def setUp(self):
super().setUp()
plugin = ImportPlugin()
op = plugin.get_operation()
from cytoflow import Tube
self.cwd = os.path.dirname(os.path.abspath(__file__))
tube = Tube(file=self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs")
op.tubes = [tube]
wi = WorkflowItem(operation=op,
status="waiting",
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
op.do_estimate = True
self.workflow.wi_waitfor(wi, 'status', 'valid')
self.assertTrue(
self.workflow.remote_eval("self.workflow[0].result is not None"))
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op, status='waiting')
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', 'valid')
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = AutofluorescencePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
super().setUp()
plugin = ThresholdPlugin()
self.op = op = plugin.get_operation()
op.name = "Thresh"
op.channel = "Y2-A"
op.threshold = 1000
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.view = view = wi.default_view = op.default_view()
view.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'view_error', "")
self.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = TasbePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.bleedthrough_list = [
_BleedthroughControl(channel="FITC-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/eyfp.fcs"),
_BleedthroughControl(channel="Pacific Blue-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/ebfp.fcs"),
_BleedthroughControl(channel="PE-Tx-Red-YG-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/mkate.fcs")
]
op.beads_name = "Spherotech RCP-30-5A Lot AG01, AF02, AD04 and AAE01"
op.beads_file = self.cwd + "/../../cytoflow/tests/data/tasbe/beads.fcs"
op.beads_unit = "MEFL"
op.to_channel = "FITC-A"
self.op.translation_list[
0].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
self.op.translation_list[
1].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation = op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 5))
plugin = BleedthroughLinearPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.controls_list = [_Control(channel = "FITC-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/eyfp.fcs'),
_Control(channel = "PE-Tx-Red-YG-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/mkate.fcs'),
_Control(channel = "Pacific Blue-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/ebfp.fcs')]
op.subset_list.append(BoolSubset(name = "Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation = op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
ImportedDataTest.setUp(self)
plugin = ThresholdPlugin()
self.op = op = plugin.get_operation()
op.name = "Thresh"
op.channel = "Y2-A"
op.threshold = 1000
self.wi = wi = WorkflowItem(operation = op)
self.view = view = wi.default_view = op.default_view()
view.subset_list.append(CategorySubset(name = "Well", values = ["A", "B"]))
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.assertTrue(wait_for(self.wi, 'status', lambda v: v == 'valid', 130))
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():
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()