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=Tabbed(PaneItem('steps.first_pane'),
PaneItem('steps.second_pane'),
PaneItem('steps.third_pane')))
def set_common_menu_29(self):
menubar = SMenuBar(
SMenu(Separator(id="NewGroup", separator=False),
Separator(id="NewGroupEnd", separator=False),
Group(OpenAction(), id="OpenGroup"),
Separator(id="OpenGroupEnd", separator=False),
Separator(id="SaveGroupEnd", separator=False),
Group(ExitAction(), id="ExitGroup"),
id='File',
name='&File'),
SMenu(PreferencesAction(), id='Edit', name='&Edit'),
SMenu(AboutAction(), id='Help', name='&Help'),
)
app = wx.GetApp()
# Create a fake task so we can use the menu creation routines
window = TaskWindow(application=self.application)
log.debug("OSXMenuBarPlugin: minimal menu extra items: %s" %
str(self.minimal_menu_actions))
task = OSXMinimalTask(menu_bar=menubar,
window=window,
extra_actions=self.minimal_menu_actions)
t = TaskActionManagerBuilder(task=task)
mgr = t.create_menu_bar_manager()
control = mgr.create_menu_bar(app)
wx.MenuBar.MacSetCommonMenuBar(control)
# Prevent wx from exiting when the last window is closed
app.SetExitOnFrameDelete(False)
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 _menu_bar_default(self):
menu_bar = SMenuBar(
SMenu(SGroup(group_factory=DockPaneToggleGroup,
id='tests.bogus_task.DockPaneToggleGroup'),
id='View',
name='&View'))
return menu_bar
def _menu_bar_default(self):
"""A menu bar with functions relevant to the Setup task.
"""
menu_bar = SMenuBar(SMenu(TaskToggleGroup(), id='File', name='&File'),
SMenu(id='Edit', name='&Edit'),
SMenu(TaskToggleGroup(), id='View', name='&View'))
return menu_bar
class PythonShellTask(Task):
"""
A task which provides a simple Python Shell to the user.
"""
# Task Interface
id = "pyface.tasks.contrib.python_shell"
name = "Python Shell"
# The list of bindings for the shell
bindings = List(Dict)
# The list of commands to run on shell startup
commands = List(Str)
# the IPythonShell instance that we are interacting with
pane = Instance(PythonShellPane)
# Task Interface
menu_bar = SMenuBar(
SMenu(
TaskAction(name="Open...", method="open", accelerator="Ctrl+O"),
id="File",
name="&File",
),
SMenu(id="View", name="&View"),
)
def create_central_pane(self):
""" Create a view pane with a Python shell
"""
logger.debug("Creating Python shell pane in central pane")
self.pane = PythonShellPane(bindings=self.bindings,
commands=self.commands)
return self.pane
# PythonShellTask API
def open(self):
""" Shows a dialog to open a file.
"""
logger.debug("PythonShellTask: opening file")
dialog = FileDialog(parent=self.window.control, wildcard="*.py")
if dialog.open() == OK:
self._open_file(dialog.path)
# Private API
def _open_file(self, path):
""" Execute the selected file in the editor's interpreter
"""
logger.debug('PythonShellTask: executing file "%s"' % path)
self.pane.editor.execute_file(path)
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),
depends_on='editor_area.active_editor')
editor_area = Instance(IEditorAreaPane)
menu_bar = SMenuBar(
SMenu(TaskAction(name='New', method='new', accelerator='Ctrl+N'),
id='File',
name='&File'),
SMenu(DockPaneToggleGroup(), id='View', name='&View'))
tool_bars = [
SToolBar(TaskAction(method='new',
tooltip='New file',
image=ImageResource('document_new')),
image_size=(32, 32)),
]
###########################################################################
# 'Task' interface.
###########################################################################
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
def _menu_bar_default(self):
menu_bar = SMenuBar(
SMenu(
SGroup(
group_factory=DockPaneToggleGroup,
id="tests.bogus_task.DockPaneToggleGroup",
),
id="View",
name="&View",
))
return menu_bar
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",
),
)
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 PikosTask(Task):
#### 'Task' interface #####################################################
id = 'pikos.live.pikos_task'
name = 'Pikos Live Plotting'
menu_bar = SMenuBar(SMenu(id='File', name='&File'),
SMenu(id='Edit', name='&Edit'),
SMenu(TaskToggleGroup(),
id='View', name='&View'))
#### 'PikosTask' interface ################################################
###########################################################################
# 'Task' interface.
###########################################################################
def create_central_pane(self):
""" Create a plot pane with a list of models. Keep track of which model
is active so that dock panes can introspect it.
"""
pane = PikosTaskPane()
return pane
class ExampleTask(Task):
""" A simple task for editing Python code.
"""
#### Task interface #######################################################
id = 'example.example_task'
name = 'Python Script Editor'
#default_layout = TaskLayout(
# left=PaneItem('example.python_script_browser_pane'))
menu_bar = SMenuBar(
SMenu(
TaskAction(
name='Open...', method='open', accelerator='Ctrl+O'),
TaskAction(
name='Save', method='save', accelerator='Ctrl+S'),
id='File',
name='&File'),
SMenu(
DockPaneToggleGroup(), id='View', name='&View'))
tool_bars = [
SToolBar(
TaskAction(
method='open',
tooltip='Open a file',
image=ImageResource('document_open')),
TaskAction(
method='save',
tooltip='Save the current file',
image=ImageResource('document_save')))
]
###########################################################################
# 'Task' interface.
###########################################################################
def _default_layout_default(self):
return TaskLayout(left=PaneItem('example.python_script_browser_pane'))
def activated(self):
""" Overriden to set the window's title.
"""
filename = self.window.central_pane.editor.path
self.window.title = filename if filename else 'Untitled'
def create_central_pane(self):
""" Create the central pane: the script editor.
"""
return PythonEditorPane()
def create_dock_panes(self):
""" Create the file browser and connect to its double click event.
"""
browser = PythonScriptBrowserPane()
handler = lambda: self._open_file(browser.selected_file)
browser.on_trait_change(handler, 'activated')
return [browser]
###########################################################################
# 'ExampleTask' interface.
###########################################################################
def open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control, wildcard='*.py')
if dialog.open() == OK:
self._open_file(dialog.path)
def save(self):
""" Attempts to save the current file, prompting for a path if
necessary. Returns whether the file was saved.
"""
editor = self.window.central_pane.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
###########################################################################
# Protected interface.
###########################################################################
def _open_file(self, filename):
""" Opens the file at the specified path in the editor.
"""
if self._prompt_for_save():
self.window.central_pane.editor.path = filename
self.activated()
def _prompt_for_save(self):
""" Prompts the user to save if necessary. Returns whether the dialog
was cancelled.
"""
if self.window.central_pane.editor.dirty:
message = 'The current file has unsaved changes. ' \
'Do you want to save your changes?'
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:
if not self.save():
return self._prompt_for_save()
return True
@on_trait_change('window:closing')
def _prompt_on_close(self, event):
""" Prompt the user to save when exiting.
"""
if not self._prompt_for_save():
event.veto = True
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),
depends_on='editor_area.active_editor')
editor_area = Instance(IEditorAreaPane)
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(top=Tabbed(PaneItem('steps.first_pane'),
PaneItem('steps.second_pane'),
PaneItem('steps.third_pane')))
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.
"""
return [FirstPane(), SecondPane(), ThirdPane()]
###########################################################################
# '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
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), depends_on="editor_area.active_editor"
)
editor_area = Instance(IEditorAreaPane)
menu_bar = SMenuBar(
SMenu(
TaskAction(name="New", method="new", accelerator="Ctrl+N"),
id="File",
name="&File",
),
SMenu(DockPaneToggleGroup(), id="View", name="&View"),
)
tool_bars = [
SToolBar(
TaskAction(
method="new",
tooltip="New file",
image=ImageResource("document_new"),
),
image_size=(32, 32),
)
]
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
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
class ImageViewerTask(Task):
""" A simple task for viewing images.
"""
#### Task interface #######################################################
id = 'example.image_viewer_task'
name = 'Image Viewer'
#default_layout = TaskLayout(
# left=PaneItem('example.python_script_browser_pane'))
menu_bar = SMenuBar(
SMenu(TaskAction(name='Open...', method='open', accelerator='Ctrl+O'),
id='File',
name='&File'),
SMenu(DockPaneToggleGroup(), id='View', name='&View'))
tool_bars = [
SToolBar(
TaskAction(method='open',
tooltip='Open a file',
image=ImageResource('document_open')))
]
###########################################################################
# 'Task' interface.
###########################################################################
def _default_layout_default(self):
return TaskLayout(left=PaneItem('image_viewer.file_browser_pane'))
def activated(self):
""" Overriden to set the window's title.
"""
filename = self.window.central_pane.model.path
self.window.title = filename if filename else 'Untitled'
def create_central_pane(self):
""" Create the central pane: the image viewer.
"""
return ImageViewerPane()
def create_dock_panes(self):
""" Create the file browser and connect to its double click event.
"""
browser = FileBrowserPane(filters=["*.jpg"])
handler = lambda: self._open_file(browser.selected_file)
browser.on_trait_change(handler, 'activated')
return [browser]
###########################################################################
# 'ExampleTask' interface.
###########################################################################
def open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control, wildcard='*.jpg')
if dialog.open() == OK:
self._open_file(dialog.path)
###########################################################################
# Protected interface.
###########################################################################
def _open_file(self, filename):
""" Opens the file at the specified path in the editor.
"""
self.window.central_pane.model.path = filename
self.activated()
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)
menu_bar = SMenuBar(
SMenu(
TaskAction(name="New", method="new", accelerator="Ctrl+N"),
id="File",
name="&File",
),
SMenu(DockPaneToggleGroup(), 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(top=PaneItem("steps.example_pane"))
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.
"""
pane = ExamplePane()
return [pane]
# ------------------------------------------------------------------------
# '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
class Visualize2dTask(Task):
""" A task for visualizing attractors in 2D.
"""
#### 'Task' interface #####################################################
id = 'example.attractors.task_2d'
name = '2D Visualization'
menu_bar = SMenuBar(SMenu(id='File', name='&File'),
SMenu(id='Edit', name='&Edit'),
SMenu(TaskToggleGroup(), id='View', name='&View'))
#### 'Visualize2dTask' interface ##########################################
# The attractor model that is currently active (visible in the center pane).
active_model = Any
# The list of available attractor models.
models = List
###########################################################################
# 'Task' interface.
###########################################################################
def create_central_pane(self):
""" Create a plot pane with a list of models. Keep track of which model
is active so that dock panes can introspect it.
"""
pane = Plot2dPane(models=self.models)
self.active_model = pane.active_model
pane.on_trait_change(self._update_active_model, 'active_model')
return pane
def create_dock_panes(self):
return [
ModelConfigPane(model=self.active_model),
ModelHelpPane(model=self.active_model)
]
###########################################################################
# Protected interface.
###########################################################################
#### Trait initializers ###################################################
def _default_layout_default(self):
return TaskLayout(
left=Tabbed(PaneItem('example.attractors.model_config_pane'),
PaneItem('example.attractors.model_help_pane')))
def _models_default(self):
from model.henon import Henon
from model.lorenz import Lorenz
from model.rossler import Rossler
return [Henon(), Lorenz(), Rossler()]
#### Trait change handlers ################################################
def _update_active_model(self):
self.active_model = self.window.central_pane.active_model
for dock_pane in self.window.dock_panes:
dock_pane.model = self.active_model
class Visualize3dTask(Task):
""" A task for visualizing attractors in 3D.
"""
#### 'Task' interface #####################################################
id = "example.attractors.task_3d"
name = "3D Visualization"
menu_bar = SMenuBar(
SMenu(id="File", name="&File"),
SMenu(id="Edit", name="&Edit"),
SMenu(TaskToggleGroup(), id="View", name="&View"),
)
#### 'Visualize3dTask' interface ##########################################
# The attractor model that is currently active (visible in the center
# pane).
active_model = Any
# The list of available attractor models.
models = List
###########################################################################
# 'Task' interface.
###########################################################################
def create_central_pane(self):
""" Create a plot pane with a list of models. Keep track of which model
is active so that dock panes can introspect it.
"""
pane = Plot3dPane(models=self.models)
self.active_model = pane.active_model
pane.on_trait_change(self._update_active_model, "active_model")
return pane
def create_dock_panes(self):
return [
ModelConfigPane(model=self.active_model),
ModelHelpPane(model=self.active_model),
]
###########################################################################
# Protected interface.
###########################################################################
#### Trait initializers ###################################################
def _default_layout_default(self):
return TaskLayout(left=Tabbed(
PaneItem("example.attractors.model_config_pane"),
PaneItem("example.attractors.model_help_pane"),
))
def _models_default(self):
from attractors.model.lorenz import Lorenz
from attractors.model.rossler import Rossler
return [Lorenz(), Rossler()]
#### Trait change handlers ################################################
def _update_active_model(self):
self.active_model = self.window.central_pane.active_model
for dock_pane in self.window.dock_panes:
dock_pane.model = self.active_model
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)
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
class ExampleTask(Task):
""" A simple task for editing Python code.
"""
# Task interface -------------------------------------------------------
id = "example.example_task"
name = "Python Script Editor"
# default_layout = TaskLayout(
# left=PaneItem('example.python_script_browser_pane'))
menu_bar = SMenuBar(
SMenu(
TaskAction(name="Open...", method="open", accelerator="Ctrl+O"),
TaskAction(name="Save", method="save", accelerator="Ctrl+S"),
id="File",
name="&File",
),
SMenu(DockPaneToggleGroup(), id="View", name="&View"),
)
tool_bars = [
SToolBar(
TaskAction(
method="open",
tooltip="Open a file",
image=ImageResource("document_open"),
),
TaskAction(
method="save",
tooltip="Save the current file",
image=ImageResource("document_save"),
),
)
]
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
def _default_layout_default(self):
return TaskLayout(left=PaneItem("example.python_script_browser_pane"))
def activated(self):
""" Overriden to set the window's title.
"""
filename = self.window.central_pane.editor.path
self.window.title = filename if filename else "Untitled"
def create_central_pane(self):
""" Create the central pane: the script editor.
"""
return PythonEditorPane()
def create_dock_panes(self):
""" Create the file browser and connect to its double click event.
"""
browser = PythonScriptBrowserPane()
handler = lambda _: self._open_file(browser.selected_file)
browser.observe(handler, "activated")
return [browser]
# ------------------------------------------------------------------------
# 'ExampleTask' interface.
# ------------------------------------------------------------------------
def open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control, wildcard="*.py")
if dialog.open() == OK:
self._open_file(dialog.path)
def save(self):
""" Attempts to save the current file, prompting for a path if
necessary. Returns whether the file was saved.
"""
editor = self.window.central_pane.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
# ------------------------------------------------------------------------
# Protected interface.
# ------------------------------------------------------------------------
def _open_file(self, filename):
""" Opens the file at the specified path in the editor.
"""
if self._prompt_for_save():
self.window.central_pane.editor.path = filename
self.activated()
def _prompt_for_save(self):
""" Prompts the user to save if necessary. Returns whether the dialog
was cancelled.
"""
if self.window.central_pane.editor.dirty:
message = ("The current file has unsaved changes. "
"Do you want to save your changes?")
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:
if not self.save():
return self._prompt_for_save()
return True
@observe("window:closing")
def _prompt_on_close(self, event):
""" Prompt the user to save when exiting.
"""
window = event.new
if not self._prompt_for_save():
window.veto = True
class ExampleTask(Task):
""" A simple task for editing Python code.
"""
# Task interface -------------------------------------------------------
id = "example.example_task"
name = "Multi-Tab Editor"
active_editor = Property(Instance(IEditor),
observe="editor_area.active_editor")
editor_area = Instance(IEditorAreaPane)
menu_bar = SMenuBar(
SMenu(
TaskAction(name="New", method="new", accelerator="Ctrl+N"),
TaskAction(name="Open...", method="open", accelerator="Ctrl+O"),
TaskAction(name="Save", method="save", accelerator="Ctrl+S"),
id="File",
name="&File",
),
SMenu(DockPaneToggleGroup(), id="View", name="&View"),
)
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"),
),
image_size=(32, 32),
show_tool_names=False,
)
]
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
def _default_layout_default(self):
return TaskLayout(left=PaneItem("example.python_script_browser_pane"))
def activated(self):
""" Overriden to set the window's title.
"""
return
filename = self.active_editor.path if self.active_editor else ""
self.window.title = filename if filename else "Untitled"
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 = PythonScriptBrowserPane()
handler = lambda _: self._open_file(browser.selected_file)
browser.observe(handler, "activated")
return [browser]
# ------------------------------------------------------------------------
# 'ExampleTask' interface.
# ------------------------------------------------------------------------
def new(self):
""" Opens a new empty window
"""
editor = PythonEditor()
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.activated()
def open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control, wildcard="*.py")
if dialog.open() == OK:
self._open_file(dialog.path)
def save(self):
""" Attempts to save the current file, prompting for a path if
necessary. Returns whether 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
# ------------------------------------------------------------------------
# Protected interface.
# ------------------------------------------------------------------------
def _open_file(self, filename):
""" Opens the file at the specified path in the editor.
"""
editor = PythonEditor(path=filename)
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.activated()
def _prompt_for_save(self):
""" Prompts the user to save if necessary. Returns whether the dialog
was cancelled.
"""
dirty_editors = dict([(editor.name, editor)
for editor in self.editor_area.editors
if editor.dirty])
if not dirty_editors.keys():
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 ------------------------------------------------
@observe("window:closing")
def _prompt_on_close(self, event):
""" Prompt the user to save when exiting.
"""
close = self._prompt_for_save()
window = event.new
window.veto = not close
# Trait property getter/setters ----------------------------------------
def _get_active_editor(self):
if self.editor_area is not None:
return self.editor_area.active_editor
return None
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 TASBETask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflowgui.tasbe_task"
name = "TASBE calibration"
menu_bar = SMenuBar(SMenu(TaskToggleGroup(),
id = 'View', name = '&View'))
# the main workflow instance.
model = Instance(Workflow)
op = Instance(IOperation)
calibration_pane = Instance(CalibrationPane)
help_pane = Instance(HelpDockPane)
_cached_help = HTML
def activated(self):
self.model.backup_workflow = self.model.workflow
self.model.workflow = []
self.model.modified = False
# add the op
self.op = TasbeCalibrationOp()
# make a new workflow item
wi = WorkflowItem(operation = self.op,
deletable = False)
wi.default_view = self.op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
self.model.workflow.append(wi)
self.model.selected = wi
self.help_pane.html = self.op.get_help()
def _default_layout_default(self):
return TaskLayout(left = PaneItem("edu.mit.synbio.cytoflowgui.calibration_pane", width = 350),
right = PaneItem("edu.mit.synbio.cytoflowgui.help_pane", width = 350))
def create_central_pane(self):
return self.application.plot_pane
def create_dock_panes(self):
self.calibration_pane = CalibrationPane(model = self.model,
task = self)
self.help_pane = HelpDockPane(task = self)
return [self.calibration_pane, self.help_pane]
@on_trait_change('op:do_exit', post_init = True)
def activate_cytoflow_task(self):
task = next(x for x in self.window.tasks if x.id == 'edu.mit.synbio.cytoflowgui.flow_task')
self.window.activate_task(task)
class ExampleTask(Task):
""" A simple task for editing Python code.
"""
#### Task interface #######################################################
id = 'example.example_task'
name = 'Multi-Tab Editor'
active_editor = Property(Instance(IEditor),
depends_on='editor_area.active_editor')
editor_area = Instance(IEditorAreaPane)
menu_bar = SMenuBar(
SMenu(TaskAction(name='New', method='new', accelerator='Ctrl+N'),
TaskAction(name='Open...', method='open', accelerator='Ctrl+O'),
TaskAction(name='Save', method='save', accelerator='Ctrl+S'),
id='File',
name='&File'),
SMenu(DockPaneToggleGroup(), id='View', name='&View'))
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')),
image_size=(32, 32),
show_tool_names=False),
]
###########################################################################
# 'Task' interface.
###########################################################################
def _default_layout_default(self):
return TaskLayout(left=PaneItem('example.python_script_browser_pane'))
def activated(self):
""" Overriden to set the window's title.
"""
return
filename = self.active_editor.path if self.active_editor else ''
self.window.title = filename if filename else 'Untitled'
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 = PythonScriptBrowserPane()
handler = lambda: self._open_file(browser.selected_file)
browser.on_trait_change(handler, 'activated')
return [browser]
###########################################################################
# 'ExampleTask' interface.
###########################################################################
def new(self):
""" Opens a new empty window
"""
editor = PythonEditor()
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.activated()
def open(self):
""" Shows a dialog to open a file.
"""
dialog = FileDialog(parent=self.window.control, wildcard='*.py')
if dialog.open() == OK:
self._open_file(dialog.path)
def save(self):
""" Attempts to save the current file, prompting for a path if
necessary. Returns whether 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
###########################################################################
# Protected interface.
###########################################################################
def _open_file(self, filename):
""" Opens the file at the specified path in the editor.
"""
editor = PythonEditor(path=filename)
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.activated()
def _prompt_for_save(self):
""" Prompts the user to save if necessary. Returns whether the dialog
was cancelled.
"""
dirty_editors = dict([(editor.name, editor)
for editor in self.editor_area.editors
if editor.dirty])
if not list(dirty_editors.keys()):
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 list(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
#### Trait property getter/setters ########################################
def _get_active_editor(self):
if self.editor_area is not None:
return self.editor_area.active_editor
return None
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 _menu_bar_default(self):
menu_bar = SMenuBar(
SMenu(SMenu(SGroup(
TaskAction(name='New Simulation',
method='new_simulation_from_datasource',
image=ImageResource('office-chart-pie')),
TaskAction(name='New Simulation from Experiment',
method='new_simulation_from_experiments',
image=ImageResource('kchart'),
accelerator='Ctrl+N'),
id='NewSimulationGroup',
name='NewSimulationGroup',
),
id='NewMenu',
name='&New Simulation'),
SGroup(TaskAction(name='Save Project',
accelerator='Ctrl+S',
method='save',
image=ImageResource('document-save')),
TaskAction(name='Save Project As...',
accelerator='Ctrl+Shift+S',
method='save_request',
image=ImageResource('document-save-as')),
id='SaveGroup',
name='SaveGroup'),
SGroup(
TaskAction(name='Save User Data',
method='save_user_ds',
image=ImageResource('drive-harddisk')),
TaskAction(name='Export User Data As...',
method='request_export_user_ds',
image=ImageResource('document-import')),
id='SaveUserDataGroup',
name='SaveUserDataGroup',
),
SGroup(
TaskWindowAction(
name='Close',
accelerator='Ctrl+W',
method='close',
),
id='CloseGroup',
name='CloseGroup',
),
id='File',
name='&File'), SMenu(id='Edit', name='&Edit'),
SMenu(DockPaneToggleGroup(), id='View', name='&View'),
SMenu(
SGroup(
TaskAction(name='Parameter Explorer',
accelerator='Ctrl+Shift+N',
method='new_simulation_grid',
enabled_name='simulations_exist'),
TaskAction(name='Parameter Optimizer',
accelerator='Ctrl+Shift+M',
method='new_optimizer',
enabled_name='experiments_and_sim_exist'),
id='ParamExplorationGroup',
name='ParamExplorationGroup',
),
SGroup(
TaskAction(name='Run Simulations',
method='run_simulations',
accelerator='Ctrl+R',
enabled_name='simulations_exist',
image=ImageResource('arrow-right')),
TaskAction(name='Run Simulation Group',
method='run_simulation_groups',
accelerator='Ctrl+Shift+R',
enabled_name='simulation_groups_exist',
image=ImageResource('arrow-right-double')),
id='RunSimulationGroup',
name='RunSimulationGroup',
),
SGroup(
TaskAction(name='Plot Chomatogram(s)',
method='new_model_calibration_plot',
accelerator='Ctrl+P',
image=ImageResource('office-chart-line')),
TaskAction(name='Particle data animation',
method='new_animation_plot'),
id='PlotsGroup',
name='PlotsGroup',
),
SGroup(
TaskAction(name=STRIP_TOOL_NAME,
method='open_strip_fraction_editor',
enabled_name='_strip_component_exist'),
id='ConfigurationGroup',
name='ConfigurationGroup',
),
SGroup(TaskAction(name='Custom Python script...',
accelerator='Ctrl+I',
method='request_run_python_script',
tooltip='Modify the current project with '
'custom script.',
image=ImageResource('text-x-python')),
TaskAction(name='Interactive Python console...',
accelerator='Ctrl+J',
tooltip="(Jupyter) Python console to "
"interactively explore Reveal's code "
"and develop new tools/scripts.",
method='request_launch_python_console',
image=ImageResource('ipython_icon')),
id='RunPythonGroup',
name='RunPythonGroup'),
id='Tools',
name='&Tools',
), SMenu(id='Help', name='&Help'))
return menu_bar