def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
# Get color and track from hypotheses graph (which is a slot in the new operator)
# TODO: Remove pgmlink section after old operator is phased out
if WITH_HYTRA:
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
else:
try:
extra = self.mainOperator.extra_track_ids
except (IndexError, KeyError):
extra = {}
# if this is a resolved merger, find which of the merged IDs we actually clicked on
if time in extra and obj in extra[time]:
colors = [self.mainOperator.label2color[time][t] for t in extra[time][obj]]
tracks = [self.mainOperator.track_id[time][t] for t in extra[time][obj]]
selected_track = self.get_color(position5d)
idx = colors.index(selected_track)
color = colors[idx]
track = tracks[idx]
else:
try:
color = self.mainOperator.label2color[time][obj]
track = [self.mainOperator.track_id[time][obj]][0]
except (IndexError, KeyError):
color = None
track = []
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(), IPCFacade().broadcast(cmd))
sub_menus = [
("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)
]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
layer = self.getLayer('Labels')
obj = self._getObject(layer.segmentationImageSlot, position5d)
if obj == 0:
return
menu = QMenu(self)
text = "Print info for object {} in the terminal".format(obj)
menu.addAction(text)
# IPC stuff
if ilastik_config.getboolean("ilastik", "debug"):
menu.addSeparator()
if any(IPCFacade().sending):
time = position5d[0]
sub = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes[:-1]:
where = Protocol.simple("and", time=time, ilastik_id=obj)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode.capitalize(),
IPCFacade().broadcast(cmd))
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start All IPC Servers", IPCFacade().start)
menu.addSeparator()
clearlabel = "Clear label for object {}".format(obj)
menu.addAction(clearlabel)
numLabels = self.labelListData.rowCount()
label_actions = []
for l in range(numLabels):
color_icon = self.labelListData.createIconForLabel(l)
act_text = 'Label object {} as "{}"'.format(
obj, self.labelListData[l].name)
act = QAction(color_icon, act_text, menu)
act.setIconVisibleInMenu(True)
label_actions.append(act_text)
menu.addAction(act)
action = menu.exec_(globalWindowCoordinate)
if action is None:
return
if action.text() == text:
numpy.set_printoptions(precision=4)
print(
"------------------------------------------------------------")
print("object: {}".format(obj))
t = position5d[0]
labels = self.op.LabelInputs([t]).wait()[t]
if len(labels) > obj:
label = int(labels[obj])
else:
label = "none"
print("label: {}".format(label))
print('features:')
feats = self.op.ObjectFeatures([t]).wait()[t]
selected = self.op.SelectedFeatures([]).wait()
for plugin in sorted(feats.keys()):
if plugin == default_features_key or plugin not in selected:
continue
print("Feature category: {}".format(plugin))
for featname in sorted(feats[plugin].keys()):
if featname not in selected[plugin]:
continue
value = feats[plugin][featname]
ft = numpy.asarray(value.squeeze())[obj]
print("{}: {}".format(featname, ft))
if len(selected) > 0:
pred = 'none'
if self.op.Predictions.ready():
preds = self.op.Predictions([t]).wait()[t]
if len(preds) >= obj:
pred = int(preds[obj])
prob = 'none'
if self.op.Probabilities.ready():
probs = self.op.Probabilities([t]).wait()[t]
if len(probs) >= obj:
prob = probs[obj]
print("probabilities: {}".format(prob))
print("prediction: {}".format(pred))
uncertainty = 'none'
if self.op.UncertaintyEstimate.ready():
uncertainties = self.op.UncertaintyEstimate([t]).wait()[t]
if len(uncertainties) >= obj:
uncertainty = uncertainties[obj]
print("uncertainty: {}".format(uncertainty))
print(
"------------------------------------------------------------")
elif action.text() == clearlabel:
topLevelOp = self.topLevelOperatorView.viewed_operator()
imageIndex = topLevelOp.LabelInputs.index(
self.topLevelOperatorView.LabelInputs)
self.topLevelOperatorView.assignObjectLabel(
imageIndex, position5d, 0)
#todo: remove old
elif self.applet.connected_to_knime:
if action.text() == knime_hilite:
data = {'command': 0, 'objectid': 'Row' + str(obj)}
self.applet.sendMessageToServer('knime', data)
elif action.text() == knime_unhilite:
data = {'command': 1, 'objectid': 'Row' + str(obj)}
self.applet.sendMessageToServer('knime', data)
elif action.text() == knime_clearhilite:
data = {'command': 2}
self.applet.sendMessageToServer('knime', data)
else:
try:
label = label_actions.index(action.text())
except ValueError:
return
topLevelOp = self.topLevelOperatorView.viewed_operator()
imageIndex = topLevelOp.LabelInputs.index(
self.topLevelOperatorView.LabelInputs)
self.topLevelOperatorView.assignObjectLabel(
imageIndex, position5d, label + 1)
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
try:
color = self.mainOperator.label2color[time][obj]
tracks = [self.mainOperator.track_id[time][obj]]
extra = self.mainOperator.extra_track_ids
except (IndexError, KeyError):
color = None
tracks = []
extra = {}
if time in extra and obj in extra[time]:
tracks.extend(extra[time][obj])
if tracks:
children, parents = self.mainOperator.track_family(tracks[0])
else:
children, parents = None, None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track ids: " + (", ".join(map(str, set(tracks))) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(),
IPCFacade().broadcast(cmd))
sub_menus = [("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(),
IPCFacade().broadcast(cmd))
sub_menus = [("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
def handshake(_, protocol, name, **address):
from ilastik.shell.gui.ipcManager import IPCFacade
if "host" in address and "port" in address:
address = (address["host"], address["port"])
IPCFacade().handshake(protocol, name, address)