* remove trailing whitespace from lines in all files

* remove shell commands from tops of files that do not contain main or test for __main__

py/fastspecfit/continuum.py

@@ -857,13 +857,13 @@ def _stellar_objective(self, params, templateflux,
             spec_resid = resid[:resid_split]
             np.subtract(modelflux, specflux, spec_resid)
             spec_resid *= specistd
-        
+
         if synthphot:
             modelflam = self.continuum_to_photometry(fullmodel)
             phot_resid = resid[resid_split:]
             np.subtract(modelflam, objflam, phot_resid)
             phot_resid *= objflamistd
-        
+
         return resid
 
 

py/fastspecfit/emlines.py

@@ -134,33 +134,33 @@ def compute_inrange_lines(self, redshift, wavelims=(3600., 9900.), wavepad=5*0.8
             ((zlinewave > (wavelims[0] + wavepad)) & \
              (zlinewave < (wavelims[1] - wavepad)))
 
-    
+
     def build_linemodels(self, separate_oiii_fit=True):
         """Build emission line model tables, with and without
         suppression of broad lines.  Establish fixed (i.e., forced to
         zero) params, tying relationships between params, and doublet
         relationships for each model, as well as the relationship
         between lines and their parameters, which we record in the
         line table.
-        
+
         Parameter fixing needs to know which lines are within the
         observed wavelength ranges of the cameras, so we first add
         this information to the line table.
 
         """
-        
+
         def create_model(tying_info, forceFixed=[]):
             """Given the tying info for the model and the list of
             in-range lines, determine which parameters of the model
             are fixed and free, and create the model's table.
-            
+
             We fix all parameters for out-of-range lines to zero,
             unless the parameter is tied to a parameter for an
             in-range line.  We also allow the caller to specify
             parameters that should be fixed regardless.
 
             """
-            
+
             n_params = len(self.param_table)
             isfixed = np.full(n_params, False, dtype=bool)
 
@@ -355,7 +355,7 @@ def tie_line(tying_info, line_params, source_linename, amp_factor=None):
 
     def summarize_linemodel(self, linemodel):
         """Simple function to summarize an input linemodel."""
-        
+
         def _print(line_mask):
             for line in np.where(line_mask)[0]:
                 line_name   = self.line_table['name'][line]

py/fastspecfit/fastspecfit.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 fastspecfit.fastspecfit
 =======================
@@ -15,6 +14,10 @@
 from fastspecfit.singlecopy import sc_data
 from fastspecfit.util import BoxedScalar, MPPool
 
+import cProfile as profile
+import pstats
+pr = profile.Profile()
+shot = 0
 
 def fastspec_one(iobj, data, out_dtype, broadlinefit=True, fastphot=False,
                  constrain_age=False, no_smooth_continuum=False,
@@ -41,11 +44,20 @@ def fastspec_one(iobj, data, out_dtype, broadlinefit=True, fastphot=False,
     # output structure
     out = BoxedScalar(out_dtype)
 
+    global shot
+    if shot > 0:
+        pr.enable()
+
     continuummodel, smooth_continuum = continuum_specfit(
         data, out, templates, igm, phot, constrain_age=constrain_age,
         no_smooth_continuum=no_smooth_continuum,
         fastphot=fastphot, debug_plots=debug_plots)
 
+    if shot > 0:
+        pr.disable()
+    else:
+        shot = 1
+
     # Optionally fit the emission-line spectrum.
     if fastphot:
         emmodel = None
@@ -212,6 +224,10 @@ def fastspec(fastphot=False, stackfit=False, args=None, comm=None, verbose=False
 
     log.info(f'Fitting {Spec.ntargets} object(s) took {time.time()-t0:.2f} seconds.')
 
+    st = pstats.Stats(pr).strip_dirs().sort_stats("cumulative")
+    st.print_stats()
+    st.print_callees()
+
     write_fastspecfit(results, meta, modelspectra=modelspectra, outfile=args.outfile,
                       specprod=Spec.specprod, coadd_type=Spec.coadd_type,
                       fphotofile=sc_data.photometry.fphotofile,
@@ -235,7 +251,7 @@ def fastphot(args=None, comm=None):
     Parameters
     ----------
     args : :class:`argparse.Namespace` or ``None``
-        Required and optional arguments parsed via inputs to the command line. 
+        Required and optional arguments parsed via inputs to the command line.
     comm : :class:`mpi4py.MPI.MPI.COMM_WORLD` or `None`
         Intracommunicator used with MPI parallelism.
 
@@ -606,4 +622,3 @@ def create_output_table(result_records, meta, units, stackfit=False):
     results = hstack((results, Table(np.array(result_records), units=units)))
 
     return results
-

py/fastspecfit/igm.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 fastspecfit.igm
 ===============
@@ -198,7 +197,7 @@ def _tLCDLA(zS, lobs):
                         0.04696 * z**3 - \
                         0.01779 * z**3.3 * (lobs[i]/lamL) ** -0.3 - \
                         0.1347  * (lobs[i]/lamL) ** 2 - \
-                        0.2905  * (lobs[i]/lamL) ** -0.3 
+                        0.2905  * (lobs[i]/lamL) ** -0.3
                 else:
                     r[i] = \
                         0.04696 * z**3 - \

py/fastspecfit/io.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 fastspecfit.io
 ==============
@@ -36,8 +35,8 @@
 # fibermap and exp_fibermap columns to read
 FMCOLS = ('TARGETID', 'TARGET_RA', 'TARGET_DEC', 'COADD_FIBERSTATUS', 'OBJTYPE',
           'PHOTSYS', 'RELEASE', 'BRICKNAME', 'BRICKID', 'BRICK_OBJID',
-          #'FIBERFLUX_G', 'FIBERFLUX_R', 'FIBERFLUX_Z', 
-          #'FIBERTOTFLUX_G', 'FIBERTOTFLUX_R', 'FIBERTOTFLUX_Z', 
+          #'FIBERFLUX_G', 'FIBERFLUX_R', 'FIBERFLUX_Z',
+          #'FIBERTOTFLUX_G', 'FIBERTOTFLUX_R', 'FIBERTOTFLUX_Z',
           #'FLUX_G', 'FLUX_R', 'FLUX_Z', 'FLUX_W1', 'FLUX_W2',
           #'FLUX_IVAR_G', 'FLUX_IVAR_R', 'FLUX_IVAR_Z', 'FLUX_IVAR_W1', 'FLUX_IVAR_W2'
           )
@@ -945,7 +944,7 @@ def one_spectrum(iobj, specdata, meta, ebv, fastphot,
                         specdata['mask'].append(specdata['mask0'][icam])
 
                         specdata['res'].append(Resolution(res))
-                        
+
             if len(cameras) == 0:
                 errmsg = 'No good data, which should never happen.'
                 log.critical(errmsg)
@@ -956,7 +955,7 @@ def one_spectrum(iobj, specdata, meta, ebv, fastphot,
             for key in ('wave', 'flux', 'ivar', 'mask', 'res'):
                 del specdata[key + '0']
                 specdata[key] = tuple(specdata[key])
-            
+
             # Pre-compute some convenience variables for "un-hstacking"
             # an "hstacked" spectrum.
             specdata['cameras'] = np.array(cameras)
@@ -968,7 +967,7 @@ def one_spectrum(iobj, specdata, meta, ebv, fastphot,
             specdata['camerapix'] = np.zeros((ncam, 2), np.int16)
             specdata['camerapix'][:, 0] = c_starts
             specdata['camerapix'][:, 1] = c_ends
-            
+
             # use the coadded spectrum to build a robust emission-line mask
             LM = LineMasker(emline_table)
             pix = LM.build_linemask(
@@ -1351,7 +1350,7 @@ def one_stacked_spectrum(iobj, specdata, synthphot):
         for key in ('wave', 'flux', 'ivar', 'mask', 'res'):
             del specdata[key + '0']
             specdata[key] = tuple(specdata[key])
-            
+
         # Pre-compute some convenience variables for "un-hstacking"
         # an "hstacked" spectrum.
         specdata['cameras'] = np.array(cameras)

py/fastspecfit/linemasker.py

@@ -84,7 +84,7 @@ def _get_contpix(zlinewaves, sigmas, nsigma_factor=2., linemask=None, lya=False)
         for linename, zlinewave, sigma in zip(linenames, zlinewaves, linesigmas_ang):
             # skip fixed (e.g., hbeta_broad) lines
             if sigma <= 0.:
-                continue 
+                continue
             I = _get_linepix(zlinewave, sigma)
             if len(I) > 0:
                 linemask[I] = True
@@ -424,7 +424,7 @@ def _fit_patches(continuum_patches, patchMap, linemodel, debug_plots=False,
             else:
                 isNarrow = EMFit.isNarrow * Ifree
                 if np.any(isNarrow):
-                    linesigma_narrow = np.atleast_1d(linesigmas[isNarrow])[0] 
+                    linesigma_narrow = np.atleast_1d(linesigmas[isNarrow])[0]
                     linevshift_narrow = np.atleast_1d(linevshifts[isNarrow])[0]
                     maxsnr_narrow = np.max(linesnrs[isNarrow])
                 else:
@@ -785,4 +785,3 @@ def _niceline(line):
         }
 
         return out
-

py/fastspecfit/qa.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 fastspecfit.qa
 ==============
@@ -300,7 +299,7 @@ def major_formatter(x, pos):
         elif fastspec['HGAMMA_BROAD_AMP']*np.sqrt(fastspec['HGAMMA_BROAD_AMP_IVAR']) > snrcut:
             leg_broad['ewbalmer_broad'] = r'EW(H$\gamma)_{\mathrm{broad}}=$'+r'${:.1f}$'.format(fastspec['HGAMMA_BROAD_EW'])+r' $\AA$'
 
-        if (fastspec['OII_3726_AMP']*np.sqrt(fastspec['OII_3726_AMP_IVAR']) > snrcut or 
+        if (fastspec['OII_3726_AMP']*np.sqrt(fastspec['OII_3726_AMP_IVAR']) > snrcut or
             fastspec['OII_3729_AMP']*np.sqrt(fastspec['OII_3729_AMP_IVAR']) > snrcut):
             leg_narrow['ewoii'] = r'EW([OII])'+r'$={:.1f}$'.format(fastspec['OII_3726_EW']+fastspec['OII_3729_EW'])+r' $\AA$'
 
@@ -315,24 +314,24 @@ def major_formatter(x, pos):
         elif fastspec['HGAMMA_AMP']*np.sqrt(fastspec['HGAMMA_AMP_IVAR']) > snrcut:
             leg_narrow['ewbalmer_narrow'] = r'EW(H$\gamma)=$'+r'${:.1f}$'.format(fastspec['HGAMMA_EW'])+r' $\AA$'
 
-        if (fastspec['HALPHA_AMP']*np.sqrt(fastspec['HALPHA_AMP_IVAR']) > snrcut and 
+        if (fastspec['HALPHA_AMP']*np.sqrt(fastspec['HALPHA_AMP_IVAR']) > snrcut and
             fastspec['HBETA_AMP']*np.sqrt(fastspec['HBETA_AMP_IVAR']) > snrcut):
             leg_narrow['hahb'] = r'$\mathrm{H}\alpha/\mathrm{H}\beta=$'+r'${:.3f}$'.format(fastspec['HALPHA_FLUX']/fastspec['HBETA_FLUX'])
-        if 'hahb' not in leg_narrow.keys() and (fastspec['HBETA_AMP']*np.sqrt(fastspec['HBETA_AMP_IVAR']) > snrcut and 
+        if 'hahb' not in leg_narrow.keys() and (fastspec['HBETA_AMP']*np.sqrt(fastspec['HBETA_AMP_IVAR']) > snrcut and
             fastspec['HGAMMA_AMP']*np.sqrt(fastspec['HGAMMA_AMP_IVAR']) > snrcut):
             leg_narrow['hbhg'] = r'$\mathrm{H}\beta/\mathrm{H}\gamma=$'+r'${:.3f}$'.format(fastspec['HBETA_FLUX']/fastspec['HGAMMA_FLUX'])
-        if (fastspec['HBETA_AMP']*np.sqrt(fastspec['HBETA_AMP_IVAR']) > snrcut and 
-            fastspec['OIII_5007_AMP']*np.sqrt(fastspec['OIII_5007_AMP_IVAR']) > snrcut and 
+        if (fastspec['HBETA_AMP']*np.sqrt(fastspec['HBETA_AMP_IVAR']) > snrcut and
+            fastspec['OIII_5007_AMP']*np.sqrt(fastspec['OIII_5007_AMP_IVAR']) > snrcut and
             fastspec['HBETA_FLUX'] > 0 and fastspec['OIII_5007_FLUX'] > 0):
             leg_narrow['oiiihb'] = r'$\log_{10}(\mathrm{[OIII]/H}\beta)=$'+r'${:.3f}$'.format(
                 np.log10(fastspec['OIII_5007_FLUX']/fastspec['HBETA_FLUX']))
-        if (fastspec['HALPHA_AMP']*np.sqrt(fastspec['HALPHA_AMP_IVAR']) > snrcut and 
-            fastspec['NII_6584_AMP']*np.sqrt(fastspec['NII_6584_AMP_IVAR']) > snrcut and 
+        if (fastspec['HALPHA_AMP']*np.sqrt(fastspec['HALPHA_AMP_IVAR']) > snrcut and
+            fastspec['NII_6584_AMP']*np.sqrt(fastspec['NII_6584_AMP_IVAR']) > snrcut and
             fastspec['HALPHA_FLUX'] > 0 and fastspec['NII_6584_FLUX'] > 0):
             leg_narrow['niiha'] = r'$\log_{10}(\mathrm{[NII]/H}\alpha)=$'+r'${:.3f}$'.format(
                 np.log10(fastspec['NII_6584_FLUX']/fastspec['HALPHA_FLUX']))
 
-        if (fastspec['OII_3726_AMP']*np.sqrt(fastspec['OII_3726_AMP_IVAR']) > snrcut or 
+        if (fastspec['OII_3726_AMP']*np.sqrt(fastspec['OII_3726_AMP_IVAR']) > snrcut or
             fastspec['OII_3729_AMP']*np.sqrt(fastspec['OII_3729_AMP_IVAR']) > snrcut):
             #if fastspec['OII_DOUBLET_RATIO'] != 0:
             leg_narrow['oii_doublet'] = r'[OII] $\lambda3726/\lambda3729={:.3f}$'.format(fastspec['OII_DOUBLET_RATIO'])
@@ -347,7 +346,7 @@ def major_formatter(x, pos):
             sedmodel, sedphot = CTools.templates2data(
                 templates.flux, templates.wave,
                 redshift=redshift, dluminosity=dlum, photsys=metadata['PHOTSYS'],
-                synthphot=True, coeff=fastspec['COEFF'] * CTools.massnorm, 
+                synthphot=True, coeff=fastspec['COEFF'] * CTools.massnorm,
                 get_abmag=True)
         else:
             sedmodel = CTools.build_stellar_continuum(
@@ -398,7 +397,7 @@ def major_formatter(x, pos):
         else:
             contmodel = CTools.build_stellar_continuum(
                 templates.flux_nolines, fastspec['COEFF'],
-                vdisp=fastspec['VDISP'], conv_pre=templates.conv_pre_nolines, 
+                vdisp=fastspec['VDISP'], conv_pre=templates.conv_pre_nolines,
                 ebv=fastspec['AV'] / Templates.klambda(5500.)
             )
 
@@ -421,7 +420,7 @@ def major_formatter(x, pos):
             fullsmoothcontinuum = np.zeros_like(fullwave)
         else:
             fullsmoothcontinuum = CTools.smooth_continuum(
-                fullwave, np.hstack(desiresiduals), np.hstack(data['ivar']), 
+                fullwave, np.hstack(desiresiduals), np.hstack(data['ivar']),
                 np.hstack(data['linemask']), camerapix=data['camerapix'])
 
         desismoothcontinuum = []
@@ -460,7 +459,7 @@ def major_formatter(x, pos):
         if not os.path.isfile(cutoutjpeg):
             wait = 5 # seconds
             cmd = 'wget -q -O {outfile} https://www.legacysurvey.org/viewer/jpeg-cutout?ra={ra}&dec={dec}&width={width}&height={height}&layer={layer}'
-            cmd = cmd.format(outfile=cutoutjpeg, ra=metadata['RA'], dec=metadata['DEC'], 
+            cmd = cmd.format(outfile=cutoutjpeg, ra=metadata['RA'], dec=metadata['DEC'],
                              width=width, height=height, layer=layer)
             log.info(cmd)
             try:
@@ -646,7 +645,7 @@ def major_formatter(x, pos):
             sedmodel_abmag = -2.5*np.log10(sedmodel * factor)
             sedax.plot(sedwave / 1e4, sedmodel_abmag, color='slategrey', alpha=0.9, zorder=1)
 
-        sedax.scatter(sedphot['lambda_eff']/1e4, sedphot['abmag'], marker='s', 
+        sedax.scatter(sedphot['lambda_eff']/1e4, sedphot['abmag'], marker='s',
                       s=400, color='k', facecolor='none', linewidth=2, alpha=1.0, zorder=2)
 
         if not fastphot:
@@ -694,11 +693,11 @@ def major_formatter(x, pos):
             raise('Problem here!')
         #print(sed_ymin, sed_ymax)
 
-        #sedax.set_xlabel(r'Observed-frame Wavelength ($\mu$m)') 
+        #sedax.set_xlabel(r'Observed-frame Wavelength ($\mu$m)')
         sedax.set_xlim(phot_wavelims[0], phot_wavelims[1])
         sedax.set_xscale('log')
-        sedax.set_ylabel('AB mag') 
-        #sedax.set_ylabel(r'Apparent Brightness (AB mag)') 
+        sedax.set_ylabel('AB mag')
+        #sedax.set_ylabel(r'Apparent Brightness (AB mag)')
         sedax.set_ylim(sed_ymin, sed_ymax)
 
         sedax.xaxis.set_major_formatter(major_formatter)
@@ -712,7 +711,7 @@ def major_formatter(x, pos):
         sedax_twin = sedax.twiny()
         sedax_twin.set_xlim(phot_wavelims[0]/(1+redshift), phot_wavelims[1]/(1+redshift))
         sedax_twin.set_xscale('log')
-        #sedax_twin.set_xlabel(r'Rest-frame Wavelength ($\mu$m)') 
+        #sedax_twin.set_xlabel(r'Rest-frame Wavelength ($\mu$m)')
 
         sedax_twin.xaxis.set_major_formatter(major_formatter)
         restticks = np.array([0.02, 0.05, 0.1, 0.2, 0.5, 1.0, 1.5, 3.0, 5.0, 10.0, 15.0, 20.0])
@@ -865,7 +864,7 @@ def major_formatter(x, pos):
                             thislinename = thislinename.replace('-', ' ')
                             if 'CIII]'  in thislinename:
                                 thislinename = thislinename+'\n'
-                            specax.text(oneline['restwave']*(1+redshift)/1e4, spec_ymax*0.97, thislinename, 
+                            specax.text(oneline['restwave']*(1+redshift)/1e4, spec_ymax*0.97, thislinename,
                                         ha='center', va='top', rotation=270, fontsize=12, alpha=0.5)
                     else:
                         if '4363' in linename:
@@ -932,7 +931,7 @@ def major_formatter(x, pos):
                                 plotline[s:e] = oneline
                                 # stupid hack; where cameras overlap (e.g.,
                                 # Halpha on sv1-bright-22923-39627731570268174),
-                                # the wavelengths are out of order. 
+                                # the wavelengths are out of order.
                                 srt = np.argsort(fullwave)
                                 xx.plot(fullwave[srt] / 1e4, plotline[srt], lw=1, alpha=0.8, color=col2[icam])
 
@@ -1131,23 +1130,23 @@ def major_formatter(x, pos):
             _ = leg_broad.pop('dv_broad')
 
         ibox = 0
-        #fig.text(startpos, toppos, '\n'.join(txt), ha='left', va='top', fontsize=legfntsz, 
-        fig.text(boxpos[ibox], toppos, '\n'.join(txt), ha='left', va='top', fontsize=legfntsz, 
+        #fig.text(startpos, toppos, '\n'.join(txt), ha='left', va='top', fontsize=legfntsz,
+        fig.text(boxpos[ibox], toppos, '\n'.join(txt), ha='left', va='top', fontsize=legfntsz,
                  bbox=bbox, linespacing=1.4)
         ibox += 1
 
         txt = [
             r'{}'.format(leg['absmag_r']),
             r'{}'.format(leg['absmag_gr']),
-            r'{}'.format(leg['absmag_rz']), 
+            r'{}'.format(leg['absmag_rz']),
             '',
             r'{}'.format(leg['dn4000_model'])
         ]
         if 'dn4000_spec' in legkeys:
             txt += [r'{}'.format(leg['dn4000_spec'])]
 
-        #fig.text(startpos+deltapos, toppos, '\n'.join(txt), ha='left', va='top', 
-        fig.text(boxpos[ibox], toppos, '\n'.join(txt), ha='left', va='top', 
+        #fig.text(startpos+deltapos, toppos, '\n'.join(txt), ha='left', va='top',
+        fig.text(boxpos[ibox], toppos, '\n'.join(txt), ha='left', va='top',
                  fontsize=legfntsz, bbox=bbox, linespacing=1.4)
         ibox += 1
 
@@ -1488,4 +1487,3 @@ def _wrap_qa(redrockfile, indx=None, stackfit=False):
 
     # if multiprocessing, clean up workers
     mp_pool.close()
-