SMART Spectral Extraction Types

Choosing to perform a spectral extraction displays a window titled "Extraction", listing the different extraction types available :

• Full Aperture Extraction
• Automatic Source Finder - Tapered Column Point Source Extraction
• Automatic Source Finder - Gaussian Point Source Extraction
• Manual Source Finder - Extraction - invokes the Manual Source Finder.

Select one type by clicking on it and then click "Extract" to run an extraction. Clicking "Cancel" will return to the "Dataset" window without running an extraction.

Note about Wavesamp

All SMART extraction options use a look-up table (supplied by the SSC) that traces the spectral orders on the BCD image. This table is converted into an IDL structure known as the "wavesamp". The extraction options use the wavesamp in order to subset the relevant group of pixels in each resolution element on the array. (IE. Assign a given pixel to an order.). Since the image of a spectral order can be curved a curved spectral order is subdivided into spectral resolution elements. The curvature results in fractional pixels being assigned to a given resolution element. The value of each fractional pixel is scaled by its geometrical area. The BCD data is in units of e.s-1 (electrons per second). Each routine estimates the total number of e.s-1 in each individual resolution element. The final step is to apply the flux calibration (IE. e.s-1 to Janskys) and stitch the orders together into a single spectrum, using the pipeline "fluxcon" tables.

Full Aperture Extraction

Full aperture extraction assumes that the relevant source fills (or approximately fills) the spectrograph slit aperture. This is usually true for all high resoloution observations and for extended source low resoloution ones. Once selected the following steps are carried out :

1. Any flux (signal) at all within the bounds of each order is extracted.
2. Pixel values that are set to NaN (not-a-number) in the pipeline or flagged by the bad-pixel mask are replaced with an average value
   that is estimated from the values of the pixels in the same resolution element as the bad pixel.
3. The flux in all detector pixels for a given wavelength (as defined by the relevant wavesamp file) is summed together.
   (Summation is in the cross dispersion direction.) This gives a total flux for that wavelength.
4. The flux summation process is repeated for each wavelength in the order.
5. A tabel of Flux against Wavelength is written, which is the new 1-D spectrum.
6. The flux summation process is then repeated for each order in the BCD (file).
7. Sets of Flux against Wavelength data are successively appended to the 1-D spectrum.

Automatic Source Finder - Tapered Column Point Source Extraction

This is the simplest extraction method for SL and LL observations of point sources. The region of image pixels extracted is tapered along each spectral order, wider at longer wavelengths, narrower at shorter wavelengths. Once selected the following steps are carried out :

1. The Automatic Source Finder finds the position of the source in each order.
2. Pixel values that are set to NaN (not-a-number) in the pipeline or flagged by the bad-pixel mask are replaced with an average value
   that is estimated from the pixels in the column within the same resolution element as the bad pixel.
3. A column of pixels centered on the point source is extracted.
4. The column traces the spectral order, and its width in the cross-dispersion direction is scaled with the instrumental point-spread function.
5. If required a pop-up window displaying the source finding can be displayed. See Automatic Source Finder for more information.
6. In the event of there not being enough data points to fit a curve a warning message will be displayed in a pop-up box : "Curvefit - not enough data points". Click "OK" to continue.

Automatic Source Finder - Gaussian Point Source Extraction

Automatic Gaussian point source extraction assumes that the source(s) extracted can be fitted with a Gaussian distribution in the cross dispersion direction. The region of image pixels extracted is tapered along each spectral order, wider at longer wavelengths, narrower at shorter wavelengths. Gaussian extraction should only be used with care, as it requires additional on-the-fly calibration. Once selected the following steps are carried out :

1. The Automatic Source Finder finds the position of the source in each order.
2. Pixel values that are set to NaN (not-a-number) in the pipeline or flagged by the bad-pixel mask are excluded from the fit.
3. For a given order (as defined by the relevant wavesamp file) the flux in each line of pixels (in the dispersion direction) is summed together.
4. This gives the "collapsed" order, effectively a measure of total flux per line of pixels versus cross dispersion distance. (Measured in pixels.)
5. A baseline noise floor is defined.
6. The collapsed order is then scanned for any peak above the baseline noise floor.
7. Any detected peak more than 1.5 pixels wide (FWHM resoloution limit) is assumed to be a source.
8. A Gaussian fit is then made to this source.
9. If the Gaussian fit is successful the source details are written to the data header. (Position in cross dispersion direction in pixels, FWHM and RA/DEC of particular source.)
   (For a given observation RA and DEC are constant along the dispersion direction and vary across it.)
10. The source is then removed from the collapsed order.
11. The collapsed order is then scanned again for a peak and if found the fitting/removal process is repeated.
12. Scanning continues until no further peaks can be found.
13. If required a pop-up window displaying the source finding can be displayed. See Automatic Source Finder for more information.
14. In the event of there not being enough data points to fit a curve a warning message will be displayed in a pop-up box : "Curvefit - not enough data points". Click "OK" to continue.

Manual Source Finder - Extraction

Please refer to the Manual Source Finder page for more information on performing extractions with the Manual Source Finder.

Effects of "sm_fwhmfactor" setting on Extraction

The "sm_fwhmfactor" is set in the User Parameters window. Its SMART default value is "-1.0". Its value is displayed in the "Extraction" window (see above).

If "sm_fwhmfactor" is set to "-1.0" :

1. Low Resolution Data.
   For ALL extraction types setting "sm_fwhmfactor" = -1.0 directs SMART to use the appropriate "psf_fov" table file, (from the SMART Calibration Files), where the extraction widths (in pixels) are defined for each order, at specified wavelength anchor points (microns).
2. High Resolution Data.
   For ALL extraction types setting "sm_fwhmfactor" = -1.0 will cause SMART to override it and set the value to "sm_fwhmfactor" = 1.0 (IE. Positive 1.0). The data will then be extracted with "sm_fwhmfactor" = 1.0.

If "sm_fwhmfactor" is not set to "-1.0" (IE. It is in the range 1.0 - 30.0) :

1. Full Aperture Extraction The "sm_fwhmfactor" has no effect on Full Aperture extraction.
2. Automatic Source Finder - Tapered Column Point Source Extraction
   1. A Gaussian fit is made to the fully collapsed ("accordianized") order (IE. entire wavelength range), exactly the same as in a Gaussian extraction.
   2. The Gaussian fit is then used to determine the center and the full width at zero (FWZ). The FWZ is used to set the column width.
   3. The line center is applied at the reference wavelength for the relevant order :
      • LL1 = 30.90 microns
      • LL2 = 17.69 microns
      • LL3 = 20.57 microns
      • SL1 = 11.42 microns
      • SL2 = 6.37 microns
      • SL3 = 8.00 microns
   4. For all other wavelengths in the order the line center is determined by following the wavesamp values corresponding to the value at the reference wavelength.
   5. The line width is applied at the reference wavelength for the relevant order :
      • LL1 = 30.90 microns
      • LL2 = 17.69 microns
      • LL3 = 20.57 microns
      • SL1 = 11.42 microns
      • SL2 = 6.37 microns
      • SL3 = 8.00 microns
   6. For all other wavelengths in the order the line width at the reference wavelength is scaled by the particular wavelength.
   7. The parameter value of "sm_fwhmfactor" moderates the width of the column, EG. sm_fwhmfactor=0.5 decreases the column width by 50%. sm_fwhmfactor=2.0 increases the column width by 100%.

3. Automatic Source Finder - Gaussian Point Source Extraction
   1. The Gaussian width AND center is determined at EACH resolution element by fitting a Gaussian curve to it.
   2. Line center and width can only be frozen for Gaussian extractions.
   3. The line center can be frozen (IE. follow the "wavesamp" specifications) ONLY when the "Line Center" option is chosen in the User Parameters for the "sm_fitfreeze" parameter. (Default = Off, IE. Not frozen). IE: If line center freeze is "On" then :
      1. The order is collapsed.
      2. Line center is determined from a fit to the collapsed spectrum.
      3. The line center is applied at the reference wavelength for the relevant order :
         • LL1 = 30.90 microns
         • LL2 = 17.69 microns
         • LL3 = 20.57 microns
         • SL1 = 11.42 microns
         • SL2 = 6.37 microns
         • SL3 = 8.00 microns
      4. For all other wavelengths in the order the line center is determined by following the wavesamp values corresponding to the value at the reference wavelength.

   4. The line width can be frozen (IE. follow the "wavesamp" specifications) ONLY when the "Line Width" option is chosen
      in the User Parameters for the "sm_fitfreeze" parameter.
      (Default = Off, IE. Not frozen). IE. If line width freeze is "On" then
      1. The order is collapsed.
      2. Line width is determined from a fit to the collapsed spectrum.
      3. The line width is applied at the reference wavelength for the relevant order :
         • LL1 = 30.90 microns
         • LL2 = 17.69 microns
         • LL3 = 20.57 microns
         • SL1 = 11.42 microns
         • SL2 = 6.37 microns
         • SL3 = 8.00 microns
      4. For all other wavelengths in the order the line width at the reference wavelength is scaled by the particular wavelength.

4. Manual Source Finder - Extraction

   Please refer to the Manual Source Finder page for more information on performing extractions with the Manual Source Finder.