def default_traits_view(self):
return View(
VGroup(Item('controls_list',
editor=VerticalListEditor(editor=InstanceEditor(
view=self.control_traits_view()),
style='custom',
mutable=False),
style='custom'),
Item('handler.add_control',
editor=ButtonEditor(value=True,
label="Add a control")),
Item('handler.remove_control',
editor=ButtonEditor(value=True,
label="Remove a control")),
label="Controls",
show_labels=False),
VGroup(Item(
'subset_list',
show_label=False,
editor=SubsetListEditor(
conditions="handler.context.previous_wi.conditions",
metadata="handler.context.previous_wi.metadata",
when="'experiment' not in vars() or not experiment")),
label="Subset",
show_border=False,
show_labels=False), Heading("WARNING: Very slow!"),
Heading("Give it a few minutes..."),
Item('do_estimate',
editor=ButtonEditor(value=True, label="Estimate!"),
show_label=False), shared_op_traits)
def traits_view(self):
v = View(VGroup(VGroup(HGroup(Heading('Lower Bound'), UItem('use_low_post')),
UItem('low_post', style='custom', enabled_when='use_low_post')),
VGroup(HGroup(Heading('Upper Bound'), UItem('use_high_post')),
UItem('high_post', style='custom', enabled_when='use_high_post')),
VGroup(HGroup(Heading('Named Range'), UItem('use_named_date_range')),
UItem('named_date_range', enabled_when='use_named_date_range'))),
buttons=['OK', 'Cancel'],
resizable=True,
kind='livemodal')
return v
def _workflow_group_default(self):
workflow_group = Group(
Heading("Chemical Ingredient Settings", springy=True),
Group(Item('execution_layers_template',
editor=InstanceEditor(),
style='custom'),
show_labels=False),
Heading("Concentration Settings", springy=True),
Group(Item('mco_template', editor=InstanceEditor(),
style='custom'),
show_labels=False))
return workflow_group
def default_traits_view(self):
return View(
Item("channels",
editor=CheckListEditor(cols=2,
name='context.previous_channels'),
style='custom'),
VGroup(Item('blank_file'), label="Autofluorescence"),
VGroup(Item('bleedthrough_list',
editor=VerticalListEditor(editor=InstanceEditor(
view=self.bleedthrough_traits_view()),
style='custom',
mutable=False),
style='custom'),
label="Bleedthrough Correction",
show_border=False,
show_labels=False),
VGroup(Item('beads_name',
editor=EnumEditor(name='handler.beads_name_choices'),
label="Beads",
width=-125),
Item('beads_file'),
Item('beads_unit',
editor=EnumEditor(name='handler.beads_units')),
Item('bead_peak_quantile', label="Peak\nQuantile"),
Item('bead_brightness_threshold', label="Peak\nThreshold "),
Item('bead_brightness_cutoff', label="Peak\nCutoff"),
label="Bead Calibration",
show_border=False),
VGroup(Item('to_channel',
editor=EnumEditor(name='object.channels')),
Item('mixture_model', label="Use mixture\nmodel?"),
label="Color Translation"),
VGroup(Item('translation_list',
editor=VerticalListEditor(editor=InstanceEditor(
view=self.translation_traits_view()),
style='custom',
mutable=False),
style='custom'),
show_labels=False),
VGroup(Item(
'subset_list',
show_label=False,
editor=SubsetListEditor(
conditions="context.previous_conditions",
metadata="context.previous_metadata",
when="'experiment' not in vars() or not experiment")),
label="Subset",
show_border=False,
show_labels=False), Heading("WARNING: Very slow!"),
Heading("Give it a few minutes..."),
Item('context.do_estimate',
editor=ButtonEditor(value=True, label="Estimate!"),
show_label=False), shared_op_traits)
def default_traits_view(self):
return View(Item('object.name'),
Heading('THE HEXBIN PLUGIN IS BROKEN.'),
Item('object.xchannel',
editor=EnumEditor(name='handler.channels'),
label = "X Channel"),
Item('object.xscale',
label = "X Scale"),
Item('object.ychannel',
editor=EnumEditor(name='handler.channels'),
label = "Y Channel"),
Item('object.yscale',
label = "Y Scale"),
Item('object.xfacet',
editor=EnumEditor(name='handler.conditions'),
label = "Horizontal\nFacet"),
Item('object.yfacet',
editor=EnumEditor(name='handler.conditions'),
label = "Vertical\nFacet"),
Item('object.huefacet',
editor=EnumEditor(name='handler.conditions'),
label="Color\nFacet"),
Item('_'),
Item('object.subset',
label="Subset",
editor = SubsetEditor(experiment = "handler.wi.result")),
shared_view_traits)
class DemoButton(HasPrivateTraits):
# -------------------------------------------------------------------------
# Trait definitions:
# -------------------------------------------------------------------------
#: The demo to be launched via a button:
demo = Instance(HasTraits)
#: The demo view item to use:
demo_item = Item(
"demo",
show_label=False,
editor=InstanceEditor(label="Run demo...", kind="live"),
)
# -------------------------------------------------------------------------
# Traits view definitions:
# -------------------------------------------------------------------------
traits_view = View(
VGroup(
VGroup(Heading("Click the button to run the demo:"), "20"),
HGroup(spring, Include("demo_item"), spring),
),
resizable=True,
)
class DemoButton ( HasPrivateTraits ):
#---------------------------------------------------------------------------
# Trait definitions:
#---------------------------------------------------------------------------
# The demo to be launched via a button:
demo = Instance( HasTraits )
# The demo view item to use:
demo_item = Item( 'demo',
show_label = False,
editor = InstanceEditor( label = 'Run demo...', kind = 'live' )
)
#---------------------------------------------------------------------------
# Traits view definitions:
#---------------------------------------------------------------------------
traits_view = View(
VGroup(
VGroup(
Heading( 'Click the button to run the demo:' ),
'20'
),
HGroup(
spring,
Include( 'demo_item' ),
spring
)
),
resizable = True
)
def _workflow_group_default(self):
workflow_group = Group(
Heading("Ray Example Settings"),
Item("lower", label="Lower bound"),
Item("upper", label="Upper bound"),
Item("ray", label="Ray"),
)
return workflow_group
def _workflow_group_default(self):
workflow_group = Group(
Heading("Power Example Settings"),
Item("lower", label="Lower bound"),
Item("upper", label="Upper bound"),
Item("power", label="Exponent"),
)
return workflow_group
def traits_view(self):
v = View(
VGroup(
HGroup(Heading(self.name),
UItem('visible')),
self._get_group()
)
)
return v
def traits_view(self):
v = okcancel_view(
VGroup(
VGroup(
HGroup(Heading('Lower Bound'), UItem('use_low_post')),
UItem('low_post',
style='custom',
enabled_when='use_low_post')),
VGroup(
HGroup(Heading('Upper Bound'), UItem('use_high_post')),
UItem('high_post',
style='custom',
enabled_when='use_high_post')),
VGroup(
HGroup(Heading('Named Range'),
UItem('use_named_date_range')),
UItem('named_date_range',
enabled_when='use_named_date_range'))))
return v
def _get_date_group(self):
f_grp = HGroup(
UItem('analysis_type', editor=EnumEditor(name='analysis_types')),
UItem('mass_spectrometer',
editor=EnumEditor(name='mass_spectrometers')),
UItem('extraction_device',
editor=EnumEditor(name='extraction_devices')))
grp = VGroup(
f_grp, Heading('Start'),
UItem('start_date',
editor=DateEditor(allow_future=False),
style='custom'), UItem('start_time', ), Item('_'),
Heading('End'),
UItem('end_date',
editor=DateEditor(allow_future=False),
style='custom'), UItem('end_time', ))
return VSplit(grp,
self._get_analysis_group(base='danalysis'),
label='Date')
def default_traits_view(self):
return View(
VGroup(
VGroup(Heading("WARNING: Very slow!"),
Item('name'),
Item('xchannel',
editor=EnumEditor(name='context.channels'),
label="X Channel"),
Item('xscale', label="X Scale"),
Item('ychannel',
editor=EnumEditor(name='context.channels'),
label="Y Channel"),
Item('yscale', label="Y Scale"),
Item('xfacet',
editor=ExtendableEnumEditor(
name='context.conditions_names',
extra_items={"None": ""}),
label="Horizontal\nFacet"),
Item('yfacet',
editor=ExtendableEnumEditor(
name='context.conditions_names',
extra_items={"None": ""}),
label="Vertical\nFacet"),
Item('huefacet',
editor=ExtendableEnumEditor(
name='context.conditions_names',
extra_items={"None": ""}),
label="Color\nFacet"),
Item('plotfacet',
editor=ExtendableEnumEditor(
name='context.conditions_names',
extra_items={"None": ""}),
label="Tab\nFacet"),
label="2D Kernel Density Estimate",
show_border=False),
VGroup(Item(
'subset_dict',
show_label=False,
editor=SubsetEditor(conditions="context.conditions")),
label="Subset",
show_border=False,
show_labels=False),
Item('context.view_warning',
resizable=True,
visible_when='context.view_warning',
editor=ColorTextEditor(foreground_color="#000000",
background_color="#ffff99")),
Item('context.view_error',
resizable=True,
visible_when='context.view_error',
editor=ColorTextEditor(foreground_color="#000000",
background_color="#ff9191"))))
def default_traits_view(self):
table_editor = TableEditor(
columns=[
ObjectColumn(name='chemical',
editor=EnumEditor(name='available')),
ObjectColumn(name='concentration',
editor=EnumEditor(name='available'))
],
sortable=False,
deletable=True,
row_factory=self._row_factory,
)
return View(
Heading('Formulation Mapping'),
Label("Select the variables that correspond to each "
"formulation component's name and concentration"),
UItem("table_rows", editor=table_editor),
)
class DemoError(HasPrivateTraits):
# -------------------------------------------------------------------------
# Trait definitions:
# -------------------------------------------------------------------------
#: The error message text:
msg = Code()
# -------------------------------------------------------------------------
# Traits view definitions:
# -------------------------------------------------------------------------
traits_view = View(
VGroup(
Heading("Error in source file"),
Item("msg", style="custom", show_label=False),
))
class DemoError(HasPrivateTraits):
#---------------------------------------------------------------------------
# Trait definitions:
#---------------------------------------------------------------------------
# The error message text:
msg = Code
#---------------------------------------------------------------------------
# Traits view definitions:
#---------------------------------------------------------------------------
traits_view = View(
VGroup(
Heading('Error in source file'),
Item('msg', style='custom', show_label=False),
))
class SensorOperationController(tui.Controller):
""" UI for controlling the hardware. """
model = t.Instance(EEGSensor)
connect = t.Button()
disconnect = t.Button()
def _connect_changed(self):
self.model.connect()
def _disconnect_changed(self):
self.model.disconnect()
traits_view = View(
HGroup(
spring,
VGroup(
HGroup(spring, Heading('EEG Sensor Controls'), spring),
VGroup(
Item('com_port',
style='simple',
enabled_when="not object.connected"),
Item('object.connected', style='readonly'),
# Item('history_length', style='readonly'),
# Item('timeseries_length', style='readonly'),
show_labels=True),
HGroup( # spring,
Item('controller.connect',
enabled_when='not object.connected'),
Item('controller.disconnect',
enabled_when='object.connected'),
spring,
show_labels=False),
Label('Last %d points saved to disk on exit.' %
MAX_HISTORY_LENGTH),
),
spring,
tui.VGrid(Heading('Activate Ch:'),
Item('channel_1_on',
label='1',
enabled_when='not channel_1_enabled'),
Item('channel_2_on',
label='2',
enabled_when='not channel_2_enabled'),
Item('channel_3_on',
label='3',
enabled_when='not channel_3_enabled'),
Item('channel_4_on',
label='4',
enabled_when='not channel_4_enabled'),
Item('channel_5_on',
label='5',
enabled_when='not channel_5_enabled'),
Item('channel_6_on',
label='6',
enabled_when='not channel_6_enabled'),
Item('channel_7_on',
label='7',
enabled_when='not channel_7_enabled'),
Item('channel_8_on',
label='8',
enabled_when='not channel_8_enabled'),
Heading('Deactivate Ch:'),
Item('channel_1_off',
label='1',
enabled_when='channel_1_enabled'),
Item('channel_2_off',
label='2',
enabled_when='channel_2_enabled'),
Item('channel_3_off',
label='3',
enabled_when='channel_3_enabled'),
Item('channel_4_off',
label='4',
enabled_when='channel_4_enabled'),
Item('channel_5_off',
label='5',
enabled_when='channel_5_enabled'),
Item('channel_6_off',
label='6',
enabled_when='channel_6_enabled'),
Item('channel_7_off',
label='7',
enabled_when='channel_7_enabled'),
Item('channel_8_off',
label='8',
enabled_when='channel_8_enabled'),
show_labels=False,
show_border=True,
columns=9,
enabled_when='object.connected'),
spring,
), )
class Demo(HasTraits):
list1 = List(Int)
list2 = List(Float)
list3 = List(Str, maxlen=3)
list4 = List(Enum('red', 'green', 'blue', 2, 3))
list5 = List(Range(low=0.0, high=10.0))
# 'low' and 'high' are used to demonstrate lists containing dynamic ranges.
low = Float(0.0)
high = Float(1.0)
list6 = List(Range(low=-1.0, high='high'))
list7 = List(Range(low='low', high='high'))
pop1 = Button("Pop from first list")
sort1 = Button("Sort first list")
# This will be str(self.list1).
list1str = Property(Str, depends_on='list1')
traits_view = \
View(
HGroup(
# This VGroup forms the column of CSVListEditor examples.
VGroup(
Item('list1', label="List(Int)",
editor=CSVListEditor(ignore_trailing_sep=False),
tooltip='options: ignore_trailing_sep=False'),
Item('list1', label="List(Int)", style='readonly',
editor=CSVListEditor()),
Item('list2', label="List(Float)",
editor=CSVListEditor(enter_set=True, auto_set=False),
tooltip='options: enter_set=True, auto_set=False'),
Item('list3', label="List(Str, maxlen=3)",
editor=CSVListEditor()),
Item('list4',
label="List(Enum('red', 'green', 'blue', 2, 3))",
editor=CSVListEditor(sep=None),
tooltip='options: sep=None'),
Item('list5', label="List(Range(low=0.0, high=10.0))",
editor=CSVListEditor()),
Item('list6', label="List(Range(low=-1.0, high='high'))",
editor=CSVListEditor()),
Item('list7', label="List(Range(low='low', high='high'))",
editor=CSVListEditor()),
springy=True,
),
# This VGroup forms the right column; it will display the
# Python str representation of the lists.
VGroup(
UItem('list1str', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list1str', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list2', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list3', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list4', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list5', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list6', editor=TextEditor(),
enabled_when='False', width=240),
UItem('list7', editor=TextEditor(),
enabled_when='False', width=240),
),
),
'_',
HGroup('low', 'high', spring, UItem('pop1'), UItem('sort1')),
Heading("Notes"),
Label("Hover over a list to see which editor options are set, "
"if any."),
Label("The editor of the first list, List(Int), uses "
"ignore_trailing_sep=False, so a trailing comma is "
"an error."),
Label("The second list is a read-only view of the first list."),
Label("The editor of the List(Float) example has enter_set=True "
"and auto_set=False; press Enter to validate."),
Label("The List(Str) example will accept at most 3 elements."),
Label("The editor of the List(Enum(...)) example uses sep=None, "
"i.e. whitespace acts as a separator."),
Label("The last two List(Range(...)) examples take one or both "
"of their limits from the Low and High fields below."),
width=720,
title="CSVListEditor Demonstration",
)
def _list1_default(self):
return [1, 4, 0, 10]
def _get_list1str(self):
return str(self.list1)
def _pop1_fired(self):
if len(self.list1) > 0:
x = self.list1.pop()
print x
def _sort1_fired(self):
self.list1.sort()
class AtmosViewer(HasTraits):
central_wavenumber = CFloat(1000)
bandwidth = CFloat(10)
selected_line_wavenumber = Float(-1.)
figure = Instance(Figure, ())
all_on = Button()
all_off = Button()
selected_molecules = List(editor=CheckListEditor(
values=molecules.keys(), cols=2, format_str='%s'))
mplFigureEditor = MPLFigureEditor()
trait_view = View(VGroup(
Item('figure', editor=mplFigureEditor, show_label=False),
HGroup(
'10',
VGroup('40',
Item(name='central_wavenumber',
editor=TextEditor(auto_set=False, enter_set=True)),
Item(name='bandwidth',
editor=TextEditor(auto_set=False, enter_set=True)),
HGroup(Item(name='selected_line_wavenumber'),
show_border=True),
show_border=True),
HGroup(VGroup('20', Heading("Molecules"),
Item(name='all_on', show_label=False),
Item(name='all_off', show_label=False)),
Item(name='selected_molecules',
style='custom',
show_label=False),
show_border=True), '10'), '10'),
handler=MPLInitHandler,
resizable=True,
title=title,
width=size[0],
height=size[1])
def __init__(self):
super(AtmosViewer, self).__init__()
self.colors = {'telluric': 'black', 'orders': 'black'}
self.molecules = molecules
self.selected_molecules = []
orders_filename = resource_filename(__name__, 'orders.txt')
self.texes_orders = pandas.io.parsers.read_csv(orders_filename,
sep='\t',
header=None,
skiprows=3)
atmos_filename = resource_filename(__name__, 'atmos.txt.gz')
self.atmos = pandas.io.parsers.read_csv(gzip.open(atmos_filename, 'r'),
sep='\t',
skiprows=7,
index_col='# wn')
self.molecule_lookup_points = {
} # keys are e.g. 'O3', with a dict of {'wn':..., 'y':...}
self.axes = self.figure.add_subplot(111)
self.axes.plot(self.atmos.index,
self.atmos['trans1mm'],
color=self.colors['telluric'])
self.axes.plot(self.atmos.index,
self.atmos['trans4mm'],
color=self.colors['telluric'])
for i in self.texes_orders.index:
self.axes.plot(self.texes_orders.ix[i].values, [0.05, 0.07],
color=self.colors['orders'])
self.axes.set_xlim(self.central_wavenumber - self.bandwidth / 2.,
self.central_wavenumber + self.bandwidth / 2.)
self.axes.set_ylim(0, 1.0)
self.axes.set_xlabel('Wavenumber (cm-1)')
self.axes.xaxis.set_major_formatter(FormatStrFormatter('%6.1f'))
self.onclick_connected = False # I don't understand why I can't do the connection here.
self.selected_line = None
self.selected_line_text = None
def on_click(self, event):
if event.xdata is None or event.ydata is None:
return
if self.selected_line in self.axes.lines:
self.axes.lines.pop(self.axes.lines.index(self.selected_line))
if self.selected_line_text in self.axes.texts:
self.axes.texts.remove(self.selected_line_text)
self.selected_line = None
self.selected_line_text = None
self.selected_line_wavenumber = -1
if len(self.molecule_lookup_points) == 0:
return
closest = {'name': None, 'wn': -1., 'dist': 9e9}
for cur_molecule in self.molecule_lookup_points:
wn = self.molecule_lookup_points[cur_molecule]['wn']
ys = self.molecule_lookup_points[cur_molecule]['y']
dist_x2 = (wn - event.xdata)**2
xlim = self.axes.get_xlim()
scale = ((xlim[1] - xlim[0]) / # this is like wavenumbers/inch
(self.axes.figure.get_figwidth() *
self.axes.get_position().bounds[2]))
dist_y2 = ((ys - event.ydata) *
(self.axes.figure.get_figheight() *
self.axes.get_position().bounds[3]) * scale)**2
dist = np.sqrt(dist_x2 + dist_y2)
if dist.min() < closest['dist']:
closest = {
'name': cur_molecule,
'wn': wn[dist.argmin()],
'dist': dist.min()
}
self.selected_line_wavenumber = closest['wn']
self.selected_line = self.axes.plot([closest['wn'], closest['wn']],
[0, 1],
'-.',
color='black')[0]
self.selected_line_text = self.axes.annotate(
closest['name'] + ('%11.5f' % closest['wn']),
(closest['wn'], 1.03),
ha='center',
annotation_clip=False)
self.redraw()
def on_scroll(self, event):
self.central_wavenumber += self.bandwidth * event.step
def _all_on_fired(self):
self.selected_molecules = self.molecules.keys()
def _all_off_fired(self):
self.selected_molecules = []
def mpl_setup(self):
self.axes_widget = AxesWidget(self.figure.gca())
self.axes_widget.connect_event('button_press_event', self.on_click)
self.axes_widget.connect_event('scroll_event', self.on_scroll)
@on_trait_change("central_wavenumber, bandwidth")
def replot_molecular_overplots(self):
for i, cur_molecule in enumerate(self.selected_molecules):
if self.molecules[cur_molecule]['hitran'] is None:
self.molecules[cur_molecule][
'hitran'] = pandas.io.parsers.read_csv(gzip.open(
self.molecules[cur_molecule]['hitran_filename'], 'r'),
skiprows=2)
wn = self.molecules[cur_molecule]['hitran']['wavenumber']
intensity = self.molecules[cur_molecule]['hitran']['intensity']
w = ((wn >= self.central_wavenumber - self.bandwidth / 2.) &
(wn <= self.central_wavenumber + self.bandwidth / 2.))
wn = wn[w]
intensity = intensity[w]
plot_orders_of_magnitude = 2.
max_line_intensity = intensity.max()
min_line_intensity = max_line_intensity / 10**plot_orders_of_magnitude
wn = wn[intensity >= min_line_intensity]
intensity = intensity[intensity >= min_line_intensity]
intensity = (
(np.log10(intensity) - np.log10(min_line_intensity)) /
(np.log10(max_line_intensity) - np.log10(min_line_intensity)))
intensity = intensity * 0.1
self.molecule_lookup_points[cur_molecule] = {
'wn': wn,
'y': intensity + (i * 0.1) + 0.05
}
wn = wn.repeat(3)
intensity = np.column_stack(
(np.zeros(len(intensity)), intensity, np.zeros(
len(intensity)))).flatten() + (i * 0.1) + 0.05
newplot = self.axes.plot(wn, intensity,
self.molecules[cur_molecule]['color'])
newtext = self.axes.annotate(
cur_molecule, (self.central_wavenumber + self.bandwidth * 0.51,
i * 0.1 + 0.065),
ha='left',
va='center',
annotation_clip=False,
color=self.molecules[cur_molecule]['color'])
if self.molecules[cur_molecule]['plot_lines'] in self.axes.lines:
self.axes.lines.pop(
self.axes.lines.index(
self.molecules[cur_molecule]['plot_lines']))
self.molecules[cur_molecule]['plot_lines'] = None
if self.molecules[cur_molecule]['plot_text'] in self.axes.texts:
self.axes.texts.remove(
self.molecules[cur_molecule]['plot_text'])
self.molecules[cur_molecule]['plot_text'] = None
self.molecules[cur_molecule]['plot_lines'] = newplot[0]
self.molecules[cur_molecule]['plot_text'] = newtext
self.redraw()
def _selected_molecules_changed(self, old, new):
self.replot_molecular_overplots()
for cur_molecule in old:
if cur_molecule not in new:
if self.molecules[cur_molecule][
'plot_lines'] in self.axes.lines:
self.axes.lines.pop(
self.axes.lines.index(
self.molecules[cur_molecule]['plot_lines']))
if self.molecules[cur_molecule][
'plot_text'] in self.axes.texts:
self.axes.texts.remove(
self.molecules[cur_molecule]['plot_text'])
self.molecules[cur_molecule]['plot_lines'] = None
self.molecules[cur_molecule]['plot_text'] = None
self.molecule_lookup_points.pop(cur_molecule, None)
self.redraw()
@on_trait_change("central_wavenumber, bandwidth")
def redraw(self):
self.axes.set_xlim(self.central_wavenumber - self.bandwidth / 2.,
self.central_wavenumber + self.bandwidth / 2.)
self.axes.set_ylim(0, 1.0)
self.figure.canvas.draw()
class MCOTemplate(BaseTemplate):
"""BaseTemplate subclass to generate MCO options for
SurfactantContributedUI"""
# ------------------
# Regular Attributes
# ------------------
#: Name of the MCO for Workflow plugin id reference
mco_name = Unicode("surfactant_mco")
#: Template referring to the primary surfactant concentration
primary_surfactant_conc = Instance(ParameterTemplate)
#: Template referring to the secondary surfactant concentration
secondary_surfactant_conc = Instance(ParameterTemplate)
#: Template referring to the salt concentration
salt_conc = Instance(ParameterTemplate)
#: List of all template objects required to build Workflow
parameter_templates = List(Instance(ParameterTemplate))
#: Determines whether or not to enable secondary surfactant UI
#: options
enable_secondary_surfactant = Bool(False)
# ------------------
# Properties
# ------------------
#: Factory ID for Workflow
id = Property(Unicode, depends_on='plugin_id,mco_name')
# ------------------
# View
# ------------------
traits_view = View(
HGroup(
Group(Heading("Primary Surfactant"),
Item("primary_surfactant_conc",
editor=InstanceEditor(),
style='custom'),
show_labels=False),
Group(Heading("Secondary Surfactant"),
Item("secondary_surfactant_conc",
editor=InstanceEditor(),
style='custom',
enabled_when='enable_secondary_surfactant'),
show_labels=False),
Group(Heading("Salt (NaCl)"),
Item("salt_conc", editor=InstanceEditor(), style='custom'),
show_labels=False)))
# ------------------
# Defaults
# ------------------
def _primary_surfactant_conc_default(self):
return ParameterTemplate(plugin_id=self.id,
name='primary_surfactant',
parameter_type='Fixed')
def _secondary_surfactant_conc_default(self):
return ParameterTemplate(plugin_id=self.id,
name='secondary_surfactant',
parameter_type='Fixed')
def _salt_conc_default(self):
return ParameterTemplate(plugin_id=self.id,
name='salt',
parameter_type='Ranged')
def _parameter_templates_default(self):
return [self.primary_surfactant_conc, self.salt_conc]
# ------------------
# Listeners
# ------------------
def _get_id(self):
return '.'.join([self.plugin_id, "factory", self.mco_name])
@on_trait_change('enable_secondary_surfactant')
def update_secondary_surf_conc(self):
if not self.enable_secondary_surfactant:
self.secondary_surfactant_conc = (
self._secondary_surfactant_conc_default())
self.parameter_templates = self._parameter_templates_default()
else:
if self.secondary_surfactant_conc not in self.parameter_templates:
self.parameter_templates.insert(1,
self.secondary_surfactant_conc)
@on_trait_change('id')
def update_plugin_id(self):
self.primary_surfactant_conc.plugin_id = self.id
self.secondary_surfactant_conc.plugin_id = self.id
self.salt_conc.plugin_id = self.id
# ------------------
# Public Methods
# ------------------
def create_template(self):
return {
"id": self.id,
"model_data": {
"parameters": [
parameter_template.create_template()
for parameter_template in self.parameter_templates
],
"kpis": [{
"name": "micelle",
"objective": "MAXIMISE"
}, {
"name": "cost",
"objective": "MINIMISE"
}],
},
}
class ExecutionLayerTemplate(BaseTemplate):
# ------------------
# Regular Attributes
# ------------------
#: Template referring to the primary surfactant data
primary_surfactant_template = Instance(IngredientTemplate)
#: Template referring to the secondary surfactant data
secondary_surfactant_template = Instance(IngredientTemplate)
#: A list of possible surfactant ingredient to choose from
surfactant_template_list = List(IngredientTemplate)
#: An empty surfactant Template
empty_surfactant_template = Instance(IngredientTemplate)
#: Template referring to the chloride ion data
salt_template = Instance(IngredientTemplate)
#: Template referring to the solvent data
solvent_template = Instance(IngredientTemplate)
#: Internal database of available Ingredient objects
_gromacs_database = Instance(GromacsDatabase)
# ------------------
# Properties
# ------------------
#: Factory ID for Workflow
id = Property(Unicode, depends_on='plugin_id')
#: List containing all fragment templates to be used in
#: a generated Workflow
ingredient_templates = Property(List(IngredientTemplate),
depends_on='primary_surfactant_template,'
'secondary_surfactant_template')
#: Number of Ingredients
n_ingredients = Property(Int, depends_on='ingredient_templates[]')
# ------------------
# Properties
# ------------------
#: A list of possible secondary surfactant ingredient, including an
#: empty ingredient option
secondary_surfactant_list = Property(List(IngredientTemplate),
depends_on='surfactant_template_list,'
'primary_surfactant_template')
# ------------------
# View
# ------------------
traits_view = View(
HGroup(
Group(Heading("Primary Surfactant"),
Item("primary_surfactant_template",
editor=InstanceEditor(name='surfactant_template_list'),
style='custom'),
show_labels=False),
Group(Heading("Secondary Surfactant"),
Item("secondary_surfactant_template",
editor=InstanceEditor(name='secondary_surfactant_list'),
style='custom'),
show_labels=False)))
# ------------------
# Defaults
# ------------------
def _empty_surfactant_template_default(self):
return IngredientTemplate(plugin_id=self.id)
def __gromacs_database_default(self):
return GromacsDatabase()
def _surfactant_template_list_default(self):
surfactants = self._gromacs_database.get_role('Surfactant')
surfactant_templates = [
IngredientTemplate(plugin_id=self.id, ingredient=surfactant)
for surfactant in surfactants
]
return surfactant_templates
def _primary_surfactant_template_default(self):
return self.surfactant_template_list[0]
def _secondary_surfactant_template_default(self):
return self.empty_surfactant_template
def _salt_template_default(self):
salt = self._gromacs_database.get_ingredient('Sodium Chloride')
return IngredientTemplate(plugin_id=self.id, ingredient=salt)
def _solvent_template_default(self):
water = self._gromacs_database.get_ingredient('Water')
return IngredientTemplate(plugin_id=self.id, ingredient=water)
# ------------------
# Listeners
# ------------------
def _get_id(self):
return '.'.join([self.plugin_id, "factory"])
@cached_property
def _get_ingredient_templates(self):
templates = [
self.primary_surfactant_template, self.salt_template,
self.solvent_template
]
if self.secondary_surfactant_template.ingredient:
templates.insert(1, self.secondary_surfactant_template)
return templates
@cached_property
def _get_n_ingredients(self):
return len(self.ingredient_templates)
@cached_property
def _get_secondary_surfactant_list(self):
secondary_list = [self.empty_surfactant_template]
secondary_list += [
surfactant for surfactant in self.surfactant_template_list
if surfactant != self.primary_surfactant_template
]
return secondary_list
@on_trait_change('primary_surfactant_template')
def update_secondary_surfactant_template(self):
if (self.primary_surfactant_template ==
self.secondary_surfactant_template):
self.secondary_surfactant_template = (
self._secondary_surfactant_template_default())
@on_trait_change('plugin_id')
def update_plugin_id(self):
for surfactant_template in self.surfactant_template_list:
surfactant_template.plugin_id = self.id
self.empty_surfactant_template.plugin_id = self.id
self.salt_template.plugin_id = self.id
self.solvent_template.plugin_id = self.id
# ------------------
# Public Methods
# ------------------
def create_database_templates(self):
templates = []
for ingredient_template in self.ingredient_templates:
template = ingredient_template.create_template()
templates.append(template)
return templates
def create_formulation_template(self):
input_slot_info = []
for template in self.ingredient_templates:
if template.ingredient.role != 'Solvent':
input_slot_info.append(
{"name": f"{template.variable_name}_ingredient"})
input_slot_info.append(
{"name": f"{template.variable_name}_conc"})
else:
input_slot_info.append(
{"name": f"{template.variable_name}_ingredient"})
return {
"id": f"{self.id}.formulation",
"model_data": {
"n_surfactants": self.n_ingredients - 2,
"input_slot_info": input_slot_info,
"output_slot_info": [{
"name": "formulation"
}]
}
}
def create_simulation_template(self):
return {
"id": f"{self.id}.simulation",
"model_data": {
"name": "surfactant_experiment",
"size": 500,
"dry_run": False,
"input_slot_info": [{
"name": "formulation"
}],
"output_slot_info": [{
"name": "results"
}]
}
}
def create_micelle_template(self):
surfactants = [
template.ingredient for template in self.ingredient_templates
if template.ingredient.role == 'Surfactant'
]
fragment_symbols = [
surfactant.fragments[0].symbol for surfactant in surfactants
]
return {
"id": f"{self.id}.micelle",
"model_data": {
"method": 'atomic',
"fragment_symbols": fragment_symbols,
"r_thresh": 0.98,
"input_slot_info": [{
"name": "formulation"
}, {
"name": "results"
}],
"output_slot_info": [{
"name": "micelle"
}]
}
}
def create_viscosity_template(self):
return {
"id": f"{self.id}.viscosity",
"model_data": {
"input_slot_info": [{
"name": "results"
}],
"output_slot_info": [{
"name": "viscosity"
}]
}
}
def create_cost_template(self):
return {
"id": f"{self.id}.cost",
"model_data": {
"input_slot_info": [{
"name": "formulation"
}],
"output_slot_info": [{
"name": "cost"
}]
}
}
def create_template(self):
return [{
'data_sources': self.create_database_templates()
}, {
'data_sources': [self.create_formulation_template()]
}, {
'data_sources': [self.create_simulation_template()]
}, {
'data_sources':
[self.create_micelle_template(),
self.create_cost_template()]
}]
class NoDemo(HasPrivateTraits):
view = View(Heading('No demo defined for this lab.'), resizable=True)
