def start(self, application):
""" Starts the plugin.
"""
# Tell the FBI to wiretap all unauthorized exceptions:
enable_fbi()
push_exception_handler(
handler=lambda obj, name, old, new: fbi(), locked=False, main=True)
def setup():
# If a trait exception occurs, fail the test.
push_exception_handler(
handler=lambda o, t, ov, nv: None,
reraise_exceptions=True,
main=True,
)
def remote_main(parent_workflow_conn, parent_mpl_conn, log_q, running_event):
# this should only ever be main method after a spawn() call
# (not fork). So we should have a fresh logger to set up.
# messages that end up at the root logger to go log_q
from logging.handlers import QueueHandler
h = QueueHandler(log_q)
logging.getLogger().addHandler(h)
# We want matplotlib to use our backend .... in both the GUI and the
# remote process. Must be called BEFORE cytoflow is imported
import matplotlib
matplotlib.use('module://cytoflowgui.matplotlib_backend_remote')
from traits.api import push_exception_handler
from cytoflowgui.workflow import RemoteWorkflow
# install a global (gui) error handler for traits notifications
push_exception_handler(handler=log_notification_handler,
reraise_exceptions=False,
main=True)
sys.excepthook = log_excepthook
# take care of the 3 places in the cytoflow module that
# need different behavior in a GUI
import cytoflow
cytoflow.RUNNING_IN_GUI = True
running_event.set()
RemoteWorkflow().run(parent_workflow_conn, parent_mpl_conn)
def start ( self, application ):
""" Starts the plugin.
"""
# Tell the FBI to wiretap all unauthorized exceptions:
enable_fbi()
push_exception_handler( handler = lambda obj, name, old, new: fbi(),
locked = False,
main = True )
def traits_test_context():
"""Context to raise errors in trait handlers."""
from traits.api import push_exception_handler
push_exception_handler(reraise_exceptions=True)
try:
yield
finally:
push_exception_handler(reraise_exceptions=False)
def traits_test_context():
"""Context to raise errors in trait handlers."""
from traits.api import push_exception_handler
push_exception_handler(reraise_exceptions=True)
try:
yield
finally:
push_exception_handler(reraise_exceptions=False)
def setUp(self):
self.binder = DummyBinder()
self.model = DummyModel()
self.blah = DummyBinder()
self.context = dict(
object=self.model,
blah=self.blah,
)
push_exception_handler(lambda *args, **kwds: None,
reraise_exceptions=True)
def setUp(self):
self.binder = DummyBinder()
self.model = DummyModel()
self.blah = DummyBinder()
self.context = dict(
object=self.model,
blah=self.blah,
)
push_exception_handler(lambda *args, **kwds: None,
reraise_exceptions=True)
def remote_main(parent_workflow_conn, parent_mpl_conn, log_q):
from cytoflowgui.workflow import RemoteWorkflow
# install a global (gui) error handler for traits notifications
push_exception_handler(handler=log_notification_handler,
reraise_exceptions=debug,
main=True)
sys.excepthook = log_excepthook
RemoteWorkflow().run(parent_workflow_conn, parent_mpl_conn, log_q)
def test_validator_change(self):
""" Check that changing a validator works properly.
"""
output = [False]
def handler(obj, name, old, new):
output[0] = True
push_exception_handler(handler)
old = self.component.validator
self.component.validator = IntValidator()
self.component.validator = old
pop_exception_handler()
self.assertTrue(output[0])
def reraise_exceptions(logger=_TRAITSUI_LOGGER):
""" Context manager to capture all exceptions occurred in the context and
then reraise a RuntimeError if there are any exceptions captured.
Exceptions from traits change notifications are also captured and reraised.
Depending on the GUI toolkit backend, unexpected exceptions occurred in the
GUI event loop may (1) cause fatal early exit of the test suite or (2) be
printed to the console without causing the test to error. This context
manager is intended for testing purpose such that unexpected exceptions
will result in a test error.
Parameters
----------
logger : logging.Logger
Logger to use for logging errors.
"""
serialized_exceptions = []
def excepthook(type, value, tb):
serialized = _serialize_exception(type, value, tb)
serialized_exceptions.append(serialized)
logger.error("Unexpected error captured in sys excepthook. \n%s",
serialized[-1])
def handler(object, name, old, new):
type, value, tb = sys.exc_info()
serialized_exceptions.append(_serialize_exception(type, value, tb))
logger.exception(
"Unexpected error occurred from change handler "
"(object: %r, name: %r, old: %r, new: %r).",
object,
name,
old,
new,
)
push_exception_handler(handler=handler)
sys.excepthook = excepthook
try:
yield
finally:
sys.excepthook = sys.__excepthook__
pop_exception_handler()
if serialized_exceptions:
msg = "Uncaught exceptions found.\n"
msg += "\n".join("=== Exception (type: {}, value: {}) ===\n"
"{}".format(*record)
for record in serialized_exceptions)
raise RuntimeError(msg)
def test_validator_change(self):
""" Check that changing a validator works properly.
"""
output = [False]
def handler(obj, name, old, new):
output[0] = True
push_exception_handler(handler)
old = self.component.validator
self.component.validator = IntValidator()
self.component.validator = old
pop_exception_handler()
self.assertTrue(output[0])
def setUp(self):
""" Prepares the test fixture before each test method is called. """
self.preferences = set_default_preferences(Preferences())
# The filename of the example preferences file.
self.example = os.fspath(files(PKG) / "example.ini")
# A temporary directory that can safely be written to.
self.tmpdir = tempfile.mkdtemp()
# Path to a temporary file
self.tmpfile = os.path.join(self.tmpdir, "tmp.ini")
push_exception_handler(reraise_exceptions=True)
self.addCleanup(pop_exception_handler)
def init_error_handlers(debug = False):
""" Initialize application error handlers.
"""
# Configure logging.
logging.basicConfig()
logger = logging.getLogger('nemesis')
logger.setLevel(logging.DEBUG if debug else logging.WARN)
# Prevent Traits from suppressing errors.
push_exception_handler(handler = lambda o, t, ov, nv: None,
reraise_exceptions = True,
main = True, locked = True)
# Install GUI exception handler.
if not debug:
sys.excepthook = gui_except_hook
def setUp(self):
# Start up a QApplication if needed.
self.app = QtGui.QApplication.instance()
if self.app is None:
self.app = QtGui.QApplication([])
push_exception_handler(reraise_exceptions=True)
# We make a new class here to test that the traits get added only at
# the right time.
# WARNING: If anyone instantiates Binder() itself, this subclass will
# see its added traits, and the test will fail.
class Object(Binder):
qclass = QtCore.QObject
x = QtDynamicProperty(10)
self.Object = Object
def setUp(self):
# Start up a QApplication if needed.
self.app = QtGui.QApplication.instance()
if self.app is None:
self.app = QtGui.QApplication([])
push_exception_handler(reraise_exceptions=True)
# We make a new class here to test that the traits get added only at
# the right time.
# WARNING: If anyone instantiates Binder() itself, this subclass will
# see its added traits, and the test will fail.
class Object(Binder):
qclass = QtCore.QObject
x = QtDynamicProperty(10)
self.Object = Object
def remote_main(parent_workflow_conn, parent_mpl_conn, log_q, running_event):
# We want matplotlib to use our backend .... in both the GUI and the
# remote process. Must be called BEFORE cytoflow is imported
import matplotlib
matplotlib.use('module://cytoflowgui.matplotlib_backend')
from traits.api import push_exception_handler
from cytoflowgui.workflow import RemoteWorkflow
# install a global (gui) error handler for traits notifications
push_exception_handler(handler=log_notification_handler,
reraise_exceptions=False,
main=True)
sys.excepthook = log_excepthook
running_event.set()
RemoteWorkflow().run(parent_workflow_conn, parent_mpl_conn, log_q)
def notification_context(handler=null_handler, reraise_exceptions=True, main=False, locked=True):
""" Context manager to temporarily add a TraitsExceptionHandler
We use a context manager to ensure that the exception handler gets cleared
no matter what. Default behaviour is to use the null_handler with
exceptions re-raised, which means any exceptions which occur will be passed
through.
"""
yield push_exception_handler(handler, reraise_exceptions, main, locked)
pop_exception_handler()
def main():
""" A program for visualizing Sim4Life EM fields from scES simulations
"""
configuration = ConfigParser()
configuration.read_file(open('src/default.ini'))
configuration.read(['config.ini'])
push_exception_handler(reraise_exceptions=True)
# Create the GUI (this does NOT start the GUI event loop).
gui = GUI()
# Create a Task and add it to a TaskWindow.
task = S4LVisualizationTask(configuration=configuration)
window = TaskWindow(
size=(configuration.getint('Display', 'window_width'),
configuration.getint('Display', 'window_height')))
window.add_task(task)
# Show the window.
window.open()
# Start the GUI event loop.
gui.start_event_loop()
def run(self):
options, args = self.parseargs()
logger = logging.getLogger()
if options.debug:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.WARNING)
sys.excepthook = self.excepthook
traits.push_exception_handler(self.trait_exception_handler, main=True, locked=True)
if options.pypy:
if platform.system() == 'Windows' and sys.executable:
prefix = os.path.dirname(sys.executable)
pypymanager.set_executable(os.path.join(prefix, 'pypy', 'pypy.exe'))
else:
pypymanager.set_executable('pypy')
pypymanager.launch_delegate()
try:
app = wx.App(False)
self.moduleloader = modules.loader.Loader()
self.ui = self.edit_traits()
self.context.uiparent = self.ui.control
self.context.plot = self.plot
self.prefs.restore_window('main', self.ui)
self.init_recent_menu()
if args:
# passing in 'self' for the info argument is a bit of a hack, but fortunately self.ui.context seems to be working fine
self.ui.handler.do_open(self, args[0])
# silently ignore multiple projects for Windows Explorer integration
app.MainLoop()
finally:
pypymanager.shutdown_delegate()
def notification_context(handler=null_handler,
reraise_exceptions=True,
main=False,
locked=True):
""" Context manager to temporarily add a TraitsExceptionHandler
We use a context manager to ensure that the exception handler gets cleared
no matter what. Default behaviour is to use the null_handler with
exceptions re-raised, which means any exceptions which occur will be passed
through.
"""
yield push_exception_handler(handler, reraise_exceptions, main, locked)
pop_exception_handler()
def remote_main(parent_workflow_conn, parent_mpl_conn, log_q, running_event):
# We want matplotlib to use our backend .... in both the GUI and the
# remote process. Must be called BEFORE cytoflow is imported
import matplotlib
matplotlib.use('module://cytoflowgui.matplotlib_backend_remote')
from traits.api import push_exception_handler
from cytoflowgui.workflow import RemoteWorkflow
# install a global (gui) error handler for traits notifications
push_exception_handler(handler = log_notification_handler,
reraise_exceptions = False,
main = True)
sys.excepthook = log_excepthook
# take care of the 3 places in the cytoflow module that
# need different behavior in a GUI
import cytoflow
cytoflow.RUNNING_IN_GUI = True
running_event.set()
RemoteWorkflow().run(parent_workflow_conn, parent_mpl_conn, log_q)
import pandas as pd
from traits.api import (HasTraits, File, Property, Int, Str, Dict, List, Type,
Bool, Either, push_exception_handler, cached_property,
Array, Instance, Float, Any)
from pysemantic.utils import TypeEncoder, get_md5_checksum, colnames
from pysemantic.custom_traits import (DTypesDict, NaturalNumber, AbsFile,
ValidTraitList)
try:
from yaml import CDumper as Dumper
from yaml import CLoader as Loader
except ImportError:
from yaml import Dumper, Loader
push_exception_handler(lambda *args: None, reraise_exceptions=True)
logger = logging.getLogger(__name__)
class DataFrameValidator(HasTraits):
"""A validator class for `pandas.DataFrame` objects."""
# The dataframe in question
data = Instance(pd.DataFrame)
# the column rules to be enforced
column_rules = Dict
# rules related to the dataset itself
rules = Dict
def setUp(self):
super(TestUiLoader, self).setUp()
push_exception_handler(reraise_exceptions=True)
def setup_package():
push_exception_handler(handler=lambda *args, **kwds: None, reraise_exceptions=True)
def __enter__(self):
self.notification_handler = push_exception_handler(self.handler,
self.reraise_exceptions, self.main, self.locked)
return self
def run_gui():
debug = ("--debug" in sys.argv)
remote_process, remote_connection = start_remote_process(debug)
import matplotlib
# We want matplotlib to use our backend
matplotlib.use('module://cytoflowgui.matplotlib_backend')
# getting real tired of the matplotlib deprecation warnings
import warnings
warnings.filterwarnings('ignore', '.*is deprecated and replaced with.*')
from traits.api import push_exception_handler
def QtMsgHandler(msg_type, msg_string):
# Convert Qt msg type to logging level
log_level = [
logging.DEBUG, logging.WARN, logging.ERROR, logging.FATAL
][int(msg_type)]
logging.log(log_level, 'Qt message: ' + msg_string.decode('utf-8'))
## monkey-patch envisage for a py3k bug. this is fixed in envisage HEAD,
## so check for version
import envisage
if envisage.__version__ == '4.6.0':
import pickle
from envisage.ui.tasks.tasks_application import TasksApplication, TasksApplicationState
logger = logging.getLogger(__name__)
logger.info("Monkey-patching envisage 4.6.0")
def _envisage_load_state(self):
""" Loads saved application state, if possible.
"""
state = TasksApplicationState()
filename = os.path.join(self.state_location, 'application_memento')
if os.path.exists(filename):
# Attempt to unpickle the saved application state.
try:
with open(filename, 'rb') as f:
restored_state = pickle.load(f)
if state.version == restored_state.version:
state = restored_state
else:
logger.warn('Discarding outdated application layout')
except:
# If anything goes wrong, log the error and continue.
logger.exception('Restoring application layout from %s',
filename)
self._state = state
def _envisage_save_state(self):
""" Saves the application state.
"""
# Grab the current window layouts.
window_layouts = [w.get_window_layout() for w in self.windows]
self._state.previous_window_layouts = window_layouts
# Attempt to pickle the application state.
filename = os.path.join(self.state_location, 'application_memento')
try:
with open(filename, 'wb') as f:
pickle.dump(self._state, f)
except:
# If anything goes wrong, log the error and continue.
logger.exception('Saving application layout')
TasksApplication._load_state = _envisage_load_state
TasksApplication._save_state = _envisage_save_state
from envisage.core_plugin import CorePlugin
from envisage.ui.tasks.tasks_plugin import TasksPlugin
from pyface.image_resource import ImageResource
from cytoflowgui.flow_task import FlowTaskPlugin
from cytoflowgui.cytoflow_application import CytoflowApplication
from cytoflowgui.op_plugins import (
ImportPlugin,
ThresholdPlugin,
RangePlugin,
QuadPlugin,
Range2DPlugin,
PolygonPlugin,
BinningPlugin,
GaussianMixture1DPlugin,
GaussianMixture2DPlugin,
BleedthroughLinearPlugin, #BleedthroughPiecewisePlugin,
BeadCalibrationPlugin,
AutofluorescencePlugin,
ColorTranslationPlugin,
TasbePlugin,
ChannelStatisticPlugin,
TransformStatisticPlugin,
RatioPlugin)
from cytoflowgui.view_plugins import (
HistogramPlugin,
Histogram2DPlugin,
ScatterplotPlugin,
BarChartPlugin,
Stats1DPlugin,
Kde1DPlugin, #Kde2DPlugin,
ViolinPlotPlugin,
TablePlugin,
Stats2DPlugin)
# assert(multiprocessing.get_start_method() == "spawn")
from cytoflow.utility.custom_traits import Removed, Deprecated
Removed.gui = True
Deprecated.gui = True
from pyface.qt import qt_api
cmd_line = " ".join(sys.argv)
if qt_api == "pyside":
print("Cytoflow uses PyQT; but it is trying to use PySide instead.")
print(" - Make sure PyQT is installed.")
print(
" - If both are installed, and you don't need both, uninstall PySide."
)
print(" - If you must have both installed, select PyQT by setting the")
print(" environment variable QT_API to \"pyqt\"")
print(" * eg, on Linux, type on the command line:")
print(" QT_API=\"pyqt\" " + cmd_line)
print(" * on Windows, try: ")
print(" setx QT_API \"pyqt\"")
sys.exit(1)
from pyface.qt.QtCore import qInstallMsgHandler
qInstallMsgHandler(QtMsgHandler)
# if we're frozen, add _MEIPASS to the pyface search path for icons etc
if getattr(sys, 'frozen', False):
from pyface.resource_manager import resource_manager
resource_manager.extra_paths.append(sys._MEIPASS) # @UndefinedVariable
# install a global (gui) error handler for traits notifications
push_exception_handler(handler=log_notification_handler,
reraise_exceptions=debug,
main=True)
sys.excepthook = log_excepthook
plugins = [
CorePlugin(),
TasksPlugin(),
FlowTaskPlugin(debug=debug, remote_connection=remote_connection)
]
# reverse of the order on the toolbar
view_plugins = [
TablePlugin(),
Stats2DPlugin(),
Stats1DPlugin(),
BarChartPlugin(),
ViolinPlotPlugin(),
# Kde2DPlugin(), # disabled until we can make it faster
Kde1DPlugin(),
Histogram2DPlugin(),
ScatterplotPlugin(),
HistogramPlugin()
]
plugins.extend(view_plugins)
op_plugins = [
RatioPlugin(),
TransformStatisticPlugin(),
ChannelStatisticPlugin(),
TasbePlugin(),
ColorTranslationPlugin(),
AutofluorescencePlugin(),
BeadCalibrationPlugin(),
# BleedthroughPiecewisePlugin(),
BleedthroughLinearPlugin(),
GaussianMixture2DPlugin(),
GaussianMixture1DPlugin(),
BinningPlugin(),
PolygonPlugin(),
QuadPlugin(),
Range2DPlugin(),
RangePlugin(),
ThresholdPlugin(),
ImportPlugin()
]
plugins.extend(op_plugins)
# these two lines stop pkg_resources from trying to load resources
# from the __main__ module, which is frozen (and thus not loadable.)
icon = ImageResource('icon')
icon.search_path = []
app = CytoflowApplication(id='edu.mit.synbio.cytoflow',
plugins=plugins,
icon=icon,
debug=debug)
app.run()
remote_process.join()
logging.shutdown()
def setUp(self):
push_exception_handler(lambda *args: None, reraise_exceptions=True)
def setUp(self):
push_exception_handler(reraise_exceptions=True)
def setUp(self):
def ignore(*args):
pass
push_exception_handler(handler=ignore, reraise_exceptions=True)
def setUp(self):
push_exception_handler(reraise_exceptions=True)
self.addCleanup(pop_exception_handler)
def rotate_scene(t):
"""
Rotate the camera of the mayavi scene at time t.
:param t: time in the range [0, duration]
:return: a screenshot of the scene
"""
mlab.view(azimuth=360 / duration * t, elevation=63, distance=distance)
return mlab.screenshot(figure=myfig, mode='rgb',
antialiased=True) # return a RGB image
#############
# load data #
#############
push_exception_handler(
reraise_exceptions=True) # force exceptions to be re-raised in Traits
root = tk.Tk()
root.withdraw()
file_path = filedialog.askopenfilename(initialdir=homedir,
title="Select the diffraction pattern",
filetypes=[("NPZ", "*.npz")])
data, _ = util.load_file(file_path)
assert data.ndim == 3, 'data should be a 3D array'
nz, ny, nx = data.shape
print("Initial data shape: ", nz, ny, nx)
file_path = filedialog.askopenfilename(initialdir=homedir,
title="Select q values",
filetypes=[("NPZ", "*.npz")])
from mayavi import mlab
from mayavi.core import lut_manager
from mayavi.core.ui.api import MlabSceneModel, SceneEditor
from mayavi.core.ui.mayavi_scene import MayaviScene
from pyface.api import FileDialog, OK, confirm, YES, GUI
from tvtk.api import tvtk
from traits.api import push_exception_handler
push_exception_handler( handler = lambda o,t,ov,nv: None,
reraise_exceptions = True,
main = True,
locked = True )
class MouseHandler(object):
"""
interactor style for escher application. how to do right clicking on mousepad?
create toggle button for mousepad?
rotation needs be improved; pick point on right click and match it to raycasted point
left click; for spline manipulation, raycast to sphere
for height editor, pick world coord on surface
"""
def __init__(self, interactor):
self.interactor = interactor
def setUp(self):
push_exception_handler(lambda *args: None, reraise_exceptions=True)
def __enter__(self):
self.notification_handler = push_exception_handler(
self.handler, self.reraise_exceptions, self.main, self.locked)
return self
def run_gui():
import os, sys
try:
# if we're running as a one-click from a MacOS app,
# we need to reset the working directory
os.chdir(sys._MEIPASS)
except:
# if we're not running as a one-click, fail gracefully
pass
# take care of the 3 places in the cytoflow module that
# need different behavior in a GUI
import cytoflow
cytoflow.RUNNING_IN_GUI = True
# this is ridiculous, but here's the situation. Qt5 now uses Chromium
# as their web renderer. Chromium needs OpenGL. if you don't
# initialize OpoenGL here, things crash on some platforms.
# so now i guess we depend on opengl too.
from OpenGL import GL # @UnresolvedImport @UnusedImport
# check that we're using the right Qt API
from pyface.qt import qt_api
cmd_line = " ".join(sys.argv)
if qt_api == "pyside":
print("Cytoflow uses PyQT; but it is trying to use PySide instead.")
print(" - Make sure PyQT is installed.")
print(
" - If both are installed, and you don't need both, uninstall PySide."
)
print(" - If you must have both installed, select PyQT by setting the")
print(" environment variable QT_API to \"pyqt5\"")
print(" * eg, on Linux, type on the command line:")
print(" QT_API=\"pyqt5\" " + cmd_line)
print(" * on Windows, try: ")
print(" setx QT_API \"pyqt5\"")
sys.exit(1)
# parse args
parser = argparse.ArgumentParser(description='Cytoflow GUI')
parser.add_argument("--debug", action='store_true')
parser.add_argument("filename", nargs='?', default="")
args = parser.parse_args()
# start the remote process
remote_process, remote_connection, queue_listener = start_remote_process()
# getting real tired of the matplotlib deprecation warnings
import warnings
warnings.filterwarnings('ignore', '.*is deprecated and replaced with.*')
# if we're frozen, add _MEIPASS to the pyface search path for icons etc
if getattr(sys, 'frozen', False):
from pyface.resource_manager import resource_manager
resource_manager.extra_paths.append(sys._MEIPASS) # @UndefinedVariable
# these three lines stop pkg_resources from trying to load resources
# from the __main__ module, which is frozen (and thus not loadable.)
from pyface.image_resource import ImageResource
icon = ImageResource('icon')
icon.search_path = []
# monkey patch the resource manager to use SVGs for icons
import pyface.resource.resource_manager
pyface.resource.resource_manager.ResourceManager.IMAGE_EXTENSIONS.append(
'.svg')
# monkey patch checklist editor to stop lowercasing
import traitsui.qt4.check_list_editor # @UnusedImport
traitsui.qt4.check_list_editor.capitalize = lambda s: s
# define and install a message handler for Qt errors
from traits.api import push_exception_handler
def QtMsgHandler(msg_type, msg_context, msg_string):
# Convert Qt msg type to logging level
log_level = [
logging.DEBUG, logging.WARN, logging.ERROR, logging.FATAL
][int(msg_type)]
logging.log(log_level, 'Qt message: ' + msg_string)
from pyface.qt.QtCore import qInstallMessageHandler # @UnresolvedImport
qInstallMessageHandler(QtMsgHandler)
# install a global (gui) error handler for traits notifications
push_exception_handler(handler=log_notification_handler,
reraise_exceptions=False,
main=True)
sys.excepthook = log_excepthook
# Import, then load, the envisage plugins
from envisage.core_plugin import CorePlugin
from envisage.ui.tasks.tasks_plugin import TasksPlugin
from cytoflowgui.flow_task import FlowTaskPlugin
from cytoflowgui.tasbe_task import TASBETaskPlugin
from cytoflowgui.export_task import ExportFigurePlugin
from cytoflowgui.cytoflow_application import CytoflowApplication
from cytoflowgui.op_plugins import (
ImportPlugin, ThresholdPlugin, RangePlugin, QuadPlugin, Range2DPlugin,
PolygonPlugin, BinningPlugin, GaussianMixture1DPlugin,
GaussianMixture2DPlugin, BleedthroughLinearPlugin,
BeadCalibrationPlugin, AutofluorescencePlugin, ColorTranslationPlugin,
TasbePlugin, ChannelStatisticPlugin, TransformStatisticPlugin,
RatioPlugin, DensityGatePlugin, FlowPeaksPlugin, KMeansPlugin,
PCAPlugin)
from cytoflowgui.view_plugins import (
HistogramPlugin, Histogram2DPlugin, ScatterplotPlugin, BarChartPlugin,
Stats1DPlugin, Kde1DPlugin, Kde2DPlugin, ViolinPlotPlugin, TablePlugin,
Stats2DPlugin, DensityPlugin, ParallelCoordinatesPlugin, RadvizPlugin)
plugins = [
CorePlugin(),
TasksPlugin(),
FlowTaskPlugin(),
TASBETaskPlugin(),
ExportFigurePlugin()
]
# ordered as we want them to show up in the toolbar
view_plugins = [
HistogramPlugin(),
ScatterplotPlugin(),
Histogram2DPlugin(),
DensityPlugin(),
Kde1DPlugin(),
Kde2DPlugin(),
RadvizPlugin(),
ParallelCoordinatesPlugin(),
ViolinPlotPlugin(),
BarChartPlugin(),
Stats1DPlugin(),
Stats2DPlugin(),
TablePlugin()
]
plugins.extend(view_plugins)
op_plugins = [
ImportPlugin(),
ThresholdPlugin(),
RangePlugin(),
QuadPlugin(),
Range2DPlugin(),
PolygonPlugin(),
RatioPlugin(),
ChannelStatisticPlugin(),
TransformStatisticPlugin(),
BinningPlugin(),
GaussianMixture1DPlugin(),
GaussianMixture2DPlugin(),
DensityGatePlugin(),
KMeansPlugin(),
FlowPeaksPlugin(),
PCAPlugin(),
AutofluorescencePlugin(),
BleedthroughLinearPlugin(),
BeadCalibrationPlugin(),
ColorTranslationPlugin(),
TasbePlugin()
]
plugins.extend(op_plugins)
# start the app
app = CytoflowApplication(id='edu.mit.synbio.cytoflow',
plugins=plugins,
icon=icon,
remote_process=remote_process,
remote_connection=remote_connection,
filename=args.filename,
debug=args.debug)
from pyface.qt import QtGui
QtGui.QApplication.instance().setStyle(
QtGui.QStyleFactory.create('Fusion'))
app.run()
remote_process.join()
queue_listener.stop()
logging.shutdown()
def setup():
# If a trait exception occurs, fail the test.
push_exception_handler( handler = lambda o,t,ov,nv: None,
reraise_exceptions = True,
main = True,
)
def setUp(self):
push_exception_handler(reraise_exceptions=True)
import numpy as np
from numpy.testing import assert_allclose
from traits.testing.unittest_tools import UnittestTools
from traits.api import push_exception_handler
import vtk
from mayavi import mlab
from mayavi.core.engine import Engine
from tvtk.api import tvtk
from mayavi.tools.engine_manager import engine_manager
from mayavi.core.registry import registry
from mayavi.tests.common import get_example_data
push_exception_handler(reraise_exceptions=True) # XXX should probably be elsewhere
################################################################################
# class `TestMlabNullEngine`
###############################################################################
class TestMlabNullEngine(unittest.TestCase):
""" Stub mlab to isolate as well as possible from creation of a new
figure.
"""
def _stop_unregister_all_engines(self):
# Some tests leave around engines hanging around, so we clean them
# up to avoid strange test errors.
for engine in list(registry.engines.values()):
engine.stop()
import numpy as np
from numpy.testing import assert_allclose
from traits.testing.unittest_tools import UnittestTools
from traits.api import push_exception_handler
import vtk
from mayavi import mlab
from mayavi.core.engine import Engine
from tvtk.api import tvtk
from mayavi.tools.engine_manager import engine_manager
from mayavi.core.registry import registry
from mayavi.tests.common import get_example_data
# XXX should probably be elsewhere
push_exception_handler(reraise_exceptions=True)
class TestMlabNullEngine(unittest.TestCase):
""" Stub mlab to isolate as well as possible from creation of a new
figure.
"""
def _stop_unregister_all_engines(self):
# Some tests leave around engines hanging around, so we clean them
# up to avoid strange test errors.
for engine in list(registry.engines.values()):
engine.stop()
registry.unregister_engine(engine)
def setUp(self):
def main():
# show complete stacktraces for debugging
push_exception_handler(reraise_exceptions=True)
gui = CiteOverlapGUI()
gui.configure_traits()
def setUp(self):
push_exception_handler(handler=lambda *args: None,
reraise_exceptions=True)
self.addTypeEqualityFunc(traits_listener.ListenerItem,
partial(assert_listener_item_equal, self))
import logging
import click
from envisage.core_plugin import CorePlugin
from envisage.ui.tasks.tasks_plugin import TasksPlugin
from stevedore import extension
from stevedore.exception import NoMatches
from traits.api import push_exception_handler
from force_bdss.core_plugins.factory_registry_plugin import (
FactoryRegistryPlugin)
from force_wfmanager.version import __version__
from force_wfmanager.wfmanager import WfManager
from force_wfmanager.plugins.wfmanager_plugin import WfManagerPlugin
push_exception_handler(lambda *args: None, reraise_exceptions=True)
@click.command()
@click.version_option(version=__version__)
@click.option('--debug',
is_flag=True,
default=False,
help="Prints extra debug information in force_wfmanager.log")
@click.option('--profile',
is_flag=True,
default=False,
help="Run GUI under cProfile, creating .prof and .pstats "
"files in the current directory.")
@click.option('--window-size',
nargs=2,
except Exception:
pass
else:
scrapers += ('mayavi',)
try:
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
import pyvista
pyvista.OFF_SCREEN = False
except Exception:
pass
else:
scrapers += ('pyvista',)
if any(x in scrapers for x in ('pyvista', 'mayavi')):
from traits.api import push_exception_handler
push_exception_handler(reraise_exceptions=True)
report_scraper = mne.report._ReportScraper()
scrapers += (report_scraper,)
else:
report_scraper = None
if 'pyvista' in scrapers:
brain_scraper = mne.viz._brain._BrainScraper()
scrapers = list(scrapers)
scrapers.insert(scrapers.index('pyvista'), brain_scraper)
scrapers = tuple(scrapers)
def append_attr_meth_examples(app, what, name, obj, options, lines):
"""Append SG examples backreferences to method and attr docstrings."""
# NumpyDoc nicely embeds method and attribute docstrings for us, but it
# does not respect the autodoc templates that would otherwise insert
def setUp(self):
super(TestUiLoader, self).setUp()
push_exception_handler(reraise_exceptions=True)
def setup_package():
push_exception_handler(handler=lambda *args, **kwds: None,
reraise_exceptions=True)
def setUp(self):
def ignore(*args):
pass
push_exception_handler(handler=ignore, reraise_exceptions=True)