File¶
lumicks.pylake.File
- class File(filename, *, rgb_to_detectors=None)¶
A convenient HDF5 file wrapper for reading data exported from Bluelake
- Parameters:
filename (str | os.PathLike) – The HDF5 file to open in read-only mode
rgb_to_detectors (Dict[Color, str]) – Dictionary that maps RGB colors to a photon detector channel (either photon counts, or photon time tags)
Examples
from lumicks import pylake file = pylake.File("example.h5") file.force1x.plot() file.kymos["name"].plot() # Open with custom detector mapping file = pylake.File("example.h5", rgb_to_detectors={"Red": "Detector 1", "Green": "Detector 2", "Blue": "Detector 3"})
- __getitem__(item)¶
Return a subgroup or a bluelake timeline channel
- save_as(filename, compression_level=5, omit_data=None, *, crop_time_range=None, verbose=True)¶
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 | os.PathLike) – Output file name.
compression_level (int) – Compression level for gzip compression (default: 5).
omit_data (str or iterable of str, optional) – Which data sets to omit. Should be a set of h5 paths (e.g. {“Force HF/Force 1y”}).
fnmatchpatterns are used to specify which fields to omit, which means you can use wildcards as well (see examples below).crop_time_range (tuple of np.int64, optional) – Specify a time interval to crop to (tuple of a start and stop time). Interval must be specified in nanoseconds since epoch (the same format as timestamps).
verbose (bool, optional) – Print verbose output. Default: True.
Examples
import lumicks.pylake as lk file = lk.File("example.h5") # Saves a file with a high compression level file.save_as("smaller.h5", compression_level=9) # Omit high frequency force data. file.save_as("no_hf.h5", omit_data="Force HF/*") # Omit Force 1y data file.save_as("no_hf.h5", omit_data="*/Force 1y") # Omit Force 1y and 2y data file.save_as("no_hf.h5", omit_data=("*/Force 1y", "*/Force 2y")) # Omit high frequency force data for channel 1y file.save_as("no_1y.h5", omit_data="Force HF/Force 1y") # Omit Scan "1" file.save_as("no_scan_1.h5", omit_data="Scan/1") # Save only the region that contains the kymograph `kymo1`. kymo = file.kymos["kymo1"] file.save_as("only_kymo.h5", crop_time_range=(kymo.start, kymo.stop))