Spectrum ( 0 and 1 representing negative and polarity integer(1): the polarity of the.mz numeric: the m/z values for the spectrum’s.msLevel integer(1): the MS level of the.isolationWindowUpperMz numeric(1): upper m/z.M/z for the isolation window in which the (MSn) spectrum was isolationWindowTargetMz numeric(1): the target.isolationWindowLowerMz numeric(1): lower m/zįor the isolation window in which the (MSn) spectrum was measured.intensity numeric: intensity values for the.Where the spectrum’s peak data is stored. MsBackendHdf5Peaks it will be the name of the HDF5 file dataStorage character(1): the (current). Of the spectrum’s data, e.g. the mzML file from which it was read. collisionEnergy numeric(1): collision energy.centroided logical(1): whether the spectrum is.acquisitionNum integer(1): the index ofĪcquisition of a spectrum during a MS run.The core variables and their data type are (alphabetically ordered): Returned by it (or NA if the information is not available). Have their own accessor method and it is guaranteed that a value is (such as MS level or retention time) an arbitrary number of optional Of as a list of individual spectra, with each spectrum having a set of P.title(zstruc.field('class') + ', z = ' + str(zstruc.Mass spectrometry data in Spectra objects can be thought P.plot(wave, flux * (ivar > 0), 'k', hold=False) #p.plot(wave, (flux-bzero) * (ivar > 0), 'k', hold=False) # the following repeatedly to loop over spectra: # Set starting fiber point (above), then copy and paste # Following commented-out bit was needed for some of the early redux: Zbfile = topdir + plate + '/spZbest-' + plate + '-' + mjd + '.fits' Spfile = topdir + plate + '/spPlate-' + plate + '-' + mjd + '.fits' # Licensed for free and unencumbered use in public domain. # Example script for looking at BOSS spectra and redshift fits via Python. This worked for Python 2.5 under Mac OS X v10.5.8 in 2009. It requires numpy, matplotlib, and pyfits. The following script is nothing fancy, and would most likely need to be updated to work with your Python distribution and data path, but gives a simple example of visualizing BOSS spectra with Python. Will run plotspec in turn on each of the fibers 501-1000 of plate 3615. If you want to look at lots of spectra, use the look command: look 36 See all the options by typing h at the prompt. You are then put in an interactive mode where you can play with the spectra: zoom in and out, change the assumed redshift, change the smoothing (a boxcar smooth of 5 pixels is the default for plotting), and so on. Superposed will be positions of emission and absorption lines, assuming the redshift given in the spZbest file. You should see a spectrum in one panel, and then 3 smaller panels with various zooms. For fiber, use any number between 5 the spectra from the first spectrograph are not yet available due to the problems with the b1 camera. You are now ready to look at spectra! The basic command is: plotspec įor plate, use one of the plates available (see above for available plates). Tell the MJD of the observations you want to plot: mjd 55098 define SPECTRO_DATA ('/u/dss/spectro/boss') Princeton folks need not type this, as it is the current default. Of course, use the proper path for your own directory structure. The last is “xterm underscore ell” for landscape Then load the macros for BOSS spectra: restore spectro.boss Enter SM in the directory where spectro.boss lives, and type the following:įirst we remove any previous things in SM’s macro buffer: DELETE HISTORY 0 10000.Contact Michael Strauss (strauss at astro dot princeton dot edu) to obtain the SM macro file (called spectro.boss).(At Princeton, for example, these files are in /u/dss/spectro/boss, and thus have directories called /u/dss/spectro/boss/3615, and so on.) Pull the reduced spectra (spPlate and spZbest files) off the SAS, creating one directory per plate.Another approach is to use SM tools, written by Michael Strauss. The above IDL tools can be used to examining the spectra. Help is available for these commands with “doc_library”: IDL> doc_library,'plotspec' From IDL, use “plotspec” to display spectra.If you are at Princeton, set export BOSS_SPECTRO_REDUX=/u/dss/spectro/boss If you are on setĮxport BOSS_SPECTRO_REDUX=/clusterfs/riemann/raid006/dr10/boss/spectro/redux Set environment variables to point to your downloaded data.Download the “idlutils” and “idlspec2d” products, set some environment variables, and put the “pro” subdirectories of each in your path:įrom bash shell: export IDLUTILS_DIR=$.
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