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)

• /(8)
  • format_name: Photon-HDF5
  • format_url: http://photon-hdf5.org/
  • format_version: 0.4
  acquisition_duration 2268.0 [float64]
  description: [|S42] data=b'A demonstrative smFRET-nsALEX measurement.'
  • identity(12)
    author: [|S12] data=b'Eitan Lerner'
    author_affiliation: [|S4] data=b'UCLA'
    creation_time: [|S19] data=b'2015-07-20 15:34:51'
    creator: [|S19] data=b'Antonino Ingargiola'
    creator_affiliation: [|S4] data=b'UCLA'
    filename: [|S25] data=b'dsdna_d7_d17_50_50_1.hdf5'
    filename_full: [|S79] data=b'C:\\Data\\Antonio\\software\\src\\phconvert\\notebooks\\data\\dsdna_d7_d17_50_50_1.hdf5'
    format_name: [|S11] data=b'Photon-HDF5'
    format_url: [|S23] data=b'http://photon-hdf5.org/'
    format_version: [|S3] data=b'0.4'
    software: [|S9] data=b'phconvert'
    software_version: [|S5] data=b'0.6.4'
  • photon_data(6)
    detectors (9716848) [uint8]
    nanotimes (9716848) [uint16]
    timestamps (9716848) [int64]
    • measurement_specs(5)
      alex_excitation_period1 (2) [int32]
      alex_excitation_period2 (2) [int32]
      laser_repetition_rate 40000000.0 [float64]
      measurement_type: [|S13] data=b'smFRET-nsALEX'
      • detectors_specs(2)
        spectral_ch1 (1) [int32]
        spectral_ch2 (1) [int32]
    • nanotimes_specs(3)
      tcspc_num_bins 4096 [int32]
      tcspc_range 6.0122042368e-08 [float64]
      tcspc_unit 1.4678233e-11 [float64]
    • timestamps_specs(1)
      timestamps_unit 6.0122042368e-08 [float64]
  • provenance(5)
    creation_time: [|S19] data=b'2014-03-25 15:58:14'
    filename: [|S24] data=b'dsdna_d7_d17_50_50_1.spc'
    filename_full: [|S78] data=b'C:\\Data\\Antonio\\software\\src\\phconvert\\notebooks\\data\\dsdna_d7_d17_50_50_1.spc'
    modification_time: [|S19] data=b'2015-01-24 08:24:34'
    software: [|S19] data=b'Becker & Hickl SPCM'
  • sample(4)
    buffer_name: [|S4] data=b'TE50'
    dye_names: [|S17] data=b'ATTO550, ATTO647N'
    num_dyes 2 [int32]
    sample_name: [|S33] data=b'50-50 mixture of two FRET samples'
  • setup(10)
    detection_wavelengths (2) [float64]
    excitation_cw (2) [uint8]
    excitation_wavelengths (2) [float64]
    lifetime 1 [uint8]
    modulated_excitation 1 [uint8]
    num_pixels 2 [int32]
    num_polarization_ch 1 [int32]
    num_spectral_ch 2 [int32]
    num_split_ch 1 [int32]
    num_spots 1 [int32]
  • user(1)
    • becker_hickl(2)
      • identification(9)
        Author: [|S6] data=b'System'
        Company: [|S7] data=b'Unknown'
        Contents: [|S93] data=b'Setup file made by system at the end of FIFO measurement with module SPC-630 (Ser.No. 3A0067)'
        Date: [|S10] data=b'2014-03-25'
        ID: [|S23] data=b'\x04SPC Setup Script File\x04'
        Revision: [|S11] data=b'12 bits ADC'
        Time: [|S8] data=b'15:58:14'
        Title: [|S20] data=b'dsdna_d7+d17_50_50_1'
        Version: [|S8] data=b'2 872 M'
      • sys_params(160)
        DI_2DC1 1 [uint8]
        DI_2DC1C 10 [int32]
        DI_2DC1S 0 [int32]
        DI_2DC2 1 [uint8]
        DI_2DC2C 13 [int32]
        DI_2DC2S 0 [int32]
        DI_2DDIS 0 [int32]
        DI_2DTRNO 3 [int32]
        DI_3DC1C 12 [int32]
        DI_3DC2C 14 [int32]
        DI_3DCOL 0 [int32]
        DI_3DINCX 0 [int32]
        DI_3DMODE 3 [int32]
        DI_3DOFFX 3 [int32]
        DI_3DOFFY 1 [int32]
        DI_3DSTYL 1 [int32]
        DI_ASCALE 1 [int32]
        DI_BLINE 0 [int32]
        DI_BOD_C 32896 [int32]
        DI_COL2 65280 [int32]
        DI_COL3 255 [int32]
        DI_COL4 13408716 [int32]
        DI_COL5 13421823 [int32]
        DI_COLMAX 16777215 [int32]
        DI_COLMIN 0 [int32]
        DI_COL_NO 3 [int32]
        DI_CUR 1 [uint8]
        DI_DETAIL 1 [uint8]
        DI_GCOL_B 16777215 [int32]
        DI_GCOL_F 14737632 [int32]
        DI_GRID 1 [uint8]
        DI_HICOL 16711680 [int32]
        DI_INTCOL 1 [int32]
        DI_INTPIX 1 [int32]
        DI_LBLINE 1 [int32]
        DI_MAXCNT 65000 [int32]
        DI_PFREQ 1 [int32]
        DI_PSTYLE 1 [int32]
        DI_RATE 1 [uint8]
        DI_SCALE 1 [int32]
        DI_SIZE 0 [int32]
        DI_SXWIN 1 [int32]
        DI_SYWIN 3 [int32]
        DI_TRACE 0 [int32]
        DI_TWIN 1 [int32]
        DI_XREV 1 [uint8]
        DI_XWIN 1 [int32]
        DI_YREV 1 [uint8]
        DI_YWIN 1 [int32]
        PR_PAUTO 1 [uint8]
        PR_PDEV 2 [int32]
        PR_PEJECT 1 [uint8]
        PR_PF 1 [uint8]
        PR_PFNAME: [|S35] data=b'D:\\SPC400\\APPLICAT\\LW_CVI\\IMAGE.PRT'
        PR_PFULL 1 [uint8]
        PR_PHEIGH 100.0 [float64]
        PR_PORIEN 1 [int32]
        PR_PPORT 2 [int32]
        PR_PWHAT 1 [int32]
        PR_PWIDTH 100.0 [float64]
        PR_SAVE_T 0 [int32]
        PR_SLEEP 5 [int32]
        PR_STP_FN: [|S32] data=b'C:\\PROGRAM FILES\\BH\\SPCM\\STP.CFG'
        SP_ACCUM 1 [uint8]
        SP_ADC_DE 0 [int32]
        SP_ADC_RE 4096 [int32]
        SP_ADC_ZOOM 0 [int32]
        SP_ADD_SEL 0 [int32]
        SP_ASAVE 32 [int32]
        SP_BORD_L 6 [int32]
        SP_BORD_U 1 [int32]
        SP_CFD_HF 5.0 [float64]
        SP_CFD_LH 5.019608 [float64]
        SP_CFD_LL -100.0 [float64]
        SP_CFD_ZC 0.0 [float64]
        SP_CH_EN 4191231 [int32]
        SP_CH_F1 0 [int32]
        SP_CH_F2 136314880 [int32]
        SP_CH_SL 16777215 [int32]
        SP_COL_T 1000.0 [float64]
        SP_CYCLES 1 [int32]
        SP_DAEC 1 [uint8]
        SP_DAES 1 [uint8]
        SP_DET_TYP 0 [int32]
        SP_DIS_T 0.1 [float64]
        SP_DITH 128 [int32]
        SP_DLIM 204800 [int32]
        SP_DTCOMP 1 [uint8]
        SP_EAL_DE 0 [int32]
        SP_EN_DLIM 1 [uint8]
        SP_EN_INT 1 [uint8]
        SP_EPX_DIV 4 [int32]
        SP_EXTST 1 [uint8]
        SP_FCYCLES 1 [int32]
        SP_FIF_FNO 1 [int32]
        SP_FIF_TYP 1 [int32]
        SP_FLB_X 0 [int32]
        SP_FLB_Y 0 [int32]
        SP_IMG_RX 1 [int32]
        SP_IMG_RY 1 [int32]
        SP_IMG_X 128 [int32]
        SP_IMG_Y 128 [int32]
        SP_INCR 1 [int32]
        SP_LDIV 2 [int32]
        SP_MEM_BANK 0 [int32]
        SP_MODE 10 [int32]
        SP_MST_CLK 0 [int32]
        SP_MTCLK 0 [int32]
        SP_NCX 8 [int32]
        SP_NCY 1 [int32]
        SP_OFFSET 0.0 [float64]
        SP_OVERFL: [|S3] data=b'C,N'
        SP_PAGE 1 [int32]
        SP_PHOT_F 34952533 [int32]
        SP_PH_BUF 204800 [int32]
        SP_PIX 0 [int32]
        SP_PIX_CLK 1 [int32]
        SP_PIX_T 2e-07 [float64]
        SP_POL_F 1 [int32]
        SP_POL_L 1 [int32]
        SP_POL_P 1 [int32]
        SP_REPEAT 1 [uint8]
        SP_REP_T 1000.0 [float64]
        SP_ROUT 1 [uint8]
        SP_SCAN_RX 1 [int32]
        SP_SCAN_RY 1 [int32]
        SP_SCAN_X 32 [int32]
        SP_SCAN_Y 32 [int32]
        SP_SCF 0 [int32]
        SP_SPE_FN: [|S44] data=b'd:\\eitan\\03_24_2014\\dsdna_d7+d17_50_50_1.spc'
        SP_STEPS 1 [int32]
        SP_STOPT 1 [uint8]
        SP_SXWIN_N 8 [int32]
        SP_SX_EQU 1 [uint8]
        SP_SYN_FD 2 [int32]
        SP_SYN_FQ -200.0 [float64]
        SP_SYN_HF 4.0 [float64]
        SP_SYN_ZC 0.0 [float64]
        SP_SYWIN_N 8 [int32]
        SP_SY_EQU 1 [uint8]
        SP_TAC_EH 10.0 [float64]
        SP_TAC_G 1 [int32]
        SP_TAC_LH 90.588234 [float64]
        SP_TAC_LL 18.82353 [float64]
        SP_TAC_OF 0.0 [float64]
        SP_TAC_R 6.0122041e-08 [float64]
        SP_TAC_TC 1.4678233e-11 [float64]
        SP_TAC_TD 6.0122041e-09 [float64]
        SP_TRIGGER 16 [int32]
        SP_TWIN_N 1 [int32]
        SP_T_EQU 1 [uint8]
        SP_WL_STA 500.0 [float64]
        SP_WL_STE 0.1 [float64]
        SP_WL_STO 551.09998 [float64]
        SP_XWIN_N 8 [int32]
        SP_XY_GAIN 1 [int32]
        SP_X_AXIS 0 [int32]
        SP_X_EQU 1 [uint8]
        SP_YWIN_N 8 [int32]
        SP_Y_EQU 1 [uint8]