clophfit.prtecan.parsers#

Prtecan/prtecan.py.

Classes#

Metadata

Represents the value of a metadata dictionary.

Functions#

`read_xls`(path)	Read first sheet of an xls file.
`lookup_listoflines`(…)	Lookup line numbers (row index) where given pattern occurs.
`strip_lines`(lines)	Remove empty fields/cells from lines read from a csv file.
`extract_metadata`(lines)	Extract metadata into both Tecanfile and Labelblock.
`merge_md`(mds)	Merge a list of metadata dict if the key value is the same in the list.
`calculate_conc`(additions, conc_stock[, conc_ini])	Calculate concentration values.
`dilution_correction`(additions)	Apply dilution correction.

Module Contents#

clophfit.prtecan.parsers.read_xls(path)#

Read first sheet of an xls file.

Parameters:: path (Path) – Path to .xls file.
Returns:: Lines as list_of_lines.
Return type:: list[list[str | int | float]]

clophfit.prtecan.parsers.lookup_listoflines(csvl: list[list[str]], pattern: str, col: int) → list[int]#

clophfit.prtecan.parsers.lookup_listoflines(csvl: list[list[str | int | float]], pattern: str = 'Label: Label', col: int = 0) → list[int]

Lookup line numbers (row index) where given pattern occurs.

Parameters:

csvl (list[list[str | int | float]] | list[list[str]]) – Lines (list_of_lines) of a csv/xls file.
pattern (str) – Pattern to be searched (default=”Label: Label”).
col (int) – Column to search (default=0).

Returns:

Row/line index for all occurrences of pattern. Empty list for no occurrences.

Return type:

list[int]

clophfit.prtecan.parsers.strip_lines(lines)#

Remove empty fields/cells from lines read from a csv file.

Parameters:: lines (list[list[str | int | float]]) – Lines (list_of_lines) that are a list of fields, typically from a csv/xls file.
Returns:: Lines (list_of_lines) removed from blank cells.
Return type:: list[list[str | int | float]]

Examples

>>> lines = [
...     ["Shaking (Linear) Amplitude:", "", "", "", 2, "mm", "", "", "", "", ""]
... ]
>>> strip_lines(lines)
[['Shaking (Linear) Amplitude:', 2, 'mm']]

class clophfit.prtecan.parsers.Metadata#

Represents the value of a metadata dictionary.

Parameters:: value (int | str | float | None) – The value for the dictionary key.

unit: collections.abc.Sequence[str | float | int] | None = None#: The first element represents the unit, while the following elements are only listed.

clophfit.prtecan.parsers.extract_metadata(lines)#

Extract metadata into both Tecanfile and Labelblock.

From a list of stripped lines takes the first field as the key of the metadata dictionary, remaining fields goes into a list of values with the exception of Label ([str]) and Temperature ([float]).

Parameters:: lines (list[list[str | int | float]]) – Lines (list_of_lines) that are a list of fields, typically from a csv/xls file.
Returns:: Metadata for Tecanfile or Labelblock.
Return type:: dict[str, Metadata]

Examples

>>> lines = [
...     ["Shaking (Linear) Amplitude:", "", "", "", 2, "mm", "", "", "", "", ""]
... ]
>>> extract_metadata(lines)
{'Shaking (Linear) Amplitude:': Metadata(value=2, unit=['mm'])}

>>> lines = [["", "Temperature: 26 °C", "", "", "", "", "", "", "", "", ""]]
>>> extract_metadata(lines)
{'Temperature': Metadata(value=26.0, unit=['°C'])}

>>> lines = [["Excitation Wavelength", "", "", "", 400, "nm", "", "", "", "", ""]]
>>> extract_metadata(lines)
{'Excitation Wavelength': Metadata(value=400, unit=['nm'])}

>>> lines = [["Label: Label1", "", "", "", "", "", "", "", "", "", "", "", ""]]
>>> extract_metadata(lines)
{'Label': Metadata(value='Label1', unit=None)}

>>> lines = [["Mode", "", "", "", "Fluorescence Top Reading", "", "", "", "", ""]]
>>> extract_metadata(lines)["Mode"].value
'Fluorescence Top Reading'

clophfit.prtecan.parsers.merge_md(mds)#

Merge a list of metadata dict if the key value is the same in the list.

Parameters:: mds (list[dict[str, Metadata]])
Return type:: dict[str, Metadata]

clophfit.prtecan.parsers.calculate_conc(additions, conc_stock, conc_ini=0.0)#

Calculate concentration values.

additions[0]=vol_ini; Stock concentration is a parameter.

Parameters:

additions (Sequence[float]) – Initial volume and all subsequent additions.
conc_stock (float) – Concentration of the stock used for additions.
conc_ini (float) – Initial concentration (default=0).

Returns:

Concentrations as vector.

Return type:

ArrayF

clophfit.prtecan.parsers.dilution_correction(additions)#

Apply dilution correction.

Parameters:: additions (list[float]) – List of initial volume (index=0) followed by all additions.
Returns:: Dilution correction vector.
Return type:: ArrayF
Raises:: ValueError – If additions list is empty or if initial volume is zero.