In situ NMR Spectroscopy¶

NMR module for in situ data.

InsituBlock ¶

Bases: DataBlock

This datablock processes in situ NMR data from an input .zip file containing two specific directories:

NMR Data Directory: Contains multiple Bruker in-situ NMR experiment datasets.
Echem Data Directory: Contains echem data files in .mpr format.

If multiple echem experiments are present, their filenames must include GCPL.

Attributes:

Name	Type	Description
`accepted_file_extensions`
`blocktype`
`defaults`
`description`
`name`
`plot_functions`
`version`	`str`

accepted_file_extensions ¶

accepted_file_extensions = ('.zip',)

blocktype ¶

blocktype = 'insitu-nmr'

defaults ¶

defaults = {'ppm1': 0.0, 'ppm2': 0.0, 'start_exp': 1, 'end_exp': None, 'step_exp': None, 'exclude_exp': None}

description ¶

description = __doc__

name ¶

name = 'NMR insitu'

plot_functions ¶

plot_functions

version ¶

version: str = __version__

count_experiments_in_nmr_folder ¶

count_experiments_in_nmr_folder(file_path: Path, nmr_folder_name: str) -> int

Count the number of experiments in the selected NMR folder.

generate_insitu_nmr_plot ¶

generate_insitu_nmr_plot(file_path: str | Path | None = None, link_plots: bool = True)

Generate combined NMR and electrochemical plots using the operando-style layout.

This method coordinates the creation of various plot components and combines them into a unified visualization.

Parameters:

Name	Type	Description	Default
`file_path`	`str \| Path \| None`	Optional path to the zip file containing NMR and echem data, removing the need to lookup in a database.	`None`
`link_plots`	`bool`	If True, links the plots for synchronized interaction, otherwise time can be saved by leaving them unlinked.	`True`

get_available_folders ¶

get_available_folders(file_path: Path) -> List[str]

Extract and return a list of available folders from the zip file.

This method opens the zip file identified by file_id, extracts the main folder and its subfolders, and returns a sorted list of subfolder names.

Parameters:

Name	Type	Description	Default
`file_path`	`Path`	Path to the zip file from which to extract folder names.	required

Returns:

Type	Description
`List[str]`	List[str]: Sorted list of subfolder names, or empty list if file not found or on error.

process_and_store_data ¶

process_and_store_data(file_path: str | Path) -> tuple[DataFrame, DataFrame]

Process insitu NMR and electrochemical data and store results.

This method validates input parameters, extracts data from the specified folders, and stores the processed data in the block's data attribute.

Returns:

Type	Description
`tuple[DataFrame, DataFrame]`	A tuple containing NMR and electrochemical data as dataframes.

process_datalab_data ¶

process_datalab_data(api_url: str, item_id: str, folder_name: str, nmr_folder_name: str, echem_folder_name: str, start_at: int = 1, end_at: Optional[int] = None, step: Optional[int] = None, exclude_exp: Optional[List[int]] = None) -> Dict

Process NMR spectroscopy data from Datalab API.

Parameters:

Name	Type	Description	Default
`api_url`	`str`	URL of the Datalab API	required
`item_id`	`str`	ID of the item to process	required
`folder_name`	`str`	Base folder name	required
`nmr_folder_name`	`str`	Folder containing NMR experiments	required
`echem_folder_name`	`str`	Folder containing Echem data	required
`start_at`	`int`	Starting experiment number (default: 1)	`1`
`exclude_exp`	`Optional[List[int]]`	List of experiment numbers to exclude (default: None)	`None`

Returns:

Type	Description
`Dict`	Dictionary containing processed NMR and electrochemical data

process_local_data ¶

process_local_data(folder_name: str, nmr_folder_name: str, echem_folder_name: str, start_at: int = 1, end_at: Optional[int] = None, step: Optional[int] = None, exclude_exp: Optional[List[int]] = None) -> Dict

Process NMR spectroscopy data from local zip files.

Parameters:

Name	Type	Description	Default
`folder_name`	`str`	Path to the ZIP file or folder containing the NMR data.	required
`nmr_folder_name`	`str`	Name of the folder inside `folder_name` containing NMR experiments.	required
`echem_folder_name`	`str`	Name of the folder inside `folder_name` containing electrochemical data.	required
`start_at`	`int`	Starting experiment number (default: 1).	`1`
`exclude_exp`	`Optional[List[int]]`	List of experiment numbers to exclude (default: None).	`None`

Returns:

Name	Type	Description
`Dict`	`Dict`	Dictionary containing processed NMR and electrochemical data.