added more parameters for hypergraph function

and added fix for negative vertices

viziphant/patterns.py

@@ -399,8 +399,8 @@ def plot_patterns(spiketrains, patterns, circle_sizes=(3, 50, 70),
     axes.yaxis.set_label_coords(-0.01, 0.5)
     return axes
 
-def plot_patterns_hypergraph(patterns, node_size=3, pattern_size=None, num_neurons=None,\
-                             highlight_patterns=None, mark_neuron=None, node_color='white'):
+def plot_patterns_hypergraph(patterns, pattern_size=None, num_neurons=None,\
+                            must_involve_neuron=None, node_size=3, node_color='white', node_linewidth=1):
     """
     Hypergraph visualization of spike patterns.
 
@@ -432,17 +432,21 @@ def plot_patterns_hypergraph(patterns, node_size=3, pattern_size=None, num_neuro
         pattern detectors.
     node_size (optional): int
         Change the size of the drawen nodes
-    pattern_size (optional): tuple or int
+    pattern_size (optional): range
         Only draw patterns that are in range of pattern_size
     num_neurons: None or int
         If None, only the neurons that are part of a pattern are shown. If an
         integer is passed, it identifies the total number of recorded neurons
         including non-pattern neurons to be additionally shown in the graph.
         Default: None
-    highlight_patterns (optional) : int
+    must_involve_neuron (optional) : int
         Highlight pattern which includes neuron x
     node_color (optional) : String
         change the color of the nodes
+
+    node_linewidth (optional) : int
+            change the line width of the nodes
+
     Returns
     -------
     A handle to a matplotlib figure containing the hypergraph.
@@ -500,33 +504,18 @@ def plot_patterns_hypergraph(patterns, node_size=3, pattern_size=None, num_neuro
 
     # Create one hypergraph per dataset
     hyperedges = []
-
-    # Create "range" of pattern_size
-    if (isinstance(pattern_size, int)): pattern_size=(pattern_size, pattern_size)
-
     # Create one hyperedge from every pattern
     for pattern in patterns:
         # A hyperedge is the set of neurons of a pattern
-        if pattern_size is None:
-            hyperedges.append(pattern['neurons'])
-        # check if hyperedge(pattern) is greater or equal to min_pattern_size
-        elif len(pattern['neurons']) >= pattern_size[0] and len(pattern['neurons']) <= pattern_size[1] or highlight_patterns in pattern['neurons']:
+        if pattern_size is None or len(pattern['neurons']) in pattern_size:
             hyperedges.append(pattern['neurons'])
 
-    # check if neuron to highlight is in hyperedge
-    temp_hyperedges = []
-    if highlight_patterns is not None:
-        if isinstance(highlight_patterns, int):
-            for edge in hyperedges:
-                if highlight_patterns in edge:
-                    temp_hyperedges.append(edge)
-            hyperedges = temp_hyperedges
-
-    # TODO: highlight_patterns as a list 
-
-    if (len(hyperedges) == 0):
-        raise Exception('Could not find any hyperedges that match the given parameters')
+    if must_involve_neuron is not None and isinstance(must_involve_neuron, int):
+        hyperedges = [edge for edge in hyperedges if must_involve_neuron in edge]
 
+    elif must_involve_neuron is not None and isinstance(must_involve_neuron, list):
+        hyperedges = [edge for edge in hyperedges if any(elem in edge for elem in must_involve_neuron)]
+
     # Currently, all hyperedges receive the same weights
     weights = [weight] * len(hyperedges)
 
@@ -536,7 +525,8 @@ def plot_patterns_hypergraph(patterns, node_size=3, pattern_size=None, num_neuro
                     weights=weights,
                     repulse=repulsive)
     hypergraphs.append(hg)
-    view = View(hypergraphs, node_size, mark_neuron, node_color)
+    view = View(hypergraphs=hypergraphs, node_size=node_size, 
+                node_color=node_color, node_linewidth=node_linewidth)
     fig = view.show(subset_style=VisualizationStyle.COLOR,
                     triangulation_style=VisualizationStyle.INVISIBLE)
 

viziphant/patterns_src/hypergraph.py

@@ -104,15 +104,23 @@ def complete_and_star_associated_graph(self):
         edges = []
         weights = []
         graph_vertices = list(self.vertices.copy())
+        if isinstance(self.vertices[0], int):
+            max_vertex = max(max(hyperedge) for hyperedge in self.hyperedges)
+        else:
+            max_vertex = 0
+        if isinstance(max_vertex, str):
+            max_vertex = 0
         for i, hyperedge in enumerate(self.hyperedges):
             # Pseudo-vertex corresponding to hyperedge
-            graph_vertices.append(-i - 1)
+            pseudo_vertex = max_vertex + i + 1
+            graph_vertices.append(pseudo_vertex)
+
             for j, vertex in enumerate(hyperedge):
                 # Every vertex of a hyperedge is adjacent to the pseudo-vertex
                 # corresponding to the hyperedge
-                edges.append([-i - 1, vertex])
-                # Weight is equal to the weight of the hyperedge (if
-                # applicable)
+                edges.append([pseudo_vertex, vertex])
+
+                # Weight is equal to the weight of the hyperedge (if applicable)
                 if self.weights:
                     weights.append(self.weights[i])
                 # Unique unordered combinations of vertices of this hyperedge

viziphant/patterns_src/view.py

@@ -34,8 +34,7 @@ class View:
     In summary, this class represents an interactive tool
     for the visualization of hypergraphs.
     """
-
-    def __init__(self, hypergraphs, node_size=3, mark_neuron=None, node_color='white', title=None):
+    def __init__(self, hypergraphs, node_size=3, node_color='white', node_linewidth=1, title=None):
         """
         Constructs a View object that handles the visualization
         of the given hypergraphs.
@@ -49,11 +48,11 @@ def __init__(self, hypergraphs, node_size=3, mark_neuron=None, node_color='white
         node_size (optional) : int
             Size of the nodes in the Hypergraphs
         
-        mark_neuron (optional) : int
-            Neuron with given number will be highlighted
-        
         node_color (optional) : String
             change the color of the nodes
+
+        node_linewidth (optional) : int
+            change the line width of the nodes
         """
 
         # Hyperedge drawings
@@ -71,12 +70,12 @@ def __init__(self, hypergraphs, node_size=3, mark_neuron=None, node_color='white
         # Color of the nodes
         self.node_color = node_color
 
+        # Width of the Node lines
+        self.node_linewidth = node_linewidth
+
         # Selected title of the figure
         self.title = title
 
-        # Marked node will be in a different color
-        self.mark_neuron = mark_neuron
-
         # If no data was provided, fill in dummy data
         if hypergraphs:
             self.hypergraphs = hypergraphs
@@ -125,7 +124,7 @@ def _setup_graph_visualization(self):
         # The hv.Graph visualization is used for displaying the data
         # hv.Graph displays the nodes (and optionally binary edges) of a graph
         dynamic_map = hv.DynamicMap(hv.Graph, streams=[pipe])
-        
+
         # Define options for visualization
         dynamic_map.opts(
             # Some space around the Graph in order to avoid nodes being on the
@@ -142,7 +141,7 @@ def _setup_graph_visualization(self):
             # All in black
             cmap=['#ffffff', '#ffffff'] * 50,
             # Size of the nodes
-            node_size=self.node_size, node_color=self.node_color, show_legend=True))
+            node_size=self.node_size, node_color=self.node_color, node_linewidth=self.node_linewidth, show_legend=True))
         return dynamic_map, pipe
 
     def _setup_hyperedge_drawing(self):