class FlowTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflow.flow_task"
name = "Cytometry analysis"
# the main workflow instance.
# THIS IS WHERE IT'S INITIALLY INSTANTIATED (note the args=())
model = Instance(Workflow, args = ())
# the center pane
view = Instance(FlowTaskPane)
# plugin lists, to setup the interface
op_plugins = List(IOperationPlugin)
view_plugins = List(IViewPlugin)
menu_bar = SMenuBar(SMenu(TaskAction(name='Open...',
method='on_open',
accelerator='Ctrl+O'),
TaskAction(name='Save',
#image='save',
method='on_save',
accelerator='Ctrl+S'),
TaskAction(name='Save As...',
method='on_save_as',
accelerator='Ctrl+e'),
TaskAction(name='Export...',
method='on_export',
accelerator='Ctrl+x'),
TaskAction(name='Preferences...',
method='on_prefs',
accelerator='Ctrl+P'),
id='File', name='&File'),
SMenu(TaskAction(name='About...',
method='on_about',
accelerator="Ctrl+A"),
id="Help", name ="&Help"))
tool_bars = [ SToolBar(TaskAction(method='on_new',
name = "New",
tooltip='New workflow',
image=ImageResource('new')),
TaskAction(method='on_open',
name = "Open",
tooltip='Open a file',
image=ImageResource('open')),
TaskAction(method='on_save',
name = "Save",
tooltip='Save the current file',
image=ImageResource('save')),
TaskAction(method='on_export',
name = "Export",
tooltip='Export the current plot',
image=ImageResource('export')),
TaskAction(method='on_prefs',
name = "Prefs",
tooltip='Preferences',
image=ImageResource('prefs')),
image_size = (32, 32))]
# are we debugging? ie, do we need a default setup?
debug = Bool
worker = Instance(threading.Thread)
to_update = Instance(UniquePriorityQueue, ())
worker_flag = Instance(threading.Event, args = ())
worker_lock = Instance(threading.Lock, args = ())
def initialized(self):
# make sure that when the result changes we get notified
# can't use a static notifier because selected.result gets updated
# on the worker thread, but we need to dispatch on the UI thread
self.model.on_trait_change(self._result_updated,
"selected:result",
dispatch = 'ui')
def activated(self):
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
# if we're debugging, add a few data bits
if self.debug:
from cytoflow import Tube
wi.operation.conditions["Dox"] = "log"
tube1 = Tube(file = "../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions = {"Dox" : 0.1})
tube2 = Tube(file = "../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions = {"Dox" : 1.0})
wi.operation.tubes.append(tube1)
wi.operation.tubes.append(tube2)
self.add_operation('edu.mit.synbio.cytoflowgui.op_plugins.hlog')
self.model.selected.operation.channels = ["V2-A", "Y2-A"]
self.model.selected.operation.name = "H"
self.add_operation('edu.mit.synbio.cytoflowgui.op_plugins.threshold')
self.model.selected.operation.channel = "Y2-A"
self.model.selected.operation.threshold = 2000
self.model.selected.operation.name = "T"
def prepare_destroy(self):
self.model = None
def _default_layout_default(self):
return TaskLayout(left = PaneItem("edu.mit.synbio.workflow_pane"),
right = PaneItem("edu.mit.synbio.view_traits_pane"))
def create_central_pane(self):
self.view = FlowTaskPane(model = self.model)
return self.view
def create_dock_panes(self):
return [WorkflowDockPane(model = self.model,
plugins = self.op_plugins,
task = self),
ViewDockPane(plugins = self.view_plugins,
task = self)]
def on_new(self):
self.model.workflow = []
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
def on_open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control,
action = 'open',
wildcard='*.flow')
if dialog.open() == OK:
self.open_file(dialog.path)
def open_file(self, path):
f = open(path, 'r')
unpickler = pickle.Unpickler(f)
new_model = unpickler.load()
# update the link back to the controller (ie, self)
for wi in new_model.workflow:
wi.task = self
# and set up the view handlers
for view in wi.views:
view.handler = view.handler_factory(model = view, wi = wi)
# replace the current workflow with the one we just loaded
if False:
from event_tracer import record_events
with record_events() as container:
self.model.workflow[:] = new_model.workflow
self.model.selected = new_model.selected
container.save_to_directory(os.getcwd())
else:
self.model.workflow[:] = new_model.workflow
self.model.selected = new_model.selected
wi = self.model.workflow[0]
while True:
wi.valid = "invalid"
with self.worker_lock:
self.to_update.put_nowait((self.model.workflow.index(wi), wi))
if wi.next:
wi = wi.next
else:
break
# check to see if we have a worker thread around
if not self.worker or not self.worker.is_alive():
self.worker = threading.Thread(target = update_model,
args = (self.worker_flag,
self.worker_lock,
self.to_update))
self.worker.daemon = True
self.worker.start()
# start the worker thread processing
with self.worker_lock:
if not self.to_update.empty():
self.worker_flag.set()
def on_save(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control,
action = 'save as',
wildcard='*.flow')
if dialog.open() == OK:
self.save_file(dialog.path)
def on_save_as(self):
pass
def save_file(self, path):
# TODO - error handling
f = open(path, 'w')
pickler = pickle.Pickler(f, 0) # text protocol for now
pickler.dump(self.model)
def on_export(self):
"""
Shows a dialog to export a file
"""
dialog = FileDialog(parent = self.window.control,
action = 'save as')
if dialog.open() == OK:
self.view.export(dialog.path)
def on_prefs(self):
pass
def on_about(self):
from cytoflow import __version__ as cf_version
from fcsparser import __version__ as fcs_version
from pandas.version import version as pd_version
from numpy.version import version as np_version
from numexpr import __version__ as numexp_version
from seaborn import __version__ as sns_version
from matplotlib import __version__ as mpl_version
from pyface import __version__ as py_version
from envisage import __version__ as env_version
from traits import __version__ as trt_version
from traitsui import __version__ as trt_ui_version
text = ["<b>Cytoflow {0}</b>".format(cf_version),
"<p>",
"fcsversion {0}".format(fcs_version),
"pandas {0}".format(pd_version),
"numpy {0}".format(np_version),
"numexpr {0}".format(numexp_version),
"seaborn {0}".format(sns_version),
"matplotlib {0}".format(mpl_version),
"pyface {0}".format(py_version),
"envisage {0}".format(env_version),
"traits {0}".format(trt_version),
"traitsui {0}".format(trt_ui_version),
"Icons from the <a href=http://tango.freedesktop.org>Tango Desktop Project</a>",
"<a href=https://thenounproject.com/search/?q=setup&i=14287>Settings icon</a> by Paulo Sa Ferreira from <a href=https://thenounproject.com>The Noun Project</a>",
"Cuvette image from Wikimedia Commons user <a href=http://commons.wikimedia.org/wiki/File:Hellma_Large_cone_cytometry_cell.JPG>HellmaUSA</a>"]
dialog = AboutDialog(parent = self.window.control,
title = "About",
image = ImageResource('cuvette'),
additions = text)
dialog.open()
def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# default to inserting at the end of the list if none selected
after = self.model.selected
if after is None:
after = self.model.workflow[-1]
idx = self.model.workflow.index(after)
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
wi.next = after.next
after.next = wi
wi.previous = after
if wi.next:
wi.next.previous = wi
self.model.workflow.insert(idx+1, wi)
# set up the default view
wi.default_view = plugin.get_default_view()
if wi.default_view is not None:
wi.default_view.op = wi.operation
wi.default_view.handler = \
wi.default_view.handler_factory(model = wi.default_view, wi = wi.previous)
wi.views.append(wi.default_view)
# select (open) the new workflow item
self.model.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
# invalidate everything following
self.operation_parameters_updated()
@on_trait_change("model:workflow[]")
def _on_remove_operation(self, obj, name, old, new):
if name == "workflow_items" and len(new) == 0 and len(old) > 0:
assert len(old) == 1
wi = old[0]
if self.model.selected == wi:
self.model.selected = wi.previous
wi.previous.next = wi.next
if wi.next:
wi.next.previous = wi.previous
del wi.default_view
del wi.views
del wi
self.operation_parameters_updated()
@on_trait_change("model:selected:operation:+")
def operation_parameters_updated(self):
# invalidate this workflow item and all the ones following it
wi = self.model.selected
while True:
wi.valid = "invalid"
with self.worker_lock:
self.to_update.put_nowait((self.model.workflow.index(wi), wi))
if wi.next:
wi = wi.next
else:
break
# check to see if we have a worker thread around
if not self.worker or not self.worker.is_alive():
self.worker = threading.Thread(target = update_model,
args = (self.worker_flag,
self.worker_lock,
self.to_update))
self.worker.daemon = True
self.worker.start()
# start the worker thread processing
with self.worker_lock:
if not self.to_update.empty():
self.worker_flag.set()
def set_current_view(self, view_id):
"""
called by the view pane
"""
wi = self.model.selected
if view_id == "default":
view_id = self.model.selected.default_view.id
view = next((x for x in wi.views if x.id == view_id), None)
if not view:
plugin = next((x for x in self.view_plugins if x.view_id == view_id))
view = plugin.get_view()
view.handler = view.handler_factory(model = view, wi = wi)
wi.views.append(view)
wi.current_view = view
@on_trait_change("model:selected.current_view")
def _current_view_changed(self, obj, name, old, new):
# we get notified if *either* the currently selected workflowitem
# *or* the current view changes.
if name == 'selected':
new = new.current_view if new else None
old = old.current_view if old else None
# remove the notifications from the old view
if old:
old.on_trait_change(self.view_parameters_updated, remove = True)
# and if the old view was interactive, turn off its interactivity
# to remove the matplotlib event handlers
if "interactive" in old.traits():
old.interactive = False
# whenever the view parameters change, we need to know so we can
# update the plot(s)
if new:
new.on_trait_change(self.view_parameters_updated)
if self.model.selected:
self.view.plot(self.model.selected)
else:
self.view.clear_plot()
else:
self.view.clear_plot()
def _result_updated(self, obj, name, old, new):
print "result updated"
if self.model.selected:
self.view.plot(self.model.selected)
else:
self.view.clear_plot()
def view_parameters_updated(self, obj, name, new):
# i should be able to specify the metadata i want in the listener,
# but there's an odd interaction (bug) between metadata, dynamic
# trait listeners and instance traits. so, check for 'transient'
# here instead,
if obj.trait(name).transient:
return
print "view parameters updated: {0}".format(name)
wi = self.model.selected
if wi is None:
wi = self.model.workflow[-1]
self.view.plot(wi)
def create_central_pane(self):
self.view = FlowTaskPane(model = self.model)
return self.view
