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FCS-analysis / PyCorrFit

data analysis and fitting software for fluorescence correlation spectroscopy (FCS)
pycorrfit.craban.de
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Intensity information missing in Page Info window and fitting window for .pt3 files #118

Closed kyseerentant closed 7 years ago

kyseerentant commented 9 years ago

When loading .pt3 files, the intensity information in both, the fitting window and page info window are missing. Also, Tools--> Trace view displays a blank page.

Identical behaviour was observed with PyCorrFit 0.8.7 and 0.8.8 on Windows and Linux. Are there any limitations on which .pt3 file versions are supported?

paulmueller commented 9 years ago

The .pt3 file support is implemented in https://github.com/dwaithe/FCS_point_correlator by @dwaithe. I don't know if the intensity information is accessible right now.

Dominic (@dwaithe), could you please point me in the right direction?

dwaithe commented 9 years ago

Hi, Sorry for delay, I was at a conference. kyseerentant if you just want to view a time-trace you can use the software at: https://github.com/dwaithe/FCS_point_correlator It depends what you want to do with it.

This is for you Paul: It is possible to display the intensity information but it requires some binning.

In the file 'correlation_objects.py' you find the lines:

Time series of photon counts. For visualisation.

self.timeSeries1,self.timeSeriesScale1 = delayTime2bin(np.array(self.trueTimeArr)/1000000,np.array(self.subChanArr),self.ch_present[0],self.photonCountBin)

Converts to counts per

self.kcount_CH1 = np.average(self.timeSeries1)

The function delayTime2bin is in the file 'correlation_methods.py'. This takes the raw TCSPC data and bins it so that you can establish the intensity over-time. Furthermore if you average the output timeSeries you can get average counts, and this will be in the units of your bin size.

Hope that helps. Best, Dom.

paulmueller commented 9 years ago

Yes, thanks for the detailed answer. It should be no problem to implement this in PyCorrFit as well.

paulmueller commented 8 years ago

@kyseerentant The next version of PyCorrFit will incorporate the visualization of the trace. I am not certain if I implemented the normalization correctly. Could you provide me with a pt3 file whose average intensity you know? Then I can make sure the import works correctly.

paulmueller commented 7 years ago

Could anyone please verify that this is working correctly now? ~https://ci.appveyor.com/api/buildjobs/sqrirfel2eub2wyt/artifacts/Output%2FPyCorrFit_1.0.0_win_32bit_setup.exe~ https://ci.appveyor.com/api/buildjobs/vi39tn3qkpnfb82h/artifacts/Output%2FPyCorrFit_1.0.0_win_32bit_setup.exe

paulmueller commented 7 years ago

@kyseerentant Could you please verify that this is working correctly now?

https://ci.appveyor.com/api/buildjobs/q4huhmgwvtnvo9vb/artifacts/Output%2FPyCorrFit_1.0.0_win_64bit_setup.exe

kyseerentant commented 7 years ago

@paulmueller Thanks Paul for implementing the suggested feature and sorry for not getting back to you earlier. I just checked a couple of old .pt3 files and the traces+ average intensities computed by PyCorrFit match the ones in SymPhoTime.

paulmueller commented 7 years ago

Thanks!