An example of code cell for PIE with 2 color detection and 2 polarizations would be great

[SefAnna]

Hi,

I would like to convert a .ptu file. We have HydraHarp400, PIE with 2 color detection and 2 polarizations. When I run the notebook 'Convert PicoQuant ns-ALEX files to Photon-HDF5.ipynb' directly as it is for my file, the photons are not plotted. Only the PIE scheme is in the plot and it says that the 'data has no positive values and therefore cannot be log-scaled'. In the last cell when loading the data I see 4 detectors which fits, and the 127 detector explained in the most recent closed issue. The HDF5 file is also generated, but I doubt it will work for further H2MM analysis.

As far as I understood I need to give more details about my file. I never used python and notebooks before. It would be great to have an example of '3. Load the data' for PIE with 2 color detection and 2 polarizations so I could adjust it to my setup.

I would be grateful for any help,
Thank you!

[jacrossley]

Hey @SefAnna

I'm sure you fixed this by now, but for anyone else please refer to this comment by tritemio #27 (comment) which outlines how to convert files with different laser / detector combinations. From the description of your set up you want to be using the 'generic' measurement type with the following parameters (depending on what channels your detectors are wired up to)

/setup/excitation_cw = [False, False]
/setup/lifetime = True
/setup/num_spectral_ch = 2
/setup/num_split_ch = 1
/setup/num_polarization_ch = 2

/photon_data/measurement_specs/detectors_specs/
    polarization_ch1 = [0, 2]
    polarization_ch2 = [1, 3]
    spectral_ch1 = [0, 1]
    spectral_ch2 = [2, 3]

Thanks,
Joel