Code reference¶

class bmlab.file.BrillouinFile(path)[source]¶

Load a HDF file with Brillouin microscopy data.

Parameters: path (str) – path of the file to load
Raises: OSError – when trying to open non-existing or bad file

get_repetition(repetition_key)[source]¶

Get a repetition from the data file based on given key.

Parameters: repetition_key (str) – key to identify the repetition in the Brillouin group
Returns: out – the repetition
Return type: Repetition

repetition_count()[source]¶

Get the number of repetitions in the data file.

Returns: out – Number of repetitions in the data file
Return type: int

repetition_keys()[source]¶

Returns list of keys for the various repetitions in the file.

Returns: out
Return type: list of str

class bmlab.file.Repetition(repetition_group)[source]¶

Creates a repetition from the corresponding group of a HDF file.

Parameters: repetition_group (HDF group) – The HDF group representing a Repetition. Consists of payload, calibration and background.

class bmlab.file.Payload(payload_group)[source]¶

Creates a payload representation from the corresponding group of a HDF file.

Parameters: payload_group (HDF group) – The payload of a repetition, basically a set of images

get_image(image_key)[source]¶

Returns the image from the payload for given key.

Parameters: image_key (str) – Key for the image.
Returns: out – Array representing the image.
Return type: numpy.ndarray

image_keys()[source]¶

Returns the keys of the images stored in the payload.

Returns: out – Keys of images in payload.
Return type: list of str

class bmlab.file.Calibration(calibration_group)[source]¶

Creates a calibration representation from the corresponding group of a HDF file.

Parameters: calibration_group (HDF group) – Calibration data of a repetition from an HDF file.

Module for interacting with files containing Brillouin microscopy data.

NOTE: Ideally, the users of bmlab should not have to know about the file format in which the data are stored. So, if possible, do not expose HDF objects to the outside (like BMicro).

exception bmlab.file.BadFileException[source]¶