class FCGateManager(EventGenerator):
"""Manages gate creation widgets and gates."""
def __init__(self, ax, callback_list=None):
self.gates = []
self.fig = ax.figure
self.ax = ax
self._plt_data = None
self.active_gate = None
self.sample = None
self.canvas = self.fig.canvas
self.key_handler_cid = self.canvas.mpl_connect(
'key_press_event',
lambda event: key_press_handler(event, self.canvas, self))
self.pick_event_cid = self.canvas.mpl_connect('pick_event',
self.pick_event_handler)
self.gate_num = 1
self.current_channels = 'd1', 'd2'
self.add_callback(callback_list)
def disconnect_events(self):
self.canvas.mpl_disconnect(self.key_handler_cid)
self.canvas.mpl_disconnect(self.pick_event_cid)
def pick_event_handler(self, event):
""" Handles pick events """
info = {
'options': self.get_available_channels(),
'guiEvent': event.mouseevent.guiEvent,
}
if hasattr(self, 'xlabel_artist') and (event.artist
== self.xlabel_artist):
info['axis_num'] = 0
self.callback(Event('axis_click', info))
if hasattr(self, 'ylabel_artist') and (event.artist
== self.ylabel_artist):
info['axis_num'] = 1
self.callback(Event('axis_click', info))
def add_gate(self, gate):
self.gates.append(gate)
self.set_active_gate(gate)
def remove_active_gate(self):
if self.active_gate is not None:
self.gates.remove(self.active_gate)
self.active_gate.remove()
self.active_gate = None
def set_active_gate(self, gate):
if self.active_gate is None:
self.active_gate = gate
gate.activate()
elif self.active_gate is not gate:
self.active_gate.inactivate()
self.active_gate = gate
gate.activate()
def _get_next_gate_name(self):
gate_name = 'gate{0}'.format(self.gate_num)
self.gate_num += 1
return gate_name
def _handle_gate_events(self, event):
self.set_active_gate(event.info['caller'])
def create_gate_widget(self, kind):
def clean_drawing_tools():
self._drawing_tool.disconnect_events()
self.canvas.draw_idle()
self._drawing_tool = None
def create_gate(*args):
cancelled = False # TODO allow drawing tool to cancel
verts = args[0]
ch = self.current_channels
verts = [dict(zip(ch, v)) for v in verts]
if kind == 'poly':
gate_type = PolyGate
elif 'threshold' in kind or 'quad' in kind:
gate_type = ThresholdGate
# FIXME: This is very specific implementation
if 'vertical' in kind:
verts = [{ch[0]: v[ch[0]]} for v in verts]
elif 'horizontal' in kind:
if len(ch) == 1:
cancelled = True
else:
verts = [{ch[1]: v[ch[1]]} for v in verts]
if not cancelled:
gate = BaseGate(verts,
gate_type,
name=self._get_next_gate_name(),
callback_list=self._handle_gate_events)
gate.spawn(ch, self.ax)
self.add_gate(gate)
clean_drawing_tools()
def start_drawing(kind):
if kind == 'poly':
self._drawing_tool = PolyDrawer(self.ax,
oncreated=create_gate,
lineprops=dict(color='k',
marker='o'))
elif kind == 'quad':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=1)
elif kind == 'horizontal threshold':
self._drawing_tool = Cursor(self.ax, vertOn=0, horizOn=1)
elif kind == 'vertical threshold':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=0)
if isinstance(self._drawing_tool, Cursor):
def finish_drawing(event):
self._drawing_tool.clear(None)
return create_gate([(event.xdata, event.ydata)])
self._drawing_tool.connect_event('button_press_event',
finish_drawing)
start_drawing(kind)
####################
### Loading Data ###
####################
def load_fcs(self, filepath=None, parent=None):
ax = self.ax
if parent is None:
parent = self.fig.canvas
if filepath is None:
from FlowCytometryTools.gui import dialogs
filepath = dialogs.open_file_dialog('Select an FCS file to load',
'FCS files (*.fcs)|*.fcs',
parent=parent)
if filepath is not None:
self.sample = FCMeasurement('temp', datafile=filepath)
print('WARNING: Data is raw (not transformation).')
self._sample_loaded_event()
def load_measurement(self, measurement):
self.sample = measurement.copy()
self._sample_loaded_event()
def _sample_loaded_event(self):
if self.sample is not None:
self.current_channels = list(self.sample.channel_names[0:2])
self.set_axes(self.current_channels, self.ax)
def get_available_channels(self):
return self.sample.channel_names
def change_axis(self, axis_num, channel_name):
"""
TODO: refactor that and set_axes
what to do with ax?
axis_num: int
axis number
channel_name: str
new channel to plot on that axis
"""
current_channels = list(self.current_channels)
if len(current_channels) == 1:
if axis_num == 0:
new_channels = channel_name,
else:
new_channels = current_channels[0], channel_name
else:
new_channels = list(current_channels)
new_channels[axis_num] = channel_name
self.set_axes(new_channels, self.ax)
def set_axes(self, channels, ax):
"""
channels : iterable of string
each value corresponds to a channel names
names must be unique
"""
# To make sure displayed as hist
if len(set(channels)) == 1:
channels = channels[0],
self.current_channels = channels
# Remove existing gates
for gate in self.gates:
gate.remove_spawned_gates()
##
# Has a clear axis command inside!!
# which will "force kill" spawned gates
self.plot_data()
for gate in self.gates:
sgate = gate.spawn(channels, ax)
gate._refresh_activation()
def close(self):
for gate in self.gates:
gate.remove()
self.disconnect_events()
####################
### Plotting Data ##
####################
def plot_data(self):
"""Plots the loaded data"""
# Clear the plot before plotting onto it
self.ax.cla()
if self.sample is None:
return
if self.current_channels is None:
self.current_channels = self.sample.channel_names[:2]
channels = self.current_channels
channels_to_plot = channels[0] if len(channels) == 1 else channels
self.sample.plot(channels_to_plot, ax=self.ax)
xaxis = self.ax.get_xaxis()
yaxis = self.ax.get_yaxis()
self.xlabel_artist = xaxis.get_label()
self.ylabel_artist = yaxis.get_label()
self.xlabel_artist.set_picker(5)
self.ylabel_artist.set_picker(5)
self.fig.canvas.draw()
def get_generation_code(self):
"""Return python code that generates all drawn gates."""
if len(self.gates) < 1:
code = ''
else:
import_list = set(
[gate._gencode_gate_class for gate in self.gates])
import_list = 'from FlowCytometryTools import ' + ', '.join(
import_list)
code_list = [gate.get_generation_code() for gate in self.gates]
code_list.sort()
code_list = '\n'.join(code_list)
code = import_list + 2 * '\n' + code_list
self.callback(Event('generated_code', {'code': code}))
return code
class FCGateManager(EventGenerator):
"""Manages gate creation widgets and gates."""
def __init__(self, ax, callback_list=None):
self.gates = []
self.fig = ax.figure
self.ax = ax
self._plt_data = None
self.active_gate = None
self.sample = None
self.canvas = self.fig.canvas
self.key_handler_cid = self.canvas.mpl_connect('key_press_event',
lambda event: key_press_handler(event,
self.canvas,
self))
self.pick_event_cid = self.canvas.mpl_connect('pick_event', self.pick_event_handler)
self.gate_num = 1
self.current_channels = 'd1', 'd2'
self.add_callback(callback_list)
def disconnect_events(self):
self.canvas.mpl_disconnect(self.key_handler_cid)
self.canvas.mpl_disconnect(self.pick_event_cid)
def pick_event_handler(self, event):
""" Handles pick events """
info = {'options': self.get_available_channels(),
'guiEvent': event.mouseevent.guiEvent,
}
if hasattr(self, 'xlabel_artist') and (event.artist == self.xlabel_artist):
info['axis_num'] = 0
self.callback(Event('axis_click', info))
if hasattr(self, 'ylabel_artist') and (event.artist == self.ylabel_artist):
info['axis_num'] = 1
self.callback(Event('axis_click', info))
def add_gate(self, gate):
self.gates.append(gate)
self.set_active_gate(gate)
def remove_active_gate(self):
if self.active_gate is not None:
self.gates.remove(self.active_gate)
self.active_gate.remove()
self.active_gate = None
def set_active_gate(self, gate):
if self.active_gate is None:
self.active_gate = gate
gate.activate()
elif self.active_gate is not gate:
self.active_gate.inactivate()
self.active_gate = gate
gate.activate()
def _get_next_gate_name(self):
gate_name = 'gate{0}'.format(self.gate_num)
self.gate_num += 1
return gate_name
def _handle_gate_events(self, event):
self.set_active_gate(event.info['caller'])
def create_gate_widget(self, kind):
def clean_drawing_tools():
self._drawing_tool.disconnect_events()
self.canvas.draw_idle()
self._drawing_tool = None
def create_gate(*args):
cancelled = False # TODO allow drawing tool to cancel
verts = args[0]
ch = self.current_channels
verts = [dict(zip(ch, v)) for v in verts]
if kind == 'poly':
gate_type = PolyGate
elif 'threshold' in kind or 'quad' in kind:
gate_type = ThresholdGate
# FIXME: This is very specific implementation
if 'vertical' in kind:
verts = [{ch[0]: v[ch[0]]} for v in verts]
elif 'horizontal' in kind:
if len(ch) == 1:
cancelled = True
else:
verts = [{ch[1]: v[ch[1]]} for v in verts]
if not cancelled:
gate = BaseGate(verts, gate_type, name=self._get_next_gate_name(),
callback_list=self._handle_gate_events)
gate.spawn(ch, self.ax)
self.add_gate(gate)
clean_drawing_tools()
def start_drawing(kind):
if kind == 'poly':
self._drawing_tool = PolyDrawer(self.ax, oncreated=create_gate,
lineprops=dict(color='k', marker='o'))
elif kind == 'quad':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=1)
elif kind == 'horizontal threshold':
self._drawing_tool = Cursor(self.ax, vertOn=0, horizOn=1)
elif kind == 'vertical threshold':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=0)
if isinstance(self._drawing_tool, Cursor):
def finish_drawing(event):
self._drawing_tool.clear(None)
return create_gate([(event.xdata, event.ydata)])
self._drawing_tool.connect_event('button_press_event', finish_drawing)
start_drawing(kind)
####################
### Loading Data ###
####################
def load_fcs(self, filepath=None, parent=None):
ax = self.ax
if parent is None:
parent = self.fig.canvas
if filepath is None:
from FlowCytometryTools.gui import dialogs
filepath = dialogs.open_file_dialog('Select an FCS file to load',
'FCS files (*.fcs)|*.fcs', parent=parent)
if filepath is not None:
self.sample = FCMeasurement('temp', datafile=filepath)
print('WARNING: Data is raw (not transformation).')
self._sample_loaded_event()
def load_measurement(self, measurement):
self.sample = measurement.copy()
self._sample_loaded_event()
def _sample_loaded_event(self):
if self.sample is not None:
self.current_channels = list(self.sample.channel_names[0:2])
self.set_axes(self.current_channels, self.ax)
def get_available_channels(self):
return self.sample.channel_names
def change_axis(self, axis_num, channel_name):
"""
TODO: refactor that and set_axes
what to do with ax?
axis_num: int
axis number
channel_name: str
new channel to plot on that axis
"""
current_channels = list(self.current_channels)
if len(current_channels) == 1:
if axis_num == 0:
new_channels = channel_name,
else:
new_channels = current_channels[0], channel_name
else:
new_channels = list(current_channels)
new_channels[axis_num] = channel_name
self.set_axes(new_channels, self.ax)
def set_axes(self, channels, ax):
"""
channels : iterable of string
each value corresponds to a channel names
names must be unique
"""
# To make sure displayed as hist
if len(set(channels)) == 1:
channels = channels[0],
self.current_channels = channels
# Remove existing gates
for gate in self.gates:
gate.remove_spawned_gates()
##
# Has a clear axis command inside!!
# which will "force kill" spawned gates
self.plot_data()
for gate in self.gates:
sgate = gate.spawn(channels, ax)
gate._refresh_activation()
def close(self):
for gate in self.gates:
gate.remove()
self.disconnect_events()
####################
### Plotting Data ##
####################
def plot_data(self):
"""Plots the loaded data"""
# Clear the plot before plotting onto it
self.ax.cla()
if self.sample is None:
return
if self.current_channels is None:
self.current_channels = self.sample.channel_names[:2]
channels = self.current_channels
channels_to_plot = channels[0] if len(channels) == 1 else channels
self.sample.plot(channels_to_plot, ax=self.ax)
xaxis = self.ax.get_xaxis()
yaxis = self.ax.get_yaxis()
self.xlabel_artist = xaxis.get_label()
self.ylabel_artist = yaxis.get_label()
self.xlabel_artist.set_picker(5)
self.ylabel_artist.set_picker(5)
self.fig.canvas.draw()
def get_generation_code(self):
"""Return python code that generates all drawn gates."""
if len(self.gates) < 1:
code = ''
else:
import_list = set([gate._gencode_gate_class for gate in self.gates])
import_list = 'from FlowCytometryTools import ' + ', '.join(import_list)
code_list = [gate.get_generation_code() for gate in self.gates]
code_list.sort()
code_list = '\n'.join(code_list)
code = import_list + 2 * '\n' + code_list
self.callback(Event('generated_code',
{'code': code}))
return code
