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tritemio / FRETBursts

Burst analysis software for smFRET. **Moved to OpenSMFS organization**
https://github.com/OpenSMFS/FRETBursts
GNU General Public License v2.0
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Hdf5 file for Alex #58

Closed DanielisRutkauskas closed 7 years ago

DanielisRutkauskas commented 7 years ago

notebook and data.zip

Hi,

I am trying to process some data (data and notebook attached) using ALEX-related functions. However, I am not able to get past the bpl.plot_alternation_hist(). It all works, however, on the example data file 0023uLRpitc_NTP_20dT_0.5GndCl.hdf5. So the question is: what is so specific to the data file that it is recognized as of ALEX? Also: why doesn't the data loaded from my file contain attribute d.ph_times_t but instead d.ph_times_m which should only be present after applying loader.alex_apply_period()?

Unrelated issue: after updating to 0.6.3, the combination filename = OpenFileDialog() d = loader.photon_hdf5(filename) does not work. What is the reason?

Thank you,

Danielis

tritemio commented 7 years ago

@DanielisRutkauskas, looking at your file it says measurement_type = 'smFRET', (in /photon_data/measurements_specs). This means that the measurement is a single-laser smFRET measurement using two detectors.

If your measurement is smFRET-usALEX, i.e. is using two alternated CW lasers and two detectors, then your should use measurement_type = 'smFRET-usALEX' (see docs here). When using this measurement type you have a new mandatory field that is alex_period containing the duration of the alternation period in timestamp units. It is also suggested to add:

so that all the parameters of the alternation are fully specified and your don't need to adjust them during the analysis.

For the OpenFileDialog issue, can you please open a new issue posting the error?

DanielisRutkauskas commented 7 years ago

Reassembled the HDF5 file according to your recommendations. It worked! Thank you.

tritemio commented 7 years ago

Great, thanks for reporting back!