def main(): from astrometry.util.fits import fits_table, merge_tables from legacypipe.survey import exposure_metadata # Fake up a survey-ccds.fits table from MzLS_CP from glob import glob #fns = glob('/project/projectdirs/cosmo/staging/mosaicz/MZLS_CP/CP20160202/k4m_160203_*oki*') fns = glob('/project/projectdirs/cosmo/staging/mosaicz/MZLS_CP/CP20160202/k4m_160203_08*oki*') print('Filenames:', fns) T = exposure_metadata(fns) # HACK T.fwhm = T.seeing / 0.262 # FAKE T.ccdnmatch = np.zeros(len(T), np.int32) + 50 T.zpt = np.zeros(len(T), np.float32) + 26.518 T.ccdzpt = T.zpt.copy() T.ccdraoff = np.zeros(len(T), np.float32) T.ccddecoff = np.zeros(len(T), np.float32) fmap = {'zd':'z'} T.filter = np.array([fmap[f] for f in T.filter]) T.writeto('mzls-ccds.fits') os.system('cp mzls-ccds.fits ~/legacypipe-dir/survey-ccds.fits') os.system('gzip -f ~/legacypipe-dir/survey-ccds.fits') import sys sys.exit(0) import logging import sys from legacypipe.runbrick import run_brick, get_runbrick_kwargs, get_parser parser = get_parser() opt = parser.parse_args() if opt.brick is None and opt.radec is None: parser.print_help() return -1 survey, kwargs = get_runbrick_kwargs(opt) if kwargs in [-1, 0]: return kwargs if opt.verbose == 0: lvl = logging.INFO else: lvl = logging.DEBUG logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout) kwargs.update(splinesky=True, pixPsf=True) run_brick(opt.brick, survey, **kwargs)
def main(survey=None, opt=None): '''Driver function for forced photometry of individual DECam images. ''' if opt is None: parser = get_parser() opt = parser.parse_args() Time.add_measurement(MemMeas) t0 = Time() if os.path.exists(opt.outfn): print('Ouput file exists:', opt.outfn) sys.exit(0) if not opt.forced: opt.apphot = True zoomslice = None if opt.zoom is not None: (x0,x1,y0,y1) = opt.zoom zoomslice = (slice(y0,y1), slice(x0,x1)) ps = None if opt.plots is not None: from astrometry.util.plotutils import PlotSequence ps = PlotSequence(opt.plots) # Try parsing filename as exposure number. try: expnum = int(opt.filename) opt.filename = None except: # make this 'None' for survey.find_ccds() expnum = None # Try parsing HDU number try: opt.hdu = int(opt.hdu) ccdname = None except: ccdname = opt.hdu opt.hdu = -1 if survey is None: survey = LegacySurveyData() if opt.filename is not None and opt.hdu >= 0: # Read metadata from file T = exposure_metadata([opt.filename], hdus=[opt.hdu]) print('Metadata:') T.about() else: # Read metadata from survey-ccds.fits table T = survey.find_ccds(expnum=expnum, ccdname=ccdname) print(len(T), 'with expnum', expnum, 'and CCDname', ccdname) if opt.hdu >= 0: T.cut(T.image_hdu == opt.hdu) print(len(T), 'with HDU', opt.hdu) if opt.filename is not None: T.cut(np.array([f.strip() == opt.filename for f in T.image_filename])) print(len(T), 'with filename', opt.filename) assert(len(T) == 1) ccd = T[0] im = survey.get_image_object(ccd) tim = im.get_tractor_image(slc=zoomslice, pixPsf=True, splinesky=True, constant_invvar=opt.constant_invvar) print('Got tim:', tim) print('Read image:', Time()-t0) if opt.catfn in ['DR1', 'DR2', 'DR3']: margin = 20 TT = [] chipwcs = tim.subwcs bricks = bricks_touching_wcs(chipwcs, survey=survey) for b in bricks: # there is some overlap with this brick... read the catalog. fn = survey.find_file('tractor', brick=b.brickname) if not os.path.exists(fn): print('WARNING: catalog', fn, 'does not exist. Skipping!') continue print('Reading', fn) T = fits_table(fn) ok,xx,yy = chipwcs.radec2pixelxy(T.ra, T.dec) W,H = chipwcs.get_width(), chipwcs.get_height() I = np.flatnonzero((xx >= -margin) * (xx <= (W+margin)) * (yy >= -margin) * (yy <= (H+margin))) T.cut(I) print('Cut to', len(T), 'sources within image + margin') # print('Brick_primary:', np.unique(T.brick_primary)) T.cut(T.brick_primary) print('Cut to', len(T), 'on brick_primary') T.cut((T.out_of_bounds == False) * (T.left_blob == False)) print('Cut to', len(T), 'on out_of_bounds and left_blob') if len(T): TT.append(T) if len(TT) == 0: print('No sources to photometer.') return 0 T = merge_tables(TT, columns='fillzero') T._header = TT[0]._header del TT # Fix up various failure modes: # FixedCompositeGalaxy(pos=RaDecPos[240.51147402832561, 10.385488075518923], brightness=NanoMaggies: g=(flux -2.87), r=(flux -5.26), z=(flux -7.65), fracDev=FracDev(0.60177207), shapeExp=re=3.78351e-44, e1=9.30367e-13, e2=1.24392e-16, shapeDev=re=inf, e1=-0, e2=-0) # -> convert to EXP I = np.flatnonzero(np.array([((t.type == 'COMP') and (not np.isfinite(t.shapedev_r))) for t in T])) if len(I): print('Converting', len(I), 'bogus COMP galaxies to EXP') for i in I: T.type[i] = 'EXP' # Same thing with the exp component. # -> convert to DEV I = np.flatnonzero(np.array([((t.type == 'COMP') and (not np.isfinite(t.shapeexp_r))) for t in T])) if len(I): print('Converting', len(I), 'bogus COMP galaxies to DEV') for i in I: T.type[i] = 'DEV' if opt.write_cat: T.writeto(opt.write_cat) print('Wrote catalog to', opt.write_cat) else: T = fits_table(opt.catfn) surveydir = survey.get_survey_dir() del survey cat = read_fits_catalog(T) # print('Got cat:', cat) print('Read catalog:', Time()-t0) print('Forced photom...') opti = None forced_kwargs = {} if opt.ceres: from tractor.ceres_optimizer import CeresOptimizer B = 8 opti = CeresOptimizer(BW=B, BH=B) #forced_kwargs.update(verbose=True) for src in cat: # Limit sizes of huge models from tractor.galaxy import ProfileGalaxy if isinstance(src, ProfileGalaxy): px,py = tim.wcs.positionToPixel(src.getPosition()) h = src._getUnitFluxPatchSize(tim, px, py, tim.modelMinval) MAXHALF = 128 if h > MAXHALF: print('halfsize', h,'for',src,'-> setting to',MAXHALF) src.halfsize = MAXHALF tr = Tractor([tim], cat, optimizer=opti) tr.freezeParam('images') for src in cat: src.freezeAllBut('brightness') src.getBrightness().freezeAllBut(tim.band) disable_galaxy_cache() F = fits_table() F.brickid = T.brickid F.brickname = T.brickname F.objid = T.objid F.filter = np.array([tim.band] * len(T)) F.mjd = np.array([tim.primhdr['MJD-OBS']] * len(T)) F.exptime = np.array([tim.primhdr['EXPTIME']] * len(T)).astype(np.float32) ok,x,y = tim.sip_wcs.radec2pixelxy(T.ra, T.dec) F.x = (x-1).astype(np.float32) F.y = (y-1).astype(np.float32) if opt.forced: if opt.plots is None: forced_kwargs.update(wantims=False) R = tr.optimize_forced_photometry(variance=True, fitstats=True, shared_params=False, priors=False, **forced_kwargs) if opt.plots: (data,mod,ie,chi,roi) = R.ims1[0] ima = tim.ima imchi = dict(interpolation='nearest', origin='lower', vmin=-5, vmax=5) plt.clf() plt.imshow(data, **ima) plt.title('Data: %s' % tim.name) ps.savefig() plt.clf() plt.imshow(mod, **ima) plt.title('Model: %s' % tim.name) ps.savefig() plt.clf() plt.imshow(chi, **imchi) plt.title('Chi: %s' % tim.name) ps.savefig() F.flux = np.array([src.getBrightness().getFlux(tim.band) for src in cat]).astype(np.float32) F.flux_ivar = R.IV.astype(np.float32) F.fracflux = R.fitstats.profracflux.astype(np.float32) F.rchi2 = R.fitstats.prochi2 .astype(np.float32) print('Forced photom:', Time()-t0) if opt.apphot: import photutils img = tim.getImage() ie = tim.getInvError() with np.errstate(divide='ignore'): imsigma = 1. / ie imsigma[ie == 0] = 0. apimg = [] apimgerr = [] # Aperture photometry locations xxyy = np.vstack([tim.wcs.positionToPixel(src.getPosition()) for src in cat]).T apxy = xxyy - 1. apertures = apertures_arcsec / tim.wcs.pixel_scale() print('Apertures:', apertures, 'pixels') for rad in apertures: aper = photutils.CircularAperture(apxy, rad) p = photutils.aperture_photometry(img, aper, error=imsigma) apimg.append(p.field('aperture_sum')) apimgerr.append(p.field('aperture_sum_err')) ap = np.vstack(apimg).T ap[np.logical_not(np.isfinite(ap))] = 0. F.apflux = ap.astype(np.float32) ap = 1./(np.vstack(apimgerr).T)**2 ap[np.logical_not(np.isfinite(ap))] = 0. F.apflux_ivar = ap.astype(np.float32) print('Aperture photom:', Time()-t0) program_name = sys.argv[0] version_hdr = get_version_header(program_name, surveydir) filename = getattr(ccd, 'image_filename') if filename is None: # HACK -- print only two directory names + filename of CPFILE. fname = os.path.basename(im.imgfn) d = os.path.dirname(im.imgfn) d1 = os.path.basename(d) d = os.path.dirname(d) d2 = os.path.basename(d) filename = os.path.join(d2, d1, fname) print('Trimmed filename to', filename) version_hdr.add_record(dict(name='CPFILE', value=filename, comment='CP file')) version_hdr.add_record(dict(name='CPHDU', value=im.hdu, comment='CP ext')) version_hdr.add_record(dict(name='CAMERA', value=ccd.camera, comment='Camera')) version_hdr.add_record(dict(name='EXPNUM', value=im.expnum, comment='Exposure num')) version_hdr.add_record(dict(name='CCDNAME', value=im.ccdname, comment='CCD name')) version_hdr.add_record(dict(name='FILTER', value=tim.band, comment='Bandpass of this image')) version_hdr.add_record(dict(name='EXPOSURE', value='%s-%s-%s' % (ccd.camera, im.expnum, im.ccdname), comment='Name of this image')) keys = ['TELESCOP','OBSERVAT','OBS-LAT','OBS-LONG','OBS-ELEV', 'INSTRUME'] for key in keys: if key in tim.primhdr: version_hdr.add_record(dict(name=key, value=tim.primhdr[key])) hdr = fitsio.FITSHDR() units = {'exptime':'sec', 'flux':'nanomaggy', 'flux_ivar':'1/nanomaggy^2'} columns = F.get_columns() for i,col in enumerate(columns): if col in units: hdr.add_record(dict(name='TUNIT%i' % (i+1), value=units[col])) outdir = os.path.dirname(opt.outfn) if len(outdir): trymakedirs(outdir) fitsio.write(opt.outfn, None, header=version_hdr, clobber=True) F.writeto(opt.outfn, header=hdr, append=True) print('Wrote', opt.outfn) if opt.save_model or opt.save_data: hdr = fitsio.FITSHDR() tim.getWcs().wcs.add_to_header(hdr) if opt.save_model: print('Getting model image...') mod = tr.getModelImage(tim) fitsio.write(opt.save_model, mod, header=hdr, clobber=True) print('Wrote', opt.save_model) if opt.save_data: fitsio.write(opt.save_data, tim.getImage(), header=hdr, clobber=True) print('Wrote', opt.save_data) print('Finished forced phot:', Time()-t0) return 0