class QuadSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
op : Instance(Range2DOp)
The instance of Range2DOp that we're viewing / editing
huefacet : Str
The conditioning variable to plot multiple colors
subset : Str
The string passed to `Experiment.query()` to subset the data before
plotting
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterplotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state.
_ax = Any(transient = True)
_hline = Instance(Line2D, transient = True)
_vline = Instance(Line2D, transient = True)
_cursor = Instance(Cursor, transient = True)
def plot(self, experiment, **kwargs):
"""Plot the underlying scatterplot and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowOpError("No experiment specified")
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(QuadSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('op.xthreshold, op.ythreshold', post_init = True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.op.xthreshold and self.op.ythreshold:
self._hline = plt.axhline(self.op.ythreshold,
linewidth = 3,
color = 'blue')
self._vline = plt.axvline(self.op.xthreshold,
linewidth = 3,
color = 'blue')
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 = True,
vertOn = True,
color = 'blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.xthreshold = event.xdata
self.op.ythreshold = event.ydata
class CrossSection(object):
"""
Class to manage the axes, artists and properties associated with
showing a 2D image, a cross-hair cursor and two parasite axes which
provide horizontal and vertical cross sections of image.
You will likely need to call `CrossSection.init_artists(init_image)` after
creating this object.
Parameters
----------
fig : matplotlib.figure.Figure
The figure object to build the class on, will clear
current contents
cmap : str, colormap, or None
color map to use. Defaults to gray
norm : Normalize or None
Normalization function to use
limit_func : callable, optional
function that takes in the image and returns clim values
auto_redraw : bool, optional
interpolation : str, optional
Interpolation method to use. List of valid options can be found in
CrossSection2DView.interpolation
"""
def __init__(self,
fig,
cmap=None,
norm=None,
limit_func=None,
auto_redraw=True,
interpolation=None):
self._cursor_position_cbs = []
self._interpolation = interpolation
# used to determine if setting properties should force a re-draw
self._auto_redraw = auto_redraw
# clean defaults
if limit_func is None:
limit_func = lambda image: (image.min(), image.max())
if cmap is None:
cmap = 'gray'
# stash the color map
self._cmap = cmap
# let norm pass through as None, mpl defaults to linear which is fine
if norm is None:
norm = Normalize()
self._norm = norm
# save a copy of the limit function, we will need it later
self._limit_func = limit_func
# this is used by the widget logic
self._active = True
self._dirty = True
self._cb_dirty = True
# work on setting up the mpl axes
self._fig = fig
# blow away what ever is currently on the figure
fig.clf()
# Configure the figure in our own image
#
# +----------------------+
# | H cross section |
# +----------------------+
# +---+ +----------------------+
# | V | | |
# | | | |
# | x | | |
# | s | | Main Axes |
# | e | | |
# | c | | |
# | t | | |
# | i | | |
# | o | | |
# | n | | |
# +---+ +----------------------+
# make the main axes
self._im_ax = fig.add_subplot(1, 1, 1)
self._im_ax.set_aspect('equal')
self._im_ax.xaxis.set_major_locator(NullLocator())
self._im_ax.yaxis.set_major_locator(NullLocator())
self._imdata = None
self._im = self._im_ax.imshow([[]],
cmap=self._cmap,
norm=self._norm,
interpolation=self._interpolation,
aspect='equal',
vmin=0,
vmax=1)
# make it dividable
divider = make_axes_locatable(self._im_ax)
# set up all the other axes
# (set up the horizontal and vertical cuts)
self._ax_h = divider.append_axes('top',
.5,
pad=0.1,
sharex=self._im_ax)
self._ax_h.yaxis.set_major_locator(LinearLocator(numticks=2))
self._ax_v = divider.append_axes('left',
.5,
pad=0.1,
sharey=self._im_ax)
self._ax_v.xaxis.set_major_locator(LinearLocator(numticks=2))
self._ax_cb = divider.append_axes('right', .2, pad=.5)
# add the color bar
self._cb = fig.colorbar(self._im, cax=self._ax_cb)
# add the cursor place holder
self._cur = None
# turn off auto-scale for the horizontal cut
self._ax_h.autoscale(enable=False)
# turn off auto-scale scale for the vertical cut
self._ax_v.autoscale(enable=False)
# create line artists
self._ln_v, = self._ax_v.plot([], [],
'k-',
animated=True,
visible=False)
self._ln_h, = self._ax_h.plot([], [],
'k-',
animated=True,
visible=False)
# backgrounds for blitting
self._ax_v_bk = None
self._ax_h_bk = None
# stash last-drawn row/col to skip if possible
self._row = None
self._col = None
# make attributes for callback ids
self._move_cid = None
self._click_cid = None
self._clear_cid = None
def add_cursor_position_cb(self, callback):
""" Add a callback for the cursor position in the main axes
Parameters
----------
callback : callable(cc, rr)
Function that gets called when the cursor position moves to a new
row or column on main axes
"""
self._cursor_position_cbs.append(callback)
# set up the call back for the updating the side axes
def _move_cb(self, event):
if not self._active:
return
if event is None:
x = self._col
y = self._row
self._col = None
self._row = None
else:
# short circuit on other axes
if event.inaxes is not self._im_ax:
return
x, y = event.xdata, event.ydata
numrows, numcols = self._imdata.shape
if x is not None and y is not None:
self._ln_h.set_visible(True)
self._ln_v.set_visible(True)
col = int(x + 0.5)
row = int(y + 0.5)
if row != self._row or col != self._col:
if 0 <= col < numcols and 0 <= row < numrows:
self._col = col
self._row = row
for cb in self._cursor_position_cbs:
cb(col, row)
for data, ax, bkg, art, set_fun in zip(
(self._imdata[row, :], self._imdata[:, col]),
(self._ax_h, self._ax_v),
(self._ax_h_bk, self._ax_v_bk),
(self._ln_h, self._ln_v),
(self._ln_h.set_ydata, self._ln_v.set_xdata)):
self._fig.canvas.restore_region(bkg)
set_fun(data)
ax.draw_artist(art)
self._fig.canvas.blit(ax.bbox)
def _click_cb(self, event):
if event.inaxes is not self._im_ax:
return
self.active = not self.active
if self.active:
self._cur.onmove(event)
self._move_cb(event)
@auto_redraw
def _connect_callbacks(self):
"""
Connects all of the callbacks for the motion and click events
"""
self._disconnect_callbacks()
self._cur = Cursor(self._im_ax, useblit=True, color='red', linewidth=2)
self._move_cid = self._fig.canvas.mpl_connect('motion_notify_event',
self._move_cb)
self._click_cid = self._fig.canvas.mpl_connect('button_press_event',
self._click_cb)
self._clear_cid = self._fig.canvas.mpl_connect('draw_event',
self._clear)
self._fig.tight_layout()
self._fig.canvas.draw_idle()
def _disconnect_callbacks(self):
"""
Disconnects all of the callbacks
"""
if self._fig.canvas is None:
# no canvas -> can't do anything about the call backs which
# should not exist
self._move_cid = None
self._clear_cid = None
self._click_cid = None
return
for atr in ('_move_cid', '_clear_cid', '_click_cid'):
cid = getattr(self, atr, None)
if cid is not None:
self._fig.canvas.mpl_disconnect(cid)
setattr(self, atr, None)
# clean up the cursor
if self._cur is not None:
self._cur.disconnect_events()
del self._cur
self._cur = None
@auto_redraw
def _init_artists(self, init_image):
"""
Update the CrossSection with a new base-image. This function
takes care of setting up all of the details about the image size
in the limits/artist extent of the image and the secondary data
in the cross-section parasite plots.
Parameters
----------
init_image : ndarray
An image to serve as the new 'base' image.
"""
im_shape = init_image.shape
# first deal with the image axis
# update the image, `update_artists` takes care of
# updating the actual artist
self._imdata = init_image
# update the extent of the image artist
self._im.set_extent([-0.5, im_shape[1] + .5, im_shape[0] + .5, -0.5])
# update the limits of the image axes to match the exent
self._im_ax.set_xlim([-.05, im_shape[1] + .5])
self._im_ax.set_ylim([im_shape[0] + .5, -0.5])
# update the format coords printer
numrows, numcols = im_shape
# note, this is a closure over numrows and numcols
def format_coord(x, y):
# adjust xy -> col, row
col = int(x + 0.5)
row = int(y + 0.5)
# make sure the point falls in the array
if col >= 0 and col < numcols and row >= 0 and row < numrows:
# if it does, grab the value
z = self._imdata[row, col]
return "X: {x:d} Y: {y:d} I: {i:.2f}".format(x=col, y=row, i=z)
else:
return "X: {x:d} Y: {y:d}".format(x=col, y=row)
# replace the current format_coord function
self._im_ax.format_coord = format_coord
# net deal with the parasite axes and artist
self._ln_v.set_data(np.zeros(im_shape[0]), np.arange(im_shape[0]))
self._ax_v.set_ylim([0, im_shape[0]])
self._ln_h.set_data(np.arange(im_shape[1]), np.zeros(im_shape[1]))
self._ax_h.set_xlim([0, im_shape[1]])
# if we have a cavas, then connect/set up junk
if self._fig.canvas is not None:
self._connect_callbacks()
# mark as dirty
self._dirty = True
def _clear(self, event):
self._ax_v_bk = self._fig.canvas.copy_from_bbox(self._ax_v.bbox)
self._ax_h_bk = self._fig.canvas.copy_from_bbox(self._ax_h.bbox)
self._ln_h.set_visible(False)
self._ln_v.set_visible(False)
# this involves reaching in and touching the guts of the
# cursor widget. The problem is that the mpl widget
# skips updating it's saved background if the widget is inactive
if self._cur:
self._cur.background = self._cur.canvas.copy_from_bbox(
self._cur.canvas.figure.bbox)
@property
def interpolation(self):
return self._interpolation
@property
def active(self):
return self._active
@active.setter
def active(self, val):
self._active = val
self._cur.active = val
@auto_redraw
def update_interpolation(self, interpolation):
"""
Set the interpolation method
"""
self._dirty = True
self._im.set_interpolation(interpolation)
@auto_redraw
def update_cmap(self, cmap):
"""
Set the color map used
"""
# TODO: this should stash new value, not apply it
self._cmap = cmap
self._dirty = True
@auto_redraw
def update_image(self, image):
"""
Set the image data
The input data does not necessarily have to be the same shape as the
original image
"""
image = np.asarray(image)
if self._imdata is None or self._imdata.shape != image.shape:
self._init_artists(image)
self._imdata = image
self._move_cb(None)
self._dirty = True
@auto_redraw
def update_norm(self, norm):
"""
Update the way that matplotlib normalizes the image
"""
self._norm = norm
self._dirty = True
self._cb_dirty = True
@auto_redraw
def update_limit_func(self, limit_func):
"""
Set the function to use to determine the color scale
"""
# set the new function to use for computing the color limits
self._limit_func = limit_func
self._dirty = True
def _update_artists(self):
"""
Updates the figure by re-drawing
"""
# if the figure is not dirty, short-circuit
if not (self._dirty or self._cb_dirty):
return
# this is a tuple which is the max/min used in the color mapping.
# these values are also used to set the limits on the value
# axes of the parasite axes
# value_limits
vlim = self._limit_func(self._imdata)
# set the color bar limits
self._im.set_clim(vlim)
self._norm.vmin, self._norm.vmax = vlim
# set the cross section axes limits
self._ax_v.set_xlim(*vlim[::-1])
self._ax_h.set_ylim(*vlim)
# set the imshow data
self._im.set_cmap(self._cmap)
self._im.set_norm(self._norm)
if self._imdata is None:
return
self._im.set_data(self._imdata)
# TODO if cb_dirty, remake the colorbar, I think this is
# why changing the norm does not play well
self._dirty = False
self._cb_dirty = False
def _draw(self):
self._fig.canvas.draw_idle()
@auto_redraw
def autoscale_horizontal(self, enable):
self._ax_h.autoscale(enable=enable)
@auto_redraw
def autoscale_vertical(self, enable):
self._ax_v.autoscale(enable=False)
class ThresholdSelection(cytoflow.views.HistogramView):
"""
Plots, and lets the user interact with, a threshold on the X axis.
TODO - beautify!
Attributes
----------
op : Instance(ThresholdOp)
the ThresholdOp we're working on.
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
the string passed to Experiment.subset() defining the subset we plot
interactive : Bool
is this view interactive?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.HistogramView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> t = flow.ThresholdOp(name = "Threshold",
... channel = "Y2-A")
>>> tv = t.default_view()
>>> tv.plot(ex2)
>>> tv.interactive = True
>>> # .... draw a threshold on the plot
>>> ex3 = thresh.apply(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.threshold')
friendly_id = Constant("Threshold Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
channel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state
_ax = Any(transient = True)
_line = Instance(Line2D, transient = True)
_cursor = Instance(Cursor, transient = True)
def plot(self, experiment, **kwargs):
"""Plot the histogram and then plot the threshold on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError("ThresholdSelection.xfacet must be empty")
if self.yfacet:
raise util.CytoflowViewError("ThresholdSelection.yfacet must be empty")
super(ThresholdSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_threshold()
self._interactive()
@on_trait_change('op.threshold', post_init = True)
def _draw_threshold(self):
if not self._ax or not self.op.threshold:
return
if self._line:
# when used in the GUI, _draw_threshold gets called *twice* without
# the plot being updated inbetween: and then the line can't be
# removed from the plot, because it was never added. so check
# explicitly first. this is likely to be an issue in other
# interactive plots, too.
if self._line and self._line in self._ax.lines:
self._line.remove()
self._line = None
if self.op.threshold:
self._line = plt.axvline(self.op.threshold, linewidth=3, color='blue')
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=True,
color='blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.threshold = event.xdata
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 MaskEditor(ToolWindow, DoubleFileChooserDialog):
def __init__(self, *args, **kwargs):
self.mask = None
self._undo_stack = []
self._im = None
self._selector = None
self._cursor = None
self.exposureloader = None
self.plot2d = None
ToolWindow.__init__(self, *args, **kwargs)
DoubleFileChooserDialog.__init__(
self, self.widget, 'Open mask file...', 'Save mask file...', [('Mask files', '*.mat'), ('All files', '*')],
self.instrument.config['path']['directories']['mask'],
os.path.abspath(self.instrument.config['path']['directories']['mask']),
)
def init_gui(self, *args, **kwargs):
self.exposureloader = ExposureLoader(self.instrument)
self.builder.get_object('loadexposure_expander').add(self.exposureloader)
self.exposureloader.connect('open', self.on_loadexposure)
self.plot2d = PlotImageWidget()
self.builder.get_object('plotbox').pack_start(self.plot2d.widget, True, True, 0)
self.builder.get_object('toolbar').set_sensitive(False)
def on_loadexposure(self, exposureloader: ExposureLoader, im: Exposure):
if self.mask is None:
self.mask = im.mask
self._im = im
self.plot2d.set_image(im.intensity)
self.plot2d.set_mask(self.mask)
self.builder.get_object('toolbar').set_sensitive(True)
def on_new(self, button):
if self._im is None or self.mask is None:
return False
self.mask = np.ones_like(self.mask)
self.plot2d.set_mask(self.mask)
self.set_last_filename(None)
def on_open(self, button):
filename = self.get_open_filename()
if filename is not None:
mask = loadmat(filename)
self.mask = mask[[k for k in mask.keys() if not k.startswith('__')][0]]
self.plot2d.set_mask(self.mask)
def on_save(self, button):
filename = self.get_last_filename()
if filename is None:
return self.on_saveas(button)
maskname = os.path.splitext(os.path.split(filename)[1])[0]
savemat(filename, {maskname: self.mask})
def on_saveas(self, button):
filename = self.get_save_filename(None)
if filename is not None:
self.on_save(button)
def suggest_filename(self):
return 'mask_dist_{0.year:d}{0.month:02d}{0.day:02d}.mat'.format(datetime.date.today())
def on_selectcircle_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Ellipse selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectrectangle_button', 'selectpolygon_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = EllipseSelector(self.plot2d.axis,
self.on_ellipse_selected,
rectprops={'facecolor': 'white', 'edgecolor': 'none', 'alpha': 0.7,
'fill': True, 'zorder': 10},
button=[1, ],
interactive=False, lineprops={'zorder': 10})
self._selector.state.add('square')
self._selector.state.add('center')
else:
assert isinstance(self._selector, EllipseSelector)
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_ellipse_selected(self, pos1, pos2):
# pos1 and pos2 are mouse button press and release events, with xdata and ydata carrying
# the two opposite corners of the bounding box of the circle. These are NOT the exact
# button presses and releases!
row = np.arange(self.mask.shape[0])[:, np.newaxis]
column = np.arange(self.mask.shape[1])[np.newaxis, :]
row0 = 0.5 * (pos1.ydata + pos2.ydata)
col0 = 0.5 * (pos1.xdata + pos2.xdata)
r2 = ((pos2.xdata - pos1.xdata) ** 2 + (pos2.ydata - pos1.ydata) ** 2) / 8
tobemasked = (row - row0) ** 2 + (column - col0) ** 2 <= r2
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask &= ~tobemasked
elif self.builder.get_object('unmask_button').get_active():
self.mask |= tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.builder.get_object('selectcircle_button').set_active(False)
self.plot2d.set_mask(self.mask)
def on_selectrectangle_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Rectangle selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectcircle_button', 'selectpolygon_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = RectangleSelector(self.plot2d.axis,
self.on_rectangle_selected,
rectprops={'facecolor': 'white', 'edgecolor': 'none', 'alpha': 0.7,
'fill': True, 'zorder': 10},
button=[1, ],
interactive=False, lineprops={'zorder': 10})
else:
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_rectangle_selected(self, pos1, pos2):
# pos1 and pos2 are mouse button press and release events, with xdata and ydata
# carrying the two opposite corners of the bounding box of the rectangle. These
# are NOT the exact button presses and releases!
row = np.arange(self.mask.shape[0])[:, np.newaxis]
column = np.arange(self.mask.shape[1])[np.newaxis, :]
tobemasked = ((row >= min(pos1.ydata, pos2.ydata)) & (row <= max(pos1.ydata, pos2.ydata)) &
(column >= min(pos1.xdata, pos2.xdata)) & (column <= max(pos1.xdata, pos2.xdata)))
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask = self.mask & (~tobemasked)
elif self.builder.get_object('unmask_button').get_active():
self.mask = self.mask | tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.builder.get_object('selectrectangle_button').set_active(False)
self.plot2d.set_mask(self.mask)
def on_selectpolygon_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Polygon selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectrectangle_button', 'selectcircle_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = LassoSelector(self.plot2d.axis,
self.on_polygon_selected,
lineprops={'color': 'white', 'zorder': 10},
button=[1, ],
)
else:
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_polygon_selected(self, vertices):
path = Path(vertices)
col, row = np.meshgrid(np.arange(self.mask.shape[1]),
np.arange(self.mask.shape[0]))
points = np.vstack((col.flatten(), row.flatten())).T
tobemasked = path.contains_points(points).reshape(self.mask.shape)
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask = self.mask & (~tobemasked)
elif self.builder.get_object('unmask_button').get_active():
self.mask = self.mask | tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.plot2d.set_mask(self.mask)
self.builder.get_object('selectpolygon_button').set_active(False)
def on_mask_toggled(self, button):
pass
def on_unmask_toggled(self, button):
pass
def on_invertmask_toggled(self, button):
pass
def on_pixelhunting_toggled(self, button):
if button.get_active():
self._cursor = Cursor(self.plot2d.axis, useblit=False, color='white', lw=1)
self._cursor.connect_event('button_press_event', self.on_cursorclick)
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
else:
self._cursor.disconnect_events()
self._cursor = None
self._undo_stack.append(self.mask)
self.plot2d.replot(keepzoom=False)
def on_cursorclick(self, event):
if (event.inaxes == self.plot2d.axis) and (self.plot2d.toolbar.mode == ''):
self.mask[round(event.ydata), round(event.xdata)] ^= True
self._cursor.disconnect_events()
self._cursor = None
self.plot2d.replot(keepzoom=True)
self.on_pixelhunting_toggled(self.builder.get_object('pixelhunting_button'))
def cleanup(self):
super().cleanup()
self._undo_stack = []
def on_undo(self, button):
try:
self.mask = self._undo_stack.pop()
except IndexError:
return
self.plot2d.set_mask(self.mask)
class ThresholdSelection(cytoflow.views.HistogramView):
"""
Plots, and lets the user interact with, a threshold on the X axis.
TODO - beautify!
Attributes
----------
op : Instance(ThresholdOp)
the ThresholdOp we're working on.
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
the string passed to Experiment.subset() defining the subset we plot
interactive : Bool
is this view interactive?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.HistogramView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> t = flow.ThresholdOp(name = "Threshold",
... channel = "Y2-A")
>>> tv = t.default_view()
>>> tv.plot(ex2)
>>> tv.interactive = True
>>> # .... draw a threshold on the plot
>>> ex3 = thresh.apply(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.threshold')
friendly_id = Constant("Threshold Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
channel = DelegatesTo('op')
threshold = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state
_ax = Any(transient=True)
_line = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""Plot the histogram and then plot the threshold on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError(
"ThresholdSelection.xfacet must be empty")
if self.yfacet:
raise util.CytoflowViewError(
"ThresholdSelection.yfacet must be empty")
super(ThresholdSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_threshold()
self._interactive()
@on_trait_change('threshold', post_init=True)
def _draw_threshold(self):
if not self._ax or not self.threshold:
return
if self._line:
# when used in the GUI, _draw_threshold gets called *twice* without
# the plot being updated inbetween: and then the line can't be
# removed from the plot, because it was never added. so check
# explicitly first. this is likely to be an issue in other
# interactive plots, too.
if self._line and self._line in self._ax.lines:
self._line.remove()
self._line = None
if self.threshold:
self._line = plt.axvline(self.threshold, linewidth=3, color='blue')
plt.draw()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=False,
vertOn=True,
color='blue',
useblit=True)
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
# sometimes the axes aren't set up and we don't get xdata (??)
if event.xdata:
self.threshold = event.xdata
class CrossSection(object):
"""
Class to manage the axes, artists and properties associated with
showing a 2D image, a cross-hair cursor and two parasite axes which
provide horizontal and vertical cross sections of image.
You will likely need to call `CrossSection.init_artists(init_image)` after
creating this object.
Parameters
----------
fig : matplotlib.figure.Figure
The figure object to build the class on, will clear
current contents
init_image : 2d ndarray
The initial image
cmap : str, colormap, or None
color map to use. Defaults to gray
norm : Normalize or None
Normalization function to use
limit_func : callable, optional
function that takes in the image and returns clim values
auto_redraw : bool, optional
interpolation : str, optional
Interpolation method to use. List of valid options can be found in
CrossSection2DView.interpolation
Properties
----------
interpolation : str
The stringly-typed pixel interpolation. See _INTERPOLATION attribute
of this cross_section_2d module
cmap : str
The colormap to use for rendering the image
"""
def __init__(self, fig, cmap=None, norm=None,
limit_func=None, auto_redraw=True, interpolation=None):
self._cursor_position_cbs = []
if interpolation is None:
interpolation = _INTERPOLATION[0]
self._interpolation = interpolation
# used to determine if setting properties should force a re-draw
self._auto_redraw = auto_redraw
# clean defaults
if limit_func is None:
limit_func = fullrange_limit_factory()
if cmap is None:
cmap = 'gray'
# stash the color map
self._cmap = cmap
# let norm pass through as None, mpl defaults to linear which is fine
if norm is None:
norm = Normalize()
self._norm = norm
# save a copy of the limit function, we will need it later
self._limit_func = limit_func
# this is used by the widget logic
self._active = True
self._dirty = True
self._cb_dirty = True
# work on setting up the mpl axes
self._fig = fig
# blow away what ever is currently on the figure
fig.clf()
# Configure the figure in our own image
#
# +----------------------+
# | H cross section |
# +----------------------+
# +---+ +----------------------+
# | V | | |
# | | | |
# | x | | |
# | s | | Main Axes |
# | e | | |
# | c | | |
# | t | | |
# | i | | |
# | o | | |
# | n | | |
# +---+ +----------------------+
# make the main axes
self._im_ax = fig.add_subplot(1, 1, 1)
self._im_ax.set_aspect('equal')
self._im_ax.xaxis.set_major_locator(NullLocator())
self._im_ax.yaxis.set_major_locator(NullLocator())
self._imdata = None
self._im = self._im_ax.imshow([[]], cmap=self._cmap, norm=self._norm,
interpolation=self._interpolation,
aspect='equal', vmin=0,
vmax=1)
# make it dividable
divider = make_axes_locatable(self._im_ax)
# set up all the other axes
# (set up the horizontal and vertical cuts)
self._ax_h = divider.append_axes('top', .5, pad=0.1,
sharex=self._im_ax)
self._ax_h.yaxis.set_major_locator(LinearLocator(numticks=2))
self._ax_v = divider.append_axes('left', .5, pad=0.1,
sharey=self._im_ax)
self._ax_v.xaxis.set_major_locator(LinearLocator(numticks=2))
self._ax_cb = divider.append_axes('right', .2, pad=.5)
# add the color bar
self._cb = fig.colorbar(self._im, cax=self._ax_cb)
# add the cursor place holder
self._cur = None
# turn off auto-scale for the horizontal cut
self._ax_h.autoscale(enable=False)
# turn off auto-scale scale for the vertical cut
self._ax_v.autoscale(enable=False)
# create line artists
self._ln_v, = self._ax_v.plot([],
[], 'k-',
animated=True,
visible=False)
self._ln_h, = self._ax_h.plot([],
[], 'k-',
animated=True,
visible=False)
# backgrounds for blitting
self._ax_v_bk = None
self._ax_h_bk = None
# stash last-drawn row/col to skip if possible
self._row = None
self._col = None
# make attributes for callback ids
self._move_cid = None
self._click_cid = None
self._clear_cid = None
def add_cursor_position_cb(self, callback):
""" Add a callback for the cursor position in the main axes
Parameters
----------
callback : callable(cc, rr)
Function that gets called when the cursor position moves to a new
row or column on main axes
"""
self._cursor_position_cbs.append(fun)
# set up the call back for the updating the side axes
def _move_cb(self, event):
if not self._active:
return
if event is None:
x = self._col
y = self._row
self._col = None
self._row = None
else:
# short circuit on other axes
if event.inaxes is not self._im_ax:
return
x, y = event.xdata, event.ydata
numrows, numcols = self._imdata.shape
if x is not None and y is not None:
self._ln_h.set_visible(True)
self._ln_v.set_visible(True)
col = int(x + 0.5)
row = int(y + 0.5)
if row != self._row or col != self._col:
if 0 <= col < numcols and 0 <= row < numrows:
self._col = col
self._row = row
for cb in self._cursor_position_cbs:
cb(col, row)
for data, ax, bkg, art, set_fun in zip(
(self._imdata[row, :], self._imdata[:, col]),
(self._ax_h, self._ax_v),
(self._ax_h_bk, self._ax_v_bk),
(self._ln_h, self._ln_v),
(self._ln_h.set_ydata, self._ln_v.set_xdata)):
self._fig.canvas.restore_region(bkg)
set_fun(data)
ax.draw_artist(art)
self._fig.canvas.blit(ax.bbox)
def _click_cb(self, event):
if event.inaxes is not self._im_ax:
return
self.active = not self.active
if self.active:
self._cur.onmove(event)
self._move_cb(event)
@auto_redraw
def _connect_callbacks(self):
"""
Connects all of the callbacks for the motion and click events
"""
self._disconnect_callbacks()
self._cur = Cursor(self._im_ax, useblit=True, color='red', linewidth=2)
self._move_cid = self._fig.canvas.mpl_connect('motion_notify_event',
self._move_cb)
self._click_cid = self._fig.canvas.mpl_connect('button_press_event',
self._click_cb)
self._clear_cid = self._fig.canvas.mpl_connect('draw_event',
self._clear)
self._fig.tight_layout()
self._fig.canvas.draw()
def _disconnect_callbacks(self):
"""
Disconnects all of the callbacks
"""
if self._fig.canvas is None:
# no canvas -> can't do anything about the call backs which
# should not exist
self._move_cid = None
self._clear_cid = None
self._click_cid = None
return
for atr in ('_move_cid', '_clear_cid', '_click_cid'):
cid = getattr(self, atr, None)
if cid is not None:
self._fig.canvas.mpl_disconnect(cid)
setattr(self, atr, None)
# clean up the cursor
if self._cur is not None:
self._cur.disconnect_events()
del self._cur
self._cur = None
@auto_redraw
def _init_artists(self, init_image):
"""
Update the CrossSection with a new base-image. This function
takes care of setting up all of the details about the image size
in the limits/artist extent of the image and the secondary data
in the cross-section parasite plots.
Parameters
----------
init_image : ndarray
An image to serve as the new 'base' image.
"""
im_shape = init_image.shape
# first deal with the image axis
# update the image, `update_artists` takes care of
# updating the actual artist
self._imdata = init_image
# update the extent of the image artist
self._im.set_extent([-0.5, im_shape[1] + .5,
im_shape[0] + .5, -0.5])
# update the limits of the image axes to match the exent
self._im_ax.set_xlim([-.05, im_shape[1] + .5])
self._im_ax.set_ylim([im_shape[0] + .5, -0.5])
# update the format coords printer
numrows, numcols = im_shape
# note, this is a closure over numrows and numcols
def format_coord(x, y):
# adjust xy -> col, row
col = int(x + 0.5)
row = int(y + 0.5)
# make sure the point falls in the array
if col >= 0 and col < numcols and row >= 0 and row < numrows:
# if it does, grab the value
z = self._imdata[row, col]
return "X: {x:d} Y: {y:d} I: {i:.2f}".format(x=col, y=row, i=z)
else:
return "X: {x:d} Y: {y:d}".format(x=col, y=row)
# replace the current format_coord function
self._im_ax.format_coord = format_coord
# net deal with the parasite axes and artist
self._ln_v.set_data(np.zeros(im_shape[0]),
np.arange(im_shape[0]))
self._ax_v.set_ylim([0, im_shape[0]])
self._ln_h.set_data(np.arange(im_shape[1]),
np.zeros(im_shape[1]))
self._ax_h.set_xlim([0, im_shape[1]])
# if we have a cavas, then connect/set up junk
if self._fig.canvas is not None:
self._connect_callbacks()
# mark as dirty
self._dirty = True
def _clear(self, event):
self._ax_v_bk = self._fig.canvas.copy_from_bbox(self._ax_v.bbox)
self._ax_h_bk = self._fig.canvas.copy_from_bbox(self._ax_h.bbox)
self._ln_h.set_visible(False)
self._ln_v.set_visible(False)
# this involves reaching in and touching the guts of the
# cursor widget. The problem is that the mpl widget
# skips updating it's saved background if the widget is inactive
if self._cur:
self._cur.background = self._cur.canvas.copy_from_bbox(
self._cur.canvas.figure.bbox)
@property
def interpolation(self):
return self._interpolation
@property
def active(self):
return self._active
@active.setter
def active(self, val):
self._active = val
self._cur.active = val
@auto_redraw
def update_interpolation(self, interpolation):
"""
Set the interpolation method
"""
self._dirty = True
self._im.set_interpolation(interpolation)
@auto_redraw
def update_cmap(self, cmap):
"""
Set the color map used
"""
# TODO: this should stash new value, not apply it
self._cmap = cmap
self._dirty = True
@auto_redraw
def update_image(self, image):
"""
Set the image data
The input data does not necessarily have to be the same shape as the
original image
"""
if self._imdata is None or self._imdata.shape != image.shape:
self._init_artists(image)
self._imdata = image
self._move_cb(None)
self._dirty = True
@auto_redraw
def update_norm(self, norm):
"""
Update the way that matplotlib normalizes the image
"""
self._norm = norm
self._dirty = True
self._cb_dirty = True
@auto_redraw
def update_limit_func(self, limit_func):
"""
Set the function to use to determine the color scale
"""
# set the new function to use for computing the color limits
self._limit_func = limit_func
self._dirty = True
def _update_artists(self):
"""
Updates the figure by re-drawing
"""
# if the figure is not dirty, short-circuit
if not (self._dirty or self._cb_dirty):
return
# this is a tuple which is the max/min used in the color mapping.
# these values are also used to set the limits on the value
# axes of the parasite axes
# value_limits
vlim = self._limit_func(self._imdata)
# set the color bar limits
self._im.set_clim(vlim)
self._norm.vmin, self._norm.vmax = vlim
# set the cross section axes limits
self._ax_v.set_xlim(*vlim[::-1])
self._ax_h.set_ylim(*vlim)
# set the imshow data
self._im.set_data(self._imdata)
self._im.set_cmap(self._cmap)
self._im.set_norm(self._norm)
# TODO if cb_dirty, remake the colorbar, I think this is
# why changing the norm does not play well
self._dirty = False
self._cb_dirty = False
def _draw(self):
self._fig.canvas.draw()
@auto_redraw
def autoscale_horizontal(self, enable):
self._ax_h.autoscale(enable=enable)
@auto_redraw
def autoscale_vertical(self, enable):
self._ax_v.autoscale(enable=False)
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 QuadSelection(Op2DView, ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit :attr:`xfacet` and :attr:`yfacet` from
:class:`cytoflow.views.ScatterplotView`, but they must both be unset!
Examples
--------
In an Jupyter notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
xfacet = Constant(None)
yfacet = Constant(None)
# override the Op2DView
xscale = util.ScaleEnum
yscale = util.ScaleEnum
xthreshold = DelegatesTo('op')
ythreshold = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_hline = Instance(Line2D, transient=True)
_vline = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""
Plot the underlying scatterplot and then plot the selection on top of it.
Parameters
----------
"""
if experiment is None:
raise util.CytoflowViewError('experiment',
"No experiment specified")
super().plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('xthreshold, ythreshold', post_init=True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.xthreshold and self.ythreshold:
self._hline = plt.axhline(self.ythreshold,
linewidth=3,
color='blue')
self._vline = plt.axvline(self.xthreshold,
linewidth=3,
color='blue')
plt.draw()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=True,
vertOn=True,
color='blue',
useblit=True)
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.xthreshold = event.xdata
self.ythreshold = event.ydata
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 QuadSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
op : Instance(Range2DOp)
The instance of Range2DOp that we're viewing / editing
huefacet : Str
The conditioning variable to plot multiple colors
subset : Str
The string passed to `Experiment.query()` to subset the data before
plotting
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterplotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_hline = Instance(Line2D, transient=True)
_vline = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""Plot the underlying scatterplot and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowOpError("No experiment specified")
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(QuadSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('op.xthreshold, op.ythreshold', post_init=True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.op.xthreshold and self.op.ythreshold:
self._hline = plt.axhline(self.op.ythreshold,
linewidth=3,
color='blue')
self._vline = plt.axvline(self.op.xthreshold,
linewidth=3,
color='blue')
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=True,
vertOn=True,
color='blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.xthreshold = event.xdata
self.op.ythreshold = event.ydata