import os,sys import pygtk import gobject import gtk import matplotlib import scipy from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas from matplotlib.backends.backend_gtkagg import NavigationToolbar2GTK as NavigationToolbar2 from matplotlib.axes import Subplot from matplotlib.figure import Figure from matplotlib import cm,cbook from pylab import Polygon from matplotlib.collections import LineCollection from matplotlib.mlab import prctile import networkx from system import logger from itertools import izip class ObjectTable: """A 2D table of elements.""" def __init__(self, xsize=0, ysize=0, creator=None): self._elements = [] self._creator = creator or (lambda : None) self.xsize = xsize self.ysize = ysize self.resize(xsize, ysize) def resize(self, xsize, ysize): """Resizes the table by removing and creating elements as required.""" # Delete or append new rows del self._elements[ysize:] new_rows = ysize - len(self._elements) self._elements.extend([list() for i in range(new_rows)]) # Delete or append new columns for row in self._elements: del row[xsize:] new_elems = xsize - len(row) row.extend([self._creator() for i in range(new_elems)]) def __getitem__(self, index): x, y = index return self._elements[y][x] def __setitem__(self, index, value): x, y = index self._elements[y][x] = value class ViewFrame (gtk.Frame): """ A ViewFrame is a gtk bin that contains a view. The ViewFrame is either active or inactive, and belongs to a group of VeiwFrames of which only one can be active at any time. """ def __init__(self, view_frames): gtk.Frame.__init__(self) self.focused = False self.view_frames = view_frames self.empty_view = EmptyView() self._button_event = None view_frames.append(self) if len(view_frames) == 1: self.focus() else: self.focused = True self.unfocus() # Get dropped views self.drag_dest_set(gtk.DEST_DEFAULT_ALL, [("GTK_TREE_MODEL_ROW", gtk.TARGET_SAME_APP, 7)], gtk.gdk.ACTION_LINK) self.connect("drag-data-received", self.on_drag_data_received) # Set view self._view = self.empty_view self._view.connect("button-press-event", self.on_button_press_event) self.add(self._view) self._view.show() self.show() def focus(self): """Gets focus and ensures that no other window is in focus.""" if self.focused: self.emit('focus-changed', self, True) return self for frame in self.view_frames: frame.unfocus() self.set_shadow_type(gtk.SHADOW_IN) self.focused = True self.emit('focus-changed', self, True) return self def unfocus(self): """Removes focus from the ViewFrame. Does nothing if unfocused.""" if not self.focused: return self.set_shadow_type(gtk.SHADOW_OUT) self.focused = False self.emit('focus-changed', self, False) def set_view(self, view): """Set view to view or to empty view if parameter is None""" # if None is passed, use empty view if view == None: view = self.empty_view # do nothing if the view is already there if view == self._view: return # detach view from current parent view_parent = view.get_parent() if view_parent: view_parent.set_view(None) # switch which widget we are listening to if self._button_event: self._view.disconnect(self._button_event) self._button_event = view.connect("button-press-event", self.on_button_press_event) # remove old view, set new view self._view.hide() self.remove(self._view) self.add(view) view.show() self._view = view def get_view(self): """Returns current view, or None if the empty view is set.""" if self._view == self.empty_view: return None return self._view def on_button_press_event(self, widget, event): if not self.focused: self.focus() def on_drag_data_received(self, widget, drag_context, x, y, selection, info, timestamp): treestore, path = selection.tree_get_row_drag_data() iter = treestore.get_iter(path) obj = treestore.get_value(iter,2) if isinstance(obj, Plot): self.set_view(obj) self.focus() class MainView (gtk.Notebook): def __init__(self): gtk.Notebook.__init__(self) self.set_show_tabs(False) self.set_show_border(False) self._view_frames = [] self._views = ObjectTable(2, 2, lambda : ViewFrame(self._view_frames)) self._small_views = gtk.Table(2, 2, True) self._small_views.set_col_spacings(4) self._small_views.set_row_spacings(4) self._large_view = ViewFrame(list()) self.update_small_views() for vf in self._view_frames: vf.connect('focus-changed', self.on_view_focus_changed) self.append_page(self._small_views) self.append_page(self._large_view) self.show() self.set_current_page(0) def __getitem__(self, x, y): return self._views[x, y] def update_small_views(self): for x in range(self._views.xsize): for y in range(self._views.ysize): child = self._views[x,y] self._small_views.attach(child, x, x+1, y, y+1) def get_active_small_view(self): for vf in self._view_frames: if vf.focused: return vf return None def goto_large(self): if self.get_current_page() == 1: return vf = self.get_active_small_view() view = vf.get_view() vf.set_view(None) self._large_view.set_view(view) self.set_current_page(1) def goto_small(self): if self.get_current_page() == 0: return vf = self.get_active_small_view() view = self._large_view.get_view() self._large_view.set_view(None) vf.set_view(view) self.set_current_page(0) def insert_view(self, view): if self.get_current_page() == 0: vf = self.get_active_small_view() else: vf = self._large_view vf.set_view(view) def set_all_plots(self, plots): for vf in self._view_frames: if plots: vf.set_view(plots.pop()) else: vf.set_view(None) def show(self): for vf in self._view_frames: vf.show() self._small_views.show() gtk.Notebook.show(self) def on_view_focus_changed(self, widget, vf, focused): if focused: self.emit('view-changed', vf) class Plot (gtk.Frame): def __init__(self, title): gtk.Frame.__init__(self) self.sel_obj = None self.title = title self.selection_listener = None self.set_shadow_type(gtk.SHADOW_NONE) self._background = None self.canvas = None self.fig = Figure(figsize=(5,4), dpi=72) self.canvas = FigureCanvas(self.fig) self.fig.set_facecolor('white') self._sel_sensitive = True def set_selection_sensitive(self,event): if event: if event.get_active(): logger.log('debug','Selection freezed') self._sel_sensitive = False else: logger.log('debug','Selections active') self._sel_sensitive = True def get_title(self): return self.title def selection_changed(self, selection): if not self._sel_sensitive or not self.get_property('visible'): return self.set_current_selection(selection) def set_selection_listener(self, listener): """Allow project to listen to selections. The selection will propagate back to all plots through the selection_changed() method. The listener will be called as listener(dimension_name, ids). """ self.selection_listener = listener def get_toolbar(self): return None class EmptyView (Plot): def __init__(self): Plot.__init__(self, 'Empty view') label = gtk.Label('No view') ebox = gtk.EventBox() ebox.add(label) self.add(ebox) label.show() ebox.show() self.show() class NavToolbar(NavigationToolbar2): toolitems = (('Select', 'Select within rectangle', 'zoom_to_rect.png', 'select'),) + NavigationToolbar2.toolitems def __init__(self, *args): NavigationToolbar2.__init__(self, *args) self._select_callback = None self.message.hide() def select(self, *args): """Selection mode selected handler.""" if self._active == 'SELECT': self._active = None else: self._active = 'SELECT' if self._idPress is not None: self._idPress = self.canvas.mpl_disconnect(self._idPress) self.mode = '' if self._idRelease is not None: self._idRelease = self.canvas.mpl_disconnect(self._idRelease) self.mode = '' if self._active: self._idPress = self.canvas.mpl_connect('button_press_event', self.press_select) self._idRelease = self.canvas.mpl_connect('button_release_event', self.release_select) self.mode = 'Select rectangle mode' self.set_message(self.mode) def set_message(self, s): """Set status in toolbar to string s. Overrided to make sure message can be updated even when drawing rubberband. """ self.message.set_label(s) def press_select(self, event): """Mouse button pressed handler for selection mode.""" x, y = event.x, event.y for i, a in enumerate(self.canvas.figure.get_axes()): if event.inaxes==a and event.inaxes.get_navigate(): xmin, xmax = a.get_xlim() ymin, ymax = a.get_ylim() lim = xmin, xmax, ymin, ymax self._xypress = x, y, a, i, lim, a.transData.deepcopy() break self.press(event) def release_select(self, event): """Mouse button released handler for selection mode.""" # only release if button was pressed inside first? if self._xypress: x, y = event.x, event.y lastx, lasty, a, ind, lim, trans = self._xypress lastx, lasty = a.transData.inverse_xy_tup( (lastx, lasty) ) x, y = a.transData.inverse_xy_tup( (x, y) ) if self._select_callback: self._select_callback(lastx, lasty, x, y) self._xypress = None self.push_current() self.release(event) def mouse_move(self, event): """Extend NavigationToolbar2.mouse_move to provide selection support.""" from matplotlib.backend_bases import cursors # Only update the rubberband for selection mode when mouse is # within the plotting area. if event.inaxes and self._active=='SELECT': if self._lastCursor != cursors.SELECT_REGION: self.set_cursor(cursors.SELECT_REGION) self._lastCursor = cursors.SELECT_REGION if self._xypress is not None: x, y = event.x, event.y lastx, lasty, a, ind, lim, trans= self._xypress self.draw_rubberband(event, x, y, lastx, lasty) NavigationToolbar2.mouse_move(self, event) def set_select_callback(self, listener): """Allow plots to register a callback for selection events. The callback will be called as listener(x1, y1, x2, y2). All coordinates are in the plot coordinate system, not pixels or widget coordinates. """ self._select_callback = listener class PlotToolbar(NavToolbar): """Extensions to existing toolbar """ def __init__(self, *args): NavToolbar.__init__(self, *args) self.tb_freeze = gtk.ToolItem() self.chk = gtk.CheckButton () self.chk.set_label ('Freeze') self.tb_freeze.add (self.chk) self.tb_freeze.set_tooltip(self.tooltips, 'Freeze current selection') self.insert(self.tb_freeze,-1) toolitem = gtk.SeparatorToolItem() self.insert(toolitem, -1) self.show_all() self.message.hide() class LineViewPlot(Plot): """Line view of current selection, no interaction Only works on 2d-arrays input: -- major_axis : dim_number for line dim (see scipy.ndarray for axis def.) -- minor_axis : needs definition only for higher order arrays ps: slow (cant get linecollection and blit to work) """ def __init__(self, dataset,major_axis=1,minor_axis=None, name="Line view"): self.use_blit = False self._last_index = [] self._data = dataset.asarray() self.dataset = dataset Plot.__init__(self, name) self.ax = self.fig.add_subplot(111) self.ax.set_title(self.get_title()) self.current_dim = self.dataset.get_dim_name(major_axis) if len(self._data.shape)==2 and not minor_axis: minor_axis = major_axis-1 #initial draw x_axis = scipy.arange(self._data.shape[minor_axis]) self.line_segs=[] for xi in range(self._data.shape[major_axis]): yi = self._data.take([xi],major_axis) self.line_segs.append([(xx,yy) for xx,yy in izip(x_axis,yi)]) #background xax = scipy.arange(self._data.shape[0]) verts_0 = [] #100,0 verts_1 = [] # 90,10 verts_2 = [] # 75,25 med = [] for i in xax: pp = prctile(self._data[i,:],[0.,5.,25,50.,75.,95.,100]) verts_0.append((i,pp[0])) verts_1.append((i,pp[1])) verts_2.append((i,pp[2])) for i in xax[::-1]: pp = prctile(self._data[i,:],[0.,5.,25,50.,75.,95.,100]) verts_0.append((i,pp[-1])) verts_1.append((i,pp[-2])) verts_2.append((i,pp[-3])) med.append(pp[3]) bck0 = Polygon(verts_0,alpha=.15,lw=0) bck1 = Polygon(verts_1,alpha=.15,lw=0) bck2 = Polygon(verts_2,alpha=.15,lw=0) self.ax.add_patch(bck0) self.ax.add_patch(bck1) self.ax.add_patch(bck2) self.ax.plot(xax,med,'b') self.ax.autoscale_view() self.add(self.canvas) self.canvas.show() #FIXME: Lineview plot cannot do selections -> disable in toolbar self._toolbar = PlotToolbar(self.canvas, None) self._toolbar.set_property('show-arrow', False) self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive) self.canvas.mpl_connect('resize_event',self.clear_background) def get_toolbar(self): return self._toolbar def clear_background(self,event): self._background = None def set_current_selection(self, selection): ids = selection[self.current_dim] # current identifiers index = self.dataset.get_indices(self.current_dim, ids) if self.use_blit: if self._background is None: self._bbox = self.ax.bbox.deepcopy() self._background = self.canvas.copy_from_bbox(self.ax.bbox) self.canvas.restore_region(self._background) if len(index)>0: # do we have a selection if len(self.ax.collections)>0: self.ax.collections = [] segs = [self.line_segs[i] for i in index] line_coll = LineCollection(segs,colors=(1,0,0,1)) line_coll.set_clip_box(self.ax.bbox) self.ax.update_datalim(line_coll.get_verts(self.ax.transData)) self._toolbar.forward() if self.use_blit: self.ax.draw_artist(line_coll) #print "\nLine collection clip box:" line_coll.get_clip_box().get_bounds() #print "\nLine collection bbox:" #print self.ax.bbox.get_bounds() #print "Background bbox:" #print self._bbox.get_bounds() #self.canvas.blit(self._bbox) self.canvas.blit() #self.ax.draw_artist(line_coll) else: self.ax.add_collection(line_coll) self.canvas.draw() class ScatterMarkerPlot(Plot): """The ScatterMarkerPlot is faster than regular scatterplot, but has no color and size options.""" def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,s=6, name="Scatter plot"): Plot.__init__(self, name) self.use_blit = False self._background = None self.ax = self.fig.add_subplot(111) self.ax.axhline(0,color='k',lw=1.,zorder=1) self.ax.axvline(0,color='k',lw=1.,zorder=1) self.current_dim = id_dim self.dataset_1 = dataset_1 self.ms = s self._selection_line = None x_index = dataset_1[sel_dim][id_1] y_index = dataset_2[sel_dim][id_2] self.xaxis_data = dataset_1._array[:,x_index] self.yaxis_data = dataset_2._array[:,y_index] self.ax.plot(self.xaxis_data,self.yaxis_data,'o',markeredgewidth=0,markersize=s) self.ax.set_title(self.get_title()) self.add(self.canvas) self.canvas.show() # add toolbar self._toolbar = PlotToolbar(self.canvas, None) self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive) self._toolbar.set_property('show-arrow', False) self._toolbar.set_select_callback(self.rectangle_select_callback) def get_toolbar(self): return self._toolbar def rectangle_select_callback(self, x1, y1, x2, y2): ydata = self.yaxis_data xdata = self.xaxis_data # find indices of selected area if x1>x2: x1, x2 = x2, x1 if y1>y2: y1, y2 = y2, y1 assert x1<=x2 assert y1<=y2 index = scipy.nonzero((xdata>x1) & (xdatay1) & (ydata0: return xdata_new = self.xaxis_data.take(index) #take data ydata_new = self.yaxis_data.take(index) #remove old selection if self._selection_line: self.ax.lines.remove(self._selection_line) self._selection_line, = self.ax.plot(xdata_new,ydata_new,marker='o',markersize=self.ms,linestyle=None,markerfacecolor='r') self._toolbar.forward() #update data lims before draw if self.use_blit: self.ax.draw_artist(self._selection_line) self.canvas.blit() else: self.canvas.draw() class ScatterPlot(Plot): """The ScatterPlot is slower than scattermarker, but has size option.""" def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,c='b',s=30,sel_dim_2=None, name="Scatter plot"): Plot.__init__(self, name) self.use_blit = False self.ax = self.fig.add_subplot(111) self.current_dim = id_dim self.dataset_1 = dataset_1 x_index = dataset_1[sel_dim][id_1] if sel_dim_2: y_index = dataset_2[sel_dim_2][id_2] else: y_index = dataset_2[sel_dim][id_2] self.xaxis_data = dataset_1._array[:,x_index] self.yaxis_data = dataset_2._array[:,y_index] lw = scipy.zeros(self.xaxis_data.shape) sc = self.ax.scatter(self.xaxis_data,self.yaxis_data,s=s,c=c,linewidth=lw,edgecolor='k',alpha=.6,cmap = cm.jet) if len(c)>1: self.fig.colorbar(sc,ticks=[],fraction=.05) self.ax.axhline(0,color='k',lw=1.,zorder=1) self.ax.axvline(0,color='k',lw=1.,zorder=1) self.ax.set_title(self.get_title()) # collection self.coll = self.ax.collections[0] # add canvas to widget self.add(self.canvas) self.canvas.show() # create toolbar self._toolbar = PlotToolbar(self.canvas, None) self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive) self._toolbar.set_property('show-arrow', False) self._toolbar.set_select_callback(self.rectangle_select_callback) def get_toolbar(self): return self._toolbar def rectangle_select_callback(self, x1, y1, x2, y2): ydata = self.yaxis_data xdata = self.xaxis_data # find indices of selected area if x1>x2: x1, x2 = x2, x1 if y1>y2: y1, y2 = y2, y1 assert x1<=x2 assert y1<=y2 index = scipy.nonzero((xdata>x1) & (xdatay1) & (ydata0: lw.put(2.,index) self.coll.set_linewidth(lw) self._toolbar.forward() #update data lims before draw if self.use_blit: self.canvas.blit() self.ax.draw_artist(self.coll) else: self.canvas.draw() class NetworkPlot(Plot): def __init__(self, dataset, **kw): # Set member variables and call superclass' constructor self.graph = dataset.asnetworkx() self.dataset = dataset self.keywords = kw self.dim_name = self.dataset.get_dim_name(0) if not kw.has_key('name'): kw['name'] = self.dataset.get_name() if not kw.has_key('prog'): kw['prog'] = 'neato' if not kw.has_key('pos') or kw['pos']: kw['pos'] = networkx.pygraphviz_layout(self.graph, kw['prog']) Plot.__init__(self, kw['name']) # Keep node size and color as dicts for fast lookup self.node_size = {} if kw.has_key('node_size') and cb.iterable(kw['node_size']): kw.remove('node_size') for id, size in zip(self.dataset[self.dim_name], kw['node_size']): self.node_size[id] = size else: for id in dataset[self.dim_name]: self.node_size[id] = 40 self.node_color = {} if kw.has_key('node_color') and cb.iterable(kw['node_color']): kw.remove('node_color') for id, color in zip(self.dataset[self.dim_name], kw['node_color']): self.node_color[id] = color else: self.node_color = None # for id in self.dataset[self.dim_name]: # self.node_color[id] = 'red' if kw.has_key('node_color'): kw.pop('node_color') self.ax = self.fig.add_subplot(111) self.ax.set_position([0.01,0.01,.99,.99]) self.ax.set_xticks([]) self.ax.set_yticks([]) # FIXME: ax shouldn't be in kw at all if kw.has_key('ax'): kw.pop('ax') # Add canvas and show self.add(self.canvas) self.canvas.show() # Initial draw networkx.draw_networkx(self.graph, ax=self.ax, **kw) # Setup toolbar self._toolbar = PlotToolbar(self.canvas, None) self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive) self._toolbar.set_property('show-arrow', False) self._toolbar.set_select_callback(self.rectangle_select_callback) 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.keywords['pos'] ydata = scipy.zeros((len(pos),),'l') xdata = scipy.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 = scipy.nonzero((xdata>x1) & (xdatay1) & (ydata