def run_gui():
logging.basicConfig(level=logging.DEBUG)
debug = ("--debug" in sys.argv)
plugins = [
CorePlugin(),
TasksPlugin(),
FlowTaskPlugin(debug=debug),
ImportPlugin(),
ThresholdPlugin(),
HistogramPlugin(),
HexbinPlugin(),
ScatterplotPlugin(),
RangePlugin(),
Range2DPlugin(),
PolygonPlugin(),
BarChartPlugin(),
Stats1DPlugin(),
BinningPlugin()
]
app = CytoflowApplication(id='edu.mit.synbio.cytoflow', plugins=plugins)
app.run()
logging.shutdown()
def __init__(self):
plugins = [
CorePlugin(),
TasksPlugin(),
DummyExtensionPluginWithDataView()
]
super(DummyWfManagerWithPlugins, self).__init__(plugins=plugins)
def __init__(self):
plugins = [
CorePlugin(),
TasksPlugin(),
DummyUIPlugin(),
DummyUIPluginOld()
]
super(DummyUIWfManager, self).__init__(plugins=plugins)
def __init__(self, filename=None):
plugins = [CorePlugin(), TasksPlugin(),
ProbeWfManagerPlugin(filename)]
super(ProbeWfManager, self).__init__(plugins=plugins)
# 'Run' the application by creating windows without an event loop
self.run = self._create_windows
def __init__(self):
plugins = [CorePlugin(), TasksPlugin(),
ProbePyFibreGUIPlugin()]
super(ProbePyFibreGUI, self).__init__(plugins=plugins)
# 'Run' the application by creating windows
# without an event loop
self.run = self._create_windows
def main(argv):
""" Run the application.
"""
logging.basicConfig(level=logging.WARNING)
plugins = [CorePlugin(), TasksPlugin(), AttractorsPlugin()]
app = AttractorsApplication(plugins=plugins)
app.run()
logging.shutdown()
def launch():
root = logging.getLogger()
root.setLevel(logging.DEBUG)
shandler = logging.StreamHandler()
shandler.setLevel(logging.DEBUG)
root.addHandler(shandler)
plugins = [CorePlugin(), TasksPlugin(), WellpyPlugin()]
app = WellpyApplication(plugins=plugins)
app.run()
def test_contributes_service(self):
plugins = [
CorePlugin(),
TasksPlugin(),
FactoryRegistryPlugin(),
WfManagerPlugin(workflow_file=None),
ExampleCustomUIPlugin()
]
wfmanager = WfManager(plugins=plugins)
wfmanager.plugin_manager.start()
self.assertEqual(len(wfmanager.get_services(IContributedUI)), 2)
self.assertEqual(len(wfmanager.get_services(IDataView)), 2)
def main(workflow_file, debug, window_size, profile):
"""Launches the FORCE workflow manager application"""
if debug is False:
logging.basicConfig(filename="force_wfmanager.log", filemode="w")
else:
logging.basicConfig(filename="force_wfmanager.log",
filemode="w",
level=logging.DEBUG)
if profile:
import cProfile
import pstats
profiler = cProfile.Profile()
profiler.enable()
log = logging.getLogger(__name__)
plugins = [
CorePlugin(),
TasksPlugin(),
FactoryRegistryPlugin(),
WfManagerPlugin(workflow_file=workflow_file)
]
mgr = extension.ExtensionManager(namespace='force.bdss.extensions',
invoke_on_load=True)
def import_extensions(ext):
log.info("Found extension {}".format(ext.name))
plugins.append(ext.obj)
try:
mgr.map(import_extensions)
except NoMatches:
log.info("No extensions found")
wfmanager = WfManager(plugins=plugins, window_size=window_size)
wfmanager.run()
if profile:
profiler.disable()
from sys import version_info
fname = 'force_wfmanager-{}-{}.{}.{}'.format(__version__,
version_info.major,
version_info.minor,
version_info.micro)
profiler.dump_stats(fname + '.prof')
with open(fname + '.pstats', 'w') as fp:
stats = pstats.Stats(profiler, stream=fp).sort_stats('cumulative')
stats.print_stats()
def run(debug, profile, log_name):
if debug:
logging.basicConfig(filename=f"{log_name}.log",
filemode="w",
level=logging.DEBUG)
else:
logging.basicConfig(filename=f"{log_name}.log",
filemode="w",
level=logging.INFO)
logger = logging.getLogger(__name__)
if profile:
import cProfile
import pstats
profiler = cProfile.Profile()
profiler.enable()
logger.info(logo(__version__))
plugins = [CorePyFibrePlugin(), TasksPlugin(), PyFibreGUIPlugin()]
plugins += load_plugins()
pyfibre_gui = PyFibreGUI(plugins=plugins)
pyfibre_gui.run()
if profile:
profiler.disable()
from sys import version_info
fname = 'pyfibre-{}-{}.{}.{}'.format(__version__, version_info.major,
version_info.minor,
version_info.micro)
profiler.dump_stats(fname + '.prof')
with open(fname + '.pstats', 'w') as fp:
stats = pstats.Stats(profiler, stream=fp).sort_stats('cumulative')
stats.print_stats()
self._create_windows()
kernel = self.get_service(IPYTHON_KERNEL_PROTOCOL)
kernel.init_ipkernel('qt4')
app.connect(app, QtCore.SIGNAL("lastWindowClosed()"), app,
QtCore.SLOT("quit()"))
app.aboutToQuit.connect(kernel.cleanup_consoles)
gui.set_trait_later(self, 'application_initialized', self)
kernel.ipkernel.start()
return started
def _application_initialized_fired(self):
logger.info('APPLICATION INITIALIZED')
if __name__ == '__main__':
import logging
logging.basicConfig(level=logging.DEBUG)
app = ExampleApplication(plugins=[
CorePlugin(),
ExamplePlugin(),
IPythonKernelPlugin(),
IPythonKernelUIPlugin(),
TasksPlugin(),
])
app.run()
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 run_gui():
debug = ("--debug" in sys.argv)
remote_process, remote_connection = start_remote_process()
# We want matplotlib to use our backend .... in both the GUI and the
# remote process
import matplotlib
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'))
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.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,
BleedthroughPiecewisePlugin, 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)
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 # @UnresolvedImport
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=False,
main=True)
sys.excepthook = log_excepthook
plugins = [
CorePlugin(),
TasksPlugin(),
FlowTaskPlugin(),
TASBETaskPlugin(),
ExportFigurePlugin()
]
# reverse of the order on the toolbar
view_plugins = [
TablePlugin(),
Stats2DPlugin(),
Stats1DPlugin(),
BarChartPlugin(),
ViolinPlotPlugin(),
Kde2DPlugin(),
RadvizPlugin(),
ParallelCoordinatesPlugin(),
Kde1DPlugin(),
DensityPlugin(),
Histogram2DPlugin(),
ScatterplotPlugin(),
HistogramPlugin()
]
plugins.extend(view_plugins)
op_plugins = [
RatioPlugin(),
PCAPlugin(),
KMeansPlugin(),
FlowPeaksPlugin(),
DensityGatePlugin(),
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,
remote_connection=remote_connection,
debug=debug)
app.run()
remote_process.join()
logging.shutdown()
def main(argv):
plugins = [CorePlugin(), TasksPlugin(), PikosPlugin()]
app = PikosApplication(plugins)
app.run()
# Create windows from the default or saved application layout.
self._create_windows()
kernel = self.get_service(IPYTHON_KERNEL_PROTOCOL)
kernel.init_ipkernel('qt4')
app.connect(app, QtCore.SIGNAL("lastWindowClosed()"),
app, QtCore.SLOT("quit()"))
app.aboutToQuit.connect(kernel.cleanup_consoles)
gui.set_trait_later(self, 'application_initialized', self)
kernel.ipkernel.start()
return started
def _application_initialized_fired(self):
logger.info('APPLICATION INITIALIZED')
if __name__ == '__main__':
import logging
logging.basicConfig(level=logging.DEBUG)
app = ExampleApplication(
plugins=[
CorePlugin(), ExamplePlugin(), IPythonKernelPlugin(),
IPythonKernelUIPlugin(), TasksPlugin(),
]
)
app.run()
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 run_gui():
multiprocessing.freeze_support()
from pyface.qt import qt_api
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\" python run.py"
print " * on Windows, try: "
print " setx QT_API \"pyqt\""
sys.exit(1)
remote_connection = start_remote_process()
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
global debug
debug = ("--debug" in sys.argv)
# 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(),
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)
app = CytoflowApplication(id='edu.mit.synbio.cytoflow',
plugins=plugins,
icon=ImageResource('icon'),
debug=debug)
app.run()
logging.shutdown()
