예제 #1
0
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                        logger.warn('Discarding outdated application layout')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()
예제 #2
0
파일: run.py 프로젝트: ritika-giri/cytoflow
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()
예제 #3
0
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()