clophfit.prenspire#

Parse EnSpire files and optionally build titrations using a note file.

Exceptions:

`CsvLineError`	Exception raised when the lines list has issues.
`ManyLinesFoundError`	Raised when there are multiple lines containing a specified search string.

Classes:

`EnspireFile`(file[, verbose])	Read an EnSpire-generated csv file.
`Note`(fpath[, verbose])	Read and processes a Note csv file.

Functions:

verbose_print(verbose)

Return print function when verbose output is True.

exception clophfit.prenspire.CsvLineError#: Exception raised when the lines list has issues.

class clophfit.prenspire.EnspireFile(file, verbose=0)#

Read an EnSpire-generated csv file.

Read the files and check the formats. extract_measurements(): create the measurements dictionary structure storing all data and metadata (description of measurement).

Parameters:

file (Path) – Path to the EnSpire csv file
verbose (int) – Level of verbosity; 0 is silent, higher values are more verbose (default=0).

Raises:

Exception – If unexpected format is found.

Examples

>>> from clophfit.prenspire import EnspireFile
>>> from pathlib import Path
>>> ef = EnspireFile(Path("tests/EnSpire/h148g-spettroC.csv"), verbose=0)
>>> ef.measurements["A"]["lambda"][2]
274.0

Attributes:

`file`
`verbose`
`metadata`	General metadata.
`measurements`	Spectra and metadata for each label, such as "MeasB".
`wells`	List of exported wells.

Methods:

export_measurements([out_dir])

Save measurements, metadata and plots into out_dir.

file: Path#

verbose: int = 0#

metadata: dict[str, str | list[str]]#: General metadata.

measurements: dict[str, Any]#: Spectra and metadata for each label, such as “MeasB”.

wells: list[str]#: List of exported wells.

export_measurements(out_dir=PosixPath('Meas-0.12.0'))#

Save measurements, metadata and plots into out_dir.

Return type:: None
Parameters:: out_dir (Path)

exception clophfit.prenspire.ManyLinesFoundError#: Raised when there are multiple lines containing a specified search string.

class clophfit.prenspire.Note(fpath, verbose=0)#

Read and processes a Note csv file.

This class is responsible for handling Experimental Note files that describe an EnSpire experiment collecting spectrum.

Parameters:

fpath (Path) – The path to the Experimental Note file to be processed.
verbose (int) – Level of verbosity; 0 is silent, higher values are more verbose (default=0).

Example

>>> from clophfit.prenspire import Note
>>> n = Note("tests/EnSpire/h148g-spettroC-nota.csv")
>>> n.wells[2]
'A03'

Attributes:

`fpath`
`verbose`
`wells`	A list of wells generated from the note file.
`titrations`	A list of titrations extracted from the note file.

Methods:

build_titrations(ef)

Extract titrations from the given ef (_note file like: <well, pH, Cl>).

fpath: Path#

verbose: int = 0#

wells: list[str]#: A list of wells generated from the note file.

titrations: dict[Any, Any]#: A list of titrations extracted from the note file.

build_titrations(ef)#

Extract titrations from the given ef (_note file like: <well, pH, Cl>).

Return type:: None
Parameters:: ef (EnspireFile)

clophfit.prenspire.verbose_print(verbose)#

Return print function when verbose output is True.

Return type:: BuiltinMethodType | Callable[..., None]
Parameters:: verbose (int)

clophfit.prenspire#

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