class FlowTaskPane(TaskPane):
"""
The center pane for the UI; contains the matplotlib canvas for plotting
data views.
"""
id = 'edu.mit.synbio.cytoflow.flow_task_pane'
name = 'Cytometry Data Viewer'
layout = Instance(QtGui.QVBoxLayout) # @UndefinedVariable
canvas = Instance(FigureCanvasQTAggLocal)
waiting_image = ImageResource('gear')
def create(self, parent):
if self.canvas is not None:
return
# create a layout for the tab widget and the main view
self.layout = layout = QtGui.QVBoxLayout() # @UndefinedVariable
self.control = QtGui.QWidget() # @UndefinedVariable
self.control.setLayout(layout)
tabs_ui = self.model.edit_traits(view = 'plot_view',
kind = 'subpanel',
parent = parent)
self.layout.addWidget(tabs_ui.control)
# add the main plot
self.canvas = FigureCanvasQTAggLocal(Figure(),
self.model.child_matplotlib_conn,
self.waiting_image.create_image(size = (1000, 1000)))
self.canvas.setSizePolicy(QtGui.QSizePolicy.Expanding, # @UndefinedVariable
QtGui.QSizePolicy.Expanding) # @UndefinedVariable
layout.addWidget(self.canvas)
def export(self, filename, **kwargs):
self.canvas.print_figure(filename, bbox_inches = 'tight', **kwargs)
def image_resource(self, image_name):
""" Returns the ImageResource object for the specified **image_name**.
"""
# Get the name of the image file:
volume_name, file_name = split_image_name(image_name)
if self.is_zip_file:
# See if we already have the image file cached in the file system:
cache_file = self._check_cache(file_name)
if cache_file is None:
# If not cached, then create a zip file reference:
ref = ZipFileReference(
resource_factory=resource_manager.resource_factory,
zip_file=self.zip_file,
path=self.path,
volume_name=self.name,
file_name=file_name,
)
else:
# Otherwise, create a cache file reference:
ref = ImageReference(
resource_manager.resource_factory, filename=cache_file
)
else:
# Otherwise, create a normal file reference:
ref = ImageReference(
resource_manager.resource_factory,
filename=join(self.path, file_name),
)
# Create the ImageResource object using the reference (note that the
# ImageResource class will not allow us to specify the reference in the
# constructor):
resource = ImageResource(file_name)
resource._ref = ref
# Return the ImageResource:
return resource
class EEGSensorApp(t.HasTraits):
sensor = t.Instance(EEGSensor)
filters = t.List(t.Instance(TimeDomainFilter))
sensor_operation_controller = t.Instance(SensorOperationController)
def _sensor_operation_controller_default(self):
return SensorOperationController(model=self.sensor)
sensor_timeseries_controller = t.Instance(SensorTimeseriesController)
def _sensor_timeseries_controller_default(self):
return SensorTimeseriesController(model=self.sensor,
filters=self.filters)
sensor_fft_controller = t.Instance(SensorFFTController)
def _sensor_fft_controller_default(self):
return SensorFFTController(model=self.sensor)
traits_view = QtView(
HGroup(
VGroup(Item('sensor_timeseries_controller', style='custom'),
show_border=True,
show_labels=False),
VGroup(Item('sensor_fft_controller', style='custom'),
Item('sensor_operation_controller', style='custom'),
show_border=True,
show_labels=False),
),
title="EEG Sensor Console",
icon=ImageResource('application'),
# style_sheet_path='dark_style_sheet.qss',
style_sheet=qdarkstyle.load_stylesheet(pyside=True),
resizable=True,
handler=AppHandler(),
)
class SecondTask(ExampleTask):
""" A simple task for opening a blank editor.
"""
# Task interface -------------------------------------------------------
id = "example.second_task"
name = "Second Multi-Tab Editor"
menu_bar = SMenuBar(
SMenu(
TaskAction(name="New", method="new", accelerator="Ctrl+N"),
id="File",
name="&File",
),
SMenu(DockPaneToggleGroup(),
TaskToggleGroup(),
id="View",
name="&View"),
)
tool_bars = [
SToolBar(
TaskAction(
method="new",
tooltip="New file",
image=ImageResource("document_new"),
),
image_size=(32, 32),
)
]
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
def _default_layout_default(self):
return TaskLayout(bottom=PaneItem("steps.example_pane"))
class LorenzApplication(WorkbenchApplication):
""" The Lorenz example application. """
#### 'IApplication' interface #############################################
# The application's globally unique Id.
id = 'acme.lorenz'
#### 'WorkbenchApplication' interface #####################################
# Branding information.
#
# The icon used on window title bars etc.
icon = ImageResource('lorenz.ico')
# The name of the application (also used on window title bars etc).
name = 'Lorenz'
###########################################################################
# 'WorkbenchApplication' interface.
###########################################################################
def _about_dialog_default(self):
""" Trait initializer. """
about_dialog = AboutDialog(parent=self.workbench.active_window.control,
image=ImageResource('about'))
return about_dialog
def _splash_screen_default(self):
""" Trait initializer. """
splash_screen = SplashScreen(image=ImageResource('splash'),
show_log_messages=True,
log_level=DEBUG)
return splash_screen
def create_contents(self, parent):
"""
Create and return the toolkit-specific contents of the dock pane.
"""
self.toolbar = ToolBarManager(orientation='vertical',
show_tool_names=False,
image_size=(32, 32))
self._default_action = TaskAction(
name="Setup View",
on_perform=lambda: self.task.set_current_view("default"),
image=ImageResource('setup'),
style='toggle',
visible=False)
self._actions["default"] = self._default_action
self.toolbar.append(self._default_action)
for plugin in self.plugins:
task_action = TaskAction(name=plugin.short_name,
on_perform=lambda id=plugin.view_id: self.
task.set_current_view(id),
image=plugin.get_icon(),
style='toggle')
self._actions[plugin.view_id] = task_action
self.toolbar.append(task_action)
window = QtGui.QMainWindow()
window.addToolBar(QtCore.Qt.RightToolBarArea,
self.toolbar.create_tool_bar(window))
self.ui = self.edit_traits(kind='subpanel', parent=window)
window.setCentralWidget(self.ui.control)
window.setParent(parent)
parent.setWidget(window)
return window
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()
class CorrectedDatasetsNode(TreeNode):
# List of object classes the node applies to
node_for = [CorrectedDatasets]
# Automatically open the children underneath the node
auto_open = False
# Specify children of node (this is an attribute of the class in
# 'node_for')
children = 'datasets'
# Label of the node (this is an attribute of the class in 'node_for')
label = 'title'
# View for the node
view = View(Group('title', orientation='vertical', show_left=False))
# Class of node to add
add = [Dataset]
icon_group = ImageResource('../images/sample_and_container.png')
icon_open = icon_group
class SceneAdderNode(AdderNode):
""" Subclass for adding Scene nodes to a Mayavi Engine node.
"""
# String to be shown in the TreeEditor.
label = Str('Add a new scene')
# The name of the icon
icon_name = Str('add_scene.png')
# Button for the View.
add_scene = Button('Add a new scene',
image=ImageResource('add_scene.png'))
# Trait view to show in the Mayavi current object panel.
view = View(Group(Item('add_scene', show_label=False, style='custom'),
label='Add a scene'))
def _add_scene_fired(self):
""" Trait handler for when the add_scene button is clicked.
"""
self.object.new_scene()
def init ( self, parent ):
""" Finishes initializing the editor by creating the underlying toolkit
widget.
"""
self._uis = []
# Create a tab widget to hold each separate object's view:
self.control = QtGui.QTabWidget()
signal = QtCore.SIGNAL( 'currentChanged(int)' )
QtCore.QObject.connect( self.control, signal, self._tab_activated )
# Create the button to close tabs, if necessary:
if self.factory.deletable:
button = QtGui.QToolButton()
button.setAutoRaise( True )
button.setToolTip( 'Remove current tab ')
button.setIcon ( ImageResource( 'closetab' ).create_icon() )
self.control.setCornerWidget( button, QtCore.Qt.TopRightCorner )
signal = QtCore.SIGNAL( 'clicked()' )
QtCore.QObject.connect( button, signal, self.close_current )
self.close_button = button
if self.factory.show_notebook_menu:
# Create the necessary attributes to manage hiding and revealing of
# tabs via a context menu
self._context_menu = QtGui.QMenu()
self.control.customContextMenuRequested.connect(self._context_menu_requested)
self.control.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
# Set up the additional 'list items changed' event handler needed for
# a list based trait:
self.context_object.on_trait_change( self.update_editor_item,
self.extended_name + '_items?', dispatch = 'ui' )
# Set of selection synchronization:
self.sync_value( self.factory.selected, 'selected' )
def _tool_bars_default(self):
toolbars = [
SToolBar(TaskAction(name="Import",
method='on_import',
image=ImageResource('import')),
TaskAction(name="Open",
method='on_open',
image=ImageResource('survey')),
TaskAction(name="Save",
method='on_save',
enabled_name='dirty',
image=ImageResource('save')),
id='File',
name="File",
show_tool_names=False,
image_size=(24, 24)),
SToolBar(TaskCommandAction(name='New Group',
method='on_new_group',
command_stack_name='command_stack',
image=ImageResource('new-group')),
TaskCommandAction(name='Delete Group',
method='on_delete_group',
enabled_name='have_current_group',
command_stack_name='command_stack',
image=ImageResource('delete-group')),
TaskAction(name='Previous Line',
method='on_previous_line',
enabled_name='survey.survey_lines',
image=ImageResource("arrow-left")),
TaskAction(name='Next Line',
method='on_next_line',
enabled_name='survey.survey_lines',
image=ImageResource("arrow-right")),
id='Survey',
name="Survey",
show_tool_names=False,
image_size=(24, 24)),
]
return toolbars
class SecondTask(ExampleTask):
""" A simple task for opening a blank editor.
"""
#### Task interface #######################################################
id = 'example.second_task'
name = 'Second Multi-Tab Editor'
menu_bar = SMenuBar(
SMenu(TaskAction(name='New', method='new', accelerator='Ctrl+N'),
id='File',
name='&File'),
SMenu(DockPaneToggleGroup(),
TaskToggleGroup(),
id='View',
name='&View'))
tool_bars = [
SToolBar(TaskAction(method='new',
tooltip='New file',
image=ImageResource('document_new')),
image_size=(32, 32)),
]
###########################################################################
# 'Task' interface.
###########################################################################
def _default_layout_default(self):
return TaskLayout(left=VSplitter(
HSplitter(PaneItem('steps.pane1'), PaneItem('steps.pane2'),
PaneItem('steps.pane3')),
HSplitter(PaneItem('steps.pane4'), PaneItem('steps.pane5'),
PaneItem('steps.pane6')),
))
class EditPreferencesAction(Action):
""" An action that displays the preferences dialog. """
#### 'Action' interface ###################################################
# A longer description of the action.
description = 'Manage Preferences'
# The action's image (displayed on tool bar tools etc).
image = ImageResource('preferences')
# The action's name (displayed on menus/tool bar tools etc).
name = 'Preferences'
# A short description of the action used for tooltip text etc.
tooltip = 'Manage Preferences'
###########################################################################
# 'Action' interface.
###########################################################################
def perform(self, event):
""" Performs the action. """
from apptools.preferences.ui.api import PreferencesManager
# Lookup the preferences manager service.
manager = event.window.application.get_service(PreferencesManager)
ui = manager.edit_traits(parent=event.window.control, kind='modal')
# If the user hit the "Ok" button, then save the preferences in case
# application crashes before it exits!
if ui.result:
self.window.application.preferences.save()
return
def get_icon(self):
return ImageResource('kmeans')
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)
ObjectTreeNode(node_for=[DemoFile],
label="nice_name",
view=demo_file_view),
ObjectTreeNode(node_for=[DemoContentFile],
label="nice_name",
view=demo_content_view),
ObjectTreeNode(node_for=[DemoImageFile],
label="nice_name",
view=demo_content_view),
],
selected='selected_node',
)
next_tool = Action(
name='Next',
image=ImageResource("next"),
tooltip="Go to next file",
action="do_next",
enabled_when="_next_node is not None",
)
previous_tool = Action(
name='Previous',
image=ImageResource("previous"),
tooltip="Go to next file",
action="do_previous",
enabled_when="_previous_node is not None",
)
parent_tool = Action(
name='Parent',
def _actions_default(self):
return [
Group(
Action(
image=ImageResource(
'16x16/x-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the -X axis",
on_perform=self.x_minus_view,
),
Action(
image=ImageResource(
'16x16/x-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the +X axis",
on_perform=self.x_plus_view,
),
Action(
image=ImageResource(
'16x16/y-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the -Y axis",
on_perform=self.y_minus_view,
),
Action(
image=ImageResource(
'16x16/y-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the +Y axis",
on_perform=self.y_plus_view,
),
Action(
image=ImageResource(
'16x16/z-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the -Z axis",
on_perform=self.z_minus_view,
),
Action(
image=ImageResource(
'16x16/z-axis',
search_path=[self._get_image_path()],
),
tooltip="View along the +Z axis",
on_perform=self.z_plus_view,
),
Action(
image=ImageResource(
'16x16/isometric',
search_path=[self._get_image_path()],
),
tooltip="Obtain an isometric view",
on_perform=self.isometric_view,
),
),
Group(
Action(
image=ImageResource(
'16x16/parallel',
search_path=[self._get_image_path()],
),
tooltip='Toggle parallel projection',
style="toggle",
on_perform=self._toggle_projection,
checked=self.parallel_projection,
),
Action(
image=ImageResource(
'16x16/origin_glyph',
search_path=[self._get_image_path()],
),
tooltip='Toggle axes indicator',
style="toggle",
enabled=(self.marker is not None),
on_perform=self._toggle_axes,
checked=self.show_axes,
),
Action(
image=ImageResource(
'16x16/fullscreen',
search_path=[self._get_image_path()],
),
tooltip=
'Full Screen (press "q" or "e" or ESC to exit fullscreen)',
style="push",
on_perform=self._full_screen_fired,
),
),
Group(
Action(
image=ImageResource(
'16x16/save',
search_path=[self._get_image_path()],
),
tooltip="Save a snapshot of this scene",
on_perform=self._save_snapshot,
),
Action(
image=ImageResource(
'16x16/configure',
search_path=[self._get_image_path()],
),
tooltip='Configure the scene',
style="push",
on_perform=self._configure_scene,
),
),
]
info.object.load()
action_strings = \
[('Plot', 'replot', 'Replot current diagrams'),
('Clear', 'clear', 'Clear current diagrams'),
('Save', 'save', 'Save session'),
('Load', 'load', 'Load session'),
('Animate', 'anim', 'Animate current session'),
('Render', 'render', 'Render current session')]
toolbar_actions = [
Action(name="Run",
tooltip='Start computation',
enabled_when='enable_run',
image=ImageResource('kt-start'),
action="run_action"),
Action(name="Pause",
tooltip='Pause computation',
enabled_when='enable_pause',
image=ImageResource('kt-pause'),
action="pause_action"),
Action(name="Stop",
tooltip='Stop computation',
enabled_when='enable_stop',
image=ImageResource('kt-stop'),
action="stop_action"),
]
# toolbar_actions += [Action(name=name,
# action=action,
def get_icon(self):
return ImageResource('polygon')
class PythonEditorTask(Task):
""" A simple task for editing Python code.
"""
# 'Task' traits -----------------------------------------------------------
#: The unique id of the task.
id = 'example.python_editor_task'
#: The human-readable name of the task.
name = u"Python Editor"
#: The currently active editor in the editor area, if any.
active_editor = Property(Instance(IEditor),
depends_on='editor_area.active_editor')
#: The editor area for this task.
editor_area = Instance(IEditorAreaPane)
#: The menu bar for the task.
menu_bar = SMenuBar(
SMenu(
SGroup(
TaskAction(name='New', method='new', accelerator='Ctrl+N'),
id='new_group',
),
SGroup(
TaskAction(name='Open...', method='open',
accelerator='Ctrl+O'),
id='open_group',
),
SGroup(
TaskAction(name='Save',
method='save',
accelerator='Ctrl+S',
enabled_name='active_editor.dirty'),
TaskAction(name='Save As...',
method='save_as',
accelerator='Ctrl+Shift+S'),
id='save_group',
),
SGroup(
TaskAction(
name='Close Editor',
method='close_editor',
accelerator='Ctrl+W',
),
id='close_group',
),
id='File',
name='&File',
),
SMenu(
SGroup(
EditorAction(
name='Undo',
method='undo',
enabled_name='can_undo',
accelerator='Ctrl+Z',
),
EditorAction(
name='Redo',
method='redo',
enabled_name='can_redo',
accelerator='Ctrl+Shift+Z',
),
id='undo_group',
),
SGroup(
EditorAction(
name='Go to Line...',
method='go_to_line',
accelerator='Ctrl+G',
),
id='search_group',
),
id='Edit',
name='&Edit',
), SMenu(
DockPaneToggleGroup(),
id='View',
name='&View',
),
SMenu(
SGroup(
OpenURLAction(
name='Python Documentation',
id='python_docs',
url=PYTHON_DOCS,
),
id="documentation_group",
),
id='Help',
name='&Help',
))
#: The tool bars for the task.
tool_bars = [
SToolBar(TaskAction(
method='new',
tooltip='New file',
image=ImageResource('document_new'),
),
TaskAction(method='open',
tooltip='Open a file',
image=ImageResource('document_open')),
TaskAction(method='save',
tooltip='Save the current file',
image=ImageResource('document_save'),
enabled_name='active_editor.dirty'),
image_size=(16, 16),
show_tool_names=False),
]
#: The status bar for the window when this task is active.
status_bar = Instance(StatusBarManager, ())
# -------------------------------------------------------------------------
# 'PythonEditorTask' interface.
# -------------------------------------------------------------------------
def create_editor(self, path=''):
""" Create a new editor in the editor pane.
Parameters
----------
path : path or ''
The path to the file to edit, or '' for an empty editor.
"""
if path:
path = os.path.abspath(path)
use_existing = (path != '')
self.editor_area.edit(
path,
factory=PythonEditor,
use_existing=use_existing,
)
if path:
self.active_editor.load()
def close_editor(self):
""" Close the active editor, or if no editors, close the Task window.
"""
if self.editor_area.active_editor is not None:
self.editor_area.remove_editor(self.editor_area.active_editor)
else:
self.window.close()
def new(self):
""" Open a new empty window
"""
self.create_editor()
def open(self):
""" Shows a dialog to open a Python file.
"""
dialog = FileDialog(parent=self.window.control, wildcard='*.py')
if dialog.open() == OK:
self.create_editor(dialog.path)
def save(self):
""" Save the current file.
If needed, this code prompts for a path.
Returns
-------
saved : bool
Whether or not the file was saved.
"""
editor = self.active_editor
try:
editor.save()
except IOError:
# If you are trying to save to a file that doesn't exist, open up a
# FileDialog with a 'save as' action.
dialog = FileDialog(
parent=self.window.control,
action='save as',
wildcard='*.py',
)
if dialog.open() == OK:
editor.save(dialog.path)
else:
return False
return True
# -------------------------------------------------------------------------
# 'Task' interface.
# -------------------------------------------------------------------------
def _default_layout_default(self):
""" The default layout with the browser pane on the left.
"""
return TaskLayout(
left=PaneItem('example.python_browser_pane', width=200))
def create_central_pane(self):
""" Create the central pane: the script editor.
"""
self.editor_area = EditorAreaPane()
return self.editor_area
def create_dock_panes(self):
""" Create the file browser and connect to its double click event.
"""
browser = PythonBrowserPane()
def handler():
return self.create_editor(browser.selected_file)
browser.on_trait_change(handler, 'activated')
return [browser]
# -------------------------------------------------------------------------
# Protected interface.
# -------------------------------------------------------------------------
def _prompt_for_save(self):
""" Prompts the user to save if necessary. Returns whether the dialog
was cancelled.
"""
dirty_editors = {
editor.name: editor
for editor in self.editor_area.editors
if editor.dirty and (editor.obj or editor.code)
}
if not dirty_editors:
return True
message = 'You have unsaved files. Would you like to save them?'
dialog = ConfirmationDialog(parent=self.window.control,
message=message,
cancel=True,
default=CANCEL,
title='Save Changes?')
result = dialog.open()
if result == CANCEL:
return False
elif result == YES:
for name, editor in dirty_editors.items():
editor.save(editor.path)
return True
# Trait change handlers --------------------------------------------------
@on_trait_change('window:closing')
def _prompt_on_close(self, event):
""" Prompt the user to save when exiting.
"""
close = self._prompt_for_save()
event.veto = not close
@on_trait_change('active_editor.name')
def _change_title(self):
""" Update the window title when the active editor changes.
"""
if self.window.active_task == self:
if self.active_editor is not None:
self.window.title = self.active_editor.name
else:
self.window.title = self.name
@on_trait_change('active_editor.[line,column,selection_length]')
def _update_status(self):
if self.active_editor is not None:
editor = self.active_editor
if editor.selection_length:
self.status_bar.messages = [
"Ln {}, Col {} ({} selected)".format(
editor.line, editor.column, editor.selection_length)
]
else:
self.status_bar.messages = [
"Ln {}, Col {}".format(editor.line, editor.column)
]
else:
self.status_bar.messages = []
# Trait property getter/setters ------------------------------------------
@cached_property
def _get_active_editor(self):
if self.editor_area is not None:
return self.editor_area.active_editor
return None
def get_icon(self):
return ImageResource('gauss_1d')
class WorkflowInfo(HasTraits):
# -------------------
# Required Attributes
# -------------------
#: Filename for the current workflow (if any)
workflow_filename = Str()
#: A list of the loaded plugins
plugins = List(Plugin)
#: The factory currently selected in the SetupPane
selected_factory_name = Str()
#: An error message for the entire workflow
error_message = Str()
# ---------------------
# Dependent Attributes
# ---------------------
#: The force project logo! Stored at images/Force_Logo.png
image = ImageResource('Force_Logo.png')
#: Message indicating currently loaded file
workflow_filename_message = Str()
#: A list of plugin names
plugin_names = List(Str)
# -----------
# View
# -----------
traits_view = View(
VGroup(
horizontal_centre(
Group(UItem('image',
editor=ImageEditor(scale=True,
allow_upscaling=False,
preserve_aspect_ratio=True)),
visible_when="selected_factory_name == 'Workflow'")),
Group(UReadonly('plugin_names',
editor=ListStrEditor(editable=False)),
show_border=True,
label='Available Plugins',
visible_when="selected_factory_name not in ['KPI']"),
Group(
UReadonly('workflow_filename_message', editor=TextEditor()),
show_border=True,
label='Workflow Filename',
),
Group(UReadonly('error_message', editor=TextEditor()),
show_border=True,
label='Workflow Errors',
visible_when="selected_factory_name == 'Workflow'"),
))
# -------------------
# Defaults
# -------------------
def _plugin_names_default(self):
return [plugin.name for plugin in self.plugins]
def _workflow_filename_message_default(self):
if self.workflow_filename == '':
return 'No File Loaded'
return 'Current File: ' + self.workflow_filename
def get_icon(self):
return ImageResource('channel_stat')
class FlowTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflowgui.flow_task"
name = "Cytometry analysis"
# the main workflow instance.
model = Instance(Workflow)
# the center pane
workflow_pane = Instance(WorkflowDockPane)
view_pane = Instance(ViewDockPane)
help_pane = Instance(HelpDockPane)
plot_params_pane = Instance(PlotParamsPane)
# 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(TaskToggleGroup(),
id = 'View', name = '&View'),
SMenu(TaskAction(name = 'Online documentation...',
method = 'on_docs'),
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('jupyter')),
TaskAction(method = "on_calibrate",
name = "Calibrate FCS...",
tooltip = "Calibrate FCS files",
image = ImageResource('tasbe')),
TaskAction(method = 'on_problem',
name = "Report a bug...",
tooltib = "Report a bug",
image = ImageResource('bug')))]
# TaskAction(method='on_prefs',
# name = "Prefs",
# tooltip='Preferences',
# image=ImageResource('prefs')),
# the file to save to if the user clicks "save" and has already clicked
# "open" or "save as".
filename = Str
def initialized(self):
if self.filename:
self.open_file(self.filename)
def activated(self):
# if we're coming back from the TASBE task, re-load the saved
# workflow
if self.model.backup_workflow:
self.model.workflow = self.model.backup_workflow
self.model.backup_workflow = []
return
# else, set up a new workflow
# add the import op
if not self.model.workflow:
self.add_operation(ImportPlugin().id)
self.model.selected = self.model.workflow[0]
self.model.modified = False
def _default_layout_default(self):
return TaskLayout(left = VSplitter(PaneItem("edu.mit.synbio.cytoflowgui.workflow_pane", width = 350),
PaneItem("edu.mit.synbio.cytoflowgui.help_pane", width = 350, height = 350)),
right = VSplitter(PaneItem("edu.mit.synbio.cytoflowgui.view_traits_pane", width = 350),
PaneItem("edu.mit.synbio.cytoflowgui.params_pane", width = 350, height = 350)),
top_left_corner = 'left',
bottom_left_corner = 'left',
top_right_corner = 'right',
bottom_right_corner = 'right')
def create_central_pane(self):
# set the toolbar image size
# this isn't really the right place for this, but it's the only
# place control passes back to user code before the toolbar
# is created.
dpi = self.window.control.physicalDpiX()
self.tool_bars[0].image_size = (int(0.4 * dpi), int(0.4 * dpi))
return self.application.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)
self.help_pane = HelpDockPane(view_plugins = self.view_plugins,
op_plugins = self.op_plugins,
task = self)
self.plot_params_pane = PlotParamsPane(model = self.model,
task = self)
return [self.workflow_pane, self.view_pane, self.help_pane, self.plot_params_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):
try:
new_workflow = load_yaml(path)
# a few things to take care of when reloading.
# we do this in the try block to catch people who
# load valid YAML files that aren't from cytoflow.
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.
if wi_idx > 0:
wi.previous_wi = new_workflow[wi_idx - 1]
if wi_idx < len(new_workflow) - 1:
wi.next_wi = new_workflow[wi_idx + 1]
except yaml.parser.ParserError as e:
error(None,
"Parser error loading {} -- is it a Cytoflow file?\n\n{}"
.format(path, str(e)))
return
except Exception as e:
error(None,
"{} loading {} -- is it a Cytoflow file?\n\n{}"
.format(e.__class__.__name__, path, str(e)))
return
# are we just running a smoke test?
if 'startup_test' in new_workflow[0].metadata:
def quit_app(app):
app.exit(force = True)
from pyface.timer.api import do_after
do_after(5*1000, quit_app, self.application)
return
# check that the FCS files are all there
wi = new_workflow[0]
assert(wi.operation.id == "edu.mit.synbio.cytoflow.operations.import")
missing_tubes = 0
for tube in wi.operation.tubes:
file = pathlib.Path(tube.file)
if not file.exists():
missing_tubes += 1
if missing_tubes == len(wi.operation.tubes):
warning(self.window.control,
"Cytoflow couldn't find any of the FCS files from that "
"workflow. If they've been moved, please open one FCS "
"file to show Cytoflow where they've been moved to.")
dialog = FileDialog(parent = self.window.control,
action = 'open',
wildcard = (FileDialog.create_wildcard("FCS files", "*.fcs *.lmd"))) # @UndefinedVariable
if dialog.open() == OK:
# find the "best" file match -- ie, the one with the longest
# tail match
fcs_path = pathlib.Path(dialog.path).parts
best_path_len = -1
for tube in wi.operation.tubes:
tube_path = pathlib.Path(tube.file).parts
for i in range(len(fcs_path)):
if list(reversed(fcs_path))[:i] == list(reversed(tube_path))[:i] and i > best_path_len:
best_path_len = i
if best_path_len >= 0:
for tube in wi.operation.tubes:
tube_path = pathlib.Path(tube.file).parts
new_path = fcs_path[:-1 * best_path_len] + tube_path[-1 * best_path_len :]
tube.file = str(pathlib.Path(*new_path))
elif missing_tubes > 0:
warning(self.window.control,
"Cytoflow couldn't find some of the FCS files from that "
"workflow. You'll need to re-load them from the Import "
"operation.")
# 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()
if self.model.debug:
self.model.run_all()
else:
ret = confirm(parent = None,
message = "Do you want to execute the workflow now?",
title = "Run workflow?")
if ret == YES:
self.model.run_all()
def on_save(self):
""" Save the file to the previous filename """
if self.filename:
save_yaml(self.model.workflow, self.filename)
self.model.modified = False
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:
save_yaml(self.model.workflow, dialog.path)
self.filename = dialog.path
self.model.modified = False
self.window.title = "Cytoflow - " + self.filename
@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):
task = next(x for x in self.window.tasks if x.id == 'edu.mit.synbio.cytoflowgui.export_task')
self.window.activate_task(task)
def on_calibrate(self):
task = next(x for x in self.window.tasks if x.id == 'edu.mit.synbio.cytoflowgui.tasbe_task')
self.window.activate_task(task)
def on_notebook(self):
"""
Shows a dialog to export the workflow to an Jupyter notebook
"""
dialog = DefaultFileDialog(parent = self.window.control,
action = 'save as',
default_suffix = "ipynb",
wildcard = (FileDialog.create_wildcard("Jupyter notebook", "*.ipynb") + ';' + #@UndefinedVariable
FileDialog.create_wildcard("All files", "*"))) # @UndefinedVariable
if dialog.open() == OK:
save_notebook(self.model.workflow, dialog.path)
def on_prefs(self):
pass
def on_docs(self):
webbrowser.open_new_tab("https://cytoflow.readthedocs.io/en/stable/manual.html")
def on_problem(self):
log = str(self._get_package_versions()) + "\n" + self.application.application_log.getvalue()
msg = "The best way to report a problem is send an application log to " \
"the developers. If you click 'Yes' below, you will be given then " \
"opportunity to save the log to a file and then file a " \
"new issue on GitHub at " \
"https://github.com/cytoflow/cytoflow/issues/new"
dialog = ConfirmationDialog(message = msg,
informative = "Would you like to report an issue to the developers?")
if dialog.open() == YES:
dialog = DefaultFileDialog(parent = self.window.control,
action = 'save as',
default_suffix = "log",
wildcard = (FileDialog.create_wildcard("Log files", "*.log") + ';' + #@UndefinedVariable
FileDialog.create_wildcard("All files", "*"))) #@UndefinedVariable
if dialog.open() == OK:
with open(dialog.path, 'w') as f:
f.write(log)
webbrowser.open_new_tab("https://github.com/cytoflow/cytoflow/issues/new")
return
def _get_package_versions(self):
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 statsmodels import __version__ as stats_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
from yapf import __version__ as yapf_version
from nbformat import __version__ as nb_version
from yaml import __version__ as yaml_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,
"statsmodels" : stats_version,
"pyface" : pyf_version,
"envisage" : env_version,
"traits" : trt_version,
"traitsui" : trt_ui_version,
"nbformat" : nb_version,
"yapf" : yapf_version,
"yaml" : yaml_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=https://thenounproject.com/search/?q=processing&i=849831>Processing icon</a> by Gregor Cresnar 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 ""
self.help_pane.help_id = selected.operation.id
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
self.help_pane.help_id = view_id
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
def get_icon(self):
return ImageResource('kde_1d')
def get_icon(self):
return ImageResource('radviz')
class NodeType(HasPrivateTraits):
""" The base class for all node types. """
# The default image used to represent nodes that DO NOT allow children.
DOCUMENT = ImageResource("document")
# The default image used to represent nodes that allow children and are NOT
# expanded.
CLOSED_FOLDER = ImageResource("closed_folder")
# The default image used to represent nodes that allow children and ARE
# expanded.
OPEN_FOLDER = ImageResource("open_folder")
# 'NodeType' interface -------------------------------------------------
# The node manager that the type belongs to.
node_manager = Instance("pyface.tree.node_manager.NodeManager")
# The image used to represent nodes that DO NOT allow children.
image = Instance(ImageResource)
# The image used to represent nodes that allow children and are NOT
# expanded.
closed_image = Instance(ImageResource)
# The image used to represent nodes that allow children and ARE expanded.
open_image = Instance(ImageResource)
# The default actions/groups/menus available on nodes of this type (shown
# on the context menu).
actions = Any # List
# The default action for nodes of this type. The default action is
# performed when a node is activated (i.e., double-clicked).
default_action = Instance(Action)
# The default actions/groups/menus for creating new children within nodes
# of this type (shown in the 'New' menu of the context menu).
new_actions = Any # List
# ------------------------------------------------------------------------
# 'NodeType' interface.
# ------------------------------------------------------------------------
# These methods are specific to the 'NodeType' interface ---------------
def is_type_for(self, node):
""" Returns True if a node is deemed to be of this type. """
raise NotImplementedError()
def allows_children(self, node):
""" Does the node allow children (ie. a folder vs a file). """
return False
def get_actions(self, node):
""" Returns the node-specific actions for a node. """
return self.actions
def get_context_menu(self, node):
""" Returns the context menu for a node. """
sat = Group(id="SystemActionsTop")
nsa = Group(id="NodeSpecificActions")
sab = Group(id="SystemActionsBottom")
# The 'New' menu.
new_actions = self.get_new_actions(node)
if new_actions is not None and len(new_actions) > 0:
sat.append(MenuManager(name="New", *new_actions))
# Node-specific actions.
actions = self.get_actions(node)
if actions is not None and len(actions) > 0:
for item in actions:
nsa.append(item)
# System actions (actions available on ALL nodes).
system_actions = self.node_manager.system_actions
if len(system_actions) > 0:
for item in system_actions:
sab.append(item)
context_menu = MenuManager(sat, nsa, sab)
context_menu.dump()
return context_menu
def get_copy_value(self, node):
""" Get the value that is copied for a node.
By default, returns the node itself.
"""
return node
def get_default_action(self, node):
""" Returns the default action for a node. """
return self.default_action
def get_new_actions(self, node):
""" Returns the new actions for a node. """
return self.new_actions
def get_paste_value(self, node):
""" Get the value that is pasted for a node.
By default, returns the node itself.
"""
return node
def get_monitor(self, node):
""" Returns a monitor that detects changes to a node.
Returns None by default, which indicates that the node is not
monitored.
"""
return None
# These methods are exactly the same as the 'TreeModel' interface -----#
def has_children(self, node):
""" Returns True if a node has children, otherwise False.
You only need to implement this method if children are allowed for the
node (ie. 'allows_children' returns True).
"""
return False
def get_children(self, node):
""" Returns the children of a node.
You only need to implement this method if children are allowed for the
node.
"""
raise NotImplementedError()
def get_drag_value(self, node):
""" Get the value that is dragged for a node.
By default, returns the node itself.
"""
return node
def can_drop(self, node, data):
""" Returns True if a node allows an object to be dropped onto it. """
return False
def drop(self, obj, data):
""" Drops an object onto a node. """
raise NotImplementedError()
def get_image(self, node, selected, expanded):
""" Returns the label image for a node. """
if self.allows_children(node):
if expanded:
order = ["open_image", "closed_image", "image"]
default = self.OPEN_FOLDER
else:
order = ["closed_image", "open_image", "image"]
default = self.CLOSED_FOLDER
else:
order = ["image", "open_image", "closed_image"]
default = self.DOCUMENT
# Use the search order to look for a trait that is NOT None.
for name in order:
image = getattr(self, name)
if image is not None:
break
# If no such trait is found then use the default image.
else:
image = default
return image
def get_selection_value(self, node):
""" Get the value that is used when a node is selected.
By default the selection value is the node itself.
"""
return node
def get_text(self, node):
""" Returns the label text for a node. """
return str(node)
def can_set_text(self, node, text):
""" Returns True if the node's label can be set. """
return len(text.strip()) > 0
def set_text(self, node, text):
""" Sets the label text for a node. """
pass
def is_collapsible(self, node):
""" Returns True if the node is collapsible, otherwise False. """
return True
def is_draggable(self, node):
""" Returns True if the node is draggablee, otherwise False. """
return True
def can_rename(self, node):
""" Returns True if the node can be renamed, otherwise False. """
return False
def is_editable(self, node):
""" Returns True if the node is editable, otherwise False.
If the node is editable, its text can be set via the UI.
DEPRECATED: Use 'can_rename'.
"""
return self.can_rename(node)
def is_expandable(self, node):
""" Returns True if the node is expandanble, otherwise False. """
return True
def get_icon(self):
return ImageResource('stats_2d')
class FlowTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflowgui.flow_task"
name = "Cytometry analysis"
# the main workflow instance.
model = Instance(Workflow)
# the center pane
workflow_pane = Instance(WorkflowDockPane)
view_pane = Instance(ViewDockPane)
help_pane = Instance(HelpDockPane)
plot_params_pane = Instance(PlotParamsPane)
# 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(TaskToggleGroup(),
# TaskWindowToggleGroup(),
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_calibrate",
name = "Calibrate FCS...",
tooltip = "Calibrate FCS files",
image = ImageResource('tasbe')),
TaskAction(method = 'on_problem',
name = "Report a bug...",
tooltib = "Report a bug",
image = ImageResource('bug')),
# 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 activated(self):
# if we're coming back from the TASBE task, re-load the saved
# workflow
if self.model.backup_workflow:
self.model.workflow = self.model.backup_workflow
self.model.backup_workflow = []
return
# else, set up a new workflow
# add the import op
if not self.model.workflow:
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"}
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]
# from cytoflowgui.op_plugins import ChannelStatisticPlugin
# 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 = VSplitter(PaneItem("edu.mit.synbio.cytoflowgui.workflow_pane"),
PaneItem("edu.mit.synbio.cytoflowgui.help_pane")),
right = VSplitter(PaneItem("edu.mit.synbio.cytoflowgui.view_traits_pane"),
PaneItem("edu.mit.synbio.cytoflowgui.params_pane")),
top_left_corner = 'left',
bottom_left_corner = 'left',
top_right_corner = 'right',
bottom_right_corner = 'right')
def create_central_pane(self):
return self.application.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)
self.help_pane = HelpDockPane(view_plugins = self.view_plugins,
op_plugins = self.op_plugins,
task = self)
self.plot_params_pane = PlotParamsPane(model = self.model,
task = self)
return [self.workflow_pane, self.view_pane, self.help_pane, self.plot_params_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):
new_workflow = load_yaml(path)
# 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.
if wi_idx > 0:
wi.previous_wi = new_workflow[wi_idx - 1]
if wi_idx < len(new_workflow) - 1:
wi.next_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:
save_yaml(self.model.workflow, self.filename)
self.model.modified = False
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:
save_yaml(self.model.workflow, dialog.path)
self.filename = dialog.path
self.model.modified = False
self.window.title = "Cytoflow - " + self.filename
@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):
task = next(x for x in self.window.tasks if x.id == 'edu.mit.synbio.cytoflowgui.export_task')
self.window.activate_task(task)
def on_calibrate(self):
task = next(x for x in self.window.tasks if x.id == 'edu.mit.synbio.cytoflowgui.tasbe_task')
self.window.activate_task(task)
def on_notebook(self):
"""
Shows a dialog to export the workflow to an Jupyter notebook
"""
dialog = FileDialog(parent = self.window.control,
action = 'save as',
default_suffix = "ipynb",
wildcard = (FileDialog.create_wildcard("Jupyter notebook", "*.ipynb") + ';' + #@UndefinedVariable
FileDialog.create_wildcard("All files", "*"))) # @UndefinedVariable
if dialog.open() == OK:
save_notebook(self.model.workflow, dialog.path)
def on_prefs(self):
pass
def on_problem(self):
log = str(self._get_package_versions()) + "\n" + self.application.application_log.getvalue()
msg = "The best way to report a problem is send an application log to " \
"the developers. You can do so by either sending us an email " \
"with the log in it, or saving the log to a file and filing a " \
"new issue on GitHub at " \
"https://github.com/bpteague/cytoflow/issues/new"
dialog = ConfirmationDialog(message = msg,
informative = "Which would you like to do?",
yes_label = "Send an email...",
no_label = "Save to a file...")
if dialog.open() == NO:
dialog = DefaultFileDialog(parent = self.window.control,
action = 'save as',
default_suffix = "log",
wildcard = (FileDialog.create_wildcard("Log files", "*.log") + ';' + #@UndefinedVariable
FileDialog.create_wildcard("All files", "*"))) #@UndefinedVariable
if dialog.open() == OK:
with open(dialog.path, 'w') as f:
f.write(log)
webbrowser.open_new_tab("https://github.com/bpteague/cytoflow/issues/new")
return
information(None, "I'll now try to open your email client and 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("*****@*****.**",
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 statsmodels import __version__ as stats_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
from yapf import __version__ as yapf_version
from nbformat import __version__ as nb_version
from yaml import __version__ as yaml_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,
"statsmodels" : stats_version,
"pyface" : pyf_version,
"envisage" : env_version,
"traits" : trt_version,
"traitsui" : trt_ui_version,
"nbformat" : nb_version,
"yapf" : yapf_version,
"yaml" : yaml_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 ""
self.help_pane.help_id = selected.operation.id
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
self.help_pane.help_id = view_id
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 ExampleTask(Task):
""" A simple task for opening a blank editor.
"""
# Task interface -------------------------------------------------------
id = "example.example_task"
name = "Multi-Tab Editor"
active_editor = Property(Instance(IEditor),
observe="editor_area.active_editor")
editor_area = Instance(IEditorAreaPane)
tool_bars = [
SToolBar(
TaskAction(
method="new",
tooltip="New file",
image=ImageResource("document_new"),
),
image_size=(32, 32),
)
]
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
def _menu_bar_default(self):
return SMenuBar(
SMenu(
TaskAction(name="New", method="new", accelerator="Ctrl+N"),
id="File",
name="&File",
),
SMenu(
DockPaneToggleGroup(),
TaskToggleGroup(),
id="View",
name="&View",
),
)
def create_central_pane(self):
""" Create the central pane: the script editor.
"""
self.editor_area = EditorAreaPane()
return self.editor_area
# ------------------------------------------------------------------------
# 'ExampleTask' interface.
# ------------------------------------------------------------------------
def new(self):
""" Opens a new empty window
"""
editor = Editor()
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.activated()
# Trait property getter/setters ----------------------------------------
def _get_active_editor(self):
if self.editor_area is not None:
return self.editor_area.active_editor
return None
