lumicks.pylake.File¶

class File(filename)¶

A convenient HDF5 file wrapper for reading data exported from Bluelake

Parameters:	filename : str The HDF5 file to open in read-only mode

Examples

from lumicks import pylake

file = pylake.File("example.h5")
file.force1x.plot()
file.kymos["name"].plot()

__init__(filename)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(filename)	Initialize self.
`from_h5py`(h5py_file)	Directly load an existing `h5py.File`
`save_as`(filename[, compression_level, omit_data])	Write a modified h5 file to disk.

Attributes

`SUPPORTED_FILE_FORMAT_VERSIONS`
`blue_photon_count`
`blue_photon_time_tags`
`bluelake_version`	The version of Bluelake which exported this file
`corrected_force1x`
`corrected_force2x`
`description`	The description of the measurement as entered by the user in Bluelake
`distance1`
`distance2`
`downsampled_force1`
`downsampled_force1x`
`downsampled_force1y`
`downsampled_force2`
`downsampled_force2x`
`downsampled_force2y`
`downsampled_force3`
`downsampled_force3x`
`downsampled_force3y`
`downsampled_force4`
`downsampled_force4x`
`downsampled_force4y`
`experiment`	The name of the experiment as entered by the user in Bluelake
`export_time`	The moment this file was exported
`fdcurves`
`force1x`
`force1y`
`force2x`
`force2y`
`force3x`
`force3y`
`force4x`
`force4y`
`format_version`	The version of the Bluelake-specific HDF5 file structure
`green_photon_count`
`green_photon_time_tags`
`guid`	An ID which uniquely identifies each exported file
`kymos`
`markers`
`point_scans`
`red_photon_count`
`red_photon_time_tags`
`scans`

__getitem__(item)¶: Return a subgroup or a bluelake timeline channel

classmethod from_h5py(h5py_file)¶: Directly load an existing h5py.File

save_as(filename, compression_level=5, omit_data={})¶

Write a modified h5 file to disk.

When transferring data, it can be beneficial to omit some channels from the h5 file, or use a higher compression ratio. High frequency channels tend to take up a lot of space and aren’t always necessary for every single analysis. It is also worth mentioning that Bluelake exports files at compression level 1 for performance reasons, so this function can help reduce the file size even when no data is omitted.

Parameters:	filename : str Output file name. compression_level : int Compression level for gzip compression (default: 5). omit_data : Set[str] Which data sets to omit. Should be a set of h5 paths (e.g. {“Force HF/Force 1y”}). `fnmatch` patterns are used to specify which fields to omit, which means you can use wildcards as well (see examples below).

Examples

import lumicks.pylake as lk

file = lk.File("example.h5")
file.save_as("smaller.h5", compression_level=9)  # Saves a file with a high compression level

file.save_as("no_hf.h5", omit_data={"Force HF/*"})  # Omit high frequency force data.

file.save_as("no_hf.h5", omit_data={"*/Force 1y"})  # Omit Force 1y data

file.save_as("no_1y.h5", omit_data={"Force HF/Force 1y"})  # Omit high frequency force data for channel 1y

bluelake_version¶: The version of Bluelake which exported this file

description¶: The description of the measurement as entered by the user in Bluelake

experiment¶: The name of the experiment as entered by the user in Bluelake

export_time¶: The moment this file was exported

format_version¶: The version of the Bluelake-specific HDF5 file structure

guid¶: An ID which uniquely identifies each exported file