Merge pull request #39 from safsaf150/brain_drawings_and_measurements

Brain drawings

Author: portaloffreedom

pyrevolve/revolve_bot/brain_nn.py

@@ -44,6 +44,8 @@ def FromYaml(yaml_object):
             params.generate_params(yaml_object['params'][k_node])
             brain.params[k_node] = params
 
+        return brain
+
     def to_yaml(self):
         yaml_dict_brain = OrderedDict()
 

pyrevolve/revolve_bot/measure.py

@@ -41,7 +41,8 @@ def count_branching_bricks(self, module=None):
                 for core_slot, child_module in module.iter_children():
                     if child_module is None:
                         continue
-                    children_count += 1
+                    if not isinstance(child_module, TouchSensorModule) and not isinstance(child_module, BrickSensorModule):
+                        children_count += 1
                     self.count_branching_bricks(child_module)
                 if (isinstance(module, BrickModule) and children_count == 3) or (isinstance(module, CoreModule) and children_count == 4):
                     self.branching_modules_count += 1
@@ -70,25 +71,27 @@ def measure_branching(self):
     def calculate_extremities_extensiveness(self, module=None, extremities=False, extensiveness=False):
         """
         Calculate extremities or extensiveness in body
+        @param extremities: calculate extremities in body if true
+        @param extensiveness: calculate extensiveness in body if true
         """
         try:
             if module is None:
                 module = self.body
 
-            if module.has_children():
-                children_count = 0
-                for core_slot, child_module in module.iter_children():
-                    if child_module is None:
-                        continue
+            children_count = 0
+            for core_slot, child_module in module.iter_children():
+                if child_module is None:
+                    continue
+                if not isinstance(child_module, TouchSensorModule):
                     children_count += 1
-                    if extremities:
-                        self.calculate_extremities_extensiveness(child_module, True, False)
-                    if extensiveness:
-                        self.calculate_extremities_extensiveness(child_module, False, True)
-                if children_count == 1 and not isinstance(module, CoreModule) and extremities:
-                    self.extremities += 1
-                if children_count == 2 and not isinstance(module, CoreModule) and extensiveness:
-                    self.extensiveness += 1
+                if extremities:
+                    self.calculate_extremities_extensiveness(child_module, True, False)
+                if extensiveness:
+                    self.calculate_extremities_extensiveness(child_module, False, True)
+            if children_count == 0 and not (isinstance(module, CoreModule) or isinstance(module, TouchSensorModule)) and extremities:
+                self.extremities += 1
+            if children_count == 1 and not (isinstance(module, CoreModule) or isinstance(module, TouchSensorModule)) and extensiveness:
+                self.extensiveness += 1
         except Exception as e:
             print('Failed calculating extremities or extensiveness')
             print('Exception: {}'.format(e))
@@ -104,7 +107,7 @@ def measure_limbs(self):
         if self.absolute_size < 6:
             practical_limit_limbs = self.absolute_size - 1
         else:
-            practical_limit_limbs = 2 * math.floor((self.absolute_size-6)/3) + (self.absolute_size - 6) % 3 + 4
+            practical_limit_limbs = 2 * math.floor((self.absolute_size - 6) / 3) + ((self.absolute_size - 6) % 3) + 4
         self.calculate_extremities_extensiveness(None, True, False)
         if self.extremities == 0:
             self.limbs = 0
@@ -181,7 +184,6 @@ def count_active_hinges(self, module=None):
         try:
             if module is None:
                 module = self.body
-
             if module.has_children():
                 if isinstance(module, ActiveHingeModule):
                     self.active_hinges_count += 1
@@ -204,7 +206,10 @@ def measure_joints(self):
             self.joints = 0
             return 0
         self.count_active_hinges()
-        practical_limit_active_hinges = math.floor((self.absolute_size-1)/2)
+        practical_limit_active_hinges = self.absolute_size - 2
+        if self.active_hinges_count == 0:
+            self.joints = 0
+            return 0
         self.joints = self.active_hinges_count / practical_limit_active_hinges
         return self.joints
 
@@ -227,8 +232,9 @@ def measure_absolute_size(self, module=None):
         :return:
         """
         try:
-            self.calculate_count()
-            self.absolute_size = self.brick_count + self.hinge_count + 1
+            if self.absolute_size is None:
+                self.calculate_count()
+                self.absolute_size = self.brick_count + self.hinge_count + 1
             return self.absolute_size
         except Exception as e:
             print('Failed measuring absolute size')
@@ -298,9 +304,9 @@ def measure_all(self):
         self.measure_coverage()
         self.measure_symmetry()
         self.measure_branching()
-        return self.get_all_measurements()
+        return self.measurement_to_dict()
 
-    def get_all_measurements(self):
+    def measurement_to_dict(self):
         """
         Return dict of all measurements
         :return:
@@ -309,7 +315,9 @@ def get_all_measurements(self):
             'branching': self.branching,
             'branching_modules_count': self.branching_modules_count,
             'limbs': self.limbs,
+            'extremeties': self.extremities,
             'length_of_limbs': self.length_of_limbs,
+            'extensiveness': self.extensiveness,
             'coverage': self.coverage,
             'joints': self.joints,
             'hinge_count': self.hinge_count,

pyrevolve/revolve_bot/render/brain_graph.py

@@ -0,0 +1,60 @@
+from graphviz import Digraph, render
+# belong to TODO
+import fnmatch
+
+
+class BrainGraph:
+    def __init__(self, brain, name='brain', typename='brain'):
+        self.graph = Digraph(typename, filename=name, format='png')
+        self.brain = brain
+
+    def add_node(self, node_id, node_type, text):
+        """
+        Add node to graph
+        @param node_id: id of node
+        @param node_type: type of node
+        @param text: text to show inside node
+        """
+        if node_type == 'Input':
+            self.graph.attr('node', shape='circle')
+        elif node_type == 'Oscillator':
+            self.graph.attr('node', shape='square')
+        self.graph.node(node_id, label=text)
+
+    def add_edge(self, source_id, desitnation_id, label):
+        """
+        Add edge to graph
+        @param source_id: id of source node
+        @param destination_id: id of destination node
+        @param label: label of edge
+        """
+        self.graph.edge(source_id, desitnation_id, label)
+
+    def save_graph(self):
+        """
+        Save graph
+        """
+        self.graph.render()
+
+    def brain_to_graph(self):
+        """
+        Export complete brain to graph
+        """
+
+        nodes = self.brain.nodes
+        params = self.brain.params
+        # belongs to TODO
+        duplicates = fnmatch.filter(nodes, 'node*-*')
+        for node in nodes:
+            # TODO REMOVE condition WHEN duplicated nodes bug is fixed -- duplicated nodes end in '-[0-9]+' or '-core[0-9]+' (node2-2, node2-core1)
+            if node not in duplicates:
+                node_id = nodes[node].id
+                text = node_id
+                if node_id in params:
+                    param = params[node_id]
+                    text += '\n Oscillator {0} \n period: {1} \n phase_offset: {2} \n amplitude: {3}'.format(
+                        nodes[node].part_id, params[node_id].period, params[node_id].phase_offset, params[node_id].amplitude)
+                self.add_node(node_id, nodes[node].type, text)
+
+        for connection in self.brain.connections:
+            self.add_edge(str(connection.src), str(connection.dst), str(connection.weight))

pyrevolve/revolve_bot/render/grid.py

@@ -130,10 +130,11 @@ def move_back(self):
 		Grid.y_pos = last_movement[1]
 		Grid.orientation = last_movement[2]
 
-	def add_to_visited(self):
+	def add_to_visited(self, include_sensors=True, is_sensor=False):
 		"""Add current position to visited coordinates list"""
 		self.calculate_orientation()
-		self.visited_coordinates.append([Grid.x_pos, Grid.y_pos])
+		if (include_sensors and is_sensor) or not is_sensor:
+			self.visited_coordinates.append([Grid.x_pos, Grid.y_pos])
 		Grid.movement_stack.append([Grid.x_pos, Grid.y_pos, Grid.orientation])
 
 	def calculate_grid_dimensions(self):

pyrevolve/revolve_bot/render/render.py

@@ -53,9 +53,7 @@ def traverse_path_of_robot(self, module, slot, include_sensors=True):
 		"""
 		if isinstance(module, ActiveHingeModule) or isinstance(module, BrickModule) or isinstance(module, TouchSensorModule) or isinstance(module, BrickSensorModule):
 			self.grid.move_by_slot(slot)
-			if include_sensors or (isinstance(module, ActiveHingeModule) or isinstance(module, BrickModule)):
-				self.grid.add_to_visited()
-
+			self.grid.add_to_visited(include_sensors, isinstance(module, TouchSensorModule))
 		if module.has_children():
 			# Traverse path of children of module
 			for core_slot, child_module in module.iter_children():

pyrevolve/revolve_bot/revolve_bot.py

@@ -16,6 +16,7 @@
 from .brain_nn import BrainNN
 
 from .render.render import Render
+from .render.brain_graph import BrainGraph
 from .measure import Measure
 
 import xml.etree.ElementTree
@@ -118,8 +119,7 @@ def load_yaml(self, text):
                     brain_type = yaml_brain['type']
 
                 if brain_type == 'neural-network':
-                    self._brain = BrainNN()
-                    self._brain.FromYaml(yaml_brain)
+                    self._brain = BrainNN.FromYaml(yaml_brain)
 
             else:
                 self._brain = None
@@ -252,6 +252,21 @@ def _update_substrate(self,
                                    new_direction,
                                    substrate_coordinates_map)
 
+    def render_brain(self, img_path):
+        """
+        Render image of brain
+        @param img_path: path to where to store image
+        """
+        if self._brain == None:
+            raise RuntimeError('Brain not initialized')
+        else:
+            try:
+                brain_graph = BrainGraph(self._brain, img_path)
+                brain_graph.brain_to_graph()
+                brain_graph.save_graph()
+            except:
+                print('Failed rendering brain')
+
     def render2d(self, img_path):
         """
         Render 2d representation of robot and store as png

requirements.txt

@@ -6,5 +6,6 @@ PyYAML>=3.11
 protobuf>=3.0.0
 psutil==3.4.2
 pycairo>=1.18.0
+graphviz>=0.10.1 
 
 -e git+https://github.com/ci-group/pygazebo.git@py2to3#egg=pygazebo