732 lines
25 KiB
Python
732 lines
25 KiB
Python
import os,sys
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import pygtk
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import gobject
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import gtk
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import matplotlib
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import scipy
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from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
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from matplotlib.backends.backend_gtkagg import NavigationToolbar2GTK as NavigationToolbar2
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from matplotlib.axes import Subplot
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from matplotlib.figure import Figure
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from matplotlib.numerix import arange, sin, pi
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from matplotlib.widgets import RectangleSelector
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from matplotlib import cm
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import networkx
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from system import logger
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class ObjectTable:
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"""A 2D table of elements."""
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def __init__(self, xsize=0, ysize=0, creator=None):
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self._elements = []
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self._creator = creator or (lambda : None)
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self.xsize = xsize
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self.ysize = ysize
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self.resize(xsize, ysize)
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def resize(self, xsize, ysize):
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"""Resizes the table by removing and creating elements as required."""
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# Delete or append new rows
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del self._elements[ysize:]
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new_rows = ysize - len(self._elements)
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self._elements.extend([list() for i in range(new_rows)])
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# Delete or append new columns
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for row in self._elements:
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del row[xsize:]
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new_elems = xsize - len(row)
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row.extend([self._creator() for i in range(new_elems)])
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def __getitem__(self, index):
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x, y = index
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return self._elements[y][x]
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def __setitem__(self, index, value):
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x, y = index
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self._elements[y][x] = value
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class ViewFrame (gtk.Frame):
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"""
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A ViewFrame is a gtk bin that contains a view.
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The ViewFrame is either active or inactive, and belongs to a group of
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VeiwFrames of which only one can be active at any time.
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"""
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def __init__(self, view_frames):
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gtk.Frame.__init__(self)
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self.focused = False
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self.view_frames = view_frames
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self.empty_view = EmptyView()
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self._button_event = None
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view_frames.append(self)
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if len(view_frames) == 1:
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self.focus()
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else:
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self.focused = True
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self.unfocus()
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# Get dropped views
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self.drag_dest_set(gtk.DEST_DEFAULT_ALL,
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[("GTK_TREE_MODEL_ROW", gtk.TARGET_SAME_APP, 7)],
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gtk.gdk.ACTION_LINK)
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self.connect("drag-data-received", self.on_drag_data_received)
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# Set view
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self._view = self.empty_view
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self._view.connect("button-press-event", self.on_button_press_event)
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self.add(self._view)
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self._view.show()
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self.show()
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def focus(self):
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"""Gets focus and ensures that no other window is in focus."""
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if self.focused:
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self.emit('focus-changed', self, True)
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return self
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for frame in self.view_frames:
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frame.unfocus()
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self.set_shadow_type(gtk.SHADOW_IN)
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self.focused = True
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self.emit('focus-changed', self, True)
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return self
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def unfocus(self):
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"""Removes focus from the ViewFrame. Does nothing if unfocused."""
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if not self.focused:
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return
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self.set_shadow_type(gtk.SHADOW_OUT)
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self.focused = False
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self.emit('focus-changed', self, False)
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def set_view(self, view):
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"""Set view to view or to empty view if parameter is None"""
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# if None is passed, use empty view
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if view == None:
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view = self.empty_view
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# do nothing if the view is already there
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if view == self._view:
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return
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# detach view from current parent
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view_parent = view.get_parent()
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if view_parent:
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view_parent.set_view(None)
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# switch which widget we are listening to
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if self._button_event:
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self._view.disconnect(self._button_event)
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self._button_event = view.connect("button-press-event",
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self.on_button_press_event)
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# remove old view, set new view
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self._view.hide()
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self.remove(self._view)
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self.add(view)
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view.show()
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self._view = view
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def get_view(self):
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"""Returns current view, or None if the empty view is set."""
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if self._view == self.empty_view:
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return None
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return self._view
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def on_button_press_event(self, widget, event):
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if not self.focused:
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self.focus()
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def on_drag_data_received(self, widget, drag_context, x, y,
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selection, info, timestamp):
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treestore, path = selection.tree_get_row_drag_data()
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iter = treestore.get_iter(path)
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obj = treestore.get_value(iter,2)
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if isinstance(obj, Plot):
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self.set_view(obj)
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self.focus()
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class MainView (gtk.Notebook):
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def __init__(self):
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gtk.Notebook.__init__(self)
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self.set_show_tabs(False)
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self.set_show_border(False)
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self._view_frames = []
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self._views = ObjectTable(2, 2, lambda : ViewFrame(self._view_frames))
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self._small_views = gtk.Table(2, 2, True)
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self._small_views.set_col_spacings(4)
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self._small_views.set_row_spacings(4)
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self._large_view = ViewFrame(list())
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self.update_small_views()
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for vf in self._view_frames:
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vf.connect('focus-changed', self.on_view_focus_changed)
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self.append_page(self._small_views)
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self.append_page(self._large_view)
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self.show()
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self.set_current_page(0)
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def __getitem__(self, x, y):
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return self._views[x, y]
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def update_small_views(self):
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for x in range(self._views.xsize):
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for y in range(self._views.ysize):
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child = self._views[x,y]
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self._small_views.attach(child, x, x+1, y, y+1)
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def get_active_small_view(self):
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for vf in self._view_frames:
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if vf.focused:
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return vf
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return None
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def goto_large(self):
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if self.get_current_page() == 1:
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return
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vf = self.get_active_small_view()
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view = vf.get_view()
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vf.set_view(None)
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self._large_view.set_view(view)
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self.set_current_page(1)
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def goto_small(self):
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if self.get_current_page() == 0:
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return
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vf = self.get_active_small_view()
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view = self._large_view.get_view()
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self._large_view.set_view(None)
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vf.set_view(view)
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self.set_current_page(0)
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def insert_view(self, view):
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if self.get_current_page() == 0:
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vf = self.get_active_small_view()
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else:
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vf = self._large_view
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vf.set_view(view)
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def set_all_plots(self, plots):
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for vf in self._view_frames:
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if plots:
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vf.set_view(plots.pop())
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else:
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vf.set_view(None)
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def show(self):
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for vf in self._view_frames:
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vf.show()
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self._small_views.show()
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gtk.Notebook.show(self)
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def on_view_focus_changed(self, widget, vf, focused):
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if focused:
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self.emit('view-changed', vf)
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class Plot (gtk.Frame):
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def __init__(self, title):
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gtk.Frame.__init__(self)
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self.sel_obj = None
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self.title = title
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self.selection_listener = None
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self.set_shadow_type(gtk.SHADOW_NONE)
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self._background = None
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self.canvas = None
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self.fig = Figure(figsize=(5,4), dpi=72)
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self.canvas = FigureCanvas(self.fig)
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self.fig.set_facecolor('white')
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self._sel_sensitive = True
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def set_selection_sensitive(self,event):
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if event:
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if event.get_active():
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logger.log('debug','Selection freezed')
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self._sel_sensitive = False
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else:
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logger.log('debug','Selections active')
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self._sel_sensitive = True
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def get_title(self):
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return self.title
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def selection_changed(self, selection):
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if not self._sel_sensitive or not self.get_property('visible'):
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return
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self.set_current_selection(selection)
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def set_selection_listener(self, listener):
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"""Allow project to listen to selections.
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The selection will propagate back to all plots through the
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selection_changed() method. The listener will be called as
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listener(dimension_name, ids).
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"""
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self.selection_listener = listener
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def get_toolbar(self):
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return None
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class EmptyView (Plot):
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def __init__(self):
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Plot.__init__(self, 'Empty view')
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label = gtk.Label('No view')
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ebox = gtk.EventBox()
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ebox.add(label)
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self.add(ebox)
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label.show()
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ebox.show()
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self.show()
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class NavToolbar(NavigationToolbar2):
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toolitems = (('Select', 'Select within rectangle', 'zoom_to_rect.png',
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'select'),) + NavigationToolbar2.toolitems
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def __init__(self, *args):
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NavigationToolbar2.__init__(self, *args)
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self._select_callback = None
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self.message.hide()
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def select(self, *args):
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"""Selection mode selected handler."""
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if self._active == 'SELECT':
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self._active = None
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else:
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self._active = 'SELECT'
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if self._idPress is not None:
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self._idPress = self.canvas.mpl_disconnect(self._idPress)
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self.mode = ''
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if self._idRelease is not None:
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self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
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self.mode = ''
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if self._active:
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self._idPress = self.canvas.mpl_connect('button_press_event', self.press_select)
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self._idRelease = self.canvas.mpl_connect('button_release_event', self.release_select)
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self.mode = 'Select rectangle mode'
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self.set_message(self.mode)
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def set_message(self, s):
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"""Set status in toolbar to string s.
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Overrided to make sure message can be updated even when
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drawing rubberband.
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"""
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self.message.set_label(s)
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def press_select(self, event):
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"""Mouse button pressed handler for selection mode."""
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x, y = event.x, event.y
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for i, a in enumerate(self.canvas.figure.get_axes()):
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if event.inaxes==a and event.inaxes.get_navigate():
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xmin, xmax = a.get_xlim()
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ymin, ymax = a.get_ylim()
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lim = xmin, xmax, ymin, ymax
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self._xypress = x, y, a, i, lim, a.transData.deepcopy()
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break
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self.press(event)
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def release_select(self, event):
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"""Mouse button released handler for selection mode."""
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# only release if button was pressed inside first?
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if self._xypress:
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x, y = event.x, event.y
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lastx, lasty, a, ind, lim, trans = self._xypress
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lastx, lasty = a.transData.inverse_xy_tup( (lastx, lasty) )
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x, y = a.transData.inverse_xy_tup( (x, y) )
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if self._select_callback:
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self._select_callback(lastx, lasty, x, y)
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self._xypress = None
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self.push_current()
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self.release(event)
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def mouse_move(self, event):
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"""Extend NavigationToolbar2.mouse_move to provide selection support."""
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from matplotlib.backend_bases import cursors
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# Only update the rubberband for selection mode when mouse is
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# within the plotting area.
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if event.inaxes and self._active=='SELECT':
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if self._lastCursor != cursors.SELECT_REGION:
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self.set_cursor(cursors.SELECT_REGION)
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self._lastCursor = cursors.SELECT_REGION
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if self._xypress is not None:
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x, y = event.x, event.y
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lastx, lasty, a, ind, lim, trans= self._xypress
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self.draw_rubberband(event, x, y, lastx, lasty)
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NavigationToolbar2.mouse_move(self, event)
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def set_select_callback(self, listener):
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"""Allow plots to register a callback for selection events.
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The callback will be called as listener(x1, y1, x2, y2). All
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coordinates are in the plot coordinate system, not pixels or
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widget coordinates.
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"""
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self._select_callback = listener
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class PlotToolbar(NavToolbar):
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"""Extensions to existing toolbar
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"""
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def __init__(self, *args):
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NavToolbar.__init__(self, *args)
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self.tb_freeze = gtk.ToolItem()
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self.chk = gtk.CheckButton ()
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self.chk.set_label ('Freeze')
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self.tb_freeze.add (self.chk)
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self.tb_freeze.set_tooltip(self.tooltips, 'Freeze current selection')
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self.insert(self.tb_freeze,-1)
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toolitem = gtk.SeparatorToolItem()
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self.insert(toolitem, -1)
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self.show_all()
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self.message.hide()
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class LineViewPlot(Plot):
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"""Line view of current selection, no interaction
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Only works on 2d-arrays
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input:
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-- major_axis : dim_number for line dim (see scipy.ndarray for axis def.)
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-- minor_axis : needs definition only for higher order arrays
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ps: slow (cant get linecollection and blit to work)
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"""
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def __init__(self, dataset,major_axis=1,minor_axis=None, name="Line view"):
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self.use_blit = False
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self._last_index = []
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self._data = dataset.asarray()
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self.dataset = dataset
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Plot.__init__(self, name)
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self.ax = self.fig.add_subplot(111)
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self.ax.set_title(self.get_title())
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self.current_dim = self.dataset.get_dim_name(major_axis)
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if len(self._data.shape)==2 and not minor_axis:
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minor_axis = major_axis-1
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#initial draw
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self.line_collection = {}
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x_axis = scipy.arrayrange(self._data.shape[minor_axis])
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for i in range(self._data.shape[major_axis]):
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yi = self._data.take([i],major_axis)
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if self.use_blit:
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l,=self.ax.plot(x_axis,yi,'k',alpha=.05,animated=True)
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else:
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l,=self.ax.plot(x_axis,yi,'k',alpha=.05)
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self.line_collection[i] = l
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self.add(self.canvas)
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self.canvas.show()
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#FIXME: Lineview plot cannot do selections -> disable in toolbar
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self._toolbar = PlotToolbar(self.canvas, None)
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self._toolbar.set_property('show-arrow', False)
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self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive)
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self.canvas.mpl_connect('resize_event',self.clear_background)
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def get_toolbar(self):
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return self._toolbar
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def clear_background(self,event):
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self._background = None
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def set_current_selection(self, selection):
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ids = selection[self.current_dim] # current identifiers
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index = self.dataset.get_indices(self.current_dim, ids)
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if self.use_blit:
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if self._background is None:
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self._last_index = None
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self._background = self.canvas.copy_from_bbox(self.ax.bbox)
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self.canvas.restore_region(self._background)
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if index:
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if self._last_index:
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for i in self._last_index:
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# if not using blit: reset last selection
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self.ax.lines[i].set_color('k')
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self.ax.lines[i].set_alpha(.05)
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self.ax.lines[i].set_zorder(1)
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for i in index:
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self.ax.lines[i].set_color('r')
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self.ax.lines[i].set_alpha(1.0)
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self.ax.lines[i].set_visible(True)
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self.ax.lines[i].set_zorder(3)
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if self.use_blit:
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self.ax.draw_artist(self.ax.lines[i])
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self._last_index = index
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if self.use_blit:
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self.canvas.blit()
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else:
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self.canvas.draw()
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class ScatterMarkerPlot(Plot):
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"""The ScatterMarkerPlot is faster than regular scatterplot, but
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has no color and size options."""
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def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,s=6, name="Scatter plot"):
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Plot.__init__(self, name)
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self.ax = self.fig.add_subplot(111)
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self.ax.axhline(0,color='k',lw=1.5,zorder=0)
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self.ax.axvline(0,color='k',lw=1.5,zorder=0)
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self.current_dim = id_dim
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self.dataset_1 = dataset_1
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self.ms = s
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self._selection_line = None
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x_index = dataset_1[sel_dim][id_1]
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y_index = dataset_2[sel_dim][id_2]
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self.xaxis_data = dataset_1._array[:,x_index]
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self.yaxis_data = dataset_2._array[:,y_index]
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self.ax.plot(self.xaxis_data,self.yaxis_data,'o',markeredgewidth=0,markersize=s)
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self.ax.set_title(self.get_title())
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self.add(self.canvas)
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self.canvas.show()
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# add toolbar
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self._toolbar = PlotToolbar(self.canvas, None)
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self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive)
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self._toolbar.set_property('show-arrow', False)
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self._toolbar.set_select_callback(self.rectangle_select_callback)
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def get_toolbar(self):
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return self._toolbar
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def rectangle_select_callback(self, x1, y1, x2, y2):
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ydata = self.yaxis_data
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xdata = self.xaxis_data
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|
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# find indices of selected area
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|
if x1>x2:
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x1, x2 = x2, x1
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if y1>y2:
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|
y1, y2 = y2, y1
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assert x1<=x2
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assert y1<=y2
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index = scipy.nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0]
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ids = self.dataset_1.get_identifiers(self.current_dim, index)
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self.selection_listener(self.current_dim, ids)
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|
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|
def set_current_selection(self, selection):
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|
ids = selection[self.current_dim] # current identifiers
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index = self.dataset_1.get_indices(self.current_dim, ids)
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xdata_new = self.xaxis_data.take(index) #take data
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|
ydata_new = self.yaxis_data.take(index)
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|
#remove old selection
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|
if self._selection_line:
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self.ax.lines.remove(self._selection_line)
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|
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self._selection_line, = self.ax.plot(xdata_new,ydata_new,marker='o',markersize=self.ms,linestyle=None,markerfacecolor='r')
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|
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|
self._toolbar.forward() #update data lims before draw
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self.canvas.draw()
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|
|
|
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|
class ScatterPlot(Plot):
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|
"""The ScatterMarkerPlot is faster than regular scatterplot, but
|
|
has no color and size options."""
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|
def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,c='b',s=30, name="Scatter plot"):
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|
Plot.__init__(self, name)
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|
self.ax = self.fig.add_subplot(111)
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|
self.current_dim = id_dim
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|
self.dataset_1 = dataset_1
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|
x_index = dataset_1[sel_dim][id_1]
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|
y_index = dataset_2[sel_dim][id_2]
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|
self.xaxis_data = dataset_1._array[:,x_index]
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|
self.yaxis_data = dataset_2._array[:,y_index]
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|
lw = scipy.zeros(self.xaxis_data.shape)
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|
self.ax.scatter(self.xaxis_data,self.yaxis_data,s=s,c=c,linewidth=lw,edgecolor='k',alpha=.6,cmap = cm.Set1)
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|
self.ax.set_title(self.get_title())
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|
# collection
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|
self.coll = self.ax.collections[0]
|
|
|
|
# add canvas to widget
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|
self.add(self.canvas)
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|
self.canvas.show()
|
|
|
|
# create toolbar
|
|
self._toolbar = PlotToolbar(self.canvas, None)
|
|
self._toolbar.chk.connect ('toggled' ,self.set_selection_sensitive)
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|
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) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0]
|
|
ids = self.dataset_1.get_identifiers(self.current_dim, index)
|
|
self.selection_listener(self.current_dim, ids)
|
|
|
|
def set_current_selection(self, selection):
|
|
ids = selection[self.current_dim] # current identifiers
|
|
index = self.dataset_1.get_indices(self.current_dim, ids)
|
|
lw = scipy.zeros(self.xaxis_data.shape)
|
|
scipy.put(lw,index,2.)
|
|
self.coll.set_linewidth(lw)
|
|
self._toolbar.forward() #update data lims before draw
|
|
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.drawing.nx_pydot.graphviz_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) & (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 set_current_selection(self, selection):
|
|
ids = selection[self.dataset.get_dim_name(0)] # current identifiers
|
|
node_set = set(self.graph.nodes())
|
|
|
|
selected_nodes = list(ids.intersection(node_set))
|
|
unselected_nodes = list(node_set.difference(ids))
|
|
|
|
if self.node_color:
|
|
unselected_colors = [self.node_color[x] for x in unselected_nodes]
|
|
else:
|
|
unselected_colors = 'red'
|
|
|
|
if self.node_size:
|
|
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, edge_list=self.graph.edges(), \
|
|
ax=self.ax, **self.keywords)
|
|
networkx.draw_networkx_labels(self.graph,**self.keywords)
|
|
if unselected_nodes:
|
|
networkx.draw_networkx_nodes(self.graph, nodelist=unselected_nodes, \
|
|
node_color='r', node_size=unselected_sizes, ax=self.ax, **self.keywords)
|
|
|
|
if selected_nodes:
|
|
networkx.draw_networkx_nodes(self.graph, nodelist=selected_nodes, \
|
|
node_color='k', node_size=selected_sizes, ax=self.ax, **self.keywords)
|
|
|
|
self.canvas.draw()
|
|
|
|
|
|
# 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,))
|
|
|