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 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 _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):
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"),
),
)
)
def get_actions_Menu_View_TaskGroup(self):
return [
DocumentationOnlyAction(
name="Pane Visibility:",
description=
"Toggles whether or not the named extra pane is shown or hidden in the current window."
),
DockPaneToggleGroup(separator=False),
DocumentationOnlyAction(
name="Current Task:",
description=
"Changes the view in the entire window to a new editing task. The files in the current task are not lost, it's just a way to edit different types of files while using the same top level window on the desktop."
),
TaskToggleGroup(separator=False),
]
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 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 ExportTask(Task):
"""
classdocs
"""
id = "edu.mit.synbio.cytoflowgui.export_task"
name = "Export figure"
menu_bar = SMenuBar(SMenu(TaskToggleGroup(), id='View', name='&View'))
# the main workflow instance.
model = Instance(Workflow)
params_pane = Instance(TraitsDockPane)
export_pane = Instance(TraitsDockPane)
def _default_layout_default(self):
return TaskLayout(right=VSplitter(
PaneItem("edu.mit.synbio.cytoflowgui.plot_params_pane", width=350),
PaneItem("edu.mit.synbio.cytoflowgui.export_pane", width=350)))
def create_central_pane(self):
return self.application.plot_pane
def create_dock_panes(self):
self.params_pane = PlotParamsPane(model=self.model, task=self)
self.export_pane = ExportPane(task=self)
return [self.params_pane, self.export_pane]
@on_trait_change('export_pane: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)
@on_trait_change('export_pane:do_export', post_init=True)
def on_export(self):
"""
Shows a dialog to export a file
"""
f = ""
filetypes_groups = self.application.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.application.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
if (self.export_pane.width * self.export_pane.dpi > 2**16 or \
self.export_pane.height * self.export_pane.dpi > 2**16 or \
self.export_pane.width * self.export_pane.height * self.export_pane.dpi ** 2 > 2 ** 30) and \
pathlib.Path(dialog.path).suffix in ['png', 'pgf', 'raw', 'rgba', 'jpg', 'jpeg', 'bmp', 'pcx', 'tif', 'tiff', 'xpm']:
error(
None,
"Can't export raster images with a height or width larger than 65535 pixels, "
"or a total image size of greater than 2**30 pixels. "
"Decrease your image size or DPI, or use a vector format (like PDF or SVG)."
)
return
self.application.plot_pane.export(dialog.path,
width=self.export_pane.width,
height=self.export_pane.height,
dpi=self.export_pane.dpi)
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
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 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 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 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"),
TaskAction(name="Add Task",
method="add_task",
accelerator="Ctrl+A"),
TaskAction(name="Remove Task",
method="remove_task",
accelerator="Ctrl+R"),
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=VSplitter(
HSplitter(PaneItem("steps.pane1"), PaneItem("steps.pane2"))))
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 [Pane1(), Pane2()]
# ------------------------------------------------------------------------
# '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()
def add_task(self):
""" Opens a new empty window
"""
task3 = ThirdTask()
self.window.add_task(task3)
self.window.activate_task(task3)
def remove_task(self):
""" Opens a new empty window
"""
task = self.window.tasks[0]
window = self.window
window.remove_task(self)
window.activate_task(task)
# 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 SkeletonTask(Task):
""" A simple task for opening a blank editor.
"""
#### Task interface #######################################################
id = 'omnivore.framework.text_edit_task'
name = 'Skeleton'
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(id='Edit', name='&Edit'),
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(
PaneItem('text_edit.pane1'),
HSplitter(
PaneItem('text_edit.pane2'),
PaneItem('text_edit.pane3'),
),
))
def create_central_pane(self):
""" Create the central pane: the text 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 [SkeletonPane1(), SkeletonPane2(), SkeletonPane3()]
###########################################################################
# '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
