prsctrl.data.prsdata.PrsData

class PrsData(data_path: str | None = None, data: dict | None = None, metadata: dict | None = None, data_name: str | None = None, file_mode='r', exp_mode=None)

Bases: Data

Class managing data and metadata. Can be initialized from data directly, or from a file or directory path.

data is a dictionary with:

• key: wavelength as int or float, or “offset_<name>”

• value: dictionary with:

  • key: quantity as string: [“lock-in-R_raw”, “lock-in-theta”, “slock-in-theta”, “lock-in-aux_raw”, … ]

  • value: quantity value, or array if “_raw”

Keys for a given wavelength/offset:

• dI: delta I, the change in reflectance/transmittance/absorbance. (This is the signal amplitude “R” from the lock-in)

• I: the baseline reflectivity. (DC signal measured using Aux In of the lock-in)

• theta: phase

• theta-corr: theta between [-90, 90], assuming |theta| > 90 simply means lock-in-R is negative

• lock-in-R: magnitude value of lock-in

• lock-in-theta: phase value of lock-in

• lock-in-aux: value if lock-in aux port

• <qty>_raw: The raw measurement data (all individual samples)

• s<qty>: Standard error of the quantity

Methods

get_column_color
get_column_label
get_column_label_with_unit
get_column_scale
get_column_tex_label
get_column_tex_label_with_unit
get_column_tex_label_with_unit_and_scale
get_column_tex_unit
get_column_unit
get_csv
get_for_wl	Return the value for <key> at a given wavelength <wl> (in nanometers)
get_spectrum_data	Return the spectral data for the specified keys and wavelengths as numpy array :param wavelengths: List of wavelengths, range of wavelenthgs (as tuple, with at least (min, max)), or None to use all wavelengths.
has_AC
has_DC
has_wavelengths
load_data_from_csv	Loads data from a single csv file.
load_data_from_dir	Load prs data from a directory path.
load_data_from_pkl	Loads data from a single pkl file. If the file is compressed with gzip, it must end with '.gz' extension. Parameters ---------- :param filepath Path to the file. :return data 2D numpy array with shape (n, 4) where n is the number of data points. metadata Dictionary with metadata.
plot_raw_for_wl	Plot raw data against index (time) for a particular wavelength.
remove_calculated_values	Delete all calculated data values
save_csv
save_csv_at
to_csv	Return a csv of the spectrum data as csv :param sep: csv separator :param columns: List of column names.
update_wavelengths
write_full_file	Write the entire data to a single pickle file in the data directory.
write_metadata
write_partial_file

Attributes

CALC_KEYS
OLD_KEYS
default_spectrum_columns
spectrum_columns_abs
spectrum_columns_reference
data_path	Absolute path to the data file or directory
dir_path	Absolute path to the data directory
dir_name	Name of the data directory

data_path

Absolute path to the data file or directory

dir_name: str

Name of the data directory

dir_path: str

Absolute path to the data directory

get_for_wl(wl, key) → float

Return the value for <key> at a given wavelength <wl> (in nanometers)

Parameters:

• wl – Wavelength in nm

• key – Key of the quantity to return.

if relative_time:

• I: the DC signal (measured by lock-in aux port and calculated from the “lock-in-aux_raw” values)

• dI: sqrt(dI-X^2 + dI-Y^2)

• dI-X: delta I = I * cos(theta) where I is the I value from the lock-in (peak-peak, calculated from the “lock-in-R_raw” values)

• dI-Y: delta I = I * sin(theta) where I is the I value from the lock-in (peak-peak, calculated from the “lock-in-R_raw” values)

• theta: the phase (calculated from the “lock-in-theta_raw” values)

• dI_I, dI-X_I, dI-Y_I: dI/I each

• lock-in-<key>: mean (error) value calculated from the “lock-in-<key>_raw” values

Returns:

float, or np.ndarray if a _raw value was requested

get_spectrum_data(wavelengths=None, columns=None, Es=None, transforms: list[Callable[[ndarray[tuple[Any, ...], dtype[_ScalarT]], list[str]], tuple[ndarray[tuple[Any, ...], dtype[_ScalarT]], list[str]]]] | None = None) → tuple[ndarray[tuple[Any, ...], dtype[_ScalarT]], list[str]]

Return the spectral data for the specified keys and wavelengths as numpy array :param wavelengths: List of wavelengths, range of wavelenthgs (as tuple, with at least (min, max)), or None to use all wavelengths. Conflicts with Es. :param Es: List of energies (eV), range of energies (as tuple, with at least (min, max)), or None to use all wavelengths. Conflicts with wavelengths :param columns: List of column keys, or None to use default_spectrum_columns. :param transforms: List of transformations to apply to the data :return: numpy.ndarray where the first index is the wavelength/index and the second is the keys/columns. (wavelength=0, <keys>…=1…)

static load_data_from_csv(filepath: str, mode=None, **csv_kw) → tuple[dict, dict]

Loads data from a single csv file. :param filepath: Path to the csv file.

static load_data_from_dir(dirpath: str) → tuple[dict, dict]

Load prs data from a directory path. If PREFER_LOAD_FROM_FULL_FILE is True, the data is loaded from the FULL_DATA_FILENAME, if it exists. Otherwise all data files with the PARTIAL_PREFIX are loaded and combined.

:param dirpath Path to the data directory :return data, metadata

classmethod load_data_from_pkl(filepath: str) → tuple[dict, dict]

Loads data from a single pkl file. If the file is compressed with gzip, it must end with ‘.gz’ extension. Parameters ———- :param filepath Path to the file. :return

data

2D numpy array with shape (n, 4) where n is the number of data points.

metadata

Dictionary with metadata.

plot_raw_for_wl(wl, what=['lock-in-R', 'lock-in-aux', 'lock-in-theta'], fig=None, axs=None, **plot_kw)

Plot raw data against index (time) for a particular wavelength.

remove_calculated_values()

Delete all calculated data values

to_csv(columns=None, sep=',')

Return a csv of the spectrum data as csv :param sep: csv separator :param columns: List of column names. If None, uses the default_spectrum_columns :return: csv as string

write_full_file(compress=False)

Write the entire data to a single pickle file in the data directory. :param compress: If True, file is compressed using gzip