def default_traits_view(self):
view = KromView(
VGroup(
HGroup(
Item("model.name",
editor=TextEditor(auto_set=True, enter_set=True)),
Spring(),
Item("model.model_type", style='readonly', label="Type"),
Spring(), Item("model.target_product", style='readonly')),
VGroup(
Item("model.is_kinetic",
label="Is Kinetic",
editor=BooleanEditor()),
VGroup(
Item('param_formula_str',
style="readonly",
show_label=False),
Item("component_array",
label="Comp. Coeff.",
show_label=False,
editor=self._tabular_editor),
),
label="Parameters",
show_border=True,
),
),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
default_button=OKButton,
title="Configure {} model".format(self.model.model_type))
return view
def default_traits_view(self):
if self.standalone:
std_buttons = OKCancelButtons
else:
std_buttons = [CancelButton]
view = KromView(
VGroup(
make_window_title_group(title="User Preferences",
include_blank_spaces=False),
Item("instructions", style="readonly", resizable=True,
show_label=False),
Tabbed(
Item("ui_prefs_view", editor=InstanceEditor(),
style="custom", label="Interface", show_label=False),
Item("file_pref_view", editor=InstanceEditor(),
style="custom", label="File loading",
show_label=False),
Item("app_pref_view", editor=InstanceEditor(),
style="custom",
# even though the group's label is not shown in the
# UI, it needs to be set to set the tab name:
label="Application", show_label=False),
Item("solver_prefs_view",
editor=InstanceEditor(), style="custom",
label="Solver", show_label=False),
),
),
buttons=[save_button, factory_reset_button] + std_buttons,
handler=RevealChromatographyPreferenceViewHandler(),
default_button=save_button,
width=700,
title="Edit Reveal Chromatography Preferences",
)
return view
def default_traits_view(self):
view = KromView(
HGroup(
VGroup(
Group(
Item("select_all_collections", label="All"),
UItem('displayed_log_collection_names',
editor=CheckListEditor(
values=self._all_log_collection_names),
style='custom'),
HGroup(
UItem("color_editor"),
),
label='Experiments/Simulations',
show_border=True,
),
Group(
UItem('displayed_log_family_names',
editor=CheckListEditor(
values=self._all_log_family_names,
format_func=lambda a: a),
style='custom'),
label='Plot Grouping', show_border=True,
),
visible_when='_show_control'
),
VGroup(
UItem('_container', editor=ComponentEditor(),
show_label=False),
show_border=True,
),
),
title="Chromatogram Plot",
)
return view
class AppPreferencesView(HasStrictTraits):
model = Instance(AppPreferenceGroup)
view = KromView(
VGroup(
Item("object.model.user_ds_folder", label="User data storage"),
Item("object.model.python_script_folder",
label="Python scripts storage"),
),
)
class UIPreferencesView(HasStrictTraits):
model = Instance(UIPreferenceGroup)
view = KromView(
VGroup(
VGroup(
Label("(Requires restart)"),
),
Item("object.model.confirm_on_window_close",
label="Confirm on project close?"),
Item("object.model.auto_close_empty_windows_on_open",
label="Auto close empty projects?",
tooltip="Auto close empty projects when opening a new one?"),
Item("object.model.app_width", label="Default app window width"),
Item("object.model.app_height", label="Default app window height"),
)
)
class ProjectFileSelector(HasStrictTraits):
path_list = List(Str)
selected = Either(Str, List(Str))
view = KromView(
Item("path_list", show_label=False,
editor=ListStrEditor(title='Project(s) to load',
selected="selected",
editable=False, multi_select=True)),
title="Select the project(s) to load",
buttons=OKCancelButtons,
width=500
)
def _selected_default(self):
return []
def default_traits_view(self):
from app_common.traitsui.common_traitsui_groups import \
make_window_title_group
title = make_window_title_group("Select Plot Colors")
msg = "By default, a simulation and the experiment it was built from "\
"share the same color. Check the box to control the color of " \
"all plots and\nun-check to keep simulation colors the same as" \
" their source experiments."
connected_colors = VGroup(
Label(msg),
HGroup(
Spring(),
Item("disconnected_plots", label="Control simulation colors")
),
show_border=False
)
items = []
for i, name in enumerate(self.collection_list):
if name not in self.collection_map:
continue
always_visible = "plot_always_visible_{}".format(i)
name_attr = "plot_name_{}".format(i)
label = getattr(self, name_attr)
items.append(
Item("plot_color_{}".format(i), label=label,
visible_when="disconnected_plots or " + always_visible),
)
view = KromView(
VGroup(
title,
connected_colors,
VGroup(
*items,
show_border=True,
label="Experiments/Simulations"
),
),
buttons=OKCancelButtons,
title="Chromatogram Plot Styles",
width=400
)
return view
class ComponentSelector(HasStrictTraits):
""" Class to support select a set of experiments from a study
"""
product = Instance(Product)
ignore_strip_by_default = Bool(True)
component_selected = List(Str)
component_name_available = List(Str)
view = KromView(Item("component_name_available",
editor=ListStrEditor(title='Component List',
selected="component_selected",
multi_select=True,
editable=False),
show_label=False),
buttons=OKCancelButtons,
title="Select components")
# Traits listener methods -------------------------------------------------
def _product_changed(self):
self.component_name_available = \
self._component_name_available_default()
self.component_selected = self._component_selected_default()
# Traits initialization methods -------------------------------------------
def _component_selected_default(self):
ignore = []
if self.ignore_strip_by_default:
ignore.append(STRIP_COMP_NAME)
return [
name for name in self.component_name_available
if name not in ignore
]
def _component_name_available_default(self):
if self.product is None:
return []
return self.product.product_component_names
class FilePreferencesView(HasStrictTraits):
model = Instance(FilePreferenceGroup)
view = KromView(
VGroup(
HGroup(
Item("object.model.max_recent_files", editor=spinner_editor,
label="Num. Recent Projects (requires restart)",
tooltip="Maximum number of recent project paths to "
"remember."),
),
HGroup(
Item("object.model.exp_importer_mass_threshold",
label="Experiment import mass balance threshold",
tooltip="Max relative mass difference to warn during "
"experiment import"),
),
),
)
class ExperimentSelector(HasStrictTraits):
""" Class to support select a set of experiments from a study
"""
study = Instance(Study)
experiment_selected = List(Str)
experiment_name_available = List(Str)
view = KromView(Item("experiment_name_available",
editor=ListStrEditor(title='Experiment List',
selected="experiment_selected",
multi_select=True,
editable=False),
show_label=False),
buttons=OKCancelButtons,
title="Select experiments")
def _experiment_name_available_default(self):
return [exp.name for exp in self.study.experiments]
def default_traits_view(self):
view = KromView(
Item("model.name",
tooltip=COMPONENT_NAME_TOOLTIP,
editor=TextEditor(invalid='_invalid_name'),
enabled_when='name_editable'),
Item("model.target_product",
enabled_when="target_product_editable"),
Item("model.extinction_coefficient",
editor=UnitScalarEditor(),
width=200),
Item("model.molecular_weight",
editor=UnitScalarEditor(),
tooltip="Molecular weight of the component in kilo-Daltons "
"(1 kDa=1 kg/mol)"),
# Relevant when used as standalone view:
buttons=OKCancelButtons,
title=self.title)
return view
def traits_view(self):
no_comp_msg = ('No components were found targeting the requested '
'product ({}). Please create the needed components '
'first.'.format(self.target_product))
view = KromView(
# Embedding the label in a Group to give it space and work around a
# traitsui bug with Label and visible_when (traitsui issues #298)
HGroup(
Label(no_comp_msg),
visible_when='component_names == []'
),
Item('component_names',
editor=ListStrEditor(selected='selected_component_names',
multi_select=True),
label="Select component(s)"),
Item('create_comp_button', show_label=False),
title="Select components to build the product.",
resizable=True,
buttons=OKCancelButtons,
)
return view
def traits_view(self):
# Build the view such that the SLURM stuff isn't visible if not
# available on the machine
elements = [
VGroup(
Item("object.model.solver_binary_path",
label="Cadet executable"),
Item("object.model.input_file_location",
label="CADET input folder"),
Item("object.model.executor_num_worker", editor=spinner_editor,
label="Cadet num. workers (requires restart)"),
Item("object.model.cadet_num_threads", editor=spinner_editor,
label="Cadet num. threads"),
Item('object.model.auto_delete_solver_files_on_exit'),
)
]
executable = self.model.slurm_binary
if check_slurm_installed(executable=executable):
elements[0].label = "General"
elements.append(
VGroup(
Item("object.model.use_slurm_scheduler",
tooltip="Submit solver run to SLURM scheduler"),
Item("object.model.slurm_binary",
visible_when="object.model.use_slurm_scheduler",
width=300, tooltip="Command to submit SLURM jobs"),
Item("object.model.slurm_partition",
visible_when="object.model.use_slurm_scheduler",
width=300,
tooltip="SLURM scheduler partition to submit jobs."),
Item("object.model.slurm_job_name",
visible_when="object.model.use_slurm_scheduler",
width=300, tooltip="SLURM scheduler job name."),
label="SLURM scheduler",
)
)
elements = [Tabbed(*elements)]
return KromView(*elements)
def traits_view(self):
visible_when_sma = "binding_model_type == '{}'".format(
STERIC_BINDING_MODEL)
visible_when_ph_sma = "binding_model_type == '{}'".format(
PH_STERIC_BINDING_MODEL)
visible_when_langmuir = "binding_model_type == '{}'".format(
LANGMUIR_BINDING_MODEL)
visible_when_extern_langmuir = "binding_model_type == '{}'".format(
PH_LANGMUIR_BINDING_MODEL)
view = KromView(VGroup(
HGroup(Spring(), Item("binding_model_type"), Spring()),
HGroup(Item('_sma_model_view',
editor=InstanceEditor(),
show_label=False,
style="custom",
visible_when=visible_when_sma),
Item('_ph_sma_model_view',
editor=InstanceEditor(),
show_label=False,
style="custom",
visible_when=visible_when_ph_sma),
Item('_langmuir_model_view',
editor=InstanceEditor(),
show_label=False,
style="custom",
visible_when=visible_when_langmuir),
Item('_ext_langmuir_model_view',
editor=InstanceEditor(),
show_label=False,
style="custom",
visible_when=visible_when_extern_langmuir),
show_border=True,
label="Model parameters"),
),
buttons=OKCancelButtons,
default_button=OKButton,
handler=BindingModelBuilderHandler(),
title="Configure new binding model")
return view
def default_traits_view(self):
view_items = []
for i, calc in enumerate(self.fraction_calculators):
calc_name = "_calc_view_{}".format(i)
self.add_trait(calc_name, Instance(StripFractionCalculatorView))
calc_view = StripFractionCalculatorView(model=calc)
self.trait_set(**{calc_name: calc_view})
view_item = VGroup(
Item(calc_name, editor=InstanceEditor(),
style="custom", show_label=False),
label=calc.experim.name
)
view_items.append(view_item)
view = KromView(
Tabbed(*view_items),
title="Strip Fraction Estimation Assistant",
buttons=[ResetAllButton, ApplyAllButton],
handler=MultiExpStripFractionCalculatorHandler(),
)
return view
def default_traits_view(self):
view = KromView(
VGroup(
HGroup(
Item("model.name"),
Spring(),
Item("model.target_product", style='readonly'),
),
VGroup(
HGroup(Item("model.column_porosity",
label="Column Porosity",
editor=PositiveFloatEditor()),
Item("model.bead_porosity",
label="Bead Porosity",
editor=PositiveFloatEditor(),
tooltip="Protein bead porosity"),
label="Porosity",
show_border=True), ),
VGroup(
VGroup(
Item("model.axial_dispersion",
label="Axial Dispersion",
editor=PositiveFloatEditor()), ),
VGroup(
Item("component_array",
label="Comp. Coeff.",
show_label=False,
editor=self._tabular_editor), ),
label="Transport Parameters",
show_border=True,
),
),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
default_button=OKButton,
title="Configure General Rate model")
return view
def default_traits_view(self):
landing_text = r"Strip contribution estimation for Experiment " \
r"'<i>{}</i>' (load '<i>{}</i>'), from the specified " \
r"load concentration, method step <br>start times and "\
r"estimated product extinction coefficient:"
landing_text = landing_text.format(self.model.experim.name,
self._load_solution_name)
formula = "strip_fraction = 1 - mass_eluting_before_strip / " \
"loaded_mass"
view = KromView(
VGroup(
VGroup(Label(landing_text),
HGroup(
Spring(),
Label(formula),
Spring(),
),
show_border=True),
VGroup(HGroup(
VGroup(
Item("object.model.load_concentration",
editor=UnitScalarEditor()),
Item("object.model.loaded_volume",
editor=UnitScalarEditor())),
Spring(),
VGroup(
Spring(),
Item("object.model.loaded_mass",
editor=UnitScalarEditor(),
style="readonly"),
Spring(),
),
),
show_border=True,
label="Product loaded into the column"),
HGroup(VGroup(
Item("object.model.product_ext_coeff",
editor=UnitScalarEditor(),
label="Est. product extinction coef."),
Item("object.model.load_start",
label="Load start time",
editor=UnitScalarEditor()),
Item("object.model.strip_start",
label="Strip start time",
editor=UnitScalarEditor()),
),
Spring(),
VGroup(
Spring(),
Item("object.model.integrated_mass_before_strip",
label="Mass eluting before strip",
editor=UnitScalarEditor(),
style="readonly"), Spring()),
show_border=True,
label="Product recovered before Strip"),
HGroup(
Spring(),
Item("object.model.strip_mass_fraction",
editor=UnitScalarEditor(),
label="Proposed Strip Mass Fraction"),
Item("_current_strip_mass_fraction",
editor=UnitScalarEditor(),
style="readonly",
label="Current Strip Mass Fraction"), Spring()),
),
title="Strip Fraction Estimation Assistant",
buttons=[ResetButton, ApplyButton],
handler=StripFractionCalculatorHandler(),
)
return view
def traits_view(self):
view = KromView(
Item("plot", editor=ComponentEditor(), show_label=False))
return view
def traits_view(self):
col_pattern_editor = build_col_name_editor(self.all_col_names)
filename = basename(self.akta_filepath)
spinner_editor = RangeEditor(low=5, high=9999, mode='spinner')
time_orig = 'AKTA time from which to import AKTA data and name' \
' of the corresponding step (typically the load).'
search_instructions = 'Hit {}-f to search for a word'
search_instructions = search_instructions.format(get_ctrl())
view = KromView(
Tabbed(
VGroup(
VGroup(
Label(time_orig),
HGroup(
Item('time_of_origin', editor=UnitScalarEditor(),
show_label=False),
Item("akta_start_method_step",
label="Method step @ t=0"),
),
Item('origin_error_msg', emphasized=True,
visible_when='origin_error_msg',
style='readonly', label="Note"),
show_border=True, label="Time of origin"
),
VGroup(
Item('patterns_as_list', editor=col_pattern_editor,
show_label=False, height=200),
Item('pattern_error_msg', emphasized=True,
visible_when='pattern_error_msg',
style='readonly', label="Error"),
show_border=True, label="AKTA Column Types"
),
label="AKTA File Settings"
),
VGroup(
Item('file_preview', editor=CodeEditor(),
show_label=False, tooltip=search_instructions),
VGroup(Item('length_of_preview', editor=spinner_editor)),
show_border=True,
label="AKTA File Preview".format(filename),
),
VGroup(
# Information used to evaluate the loaded product mass
Item("mass_bal_analyzer", editor=InstanceEditor(),
style="custom", show_label=False),
VGroup(
HGroup(
Item("mass_bal_msg", emphasized=True,
style='readonly', show_label=False),
),
Item("mass_bal_strategy",
label="Adjustment strategy",
enabled_when="not mass_balanced"),
HGroup(
Item("mass_bal_strategy_msg", emphasized=True,
style='readonly', show_label=False,
enabled_when="not mass_balanced"),
),
visible_when="target_experiment and pure_protein_exp"
),
label="UV and Mass Balance",
),
),
buttons=OKCancelButtons,
title="Experiment Importer: {}".format(self.experiment_name),
width=900,
)
return view
def traits_view(self):
component_descr_simple_editor = build_component_descr_editor(False)
component_descr_expert_editor = build_component_descr_editor(True)
known_products = self.datasource.get_object_names_by_type('products')
name_editor = TextWithExcludedValuesEditor(
forbidden_values=set(known_products)
)
expert_mode_tooltip = "Expert mode: customize assay names, and " \
"control concentration expressions."
strip_label = 'Strip component, automatically added to account for' \
' load mass eluting during the Strip step, if any.'
view = KromView(
VGroup(
HGroup(
Item('name', editor=name_editor, width=300),
Item('product_type'),
),
Item("description", style="custom"),
Item('pI', editor=UnitScalarEditor(), label="pI"),
HGroup(
Spring(),
Item('expert_mode', tooltip=expert_mode_tooltip),
),
VGroup(
Item('component_descs', show_label=False,
editor=component_descr_simple_editor),
Item('_add_comp_button', show_label=False),
HGroup(
Spring(),
Item('add_strip', tooltip=expert_mode_tooltip),
),
VGroup(
Label(strip_label),
HGroup(
Item('strip_component_descs', style='readonly',
editor=component_descr_simple_editor,
show_label=False, height=40),
Item('_edit_strip_comp_button', show_label=False),
),
visible_when="add_strip"
),
label="Product component names",
show_border=True, visible_when="not expert_mode"
),
VGroup(
Item('component_descs', show_label=False,
editor=component_descr_expert_editor,
visible_when="expert_mode"),
Item('_add_comp_button', show_label=False),
label="Product components and concentration expressions",
show_border=True, visible_when="expert_mode"
),
VGroup(
Item('component_assay_names', editor=ASSAY_TABLE_EDITOR,
show_label=False),
Item("_add_assay_button", show_label=False),
label="Component assay values",
show_border=True, visible_when="expert_mode"
),
),
width=600, height=600, title="Specify New Product Characteristics",
buttons=OKCancelButtons
)
return view
def traits_view(self):
additional_param_controls = self._build_additional_param_editors()
param_list_with_cost = [ALL_COST_COL_NAME] + self.param_list
two_d_plot_shown = "show_cost_data_nd == '2D' and y_axis_param != " \
"'{}'".format(ALL_COST_COL_NAME)
weight_range_editor = RangeEditor(low=0., high=MAX_WEIGHT)
weight_doc = Label("The following control the relative importance or "
"the various components that go into computing the"
" cost of a model,\nthat is the difference between "
"a simulation with that model and the corresponding"
" experiment."),
view = KromView(VGroup(
VGroup(weight_doc,
HGroup(
Item("peak_time_weight", label="Peak time"),
Item("peak_height_weight", label="Peak height"),
Item("peak_slope_weight", label="Peak slope"),
),
show_border=True,
label="Weights",
enabled_when="False",
visible_when="not weight_edit_mode"),
VGroup(weight_doc,
Item("peak_time_weight",
label="Peak time",
editor=weight_range_editor),
Item("peak_height_weight",
label="Peak height",
editor=weight_range_editor),
Item("peak_slope_weight",
label="Peak slope",
editor=weight_range_editor),
show_border=True,
label="Weights",
visible_when="weight_edit_mode"),
HGroup(
Spring(),
Item("edit_weights_button",
show_label=False,
enabled_when="can_change_weights")),
VGroup(HGroup(
Item("show_cost_data_nd",
label="Plot type",
style="custom",
enabled_when="len(param_list) > 1"),
Item("x_axis_param",
editor=EnumEditor(values=self.param_list)),
Item("y_axis_param",
editor=EnumEditor(values=param_list_with_cost),
enabled_when="show_cost_data_nd != '1D'"),
),
Item("plot1_2d_container",
editor=ComponentEditor(),
show_label=False),
HGroup(
Spring(),
Item('color_bar_max_percentile',
editor=RangeEditor(low=1, high=100,
mode='spinner'),
label='Colorbar high percentile (%)',
visible_when=two_d_plot_shown)),
VGroup(*additional_param_controls),
label="Cost function plot",
show_border=True,
visible_when="not no_cost_data"),
),
buttons=[OKButton],
title="View/Edit optimizer cost function")
return view