source: framspy/FramsticksLib.py @ 1078

from typing import List  # to be able to specify a type hint of list(something)
import json
import sys, os
import argparse
import numpy as np
import frams


class FramsticksLib:
        """Communicates directly with Framsticks DLL/SO.
        You can perform basic operations like mutation, crossover, and evaluation of genotypes.
        This way you can perform evolution controlled by python as well as access and manipulate genotypes.
        You can even design and use in evolution your own genetic representation implemented entirely in python.

        You need to provide one or two parameters when you run this class: the path to Framsticks CLI where .dll/.so resides
        and the name of the Framsticks dll/so (if it is non-standard). See::
                FramsticksLib.py -h"""

        DETERMINISTIC: bool = False  # set to True to have the same results in each run

        GENOTYPE_INVALID = "/*invalid*/"  # this is how genotype invalidity is represented in Framsticks
        EVALUATION_SETTINGS_FILE = "eval-allcriteria.sim"  # MUST be compatible with standard-eval expdef


        def __init__(self, framspath, framsexe, pid=""):
                self.pid = pid if pid is not None else ""
                self.frams_path = framspath
                self.frams_exe = framsexe if framsexe is not None else 'frams.exe' if os.name == "nt" else 'frams.linux'
                self.writing_path = None
                mainpath = os.path.join(self.frams_path, self.frams_exe)
                # exe_call = [mainpath, '-Q', '-s', '-c', '-icliutils.ini']  # -c will be ignored in Windows Framsticks (this option is meaningless because the Windows version does not support color console, so no need to deactivate this feature using -c)
                # exe_call_to_get_version = [mainpath, '-V']
                # exe_call_to_get_path = [mainpath, '-?']

                frams.init(framspath, "-Ddata")  # "-D"+os.path.join(framspath,"data")) # not possible (maybe python windows issue) because of the need for os.chdir(). So we assume "data" is where the dll/so is

                print('Available objects:', dir(frams))
                print()

                self.__spawnFramsticksCLI()


        def __spawnFramsticksCLI(self):
                print('Performing a basic test 1/2... ', end='')
                simplest = self.getSimplest("1")
                assert simplest == "X" and type(simplest) is str
                print('OK.')
                print('Performing a basic test 2/2... ', end='')
                assert self.isValid(["X[0:0],", "X[0:0]", "X[1:0]"]) == [False, True, False]
                print('OK.')
                if not self.DETERMINISTIC:
                        frams.Math.randomize();
                frams.Simulator.expdef = "standard-eval"  # this expdef must be used by EVALUATION_SETTINGS_FILE


        def getSimplest(self, genetic_format) -> str:
                return frams.GenMan.getSimplest(genetic_format).genotype._string()


        def evaluate(self, genotype_list: List[str]):
                """
                Returns:
                        List of dictionaries containing the performance of genotypes evaluated using self.EVALUATION_SETTINGS_FILE.
                        Note that for whatever reason (e.g. incorrect genotype), the dictionaries you will get may be empty or
                        partially empty and may not have the fields you expected, so handle such cases properly.
                """
                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity

                # TODO use Logger to mute stdout (optinally just like in FramsticksCLI.py)
                frams.GenePools[0].clear()
                frams.Simulator.ximport(self.EVALUATION_SETTINGS_FILE, 2 + 4 + 8 + 16)
                for g in genotype_list:
                        frams.GenePools[0].add(g)
                frams.ExpProperties.evalsavefile = ""  # no need to store results in a file - we will get evaluations directly from Genotype's "data" field
                frams.Simulator.init()
                frams.Simulator.start()
                step = frams.Simulator.step  # cache reference to avoid repeated lookup in the loop
                while frams.Simulator.running._int():  # standard-eval.expdef sets running to 0 when the evaluation is complete
                        step()

                results = []
                for g in frams.GenePools[0]:
                        serialized_dict = frams.String.serialize(g.data[frams.ExpProperties.evalsavedata._value()])
                        evaluations = json.loads(serialized_dict._string())
                        # now, for consistency with FramsticksCLI.py, add "num" and "name" keys that are missing because we got data directly from Genotype, not from the file produced by standard-eval.expdef's function printStats(). What we do below is what printStats() does.
                        result = {"num": g.num._value(), "name": g.name._value(), "evaluations": evaluations}
                        results.append(result)

                return results


        def mutate(self, genotype_list: List[str]) -> List[str]:
                """
                Returns:
                        The genotype(s) of the mutated source genotype(s). self.GENOTYPE_INVALID for genotypes whose mutation failed (for example because the source genotype was invalid).
                """
                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity

                mutated = []
                for g in genotype_list:
                        mutated.append(frams.GenMan.mutate(frams.Geno.newFromString(g)).genotype._string())
                assert len(genotype_list) == len(mutated), "Submitted %d genotypes, received %d validity values" % (len(genotype_list), len(mutated))
                return mutated


        def crossOver(self, genotype_parent1: str, genotype_parent2: str) -> str:
                """
                Returns:
                        The genotype of the offspring. self.GENOTYPE_INVALID if the crossing over failed.
                """
                return frams.GenMan.crossOver(frams.Geno.newFromString(genotype_parent1), frams.Geno.newFromString(genotype_parent2)).genotype._string()


        def dissimilarity(self, genotype_list: List[str]) -> np.ndarray:
                """
                Returns:
                        A square array with dissimilarities of each pair of genotypes.
                """
                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity

                frams.SimilMeasure.type = 1  # adjust to your needs. Set here because loading EVALUATION_SETTINGS_FILE during evaluation may overwrite these parameters
                frams.SimilMeasureHungarian.simil_weightedMDS = 1
                frams.SimilMeasureHungarian.simil_partgeom = 1

                n = len(genotype_list)
                square_matrix = np.zeros((n, n))
                genos = []  # prepare an array of Geno objects so we don't need to convert raw strings to Geno objects all the time
                for g in genotype_list:
                        genos.append(frams.Geno.newFromString(g))
                for i in range(n):
                        for j in range(n):  # maybe calculate only one triangle if you really need a 2x speedup
                                square_matrix[i][j] = frams.SimilMeasure.evaluateDistance(genos[i], genos[j])._double()

                for i in range(n):
                        assert square_matrix[i][i] == 0, "Not a correct dissimilarity matrix, diagonal expected to be 0"
                assert (square_matrix == square_matrix.T).all(), "Probably not a correct dissimilarity matrix, expecting symmetry, verify this"  # could introduce tolerance in comparison (e.g. class field DISSIMIL_DIFF_TOLERANCE=10^-5) so that miniscule differences do not fail here
                return square_matrix


        def isValid(self, genotype_list: List[str]) -> List[bool]:
                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity
                valid = []
                for g in genotype_list:
                        valid.append(frams.Geno.newFromString(g).is_valid._int() == 1)
                assert len(genotype_list) == len(valid), "Submitted %d genotypes, received %d validity values" % (len(genotype_list), len(valid))
                return valid


def parseArguments():
        parser = argparse.ArgumentParser(description='Run this program with "python -u %s" if you want to disable buffering of its output.' % sys.argv[0])
        parser.add_argument('-path', type=ensureDir, required=True, help='Path to Framsticks CLI without trailing slash.')
        parser.add_argument('-exe', required=False, help='Library name. If not given, "frams.dll" or "frams.so" is assumed depending on the platform.')  # TODO dll,so, allow to change name?
        parser.add_argument('-genformat', required=False, help='Genetic format for the demo run, for example 4, 9, or S. If not given, f1 is assumed.')
        return parser.parse_args()


def ensureDir(string):
        if os.path.isdir(string):
                return string
        else:
                raise NotADirectoryError(string)


if __name__ == "__main__":
        # A demo run.

        # TODO ideas:
        # - check_validity with three levels (invalid, corrected, valid)
        # - a pool of binaries running simultaneously, balance load - in particular evaluation

        parsed_args = parseArguments()
        framsDLL = FramsticksLib(parsed_args.path, parsed_args.exe, None)  # parsed_args.pid)

        print("Sending a direct command to Framsticks CLI that calculates \"4\"+2 yields", frams.Simulator.eval("return \"4\"+2;"))

        simplest = framsDLL.getSimplest('1' if parsed_args.genformat is None else parsed_args.genformat)
        print("\tSimplest genotype:", simplest)
        parent1 = framsDLL.mutate([simplest])[0]
        parent2 = parent1
        MUTATE_COUNT = 10
        for x in range(MUTATE_COUNT):  # example of a chain of 10 mutations
                parent2 = framsDLL.mutate([parent2])[0]
        print("\tParent1 (mutated simplest):", parent1)
        print("\tParent2 (Parent1 mutated %d times):" % MUTATE_COUNT, parent2)
        offspring = framsDLL.crossOver(parent1, parent2)
        print("\tCrossover (Offspring):", offspring)
        print('\tDissimilarity of Parent1 and Offspring:', framsDLL.dissimilarity([parent1, offspring])[0, 1])
        print('\tPerformance of Offspring:', framsDLL.evaluate([offspring]))
        print('\tValidity of Parent1, Parent 2, and Offspring:', framsDLL.isValid([parent1, parent2, offspring]))