TaskingSoup, TaskingSoupExperiment

code/experiment.py

@@ -27,12 +27,21 @@ class Experiment(ABC):
     def __init__(self, name=None, ident=None, **kwargs):
         self.experiment_id = f'{ident or ""}_{time.time()}'
         self.experiment_name = name or 'unnamed_experiment'
-        self.next_iteration = 0
+        self.iteration = 0
         self.log_messages = list()
         self.historical_particles = dict()
+        self.params = dict(exp_iterations=100, application_steps=100, prints=True, trains_per_application=100)
+        self.with_params(**kwargs)
+
+    def __copy__(self):
+
+        self_copy = self.__class__(name=self.experiment_name, **self.params)
+        self_copy.__dict__ = {attr: self.__dict__[attr] for attr in self.__dict__ if
+                              attr not in ['particles', 'historical_particles']}
+        return self_copy
 
     def __enter__(self):
-        self.dir = os.path.join('experiments', f'exp-{self.experiment_name}-{self.experiment_id}-{self.next_iteration}')
+        self.dir = os.path.join('experiments', f'exp-{self.experiment_name}-{self.experiment_id}-{self.iteration}')
         os.makedirs(self.dir)
         print(f'** created {self.dir} **')
         return self
@@ -40,7 +49,14 @@ class Experiment(ABC):
     def __exit__(self, exc_type, exc_value, traceback):
         self.save(experiment=self.without_particles())
         self.save_log()
-        self.next_iteration += 1
+        # Clean Exit
+        self.reset_all()
+        # self.iteration += 1  Taken From here!
+
+    def with_params(self, **kwargs):
+        # Make them your own
+        self.params.update(kwargs)
+        return self
 
     def log(self, message, **kwargs):
         self.log_messages.append(message)
@@ -51,12 +67,6 @@ class Experiment(ABC):
             for log_message in self.log_messages:
                 print(str(log_message), file=log_file)
 
-    def __copy__(self):
-        self_copy = self.__class__(name=self.experiment_name,)
-        self_copy.__dict__ = {attr: self.__dict__[attr] for attr in self.__dict__ if
-                              attr not in ['particles', 'historical_particles']}
-        return self_copy
-
     def without_particles(self):
         self_copy = copy.copy(self)
         # self_copy.particles = [particle.states for particle in self.particles]
@@ -68,23 +78,28 @@ class Experiment(ABC):
             with open(os.path.join(self.dir, f"{name}.dill"), "wb") as dill_file:
                 dill.dump(value, dill_file)
 
+    def reset_log(self):
+        self.log_messages = list()
+
     @abstractmethod
-    def run_net(self, net, trains_per_application=100, step_limit=100, run_id=0, **kwargs):
+    def run_net(self, net, **kwargs):
         raise NotImplementedError
         pass
 
-    def run_exp(self, network_generator, exp_iterations, step_limit=100, prints=False, reset_model=False, **kwargs):
+    def run_exp(self, network_generator, reset_model=False, **kwargs):
         # INFO Run_ID needs to be more than 0, so that exp stores the trajectories!
-        for run_id in range(exp_iterations):
+        for run_id in range(self.params.get('exp_iterations')):
             network = network_generator()
-            self.run_net(network, step_limit, run_id=run_id + 1, **kwargs)
+            self.run_net(network, **kwargs)
             self.historical_particles[run_id] = network
-            if prints:
+            if self.params.get('prints'):
                 print("Fixpoint? " + str(network.is_fixpoint()))
-        if reset_model:
-            self.reset_model()
+            self.iteration += 1
+            if reset_model:
+                self.reset_model()
 
     def reset_all(self):
+        self.reset_log()
         self.reset_model()
 
 
@@ -96,22 +111,22 @@ class FixpointExperiment(Experiment):
         self.counters = dict(divergent=0, fix_zero=0, fix_other=0, fix_sec=0, other=0)
         self.interesting_fixpoints = []
 
-    def run_exp(self, network_generator, exp_iterations, logging=True, reset_model=False, **kwargs):
+    def run_exp(self, network_generator, logging=True, reset_model=False, **kwargs):
         kwargs.update(reset_model=False)
-        super(FixpointExperiment, self).run_exp(network_generator, exp_iterations, **kwargs)
+        super(FixpointExperiment, self).run_exp(network_generator, **kwargs)
         if logging:
             self.log(self.counters)
         if reset_model:
             self.reset_model()
 
-    def run_net(self, net, step_limit=100, run_id=0, **kwargs):
+    def run_net(self, net, **kwargs):
         if len(kwargs):
             raise IllegalArgumentError
-        for i in range(step_limit):
+        for i in range(self.params.get('application_steps')):
             if net.is_diverged() or net.is_fixpoint():
                 break
             net.set_weights(net.apply_to_weights(net.get_weights()))
-            if run_id:
+            if self.iteration and hasattr(self, 'save_state'):
                 net.save_state(time=i)
         self.count(net)
 
@@ -145,21 +160,32 @@ class MixedFixpointExperiment(FixpointExperiment):
         kwargs['name'] = self.__class__.__name__ if 'name' not in kwargs else kwargs['name']
         super(MixedFixpointExperiment, self).__init__(**kwargs)
 
-    def run_net(self, net, step_limit=100, run_id=0, trains_per_application=100, **kwargs):
+    def run_net(self, net, **kwargs):
         assert hasattr(net, 'train'), 'This Network must be trainable, i.e. use the "TrainingNeuralNetworkDecorator"!'
 
-        for evolution_step in range(step_limit):
+        for application in range(self.params.get('application_steps')):
+            epoch_num = self.params.get('trains_per_application') * application
             net.set_weights(net.apply_to_weights(net.get_weights()))
             if net.is_diverged() or net.is_fixpoint():
                 break
-            epoch_num = run_id * trains_per_application * evolution_step
-            with tqdm(postfix={"epoch": 0, "loss": 0, None: None},
-                      bar_format="This Epoch:{postfix[epoch]} Loss: {postfix[loss]}%|{r_bar}") as bar:
-                for epoch in range(epoch_num, epoch_num + trains_per_application):
+            barformat = "Experiment Iteration: {postfix[iteration]} | "
+            barformat += "Evolution Step:{postfix[step]}| "
+            barformat += "Training Epoch:{postfix[epoch]}| "
+            barformat += "Loss: {postfix[loss]} | {bar}"
+            with tqdm(total=self.params.get('trains_per_application'),
+                      postfix={'step': 0, 'loss': 0, 'iteration': self.iteration, 'epoch': 0, None: None},
+                      bar_format=barformat) as bar:
+                # This iterates for self.trains_per_application times, the addition is just for  epoch enumeration
+                for epoch in range(epoch_num, epoch_num + self.params.get('trains_per_application')):
+                    if net.is_diverged():
+                        print('Network diverged to either inf or nan... breaking')
+                        break
                     loss = net.train(epoch=epoch)
-                    bar.postfix.update(epoch=epoch, loss=loss)
+                    if epoch % 10 == 0:
+                        bar.postfix.update(step=application, epoch=epoch, loss=loss, iteration=self.iteration)
                     bar.update()
-            if run_id and hasattr(net, 'save_sate'):
+                    epoch_num += 1
+            if self.iteration and hasattr(net, 'save_sate'):
                 net.save_state()
         self.count(net)
 
@@ -169,60 +195,71 @@ class TaskExperiment(MixedFixpointExperiment):
     def __init__(self, **kwargs):
         kwargs['name'] = self.__class__.__name__ if 'name' not in kwargs else kwargs['name']
         super(TaskExperiment, self).__init__(**kwargs)
-        self.task_performance = []
-        self.self_performance = []
 
-    def run_exp(self, network_generator, exp_iterations, logging=True, reset_model=False, **kwargs):
+    def run_exp(self, network_generator, logging=True, reset_model=False, **kwargs):
         kwargs.update(reset_model=False, logging=logging)
-        super(FixpointExperiment, self).run_exp(network_generator, exp_iterations, **kwargs)
+        super(FixpointExperiment, self).run_exp(network_generator, **kwargs)
         if reset_model:
             self.reset_model()
         pass
 
-    def run_net(self, net, step_limit=100, run_id=0, **kwargs):
+    def run_net(self, net, **kwargs):
         assert hasattr(net, 'evaluate')
-        kwargs.update(step_limit=step_limit, run_id=run_id)
         super(TaskExperiment, self).run_net(net, **kwargs)
 
         # Get Performance without Training
-        selfX, selfY = net.get_samples(self_samples=True)
+        task_performance = net.evaluate(*net.get_samples(task_samples=True),
+                                        batchsize=net.get_amount_of_weights())
+        self_performance = net.evaluate(*net.get_samples(self_samples=True),
+                                        batchsize=net.get_amount_of_weights())
 
-        self.task_performance.append(net.evaluate(*net.get_samples(task_samples=True),
-                                                  batchsize=net.get_amount_of_weights()))
-        self.self_performance.append(net.evaluate(*net.get_samples(self_samples=True),
-                                                  batchsize=net.get_amount_of_weights()))
+        current_performance = dict(task_performance=task_performance,
+                                   self_performance=self_performance,
+                                   counters=self.counters, id=self.iteration)
+
+        self.log(current_performance)
         pass
 
 
 class SoupExperiment(Experiment):
 
-    def __init__(self, **kwargs):
+    def __init__(self, soup_generator, **kwargs):
         kwargs['name'] = self.__class__.__name__ if 'name' not in kwargs else kwargs['name']
+        self.soup_generator = soup_generator
         super(SoupExperiment, self).__init__(**kwargs)
 
-    def run_exp(self, network_generator, exp_iterations,
-                soup_generator=None, soup_iterations=0, prints=False, **kwargs):
-        for i in range(soup_iterations):
-            if not soup_generator:
-                raise ValueError('A Soup Generator needs to be given!')
-            soup = soup_generator()
+    def run_exp(self, network_generator, **kwargs):
+        for i in range(self.params.get('exp_iterations')):
+            soup = self.soup_generator()
             soup.seed()
-            for _ in tqdm(range(exp_iterations)):
+            for _ in tqdm(range(self.params.get('application_steps'))):
                 soup.evolve()
             self.log(soup.count())
             self.save(soup=soup.without_particles())
             K.clear_session()
 
-    def run_net(self, net, trains_per_application=100, step_limit=100, run_id=0, **kwargs):
+    def run_net(self, net, **kwargs):
         raise NotImplementedError
         pass
 
 
-class IdentLearningExperiment(Experiment):
+class TaskingSoupExperiment(Experiment):
 
-    def __init__(self, **kwargs):
+    def __init__(self, soup_generator, **kwargs):
         kwargs['name'] = self.__class__.__name__ if 'name' not in kwargs else kwargs['name']
-        super(IdentLearningExperiment, self).__init__(**kwargs)
+        self.soup_generator = soup_generator
+        super(TaskingSoupExperiment, self).__init__(**kwargs)
 
-    def run_net(self, net, trains_per_application=100, step_limit=100, run_id=0, **kwargs):
+    def run_exp(self, network_generator, **kwargs):
+        for i in range(self.params.get('exp_iterations')):
+            soup = self.soup_generator()
+            soup.seed()
+            for _ in tqdm(range(self.params.get('application_steps'))):
+                soup.evolve()
+            self.log(soup.count())
+            self.save(soup=soup.without_particles())
+            K.clear_session()
+
+    def run_net(self, net, **kwargs):
+        raise NotImplementedError()
         pass

code/network.py

@@ -3,6 +3,7 @@ import numpy as np
 from abc import abstractmethod, ABC
 from typing import List, Union, Tuple
 from types import FunctionType
+import warnings
 
 # Functions and Operators
 from operator import mul
@@ -38,6 +39,25 @@ class SaveStateCallback(Callback):
         return
 
 
+class EarlyStoppingByInfNanLoss(Callback):
+    def __init__(self, monitor='loss', verbose=0):
+        super(Callback, self).__init__()
+        self.monitor = monitor
+        self.verbose = verbose
+
+    def on_epoch_end(self, epoch, logs: dict = None):
+        logs = logs or dict()
+        current = logs.get(self.monitor)
+        if current is None:
+            warnings.warn(f'Early stopping requires {self.monitor} available!', RuntimeWarning)
+            pass
+
+        if np.isnan(current) or np.isinf(current):
+            if self.verbose > 0:
+                print(f'Epoch {epoch}: early stopping THR')
+            self.model.stop_training = True
+
+
 class NeuralNetwork(ABC):
     """
     This is the Base Network Class, including abstract functions that must be implemented.
@@ -84,7 +104,7 @@ class NeuralNetwork(ABC):
 
     def __init__(self, **params):
         super().__init__()
-        self.params = dict(epsilon=0.00000000000001)
+        self.params = dict(epsilon=0.00000000000001, early_nan_stopping=True, store_states=False)
         self.params.update(params)
         self.name = params.get('name', self.__class__.__name__)
         self.keras_params = dict(activation='linear', use_bias=False)
@@ -233,21 +253,23 @@ class ParticleDecorator:
     def get_states(self):
         return self.states
 
-    def attack(self, other_network):
+    def attack(self, other_network, iterations: int = 1):
         """
         Set a networks weights based on the output of the application of my function to its weights.
         "Alter a networks weights based on my evaluation"
         :param other_network:
+        :param iterations:
         :return:
         """
-        other_network.set_weights(self.apply_to_network(other_network))
+        for _ in range(iterations):
+            other_network.set_weights(self.apply_to_network(other_network))
         return self
 
-    def self_attack(self, iterations=1):
+    def self_attack(self, iterations: int = 1):
         """
         Set my weights based on the output of the application of my function to its weights.
         "Alter my network weights based on my evaluation"
-        :param other_network:
+        :param iterations:
         :return:
         """
         for _ in range(iterations):
@@ -255,7 +277,7 @@ class ParticleDecorator:
         return self
 
 
-class TaskDecorator(TaskAdditionOf2):
+class TaskDecorator(ParticleTaskAdditionOf2):
 
     def __init__(self, network, **kwargs):
         super(TaskDecorator, self).__init__(**kwargs)
@@ -271,12 +293,21 @@ class TaskDecorator(TaskAdditionOf2):
 
         if task_samples:
             return super(TaskDecorator, self).get_samples()
+
         elif self_samples:
             return self.network.get_samples()
-        elif prng() >= kwargs.get('split', 0.5):
-            return super(TaskDecorator, self).get_samples()
+
         else:
-            return self.network.get_samples()
+            self_x, self_y = self.network.get_samples()
+            task_x, task_y = super(TaskDecorator, self).get_samples()
+
+            amount_of_weights = self.network.get_amount_of_weights()
+            random_idx = np.random.choice(np.arange(amount_of_weights), amount_of_weights//2)
+
+            x = self_x[random_idx] = task_x[random_idx]
+            y = self_y[random_idx] = task_y[random_idx]
+
+            return x, y
 
 
 class WeightwiseNeuralNetwork(NeuralNetwork):
@@ -304,7 +335,7 @@ class WeightwiseNeuralNetwork(NeuralNetwork):
         # normalize [layer, cell, position]
         for idx in range(1, sample.shape[1]):
             sample[:, idx] = sample[:, idx] / np.max(sample[:, idx])
-        return sample, sample
+        return sample, sample[:, 0]
 
     def apply_to_weights(self, weights) -> List[np.ndarray]:
         # ToDo: Insert DocString
@@ -427,6 +458,7 @@ class AggregatingNeuralNetwork(NeuralNetwork):
 class RecurrentNeuralNetwork(NeuralNetwork):
 
     def __init__(self, width, depth, **kwargs):
+        raise NotImplementedError
         super().__init__(**kwargs)
         self.features = 1
         self.width = width
@@ -510,10 +542,17 @@ class TrainingNeuralNetworkDecorator:
             self.model_compiled = True
         return self
 
-    def train(self, batchsize=1, store_states=False, epoch=0):
+    def train(self, batchsize=1, epoch=0):
         self.compiled()
         x, y = self.network.get_samples()
-        savestatecallback = [SaveStateCallback(network=self, epoch=epoch)] if store_states else None
+        callbacks = []
+        if self.get_params().get('store_states'):
+            callbacks.append(SaveStateCallback(network=self, epoch=epoch))
+        if self.get_params().get('early_nan_stopping'):
+            callbacks.append(EarlyStoppingByInfNanLoss())
+
+        # 'or' does not work on empty lists
+        callbacks = callbacks if callbacks else None
         """
         Please Note:
         
@@ -526,7 +565,7 @@ class TrainingNeuralNetworkDecorator:
             given by `epochs`, but merely until the epoch
             of index `epochs` is reached."""
         history = self.network.model.fit(x=x, y=y, initial_epoch=epoch, epochs=epoch+1, verbose=0,
-                                         batch_size=batchsize, callbacks=savestatecallback)
+                                         batch_size=batchsize, callbacks=callbacks)
         return history.history['loss'][-1]
 
     def learn_from(self, other_network, batchsize=1):
@@ -558,11 +597,10 @@ if __name__ == '__main__':
 
     if True:
         # WeightWise Neural Network
-        net_generator = lambda: TrainingNeuralNetworkDecorator(TaskDecorator(
-            WeightwiseNeuralNetwork(width=2, depth=2))).with_keras_params(activation='linear')
-        with TaskExperiment() as exp:
-            exp.run_exp(net_generator, 10, trains_per_application=10)
-            exp.reset_all()
+        with TaskExperiment().with_params(application_steps=10, trains_per_application=1000, exp_iterations=30) as exp:
+            net_generator = lambda: TrainingNeuralNetworkDecorator(TaskDecorator(
+                WeightwiseNeuralNetwork(width=4, depth=3))).with_keras_params(activation='linear')
+            exp.run_exp(net_generator, reset_model=True)
 
     if False:
         # Aggregating Neural Network
@@ -585,8 +623,7 @@ if __name__ == '__main__':
         # ok so this works quite realiably
         run_count = 1000
         net_generator = lambda: TrainingNeuralNetworkDecorator(WeightwiseNeuralNetwork(
-            width=2, depth=2).with_params(epsilon=0.0001, steplimit=2, trains_per_application=10
-                                          )).with_keras_params(optimizer='sgd')
+            width=2, depth=2).with_params(epsilon=0.0001)).with_keras_params(optimizer='sgd')
         with MixedFixpointExperiment() as exp:
             for run_id in tqdm(range(run_count+1)):
                 exp.run_exp(net_generator, 1)
@@ -600,7 +637,7 @@ if __name__ == '__main__':
             net = TrainingNeuralNetworkDecorator(
                 AggregatingNeuralNetwork(4, width=2, depth=2).with_params(epsilon=0.1e-6))
             for run_id in tqdm(range(run_count+1)):
-                loss = net.compiled().train()
+                current_loss = net.compiled().train()
                 if run_id % 100 == 0:
                     net.print_weights()
                     old_aggs, _ = net.get_aggregated_weights()
@@ -609,7 +646,7 @@ if __name__ == '__main__':
                     print("new weights agg: " + str(new_aggs))
                     print("Fixpoint? " + str(net.is_fixpoint()))
                     print("Fixpoint after Agg? " + str(fp))
-                    print("Loss " + str(loss))
+                    print("Loss " + str(current_loss))
                     print()
 
     if False:
@@ -620,10 +657,10 @@ if __name__ == '__main__':
             net = TrainingNeuralNetworkDecorator(RecurrentNeuralNetwork(width=2, depth=2)
                                                  ).with_keras_params(optimizer='sgd', activation='linear')
             for run_id in tqdm(range(run_count+1)):
-                loss = net.compiled().train()
+                current_loss = net.compiled().train()
                 if run_id % 500 == 0:
                     net.print_weights()
                     # print(net.apply_to_network(net))
                     print("Fixpoint? " + str(net.is_fixpoint()))
-                    print("Loss " + str(loss))
+                    print("Loss " + str(current_loss))
                     print()

code/plotting/plotting_class.py

@@ -0,0 +1,66 @@
+import os
+
+from experiment import Experiment
+# noinspection PyUnresolvedReferences
+from soup import Soup
+
+from argparse import ArgumentParser
+import numpy as np
+
+import plotly as pl
+import plotly.graph_objs as go
+
+import colorlover as cl
+
+import dill
+
+from sklearn.manifold.t_sne import TSNE, PCA
+
+
+def build_args():
+    arg_parser = ArgumentParser()
+    arg_parser.add_argument('-i', '--in_file', nargs=1, type=str)
+    arg_parser.add_argument('-o', '--out_file', nargs='?', default='out', type=str)
+    return arg_parser.parse_args()
+
+
+class DataPlotter:
+
+    def __init__(self, path=None):
+        self.path = path or os.getcwd()
+        pass
+
+    def search_and_apply(self, plotting_function, files_to_look_for=None, absolut_file_or_folder=None):
+        absolut_file_or_folder, files_to_look_for = self.path or absolut_file_or_folder, list() or files_to_look_for
+        if os.path.isdir(absolut_file_or_folder):
+            for sub_file_or_folder in os.scandir(absolut_file_or_folder):
+                self.search_and_apply(plotting_function, files_to_look_for=files_to_look_for,
+                                      absolut_file_or_folder=sub_file_or_folder.path)
+        elif absolut_file_or_folder.endswith('.dill'):
+            file_or_folder = os.path.split(absolut_file_or_folder)[-1]
+            if file_or_folder in files_to_look_for and not os.path.exists(
+                    '{}.html'.format(absolut_file_or_folder[:-5])):
+                print('Apply Plotting function "{func}" on file "{file}"'.format(func=plotting_function.__name__,
+                                                                                 file=absolut_file_or_folder)
+                      )
+                with open(absolut_file_or_folder, 'rb') as in_f:
+                    exp = dill.load(in_f)
+
+                names_dill_location = os.path.join(*os.path.split(absolut_file_or_folder)[:-1], 'all_names.dill')
+                with open(names_dill_location, 'rb') as in_f:
+                    names = dill.load(in_f)
+
+                try:
+                    plotting_function((names, exp), filename='{}.html'.format(absolut_file_or_folder[:-5]))
+                except ValueError:
+                    pass
+                except AttributeError:
+                    pass
+            else:
+                # This was either another FilyType or Plot.html already exists.
+                pass
+
+
+if __name__ == '__main__':
+    plotter = DataPlotter
+    pass

code/plotting/task_learning_curves.py

@@ -0,0 +1,109 @@
+import os
+from collections import defaultdict
+
+# noinspection PyUnresolvedReferences
+from soup import Soup
+from experiment import TaskExperiment
+
+from argparse import ArgumentParser
+
+import plotly as pl
+import plotly.graph_objs as go
+
+import colorlover as cl
+
+import dill
+import numpy as np
+
+
+def build_args():
+    arg_parser = ArgumentParser()
+    arg_parser.add_argument('-i', '--in_file', nargs=1, type=str)
+    arg_parser.add_argument('-o', '--out_file', nargs='?', default='out', type=str)
+    return arg_parser.parse_args()
+
+
+def line_plot(exp: TaskExperiment, filename='lineplot'):
+    assert isinstance(exp, TaskExperiment), ' This has to be a TaskExperiment!'
+    traces, data = [], defaultdict(list)
+
+    color_scale = cl.scales['3']['div']['RdYlBu']
+
+    # Sort data per Key
+    for message in exp.log_messages:
+        for key in message.keys():
+            try:
+                data[key].append(-0.1 if np.isnan(message[key]) or np.isinf(message[key]) else message[key])
+            except:
+                data[key].append(message[key])
+
+    for line_id, key in enumerate(data.keys()):
+        if key not in ['counters', 'id']:
+            trace = go.Scatter(
+                x=[x for x in range(len(data[key]))],
+                y=data[key],
+                name=key,
+                line=dict(
+                    color=color_scale[line_id],
+                    width=5
+                ),
+            )
+
+            traces.append(trace)
+        else:
+            continue
+
+    layout = dict(xaxis=dict(title='Trains per self-application', titlefont=dict(size=20)),
+                  yaxis=dict(title='Average amount of fixpoints found',
+                             titlefont=dict(size=20),
+                             # type='log',
+                             # range=[0, 2]
+                             ),
+                  legend=dict(orientation='h', x=0.3, y=-0.3),
+                  # height=800, width=800,
+                  margin=dict(b=0)
+                  )
+
+    fig = go.Figure(data=traces, layout=layout)
+    pl.offline.plot(fig, auto_open=True, filename=filename)
+    pass
+
+
+def search_and_apply(absolut_file_or_folder, plotting_function, files_to_look_for=None, override=False):
+    # ToDo: Clean this Mess
+    assert os.path.exists(absolut_file_or_folder), f'The given path does not exist! Given: {absolut_file_or_folder}'
+    files_to_look_for = files_to_look_for or list()
+    if os.path.isdir(absolut_file_or_folder):
+        for sub_file_or_folder in os.scandir(absolut_file_or_folder):
+            search_and_apply(sub_file_or_folder.path, plotting_function,
+                             files_to_look_for=files_to_look_for, override=override)
+    elif absolut_file_or_folder.endswith('.dill'):
+        file_or_folder = os.path.split(absolut_file_or_folder)[-1]
+        if file_or_folder in files_to_look_for or not files_to_look_for:
+            if not os.path.exists('{}.html'.format(absolut_file_or_folder[:-5])) or override:
+                print('Apply Plotting function "{func}" on file "{file}"'.format(func=plotting_function.__name__,
+                                                                                 file=absolut_file_or_folder)
+                      )
+                with open(absolut_file_or_folder, 'rb') as in_f:
+                    exp = dill.load(in_f)
+
+                try:
+                    plotting_function(exp, filename='{}.html'.format(absolut_file_or_folder[:-5]))
+                except ValueError:
+                    pass
+                except AttributeError:
+                    pass
+            else:
+                # Plot.html already exists.
+                pass
+        else:
+            # This was a wrong FilyType.
+            pass
+
+
+if __name__ == '__main__':
+    args = build_args()
+    in_file = args.in_file[0]
+    out_file = args.out_file
+
+    search_and_apply(in_file, line_plot, override=True)

code/setups/network_trajectorys.py

@@ -104,7 +104,7 @@ if __name__ == '__main__':
             for run_id in range(10):
                 net = TrainingNeuralNetworkDecorator(FFTNeuralNetwork(2, width=2, depth=2))\
                     .with_params(epsilon=0.0001, activation='sigmoid')
-                exp.run_net(net, 500, 10)
+                exp.run_net(net)
 
                 net.print_weights()
 

code/soup.py

@@ -1,30 +1,30 @@
 import random
-from operator import mul
-from functools import reduce
-
 from tensorflow.python.keras.layers import Dense, Dropout, BatchNormalization
+from tensorflow.python.keras import backend as K
 
 from network import *
 
+from math import sqrt
 
 def prng():
     return random.random()
 
 
 class Soup(object):
-    
+
     def __init__(self, size, generator, **kwargs):
         self.size = size
         self.generator = generator
         self.particles = []
         self.historical_particles = {}
-        self.params = dict(attacking_rate=0.1, learn_from_rate=0.1, train=0, learn_from_severity=1)
-        self.params.update(kwargs)
+        self.soup_params = dict(attacking_rate=0.1, learn_from_rate=0.1, train=0, learn_from_severity=1)
+        self.soup_params.update(kwargs)
         self.time = 0
         self.is_seeded = False
+        self.is_compiled = False
 
     def __copy__(self):
-        copy_ = Soup(self.size, self.generator, **self.params)
+        copy_ = Soup(self.size, self.generator, **self.soup_params)
         copy_.__dict__ = {attr: self.__dict__[attr] for attr in self.__dict__ if
                           attr not in ['particles', 'historical_particles']}
         return copy_
@@ -35,18 +35,18 @@ class Soup(object):
         self_copy.historical_particles = {key: val.states for key, val in self.historical_particles.items()}
         return self_copy
 
-    def with_params(self, **kwargs):
-        self.params.update(kwargs)
+    def with_soup_params(self, **kwargs):
+        self.soup_params.update(kwargs)
         return self
-    
+
     def generate_particle(self):
         new_particle = ParticleDecorator(self.generator())
         self.historical_particles[new_particle.get_uid()] = new_particle
         return new_particle
-        
+
     def get_particle(self, uid, otherwise=None):
         return self.historical_particles.get(uid, otherwise)
-    
+
     def seed(self):
         if not self.is_seeded:
             self.particles = []
@@ -55,43 +55,43 @@ class Soup(object):
         else:
             print('already seeded!')
         self.is_seeded = True
-        return self       
-    
+        return self
+
     def evolve(self, iterations=1):
         for _ in range(iterations):
             self.time += 1
             for particle_id, particle in enumerate(self.particles):
                 description = {'time': self.time}
-                if prng() < self.params.get('attacking_rate'):
+                if prng() < self.soup_params.get('attacking_rate'):
                     other_particle_id = int(prng() * len(self.particles))
                     other_particle = self.particles[other_particle_id]
                     particle.attack(other_particle)
                     description['action'] = 'attacking'
                     description['counterpart'] = other_particle.get_uid()
 
-                if prng() < self.params.get('learn_from_rate'):
+                if prng() < self.soup_params.get('learn_from_rate'):
                     other_particle_id = int(prng() * len(self.particles))
                     other_particle = self.particles[other_particle_id]
-                    for _ in range(self.params.get('learn_from_severity', 1)):
+                    for _ in range(self.soup_params.get('learn_from_severity', 1)):
                         particle.learn_from(other_particle)
                     description['action'] = 'learn_from'
                     description['counterpart'] = other_particle.get_uid()
 
-                for _ in range(self.params.get('train', 0)):
+                for _ in range(self.soup_params.get('train', 0)):
                     # callbacks on save_state are broken for TrainingNeuralNetwork
                     loss = particle.train(store_states=False)
-                    description['fitted'] = self.params.get('train', 0)
+                    description['fitted'] = self.soup_params.get('train', 0)
                     description['loss'] = loss
                     description['action'] = 'train_self'
                     description['counterpart'] = None
 
-                if self.params.get('remove_divergent') and particle.is_diverged():
+                if self.soup_params.get('remove_divergent') and particle.is_diverged():
                     new_particle = self.generate_particle()
                     self.particles[particle_id] = new_particle
                     description['action'] = 'divergent_dead'
                     description['counterpart'] = new_particle.get_uid()
 
-                if self.params.get('remove_zero') and particle.is_zero():
+                if self.soup_params.get('remove_zero') and particle.is_zero():
                     new_particle = self.generate_particle()
                     self.particles[particle_id] = new_particle
                     description['action'] = 'zweo_dead'
@@ -113,7 +113,7 @@ class Soup(object):
             else:
                 counters['other'] += 1
         return counters
-        
+
     def print_all(self):
         for particle in self.particles:
             particle.print_weights()
@@ -122,62 +122,171 @@ class Soup(object):
 
 class SolvingSoup(Soup):
 
-    def __init__(self, task: Task, particle_amount: int, particle_generator, depth: int=None, **kwargs):
-        super(SolvingSoup, self).__init__(particle_amount, particle_generator, **kwargs)
-        self.model = Sequential()
-        self.depth = depth or particle_amount - 1
-        self.task = task
+    @staticmethod
+    def weights_to_flat_array(weights: List[np.ndarray]) -> np.ndarray:
+        return np.concatenate([d.ravel() for d in weights])
 
-        self.network_params = dict()
+    @staticmethod
+    def reshape_flat_array(array, shapes: List[Tuple[int]]) -> List[np.ndarray]:
+        # Same thing, but with an additional np call
+        # sizes: List[int] = [int(np.prod(shape)) for shape in shapes]
+
+        sizes = [reduce(mul, shape) for shape in shapes]
+        # Split the incoming array into slices for layers
+        slices = [array[x: y] for x, y in zip(accumulate([0] + sizes), accumulate(sizes))]
+        # reshape them in accordance to the given shapes
+        weights = [np.reshape(weight_slice, shape) for weight_slice, shape in zip(slices, shapes)]
+        return weights
+
+    def __init__(self, population_size: int, task: Task, particle_generator, **kwargs):
+        super(SolvingSoup, self).__init__(population_size, particle_generator, **kwargs)
+        self.task = task
+        self.model: Sequential
+
+        self.network_params = dict(sparsity_rate=0.1, early_nan_stopping=True)
         self.compile_params = dict(loss='mse', optimizer='sgd')
         self.compile_params.update(kwargs.get('compile_params', {}))
 
     def with_network_params(self, **params):
         self.network_params.update(params)
 
+    def _generate_model(self):
+        model = Sequential()
+        weights, last_weights = self.get_total_weight_amount(), 0
+        while weights:
+            n = int(sqrt(weights))
+            this_weights = sqrt(weights / n)
+            if not this_weights:
+                break
+            if not model.layers:
+                # First Input layer
+                model.add(Dense(this_weights, activation='linear', input_shape=self.task.input_shape))
+            else:
+                # Intermediate Layers
+                model.add(Dense(this_weights, activation='linear'))
+                self.model.add(BatchNormalization())
+                self.model.add(Dropout(rate=self.soup_params.get('sparsity_rate')))
+            weights -= this_weights * last_weights
+            last_weights = this_weights
+        # Last Layer
+        model.add(Dense(self.task.output_shape))
+        return model
+
+    def get_weights(self):
+        return self.model.get_weights()
+
+    def set_weights(self, weights: List[np.ndarray]):
+        self.model.set_weights(weights)
+
+    def set_intermediate_weights(self, weights: List[np.ndarray]):
+        all_weights = self.get_weights()
+        all_weights[1:-1] = weights
+        self.set_weights(all_weights)
+
     def seed(self):
         super(SolvingSoup, self).seed()
-
-        # Static First Layer
-        self.model.add(Dense(self.network_params.get('first_layer_units', 10), input_shape=self.task.input_shape))
-        self.model.add(BatchNormalization())
-
-        for layer_num in range(self.depth):
-            # ToDo !!!!!!!!!!
-            self.model.add(Dense())
-            self.model.add(Dropout(rate=self.params.get('sparsity_rate', 0.1)))
-
-        has_to_be_zero =
-
-        if has_to_be_zero:
-            raise ValueError(f'This Combination does not Work!, There are still {has_to_be_zero} unnassigned Weights!')
-        self.model.add(Dense(left_over_units))
-        self.model.add(Dense(self.task.output_shape))
+        K.clear_session()
+        self.model = self._generate_model()
         pass
 
     def compile_model(self, **kwargs):
-        compile_params = copy.deepcopy(self.compile_params)
-        compile_params.update(kwargs)
-        return self.model.compile(**compile_params)
+        if not self.is_compiled:
+            compile_params = copy.deepcopy(self.compile_params)
+            compile_params.update(kwargs)
+            return self.model.compile(**compile_params)
+        else:
+            raise BrokenPipeError('This Model is not compiled yet! Something went wrong in the Pipeline!')
 
     def get_total_weight_amount(self):
         if self.is_seeded:
             return sum([x.get_amount_of_weights for x in self.particles])
+        else:
+            return 0
+
+    def get_shapes(self):
+        return [x.shape for x in self.get_weights()]
+
+    def get_intermediate_shapes(self):
+        weights = [x.shape for x in self.get_weights()]
+        return weights[1:-1]
 
     def predict(self, x):
         return self.model.predict(x)
 
+    def evolve(self, **kwargs):
+        super(SolvingSoup, self).evolve(iterations=1)
 
+    def get_particle_weights(self):
+        return np.concatenate([x.get_weights_flat() for x in self.particles])
+
+    def set_particle_weights(self, weights):
+        particle_weight_shape = self.particles[0].shapes(self.particles[0].get_weights())
+        sizes = [x.get_amount_of_weights() for x in self.particles]
+        flat_weights = self.weights_to_flat_array(weights)
+        slices = [flat_weights[x: y] for x, y in zip(accumulate([0] + sizes), accumulate(sizes))]
+        for particle, weight in zip((self.particles, slices)):
+            self.reshape_flat_array(weight, particle_weight_shape)
+        return True
+
+    def compiled(self, **kwargs):
+        if not self.is_compiled:
+            self.seed()
+            self.compile_model(**kwargs)
+            self.is_compiled = True
+        return self
+
+    def train(self, batchsize=1, epoch=0):
+        self.compiled()
+        x, y = self.task.get_samples()
+        callbacks = []
+        if self.network_params.get('early_nan_stopping'):
+            callbacks.append(EarlyStoppingByInfNanLoss())
+
+        # 'or' does not work on empty lists
+        callbacks = callbacks if callbacks else None
+        """
+        Please Note:
+
+        epochs: Integer. Number of epochs to train the model.
+            An epoch is an iteration over the entire `x` and `y`
+            data provided.
+            Note that in conjunction with `initial_epoch`,
+            `epochs` is to be understood as "final epoch".
+            The model is not trained for a number of iterations
+            given by `epochs`, but merely until the epoch
+            of index `epochs` is reached."""
+        history = self.model.fit(x=x, y=y, initial_epoch=epoch, epochs=epoch + 1, verbose=0,
+                                 batch_size=batchsize, callbacks=callbacks)
+        return history.history['loss'][-1]
+
+    def train_at_particle_level(self):
+        self.compiled()
+
+        weights = self.get_particle_weights()
+        shaped_weights = self.reshape_flat_array(weights, self.get_intermediate_shapes())
+        self.set_intermediate_weights(shaped_weights)
+
+        return
 
 
 if __name__ == '__main__':
     if True:
-        with SoupExperiment(name='soup') as exp:
+        from task import TaskAdditionOf2
+        soup_generator = SolvingSoup(20, ParticleTaskAdditionOf2(), net_generator)
+        with SoupExperiment(soup_generator, name='solving_soup') as exp:
             net_generator = lambda: TrainingNeuralNetworkDecorator(
                 WeightwiseNeuralNetwork(2, 2).with_keras_params(activation='linear').with_params()
             )
-            soup_generator = lambda: Soup(10, net_generator).with_params(remove_divergent=True, remove_zero=True)
-            exp.run_exp(net_generator, 10, soup_generator, 1, False)
+            exp.run_exp(net_generator)
+
+    if True:
+        soup_generator = lambda: Soup(10, net_generator).with_soup_params(remove_divergent=True, remove_zero=True)
+        with SoupExperiment(soup_generator, name='soup') as exp:
+            net_generator = lambda: TrainingNeuralNetworkDecorator(
+                WeightwiseNeuralNetwork(2, 2).with_keras_params(activation='linear').with_params()
+            )
+
+            exp.run_exp(net_generator)
 
             # net_generator = lambda: FFTNeuralNetwork(2, 2).with_keras_params(activation='linear').with_params()
             # net_generator = lambda: AggregatingNeuralNetwork(4, 2, 2).with_keras_params(activation='sigmoid')\
@@ -185,12 +294,12 @@ if __name__ == '__main__':
             # net_generator = lambda: RecurrentNeuralNetwork(2, 2).with_keras_params(activation='linear').with_params()
 
     if True:
-        with SoupExperiment(name='soup') as exp:
+        soup_generator = lambda: Soup(10, net_generator).with_soup_params(remove_divergent=True, remove_zero=True)
+        with SoupExperiment(soup_generator, name='soup') as exp:
             net_generator = lambda: TrainingNeuralNetworkDecorator(WeightwiseNeuralNetwork(2, 2)) \
                 .with_keras_params(activation='linear').with_params(epsilon=0.0001)
-            soup_generator = lambda: Soup(10, net_generator).with_params(remove_divergent=True, remove_zero=True, train=20)
 
-            exp.run_exp(net_generator, 10, soup_generator, 1, False)
+            exp.run_exp(net_generator)
 
             # net_generator = lambda: TrainingNeuralNetworkDecorator(AggregatingNeuralNetwork(4, 2, 2))
             # .with_keras_params(activation='linear')\

code/task.py

@@ -15,14 +15,24 @@ class Task(ABC):
         raise NotImplementedError
 
 
-class TaskAdditionOf2(Task):
+class ParticleTaskAdditionOf2(Task):
 
     def __init__(self, **kwargs):
-        super(TaskAdditionOf2, self).__init__(input_shape=(4,), output_shape=(1, ), **kwargs)
+        super(ParticleTaskAdditionOf2, self).__init__(input_shape=(4,), output_shape=(1, ), **kwargs)
 
     def get_samples(self) -> Tuple[np.ndarray, np.ndarray]:
         x = np.zeros((self.batchsize, *self.input_shape))
         x[:, :2] = np.random.standard_normal((self.batchsize, 2)) * 0.5
-        y = np.zeros_like(x)
-        y[:, -1] = np.sum(x, axis=1)
-        return x, y
+        y = np.sum(x, axis=1)
+        return x, y
+
+
+class SoupTask(Task):
+
+    def __init__(self, input_shape, output_shape):
+        super(SoupTask, self).__init__(input_shape, output_shape)
+        pass
+
+    def get_samples(self) -> Tuple[np.ndarray, np.ndarray]:
+        raise NotImplementedError
+        # ToDo Hier geht es weiter.