PhoenicsParseError: 'parameters'

[comnGuy]

Hi,

I tried to execute an example of your repository, e.g. Sequential optimization. I run into the following error.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/site-packages/phoenics/utilities/decorators.py", line 36, in wrapper
    function(*args, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/phoenics/utilities/config_parser.py", line 368, in parse_config_file
    self._parse(self.config_dict)
  File "/opt/conda/lib/python3.7/site-packages/phoenics/utilities/config_parser.py", line 356, in _parse
    self._parse_parameters(self.config['parameters'])

PhoenicsParseError: 'parameters'

It looks like that the error has something to do with config.json.

Steps

1. I used the image docker pull jupyter/datascience-notebook
2. Cloned your repository.
3. Navigated to phoenics/examples/optimization_sequential/
4. python optimize_branin.py

Container Information

• Ubuntu 18.04.4 LTS
• Python 3.7.6
• GCC 7.3.0

Thanks!

If you need additional information, let me know.

Best Regards
Bernhard

[FreakyJ]

I've got it working using this config file:

{
	"general": {
		"num_batches": 1,
		"batch_size":  2,
		"backend": "tfprob",
		"parallel_evaluations": "True"
	},
	"parameters": [{"name": "param_0", "type": "continuous", "low":  -4.0, "high": 4.0, "size": 1},
				  {"name": "param_1", "type": "continuous", "low": -4.0, "high":  4.0, "size": 1}],
	"objectives": [{"name": "obj_0", "goal": "minimize", "hierarchy": 0, "tolerance": 0.2}, 
				   {"name": "obj_1", "goal": "maximize", "hierarchy": 1, "tolerance": 0.2}]
}

However, the rest of the example code seems to be out of dated, too,

import sys 
sys.path.append('../../phoenics')
import pickle
from phoenics import Phoenics 
import numpy as np

def fonseca(params):
    vector = np.array([params[key_name][0] for key_name in ['param_0', 'param_1']])
    obj_0  = 1 - np.exp( - np.sum((vector - 1. / np.sqrt(len(vector)))**2))
    obj_1  = 1 - np.exp( - np.sum((vector + 1. / np.sqrt(len(vector)))**2))
    params['obj_0'] = obj_0
    params['obj_1'] = obj_1
    return params


class OptimizationManager(object):

    def __init__(self, config_file, loss_function):

        # creates instance of Phoenics optimizer
        self.phoenics      = Phoenics(config_file)
        self.loss_function = loss_function 


    def optimize(self, max_iter = 100):

        observations = []

        for num_iter in range(max_iter):

            # query for new parameters based on prior observations
            params = self.phoenics.recommend(observations = observations)
            print('LEN_PARAMS', len(params))

            # use parameters for evaluation ...
            # ... experimentally or computationally
            for param in params:
                observation = self.loss_function(param)
                observations.append(observation)

            # log observations in a pickle file for future analysis
            pickle.dump(observations, open('observations.pkl', 'wb'))

            # print observations to file 
            logfile = open('logfile.dat', 'a')
            for param in params:
                new_line = ''
                for var_name in sorted(self.phoenics.config.parameters.name):
                    for param_value in param[var_name]:
                        new_line += '%.5e\t' % (param[var_name])
                for obj_name in sorted(self.phoenics.config.objectives.name):
                    new_line += '%.5e\t' % (param[obj_name])
                logfile.write(new_line + '\n')
            logfile.close()

#========================================================================

if __name__ == '__main__':

    logfile = open('config.json', 'r')
    print(logfile.read())
    logfile.close()

    manager = OptimizationManager('config.json', fonseca)
    manager.optimize()

[FreakyJ]

And you can plot it like this:

import pandas as pd
import matplotlib.pyplot as plt

observations = pickle.load(open('observations.pkl', 'rb'))
df_observations = pd.DataFrame(observations)

fig = plt.figure(figsize=[10, 10])
ax = fig.add_subplot(111, projection='3d')
ax.scatter(df_observations["param_0"], df_observations["param_1"], df_observations["obj_0"], zdir='z', s=20, c=None, depthshade=True)
ax.scatter(df_observations["param_0"], df_observations["param_1"], df_observations["obj_1"], zdir='z', s=20, c=None, depthshade=True)

[FreakyJ]

And in case you would like to plot the "problem"

import pandas as pd
import matplotlib.pyplot as plt

df_params = pd.DataFrame({'x': [], 'y': [], 'obj_0': [], 'obj_1': []})
for x in range(-400, 400, 10):
    for y in range(-400, 400, 10):
        res = fonseca({"param_0": [x/100], "param_1": [y/100]})
        df_params = df_params.append({'x': x/100, 'y': y/100, 'obj_0': res["obj_0"], 'obj_1': res["obj_1"]}, ignore_index=True)
        

fig = plt.figure(figsize=[10, 10])
ax = fig.add_subplot(111, projection='3d')
ax.scatter(df_params["x"], df_params["y"], df_params["obj_0"], zdir='z', s=20, c=None, depthshade=True)
ax.scatter(df_params["x"], df_params["y"], df_params["obj_1"], zdir='z', s=20, c=None, depthshade=True)

[rikoimade]

I tried to run with the following config file (basically replacing 'variables' key with 'parameters' key:

{
"general": {
"num_batches": 1,
"batch_size": 1,
"backend": "tfprob",
"parallel_evaluations": "True"
},
"parameters": [{"x": {"low": -5.0, "high": 10.0, "type": "float", "size": 1}},
{"y": {"low": 0.0, "high": 15.0, "type": "float", "size": 1}}],
"objectives": [{"branin": {"hierarchy": 0, "type": "minimum", "tolerance": 0.0}}]
}

and I get another error about 'size'

from phoenics import Phoenics
phoenics = Phoenics('config.json')
Traceback (most recent call last):
File "C:\Users\xxx\anaconda3\envs\chimera\lib\site-packages\phoenics\utilities\decorators.py", line 36, in wrapper
function(*args, **kwargs)
File "C:\Users\xxx\anaconda3\envs\chimera\lib\site-packages\phoenics\utilities\config_parser.py", line 369, in parse_config_file
self._parse(self.config_dict)
File "C:\Users\xxx\anaconda3\envs\chimera\lib\site-packages\phoenics\utilities\config_parser.py", line 356, in _parse
self._parse_parameters(self.config['parameters'])
File "C:\Users\xxx\anaconda3\envs\chimera\lib\site-packages\phoenics\utilities\config_parser.py", line 139, in _parse_parameters
size = setting['size']

←[0;31mPhoenicsParseError: 'size'←[0m