def run(self):
# Clear the default logging so we can use our own format
rootLogger = logging.getLogger()
list(map(rootLogger.removeHandler, rootLogger.handlers[:]))
list(map(rootLogger.removeFilter, rootLogger.filters[:]))
logging.getLogger().setLevel(logging.DEBUG)
## send the log to STDERR
try:
console_handler = logging.StreamHandler()
console_handler.setFormatter(
logging.Formatter(
"%(asctime)s %(levelname)s:%(name)s:%(message)s"))
console_handler.setLevel(
logging.DEBUG if self.debug else logging.ERROR)
logging.getLogger().addHandler(console_handler)
except:
# if there's no console, this fails
pass
## capture log in memory
mem_handler = logging.StreamHandler(self.application_log)
mem_handler.setFormatter(
logging.Formatter(
"%(asctime)s %(levelname)s:%(name)s:%(message)s"))
mem_handler.setLevel(logging.DEBUG)
logging.getLogger().addHandler(mem_handler)
## and display gui messages for exceprions
gui_handler = multiprocess_logging.CallbackHandler(
lambda msg, app=self: gui_handler_callback(msg, app))
gui_handler.setLevel(logging.ERROR)
logging.getLogger().addHandler(gui_handler)
# must redirect to the gui thread
self.on_trait_change(self.show_error,
'application_error',
dispatch='ui')
# set up the model
self.model = Workflow(remote_connection=self.remote_connection,
debug=self.debug)
# and the shared central pane
self.plot_pane = FlowTaskPane(model=self.model)
# run the GUI
super(CytoflowApplication, self).run()
def run(self):
# set the root logger level to DEBUG; decide what to do with each
# message on a handler-by-handler basis
logging.getLogger().setLevel(logging.DEBUG)
## send the log to STDERR
try:
console_handler = logging.StreamHandler()
console_handler.setFormatter(
logging.Formatter(
"%(asctime)s %(levelname)s:%(name)s:%(message)s"))
console_handler.setLevel(
logging.DEBUG if self.debug else logging.ERROR)
logging.getLogger().addHandler(console_handler)
except:
# if there's no console, this fails
pass
## capture log in memory
mem_handler = logging.StreamHandler(self.application_log)
mem_handler.setFormatter(
logging.Formatter(
"%(asctime)s %(levelname)s:%(name)s:%(message)s"))
mem_handler.setLevel(logging.DEBUG)
logging.getLogger().addHandler(mem_handler)
## and display gui messages for exceptions
gui_handler = CallbackHandler(
lambda rec, app=self: gui_handler_callback(rec.getMessage(), app))
gui_handler.setLevel(logging.ERROR)
logging.getLogger().addHandler(gui_handler)
# must redirect to the gui thread
self.on_trait_change(self.show_error,
'application_error',
dispatch='ui')
# set up the model
self.model = Workflow(remote_connection=self.remote_connection,
debug=self.debug)
# and the shared central pane
self.plot_pane = FlowTaskPane(model=self.model)
# run the GUI
super(CytoflowApplication, self).run()
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 image...',
method='on_export',
accelerator='Ctrl+x'),
TaskAction(name='Export IPython notebook...',
method='on_ipython',
accelerator='Ctrl+I'),
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_ipython',
name='IPython',
tooltip="Export to an IPython notebook...",
image=ImageResource('ipython')),
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.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(model=self.model,
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.status = "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_ipython(self):
"""
Shows a dialog to export the workflow to an IPython notebook
"""
dialog = FileDialog(parent=self.window.control,
action='save as',
wildcard='*.ipynb')
if dialog.open() == OK:
writer = IPythonNotebookWriter(file=dialog.path)
writer.export(self.workflow)
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.status = "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
class FlowTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflow.flow_task"
name = "Cytometry analysis"
# the main workflow instance.
# THIS IS WHERE IT'S INSTANTIATED (note the args=() )
model = Instance(LocalWorkflow, 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='Save Plot...',
method='on_export',
accelerator='Ctrl+x'),
TaskAction(name='Export Jupyter notebook...',
method='on_notebook',
accelerator='Ctrl+I'),
TaskAction(name='Preferences...',
method='on_prefs',
accelerator='Ctrl+P'),
id='File', name='&File'),
SMenu(id = 'View', name = '&View'),
SMenu(TaskAction(name = 'Report a problem....',
method = 'on_problem'),
TaskAction(name='About...',
method='on_about'),
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 = "Save Plot",
tooltip='Save the current plot',
image=ImageResource('export')),
TaskAction(method='on_notebook',
name='Notebook',
tooltip="Export to an Jupyter notebook...",
image=ImageResource('ipython')),
TaskAction(method='on_prefs',
name = "Prefs",
tooltip='Preferences',
image=ImageResource('prefs'),
enabled = False),
image_size = (32, 32))]
# are we debugging? ie, do we need a default setup?
debug = Bool
def activated(self):
# add an import plugin
import_op = ImportPlugin().get_operation()
# if we're debugging, add a few data bits
if self.debug:
from cytoflow import Tube
import_op.conditions["Dox"] = "float"
import_op.conditions["Replicate"] = "int"
tube1 = Tube(file = "../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions = {"Dox" : 1.0, "Replicate" : 1})
tube2 = Tube(file = "../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions = {"Dox" : 10.0, "Replicate" : 1})
tube3 = Tube(file = "../cytoflow/tests/data/Plate01/CFP_Well_B4.fcs",
conditions = {"Dox" : 1.0, "Replicate" : 2})
tube4 = Tube(file = "../cytoflow/tests/data/Plate01/RFP_Well_A6.fcs",
conditions = {"Dox" : 10.0, "Replicate" : 2})
import_op.tubes = [tube1, tube2, tube3, tube4]
self.model.add_operation(import_op)
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(model = self.model,
plugins = self.view_plugins,
task = self)]
def on_new(self):
self.model.workflow = []
# add an import operation
import_op = ImportPlugin().get_operation()
self.model.add_operation(import_op)
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_workflow = unpickler.load()
# 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_workflow
container.save_to_directory(os.getcwd())
else:
self.model.workflow = new_workflow
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.workflow)
def on_export(self):
"""
Shows a dialog to export a file
"""
information(None, "This will save exactly what you see on the screen "
"to a file. Choose the file type via the file "
"extension (ie .png, .pdf, .jpg)", "Export")
dialog = FileDialog(parent = self.window.control,
action = 'save as')
if dialog.open() == OK:
self.view.export(dialog.path)
def on_notebook(self):
"""
Shows a dialog to export the workflow to an Jupyter notebook
"""
return
dialog = FileDialog(parent = self.window.control,
action = 'save as',
wildcard = '*.ipynb')
if dialog.open() == OK:
writer = JupyterNotebookWriter(file = dialog.path)
writer.export(self.workflow)
def on_prefs(self):
pass
def on_problem(self):
information(None, "Your email client will now create a new message to the "
"developer. Debugging logs are attached. Please fill "
"out the template bug report and send -- thank you for "
"reporting a bug!")
# import tempfile
log = guiutil.parent_log.getvalue()
log += self.model.get_child_log()
#
# logfile = tempfile.NamedTemporaryFile(delete = False)
# logfile.write(parent_log)
# logfile.write(child_log)
# logfile.close()
versions = ["{0} {1}".format(key, value) for key, value in self._get_package_versions().iteritems()]
body = """
Thank you for your bug report! Please fill out the following template.
PLATFORM (Mac, PC, Linux, other):
OPERATING SYSTEM (eg OSX 10.7, Windows 8.1):
SEVERITY (Critical? Major? Minor? Enhancement?):
DESCRIPTION:
- What were you trying to do?
- What happened?
- What did you expect to happen?
PACKAGE VERSIONS: {0}
DEBUG LOG: {1}
""".format(versions, log)
mailto.mailto("*****@*****.**",
subject = "Cytoflow bug report",
body = body)
def _get_package_versions(self):
import sys
from cytoflow import __version__ as cf_version
from fcsparser import __version__ as fcs_version
from pandas import __version__ as pd_version
from numpy import __version__ as np_version
from numexpr import __version__ as nxp_version
from bottleneck import __version__ as btl_version
from seaborn import __version__ as sns_version
from matplotlib import __version__ as mpl_version
from scipy import __version__ as scipy_version
from sklearn import __version__ as skl_version
from pyface import __version__ as pyf_version
from envisage import __version__ as env_version
from traits import __version__ as trt_version
from traitsui import __version__ as trt_ui_version
return {"python" : sys.version,
"cytoflow" : cf_version,
"fcsparser" : fcs_version,
"pandas" : pd_version,
"numpy" : np_version,
"numexpr" : nxp_version,
"bottleneck" : btl_version,
"seaborn" : sns_version,
"matplotlib" : mpl_version,
"scipy" : scipy_version,
"scikit-learn" : skl_version,
"pyface" : pyf_version,
"envisage" : env_version,
"traits" : trt_version,
"traitsui" : trt_ui_version}
def on_about(self):
versions = self._get_package_versions()
text = ["<b>Cytoflow {0}</b>".format(versions['cytoflow']),
"<p>"]
ver_text = ["{0} {1}".format(key, value) for key, value in versions.iteritems()]
text.extend(ver_text)
text.extend(["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>",
"<a href=http://www.freepik.com/free-photos-vectors/background>App icon from Starline - Freepik.com</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(text = text,
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))
# add the operation and the operation's default view
self.model.add_operation(plugin.get_operation())
def set_current_view(self, view_id):
"""
called by the view pane
"""
if view_id == "default":
self.model.set_current_view(self.model.selected.default_view)
else:
plugin = next((x for x in self.view_plugins if x.view_id == view_id))
self.model.set_current_view(plugin.get_view())
def create_central_pane(self):
self.view = FlowTaskPane(model = self.model)
return self.view
class FlowTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflow.flow_task"
name = "Cytometry analysis"
# the main workflow instance.
model = Instance(Workflow)
# the center pane
plot_pane = Instance(FlowTaskPane)
workflow_pane = Instance(WorkflowDockPane)
view_pane = Instance(ViewDockPane)
# 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='Save Plot...',
method='on_export',
accelerator='Ctrl+x'),
# TaskAction(name='Export Jupyter notebook...',
# method='on_notebook',
# accelerator='Ctrl+I'),
# TaskAction(name='Preferences...',
# method='on_prefs',
# accelerator='Ctrl+P'),
id='File',
name='&File'),
SMenu(id='View', name='&View'),
SMenu(TaskAction(name='Report a problem....', method='on_problem'),
TaskAction(name='About...', method='on_about'),
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="Save Plot",
tooltip='Save the current plot',
image=ImageResource('export')),
# TaskAction(method='on_notebook',
# name='Notebook',
# tooltip="Export to an Jupyter notebook...",
# image=ImageResource('ipython')),
# TaskAction(method='on_prefs',
# name = "Prefs",
# tooltip='Preferences',
# image=ImageResource('prefs')),
image_size=(32, 32))
]
# the file to save to if the user clicks "save" and has already clicked
# "open" or "save as".
filename = Unicode
def prepare_destroy(self):
self.model.shutdown_remote_process()
def activated(self):
# add the import op
self.add_operation(ImportPlugin().id)
self.model.selected = self.model.workflow[0]
# if we're debugging, add a few data bits
if self.model.debug:
from cytoflow import Tube
import_op = self.model.workflow[0].operation
import_op.conditions = {"Dox": "float", "Well": "category"}
# import_op.conditions["Dox"] = "float"
# import_op.conditions["Well"] = "category"
tube1 = Tube(file="../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions={
"Dox": 0.0,
"Well": 'A'
})
tube2 = Tube(file="../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions={
"Dox": 10.0,
"Well": 'A'
})
tube3 = Tube(file="../cytoflow/tests/data/Plate01/CFP_Well_B4.fcs",
conditions={
"Dox": 0.0,
"Well": 'B'
})
tube4 = Tube(file="../cytoflow/tests/data/Plate01/RFP_Well_A6.fcs",
conditions={
"Dox": 10.0,
"Well": 'B'
})
import_op.tubes = [tube1, tube2, tube3, tube4]
# self.add_operation(ChannelStatisticPlugin().id)
# stat_op = self.model.workflow[1].operation
# stat_op.name = "Test"
# stat_op.channel = "Y2-A"
# stat_op.statistic_name = "Geom.Mean"
# stat_op.by = ["Dox", "Well"]
# self.model.selected = self.model.workflow[1]
self.model.modified = False
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.plot_pane = FlowTaskPane(model=self.model)
return self.plot_pane
def create_dock_panes(self):
self.workflow_pane = WorkflowDockPane(model=self.model,
plugins=self.op_plugins,
task=self)
self.view_pane = ViewDockPane(model=self.model,
plugins=self.view_plugins,
task=self)
return [self.workflow_pane, self.view_pane]
def on_new(self):
if self.model.modified:
ret = confirm(
parent=None,
message=
"Are you sure you want to discard the current workflow?",
title="Clear workflow?")
if ret != YES:
return
self.filename = ""
self.window.title = "Cytoflow"
# clear the workflow
self.model.workflow = []
# add the import op
self.add_operation(ImportPlugin().id)
# and select the operation
self.model.selected = self.model.workflow[0]
self.model.modified = False
def on_open(self):
"""
Shows a dialog to open a file.
"""
if self.model.modified:
ret = confirm(
parent=None,
message=
"Are you sure you want to discard the current workflow?",
title="Clear workflow?")
if ret != YES:
return
dialog = FileDialog(
parent=self.window.control,
action='open',
wildcard=(
FileDialog.create_wildcard("Cytoflow workflow", "*.flow") +
';' + #@UndefinedVariable
FileDialog.create_wildcard("All files",
"*"))) #@UndefinedVariable
if dialog.open() == OK:
self.open_file(dialog.path)
self.filename = dialog.path
self.window.title = "Cytoflow - " + self.filename
def open_file(self, path):
f = open(path, 'r')
unpickler = pickle.Unpickler(f)
try:
version = unpickler.load()
except TraitError:
error(parent=None,
message="This doesn't look like a Cytoflow file. Or maybe "
"you tried to load a workflow older than version "
"0.5?")
return
if version != self.model.version:
ret = confirm(
parent=None,
message="This is Cytoflow {}, but you're trying "
"to load a workflow from version {}. This may or "
"may not work! Are you sure you want to proceed?".format(
self.model.version, version),
title="Load workflow?")
if ret != YES:
return
try:
new_workflow = unpickler.load()
except TraitError as e:
error(parent=None, message="Error trying to load the workflow.")
return
# a few things to take care of when reloading
for wi_idx, wi in enumerate(new_workflow):
# get wi lock
wi.lock.acquire()
# clear the wi status
wi.status = "loading"
# re-link the linked list. i thought this would get taken care
# of in deserialization, but i guess not...
if wi_idx > 0:
wi.previous_wi = new_workflow[wi_idx - 1]
# replace the current workflow with the one we just loaded
if False: # for debugging the loading of things
from .event_tracer import record_events
with record_events() as container:
self.model.workflow = new_workflow
container.save_to_directory(os.getcwd())
else:
self.model.workflow = new_workflow
self.model.modified = False
for wi in self.model.workflow:
wi.lock.release()
def on_save(self):
""" Save the file to the previous filename """
if self.filename:
self.save_file(self.filename)
else:
self.on_save_as()
def on_save_as(self):
dialog = DefaultFileDialog(
parent=self.window.control,
action='save as',
default_suffix="flow",
wildcard=(
FileDialog.create_wildcard("Cytoflow workflow", "*.flow") +
';' + #@UndefinedVariable
FileDialog.create_wildcard("All files",
"*"))) #@UndefinedVariable
if dialog.open() == OK:
self.save_file(dialog.path)
self.filename = dialog.path
self.window.title = "Cytoflow - " + self.filename
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.version)
pickler.dump(self.model.workflow)
self.model.modified = False
@on_trait_change('model.modified', post_init=True)
def _on_model_modified(self, val):
if val:
if not self.window.title.endswith("*"):
self.window.title += "*"
else:
if self.window.title.endswith("*"):
self.window.title = self.window.title[:-1]
def on_export(self):
"""
Shows a dialog to export a file
"""
information(
None, "This will save exactly what you see on the screen "
"to a file.", "Export")
f = ""
filetypes_groups = self.plot_pane.canvas.get_supported_filetypes_grouped(
)
filename_exts = []
for name, ext in filetypes_groups.items():
if f:
f += ";"
f += FileDialog.create_wildcard(name,
" ".join(["*." + e for e in ext
])) #@UndefinedVariable
filename_exts.append(ext)
dialog = FileDialog(parent=self.window.control,
action='save as',
wildcard=f)
if dialog.open() == OK:
filetypes = list(
self.plot_pane.canvas.get_supported_filetypes().keys())
if not [
ext for ext in ["." + ext for ext in filetypes]
if dialog.path.endswith(ext)
]:
selected_exts = filename_exts[dialog.wildcard_index]
ext = sorted(selected_exts, key=len)[0]
dialog.path += "."
dialog.path += ext
self.plot_pane.export(dialog.path)
def on_notebook(self):
"""
Shows a dialog to export the workflow to an Jupyter notebook
"""
return
dialog = FileDialog(parent=self.window.control,
action='save as',
wildcard='*.ipynb')
if dialog.open() == OK:
writer = JupyterNotebookWriter(file=dialog.path)
writer.export(self.model.workflow)
def on_prefs(self):
pass
def on_problem(self):
information(
None, "Your email client will now create a new message to the "
"developer. Debugging logs are attached. Please fill "
"out the template bug report and send -- thank you for "
"reporting a bug!")
log = self.application.application_log.getvalue()
versions = [
"{0} {1}".format(key, value)
for key, value in self._get_package_versions().items()
]
body = """
Thank you for your bug report! Please fill out the following template.
PLATFORM (Mac, PC, Linux, other):
OPERATING SYSTEM (eg OSX 10.7, Windows 8.1):
SEVERITY (Critical? Major? Minor? Enhancement?):
DESCRIPTION:
- What were you trying to do?
- What happened?
- What did you expect to happen?
PACKAGE VERSIONS: {0}
DEBUG LOG: {1}
""".format(versions, log)
# mailto.mailto("*****@*****.**",
# subject = "Cytoflow bug report",
# body = body)
def _get_package_versions(self):
import sys
from cytoflow import __version__ as cf_version
from fcsparser import __version__ as fcs_version
from pandas import __version__ as pd_version
from numpy import __version__ as np_version
from numexpr import __version__ as nxp_version
from bottleneck import __version__ as btl_version
from seaborn import __version__ as sns_version
from matplotlib import __version__ as mpl_version
from scipy import __version__ as scipy_version
from sklearn import __version__ as skl_version
from pyface import __version__ as pyf_version
from envisage import __version__ as env_version
from traits import __version__ as trt_version
from traitsui import __version__ as trt_ui_version
return {
"python": sys.version,
"cytoflow": cf_version,
"fcsparser": fcs_version,
"pandas": pd_version,
"numpy": np_version,
"numexpr": nxp_version,
"bottleneck": btl_version,
"seaborn": sns_version,
"matplotlib": mpl_version,
"scipy": scipy_version,
"scikit-learn": skl_version,
"pyface": pyf_version,
"envisage": env_version,
"traits": trt_version,
"traitsui": trt_ui_version
}
def on_about(self):
versions = self._get_package_versions()
text = ["<b>Cytoflow {0}</b>".format(versions['cytoflow']), "<p>"]
ver_text = [
"{0} {1}".format(key, value) for key, value in versions.items()
]
text.extend(ver_text)
text.extend([
"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>",
"<a href=http://www.freepik.com/free-photos-vectors/background>App icon from Starline - Freepik.com</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(text=text,
parent=self.window.control,
title="About",
image=ImageResource('cuvette'),
additions=text)
dialog.open()
@on_trait_change('model.selected', post_init=True)
def _on_select_op(self, selected):
if selected:
self.view_pane.enabled = (selected is not None)
self.view_pane.default_view = selected.default_view.id if selected.default_view else ""
self.view_pane.selected_view = selected.current_view.id if selected.current_view else ""
else:
self.view_pane.enabled = False
@on_trait_change('view_pane.selected_view', post_init=True)
def _on_select_view(self, view_id):
if not view_id:
return
# if we already have an instantiated view object, find it
try:
self.model.selected.current_view = next(
(x for x in self.model.selected.views if x.id == view_id))
except StopIteration:
# else make the new view
plugin = next(
(x for x in self.view_plugins if x.view_id == view_id))
view = plugin.get_view()
self.model.selected.views.append(view)
self.model.selected.current_view = view
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))
# next, get an operation
op = plugin.get_operation()
# make a new workflow item
wi = WorkflowItem(
operation=op,
deletable=(op_id !=
'edu.mit.synbio.cytoflowgui.op_plugins.import'))
# if the op has a default view, add it to the wi
try:
wi.default_view = op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
except AttributeError:
pass
# figure out where to add it
if self.model.selected:
idx = self.model.workflow.index(self.model.selected) + 1
else:
idx = len(self.model.workflow)
# the add_remove_items handler takes care of updating the linked list
self.model.workflow.insert(idx, wi)
# and make sure to actually select the new wi
self.model.selected = wi
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 image...',
method='on_export',
accelerator='Ctrl+x'),
TaskAction(name='Export IPython notebook...',
method='on_ipython',
accelerator='Ctrl+I'),
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_ipython',
name='IPython',
tooltip="Export to an IPython notebook...",
image=ImageResource('ipython')),
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.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(model = self.model,
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.status = "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_ipython(self):
"""
Shows a dialog to export the workflow to an IPython notebook
"""
dialog = FileDialog(parent = self.window.control,
action = 'save as',
wildcard = '*.ipynb')
if dialog.open() == OK:
writer = IPythonNotebookWriter(file = dialog.path)
writer.export(self.workflow)
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.status = "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)
