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Photon-HDF5 / phconvert

Convert Beker&Hickl, PicoQuant and other formats to Photon-HDF5
http://photon-hdf5.github.io/phconvert
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Decoding spatial features of HydraHarpT3V2 data #29

Closed jrivers96 closed 5 years ago

jrivers96 commented 6 years ago

I can't seem to get spatial features from the detections, only a 1D array. The meta data clearly shows a 256 x 256 x 10 array with 1560 time points per pixel.

image

The below shows a pprint on some of the meta fields showing spatial dimensions for the data.

image

jrivers96 commented 6 years ago

FYI @apoliakov

tritemio commented 6 years ago

load_ptu returns 3 arrays (timestamps, detectors, nanotimes) and a dictionary (meta). In meta you find a few items such as measurement duration, but for the most part it is just a direct mapping of the header data. If the header contains the information you need, you should be able to extract it from meta['tags'].

That said, you have only 5 detectors IDs. I'm guessing this some kind of scanning confocal data? In this case you probably have markers in your arrays to mark the line, and frame end. We currently have no support for reconstructing images or volumes from this data. You need to do it manually from the arrays.

snizzleorg commented 6 years ago

Please check the principles of TCSPC available for example here: https://www.picoquant.com/images/uploads/page/files/7253/technote_tcspc.pdf (specifically page 12). As @tritemio pointed out, the markers coming from your scanner are interlaced with the photons and are needed for reconstructing the image out of your photo data stream.