import os,sys from itertools import izip import pygtk import gobject import gtk import fluents from system import logger import matplotlib from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas from matplotlib.backend_bases import NavigationToolbar2,cursors from matplotlib.backends.backend_gtk import FileChooserDialog,cursord from matplotlib.widgets import SubplotTool,RectangleSelector 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 import scipy # global active mode. Used by toolbars to communicate correct mode active_mode = 'default' 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 ## Set up a VBox with a label wrapped in an event box. label = gtk.Label() ebox = gtk.EventBox() ebox.add(label) vbox = gtk.VBox() vbox.pack_start(ebox, expand=False) vbox.pack_start(gtk.HSeparator(), expand=False) self._ebox_button_event = ebox.connect("button-press-event", self.on_button_press_event) ## Keep the references for later use. self._vbox = vbox self._ebox = ebox self._view_title = label self.add(vbox) 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._vbox.add(self._view) self._view_title.set_text(self._view.title) self.show_all() self._view.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._ebox.set_state(gtk.STATE_ACTIVE) 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._ebox.set_state(gtk.STATE_NORMAL) 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 if view._view_frame: view._view_frame.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 if self._view: self._view.hide() self._vbox.remove(self._view) self._view._view_frame = None self._view_title.set_text(view.title) self._vbox.add(view) view.show() view._view_frame = self 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 get_active_view_frame(self): if self.get_current_page() == 0: return self.get_active_small_view() else: return self._large_view 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 View (gtk.Frame): """The base class of everything that is shown in the center view of fluents. Most views should rather subclass Plot, which automatically handles freezing and toolbars, and sets up matplotlib Figure and Canvas objects. """ def __init__(self, title): gtk.Frame.__init__(self) self.title = title self.set_shadow_type(gtk.SHADOW_NONE) self._view_frame = None def get_toolbar(self): return None class EmptyView (View): """EmptyView is shown in ViewFrames that are unused.""" def __init__(self): View.__init__(self, 'Empty view') self.set_label(None) label = gtk.Label('No view') ebox = gtk.EventBox() ebox.add(label) self.add(ebox) label.show() ebox.show() self.show() class Plot (View): def __init__(self, title): View.__init__(self, title) self.selection_listener = None self.fig = Figure() self.canvas = FigureCanvas(self.fig) self._background = None self._frozen = False self._toolbar = PlotToolbar(self) self.canvas.add_events(gtk.gdk.ENTER_NOTIFY_MASK) self.current_dim = None self._current_selection = None def set_frozen(self, frozen): """A frozen plot will not be updated when the current selection is changed.""" self._frozen = frozen if not frozen and self._current_selection != None: self.set_current_selection(self._current_selection) def get_title(self): return self.title def get_toolbar(self): return self._toolbar def selection_changed(self, dim_name, selection): """ Selection observer handle. A selection change in a plot is only drawn if: 1.) plot is sensitive to selections (not freezed) 2.) plot is visible (has a view) 3.) the selections dim_name is the plot's dimension. """ self._current_selection = selection if self._frozen \ or not self.get_property('visible') \ or self.current_dim != dim_name: 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 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) self.canvas.mpl_connect('resize_event', self.clear_background) 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)) if self.use_blit: self.ax.draw_artist(line_coll) line_coll.get_clip_box().get_bounds() self.canvas.blit() 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() 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() 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) 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) self.current_dim = self.dim_name 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) def get_toolbar(self): return self._toolbar def rectangle_select_callback(self, x1, y1, x2, y2): 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) & (ydataabs(dy)): dy = dx else: dx = dy elif event.key=='x': dy = 0 elif event.key=='y': dx = 0 elif event.key=='shift': if 2*abs(dx) < abs(dy): dx=0 elif 2*abs(dy) < abs(dx): dy=0 elif(abs(dx)>abs(dy)): dy=dy/abs(dy)*abs(dx) else: dx=dx/abs(dx)*abs(dy) return (dx,dy) for cur_xypress in self._xypress: lastx, lasty, a, ind, lim, trans = cur_xypress xmin, xmax, ymin, ymax = lim #safer to use the recorded button at the press than current button: #multiple button can get pressed during motion... if self._button_pressed==1: lastx, lasty = trans.inverse_xy_tup( (lastx, lasty) ) x, y = trans.inverse_xy_tup( (event.x, event.y) ) if a.get_xscale()=='log': dx=1-lastx/x else: dx=x-lastx if a.get_yscale()=='log': dy=1-lasty/y else: dy=y-lasty dx,dy=format_deltas(event,dx,dy) if a.get_xscale()=='log': xmin *= 1-dx xmax *= 1-dx else: xmin -= dx xmax -= dx if a.get_yscale()=='log': ymin *= 1-dy ymax *= 1-dy else: ymin -= dy ymax -= dy elif self._button_pressed==3: try: dx=(lastx-event.x)/float(a.bbox.width()) dy=(lasty-event.y)/float(a.bbox.height()) dx,dy=format_deltas(event,dx,dy) if a.get_aspect() != 'auto': dx = 0.5*(dx + dy) dy = dx alphax = pow(10.0,dx) alphay = pow(10.0,dy) lastx, lasty = trans.inverse_xy_tup( (lastx, lasty) ) if a.get_xscale()=='log': xmin = lastx*(xmin/lastx)**alphax xmax = lastx*(xmax/lastx)**alphax else: xmin = lastx+alphax*(xmin-lastx) xmax = lastx+alphax*(xmax-lastx) if a.get_yscale()=='log': ymin = lasty*(ymin/lasty)**alphay ymax = lasty*(ymax/lasty)**alphay else: ymin = lasty+alphay*(ymin-lasty) ymax = lasty+alphay*(ymax-lasty) except OverflowError: warnings.warn('Overflow while panning') return a.set_xlim(xmin, xmax) a.set_ylim(ymin, ymax) self.canvas.draw() def _on_button_release(self, event): 'the release mouse button callback in pan/zoom mode' self.canvas.mpl_disconnect(self._motion_notify) if not self._xypress: return self._xypress = None self._button_pressed=None self.canvas.draw() class ZoomPlotMode (PlotMode): def __init__(self, plot): PlotMode.__init__(self, plot, 'zoom', 'Zoom to rectangle','zoom_to_rect.png') self._selectors = {} def activate(self): for ax in self.canvas.figure.get_axes(): props = dict(facecolor = 'blue', edgecolor = 'black', alpha = 0.3, fill = True) rs = RectangleSelector(ax, self._on_select, drawtype='box', useblit=True, rectprops = props) self.canvas.draw() self._selectors[rs] = ax def deactivate(self): self._mpl_disconnect_all() self._selectors = {} def _on_select(self, start, end): ax = start.inaxes ax.set_xlim((min(start.xdata, end.xdata), max(start.xdata, end.xdata))) ax.set_ylim((min(start.ydata, end.ydata), max(start.ydata, end.ydata))) self.canvas.draw() class SelectPlotMode (PlotMode): def __init__(self, plot): PlotMode.__init__(self, plot, 'select', 'Select within rectangle', 'select.png') self._selectors = {} def activate(self): for ax in self.canvas.figure.get_axes(): props = dict(facecolor = 'blue', edgecolor = 'black', alpha = 0.3, fill = True) rs = RectangleSelector(ax, self._on_select, drawtype='box', useblit=True, rectprops = props) self.canvas.draw() self._selectors[rs] = ax def deactivate(self): self._mpl_disconnect_all() self._selectors = {} def _on_select(self, start, end): self.plot.rectangle_select_callback(start.xdata, start.ydata, end.xdata, end.ydata) class PlotToolbar(gtk.Toolbar): def __init__(self, plot): gtk.Toolbar.__init__(self) self.plot = plot self.canvas = plot.canvas self._current_mode = None self.tooltips = gtk.Tooltips() ## Maps toolbar buttons to PlotMode objects. self._mode_buttons = {} self.set_property('show-arrow', False) self.canvas.connect('enter-notify-event', self.on_enter_notify) self.show() self.add_mode(DefaultPlotMode(self.plot)) self.add_mode(PanPlotMode(self.plot)) self.add_mode(ZoomPlotMode(self.plot)) self.add_mode(SelectPlotMode(self.plot)) self.insert(gtk.SeparatorToolItem(), -1) self.set_style(gtk.TOOLBAR_ICONS) # Set up freeze button btn = gtk.ToggleToolButton() fname = os.path.join(fluents.ICONDIR, "freeze.png") image = gtk.Image() image.set_from_file(fname) btn.set_icon_widget(image) btn.connect('toggled', self._on_freeze_toggle) self.insert(btn, -1) self.show_all() def add_mode(self, mode): """Adds a new mode to the toolbar.""" if len(self._mode_buttons) > 0: other = self._mode_buttons.keys()[0] else: other = None btn = gtk.RadioToolButton(other) btn.set_icon_widget(mode.get_icon()) btn.set_tooltip(self.tooltips, mode.tooltip, 'Private') btn.connect('toggled', self._on_mode_toggle) self._mode_buttons[btn] = mode self.insert(btn, -1) if self._current_mode == None: self._current_mode = mode def get_mode(self): """Returns the active mode name.""" if self._current_mode: return self._current_mode.name return None def get_mode_by_name(self, mode_name): """Returns the mode with the given name or None.""" for m in self._mode_buttons.values(): if m.name == mode_name: return m return None def get_button(self, mode_name): """Returns the button that corresponds to a mode name.""" for b, m in self._mode_buttons.items(): if m.name == mode_name: return b return None def set_mode(self, mode_name): """Sets a mode by name. Returns the mode or None""" if mode_name == self._current_mode.name: return None if self._current_mode: self._current_mode.deactivate() new_mode = self.get_mode_by_name(mode_name) if new_mode: new_mode.activate() self._current_mode = self.get_mode_by_name(mode_name) else: logger.log('warning', 'No such mode: %s' % mode_name) if self.get_button(mode_name) and \ not self.get_button(mode_name).get_active(): self.get_button(mode_name).set_active(True) globals()['active_mode'] = mode_name return self._current_mode def _on_mode_toggle(self, button): if button.get_active(): self.set_mode(self._mode_buttons[button].name) def _on_freeze_toggle(self, button): self.plot.set_frozen(button.get_active()) def on_enter_notify(self, widget, event): self.set_mode(active_mode) # Create a view-changed signal that should be emitted every time # the active view changes. gobject.signal_new('view-changed', MainView, gobject.SIGNAL_RUN_LAST, gobject.TYPE_NONE, (gobject.TYPE_PYOBJECT,)) # Create focus-changed signal gobject.signal_new('focus-changed', ViewFrame, gobject.SIGNAL_RUN_LAST, gobject.TYPE_NONE, (gobject.TYPE_PYOBJECT, gobject.TYPE_BOOLEAN,))