Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
#
# Modified BSD License
# Enthought library imports
from envisage.api import Plugin
from envisage.api import Service
from traits.api import List
# This module's package.
PKG = '.'.join(__name__.split('.')[:-1])
# Logging imports
import logging
logger = logging.getLogger('root.'+__name__)
class OraclePlugin(Plugin):
""" This plugin allows to create code """
ACTION_SETS = 'envisage.ui.workbench.action_sets'
# The plugin's unique identifier.
id = 'connectome.codeoracle'
# The plugin's name (suitable for displaying to the user).
name = 'Oracle Plugin'
# adding the action sets
action_sets = List(contributes_to=ACTION_SETS)
def _action_sets_default(self):
""" Trait initializer. """
from oracle_action_set import OracleActionSet
# Author: Prabhu Ramachandran
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
from traits.api import List
from envisage.api import Plugin, ServiceOffer
# This module's package.
PKG = '.'.join(__name__.split('.')[:-1])
# The mayavi package ID.
ID = 'mayavi'
###############################################################################
# `MayaviPlugin` class.
###############################################################################
class MayaviPlugin(Plugin):
# Extension point Ids.
SERVICE_OFFERS = 'envisage.ui.workbench.service_offers'
PREFERENCES = 'envisage.preferences'
# The plugins name.
name = 'Mayavi plugin'
# Our ID.
id = ID
###### Contributions to extension points made by this plugin ######
# Services we contribute.
service_offers = List(contributes_to=SERVICE_OFFERS)
recognizers = []
from .image import ImageRecognizer
recognizers.append(ImageRecognizer())
from .text import PlainTextRecognizer, PoundBangTextRecognizer, XMLTextRecognizer
recognizers.append(PlainTextRecognizer())
recognizers.append(PoundBangTextRecognizer())
recognizers.append(XMLTextRecognizer())
from .meta import OmnivoreRecognizer
recognizers.append(OmnivoreRecognizer())
# [[[end]]]
from envisage.api import Plugin
from traits.api import List
class BuiltinFileRecognizerPlugin(Plugin):
""" A plugin that contributes to the omnivore_framework.file_type.recognizer extension point. """
#### 'IPlugin' interface ##################################################
# The plugin's unique identifier.
id = 'omnivore_framework.file_type.recognizer.builtin'
# The plugin's name (suitable for displaying to the user).
name = 'Builtin File Recognizer Plugin'
# This tells us that the plugin contributes the value of this trait to the
# 'greetings' extension point.
recognizer = List(recognizers, contributes_to='omnivore_framework.file_recognizer')
plugins = [BuiltinFileRecognizerPlugin()]
return False
def get_notebook_code(self, idx):
view = AutofluorescenceDiagnosticView()
view.copy_traits(self, view.copyable_trait_names())
return dedent("""
op_{idx}.default_view({traits}).plot(ex_{prev_idx})
"""
.format(traits = traits_str(view),
idx = idx,
prev_idx = idx - 1))
@provides(IOperationPlugin)
class AutofluorescencePlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.autofluorescence'
operation_id = 'edu.mit.synbio.cytoflow.operations.autofluorescence'
short_name = "Autofluorescence correction"
menu_group = "Calibration"
def get_operation(self):
return AutofluorescencePluginOp()
def get_icon(self):
return ImageResource('autofluorescence')
@contributes_to(OP_PLUGIN_EXT)
def get_plugin(self):
return self
# Standard library imports.
import os.path
# Enthought library imports.
from envisage.api import ExtensionPoint, Plugin, ServiceOffer
from traits.api import List, Instance
from .i_file_recognizer import IFileRecognizer, IFileRecognizerDriver
import logging
log = logging.getLogger(__name__)
class FileTypePlugin(Plugin):
""" Plugin for identifying file types
"""
# The Ids of the extension points that this plugin offers.
RECOGNIZER = 'omnivore_framework.file_recognizer'
# Extension point IDs.
SERVICE_OFFERS = 'envisage.service_offers'
#### 'IPlugin' interface ##################################################
# The plugin's unique identifier.
id = 'omnivore_framework.file_type.plugin'
# The plugin's name (suitable for displaying to the user).
name = 'File Type'
for channel in self.channels_list:
view.channels.append(channel.channel)
view.scale[channel.channel] = channel.scale
plot_params_str = traits_str(self.plot_params)
return dedent("""
{repr}.plot(ex_{idx}{plot}{plot_params})
"""
.format(repr = repr(view),
idx = idx,
plot = ", plot_name = " + repr(self.current_plot) if self.plot_names else "",
plot_params = ", " + plot_params_str if plot_params_str else ""))
@provides(IViewPlugin)
class RadvizPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.view.radviz'
view_id = 'edu.mit.synbio.cytoflow.view.radviz'
short_name = "Radviz Plot"
def get_view(self):
return RadvizPluginView()
def get_icon(self):
return ImageResource('radviz')
@contributes_to(VIEW_PLUGIN_EXT)
def get_plugin(self):
return self
### Serialization
return False
def get_notebook_code(self, idx):
view = BeadCalibrationDiagnostic()
view.copy_traits(self, view.copyable_trait_names())
return dedent("""
op_{idx}.default_view({traits}).plot(ex_{prev_idx})
"""
.format(traits = traits_str(view),
idx = idx,
prev_idx = idx - 1))
@provides(IOperationPlugin)
class BeadCalibrationPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.beads_calibrate'
operation_id = 'edu.mit.synbio.cytoflow.operations.beads_calibrate'
short_name = "Bead Calibration"
menu_group = "Calibration"
def get_operation(self):
return BeadCalibrationPluginOp()
def get_icon(self):
return ImageResource('bead_calibration')
@contributes_to(OP_PLUGIN_EXT)
def get_plugin(self):
return self
plot_params_str = traits_str(self.density_plot_params)
else:
plot_params_str = traits_str(self.scatterplot_plot_params)
return dedent("""
op_{idx}.default_view({traits}).plot(ex_{idx}{plot_params})
"""
.format(traits = traits_str(view),
idx = idx,
plot_params = ", " + plot_params_str if plot_params_str else ""))
@provides(IOperationPlugin)
class FlowPeaksPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.flowpeaks'
operation_id = 'edu.mit.synbio.cytoflow.operations.flowpeaks'
short_name = "Flow Peaks"
menu_group = "Gates"
def get_operation(self):
return FlowPeaksPluginOp()
def get_icon(self):
return ImageResource('flowpeaks')
@contributes_to(OP_PLUGIN_EXT)
def get_plugin(self):
return self
def get_notebook_code(self, idx):
op = PolygonOp()
op.copy_traits(self, op.copyable_trait_names())
return dedent("""
op_{idx} = {repr}
ex_{idx} = op_{idx}.apply(ex_{prev_idx})
"""
.format(repr = repr(op),
idx = idx,
prev_idx = idx - 1))
@provides(IOperationPlugin)
class PolygonPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.polygon'
operation_id = 'edu.mit.synbio.cytoflow.operations.polygon'
short_name = "Polygon Gate"
menu_group = "Gates"
def get_operation(self):
return PolygonPluginOp()
def get_icon(self):
return ImageResource('polygon')
@contributes_to(OP_PLUGIN_EXT)
def get_plugin(self):
return self
# Bleedthrough
op_{idx}_bleedthrough.default_view().plot(ex_{idx}_af)
# Bead calibration
op_{idx}_beads.default_view().plot(ex_{idx}_bleedthrough)
# Color translation
op_{idx}_color.default_view().plot(ex_{idx}_beads)
"""
.format(idx = idx,
prev_idx = idx - 1))
@provides(IOperationPlugin)
class TasbePlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.tasbe'
operation_id = 'edu.mit.synbio.cytoflowgui.op_plugins.tasbe'
short_name = "TASBE Calibration"
menu_group = "Gates"
def get_operation(self):
return TasbePluginOp()
def get_icon(self):
return ImageResource('tasbe')
@contributes_to(OP_PLUGIN_EXT)
def get_plugin(self):
return self