mainly play in plots

fluent

@@ -130,3 +130,5 @@ if __name__ == '__main__':
     app.show()
     gtk.main()
 
+
+

system/dataset.py

@@ -1,7 +1,6 @@
-#import logger
+import logger
 from scipy import array,take,asarray,shape
 import project
-#from sets import Set as set
 from itertools import izip 
 
 
@@ -30,15 +29,21 @@ class Dataset:
             enum_ids = {}
             if dim_name not in project.c_p.dim_names:
                 dim_name = project.c_p.suggest_dim_name(dim_name)
-            if not ids:
+                if not ids:
-                ids = self._create_identifiers(axis)
+                    ids = self._create_identifiers(axis)
             for num,name in enumerate(ids):
                 enum_ids[name] = num
             self.ids[dim_name] = enum_ids
             self._ids_set = self._ids_set.union(set(ids))
             self._dim_num[dim_name] = axis
             self._dim_names.append(dim_name)
-        for df,d in izip(def_list,self.dims):
+            #if dim_name in project.c_p.dim_names:
+            #    if ids:
+            #        # check that identifers are same as before
+            #        raise NotImplementedError
+            #    else:
+                    
+        for df,d in izip(def_list,self.dims): #check that data and labels match 
             df=df[1]
             if len(df)!=d and df:
                 raise ValueError,"dim size and identifyer mismatch"
@@ -70,6 +75,10 @@ class Dataset:
         n_dim = self.dims[axis]
         return [str(axis) + '_' + str(i) for i in range(n_dim)]
 
+    def index_to_id(self,dim_name,index):
+        dim_ids = self.ids[dim_name]
+        return [id for id,ind in dim_ids.items() if ind in index]
+    
 class Selection:
     """Handles selected identifiers along each dimension of a dataset"""
     def __init__(self):

system/plots.py

@@ -2,6 +2,7 @@
 import pygtk
 import gtk
 import matplotlib
+import project
 from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
 from matplotlib.axes import Subplot
 from matplotlib.figure import Figure
@@ -12,6 +13,7 @@ from matplotlib.widgets import RectangleSelector
 
 import scipy
 import logger
+import project
 
 class MainView (gtk.Notebook):
     def __init__(self):
@@ -167,6 +169,8 @@ class Plot (gtk.Frame):
         gtk.Frame.__init__(self)
         self.mark_active(False)
         self.connect('button_press_event', self.on_button_press)
+        self.sel_obj = None
+        project.c_p.attach(self)
         
     def on_button_press(self, *rest):
         logger.log('debug', 'button pressed in plot')
@@ -181,6 +185,9 @@ class Plot (gtk.Frame):
         else:
             self.set_shadow_type(gtk.SHADOW_OUT)
 
+    def update_selection(self,project):
+        self.selection_object = project.get_selection()
+    
 class EmptyView (Plot):
     def __init__(self):
         Plot.__init__(self)
@@ -228,18 +235,20 @@ class ScatterPlot (Plot):
         Plot.__init__(self)
         fig = Figure(figsize=(5,4), dpi=72)
         self.ax = ax = fig.add_subplot(111)
-        N = 200
+        self.x_dataset = project.c_p.datasets[0]
-        self.a = a = scipy.randn(N)
+        x = self.x_dataset._data
-        self.b = b = scipy.randn(N)
+        self.a = a =  x[:,0]
+        self.b = b = x[:,1]
         ax.plot(a,b,'og')
         self.canvas = FigureCanvas(fig)
         self.add(self.canvas)
+        rectprops = dict(facecolor='blue', edgecolor = 'black',
+                                 alpha=0.2, fill=True)
         sel = RectangleSelector(ax, self.line_select_callback,
-                      drawtype='box',useblit=True)
+                      drawtype='box',useblit=True,rectprops=rectprops)
         
         self.canvas.show()
 
-        
     def line_select_callback(self,event1, event2):
         'event1 and event2 are the press and release events'
         x1, y1 = event1.xdata, event1.ydata
@@ -250,11 +259,17 @@ class ScatterPlot (Plot):
         ydata = self.b
         xdata = self.a
         index =scipy.nonzero((xdata<x2) & (xdata>x1) & (ydata<y1) & (ydata>y2))
-        xdata_new = scipy.take(xdata,index)
+        if len(index)==0:
-        ydata_new = scipy.take(ydata,index)
+            logger.log('debug','No points selected!')
-        #self.ax.plot(xdata,ydata,'og')
+        else:
-        self.ax.plot(xdata_new,ydata_new,'or')
+            logger.log('debug','Selected:\n%s'%index)
-        self.canvas.draw()
+            ids = self.x_dataset.index_to_id('samples',index)
+            logger.log('debug','Selected identifiers:\n%s'%ids)
+            xdata_new = scipy.take(xdata,index)
+            ydata_new = scipy.take(ydata,index)
+            # self.ax.plot(xdata,ydata,'og')
+            self.ax.plot(xdata_new,ydata_new,'or')
+            self.canvas.draw()
     
     def get_toolbar(self, window):
         self.toolbar = NavigationToolbar(self.canvas, window)

system/project.py

@@ -1,4 +1,5 @@
 import dataset
+import scipy
 
 class Project:
     def __init__(self,name="Testing"):
@@ -27,9 +28,10 @@ class Project:
             if modifier != observer:
                 observer.update(self)
 
-    def set_selection(self,dim_name,selection):
+    def set_selection(self,sel_obj,dim_name,selection):
         """Sets selection and notifies observers"""
         current_selection = set(selection)
+        sel_obj.current_selection[dim_name] = current_selection
         self.current_selection[dim_name] = current_selection
         self.notify()
 
@@ -52,3 +54,18 @@ class Project:
         
 # FIXME: Singleton project should be removed.
 c_p = Project()
+
+#add test data
+x = scipy.rand(2000,3)
+def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
+test_data = dataset.Dataset(x,def_list)
+c_p.add_dataset(test_data)
+
+y = scipy.rand(2,2)
+def_list = [ ['samples',['1','2']], ['yclasses',['C','N']] ]
+test_data = dataset.Dataset(y,def_list)
+c_p.add_dataset(test_data)
+
+#add selection object
+c_p.sel_obj = dataset.Selection()
+