File

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()

__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

property bluelake_version: str

The version of Bluelake which exported this file

property description: str

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

property experiment: str

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

property export_time: int

The moment this file was exported

property fdcurves: Dict[str, lumicks.pylake.fdcurve.FdCurve]

FdCurves stored in the file

property format_version: int

The version of the Bluelake-specific HDF5 file structure

property guid: str

An ID which uniquely identifies each exported file

property kymos: Dict[str, lumicks.pylake.kymo.Kymo]

Kymos stored in the file

property markers: Dict[str, lumicks.pylake.marker.Marker]

Markers stored in the file

property point_scans: Dict[str, lumicks.pylake.scan.Scan]

Point Scans stored in the file

property scans: Dict[str, lumicks.pylake.scan.Scan]

Confocal Scans stored in the file