Module loader

This module contains functions to load each supported data format. Each loader function loads data from a third-party formats into a python dictionary which has the structure of a Photon-HDF5 file. These dictionaries can be passed to phconvert.hdf5.save_photon_hdf5() to save the data in Photon-HDF5 format.

The loader module contains high-level functions which “fill” the dictionary with the appropriate arrays. The actual decoding of the input binary files is performed by low-level functions in other modules (smreader.py, pqreader.py, bhreader.py). When trying to decode a new file format, these modules can provide useful examples.

phconvert.loader.nsalex_bh(filename_spc, donor=4, acceptor=6, alex_period_donor=(10, 1500), alex_period_acceptor=(2000, 3500), excitation_wavelengths=(5.32e-07, 6.35e-07), detection_wavelengths=(5.8e-07, 6.8e-07), allow_missing_set=False, tcspc_num_bins=None, tcspc_unit=None)

Load a .spc and (optionally) .set files for ns-ALEX and return 2 dict.

The first dictionary can be passed to the phconvert.hdf5.save_photon_hdf5() function to save the data in Photon-HDF5 format.

Returns:the first contains the main photon data (timestamps, detectors, nanotime, ...); the second contains the raw data from the .set file (it can be saved in a user group in Photon-HDF5).
Return type:Two dictionaries
phconvert.loader.nsalex_ht3(filename, donor=0, acceptor=1, alex_period_donor=(150, 1500), alex_period_acceptor=(1540, 3050), excitation_wavelengths=(5.23e-07, 6.28e-07), detection_wavelengths=(5.8e-07, 6.8e-07))

Load a .ht3 file containing ns-ALEX data and return a dict.

This dictionary can be passed to the phconvert.hdf5.save_photon_hdf5() function to save the data in Photon-HDF5 format.

phconvert.loader.nsalex_pt3(filename, donor=0, acceptor=1, alex_period_donor=(150, 1500), alex_period_acceptor=(1540, 3050), excitation_wavelengths=(5.23e-07, 6.28e-07), detection_wavelengths=(5.8e-07, 6.8e-07))

Load a .pt3 file containing ns-ALEX data and return a dict.

This dictionary can be passed to the phconvert.hdf5.save_photon_hdf5() function to save the data in Photon-HDF5 format.

phconvert.loader.nsalex_t3r(filename, donor=0, acceptor=1, alex_period_donor=(150, 1500), alex_period_acceptor=(1540, 3050), excitation_wavelengths=(5.23e-07, 6.28e-07), detection_wavelengths=(5.8e-07, 6.8e-07))

Load a .t3r file containing ns-ALEX data and return a dict.

This dictionary can be passed to the phconvert.hdf5.save_photon_hdf5() function to save the data in Photon-HDF5 format.

phconvert.loader.usalex_sm(filename, donor=0, acceptor=1, alex_period=4000, alex_offset=750, alex_period_donor=(2850, 580), alex_period_acceptor=(930, 2580), excitation_wavelengths=(5.32e-07, 6.35e-07), detection_wavelengths=(5.8e-07, 6.8e-07), software='LabVIEW Data Acquisition usALEX')

Load a .sm us-ALEX file and returns a dictionary.

This dictionary can be passed to the phconvert.hdf5.save_photon_hdf5() function to save the data in Photon-HDF5 format.