Changeset 947 for framspy

Timestamp:

06/10/20 10:53:01 (4 years ago)

Author:

Maciej Komosinski

Message:

Added DETERMINISTIC boolean choice

File:

• framspy/FramsticksCLI.py (modified) (6 diffs)

framspy/FramsticksCLI.py

@@ -12 +12 @@
         You can perform basic operations like mutation, crossover, and evaluation of genotypes.
         This way you can perform evolution controlled by python, 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
@@ -18 +19 @@
 
         PRINT_FRAMSTICKS_OUTPUT: bool = False  # set to True for debugging
+        DETERMINISTIC: bool = False  # set to True to have the same results on each run
 
         GENO_SAVE_FILE_FORMAT = Enum('GENO_SAVE_FILE_FORMAT', 'NATIVEFRAMS RAWGENO')  # how to save genotypes
@@ -92 +94 @@
                 assert self.isValid("X[0:0],") == False
                 print('OK.')
-                self.child.sendline(self.RANDOMIZE_CMD)
+                if not self.DETERMINISTIC:
+                        self.child.sendline(self.RANDOMIZE_CMD)
                 self.child.sendline(self.SETEXPEDEF_CMD)
 
@@ -178 +181 @@
                 Returns:
                         Dictionary -- genotype evaluated with self.EVALUATE_COMMAND. Note that for whatever reason (e.g. incorrect genotype),
-                        the dictionary you get may be empty or partially empty and may not have the fields you expected, so handle this case
-                        properly.
+                        the dictionary you will get may be empty or partially empty and may not have the fields you expected, so handle such cases properly.
                 """
                 files = self.__runCommand(self.EVALUATE_CMD, [genotype], self.EVALUATE_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
@@ -212 +214 @@
                 with open(files[-1]) as f:
                         dissimilarity_matrix = np.genfromtxt(f, dtype=np.float64, comments='#', encoding=None, delimiter='\t')
-                # 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
-                # too complicated, so strings in column #1 become NaN as floats (unless they
-                # accidentally are numbers?) - not great, not terrible
+                # 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
+                # 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
                 EXPECTED_SHAPE = (2, 4)
                 assert dissimilarity_matrix.shape == EXPECTED_SHAPE, f"Not a correct dissimilarity matrix, expected {EXPECTED_SHAPE} "
@@ -249 +250 @@
 if __name__ == "__main__":
         # A demo run.
+
+        # TODO ideas:
+        # - check_validity with three levels (invalid, corrected, valid)
+        # - use threads for non-blocking reading from frams' stdout and thus not relying on specific strings printed by frams
+        # - a pool of binaries run at the same time, balance load - in particular evaluation
+        # - if we read genotypes in "org:" format anywhere: import https://pypi.org/project/framsreader/0.1.2/ and use it if successful,
+        #    if not then print a message "framsreader not available, using simple internal method to save a genotype" and proceed as it is now.
+        #    So far we don't read, but we should use the proper writer to handle all special cases like quoting etc.
+
         parsed_args = parseArguments()
         framsCLI = FramsticksCLI(parsed_args.path, parsed_args.exe)