fit_tscan

fit tscan: fitting experimental time trace spectrum data with the convolution of the sum of

  1. exponential decay (mode = decay)

  2. damped oscillation (mode = osc)

  3. exponential decay, damped oscillation (mode=both)

and irf function. There are three types of irf function (gaussian, cauchy, pseudo voigt) are supported. To calculate the contribution of each life time component, it solve least linear square problem via scipy.linalg.lstsq function.

  • usage: fit_tscan [-h] [–mode {decay,osc,both}] [–irf {g,c,pv}] [–fwhm_G FWHM_G] [–fwhm_L FWHM_L] [–num_file NUM_FILE [NUM_FILE …]] [-t0 TIME_ZEROS [TIME_ZEROS …]] [-t0f TIME_ZEROS_FILE] [–tau [TAU …]] [–tau_osc TAU_OSC [TAU_OSC …]] [–period_osc PERIOD_OSC [PERIOD_OSC …]] [–no_base] [–same_t0] [–fix_irf] [–fix_t0] [–method_glb {basinhopping, ampgo}] [-o OUTDIR] [–save_fig] prefix [prefix …]

  • positional arguments:

    • prefix prefix for tscan files It will read prefix_i.txt

  • optional arguments:

    • -h, –help show this help message and exit

    • –mode {decay,osc,both} Mode of fitting

      • decay: fitting with the sum of the convolution of exponential decay and instrumental response function

      • osc: fitting with the sum of the convolution of damped oscillation and instrumental response function

      • both: fitting with the sum of both decay and osc

    • –irf {g,c,pv} shape of instrument response functon

      • g: gaussian distribution

      • c: cauchy distribution

      • pv: pseudo voigt profile \({PV}(f_G, f_L) = \eta(f_G, f_L) C(f(f_G, f_L)) + (1-\eta(f_G, f_L)) G(f(f_G, f_L))\) The uniform fwhm parameter \(f(f_G, f_L)\) and mixing parameter \(\eta(f_G, f_L)\) are determined according to Journal of Applied Crystallography. 33 (6): 1311–1316.

    • –fwhm_G FWHM_G full width at half maximum for gaussian shape. It would not be used when you set cauchy irf function

    • –fwhm_L FWHM_L full width at half maximum for cauchy shape. It would not be used when you did not set irf or use gaussian irf function

    • –num_file NUM_FILE [NUM_FILE …] number of scan file corresponding to each prefix

    • -t0 TIME_ZEROS [TIME_ZEROS …], –time_zeros TIME_ZEROS [TIME_ZEROS …] time zeros for each tscan

    • -t0f TIME_ZEROS_FILE, –time_zeros_file TIME_ZEROS_FILE filename for time zeros of each tscan

    • –tau [TAU …] lifetime of each decay component [mode: decay, both]

    • –tau_osc TAU_OSC [TAU_OSC …] lifetime of each damped oscillation component [mode: osc, both]

    • –period_osc PERIOD_OSC [PERIOD_OSC …] period of the vibration of each damped oscillation component [mode: osc, both]

    • –no_base exclude baseline for fitting [mode: decay, both]

    • –same_t0 set time zero of every time delay scan belong to the same dataset equal

    • –fix_irf fix irf parameter (fwhm_G, fwhm_L) during fitting process

    • –fix_t0 fix time zero parameter during fitting process.

    • –method_glb {basinhopping,ampgo} Global Optimization Method

    • ‘basinhopping’ : basinhopping

    • ‘ampgo’ : Adaptive Memory Programming for Global Optimization

    • -o OUTDIR, –outdir OUTDIR name of directory to store output files

    • –save_fig save plot instead of display

Note

  1. The number of time zero parameter should be same as the total number of scan to fit.

  2. However, if you set same_t0 then the number of time zero parameter should be same as the total number of dataset.

  3. Every scan file whose prefix of filename is same should have same scan range

  4. if you set shape of irf to pseudo voigt (pv), then you should provide two full width at half maximum value for gaussian and cauchy parts, respectively.

  5. If you did not set tau and mode=decay then --no_base option is discouraged.

  6. If you set mode=decay then any parameter whoose subscript is osc is discarded (i.e. tau_osc, period_osc).

  7. If you set mode=osc then tau parameter is discarded. Also, baseline feature is not included in fitting function.

  8. The number of tau_osc and period_osc parameter should be same

  9. If you set mode=both then you should set tau, tau_osc and period_osc. However the number of tau and tau_osc need not to be same.