def _default_layout_default(self):
return TaskLayout(left=Splitter(Splitter(PaneItem('pychron.pipeline.pane',
width=200),
PaneItem('pychron.pipeline.analyses',
width=200)),
PaneItem('pychron.pipeline.repository'),
orientation='vertical'))
def _default_layout_default(self):
return TaskLayout(left=Splitter(Splitter(
PaneItem('pychron.sys_mon.connection'),
PaneItem('pychron.processing.controls'),
orientation='vertical'),
PaneItem('pychron.sys_mon.analyses'),
orientation='horizontal'),
right=VSplitter(
Tabbed(PaneItem('pychron.console'),
PaneItem('pychron.plot_editor')),
PaneItem('pychron.dashboard.client')))
def _default_layout_default(self):
return TaskLayout(
left=Splitter(
PaneItem('pychron.labnumber.irradiation'),
Tabbed(
# PaneItem('pychron.labnumber.extractor'),
PaneItem('pychron.labnumber.editor')),
orientation='vertical'),
right=Splitter(PaneItem('pychron.entry.level'),
PaneItem('pychron.entry.chronology'),
PaneItem('pychron.entry.irradiation_canvas'),
orientation='vertical'))
def _default_layout_default(self):
return TaskLayout(
left=Splitter(
PaneItem('pychron.wait', height=100),
Tabbed(PaneItem('pychron.experiment.factory'),
PaneItem('pychron.experiment.isotope_evolution')),
orientation='vertical'),
right=Splitter(Tabbed(
PaneItem('pychron.experiment.stats'),
PaneItem('pychron.console', height=425),
PaneItem('pychron.experiment.explanation', height=425),
PaneItem('pychron.experiment.connection_status')),
PaneItem('pychron.extraction_line.canvas_dock'),
orientation='vertical'),
top=PaneItem('pychron.experiment.controls'))
def get_layout(self):
""" Returns a LayoutItem that reflects the layout of the current
splitter.
"""
ORIENTATION_MAP = {QtCore.Qt.Horizontal: 'horizontal',
QtCore.Qt.Vertical: 'vertical'}
# obtain layout based on children layouts
if not self.is_leaf():
layout = Splitter(self.leftchild.get_layout(),
self.rightchild.get_layout(),
orientation=ORIENTATION_MAP[self.orientation()])
# obtain the Tabbed layout
else:
if self.is_empty():
layout = Tabbed(PaneItem(id=-1,
width=self.width(),
height=self.height()),
active_tab=0)
else:
items = []
for i in range(self.tabwidget().count()):
widget = self.tabwidget().widget(i)
# mark identification for empty_widget
editor = self.editor_area._get_editor(widget)
item_id = self.editor_area.editors.index(editor)
item_width = self.width()
item_height = self.height()
items.append(PaneItem(id=item_id,
width=item_width,
height=item_height))
layout = Tabbed(*items, active_tab=self.tabwidget().currentIndex())
return layout
def _default_layout_default(self):
return TaskLayout(
left=Splitter(
PaneItem('pychron.spectrometer.controls'),
orientation='vertical'),
right=VSplitter(PaneItem('pychron.spectrometer.intensities'),
PaneItem('pychron.spectrometer.readout')))
def _default_layout_default(self):
return TaskLayout(
left=PaneItem('{}.stage'.format(self.id)),
top=Splitter(
PaneItem('{}.control'.format(self.id), width=200),
PaneItem('pychron.lasers.pulse', width=300),
Tabbed(PaneItem('pychron.lasers.optics'),
PaneItem('{}.supplemental'.format(self.id)))))
def _default_layout_default(self):
return TaskLayout(
# top=PaneItem('pychron.extraction_line.gauges'),
left=Splitter(PaneItem('pychron.video.source'),
PaneItem('pychron.video.controls'),
orientation='vertical'),
# width=500,
# height=500
)
def _default_layout_default(self):
#c=PaneItem('pychron.smart_selection.configure')
search = Tabbed(browser_pane_item())
#PaneItem('pychron.search.query'))
#a=Splitter(d,orientation='vertical')
unk = PaneItem('pychron.processing.unknowns')
left = Splitter(search, unk)
return TaskLayout(id='pychron.processing.batch', left=left)
def _default_layout_default(self):
return TaskLayout(
left=Splitter(PaneItem('pychron.spectrometer.controls'),
Tabbed(PaneItem('pychron.spectrometer.intensities'),
PaneItem('pychron.spectrometer.readout')),
orientation='vertical')
# right=Splitter(
# PaneItem('pychron.experiment.stats'),
# PaneItem('pychron.experiment.console'),
# orientation='vertical'
# ),
# bottom=PaneItem('pychron.experiment.console'),
# top=PaneItem('pychron.experiment.controls')
)
class S4LVisualizationTask(Task): # pylint: disable=too-many-instance-attributes
""" A task for visualizing Sim4Life EM fields from scES simulations
"""
#: The task's identifier.
id = "s4l.main_task"
#: The task's user-visible name.
name = "S4L Visualization"
#: Configuration parser.
configuration = Instance(ConfigParser)
#: Current participant's ID
participant_id = Str()
#: Temporary dictionary for editing user configuration
_to_edit = Dict()
#: Plane attributes dock pane.
plane_attributes_pane = Instance(PlaneAttributes)
#: Line attributes dock pane.
line_attributes_pane = Instance(LineAttributes)
#: Participant ID dock pane.
part_id_pane = Instance(ParticipantIDPane)
#: The currently active editor.
active_editor = Property(Instance(IEditor),
depends_on="editor_area.active_editor")
#: The editor area in which the editor belongs.
editor_area = Instance(IEditorAreaPane)
#: The opening page's editor.
start_page = Instance(StartPage)
#: The object containing the field data.
fields_model = Instance(EMFields)
#: The 3D view panel.
mayavi_scene = Instance(Mayavi3DScene)
#: The slice figure panel.
slice_figure = Instance(SliceFigureModel)
#: The line figure panel.
line_figure = Instance(LineFigureModel)
#: Has the main window been initialized?
model_initialized = Bool(False)
#: Action to run :py:meth:`toggle_full_model`.
toggle_model_action = TaskAction(name='Full Model',
method='toggle_full_model',
style='toggle',
enabled_name='model_initialized')
#: Action to run :py:meth:`change_cord_model`.
new_cord_action = TaskAction(name='New Cord Model',
method='change_cord_model',
enabled_name='model_initialized')
#: Action to run :py:meth:`toggle_log_scale`.
toggle_scale_action = TaskAction(name='Log Scale',
method='toggle_log_scale',
style='toggle',
checked=True,
enabled_name='model_initialized')
#: Action to run :py:meth:`toggle_line_cross_marker`.
toggle_line_cross_action = TaskAction(name='Line Cross Marker',
method='toggle_line_cross_marker',
style='toggle',
checked=True,
enabled_name='model_initialized')
#: The task's menu bar.
menu_bar = SMenuBar(
SMenu(
TaskAction(name="&Open...", method="open", accelerator="Ctrl+O"),
SMenu(
TaskAction(name="Export &Slice", method="export_slice"),
TaskAction(name="Export &Line", method="export_line"),
id="File.Export",
name="&Export",
),
TaskAction(name="&Settings", method="edit_configuration"),
id="File",
name="&File",
),
SMenu(SMenu(DockPaneToggleGroup(), id='View.Panes', name='&Panes'),
toggle_model_action,
toggle_scale_action,
toggle_line_cross_action,
id="View",
name="&View"),
SMenu(
new_cord_action,
SMenu(FieldSelectionGroup(),
id='Edit.Fields',
name='&Choose Field'),
id='Edit',
name='&Edit',
),
)
# ------------------------------------------------------------------------
# 'Task' interface.
# ------------------------------------------------------------------------
@observe('editor_area.active_tabwidget')
def _update_tabwidgets(self, event): # pylint: disable=unused-argument
try:
self.editor_area.active_tabwidget.setTabsClosable(False)
except AttributeError:
pass
def initialized(self):
for tabwidget in self.editor_area.tabwidgets():
tabwidget.setTabsClosable(False)
self.start_page = StartPage(task=self)
self.editor_area.add_editor(self.start_page)
self.editor_area.activate_editor(self.start_page)
self.activated()
def activated(self):
self.editor_area.active_tabwidget.setTabsClosable(False)
def create_central_pane(self):
self.editor_area = SplitEditorAreaPane(
callbacks={'open': self._new_file})
return self.editor_area
def create_dock_panes(self):
"""
Create the attribute editor panes.
"""
self.plane_attributes_pane = PlaneAttributes(
configuration=self.configuration)
self.plane_attributes_pane.sync_trait('participant_id', self)
self.line_attributes_pane = LineAttributes(
configuration=self.configuration)
self.line_attributes_pane.sync_trait('participant_id', self)
self.part_id_pane = ParticipantIDPane()
self.part_id_pane.sync_trait('participant_id', self)
return [
self.plane_attributes_pane, self.line_attributes_pane,
self.part_id_pane
]
# ------------------------------------------------------------------------
# 'S4L_Visualization_task' interface.
# ------------------------------------------------------------------------
def open(self):
"""
Show a dialog to open a new data source.
"""
dialog = FileDialog(
title='Choose Data File',
parent=self.window.control,
wildcard=FileDialog.create_wildcard('Data Files', ['*.mat']) +
FileDialog.WILDCARD_ALL)
if dialog.open() == OK:
if not self.model_initialized:
self._new_file(dialog.path)
def export_slice(self):
"""
Export data for current slice.
"""
dialog = FileDialog(
title='Export Slice Plane',
action='save as',
parent=self.window.control,
wildcard='' +
FileDialog.create_wildcard('Excel Files', ['*.xlsx']) +
FileDialog.create_wildcard('CSV Files', ['*.csv', '*.txt']) +
FileDialog.WILDCARD_ALL)
if dialog.open() == OK:
self.slice_figure.export_slice(dialog.path)
def export_line(self):
"""
Export data for current line.
"""
dialog = FileDialog(
title='Export Line Data',
action='save as',
parent=self.window.control,
wildcard='' +
FileDialog.create_wildcard('Excel Files', ['*.xlsx']) +
FileDialog.create_wildcard('CSV Files', ['*.csv', '*.txt']) +
FileDialog.WILDCARD_ALL)
if dialog.open() == OK:
self.line_figure.export_line(dialog.path)
def toggle_full_model(self):
"""
Toggle between showing the full spinal cord model and showing only below the cut plane.
"""
self.mayavi_scene.show_full_model = not self.mayavi_scene.show_full_model
def toggle_log_scale(self):
"""
Toggle between using a logarithmic scale and a linear scale.
"""
self.mayavi_scene.log_scale = not self.mayavi_scene.log_scale
self.slice_figure.log_scale = not self.slice_figure.log_scale
def toggle_line_cross_marker(self):
"""
Toggle visibility of the line cross marker on the slice figure.
"""
self.slice_figure.draw_cross = not self.slice_figure.draw_cross
def change_cord_model(self):
"""
Change the spinal cord model file used for the 3D display.
"""
dialog = FileDialog(
title='Choose Spinal Cord Model',
parent=self.window.control,
wildcard=FileDialog.create_wildcard('VTK Model', ['*.vtk']) +
FileDialog.WILDCARD_ALL)
if dialog.open() == OK:
self.mayavi_scene.csf_model = dialog.path
def reset_camera(self):
"""
Set the camera for the Mayavi scene to a pre-determined perspective.
"""
self.mayavi_scene.initialize_camera()
def edit_configuration(self):
preferences = PreferenceDialog(configuration=self.configuration,
title="S4L Visualization Preferences")
ui = preferences.edit_traits(kind='modal')
if ui.result:
self.configuration.remove_section('')
with open('config.ini', 'w') as out_file:
self.configuration.write(out_file)
def update_participant_id(self):
if self.model_initialized:
self.line_attributes_pane.set_participant_defaults()
self.mayavi_scene.reset_participant_defaults()
# ------------------------------------------------------------------------
# Protected interface.
# ------------------------------------------------------------------------
def _new_file(self, filename):
"""
Change the data source to the file at the specified path
Parameters
----------
filename : :py:class:`os.PathLike`
Path to data source file
"""
GUI.set_busy(True)
if m := re.search(r"\D(\d{3})\D", filename):
self.participant_id = m.group(1)
if self.participant_id is not None:
if self.participant_id not in self.configuration:
self.configuration[self.participant_id] = {}
default_points = self.configuration[self.participant_id]['points']
self.line_attributes_pane.set_points(default_points)
self.part_id_pane.participant_id = self.participant_id
self.editor_area.remove_editor(self.start_page)
self.window.set_layout(
TaskLayout(bottom=PaneItem('s4l.plane_attributes'),
left=VSplitter(PaneItem('s4l.line_attributes'),
PaneItem('s4l.participant_id_pane')),
top_left_corner='top',
top_right_corner='top',
bottom_left_corner='left',
bottom_right_corner='right'))
self.fields_model = EMFields(configuration=self.configuration,
data_path=filename)
self.fields_model.sync_trait('participant_id', self)
self.plane_attributes_pane.fields_model = self.fields_model
self.mayavi_scene = Mayavi3DScene(fields_model=self.fields_model,
configuration=self.configuration)
self.mayavi_scene.sync_trait('participant_id', self)
self.mayavi_scene.sync_trait('normal', self.plane_attributes_pane)
self.mayavi_scene.sync_trait('origin', self.plane_attributes_pane)
self.line_attributes_pane.sync_trait('points',
self.mayavi_scene,
mutual=False)
self.mayavi_scene.create_plot()
editor = self.mayavi_scene
self.editor_area.add_editor(editor)
self.editor_area.activate_editor(editor)
self.editor_area.active_tabwidget.setTabsClosable(False)
self.activated()
self.slice_figure = SliceFigureModel(fields_model=self.fields_model,
mayavi_scene=self.mayavi_scene,
configuration=self.configuration)
self.slice_figure.sync_trait('participant_id', self)
self.slice_figure.create_plot()
self.editor_area.add_editor(self.slice_figure)
self.editor_area.activate_editor(self.slice_figure)
self.editor_area.active_tabwidget.setTabsClosable(False)
self.activated()
self.line_figure = LineFigureModel(fields_model=self.fields_model)
self.line_figure.sync_trait('points', self.line_attributes_pane)
self.line_figure.create_plot(None)
self.editor_area.add_editor(self.line_figure)
self.editor_area.activate_editor(self.line_figure)
self.editor_area.active_tabwidget.setTabsClosable(False)
self.activated()
self.mayavi_scene.disable_widgets()
while self.editor_area.active_tabwidget.parent().is_collapsible():
self.editor_area.active_tabwidget.parent().collapse()
layout = Splitter(
Tabbed(PaneItem(1), PaneItem(2), active_tab=0),
Tabbed(PaneItem(0), active_tab=0),
)
self.editor_area.set_layout(layout)
self.editor_area.control.setSizes([900, 295])
self.editor_area.activate_editor(self.slice_figure)
self.editor_area.active_tabwidget.setTabsClosable(False)
for tabwidget in self.editor_area.tabwidgets():
tabwidget.setTabsClosable(False)
self.model_initialized = True
def split_editors(self, a, b, h1=-1, h2=-1, orientation='horizontal'):
layout = Splitter(PaneItem(id=a, height=h1),
PaneItem(id=b, height=h2),
orientation=orientation)
self.set_editor_layout(layout)
def _default_layout_default(self):
return TaskLayout(left=Splitter(
PaneItem('pychron.laser_calibration.execute', width=200),
PaneItem('pychron.laser_calibration.control', width=200),
orientation='vertical'))
def _default_layout_default(self):
#return TaskLayout(left=PaneItem('pychron.lasers.client'))
return TaskLayout(
left=Splitter(
PaneItem('pychron.experiment.wait', height=100),
Tabbed(
PaneItem('pychron.experiment.factory'),
PaneItem('pychron.experiment.isotope_evolution'),
# PaneItem('pychron.experiment.summary'),
),
orientation='vertical'
),
right=Splitter(
Tabbed(
PaneItem('pychron.experiment.stats'),
PaneItem('pychron.console', height=425),
PaneItem('pychron.experiment.explanation', height=425),
),
# PaneItem('pychron.extraction_line.canvas_dock'),
# PaneItem('pychron.experiment.wait'),
orientation='vertical'
),
top=PaneItem('pychron.experiment.controls')
)
#============= EOF =============================================
# editor = self.active_editor
# if editor is None:
# if self.editor_area.editors:
# editor = self.editor_area.editors[0]
#
# if editor:
# p = editor.path
# p = add_extension(p, '.txt')
#
# if os.path.isfile(p):
# # make a backup copy of the original experiment file
# shutil.copyfile(p, '{}.orig'.format(p))
#
# # group = editor.group
# # min_idx = editor.merge_id
# # text = open(p, 'r').read()
# # hash_val = hashlib.sha1(text).hexdigest()
# # qs = [ei.queue
# # for ei in self.editor_area.editors
# # if ei.group == group and ei.merge_id >= min_idx]
# qs = [ei.queue for ei in self.editor_area.editors]
# # launch execution thread
# # if successful open an auto figure task
# # if self.manager.execute_queues(qs, p, text, hash_val):
# if self.manager.execute_queues(qs, p):
# self._open_auto_figure()
# def merge(self):
# eqs = [self.active_editor.queue]
# self.active_editor.merge_id = 1
# self.active_editor.group = self.group_count
# self.group_count += 1
# for i, ei in enumerate(self.editor_area.editors):
# if not ei == self.active_editor:
# eqs.append(ei.queue)
# ei.merge_id = i + 2
# ei.group = self.group_count
#
# path = self.save_file_dialog()
# if path:
# self.active_editor.save(path, eqs)
# for ei in self.editor_area.editors:
# ei.path = path
