Tutorial

Here we provide a brief tutorial to start fitting with the sviewer GUI.

Loading the spectrum

The spectrum can be loaded in GUI by several ways:

  • Drag and drop method: You can load several files in one drop.
  • File/Import spectrum... in Main menu
  • File/Open... in Main menu: In that case it load the spectra specified in .spv file, whih contains saved progress of data analysis.
  • File/Import list... in Main menu: import a list of spectra from the file with list contains of path to spectra.
  • File/Import folder... in Main menu: import all spectra from the specified folder.

The basic sviewer spectral format is plain ASCII file, which stores spectrum in column-like representation with the following order: <wavelength> <flux> <uncertainty>. The spectrum do not necessary need to have <uncertainty> column, as well as can read the <continuum> provided in the additional forth column. The header of ascii file should be commented out by #.

Additionally there is possibility to load the spectrum in FITS format. The program can automatically recognize several FITS format produced by standard reduction routines, such as UVES popler, SDSS, etc.

Constructing continuum

One of the first part of the absorption line analysis is constructing of the unabsorbed continuum. In most partical cases, the continuum is not well defined a priori, and can be considered as some fixed normalization of the spectrum (fit profile) or as a nuissance parameter. There are several way to construct continuum:

  • B-spline: continuum is constructed using B-spline interpolation between data points that can be created using mouse interaction:
    • b + LEFT CLICK: add point for B-spline at the cursor position.
    • b + RIGHT CLICK: remove the closest point of B-spline at the cursor position.
    • b + MOUSE REGION: remove all points of B-spline within selected region.

    B-spline is automatically recalculated at each change in the data points array.

  • Iterative Smoothing: for quick constion of smooth continuum press q. For more options see Continuum widget

  • Savitsky-Golay interpolation: avaliable in Continuum widget

  • Chebyshev polinomials: avaliable in Continuum widget

Fine tunning options and actions to construct and modify the continuum is avaliable in Continuum widget that can be opened iether 1d spec/Continuum... in Main Menu or pressing CTRL + c.

After continuum is constructed one can normalize/denormalize the representation of the spectrum by pressing Normalize button in Control panel or using n key.

Selecting fit regions

To perform the fit it is necessary to select the spectrum pixels in which the spectrum will be compared with the fit model. This can be done by:

  • s + MOUSE REGION: select points within region drawn by mouse using Left button
  • s + SHIFT + MOUSE REGION: select points to all exposures within selected region
  • d + MOUSE REGION: deselect points within region drawn by mouse using Left button
  • d + SHIFT + MOUSE REGION: deselect points to all exposures within selected region

The representation of selected pixels (regions, points, lines) can be changed in Preferences widget (View/Preferences... in Main menu or by pressing F11)

Making fit model

The fit model should be defined in the Fit model widget, which can be opened either by Fit/Fit model... in Main Menu or pressing F3. Detailed description of the Fit Model widget is given in Fit model

After setting/modification of fit model one can update (if it was not update automatically) the fit by pressing

  • f: this will construct the model profiels in the selected regions only.
  • SHIFT + f: this will construct the model profiles for all avaliable line in the spectrum.

Fitting

There are two avaliable fit routines:

  • Minimizing likelihood using Levenberg-Marquard method. The uncertainties on the fitting parameters estimate from the covariance matrix approach. This fit is performed by the pressing Fit button in Control panel. There is a possibility to choose a particular set of the paramaters that will be varied during the fit, inside Fit parameters widget, which can be opened either by Fit/Fit paramaters... in Main Menu or pressing F4.
  • Bayessian approach by Monte Carlo Markov Chain (MCMC) technique with a set of Samplers. The options and control is provide in MCMC widget, which can be called using either by Fit/MCMC Fit... in Main Menu or pressing F5. The detailed description is provided in Bayessian inference with MCMC

Viewing results

The fit result can be provided inside Fit results widget, which can be called either by Fit/Fit results... in Main Menu or pressing F6. There various option for the output, including plain text, PyQt widget table and latex table.

The fit profiles can be constructed in the publish-ready representation with matplotlib by using Plot Lines widget, which can be called either by View/Plot line profiles... in Main Menu or pressing F7. The detailed description of Plot profiles widget is provided in Plot line profiles widget