class PolygonSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a 2D polygon selection.
Attributes
----------
op : Instance(PolygonOp)
The operation on which this selection view is operating
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
The string for subsetting the plot
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterPlotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> s = flow.ScatterplotView(xchannel = "V2-A",
... ychannel = "Y2-A")
>>> poly = s.default_view()
>>> poly.plot(ex2)
>>> poly.interactive = True
"""
id = Constant('edu.mit.synbio.cytoflow.views.polygon')
friendly_id = Constant("Polygon Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_cursor = Instance(Cursor, transient=True)
_path = Instance(mpl.path.Path, transient=True)
_patch = Instance(mpl.patches.PathPatch, transient=True)
_line = Instance(mpl.lines.Line2D, transient=True)
_drawing = Bool(transient=True)
_last_draw_time = Float(0.0, transient=True)
_last_click_time = Float(0.0, transient=True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError(
"RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError(
"RangeSelection.yfacet must be empty or `Undefined`")
super(PolygonSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_poly()
self._interactive()
@on_trait_change('op.vertices', post_init=True)
def _draw_poly(self):
if not self._ax:
return
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._drawing or not self.op.vertices or len(self.op.vertices) < 3 \
or any([len(x) != 2 for x in self.op.vertices]):
return
patch_vert = np.concatenate(
(np.array(self.op.vertices), np.array((0, 0), ndmin=2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax, horizOn=False, vertOn=False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if not self._ax:
return
if (self._cursor.ignore(event)):
return
# we have to check the wall clock time because the IPython notebook
# doesn't seem to register double-clicks
if event.dblclick or (time.clock() - self._last_click_time < 0.5):
self._drawing = False
self.op.vertices = map(tuple, self._path.vertices)
self.op._xscale = plt.gca().get_xscale()
self.op._yscale = plt.gca().get_yscale()
self._path = None
return
self._last_click_time = time.clock()
self._drawing = True
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata),
ndmin=2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin=2)
self._path = mpl.path.Path(vertices, closed=False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor="black",
fill=False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
def _onmove(self, event):
if not self._ax:
return
if (self._cursor.ignore(event) or not self._drawing or not self._path
or self._path.vertices.shape[0] == 0 or not event.xdata
or not event.ydata):
return
# only draw 5 times/sec
if (time.clock() - self._last_draw_time < 0.2):
return
self._last_draw_time = time.clock()
if self._line and self._line in self._ax.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth=1, color="black")
self._ax.add_line(self._line)
plt.gcf().canvas.draw()
class PolygonSelection(HasStrictTraits):
"""Plots, and lets the user interact with, a 2D selection.
Attributes
----------
polygon : Instance(numpy.ndarray)
The polygon vertices
view : Instance(IView)
the IView that this view is wrapping. I suggest that if it's another
ISelectionView, that its `interactive` property remain False. >.>
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
"""
id = "edu.mit.synbio.cytoflow.views.polygon"
friendly_id = "Polygon Selection"
view = Instance(IView, transient = True)
interactive = Bool(False, transient = True)
vertices = List((Float, Float))
# internal state.
_cursor = Instance(Cursor, transient = True)
_path = Instance(mpl.path.Path, transient = True)
_patch = Instance(mpl.patches.PathPatch, transient = True)
_line = Instance(mpl.lines.Line2D, transient = True)
_drawing = Bool(transient = True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
self.view.plot(experiment, **kwargs)
self._draw_poly()
def is_valid(self, experiment):
"""If the decorated view is valid, we are too."""
return self.view.is_valid(experiment)
@on_trait_change('vertices')
def _draw_poly(self):
ca = plt.gca()
if self._patch and self._patch in ca.patches:
self._patch.remove()
if self._drawing or not self.vertices or len(self.vertices) < 3 \
or any([len(x) != 2 for x in self.vertices]):
return
patch_vert = np.concatenate((np.array(self.vertices),
np.array((0,0), ndmin = 2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
ca.add_patch(self._patch)
plt.gcf().canvas.draw()
@on_trait_change('interactive')
def _interactive(self):
if self.interactive:
ax = plt.gca()
self._cursor = Cursor(ax, horizOn = False, vertOn = False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
else:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if(self._cursor.ignore(event)):
return
if event.dblclick:
self._drawing = False
self.vertices = map(tuple, self._path.vertices)
self._path = None
return
ca = plt.gca()
self._drawing = True
if self._patch and self._patch in ca.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata), ndmin = 2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin = 2)
self._path = mpl.path.Path(vertices, closed = False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor = "black",
fill = False)
ca.add_patch(self._patch)
plt.gcf().canvas.draw()
def _onmove(self, event):
if(self._cursor.ignore(event)
or not self._drawing
or not self._path
or self._path.vertices.shape[0] == 0
or not event.xdata
or not event.ydata):
return
ca = plt.gca()
if not ca:
return
if self._line and self._line in ca.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth = 1, color = "black")
ca.add_line(self._line)
plt.gcf().canvas.draw()
class PolygonSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a 2D polygon selection.
Attributes
----------
op : Instance(PolygonOp)
The operation on which this selection view is operating
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
The string for subsetting the plot
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterPlotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> s = flow.ScatterplotView(xchannel = "V2-A",
... ychannel = "Y2-A")
>>> poly = s.default_view()
>>> poly.plot(ex2)
>>> poly.interactive = True
"""
id = Constant('edu.mit.synbio.cytoflow.views.polygon')
friendly_id = Constant("Polygon Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state.
_ax = Any(transient = True)
_cursor = Instance(Cursor, transient = True)
_path = Instance(mpl.path.Path, transient = True)
_patch = Instance(mpl.patches.PathPatch, transient = True)
_line = Instance(mpl.lines.Line2D, transient = True)
_drawing = Bool(transient = True)
_last_draw_time = Float(0.0, transient = True)
_last_click_time = Float(0.0, transient = True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError("RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError("RangeSelection.yfacet must be empty or `Undefined`")
super(PolygonSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_poly()
self._interactive()
@on_trait_change('op.vertices', post_init = True)
def _draw_poly(self):
if not self._ax:
return
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._drawing or not self.op.vertices or len(self.op.vertices) < 3 \
or any([len(x) != 2 for x in self.op.vertices]):
return
patch_vert = np.concatenate((np.array(self.op.vertices),
np.array((0,0), ndmin = 2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
@on_trait_change('interactive', post_init = True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax, horizOn = False, vertOn = False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if not self._ax:
return
if(self._cursor.ignore(event)):
return
# we have to check the wall clock time because the IPython notebook
# doesn't seem to register double-clicks
if event.dblclick or (time.clock() - self._last_click_time < 0.5):
self._drawing = False
self.op.vertices = map(tuple, self._path.vertices)
self.op._xscale = plt.gca().get_xscale()
self.op._yscale = plt.gca().get_yscale()
self._path = None
return
self._last_click_time = time.clock()
self._drawing = True
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata), ndmin = 2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin = 2)
self._path = mpl.path.Path(vertices, closed = False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor = "black",
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
def _onmove(self, event):
if not self._ax:
return
if(self._cursor.ignore(event)
or not self._drawing
or not self._path
or self._path.vertices.shape[0] == 0
or not event.xdata
or not event.ydata):
return
# only draw 5 times/sec
if(time.clock() - self._last_draw_time < 0.2):
return
self._last_draw_time = time.clock()
if self._line and self._line in self._ax.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth = 1, color = "black")
self._ax.add_line(self._line)
plt.gcf().canvas.draw()
