new folder for saving the experimental data

experiments/{my_experiment}/data/{experiment_name}/{run}/

Author: portaloffreedom

experiments/examples/consolidate_experiments.py

@@ -1,13 +1,14 @@
 import os
 
 # set these variables according to your experiments #
-dirpath = '../'
+dirpath = 'data'
 experiments_type = [
                     'default_experiment'
                     ]
 runs = 1
 # set these variables according to your experiments #
 
+
 def build_headers(path):
 
     print(path + "/all_measures.txt")
@@ -36,11 +37,12 @@ def build_headers(path):
 
     return behavior_headers, phenotype_headers
 
+
 for exp in experiments_type:
     for run in range(1, runs+1):
 
         print(exp, run)
-        path = dirpath + str(exp) + '_' + str(run)
+        path = os.path.join(dirpath, str(exp), str(run))
         behavior_headers, phenotype_headers = build_headers(path)
 
         file_summary = open(path + "/all_measures.tsv", "a")

experiments/karines_experiments/consolidate_experiments.py

@@ -2,14 +2,15 @@
 
 
 # set these variables according to your experiments #
-dirpath = 'data/'
+dirpath = 'data'
 experiments_type = [
                     'plane',
                     'lava'
                     ]
 runs = 10
 # set these variables according to your experiments #
 
+
 def build_headers(path):
 
     print(path + "/all_measures.txt")
@@ -38,11 +39,12 @@ def build_headers(path):
 
     return behavior_headers, phenotype_headers
 
+
 for exp in experiments_type:
     for run in range(1, runs+1):
 
         print(exp, run)
-        path = dirpath + str(exp) + '_' + str(run)
+        path = os.path.join(dirpath, str(exp), str(run))
         behavior_headers, phenotype_headers = build_headers(path)
 
         file_summary = open(path + "/all_measures.tsv", "a")

experiments/karines_experiments/stuck-experiments_watchman.py

@@ -21,7 +21,7 @@
     for exp in experiments_names:
         for run in range(0, runs):
 
-            path = dir_path + "/" + exp +'_'+str(run+1) + "/data_fullevolution/fitness"
+            path = os.path.join(dir_path, exp, str(run+1), 'data_fullevolution', 'fitness')
             time_now = datetime.now()
             time_ago = time_now - timedelta(minutes=limit_of_minutes)
 

pyrevolve/evolution/population.py

@@ -89,26 +89,26 @@ def _new_individual(self, genotype):
         individual.develop()
         self.conf.experiment_management.export_genotype(individual)
         self.conf.experiment_management.export_phenotype(individual)
-        self.conf.experiment_management.export_phenotype_images('data_fullevolution/phenotype_images', individual)
-        individual.phenotype.measure_phenotype(self.conf.experiment_name)
-        individual.phenotype.export_phenotype_measurements(self.conf.experiment_name)
+        self.conf.experiment_management.export_phenotype_images(os.path.join('data_fullevolution', 'phenotype_images'), individual)
+        individual.phenotype.measure_phenotype()
+        individual.phenotype.export_phenotype_measurements(self.conf.experiment_management.data_folder)
 
         return individual
 
     async def load_individual(self, id):
-        path = 'experiments/'+self.conf.experiment_name
+        data_path = self.conf.experiment_management.data_folder
         genotype = self.conf.genotype_constructor(self.conf.genotype_conf, id)
-        genotype.load_genotype(f'{path}/data_fullevolution/genotypes/genotype_{id}.txt')
+        genotype.load_genotype(os.path.join(data_path, 'genotypes', f'genotype_{id}.txt'))
 
         individual = Individual(genotype)
         individual.develop()
-        individual.phenotype.measure_phenotype(self.conf.experiment_name)
+        individual.phenotype.measure_phenotype()
 
-        with open(os.path.join(path, 'data_fullevolution', 'fitness', f'fitness_{id}.txt')) as f:
+        with open(os.path.join(data_path, 'fitness', f'fitness_{id}.txt')) as f:
             data = f.readlines()[0]
             individual.fitness = None if data == 'None' else float(data)
 
-        with open(os.path.join(path, 'data_fullevolution', 'descriptors', f'behavior_desc_{id}.txt')) as f:
+        with open(os.path.join(data_path, 'descriptors', f'behavior_desc_{id}.txt')) as f:
             lines = f.readlines()
             if lines[0] == 'None':
                 individual.phenotype._behavioural_measurements = None
@@ -135,8 +135,8 @@ async def load_snapshot(self, gen_num):
         Recovers all genotypes and fitnesses of robots in the lastest selected population
         :param gen_num: number of the generation snapshot to recover
         """
-        path = 'experiments/'+self.conf.experiment_name
-        for r, d, f in os.walk(path +'/selectedpop_'+str(gen_num)):
+        data_path = self.conf.experiment_management.experiment_folder
+        for r, d, f in os.walk(data_path +'/selectedpop_'+str(gen_num)):
             for file in f:
                 if 'body' in file:
                     id = file.split('.')[0].split('_')[-2]+'_'+file.split('.')[0].split('_')[-1]

pyrevolve/experiment_management.py

@@ -10,45 +10,49 @@ class ExperimentManagement:
 
     def __init__(self, settings):
         self.settings = settings
-        self.dirpath = os.path.join('experiments', self.settings.experiment_name)
+        manager_folder = os.path.dirname(self.settings.manager)
+        self._experiment_folder = os.path.join(manager_folder, 'data', self.settings.experiment_name, self.settings.run)
+        self._data_folder = os.path.join(self._experiment_folder, 'data_fullevolution')
 
     def create_exp_folders(self):
-        if os.path.exists(self.dirpath):
-            shutil.rmtree(self.dirpath)
-        os.mkdir(self.dirpath)
-        os.mkdir(self.dirpath+'/data_fullevolution')
-        os.mkdir(self.dirpath+'/data_fullevolution/genotypes')
-        os.mkdir(self.dirpath+'/data_fullevolution/phenotypes')
-        os.mkdir(self.dirpath+'/data_fullevolution/descriptors')
-        os.mkdir(self.dirpath+'/data_fullevolution/fitness')
-        os.mkdir(self.dirpath+'/data_fullevolution/phenotype_images')
-        os.mkdir(self.dirpath+'/data_fullevolution/failed_eval_robots')
-
-    def _experiment_folder(self):
-        return self.dirpath
-
-    def _data_folder(self):
-        return os.path.join(self.dirpath, 'data_fullevolution')
+        if os.path.exists(self.experiment_folder):
+            shutil.rmtree(self.experiment_folder)
+        os.makedirs(self.experiment_folder)
+        os.mkdir(self.data_folder)
+        os.mkdir(os.path.join(self.data_folder, 'genotypes'))
+        os.mkdir(os.path.join(self.data_folder, 'phenotypes'))
+        os.mkdir(os.path.join(self.data_folder, 'descriptors'))
+        os.mkdir(os.path.join(self.data_folder, 'fitness'))
+        os.mkdir(os.path.join(self.data_folder, 'phenotype_images'))
+        os.mkdir(os.path.join(self.data_folder, 'failed_eval_robots'))
+
+    @property
+    def experiment_folder(self):
+        return self._experiment_folder
+
+    @property
+    def data_folder(self):
+        return self._data_folder
 
     def export_genotype(self, individual):
         if self.settings.recovery_enabled:
-            individual.export_genotype(self._data_folder())
+            individual.export_genotype(self.data_folder)
 
     def export_phenotype(self, individual):
         if self.settings.export_phenotype:
-            individual.export_phenotype(self._data_folder())
+            individual.export_phenotype(self.data_folder)
 
     def export_fitnesses(self, individuals):
-        folder = self._data_folder()
+        folder = self.data_folder
         for individual in individuals:
             individual.export_fitness(folder)
 
     def export_fitness(self, individual):
-        folder = os.path.join(self._data_folder(),'fitness')
+        folder = os.path.join(self.data_folder, 'fitness')
         individual.export_fitness(folder)
 
     def export_behavior_measures(self, _id, measures):
-        filename = os.path.join(self._data_folder(), 'descriptors', f'behavior_desc_{_id}.txt')
+        filename = os.path.join(self.data_folder, 'descriptors', f'behavior_desc_{_id}.txt')
         with open(filename, "w") as f:
             if measures is None:
                 f.write(str(None))
@@ -57,17 +61,17 @@ def export_behavior_measures(self, _id, measures):
                     f.write(f"{key} {val}\n")
 
     def export_phenotype_images(self, dirpath, individual):
-        individual.phenotype.render_body(self._experiment_folder() +'/'+dirpath+f'/body_{individual.phenotype.id}.png')
-        individual.phenotype.render_brain(self._experiment_folder() +'/'+dirpath+f'/brain_{individual.phenotype.id}')
+        individual.phenotype.render_body(os.path.join(self.experiment_folder, dirpath, f'body_{individual.phenotype.id}.png'))
+        individual.phenotype.render_brain(os.path.join(self.experiment_folder, dirpath, f'brain_{individual.phenotype.id}.png'))
 
     def export_failed_eval_robot(self, individual):
-        individual.genotype.export_genotype(f'{self._data_folder()}/failed_eval_robots/genotype_{str(individual.phenotype.id)}.txt')
-        individual.phenotype.save_file(f'{self._data_folder()}/failed_eval_robots/phenotype_{str(individual.phenotype.id)}.yaml')
-        individual.phenotype.save_file(f'{self._data_folder()}/failed_eval_robots/phenotype_{str(individual.phenotype.id)}.sdf', conf_type='sdf')
+        individual.genotype.export_genotype(os.path.join(self.data_folder, 'failed_eval_robots', f'genotype_{individual.phenotype.id}.txt'))
+        individual.phenotype.save_file(os.path.join(self.data_folder, 'failed_eval_robots', f'phenotype_{individual.phenotype.id}.yaml'))
+        individual.phenotype.save_file(os.path.join(self.data_folder, 'failed_eval_robots', f'phenotype_{individual.phenotype.id}.sdf'), conf_type='sdf')
 
     def export_snapshots(self, individuals, gen_num):
         if self.settings.recovery_enabled:
-            path = os.path.join(self._experiment_folder(), f'selectedpop_{gen_num}')
+            path = os.path.join(self.experiment_folder, f'selectedpop_{gen_num}')
             if os.path.exists(path):
                 shutil.rmtree(path)
             os.mkdir(path)
@@ -76,9 +80,9 @@ def export_snapshots(self, individuals, gen_num):
             logger.info(f'Exported snapshot {str(gen_num)} with {str(len(individuals))} individuals')
 
     def experiment_is_new(self):
-        if not os.path.exists(self._experiment_folder()):
+        if not os.path.exists(self.experiment_folder):
             return True
-        path, dirs, files = next(os.walk(os.path.join(self._data_folder(), 'fitness')))
+        path, dirs, files = next(os.walk(os.path.join(self.data_folder, 'fitness')))
         if len(files) == 0:
             return True
         else:
@@ -87,10 +91,10 @@ def experiment_is_new(self):
     def read_recovery_state(self, population_size, offspring_size):
         snapshots = []
 
-        for r, d, f in os.walk(self._experiment_folder()):
+        for r, d, f in os.walk(self.experiment_folder):
             for dir in d:
                 if 'selectedpop' in dir:
-                    exported_files = len([name for name in os.listdir(os.path.join(self._experiment_folder(), dir)) if os.path.isfile(os.path.join(self._experiment_folder(), dir, name))])
+                    exported_files = len([name for name in os.listdir(os.path.join(self.experiment_folder, dir)) if os.path.isfile(os.path.join(self.experiment_folder, dir, name))])
                     if exported_files == (population_size * 2): # body and brain files
                         snapshots.append(int(dir.split('_')[1]))
 
@@ -104,7 +108,7 @@ def read_recovery_state(self, population_size, offspring_size):
             n_robots = 0
 
         robot_ids = []
-        for r, d, f in os.walk(os.path.join(self._data_folder(), 'fitness')):
+        for r, d, f in os.walk(os.path.join(self.data_folder, 'fitness')):
             for file in f:
                 robot_ids.append(int(file.split('.')[0].split('_')[-1]))
         last_id = np.sort(robot_ids)[-1]

pyrevolve/revolve_bot/revolve_bot.py

@@ -68,7 +68,7 @@ def measure_behaviour(self):
         """
         pass
 
-    def measure_phenotype(self, experiment_name):
+    def measure_phenotype(self):
         self._morphological_measurements = self.measure_body()
         self._brain_measurements = self.measure_brain()
         logger.info('Robot ' + str(self.id) + ' was measured.')
@@ -86,14 +86,13 @@ def measure_body(self):
         except Exception as e:
             logger.exception('Failed measuring body')
 
-    def export_phenotype_measurements(self, path):
-        with open('experiments/' + path + '/data_fullevolution/descriptors/'
-                  + 'phenotype_desc_' + str(self.id) + '.txt', 'w+') as file:
-            # TODO this crashes
+    def export_phenotype_measurements(self, data_path):
+        filepath = os.path.join(data_path, 'descriptors', f'phenotype_desc_{self.id}.txt')
+        with open(filepath, 'w+') as file:
             for key, value in self._morphological_measurements.measurements_to_dict().items():
-                file.write('{} {}\n'.format(key, value))
+                file.write(f'{key} {value}\n')
             for key, value in self._brain_measurements.measurements_to_dict().items():
-                file.write('{} {}\n'.format(key, value))
+                file.write(f'{key} {value}\n')
 
     def measure_brain(self):
         """