Reading Photon-HDF5#

Example files can be found here

Download the file (might take a bit):

import requests
import pathlib

if not pathlib.Path('test_photon_file.hdf5').exists():
    r = requests.get('https://figshare.com/ndownloader/files/2182602')

    with open('test_photon_file.hdf5', 'wb') as f:
        f.write(r.content)
import h5rdmtoolbox as h5tbx
h5tbx.dump('test_photon_file.hdf5', collapsed=False)
http://photon-hdf5.org/
    • 2268.0 [] (float64)
      : [|S42] data=b'A demonstrative smFRET-nsALEX measurement.'
        : [|S12] data=b'Eitan Lerner'
        : [|S4] data=b'UCLA'
        : [|S19] data=b'2015-07-20 15:34:51'
        : [|S19] data=b'Antonino Ingargiola'
        : [|S4] data=b'UCLA'
        : [|S25] data=b'dsdna_d7_d17_50_50_1.hdf5'
        : [|S79] data=b'C:\\Data\\Antonio\\software\\src\\phconvert\\notebooks\\data\\dsdna_d7_d17_50_50_1.hdf5'
        : [|S11] data=b'Photon-HDF5'
        : [|S23] data=b'http://photon-hdf5.org/'
        : [|S3] data=b'0.4'
        : [|S9] data=b'phconvert'
        : [|S5] data=b'0.6.4'
        (9716848) [uint8]
        (9716848) [uint16]
        (9716848) [int64]
          (2) [int32]
          (2) [int32]
          40000000.0 [] (float64)
          : [|S13] data=b'smFRET-nsALEX'
            (1) [int32]
            (1) [int32]
          4096 [] (int32)
          6.0122042368e-08 [] (float64)
          1.4678233e-11 [] (float64)
          6.0122042368e-08 [] (float64)
        : [|S19] data=b'2014-03-25 15:58:14'
        : [|S24] data=b'dsdna_d7_d17_50_50_1.spc'
        : [|S78] data=b'C:\\Data\\Antonio\\software\\src\\phconvert\\notebooks\\data\\dsdna_d7_d17_50_50_1.spc'
        : [|S19] data=b'2015-01-24 08:24:34'
        : [|S19] data=b'Becker & Hickl SPCM'
        : [|S4] data=b'TE50'
        : [|S17] data=b'ATTO550, ATTO647N'
        2 [] (int32)
        : [|S33] data=b'50-50 mixture of two FRET samples'
        (2) [float64]
        (2) [uint8]
        (2) [float64]
        1 [] (uint8)
        1 [] (uint8)
        2 [] (int32)
        1 [] (int32)
        2 [] (int32)
        1 [] (int32)
        1 [] (int32)
            : [|S6] data=b'System'
            : [|S7] data=b'Unknown'
            : [|S93] data=b'Setup file made by system at the end of FIFO measurement with module SPC-630 (Ser.No. 3A0067)'
            : [|S10] data=b'2014-03-25'
            : [|S23] data=b'\x04SPC Setup Script File\x04'
            : [|S11] data=b'12 bits ADC'
            : [|S8] data=b'15:58:14'
            : [|S20] data=b'dsdna_d7+d17_50_50_1'
            : [|S8] data=b'2 872 M'
            1 [] (uint8)
            10 [] (int32)
            0 [] (int32)
            1 [] (uint8)
            13 [] (int32)
            0 [] (int32)
            0 [] (int32)
            3 [] (int32)
            12 [] (int32)
            14 [] (int32)
            0 [] (int32)
            0 [] (int32)
            3 [] (int32)
            3 [] (int32)
            1 [] (int32)
            1 [] (int32)
            1 [] (int32)
            0 [] (int32)
            32896 [] (int32)
            65280 [] (int32)
            255 [] (int32)
            13408716 [] (int32)
            13421823 [] (int32)
            16777215 [] (int32)
            0 [] (int32)
            3 [] (int32)
            1 [] (uint8)
            1 [] (uint8)
            16777215 [] (int32)
            14737632 [] (int32)
            1 [] (uint8)
            16711680 [] (int32)
            1 [] (int32)
            1 [] (int32)
            1 [] (int32)
            65000 [] (int32)
            1 [] (int32)
            1 [] (int32)
            1 [] (uint8)
            1 [] (int32)
            0 [] (int32)
            1 [] (int32)
            3 [] (int32)
            0 [] (int32)
            1 [] (int32)
            1 [] (uint8)
            1 [] (int32)
            1 [] (uint8)
            1 [] (int32)
            1 [] (uint8)
            2 [] (int32)
            1 [] (uint8)
            1 [] (uint8)
            : [|S35] data=b'D:\\SPC400\\APPLICAT\\LW_CVI\\IMAGE.PRT'
            1 [] (uint8)
            100.0 [] (float64)
            1 [] (int32)
            2 [] (int32)
            1 [] (int32)
            100.0 [] (float64)
            0 [] (int32)
            5 [] (int32)
            : [|S32] data=b'C:\\PROGRAM FILES\\BH\\SPCM\\STP.CFG'
            1 [] (uint8)
            0 [] (int32)
            4096 [] (int32)
            0 [] (int32)
            0 [] (int32)
            32 [] (int32)
            6 [] (int32)
            1 [] (int32)
            5.0 [] (float64)
            5.019608 [] (float64)
            -100.0 [] (float64)
            0.0 [] (float64)
            4191231 [] (int32)
            0 [] (int32)
            136314880 [] (int32)
            16777215 [] (int32)
            1000.0 [] (float64)
            1 [] (int32)
            1 [] (uint8)
            1 [] (uint8)
            0 [] (int32)
            0.1 [] (float64)
            128 [] (int32)
            204800 [] (int32)
            1 [] (uint8)
            0 [] (int32)
            1 [] (uint8)
            1 [] (uint8)
            4 [] (int32)
            1 [] (uint8)
            1 [] (int32)
            1 [] (int32)
            1 [] (int32)
            0 [] (int32)
            0 [] (int32)
            1 [] (int32)
            1 [] (int32)
            128 [] (int32)
            128 [] (int32)
            1 [] (int32)
            2 [] (int32)
            0 [] (int32)
            10 [] (int32)
            0 [] (int32)
            0 [] (int32)
            8 [] (int32)
            1 [] (int32)
            0.0 [] (float64)
            : [|S3] data=b'C,N'
            1 [] (int32)
            34952533 [] (int32)
            204800 [] (int32)
            0 [] (int32)
            1 [] (int32)
            2e-07 [] (float64)
            1 [] (int32)
            1 [] (int32)
            1 [] (int32)
            1 [] (uint8)
            1000.0 [] (float64)
            1 [] (uint8)
            1 [] (int32)
            1 [] (int32)
            32 [] (int32)
            32 [] (int32)
            0 [] (int32)
            : [|S44] data=b'd:\\eitan\\03_24_2014\\dsdna_d7+d17_50_50_1.spc'
            1 [] (int32)
            1 [] (uint8)
            8 [] (int32)
            1 [] (uint8)
            2 [] (int32)
            -200.0 [] (float64)
            4.0 [] (float64)
            0.0 [] (float64)
            8 [] (int32)
            1 [] (uint8)
            10.0 [] (float64)
            1 [] (int32)
            90.588234 [] (float64)
            18.82353 [] (float64)
            0.0 [] (float64)
            6.0122041e-08 [] (float64)
            1.4678233e-11 [] (float64)
            6.0122041e-09 [] (float64)
            16 [] (int32)
            1 [] (int32)
            1 [] (uint8)
            500.0 [] (float64)
            0.1 [] (float64)
            551.09998 [] (float64)
            8 [] (int32)
            1 [] (int32)
            0 [] (int32)
            1 [] (uint8)
            8 [] (int32)
            1 [] (uint8)