": critval}])
return database
def wrapper_handle_exceptions(x, *args, **kwargs):
try:
out = func(x, *args, **kwargs)
except (KeyboardInterrupt, SystemExit):
raise
except Exception as e:
# Adjust the criterion value at the start.
start_criterion_value = general_options[
"start_criterion_value"]
constant, slope = general_options.get(
"criterion_exception_penalty", (None, None))
constant = 2 * start_criterion_value if constant is None else constant
slope = 0.1 * start_criterion_value if slope is None else slope
raise_exc = general_options.get("criterion_exception_raise",
False)
if raise_exc:
raise e
else:
if database:
exception_info = traceback.format_exc()
p = reparametrize_from_internal(
internal=x,
fixed_values=params["_internal_fixed_value"].
to_numpy(),
pre_replacements=params["_pre_replacements"].
to_numpy().astype(int),
processed_constraints=constraints,
post_replacements=(params["_post_replacements"].
to_numpy().astype(int)),
processed_params=params,
)
msg = (exception_info + "\n\n" +
"The parameters are\n\n" +
p["value"].to_csv(sep="\t", header=True))
append_rows(database, "exceptions", {"value": msg})
out = min(
MAX_CRITERION_PENALTY,
constant + slope * np.linalg.norm(x - start_params),
)
return out
def prepare_database(
path,
params,
comparison_plot_data=None,
dash_options=None,
constraints=None,
optimization_status="scheduled",
gradient_status=0,
):
"""Return database metadata object with all relevant tables for the optimization.
This should always be used to create entirely new databases or to create the
tables needed during optimization in an existing database.
A new database is created if path does not exist yet. Otherwise the
existing database is loaded and all tables needed to log the optimization are
overwritten. Other tables remain unchanged.
The resulting database has the following tables:
- params_history: the complete history of parameters from the optimization. The
index column is "iteration", the remaining columns are parameter names taken
from params["name"].
- gradient_history: the complete history of gradient evaluations from the
optimization. Same columns as params_history.
- criterion_history: the complete history of criterion values from the optimization.
The index column is "iteration", the second column is "value".
- time_stamps: timestamps from the end of each criterion evaluation. Same columns as
criterion_history.
- convergence_history: the complete history of convergence criteria from the
optimization. The index column is "iteration", the other columns are "ftol",
"gtol" and "xtol".
- start_params: copy of user provided ``params``. This is not just the first entry
of params_history because it contains all columns and has a different index.
- optimization_status: table with one row and one column called "value" which takes
the values "scheduled", "running", "success" or "failure". Initialized to
``optimization_status``.
- gradient_status: table with one row and one column called "value" which
can be any float between 0 and 1 and indicates the progress of the gradient
calculation. Initialized to ``gradient_status``
- dash_options: table with one row and one column called "value". It contains
a dictionary with the dashboard options.
Internally this is a PickleType, so the dictionary must be pickle serializable.
Initialized to dash_options.
- exceptions: table with one column called "value" with exceptions.
- constraints: table with one row and one column called "value". It contains the
list of constraints. Internally this is a PickleType, so the list must be pickle
serializable.
Args:
path (str or pathlib.Path): location of the database file. If the file does
not exist, it will be created.
params (pd.DataFrame): see :ref:`params`.
comparison_plot_data : (numpy.ndarray or pandas.Series or pandas.DataFrame):
Contains the data for the comparison plot. Later updates will only deliver
the value column where as this input has an index and other invariant
information.
dash_options (dict): Dictionary with the dashboard options.
optimization_status (str): One of "scheduled", "running", "success", "failure".
gradient_status (float): Progress of gradient calculation between 0 and 1.
constraints (list): List of constraints.
Returns:
database (sqlalchemy.MetaData). The engine that connects
to the database can be accessed via ``database.bind``.
"""
gradient_status = float(gradient_status)
database = load_database(path)
opt_tables = [
"params_history",
"gradient_history",
"criterion_history",
"timestamps",
"convergence_history",
"start_params",
"comparison_plot",
"optimization_status",
"gradient_status",
"dash_options",
"exceptions",
"constraints",
]
for table in opt_tables:
if table in database.tables:
database.tables[table].drop(database.bind)
_define_table_formatted_with_params(database, params, "params_history")
_define_table_formatted_with_params(database, params, "gradient_history")
_define_fitness_history_table(database, "criterion_history")
_define_time_stamps_table(database)
_define_convergence_history_table(database)
_define_start_params_table(database)
_define_one_column_pickle_table(database, "comparison_plot")
_define_optimization_status_table(database)
_define_gradient_status_table(database)
_define_scalar_pickle_table(database, "dash_options")
_define_string_table(database, "exceptions")
_define_scalar_pickle_table(database, "constraints")
engine = database.bind
database.create_all(engine)
append_rows(database, "start_params", {"value": params})
append_rows(database, "optimization_status",
{"value": optimization_status})
append_rows(database, "gradient_status", {"value": gradient_status})
append_rows(database, "dash_options", {"value": dash_options})
append_rows(database, "constraints", {"value": constraints})
if comparison_plot_data is None:
comparison_plot_data = pd.DataFrame({"value": [np.nan]})
append_rows(database, "comparison_plot", {"value": comparison_plot_data})
return database