source: framspy/FramsticksCLI.py @ 1021

Last change on this file since 1021 was 1021, checked in by Maciej Komosinski, 6 days ago

Checking for genotype validity can now handle multiple genotypes at once

File size: 15.8 KB
Line 
1from subprocess import Popen, PIPE, check_output
2from enum import Enum
3from typing import List  # to be able to specify a type hint of list(something)
4from itertools import count  # for tracking multiple instances
5import json
6import sys, os
7import argparse
8import numpy as np
9
10
11class FramsticksCLI:
12        """Runs Framsticks CLI (command-line) executable and communicates with it using standard input and output.
13        You can perform basic operations like mutation, crossover, and evaluation of genotypes.
14        This way you can perform evolution controlled by python as well as access and manipulate genotypes.
15        You can even design and use in evolution your own genetic representation implemented entirely in python.
16
17        You need to provide one or two parameters when you run this class: the path to Framsticks CLI
18        and the name of the Framsticks CLI executable (if it is non-standard). See::
19                FramsticksCLI.py -h"""
20
21        PRINT_FRAMSTICKS_OUTPUT: bool = False  # set to True for debugging
22        DETERMINISTIC: bool = False  # set to True to have the same results on each run
23
24        GENO_SAVE_FILE_FORMAT = Enum('GENO_SAVE_FILE_FORMAT', 'NATIVEFRAMS RAWGENO')  # how to save genotypes
25        OUTPUT_DIR = "scripts_output"
26        STDOUT_ENDOPER_MARKER = "FileObject.write"  # we look for this message on Framsticks CLI stdout to detect when Framsticks created a file with the result we expect
27
28        FILE_PREFIX = 'framspy_'
29
30        RANDOMIZE_CMD = "Math.randomize();"
31        SETEXPEDEF_CMD = "Simulator.expdef=\"standard-eval\";"
32        GETSIMPLEST_CMD = "getsimplest"
33        GETSIMPLEST_FILE = "simplest.gen"
34        EVALUATE_CMD = "evaluate eval-allcriteria.sim"
35        EVALUATE_FILE = "genos_eval.json"
36        CROSSOVER_CMD = "crossover"
37        CROSSOVER_FILE = "child.gen"
38        DISSIMIL_CMD = "dissimil"
39        DISSIMIL_FILE = "dissimilarity_matrix.tsv"  # tab-separated values
40        ISVALID_CMD = "arevalid"
41        ISVALID_FILE = "validity.txt"
42        MUTATE_CMD = "mutate"
43        MUTATE_FILE = "mutant.gen"
44
45        CLI_INPUT_FILE = "genotypes.gen"
46
47        _next_instance_id = count(0)  # "static" counter incremented when a new instance is created. Used to ensure unique filenames for each instance.
48
49
50        def __init__(self, framspath, framsexe, pid=""):
51                self.pid = pid if pid is not None else ""
52                self.id = next(FramsticksCLI._next_instance_id)
53                self.frams_path = framspath
54                self.frams_exe = framsexe if framsexe is not None else 'frams.exe' if os.name == "nt" else 'frams.linux'
55                self.writing_path = None
56                mainpath = os.path.join(self.frams_path, self.frams_exe)
57                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)
58                exe_call_to_get_version = [mainpath, '-V']
59                exe_call_to_get_path = [mainpath, '-?']
60                try:
61                        print("\n".join(self.__readAllOutput(exe_call_to_get_version)))
62                        help = self.__readAllOutput(exe_call_to_get_path)
63                        for helpline in help:
64                                if 'dDIRECTORY' in helpline:
65                                        self.writing_path = helpline.split("'")[1]
66                except FileNotFoundError:
67                        print("Could not find Framsticks executable ('%s') in the given location ('%s')." % (self.frams_exe, self.frams_path))
68                        sys.exit(1)
69                print("Temporary files with results will be saved in detected writable working directory '%s'" % self.writing_path)
70                self.__spawnFramsticksCLI(exe_call)
71
72
73        def __readAllOutput(self, command):
74                frams_process = Popen(command, stdout=PIPE, stderr=PIPE, stdin=PIPE)
75                return [line.decode('utf-8').rstrip() for line in iter(frams_process.stdout.readlines())]
76
77
78        def __spawnFramsticksCLI(self, args):
79                # the child app (Framsticks CLI) should not buffer outputs and we need to immediately read its stdout, hence we use pexpect/wexpect
80                print('Spawning Framsticks CLI for continuous stdin/stdout communication... ', end='')
81                if os.name == "nt":  # Windows:
82                        import wexpect  # https://pypi.org/project/wexpect/
83                        # https://github.com/raczben/wexpect/tree/master/examples
84                        self.child = wexpect.spawn(' '.join(args))
85                else:
86                        import pexpect  # https://pexpect.readthedocs.io/en/stable/
87                        self.child = pexpect.spawn(' '.join(args))
88                self.child.setecho(False)  # ask the communication to not copy to stdout what we write to stdin
89                print('OK.')
90
91                self.__readFromFramsCLIUntil("UserScripts.autoload")
92                print('Performing a basic test 1/2... ', end='')
93                assert self.getSimplest("1") == "X"
94                print('OK.')
95                print('Performing a basic test 2/2... ', end='')
96                assert self.isValid(["X[0:0],", "X[0:0]", "X[1:0]"]) == [False, True, False]
97                print('OK.')
98                if not self.DETERMINISTIC:
99                        self.sendDirectCommand(self.RANDOMIZE_CMD)
100                self.sendDirectCommand(self.SETEXPEDEF_CMD)
101
102
103        def closeFramsticksCLI(self):
104                # End gracefully by sending end-of-file character: ^Z or ^D
105                # Without the -Q argument ("quiet mode"), Framsticks CLI would print "Shell closed." for goodbye.
106                self.child.sendline(chr(26 if os.name == "nt" else 4))
107
108
109        def __getPrefixedFilename(self, filename: str) -> str:
110                # Returns filename with unique instance id appended so there is no clash when many instances of this class use the same Framsticks CLI executable
111                return FramsticksCLI.FILE_PREFIX + self.pid + str(chr(ord('A') + self.id)) + '_' + filename
112
113
114        def __saveGenotypeToFile(self, genotype, name, mode, saveformat):
115                relname = self.__getPrefixedFilename(name)
116                absname = os.path.join(self.writing_path, relname)
117                if mode == 'd':  # special mode, 'delete'
118                        if os.path.exists(absname):
119                                os.remove(absname)
120                else:
121                        outfile = open(absname, mode)
122                        if saveformat == self.GENO_SAVE_FILE_FORMAT["RAWGENO"]:
123                                outfile.write(genotype)
124                        else:
125                                outfile.write("org:\n")
126                                outfile.write("genotype:~\n")
127                                outfile.write(genotype + "~\n\n")  # TODO proper quoting of special characters in genotype...
128                        outfile.close()
129                return relname, absname
130
131
132        def __readFromFramsCLIUntil(self, until_marker: str) -> str:
133                output = ""
134                while True:
135                        self.child.expect('\r\n' if os.name == "nt" else '\n')
136                        msg = str(self.child.before)
137                        if self.PRINT_FRAMSTICKS_OUTPUT or msg.startswith("[ERROR]") or msg.startswith("[CRITICAL]"):
138                                print(msg)
139                        if until_marker in msg:
140                                break
141                        else:
142                                output += msg + '\n'
143                return output
144
145
146        def __runCommand(self, command, genotypes, result_file_name, saveformat) -> List[str]:
147                filenames_rel = []  # list of file names with input data for the command
148                filenames_abs = []  # same list but absolute paths actually used
149                if saveformat == self.GENO_SAVE_FILE_FORMAT["RAWGENO"]:
150                        for i in range(len(genotypes)):
151                                # plain text format = must have a separate file for each genotype
152                                rel, abs = self.__saveGenotypeToFile(genotypes[i], "genotype" + str(i) + ".gen", "w", self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
153                                filenames_rel.append(rel)
154                                filenames_abs.append(abs)
155                elif saveformat == self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"]:
156                        self.__saveGenotypeToFile(None, self.CLI_INPUT_FILE, 'd', None)  # 'd'elete: ensure there is nothing left from the last run of the program because we "a"ppend to file in the loop below
157                        for i in range(len(genotypes)):
158                                rel, abs = self.__saveGenotypeToFile(genotypes[i], self.CLI_INPUT_FILE, "a", self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
159                        #  since we use the same file in the loop above, add this file only once (i.e., outside of the loop)
160                        filenames_rel.append(rel)
161                        filenames_abs.append(abs)
162
163                result_file_name = self.__getPrefixedFilename(result_file_name)
164                cmd = command + " " + " ".join(filenames_rel) + " " + result_file_name
165                self.child.sendline(cmd)
166                self.__readFromFramsCLIUntil(self.STDOUT_ENDOPER_MARKER)
167                filenames_abs.append(os.path.join(self.writing_path, self.OUTPUT_DIR, result_file_name))
168                return filenames_abs  # last element is a path to the file containing results
169
170
171        def __cleanUpCommandResults(self, filenames):
172                """Deletes files with results just created by the command."""
173                for name in filenames:
174                        os.remove(name)
175
176
177        sendDirectCommand_counter = count(0)  # an internal counter for the sendDirectCommand() method; should be static within that method but python does not allow
178
179
180        def sendDirectCommand(self, command: str) -> str:
181                """Sends any command to Framsticks CLI. Use when you know Framsticks and its scripting language, Framscript.
182
183                Returns:
184                        The output of the command, likely with extra \\n because for each entered command, Framsticks CLI responds with a (muted in Quiet mode) prompt and a \\n.
185                """
186                self.child.sendline(command.strip())
187                next(FramsticksCLI.sendDirectCommand_counter)
188                STDOUT_ENDOPER_MARKER = "uniqe-marker-" + str(FramsticksCLI.sendDirectCommand_counter)
189                self.child.sendline("Simulator.print(\"%s\");" % STDOUT_ENDOPER_MARKER)
190                return self.__readFromFramsCLIUntil(STDOUT_ENDOPER_MARKER)
191
192
193        def getSimplest(self, genetic_format) -> str:
194                assert len(genetic_format) == 1, "Genetic format should be a single character"
195                files = self.__runCommand(self.GETSIMPLEST_CMD + " " + genetic_format + " ", [], self.GETSIMPLEST_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
196                with open(files[-1]) as f:
197                        genotype = "".join(f.readlines())
198                self.__cleanUpCommandResults(files)
199                return genotype
200
201
202        def evaluate(self, genotype: str):
203                """
204                Returns:
205                        Dictionary -- genotype evaluated with self.EVALUATE_COMMAND. Note that for whatever reason (e.g. incorrect genotype),
206                        the dictionary you will get may be empty or partially empty and may not have the fields you expected, so handle such cases properly.
207                """
208                files = self.__runCommand(self.EVALUATE_CMD, [genotype], self.EVALUATE_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
209                with open(files[-1]) as f:
210                        data = json.load(f)
211                if len(data) > 0:
212                        self.__cleanUpCommandResults(files)
213                        return data
214                else:
215                        print("Evaluating genotype: no performance data was returned in", self.EVALUATE_FILE)  # we do not delete files here
216                        return None
217
218
219        def mutate(self, genotype: str) -> str:
220                """
221                Returns:
222                        The genotype of the mutated individual. Empty string if the mutation failed.
223                """
224                files = self.__runCommand(self.MUTATE_CMD, [genotype], self.MUTATE_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
225                with open(files[-1]) as f:
226                        newgenotype = "".join(f.readlines())
227                self.__cleanUpCommandResults(files)
228                return newgenotype
229
230
231        def crossOver(self, genotype_parent1: str, genotype_parent2: str) -> str:
232                """
233                Returns:
234                        The genotype of the offspring. Empty string if the crossing over failed.
235                """
236                files = self.__runCommand(self.CROSSOVER_CMD, [genotype_parent1, genotype_parent2], self.CROSSOVER_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
237                with open(files[-1]) as f:
238                        child_genotype = "".join(f.readlines())
239                self.__cleanUpCommandResults(files)
240                return child_genotype
241
242
243        def dissimilarity(self, genotype_list: List[str]) -> np.ndarray:
244                """
245                Returns:
246                        A square array with dissimilarities of each pair of genotypes.
247                """
248                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
249                files = self.__runCommand(self.DISSIMIL_CMD, genotype_list, self.DISSIMIL_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
250                with open(files[-1]) as f:
251                        dissimilarity_matrix = np.genfromtxt(f, dtype=np.float64, comments='#', encoding=None, delimiter='\t')
252                # We would like to skip column #1 while reading and read everything else, but... https://stackoverflow.com/questions/36091686/exclude-columns-from-genfromtxt-with-numpy
253                # This would be too complicated, so strings (names) in column #1 become NaN as floats (unless they accidentally are valid numbers) - not great, not terrible
254                square_matrix = dissimilarity_matrix[:, 2:]  # get rid of two first columns (fitness and name)
255                EXPECTED_SHAPE = (len(genotype_list), len(genotype_list))
256                # print(square_matrix)
257                assert square_matrix.shape == EXPECTED_SHAPE, f"Not a correct dissimilarity matrix, expected {EXPECTED_SHAPE} "
258                for i in range(len(square_matrix)):
259                        assert square_matrix[i][i] == 0, "Not a correct dissimilarity matrix, diagonal expected to be 0"
260                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
261                self.__cleanUpCommandResults(files)
262                return square_matrix
263
264
265        def isValid(self, genotype_list: List[str]) -> List[bool]:
266                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
267                files = self.__runCommand(self.ISVALID_CMD, genotype_list, self.ISVALID_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
268                valid = []
269                with open(files[-1]) as f:
270                        for line in f:
271                                valid.append(line.strip() == "1")
272                self.__cleanUpCommandResults(files)
273                assert len(genotype_list) == len(valid), "Submitted %d genotypes, received %d validity values" % (len(genotype_list), len(valid))
274                return valid
275
276
277def parseArguments():
278        parser = argparse.ArgumentParser(description='Run this program with "python -u %s" if you want to disable buffering of its output.' % sys.argv[0])
279        parser.add_argument('-path', type=ensureDir, required=True, help='Path to Framsticks CLI without trailing slash.')
280        parser.add_argument('-exe', required=False, help='Executable name. If not given, "frams.exe" or "frams.linux" is assumed.')
281        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.')
282        parser.add_argument('-pid', required=False, help='Unique ID of this process. Only relevant when you run multiple instances of this class simultaneously but as separate processes, and they use the same Framsticks CLI executable. This value will be appended to the names of created files to avoid conflicts.')
283        return parser.parse_args()
284
285
286def ensureDir(string):
287        if os.path.isdir(string):
288                return string
289        else:
290                raise NotADirectoryError(string)
291
292
293if __name__ == "__main__":
294        # A demo run.
295
296        # TODO ideas:
297        # - check_validity with three levels (invalid, corrected, valid)
298        # - "vectorize" some operations (isvalid, evaluate) so that a number of genotypes is handled in one call
299        # - use threads for non-blocking reading from frams' stdout and thus not relying on specific strings printed by frams
300        # - a pool of binaries run at the same time, balance load - in particular evaluation
301        # - if we read genotypes in "org:" format anywhere: import https://pypi.org/project/framsreader/0.1.2/ and use it if successful,
302        #    if not then print a message "framsreader not available, using simple internal method to save a genotype" and proceed as it is now.
303        #    So far we don't read, but we should use the proper writer to handle all special cases like quoting etc.
304
305        parsed_args = parseArguments()
306        framsCLI = FramsticksCLI(parsed_args.path, parsed_args.exe, parsed_args.pid)
307
308        print("Sending a direct command to Framsticks CLI that calculates \"4\"+2 yields", repr(framsCLI.sendDirectCommand("Simulator.print(\"4\"+2);")))
309
310        simplest = framsCLI.getSimplest('1' if parsed_args.genformat is None else parsed_args.genformat)
311        print("\tSimplest genotype:", simplest)
312        parent1 = framsCLI.mutate(simplest)
313        parent2 = parent1
314        MUTATE_COUNT = 10
315        for x in range(MUTATE_COUNT):  # example of a chain of 20 mutations
316                parent2 = framsCLI.mutate(parent2)
317        print("\tParent1 (mutated simplest):", parent1)
318        print("\tParent2 (Parent1 mutated %d times):" % MUTATE_COUNT, parent2)
319        offspring = framsCLI.crossOver(parent1, parent2)
320        print("\tCrossover (Offspring):", offspring)
321        print('\tDissimilarity of Parent1 and Offspring:', framsCLI.dissimilarity([parent1, offspring])[0, 1])
322        print('\tPerformance of Offspring:', framsCLI.evaluate(offspring))
323        print('\tValidity of Parent1, Parent 2, and Offspring:', framsCLI.isValid([parent1, parent2, offspring]))
324
325        framsCLI.closeFramsticksCLI()
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