bio_rtd.core¶

Inlet¶

class bio_rtd.core.Inlet(t, species_list, inlet_id, gui_title)[source]¶

Bases: bio_rtd.core.DefaultLoggerLogic, abc.ABC

Generates starting flow rate and concentration profiles.

Parameters

t (ndarray) –
Simulation time vector

Starts with 0 and has a constant time step.
species_list (Sequence[str]) – List with names of simulating process fluid species.
inlet_id (str) – Unique identifier of an instance. It is stored in uo_id.
gui_title (str) – Readable title of an instance.

Variables

species_list (list of str) – List with names of simulating process fluid species.
uo_id (str) – Unique identifier of the Inlet instance.
gui_title (str) – Readable title of the Inlet instance.
adj_par_list (list of bio_rtd.adj_par.AdjustableParameter) – List of adjustable parameters exposed to the GUI.

get_n_species()[source]¶

Get number of process fluid species.

Return type: int

get_result()[source]¶

Get flow rate and concentration profiles.

Return type

Tuple[ndarray, ndarray]

Returns

f_out – Flow rate profile.
c_out – Concentration profile.

get_t()[source]¶

Get simulation time vector.

Return type: ndarray

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

set_logger_from_parent(parent_id, logger)¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –

UnitOperation¶

class bio_rtd.core.UnitOperation(t, uo_id, gui_title='')[source]¶

Bases: bio_rtd.core.DefaultLoggerLogic, abc.ABC

Processes flow rate and concentration profiles.

Parameters

t (ndarray) – Global simulation time vector. It must starts with 0 and have a constant time step.
uo_id (str) – Unique identifier.
gui_title (str) – Readable title for GUI.

Variables

adj_par_list – List of adjustable parameters exposed to the GUI.
gui_hidden – Hide the of the unit operation (default False).
discard_inlet_until_t – Discard inlet until given time.
discard_inlet_until_min_c – Discard inlet until given concentration is reached.
discard_inlet_until_min_c_rel – Discard inlet until given concentration relative to is reached. Specified concentration is relative to the max concentration.
discard_inlet_n_cycles – Discard first n cycles of the periodic inlet flow rate profile.
discard_outlet_until_t – Discard outlet until given time.
discard_outlet_until_min_c – Discard outlet until given concentration is reached.
discard_outlet_until_min_c_rel – Discard outlet until given concentration relative to is reached. Specified concentration is relative to the max concentration.
discard_outlet_n_cycles – Discard first n cycles of the periodic outlet flow rate profile.

adj_par_list: _typing.Sequence[_adj_par.AdjustableParameter]¶: Settings

evaluate(f_in, c_in)[source]¶

Evaluate the propagation through the unit operation.

Parameters

c_in (ndarray) – Inlet concentration profile with shape (n_species, n_time_steps).
f_in (array) – Inlet flow rate profile with shape (n_time_steps,).

Return type

Tuple[ndarray, ndarray]

Returns

f_out – Outlet flow rate profile.
c_out – Outlet concentration profile.

get_result()[source]¶

Returns existing flow rate and concentration profiles.

Return type

Tuple[ndarray, ndarray]

Returns

f_out – Outlet flow rate profile.
c_out – Outlet concentration profile.

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

set_logger_from_parent(parent_id, logger)¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –

RtdModel¶

class bio_rtd.core.RtdModel(inlet, dsp_uo_chain, logger=None, title='RtdModel', desc='')[source]¶

Bases: bio_rtd.core.DefaultLoggerLogic, abc.ABC

Combines inlet and a train of unit operations into a model.

The logger assigned to the instance of RtdModel is propagated throughout inlet and unit operations in dsp_uo_chain.

Parameters

inlet (Inlet) – Inlet profile.
dsp_uo_chain (Sequence[UnitOperation]) – Sequence of unit operations. The sequence needs to be in order.
logger (Optional[RtdLogger]) – Logger that the model uses for sending status messages and storing intermediate data.
title (str) – Title of the model.
desc (str) – Description of the model.

recalculate(start_at, on_update_callback)[source]¶: Recalculates the process fluid propagation, starting at start_at unit operation (-1 for inlet and entire process). Callback function can be specified. It receives the index of the just updated unit operation.

get_dsp_uo(uo_id)[source]¶

Get reference to a UnitOperation with specified uo_id.

Return type: UnitOperation

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

recalculate(start_at=0, on_update_callback=None)[source]

Recalculate process fluid propagation.

Parameters

start_at (int) – The index of first unit operation that needs to be re-evaluated. Default = 0. If -1, then the inlet profile is also re-evaluated.
on_update_callback (Optional[Callable[[int], None]]) –
Optional callback function which receives an integer.

The integer corresponds to the index of re-evaluated unit operation (-1 for inlet). This can serve as a trigger for updating UI after re-evaluation of individual unit operations.

set_logger_from_parent(parent_id, logger)¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –

UserInterface¶

class bio_rtd.core.UserInterface(rtd_model)[source]¶

Bases: abc.ABC

Wrapper around RtdModel suitable for building GUI on top of it.

Parameters

rtd_model (RtdModel) – RTD model.

Variables

species_label (list of str) – Labels of the species in concentration array.
x_label – Label of x axis (time). Default = ‘t’
y_label_c – Label of y axis (concentration). Default = ‘c’
y_label_f – Label of y axis (flow rate). Default = ‘f’
start_at (int) – The index of unit operation (starting with 0) at which the re-evaluation starts. The value of -1 means that the inlet profile is also reevaluated.

abstract build_ui()[source]¶: Build the UI from scratch.

recalculate(forced=False)[source]¶

Re-evaluates the model from the start_at index onwards.

Parameters: forced – If true, the entire model (inlet + unit operations) is re-evaluated. The same can be achieved by setting self.start_at to -1.

PDF¶

class bio_rtd.core.PDF(t, pdf_id='')[source]¶

Bases: bio_rtd.core.ParameterSetList, bio_rtd.core.DefaultLoggerLogic, abc.ABC

Abstract class for defining probability distribution functions.

Parameters

t (ndarray) – Simulation time vector.
pdf_id (str) – Unique identifier of the PDF instance.

Variables

trim_and_normalize – Trim edges of the peak by the threshold at the relative signal specified by cutoff_relative_to_max. Default = True.
cutoff_relative_to_max – Cutoff as a share of max value of the pdf (default 0.0001). It is defined to avoid very long tails of the distribution.

get_p()[source]¶: Get calculated PDF.

update_pdf(**kwargs)[source]¶: Re-calculate PDF based on specified parameters.

Abstract Methods

----------------

_calc_pdf(kw_pars: dict)[source]¶: Calculate new pdf for a given set of parameters. The keys of the kw_pars include keys from one of the group in _possible_key_groups and any optional subset of keys from _optional_keys.

assert_and_get_provided_kv_pairs(**kwargs)¶

Parameters: kwargs – Inputs to calc_pdf(**kwargs) function
Returns: Filtered kwargs so the keys contain first possible key group in _possible_key_groups and any number of optional keys from _optional_keys.
Return type: dict
Raises: ValueError – If **kwargs do not contain keys from any of the groups in _possible_key_groups.

get_p()[source]

Get probability distribution.

Returns: p – Evaluated probability distribution function. sum(p * self._dt) == 1 Corresponding time axis starts with 0 and has a fixed step of self._dt.
Return type: np.ndarray

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

set_logger_from_parent(parent_id, logger)¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –

update_pdf(**kwargs)[source]

Re-calculate PDF based on specified parameters.

Parameters: kwargs – Should contain keys from one of the group in self._possible_key_groups. It may contain additional keys from self._optional_keys.

ChromatographyLoadBreakthrough¶

class bio_rtd.core.ChromatographyLoadBreakthrough(dt, bt_profile_id='ChromatographyLoadBreakthrough')[source]¶

Bases: bio_rtd.core.ParameterSetList, bio_rtd.core.DefaultLoggerLogic, abc.ABC

What parts of the load bind to the column.

Parameters: bt_profile_id (str) – Unique identifier of the PDF instance. Used for logs.

Notes

See docstring of ParameterSetList for information about key groups.

assert_and_get_provided_kv_pairs(**kwargs)¶

Parameters: kwargs – Inputs to calc_pdf(**kwargs) function
Returns: Filtered kwargs so the keys contain first possible key group in _possible_key_groups and any number of optional keys from _optional_keys.
Return type: dict
Raises: ValueError – If **kwargs do not contain keys from any of the groups in _possible_key_groups.

calc_c_bound(f_load, c_load)[source]¶

Calculates what parts of load bin to the column.

Parameters

f_load (ndarray) – Load flow rate profile.
c_load (ndarray) – Load concentration profile. Concentration profile should include only species which bind to the column.

Returns

Parts of the load that binds to the column during the load step. c_bound has the same shape as c_load.

Return type

c_bound

Notes

This is default implementation. The user is welcome to override this function in a custom child class.

abstract get_total_bc()[source]¶

Total binding capacity

Useful for determining column utilization.

Return type: float

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

set_logger_from_parent(parent_id, logger)¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –

update_btc_parameters(**kwargs)[source]¶

Update binding dynamics for a given set of parameters.

Return type: None

ParameterSetList¶

class bio_rtd.core.ParameterSetList[source]¶

Bases: abc.ABC

Abstract class for asserting keys in key-value pairs.

Key-value pairs passed to assert_and_get_provided_kv_pairs should contain all keys from (at least) one of the key groups in _possible_key_groups. The method returns key-value pars with keys from that group and all passed keys that can be also found in _optional_keys.

Examples

>>> class DummyClass(ParameterSetList):
...    _possible_key_groups = [['par_1'], ['par_2a', 'par_2b']]
...    _optional_keys = ['key_plus_1', 'key_plus_2']
>>>
>>> dc = DummyClass()
>>> dc.assert_and_get_provided_kv_pairs(par_1=1, par_2a=2)
{'par_1': 1}
>>> dc.assert_and_get_provided_kv_pairs(par_2a=1, par_2b=2,
...                                     key_plus_1=3, key_plus_9=2)
{'par_2a': 1, 'par_2b': 2, 'key_plus_1': 3}
>>> dc.assert_and_get_provided_kv_pairs(
...     key_plus_1=1) 
Traceback (most recent call last):
KeyError: "Keys ... do not contain any of the required groups: ...

assert_and_get_provided_kv_pairs(**kwargs)[source]¶

Parameters: kwargs – Inputs to calc_pdf(**kwargs) function
Returns: Filtered kwargs so the keys contain first possible key group in _possible_key_groups and any number of optional keys from _optional_keys.
Return type: dict
Raises: ValueError – If **kwargs do not contain keys from any of the groups in _possible_key_groups.

DefaultLoggerLogic¶

class bio_rtd.core.DefaultLoggerLogic(logger_parent_id)[source]¶

Bases: abc.ABC

Default binding of the RtdLogger to a class.

The class holds a reference to a RtdLogger logger instance and plants a data tree in the logger.

Parameters: logger_parent_id (str) – Custom unique id that belongs to the instance of the class. It is used to plant a data tree in the RtdLogger.

Examples

>>> logger_parent_id = "parent_unit_operation"
>>> l = DefaultLoggerLogic(logger_parent_id)
>>> isinstance(l.log, _logger.DefaultLogger)
True
>>> l.log.e("Error Description")  # log error
Traceback (most recent call last):
RuntimeError: Error Description
>>> l.log.w("Warning Description")  # log waring
Warning Description
>>> l.log.i("Info")  # log info
>>> l.log.log_data = True
>>> l.log.log_level = _logger.RtdLogger.DEBUG
>>> l.log.i_data(l._log_tree, "a", 3)  # store value in logger
>>> l.log.d_data(l._log_tree, "b", 7)  # store at DEBUG level
>>> l.log.get_data_tree(logger_parent_id)["b"]
7
>>> l.log = _logger.StrictLogger()
>>> l.log.w("Warning Info")
Traceback (most recent call last):
RuntimeError: Warning Info

Notes

See the documentation of the RtdLogger.

property log¶

Logger.

If logger is not set, then a DefaultLogger is instantiated. Setter also plants a data tree into passed logger.

Return type: RtdLogger

set_logger_from_parent(parent_id, logger)[source]¶

Inherit logger from parent.

Parameters

parent_id (str) –
logger (RtdLogger) –