Electrochemistry

CycleBlock ¶

CycleBlock(item_id: str | None = None, collection_id: str | None = None, init_data: dict | None = None, unique_id: str | None = None)

Bases: DataBlock

A data block for processing electrochemical cycling data.

This class that contains functions for processing dataframes created by navani from raw cycler files and plotting them with Bokeh.

Navani documentation: be-smith.github.io/navani/

The file formats currently supported are:

Biologic (.mpr) - requires galvani echemdata/galvani
Arbin (.res, .xls and .xlsx) - the .res format requires galvani echemdata/galvani
Neware (.nda, .ndax)
Ivium (.txt)
Lanhe/Lande (.xls, .xlsx) - most formats, certain exports may not work depending on the software version or settings
Preprocessed (.csv) - CSV files with appropriate columns ['Capacity', 'Voltage', 'half cycle', 'full cycle', 'Current', 'state']

Parameters:

Name	Type	Description	Default
`item_id`	`str \| None`	The item to which the block is attached, or	`None`
`collection_id`	`str \| None`	The collection to which the block is attached.	`None`
`init_data`	`dict \| None`	A dictionary of data to initialise the block with.	`None`
`unique_id`	`str \| None`	A unique id for the block, used in the DOM and database.	`None`

Attributes:

Name	Type	Description
`accepted_file_extensions`		A list of file extensions that the block will attempt to read.
`block_db_model`
`block_id`
`blocktype`		A short (unique) string key specifying the type of block.
`data`
`defaults`	`dict[str, Any]`	Any default values that should be set if they are not
`description`		A longer description outlining the purpose and capability
`name`		The human-readable block name specifying which technique
`plot_functions`		A list of methods that will generate plots for this block.
`version`	`str`	The implementation version of this particular block.

accepted_file_extensions ¶

accepted_file_extensions = ('.mpr', '.txt', '.xls', '.xlsx', '.res', '.nda', '.ndax', '.csv')

A list of file extensions that the block will attempt to read.

block_db_model ¶

block_db_model = DataBlockResponse

block_id ¶

block_id = unique_id or generate_random_id()

blocktype ¶

blocktype = 'cycle'

A short (unique) string key specifying the type of block.

data ¶

data = {'item_id': item_id, 'collection_id': collection_id, 'blocktype': blocktype, 'block_id': block_id, None: defaults}

defaults ¶

defaults: dict[str, Any] = {'p_spline': 5, 's_spline': 5, 'win_size_2': 101, 'win_size_1': 1001, 'derivative_mode': None}

Any default values that should be set if they are not supplied during block init.

description ¶

description = "This block can plot data from electrochemical cycling experiments from many different cycler's file formats.\n    The file formats currently supported are:\n\n    - Biologic (.mpr)\n    - Arbin (.res, .xls and .xlsx)\n    - Neware (.nda, .ndax)\n    - Ivium (.txt)\n    - Lanhe/Lande (.xls, .xlsx)\n    - Preprocessed (.csv) (previously extracted by navani or other tools)\n\n    "

A longer description outlining the purpose and capability of the block.

name ¶

name = 'Electrochemical cycling'

The human-readable block name specifying which technique or file format it pertains to.

plot_functions ¶

plot_functions

A list of methods that will generate plots for this block.

version ¶

version: str = __version__

The implementation version of this particular block.

event_names ¶

event_names() -> set[str]

Return a list of event names supported by this block.

events_by_name ¶

events_by_name() -> dict[str, Callable]

Returns a dict of registered events for this block.

from_web ¶

from_web(data: dict)

Initialise the block state from data passed via web request with a given item, collection and block ID.

Parameters:

Name	Type	Description	Default
`data`	`dict`	The block data to initialiaze the block with.	required

null_event ¶

null_event(**kwargs)

A null debug event that does nothing but logs its kwargs and overwrites the data dict with the args.

plot_cycle ¶

plot_cycle()

Plots the electrochemical cycling data from the file ID provided in the request.

process_events ¶

process_events(events: list[dict] | dict)

Handle any supported events passed to the block.

to_db ¶

to_db() -> dict

returns a dictionary with the data for this block, ready to be input into mongodb

to_web ¶

to_web() -> dict[str, Any]

Returns a JSON serializable dictionary to render the data block on the web.

update_from_web ¶

update_from_web(data: dict)

Update the block with validated data received from a web request. Will strip any fields that are "computed" or otherwise not controllable by the user.

Parameters:

Name	Type	Description	Default
`data`	`dict`	A dictionary of data to update the block with.	required