HAMMER.PRO V1.2 README
Hammer.pro is an idl code written to replace the need for several different independent spectral pipelines used primarily by the UW M star research group. Each spectra hit by the Hammer is analyzed to predict its MK spectral type on the basis of a fit to a set of 30 spectral indices, taking into account the uncertainty in each index. The spectra is then analyzed to provide information on the activity level of the star, as measured by the presence or absence of chromospheric Halpha emission, as well as for M subdwarf status, by allowing calculation of the ratio of TiO to CaH. Once the entire set of spectra submitted to the Hammer has been automatically analyzed in this manner, the user is allowed to interactively tweak the assigned spectral type before a final summary file is created.
The Hammer reads in spectra in a variety of formats, namely as sdss fits files ('sdssfits'), a standard fits spectra ('fits'), or text files with a wavelength column preceeding a column of fluxes ('txt'). Version 1.1 has added a new format ('princeton') to read in the Princeton reductions of SDSS spectra. This new format depends on the READSPEC program distributed as part of the IDLSPEC2D package -- users will need to install the IDLSPEC2D, IDLUTILS, and Goddard IDL utilities available from http://www.astro.princeton.edu/~schlegel/code.html
All formats should have wavelengths expressed in angstroms; sdss spectra should be in the standard sdss wavelength format (vacuum wavelengths & logarithmic pixels), while non-sdss spectra should be calibrated in air wavelengths.
Before being run the first time, the user add the hammerv1_1 directory to their idl path, and then must edit line 19 of hammer.pro to indicate the location of the hammerv1_1 directory in their system. These steps are required so that hammer.pro can locate and load the templates.idl and indices.idl files contained within that directory.
MAC USERS: to make the cursor input for eyecheck.pro work correctly, type the following on the command line:
defaults write com.apple.x11 wm_click_through -bool true
typing this once will allow you to use the clickable IDL interface in the eyetyping portion of the Hammer.
Hammer.pro should then be passed a table giving the data paths of spectra to be
analyzed in the first column, with a second column giving the format of each
type of spectra using the coding system indicated in the 'FORMATS' section.
The hammer will then allow the user to specify a S/N level below which
spectra should be ignored rather than included in the following analysis.
S/N is measured from the 100 Angstrom wide region with the largest mean flux;
the three possible regions have central wavelengths of 4550, 6150 and 8250.
Spectra which pass this S/N cut are then measured automatically for a best
fit MK spectral type, Halpha emission equivalent width (and the statistical
significance of the activity level thereby detected), and various spectral
indices which can indicate subdwarf status.
Once all spectra have been measured automatically, the user is prompted to determine if another S/N cut should be used to pare the list which will be examined visually. EYECUT then asks what spectra to start with -- this should usually be zero, unless the user has stopped the program previously and is now returning to type the remaining spectra. If the user is returning to eyetype the remaining spectra, there is an option to bypass the automatic spectral typing, subdwarf and magnetic activity portions of the code.
The template for the automatically determined best fit spectral type is then compared to the target spectra. The user can select other templates from the same MK sub class (Os, As, Gs, Ms, etc.) by clicking on the appropriate label along the top axis. Labels shown in green indicate valid MK spectral types; the current template selection is shown in red. Along the left axis of the plot are labels which, if clicked, allow the user to compare the target to templates from other MK sub classes. The appropriate template labels then replace those along the top axis of the plot. Along the right hand side of the screen are the 'EARLIER' and 'LATER' buttons, which allow the user to step through the template set one sub-class at a time.
Buttons along the bottom allow the user to modify the comparison routine in some additional manner:
ODD: after selecting odd, the user is prompted via the IDL XTERM window to enter a 3 letter (or less) code for the object's spectral classification. Possible notations could include C* for Carbon star, QSO for Quasars, Sdm for subdwarfs, WDM for White dwarf M dwarf pair, etc. The routine records this in place of the automatically fit spectral type, and loads the next target spectra.
BAD: indicates the spectra has such low S/N it should be discarded from the sample. Object has a spectral type recorded as 'bad' and the next target spectra is loaded for visual analysis.
SMOOTH: for noisy spectra, allows smoothing to facilitate comparison of the continuum shape with smoothed template spectra. Possible pixel smoothing window widths are displayed for the user's consideration along the top axis of the plot window. Following this selection, subsequent template comparisons will be conducted for this spectra using the same smoothing window. Users can choose to revert to the original spectrum by choosing a smoothing window of 1 in a subsequent SMOOTH operation.
DONE: the current template is assigned as the visually confirmed type.
BACK: returns to the spectra considered immediately previous to this one. As this is a kludgey feature, it reads in and re-writes the visual summary file. For long lists, this could take a significant amount of time.
BREAK: allows the user to save the results of spectral typing partway through the list. Returning to Hammer.pro will allow the user to continue visually typing spectra from the same location in the list, though automatic determination of spectral types won't be circumvented.
autoSpTresults.tbl -- results from the automatic determination of spectral type via 30 spectral indices. Columns are: the filename, the spectral format, the S/N of the spectra, and the automatically assigned spectral type.
ew.tbl -- results from A. West's subdwarf and activity codes. See the code themselves (in the /neededpros directory) to determine what each column is.
eyeout.tbl -- a minimal output from the eyecheck portion of the code, recording the filename, visual type, and automatically assigned type.
finalsummary.tbl -- a summary file containing all the outputs in one large text file. See column headings for more info.
rejectedspectra.tbl -- a file indicating spectra whose S/N were too low to be considered by Hammer.pro.
Included in this distribution are a set of test spectra and a sample list to serve as examples for users. 'testsoe.lis' is a list of input spectra for the Hammer, pointing to spectra contained within the testspecs directory.
To run the Hammer with these test files, one should start up IDL. the Hammer can then be started from within the hammer directory with the following sequence of commands:
IDL> .r hammer.pro IDL> hammer, 'testsoe.lis'
Good luck!
Hammer.pro uses a spectral typing engine created by Kevin R. Covey using a set of indices determined to track well with spectral type from measurements of a set of over 1500 calibration spectra (thanks to the authors of the STELIB, INDO-US, and MILES spectral atlases -- the value of these indices as a function of spectral type is given in the IDL save file located at /neededpros/indices.idl). K. Covey also incorporated the SUBDWARF and EW routines written by A. West for analysis of the activity and metallicity of M dwarfs, with slight modification to allow the processing of non-sdss spectra (I may have messed this up -- if you use the outputs of these routines and are getting odd answers, that's probably what happened). K. Covey also heavily modified the original EYECHECK routine by A. West to allow the comparison of target spectra to the entire range of MK spectral types, as well as adding new functionality (the ODD, SMOOTH, and BACK buttons, etc.) The creation of all the routines above were performed with the steady supervision of Suzanne Hawley and the UW astronomy Dept.
1/4/07 -- Changed cursor command option to /down instead of 3 to allow eyecheck.pro to work correctly on macs.
-- modified README file to include command necessary for macs
to allow cursor command to work correctly.
-- Fixed incorrect format statement for printing S/N of spectra
rejected from eyecheck.pro.
-- Added 'princeton' format for princeton reduced SDSS spectra.
1/30/07 -- Fixed bug that crashed eyecheck.pro when 'earlier' and 'later' buttons are used at the edge of the spectral sequence
-- Fixed bug that prevented huge numbers of spectra from going through
ew.pro
7/6/07 -- Modified readplainfits.pro to handle spectra where the reference pixel is not the first pixel in the spectrum
7/9/07 -- Fixed bug where spectra without any measurable indices were not being written to rejectedspectra.tbl
-- Made ew.pro, eyecheck.pro, and hammer.pro all output 100
character filenames in their output tables.
12/4/09 -- Modified default window size in eyecheck.pro
-- removed superfluous print statements and unnecessary comments
12/7/09 -- removed double 'vactoair' call after verifying that indices were measured from spectra that were not double 'vactoair'ed.
-- added ability to specify partial paths in list of spectra
11/7/14 -- Forked by gully