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Methods

Supported methods

The following methods are supported in PyPalmSens:

Voltammetric Techniques

Pulsed Techniques

Amperometric Techniques

Potentiometric Techniques

Coulometric techniques

Other

Setting up a method

This example creates a method for a square-wave voltammetry measurement versus the open circuit potential:

>>> import pypalmsens as ps

>>> method = ps.SquareWaveVoltammetry(
...    conditioning_potential = 2.0,  # V
...    conditioning_time = 2,  # seconds
...    versus_ocp_mode = 3,  # versus begin and end potential
...    versus_ocp_max_ocp_time = 1,  # seconds
...    begin_potential = -0.5,  # V
...    end_potential = 0.5,  # V
...    step_potential = 0.01,  # V
...    amplitude = 0.08,  # V
...    frequency = 10,  # Hz
...)

Because methods are pydantic models, all attributes can be modified afterwards:

>>> method.begin_potential = -1.0
>>> method.end_potential = 1.0
>>> method.step_potential = 0.02

Methods can be serialized to and from a dictionary:

>>> dumped = method.model_dump()
>>> dumped
{'equilibration_time': 0.0,
 'begin_potential': -1.0,
 'end_potential': 1.0,
 'step_potential': 0.02,
 'frequency': 10,
 'amplitude': 0.08,
 ...}
>>> method2 == ps.SquareWaveVoltammetry(**dumped)
>>> method == method2
True

Methods can be copied and updated:

>>> method3 = method.model_copy(update={'equilibration_time' : 10.0})
>>> method == method3
False

Tip

The VSCode Debug Console or another Python REPL environment like IPython will auto complete on the properties and functions.

Debug console in VSCode

Common settings

Many settings are shared between methods. For a full listing, see pypalmsens.settings.

If you don’t specify any arguments, the default values are loaded. These are accessible via attributes on the methods.

For example:

>>> cv = ps.CyclicVoltammetry()
>>> cv.current_range
CurrentRange(max = '10mA', min = '1uA', start = '100uA')

There are two ways to modify the current ranges, for example, if you want so set the start current at 10 μA.

  1. By passing current ranges as an argument during initialization

    >>> cv = ps.CyclicVoltammetry(current_range={'start':'10uA'})
>>> cv.current_range
CurrentRange(max='10mA', min='1uA', start='10uA') # (1)!
    1. Only the start value was set, so the min/max are populated with the defaults.

  2. By updating the attributes (after initialization)

    >>> cv = ps.CyclicVoltammetry()
>>> cv.current_range.start = '10uA'

Fixed ranges

If you want to use a fixed current (or potential) range, you can save yourself some typing by passing the current range string directly. This automatically expands into the CurrentRange object with min, max, and start equal.

>>> cv = ps.CyclicVoltammetry(current_range='10uA')
>>> cv.current_range
CurrentRange(max = '10uA',min = '10uA',start = '10uA')

Validation

Methods are defined as Pydantic Models. Pydantic is a library for defining a schema via models. They are very similar to Python dataclasses in the way that they work.

The important difference is that Pydantic offers more options for validation, serialization, and conversion.

This means is automatically converts dictionaries to the correct type (if the fields can be matched), for example:

>>> import pypalmsens as ps

>>> cv = ps.CyclicVoltammetry(
...     current_range = {'min':'10mA', 'max':'1uA', 'start':'100uA'}
... )
>>> cv.current_range
CurrentRange(max='10mA', min='1uA', start='100uA')

And gives an errorr when trying to overwrite types by invalid dictionaries or instances:

>>> cv.current_range='foo'
ValidationError: 1 validation error for CyclicVoltammetry
current_range
  Input should be a valid dictionary or instance of CurrentRange [type=model_type, input_value='foo', input_type=str]
    For further information visit https://errors.pydantic.dev/2.12/v/model_type

It is also helps prevents setting non-existant variables and guard against typos:

>>> cv = ps.CyclicVoltammetry(foo=123, scanreat=2.0)
ValidationError: 2 validation errors for CyclicVoltammetry
foo
  Extra inputs are not permitted [type=extra_forbidden, input_value=123, input_type=int]
    For further information visit https://errors.pydantic.dev/2.12/v/extra_forbidden
    scanreat
  Extra inputs are not permitted [type=extra_forbidden, input_value=1.0, input_type=float]
    For further information visit https://errors.pydantic.dev/2.12/v/extra_forbidden

'Strict' mode helps catching variable errors, for example when you set a string when a number (float) is expected:

>>> cv = ps.CyclicVoltammetry(scanrate='1.0')
ValidationError: 1 validation error for CyclicVoltammetry
scanrate
  Input should be a valid number [type=float_type, input_value='1.0', input_type=str]
    For further information visit https://errors.pydantic.dev/2.12/v/float_type

It also prevents setting non-existant attributes:

>>> cv.scanreat=1.0
ValueError: "CyclicVoltammetry" object has no field "scanreat"

Or unexpected values:

>>> cp = ps.ChronoPotentiometry(applied_current_range='1GA')
ValidationError: 1 validation error for ChronoPotentiometry
applied_current_range
  Input should be '100pA', '1nA', ... or '1A' [type=literal_error, input_value='1GA', input_type=str]
    For further information visit https://errors.pydantic.dev/2.12/v/literal_error

Starting a measurement

For further information on how to run a measurement: