8.2.3. The Sequencer Extension

Summary of the main classes of the Sequencer extension. See also Extending the Sequencer.

8.2.3.1. The Extension

`Sequencer`(parent, dashboard)
`SequenceWorker`(sequencer[, parent])

class pymodaq.extensions.sequencer.sequencer.Sequencer(parent, dashboard)[source]

Attributes:

main_sequence
module_and_data_saver: Complex but Standardized way to save data from the CustomExt and
sequence_names

Methods

`connect_things`()	Connect actions and/or other widgets signal to methods
`do_things_after_experiment_set`(experiment_name)
`do_things_after_ui_setup`()
`populate_status_bar`()
`setup_actions`()	Method where to create actions to be subclassed.
`setup_docks_and_widgets`()	Mandatory method to be subclassed to setup the docks layout
`setup_menus_and_toolbars`([menubar])	Non mandatory method to be subclassed in order to create a menubar
`update_sequence_name`(old_name, new_name)	browse all elts in the sequences for SequenceElt and modify the current seq name if it has been changed!

add_sequence
load_sequence
remove_sequence
save_sequence
show_settings

connect_things()[source]: Connect actions and/or other widgets signal to methods

setup_actions()[source]

Method where to create actions to be subclassed. Mandatory

Examples

>>> self.add_action('quit', 'Quit', 'close2', "Quit program")
>>> self.add_action('grab', 'Grab', 'camera', "Grab from camera", checkable=True)
>>> self.add_action('load', 'Load', 'Open', "Load target file (.h5, .png, .jpg) or data from camera"
    , checkable=False)
>>> self.add_action('save', 'Save', 'SaveAs', "Save current data", checkable=False)

See also

ActionManager.add_action

setup_docks_and_widgets()[source]: Mandatory method to be subclassed to setup the docks layout

See also

pyqtgraph.dockarea.Dock

setup_menus_and_toolbars(menubar=None)[source]

Non mandatory method to be subclassed in order to create a menubar

create menu for actions contained into the self._actions, for instance:

See also

pymodaq.utils.managers.action_manager.ActionManager

update_sequence_name(old_name, new_name)[source]: browse all elts in the sequences for SequenceElt and modify the current seq name if it has been changed!

class pymodaq.extensions.sequencer.sequencer.SequenceWorker(sequencer, parent=None)[source]

Attributes:

app
status_manager

Methods

save_callback
stop
stopped

class pymodaq.extensions.sequencer.utilities.sequencer.sequence.Sequence(title, parent, dashboard)[source]

Attributes:

model
root_elt

Methods

`connect_things`()	Connect actions and/or other widgets signal to methods
`do_things_after_experiment_set`(experiment_name)
`do_things_after_ui_setup`()
`set_log_callback`(log_callback)	Set a Callback for all element to log (if any) their data into the log h5 file
`setup_actions`()	Method where to create actions to be subclassed.
`setup_docks_and_widgets`()	Mandatory method to be subclassed to setup the docks layout
`setup_menus_and_toolbars`([menubar])	Non mandatory method to be subclassed in order to create a menubar

is_valid
iterate_elts
load_sequence
name_changed
pause_sequence
recursive_connect_elts
recursive_disconnect_elts
selected_index_from_entered_state
sequence_finished
sequence_stopped
setup_machine
start_sequence
update_name

connect_things()[source]: Connect actions and/or other widgets signal to methods

set_log_callback(log_callback)[source]: Set a Callback for all element to log (if any) their data into the log h5 file

setup_actions()[source]

Method where to create actions to be subclassed. Mandatory

Examples

>>> self.add_action('quit', 'Quit', 'close2', "Quit program")
>>> self.add_action('grab', 'Grab', 'camera', "Grab from camera", checkable=True)
>>> self.add_action('load', 'Load', 'Open', "Load target file (.h5, .png, .jpg) or data from camera"
    , checkable=False)
>>> self.add_action('save', 'Save', 'SaveAs', "Save current data", checkable=False)

See also

ActionManager.add_action

setup_docks_and_widgets()[source]: Mandatory method to be subclassed to setup the docks layout

See also

pyqtgraph.dockarea.Dock

setup_menus_and_toolbars(menubar=None)[source]

Non mandatory method to be subclassed in order to create a menubar

create menu for actions contained into the self._actions, for instance:

See also

pymodaq.utils.managers.action_manager.ActionManager

8.2.3.2. Elements

`SeqEltBase`(id[, parent, parent_sequence])	Base class defining the interface of all elements handled by the Sequencer
`SeqEltFactory`()	The factory class to get Sequencer Elements
`ElementError`

class pymodaq.extensions.sequencer.utilities.element_factory.SeqEltBase(id, parent=None, parent_sequence=None, **label_kwargs)[source]

Base class defining the interface of all elements handled by the Sequencer

Attributes:

children
children_without_add
dashboard
id
mstate
name
parent: Get/Set this element parent
parent_sequence

Methods

`check_set_is_valid`()	Check the validity of the element
`child`(index)	Get the child by its index within the list of children
`child_by_index`(index)	Get the child by its unique index
`create_widget`([parent])	Public API to be used to create the widget representing this elt
`deserialize`(bytes_str)	Convert bytes into a SeqEltBase object
`do_things_with_dashboard`()	If this Element is using the Dashboard, once its setter has been called, this method will be executed
`do_things_with_parent_sequence`()	If this Element is using the Dashboard, once its setter has been called, this method will be executed
`execute`([dte])	Execute the Element
`from_dict`(dict_config)	Deserialization from a dictionary
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`get_elt_from_id`(elt_id[, start_parent])	Get the Element having the specified id starting from start_parent in the tree
`get_elts`([parent_elt, without_ids, ...])	Get as a list all element in the tree starting from parent_elt
`get_elts_as_str`([parent_elt, without_ids, ...])	Get the elements name of all existing elements
`get_ids`([parent_elt, without_ids, without_types])	Get the ids of the existing elements
`initialize_element`()	Perform Initialization of the element if needed when called
`save_data`(dte[, done])	By calling this method, data will be logged using the TimeSaver
`serialize`(obj)	Convert a SeqEltBase object into a bytes string
`set_parent`(value)	to be used as a slot or ...
`size_hint`()	Returns the Size the corresponding widget will likely have
`to_dict`()	Serialization in a dictionary
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

append_child
children_signal
data_to_log_signal
done_signal
get_root_elt
go_to_signal
save_signal
set_dashboard
set_parent_sequence

classmethod deserialize(bytes_str)[source]

Convert bytes into a SeqEltBase object

Return type:

Tuple[SeqEltBase, bytes]

Returns:

SeqEltBase (the decoded object)
bytes (the remaining bytes string if any)

classmethod from_dict(dict_config)[source]

Deserialization from a dictionary

Returns:: SeqEltBase
Return type:: SeqEltBase

classmethod serialize(obj)[source]

Convert a SeqEltBase object into a bytes string

Returns:: bytes
Return type:: bytes

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

To be reimplemented

if not valid should raise an ElementError exception else return None

child(index)[source]

Get the child by its index within the list of children

Return type:: Optional[SeqEltBase]

child_by_index(index)[source]

Get the child by its unique index

Return type:: Optional[SeqEltBase]

create_widget(parent=None)[source]

Public API to be used to create the widget representing this elt

Return type:: QWidget

do_things_with_dashboard()[source]

If this Element is using the Dashboard, once its setter has been called, this method will be executed

Do whatever is needed to instantiate your element with the Dashboard

do_things_with_parent_sequence()[source]

If this Element is using the Dashboard, once its setter has been called, this method will be executed

Do whatever is needed to instantiate your element with the Dashboard

execute(dte=None)[source]

Execute the Element

Should emit the done_signal when executed (could be with empty DataToExport)

from_dict_custom(dict_config)[source]

Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to be reimplemented

get_elt_from_id(elt_id, start_parent=None)[source]

Get the Element having the specified id starting from start_parent in the tree

Parameters:

elt_id (int)
start_parent (SeqEltBase) – Optional, if not specified or None, start from the Root of this element hierarchy

Return type:

Optional[SeqEltBase]

get_elts(parent_elt=None, without_ids=(), without_types=())[source]

Get as a list all element in the tree starting from parent_elt

Parameters:

without_types (Iterable[type[SeqEltBase]])
parent_elt (SeqEltBase)
without_ids (Iterable[int]) – tuple of ids to remove from the result
without_types – tuple of elements type to remove from the result

Returns:

list[SeqEltBase]

Return type:

list[SeqEltBase]

get_elts_as_str(parent_elt=None, without_ids=(), without_types=())[source]

Get the elements name of all existing elements

Return type:: list[str]

get_ids(parent_elt=None, without_ids=(), without_types=())[source]

Get the ids of the existing elements

Return type:: list[int]

initialize_element()[source]

Perform Initialization of the element if needed when called

Will be called automatically during the machine execution if the elt it comes from (using the StateMachine) is not a child of itself

To be reimplemented

save_data(dte, done=True)[source]

By calling this method, data will be logged using the TimeSaver

Parameters:

dte (DataToExport) – data to log and eventually custom save in self._save_data (reimplemented)
done (bool) – if True (default)the done signal is emitted ending this state

set_parent(value)[source]: to be used as a slot or …

size_hint()[source]

Returns the Size the corresponding widget will likely have

Return type:: QSize

to_dict()[source]

Serialization in a dictionary

Return type:: dict[str, Any]

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

property parent: SeqEltBase: Get/Set this element parent

class pymodaq.extensions.sequencer.utilities.element_factory.SeqEltFactory[source]

The factory class to get Sequencer Elements

Attributes:

elements

Methods

`get_seq_elt`(name)	Factory command to get registered subentry handler.
`register_elt`()	Class decorator method to register SubEntryHandlers class to the internal registry.

classmethod get_seq_elt(name)[source]

Factory command to get registered subentry handler.

This method gets the appropriate executor class from the registry

Return type:: type[SeqEltBase]

classmethod register_elt()[source]

Class decorator method to register SubEntryHandlers class to the internal registry. Must be used as a decorator above the definition of an SubEntryHandler inherited class.

The entry class must implement specific class attributes and methods

Return type:: Callable

class pymodaq.extensions.sequencer.utilities.element_factory.ElementError[source]

The elements shipped with PyMoDAQ:

class pymodaq.extensions.sequencer.utilities.elements.state.StateElt(*args, **kwargs)[source]

Attributes:

experiment
state
states

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`filter_state_wrt_manager`()	Reset the state to 'default' if not declared in the StateManager of the DashBoard
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`size_hint`()
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

save_actuator_moved
set_state
set_states
update_combo_states
update_states

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

Return type:: bool

filter_state_wrt_manager()[source]: Reset the state to ‘default’ if not declared in the StateManager of the DashBoard

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.move.MoveElt(*args, **kwargs)[source]

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`initialize_element`()
`size_hint`()
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

set_wait_move_done

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or raise ElementError if the user may do something!

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.grab.GrabElt(*args, **kwargs)[source]

Attributes:

detectors
selected
status

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`filter_selected_wrt_manager`()	Filter selected given the presence of the detector in the manager
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`size_hint`()
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

clean_signals
get_selected_detectors
set_status
update_detectors_from_combo
update_modules

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

filter_selected_wrt_manager()[source]: Filter selected given the presence of the detector in the manager

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.wait.WaitElt(*args, **kwargs)[source]

Attributes:

wait_time

Methods

`check_set_is_valid`()
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

done
set_wait_time_from_spinbox

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.repeat.RepeatElt(*args, **kwargs)[source]

Attributes:

n_repeat

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`initialize_element`()
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

set_repeat_from_spinbox

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.scanner.ScannerElt(*args, **kwargs)[source]

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`initialize_element`()
`size_hint`()
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.choice.ChoiceElt(*args, **kwargs)[source]

Attributes:

choice_model
go_to_false
go_to_true
without_ids
without_types

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`set_go_to_true`(value)	set go_true given the value which is the index of the get_ids or self.get_elts_as_str return lists
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

set_choice_model
set_go_to_false
update_modules
update_params
update_target_states

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

Return type:: bool

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

set_go_to_true(value)[source]: set go_true given the value which is the index of the get_ids or self.get_elts_as_str return lists

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

class pymodaq.extensions.sequencer.utilities.elements.sequence.SequenceElt(*args, **kwargs)[source]

Attributes:

sequence
sequence_obj

Methods

`check_set_is_valid`()	Check the validity of the element
`do_things_with_dashboard`()
`do_things_with_parent_sequence`()	If this Element is using the Dashboard, once its setter has been called, this method will be executed
`from_dict_custom`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`get_sequences`()	Get the list of Sequences that can be started, removing the one this element belong to
`get_sequences_name`()	Get the list of Sequences that can be started, removing the one this element belong to
`to_dict_custom`()	adds attribute to a dict in order to produce a human readable representation/configuration for this element

register_sequence
set_sequence
unregister_sequence
update_combo_sequences

check_set_is_valid()[source]

Check the validity of the element

Will be called before executing the element. Try to make sure the element is valid or return None if the user may do something!

Return type:: bool

do_things_with_parent_sequence()[source]

If this Element is using the Dashboard, once its setter has been called, this method will be executed

Do whatever is needed to instantiate your element with the Dashboard

from_dict_custom(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

get_sequences()[source]

Get the list of Sequences that can be started, removing the one this element belong to

Return type:: list[Sequence]

get_sequences_name()[source]

Get the list of Sequences that can be started, removing the one this element belong to

Return type:: list[str]

to_dict_custom()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this element

to be reimplemented

Return type:: dict[str, Any]

8.2.3.3. Choice models

class pymodaq.extensions.sequencer.utilities.choice_models.model.ChoiceModelBase(parent_elt)[source]

Attributes:

selected

Methods

`check_set_is_valid`()	Check if the current settings of this model are valid
`from_dict`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`to_dict`()	adds attribute to a dict in order to produce a human readable representation/configuration for this model params
`updated_module_manager`()	called whenever the parent modules manager is updated

execute

check_set_is_valid()[source]

Check if the current settings of this model are valid

To be reimplemented

Should raise ElementError if not valid

from_dict(dict_config)[source]

Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to be reimplemented

to_dict()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this model params

to be reimplemented

Return type:: dict[str, Any]

updated_module_manager()[source]

called whenever the parent modules manager is updated

to be reimplemented

pymodaq.extensions.sequencer.utilities.choice_models.model.get_choice_models()[source]

Register ChoiceModels in pymodaq models entrypoints

Returns:: list
Return type:: list of dict containing the name and python module of the found models

Example

model = [{‘name’: ‘MyModel’, ‘class’: DataModel}]

class pymodaq.extensions.sequencer.utilities.choice_models.factory.ChoiceModelFactory[source]

The factory class to get Sequencer Elements

Attributes:

models

Methods

`get_model`(name)	Factory command to get registered subentry handler.
`register_choice`()	Class decorator method to register Models to be used with the Choice Element class to the internal registry.

classmethod get_model(name)[source]

Factory command to get registered subentry handler.

This method gets the appropriate executor class from the registry

Return type:: type[ChoiceModelBase]

classmethod register_choice()[source]

Class decorator method to register Models to be used with the Choice Element class to the internal registry. Must be used as a decorator above the definition of a ChoiceModelBase inherited class.

The class must implement the ChoiceModelBase interface

Return type:: Callable

The models shipped with PyMoDAQ:

class pymodaq.extensions.sequencer.models.threshold_choice_model.ThresholdChoiceModel(*args, **kwargs)[source]

Methods

`check_set_is_valid`()	Check if the current settings of this model are valid
`from_dict`(dict_config)	Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods
`to_dict`()	adds attribute to a dict in order to produce a human readable representation/configuration for this model params
`updated_module_manager`()	called whenever the parent modules manager is updated

execute
probe_data
process_dte

check_set_is_valid()[source]: Check if the current settings of this model are valid

from_dict(dict_config)[source]: Create/set the custom part of the element to finish initialization using setters, attribute assignment or methods

to_dict()[source]

adds attribute to a dict in order to produce a human readable representation/configuration for this model params

Return type:: dict[str, Any]

updated_module_manager()[source]: called whenever the parent modules manager is updated

class pymodaq.extensions.sequencer.models.user_input_choice.UserInput(parent_elt)[source]

Methods

execute

class pymodaq.extensions.sequencer.models.true_choice_model.TrueChoiceModel(parent_elt)[source]

Methods

execute

class pymodaq.extensions.sequencer.models.false_choice_model.FalseChoiceModel(parent_elt)[source]

Methods

execute

8.2.3.4. State machine

class pymodaq.extensions.sequencer.utilities.states.CompositeState(elt, *args, **kwargs)[source]

Attributes:

external_transitions

Methods

add_external_transition
clear_state_and_transitions
clear_transitions
set_do_init
setup_states

class pymodaq.extensions.sequencer.utilities.states.TrackedTransition(signal, source_state, target_state=None)[source]

Methods

is_child_of(child_state, target_parent)

Walks up the parent chain to see if target_parent is an ancestor.

eventTest
onTransition
targetState
update_target

static is_child_of(child_state, target_parent)[source]: Walks up the parent chain to see if target_parent is an ancestor.

class pymodaq.extensions.sequencer.utilities.states.ValueTransition(signal, value, source_state, target_state=None)[source]

Methods

eventTest

class pymodaq.extensions.sequencer.utilities.states.InterruptState(*args, **kwargs)[source]

Methods

onEntry