* system/plots.py: Added NetworkPlot, which may or may not work correctly.

* system/dataset.py: Removed a few lines of obsolete code.

system/dataset.py

@@ -113,9 +113,6 @@ class Dataset:
         
     def asarray(self):
         """Returns the numeric array (data) of dataset"""
-        if not self.has_array:
-            raise ValueError, "Dataset is empty"
-        else:
         return self._array
 
     def add_array(self,array):
@@ -199,13 +196,6 @@ class CategoryDataset(Dataset):
     
     def __init__(self):
         Dataset.__init__(self)
-        self.has_collection = False
-            
-    def as_array(self):
-        """Returns data as binary matrix"""
-        if not self.has_array and self.has_collection:
-            #build numeric array
-            pass
             
     def as_collection(self,dim):
         """Returns data as collection along dim"""
@@ -236,7 +226,7 @@ class GraphDataset(Dataset):
         self.has_graph = False
         
     def asnetworkx(self,nx_type='graph'):
-        dim = self.get_dim_names()[0]
+        dim = self.get_dim_name()[0]
         ids = self.get_identifiers(dim)
         adj_mat = self.asarray()
         G = self._graph_from_adj_matrix(adj_mat,labels=ids)
@@ -270,6 +260,7 @@ class GraphDataset(Dataset):
                     tail = labels[i]
                     G.add_edge(head,tail)
         return G
+
 Dataset._all_dims=set()
 
 class Selection:

system/plots.py

@@ -11,6 +11,7 @@ from matplotlib.figure import Figure
 from matplotlib.numerix import arange, sin, pi
 from matplotlib.widgets import RectangleSelector
 from matplotlib import cm
+import networkx
 from system import logger
 
 
@@ -471,44 +472,79 @@ class ScatterPlot(Plot):
 
         # find indices of selected area
         if x1>x2:
-            if y1<y2:
+            x1, x2 = x2, x1
-                index =scipy.nonzero((xdata<x1) & (xdata>x2) & (ydata>y1) & (ydata<y2))
+        if y1>y2:
-            else:
+            y1, y2 = y2, y1
-                index =scipy.nonzero((xdata<x1) & (xdata>x2) & (ydata<y1) & (ydata>y2))
+        assert x1<=x2
-        else:
+        assert y1<=y2
-            #logger.log('debug','Selection x_start less than x_end')
+
-            if y1<y2:
+        index = scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))
-                #logger.log('debug','Selection y_start less than y_end')
+        print 'index:', index
-                index =scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))
+        print 'current_dim', self.current_dim
-            else:
-                #logger.log('debug','Selection y_start bigger than y_end')
-                index =scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata<y1) & (ydata>y2))
 
         ids = self.dataset_1.get_identifiers(self.current_dim, index)
+        print 'ids', ids
         self.selection_listener(self.current_dim, ids)
 
     def selection_changed(self, selection):
         ids = selection[self.current_dim] # current identifiers
+        print 'ids: ', ids
          
         index = self.dataset_1.get_indices(self.current_dim, ids)
-        xdata_new = scipy.take(self.xaxis_data,index) #take data
+        xdata_new = scipy.take(self.xaxis_data, index) #take data
-        ydata_new = scipy.take(self.yaxis_data,index)
+        ydata_new = scipy.take(self.yaxis_data, index)
         self.ax.clear()
         self.ax.plot(self.xaxis_data,self.yaxis_data,'og')
         self.ax.plot(xdata_new,ydata_new,'or')
         self.canvas.draw()
 
 class NetworkPlot(Plot):
-    def __init__(self, dataset, name='Network Plot'):
+    def __init__(self, graph, **kw):
-        Plot.__init__(self)
+        # Set member variables and call superclass' constructor
+        self.graph = graph.asnetworkx()
+        self.dataset = graph
+        self.keywords = kw
+        self.dim_name = self.dataset.get_dim_name(0)
 
-        fig = Figure(figsize=(5,4), dpi=72)
+        if not kw.has_key('name'):
-        self.ax = ax = fig.add_subplot(111)
+            kw['name'] = self.dataset.get_name()
+        if not kw.has_key('prog'):
+            kw['prog'] = 'neato'
+        if not kw.has_key('pos') or kw['pos']:
+            print 'graph: ', self.graph, type(self.graph)
+            print 'prog:', kw['prog']
+            kw['pos'] = networkx.drawing.nx_pydot.graphviz_layout(self.graph, kw['prog'])
+        Plot.__init__(self, kw['name'])
 
-        self.canvas = FigureCanvas(fig)
+        # Keep node size and color as dicts for fast lookup
+        if kw.has_key('node_size') and cb.iterable(kw['node_size']):
+            kw.remove('node_size')
+            self.node_size = {}
+            for id, size in zip(self.dataset[self.dim_name], kw['node_size']):
+                self.node_size[id] = size
+                
+        if kw.has_key('node_color') and cb.iterable(kw['node_color']):
+            kw.remove('node_color')
+            self.node_color = {}
+            for id, color in zip(self.dataset[self.dim_name], kw['node_color']):
+                self.node_color[id] = color
+
+        # FIXME: What is figsize?
+        self.fig = Figure(figsize=(5, 4), dpi=72)
+        self.ax = self.fig.add_subplot(111)
+        # FIXME: ax shouldn't be in kw at all
+        if kw.has_key('ax'):
+            kw.pop('ax')
+
+        # Add canvas and show
+        self.canvas = FigureCanvas(self.fig)
         self.add(self.canvas)
         self.canvas.show()
 
+        # Initial draw
+        networkx.draw_networkx(self.graph, ax=self.ax, **kw)
+
+        # Setup toolbar
         self._toolbar = NavToolbar(self.canvas, None)
         self._toolbar.set_property('show-arrow', False)
         self._toolbar.set_select_callback(self.rectangle_select_callback)
@@ -516,8 +552,49 @@ class NetworkPlot(Plot):
     def get_toolbar(self):
         return self._toolbar
 
+    def rectangle_select_callback(self, x1, y1, x2, y2):
+        'event1 and event2 are the press and release events'
+        pos = self.kw['pos']
+        ydata = zeros((len(pos),),'l')
+        xdata = zeros((len(pos),),'l')
+        node_ids = []
+        c = 0
+        for name,(x,y) in pos.items():
+            node_ids.append(name)
+            xdata[c] = x
+            ydata[c] = y
+            c+=1
+        
+        # find indices of selected area
+        if x1 > x2:
+            x1, x2 = x2, x1
+        if y1 > y2:
+            y1, y2 = y2, y1
+        index = nonzero((xdata<x1) & (xdata>x2) & (ydata>y1) & (ydata<y2))
+
+        ids = [node_ids[i] for i in index]
+        self.selection_listener(self.dataset.get_dim_name(0), ids)
+
     def selection_changed(self, selection):
-        return None
+        ids = selection[self.dataset.get_dim_name(0)] # current identifiers
+        selected_nodes = list(ids.intersection(set(self.graph.nodes())))
+        unselected_nodes = list(ids.difference(selected_nodes))
+
+        unselected_colors = [self.node_color[x] for x in unselected_nodes]
+        unselected_sizes = [self.node_size[x] for x in unselected_nodes]
+        selected_sizes = [self.node_size[x] for x in selected_nodes]
+
+        self.ax.clear()
+        networkx.draw_networkx_edges(self.graph, self.kw['pos'], edge_list=self.graph.edges(), \
+            ax=self.ax, *kw)
+        
+        networkx.draw_networkx_nodes(self.graph, self.kw['pos'], node_list=unselected_nodes, \
+            node_color=unselected_colors, node_size=unselected_sizes, ax=self.ax, *kw)
+
+        networkx.draw_networkx_nodes(self.graph, self.kw['pos'], node_list=selected_nodes, \
+            node_color='black', node_size=selected_sizes, ax=self.ax, *kw)
+        
+        self.canvas.draw()
 
 
 # Create a view-changed signal that should be emitted every time

workflows/test_workflow.py

@@ -4,6 +4,7 @@ from system import dataset, logger, plots, workflow
 #import gostat
 from scipy import array,randn,log
 import cPickle
+import networkx
 
 class TestWorkflow (workflow.Workflow):
 
@@ -103,7 +104,15 @@ class TestDataFunction(workflow.Function):
         x = randn(20,30)
         X = dataset.Dataset(x)
         p = plots.ScatterPlot(X, X, 'rows', 'rows', '0_1', '0_2')
-        return [X, plots.SinePlot(), p]
+        graph = networkx.XGraph()
+        for x in 'ABCDEF':
+            for y in 'ADE':
+                graph.add_edge(x, y, 3)
+        print networkx.adj_matrix(graph)
+        ds = dataset.GraphDataset(array(networkx.adj_matrix(graph)))
+        ds_plot = plots.NetworkPlot(ds)
+            
+        return [X, ds, plots.SinePlot(), p, ds_plot]
 
 class DatasetLog(workflow.Function):
     def __init__(self):