示例#1
0
def main():
    import argparse

    parser = argparse.ArgumentParser(
        description='This script creates small self-contained data sets that '
        'are useful for test cases of the pipeline codes.')

    parser.add_argument('ccds', help='CCDs table describing region to grab')
    parser.add_argument('outdir', help='Output directory name')
    parser.add_argument('brick', help='Brick containing these images')

    parser.add_argument('--survey-dir', type=str, default=None)
    parser.add_argument('--cache-dir', type=str, default=None,
                        help='Directory to search for cached files')
    parser.add_argument('--wise', help='For WISE outputs, give the path to a WCS file describing the sub-brick region of interest, eg, a coadd image')
    parser.add_argument('--wise-wcs-hdu', help='For WISE outputs, the HDU to read the WCS from in the file given by --wise.', type=int, default=0)
    parser.add_argument('--fpack', action='store_true', default=False)
    parser.add_argument('--gzip', action='store_true', default=False)
    parser.add_argument('--pad', action='store_true', default=False,
                        help='Keep original image size, but zero out pixels outside ROI')
    
    args = parser.parse_args()

    v = 'SKY_TEMPLATE_DIR'
    if v in os.environ:
        del os.environ[v]

    C = fits_table(args.ccds)
    print(len(C), 'CCDs in', args.ccds)
    C.camera = np.array([c.strip() for c in C.camera])
    
    survey = LegacySurveyData(cache_dir=args.cache_dir, survey_dir=args.survey_dir)

    if ',' in args.brick:
        ra,dec = args.brick.split(',')
        ra = float(ra)
        dec = float(dec)
        fakebricks = fits_table()
        fakebricks.brickname = np.array([('custom-%06i%s%05i' %
                                          (int(1000*ra), 'm' if dec < 0 else 'p',
                                           int(1000*np.abs(dec))))])
        fakebricks.ra  = np.array([ra])
        fakebricks.dec = np.array([dec])
        bricks = fakebricks
        outbricks = bricks
    else:
        bricks = survey.get_bricks_readonly()
        outbricks = bricks[np.array([n == args.brick for n in bricks.brickname])]
        assert(len(outbricks) == 1)

    outsurvey = LegacySurveyData(survey_dir = args.outdir)
    trymakedirs(args.outdir)
    outbricks.writeto(os.path.join(args.outdir, 'survey-bricks.fits.gz'))

    targetwcs = wcs_for_brick(outbricks[0])
    H,W = targetwcs.shape

    tycho2fn = survey.find_file('tycho2')
    kd = tree_open(tycho2fn, 'stars')
    radius = 1.
    rc,dc = targetwcs.radec_center()
    I = tree_search_radec(kd, rc, dc, radius)
    print(len(I), 'Tycho-2 stars within', radius, 'deg of RA,Dec (%.3f, %.3f)' % (rc,dc))
    # Read only the rows within range.
    tycho = fits_table(tycho2fn, rows=I)
    del kd
    print('Read', len(tycho), 'Tycho-2 stars')
    ok,tx,ty = targetwcs.radec2pixelxy(tycho.ra, tycho.dec)
    #margin = 100
    #tycho.cut(ok * (tx > -margin) * (tx < W+margin) *
    #          (ty > -margin) * (ty < H+margin))
    print('Cut to', len(tycho), 'Tycho-2 stars within brick')
    del ok,tx,ty
    #tycho.writeto(os.path.join(args.outdir, 'tycho2.fits.gz'))
    f,tfn = tempfile.mkstemp(suffix='.fits')
    os.close(f)
    tycho.writeto(tfn)
    outfn = os.path.join(args.outdir, 'tycho2.kd.fits')
    cmd = 'startree -i %s -o %s -P -k -n stars -T' % (tfn, outfn)
    print(cmd)
    rtn = os.system(cmd)
    assert(rtn == 0)
    os.unlink(tfn)

    from legacypipe.gaiacat import GaiaCatalog
    gcat = GaiaCatalog()
    # from ps1cat.py:
    wcs = targetwcs
    step=100.
    margin=10.
    # Grid the CCD in pixel space
    W,H = wcs.get_width(), wcs.get_height()
    xx,yy = np.meshgrid(
        np.linspace(1-margin, W+margin, 2+int((W+2*margin)/step)),
        np.linspace(1-margin, H+margin, 2+int((H+2*margin)/step)))
    # Convert to RA,Dec and then to unique healpixes
    ra,dec = wcs.pixelxy2radec(xx.ravel(), yy.ravel())
    healpixes = set()
    for r,d in zip(ra,dec):
        healpixes.add(gcat.healpix_for_radec(r, d))
    for hp in healpixes:
        hpcat = gcat.get_healpix_catalog(hp)
        ok,xx,yy = wcs.radec2pixelxy(hpcat.ra, hpcat.dec)
        onccd = np.flatnonzero((xx >= 1.-margin) * (xx <= W+margin) *
                               (yy >= 1.-margin) * (yy <= H+margin))
        hpcat.cut(onccd)
        if len(hpcat):
            outfn = os.path.join(args.outdir, 'gaia', 'chunk-%05d.fits' % hp)
            trymakedirs(os.path.join(args.outdir, 'gaia'))
            hpcat.writeto(outfn)
    
    outccds = C.copy()
    cols = outccds.get_columns()
    for c in ['ccd_x0', 'ccd_x1', 'ccd_y0', 'ccd_y1',
              'brick_x0', 'brick_x1', 'brick_y0', 'brick_y1',
              'skyver', 'wcsver', 'psfver', 'skyplver', 'wcsplver',
              'psfplver' ]:
        if c in cols:
            outccds.delete_column(c)
    outccds.image_hdu[:] = 1

    # Convert to list to avoid truncating filenames
    outccds.image_filename = [fn for fn in outccds.image_filename]
    
    for iccd,ccd in enumerate(C):

        decam = (ccd.camera.strip() == 'decam')
        bok   = (ccd.camera.strip() == '90prime')

        im = survey.get_image_object(ccd)
        print('Got', im)
        if survey.cache_dir is not None:
            im.check_for_cached_files(survey)
        slc = (slice(ccd.ccd_y0, ccd.ccd_y1), slice(ccd.ccd_x0, ccd.ccd_x1))

        psfkwargs = dict(pixPsf=True, gaussPsf=False, hybridPsf=False,
                         normalizePsf=False)

        tim = im.get_tractor_image(slc, pixPsf=True,
                                   subsky=False, nanomaggies=False,
                                   no_remap_invvar=True, old_calibs_ok=True)
        print('Tim:', tim.shape)

        psfrow = psfhdr = None

        if args.pad:
            psf = im.read_psf_model(0, 0, w=im.width, h=im.height, **psfkwargs)
            psfex = psf.psfex
        else:
            psf = tim.getPsf()
            psfex = psf.psfex

            # Did the PSF model come from a merged file?
            for fn in [im.merged_psffn, im.psffn] + im.old_merged_psffns:
                if not os.path.exists(fn):
                    continue
                T = fits_table(fn)
                I, = np.nonzero((T.expnum == im.expnum) *
                                np.array([c.strip() == im.ccdname for c in T.ccdname]))
                if len(I) != 1:
                    continue
                psfrow = T[I]
                x0 = ccd.ccd_x0
                y0 = ccd.ccd_y0
                psfrow.polzero1[0] -= x0
                psfrow.polzero2[0] -= y0
                #psfhdr = fitsio.read_header(im.merged_psffn)
                break
        psfex.fwhm = tim.psf_fwhm

        #### HACK
        #psfrow = None
        assert(psfrow is not None)
        if psfrow is not None:
            print('PSF row:', psfrow)
        #else:
        #    print('PSF:', psf)
        #    print('PsfEx:', psfex)

        skyrow = skyhdr = None

        if args.pad:
            primhdr = fitsio.read_header(im.imgfn)
            imghdr = fitsio.read_header(im.imgfn, hdu=im.hdu)

            sky = im.read_sky_model(splinesky=True, primhdr=primhdr, imghdr=imghdr)
            #skyhdr = fitsio.read_header(im.splineskyfn)
            #msky = im.read_merged_splinesky_model(slc=slc, old_calibs_ok=True)
        else:
            sky = tim.getSky()

            # Did the sky model come from a merged file?
            #msky = im.read_merged_splinesky_model(slc=slc, old_calibs_ok=True)

        print('merged skyfn:', im.merged_skyfn)
        print('single skyfn:', im.skyfn)
        print('old merged skyfns:', im.old_merged_skyfns)

        for fn in [im.merged_skyfn, im.skyfn] + im.old_merged_skyfns:
            if not os.path.exists(fn):
                continue
            T = fits_table(fn)
            I, = np.nonzero((T.expnum == im.expnum) *
                            np.array([c.strip() == im.ccdname for c in T.ccdname]))
            skyrow = T[I]
            skyrow.x0[0] = ccd.ccd_x0
            skyrow.y0[0] = ccd.ccd_y0
            # s_med = skyrow.sky_med[0]
            # s_john = skyrow.sky_john[0]
            # skyhdr = fitsio.read_header(fn)

        assert(skyrow is not None)
        ### HACK
        #skyrow = None
                
        if skyrow is not None:
            print('Sky row:', skyrow)
        else:
            print('Sky:', sky)


        # Output filename format:
        fn = ccd.image_filename.strip()
        ccd.image_filename = os.path.join(os.path.dirname(fn),
                                          '%s.%s.fits' % (os.path.basename(fn).split('.')[0], ccd.ccdname.strip()))
        outim = outsurvey.get_image_object(ccd)
        print('Output image:', outim)
        
        print('Image filename:', outim.imgfn)
        trymakedirs(outim.imgfn, dir=True)

        imgdata = tim.getImage()
        ivdata = tim.getInvvar()

        # Since we remap DQ codes (always with Mosaic and Bok, sometimes with DECam),
        # re-read from the FITS file rather than using tim.dq.
        print('Reading data quality from', im.dqfn, 'hdu', im.hdu)
        dqdata = im._read_fits(im.dqfn, im.hdu, slice=tim.slice)

        print('Tim shape:', tim.shape, 'Slice', tim.slice)
        print('image shape:', imgdata.shape, 'iv', ivdata.shape, 'DQ', dqdata.shape)

        from collections import Counter
        dqvals = Counter(dqdata.ravel())
        print('DQ pixel counts:')
        for k,n in dqvals.most_common():
            print('  0x%x' % k, ':', n)

        if args.pad:
            # Create zero image of full size, copy in data.
            fullsize = np.zeros((ccd.height, ccd.width), imgdata.dtype)
            fullsize[slc] = imgdata
            imgdata = fullsize

            fullsize = np.zeros((ccd.height, ccd.width), dqdata.dtype)
            fullsize[slc] = dqdata
            dqdata = fullsize

            fullsize = np.zeros((ccd.height, ccd.width), ivdata.dtype)
            fullsize[slc] = ivdata
            ivdata = fullsize
            
        else:
            # Adjust the header WCS by x0,y0
            crpix1 = tim.hdr['CRPIX1']
            crpix2 = tim.hdr['CRPIX2']
            tim.hdr['CRPIX1'] = crpix1 - ccd.ccd_x0
            tim.hdr['CRPIX2'] = crpix2 - ccd.ccd_y0

        # Add image extension to filename
        # fitsio doesn't compress .fz by default, so drop .fz suffix
        
        #outim.imgfn = outim.imgfn.replace('.fits', '-%s.fits' % im.ccdname)
        if not args.fpack:
            outim.imgfn = outim.imgfn.replace('.fits.fz', '.fits')
        if args.gzip:
            outim.imgfn = outim.imgfn.replace('.fits', '.fits.gz')

        #outim.wtfn  = outim.wtfn.replace('.fits', '-%s.fits' % im.ccdname)
        if not args.fpack:
            outim.wtfn  = outim.wtfn.replace('.fits.fz', '.fits')
        if args.gzip:
            outim.wtfn = outim.wtfn.replace('.fits', '.fits.gz')

        if outim.dqfn is not None:
            #outim.dqfn  = outim.dqfn.replace('.fits', '-%s.fits' % im.ccdname)
            if not args.fpack:
                outim.dqfn  = outim.dqfn.replace('.fits.fz', '.fits')
            if args.gzip:
                outim.dqfn = outim.dqfn.replace('.fits', '.fits.gz')

        if bok:
            outim.psffn = outim.psffn.replace('.psf', '-%s.psf' % im.ccdname)

        ccdfn = outim.imgfn
        ccdfn = ccdfn.replace(outsurvey.get_image_dir(), '')
        if ccdfn.startswith('/'):
            ccdfn = ccdfn[1:]
        outccds.image_filename[iccd] = ccdfn

        print('Changed output filenames to:')
        print(outim.imgfn)
        print(outim.dqfn)

        ofn = outim.imgfn
        if args.fpack:
            f,ofn = tempfile.mkstemp(suffix='.fits')
            os.close(f)
        fits = fitsio.FITS(ofn, 'rw', clobber=True)
        fits.write(None, header=tim.primhdr)
        fits.write(imgdata, header=tim.hdr, extname=ccd.ccdname)
        fits.close()

        if args.fpack:
            cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, outim.imgfn, ofn)
            print('Running:', cmd)
            rtn = os.system(cmd)
            assert(rtn == 0)

        h,w = tim.shape
        if not args.pad:
            outccds.width[iccd] = w
            outccds.height[iccd] = h
            outccds.crpix1[iccd] = crpix1 - ccd.ccd_x0
            outccds.crpix2[iccd] = crpix2 - ccd.ccd_y0

        wcs = Tan(*[float(x) for x in
                    [ccd.crval1, ccd.crval2, ccd.crpix1, ccd.crpix2,
                     ccd.cd1_1, ccd.cd1_2, ccd.cd2_1, ccd.cd2_2, ccd.width, ccd.height]])

        if args.pad:
            subwcs = wcs
        else:
            subwcs = wcs.get_subimage(ccd.ccd_x0, ccd.ccd_y0, w, h)
            outccds.ra[iccd],outccds.dec[iccd] = subwcs.radec_center()

        print('Weight filename:', outim.wtfn)
        wfn = outim.wtfn
        trymakedirs(wfn, dir=True)

        ofn = wfn
        if args.fpack:
            f,ofn = tempfile.mkstemp(suffix='.fits')
            os.close(f)

        fits = fitsio.FITS(ofn, 'rw', clobber=True)
        fits.write(None, header=tim.primhdr)
        fits.write(ivdata, header=tim.hdr, extname=ccd.ccdname)
        fits.close()

        if args.fpack:
            cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, wfn, ofn)
            print('Running:', cmd)
            rtn = os.system(cmd)
            assert(rtn == 0)

        if outim.dqfn is not None:
            print('DQ filename', outim.dqfn)
            trymakedirs(outim.dqfn, dir=True)

            ofn = outim.dqfn
            if args.fpack:
                f,ofn = tempfile.mkstemp(suffix='.fits')
                os.close(f)

            fits = fitsio.FITS(ofn, 'rw', clobber=True)
            fits.write(None, header=tim.primhdr)
            fits.write(dqdata, header=tim.hdr, extname=ccd.ccdname)
            fits.close()

            if args.fpack:
                cmd = 'fpack -g -q 0 -S %s > %s && rm %s' % (ofn, outim.dqfn, ofn)
                print('Running:', cmd)
                rtn = os.system(cmd)
                assert(rtn == 0)

        psfout = outim.psffn
        #if psfrow:
        #    psfout = outim.merged_psffn
        print('PSF output filename:', psfout)
        trymakedirs(psfout, dir=True)
        if psfrow:
            psfrow.writeto(psfout, primhdr=psfhdr)
        else:
            print('Writing PsfEx:', psfout)
            psfex.writeto(psfout)
            # update header
            F = fitsio.FITS(psfout, 'rw')
            F[0].write_keys([dict(name='EXPNUM', value=ccd.expnum),
                             dict(name='PLVER',  value=psf.plver),
                             dict(name='PROCDATE', value=psf.procdate),
                             dict(name='PLPROCID', value=psf.plprocid),])
            F.close()

        skyout = outim.skyfn
        #if skyrow:
        #    skyout = outim.merged_splineskyfn

        print('Sky output filename:', skyout)
        trymakedirs(skyout, dir=True)
        if skyrow is not None:
            skyrow.writeto(skyout, primhdr=skyhdr)
        else:
            primhdr = fitsio.FITSHDR()
            primhdr['PLVER'] = sky.plver
            primhdr['PLPROCID'] = sky.plprocid
            primhdr['PROCDATE'] = sky.procdate
            primhdr['EXPNUM'] = ccd.expnum
            primhdr['IMGDSUM'] = sky.datasum
            primhdr['S_MED'] = s_med
            primhdr['S_JOHN'] = s_john
            sky.write_fits(skyout, primhdr=primhdr)

        # HACK -- check result immediately.
        outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))
        outsurvey.ccds = None
        outC = outsurvey.get_ccds_readonly()
        occd = outC[iccd]
        outim = outsurvey.get_image_object(occd)
        print('Got output image:', outim)
        otim = outim.get_tractor_image(pixPsf=True,
                                       hybridPsf=True, old_calibs_ok=True)
        print('Got output tim:', otim)

    outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))

    # WISE
    if args.wise is not None:
        from wise.forcedphot import unwise_tiles_touching_wcs
        from wise.unwise import (unwise_tile_wcs, unwise_tiles_touching_wcs,
                                 get_unwise_tractor_image, get_unwise_tile_dir)
        # Read WCS...
        print('Reading TAN wcs header from', args.wise, 'HDU', args.wise_wcs_hdu)
        targetwcs = Tan(args.wise, args.wise_wcs_hdu)
        tiles = unwise_tiles_touching_wcs(targetwcs)
        print('Cut to', len(tiles), 'unWISE tiles')
        H,W = targetwcs.shape
        r,d = targetwcs.pixelxy2radec(np.array([1,   W,   W/2, W/2]),
                                      np.array([H/2, H/2, 1,   H  ]))
        roiradec = [r[0], r[1], d[2], d[3]]

        unwise_dir = os.environ['UNWISE_COADDS_DIR']
        wise_out = os.path.join(args.outdir, 'images', 'unwise')
        print('Will write WISE outputs to', wise_out)

        unwise_tr_dir = os.environ['UNWISE_COADDS_TIMERESOLVED_DIR']
        wise_tr_out = os.path.join(args.outdir, 'images', 'unwise-tr')
        print('Will write WISE time-resolved outputs to', wise_tr_out)
        trymakedirs(wise_tr_out)

        W = fits_table(os.path.join(unwise_tr_dir, 'time_resolved_atlas.fits'))
        print('Read', len(W), 'time-resolved WISE coadd tiles')
        W.cut(np.array([t in tiles.coadd_id for t in W.coadd_id]))
        print('Cut to', len(W), 'time-resolved vs', len(tiles), 'full-depth')

        # Write the time-resolved index subset.
        W.writeto(os.path.join(wise_tr_out, 'time_resolved_atlas.fits'))

        # this ought to be enough for anyone =)
        _,Nepochs = W.epoch_bitmask.shape
        print('N epochs in time-resolved atlas:', Nepochs)

        wisedata = []

        # full depth
        for band in [1,2,3,4]:
            wisedata.append((unwise_dir, wise_out, tiles.coadd_id, band, True))

        # time-resolved
        for band in [1,2]:
            # W1 is bit 0 (value 0x1), W2 is bit 1 (value 0x2)
            bitmask = (1 << (band-1))
            for e in range(Nepochs):
                # Which tiles have images for this epoch?
                I = np.flatnonzero(W.epoch_bitmask[:,e] & bitmask)
                if len(I) == 0:
                    continue
                print('Epoch %i: %i tiles:' % (e, len(I)), W.coadd_id[I])
                edir = os.path.join(unwise_tr_dir, 'e%03i' % e)
                eoutdir = os.path.join(wise_tr_out, 'e%03i' % e)
                wisedata.append((edir, eoutdir, tiles.coadd_id[I], band, False))

        wrote_masks = set()

        model_dir = os.environ.get('UNWISE_MODEL_SKY_DIR')
        if model_dir is not None:
            model_dir_out = os.path.join(args.outdir, 'images', 'unwise-mod')
            trymakedirs(model_dir_out)

        for indir, outdir, tiles, band, fulldepth in wisedata:
            for tile in tiles:
                wanyband = 'w'
                tim = get_unwise_tractor_image(indir, tile, band,
                                               bandname=wanyband, roiradecbox=roiradec)
                print('Got unWISE tim', tim)
                print(tim.shape)

                if model_dir is not None and fulldepth and band in [1,2]:
                    print('ROI', tim.roi)
                    #0387p575.1.mod.fits
                    fn = '%s.%i.mod.fits' % (tile, band)
                    print('Filename', fn)
                    F = fitsio.FITS(os.path.join(model_dir, fn))
                    x0,x1,y0,y1 = tim.roi
                    slc = slice(y0,y1),slice(x0,x1)

                    phdr = F[0].read_header()

                    outfn = os.path.join(model_dir_out, fn)
                    for e,extname in [(1,'MODEL'), (2,'SKY')]:
                        pix = F[e][slc]
                        hdr = F[e].read_header()
                        crpix1 = hdr['CRPIX1']
                        crpix2 = hdr['CRPIX2']
                        hdr['CRPIX1'] -= x0
                        hdr['CRPIX2'] -= y0
                        #print('mod', mod)
                        #print('Model', mod.shape)
                        if e == 1:
                            fitsio.write(outfn, None, clobber=True, header=phdr)
                        fitsio.write(outfn, pix, header=hdr, extname=extname)
                    print('Wrote', outfn)

                thisdir = get_unwise_tile_dir(outdir, tile)
                print('Directory for this WISE tile:', thisdir)
                base = os.path.join(thisdir, 'unwise-%s-w%i-' % (tile, band))
                print('Base filename:', base)

                masked = True
                mu = 'm' if masked else 'u'

                imfn = base + 'img-%s.fits'       % mu
                ivfn = base + 'invvar-%s.fits.gz' % mu
                nifn = base + 'n-%s.fits.gz'      % mu
                nufn = base + 'n-u.fits.gz'

                #print('WISE image header:', tim.hdr)

                # Adjust the header WCS by x0,y0
                wcs = tim.wcs.wcs
                tim.hdr['CRPIX1'] = wcs.crpix[0]
                tim.hdr['CRPIX2'] = wcs.crpix[1]

                H,W = tim.shape
                tim.hdr['IMAGEW'] = W
                tim.hdr['IMAGEH'] = H

                print('WCS:', wcs)
                print('Header CRPIX', tim.hdr['CRPIX1'], tim.hdr['CRPIX2'])

                trymakedirs(imfn, dir=True)
                fitsio.write(imfn, tim.getImage(), header=tim.hdr, clobber=True)
                print('Wrote', imfn)
                fitsio.write(ivfn, tim.getInvvar(), header=tim.hdr, clobber=True)
                print('Wrote', ivfn)
                fitsio.write(nifn, tim.nims, header=tim.hdr, clobber=True)
                print('Wrote', nifn)
                fitsio.write(nufn, tim.nuims, header=tim.hdr, clobber=True)
                print('Wrote', nufn)

                if not (indir,tile) in wrote_masks:
                    print('Looking for mask file for', indir, tile)
                    # record that we tried this dir/tile combo
                    wrote_masks.add((indir,tile))
                    for idir in indir.split(':'):
                        tdir = get_unwise_tile_dir(idir, tile)
                        maskfn = 'unwise-%s-msk.fits.gz' % tile
                        fn = os.path.join(tdir, maskfn)
                        print('Mask file:', fn)
                        if os.path.exists(fn):
                            print('Reading', fn)
                            (x0,x1,y0,y1) = tim.roi
                            roislice = (slice(y0,y1), slice(x0,x1))
                            F = fitsio.FITS(fn)[0]
                            hdr = F.read_header()
                            M = F[roislice]
                            outfn = os.path.join(thisdir, maskfn)
                            fitsio.write(outfn, M, header=tim.hdr, clobber=True)
                            print('Wrote', outfn)
                            break

    outC = outsurvey.get_ccds_readonly()
    for iccd,ccd in enumerate(outC):
        outim = outsurvey.get_image_object(ccd)
        print('Got output image:', outim)
        otim = outim.get_tractor_image(pixPsf=True,
                                       hybridPsf=True, old_calibs_ok=True)
        print('Got output tim:', otim)
示例#2
0
def main():
    import argparse

    parser = argparse.ArgumentParser(
        description='This script creates small self-contained data sets that '
        'are useful for test cases of the pipeline codes.')

    parser.add_argument('ccds', help='CCDs table describing region to grab')
    parser.add_argument('outdir', help='Output directory name')
    parser.add_argument('brick', help='Brick containing these images')

    parser.add_argument('--wise', help='For WISE outputs, give the path to a WCS file describing the sub-brick region of interest, eg, a coadd image')
    parser.add_argument('--fpack', action='store_true', default=False)
    parser.add_argument('--pad', action='store_true', default=False,
                        help='Keep original image size, but zero out pixels outside ROI')
    
    args = parser.parse_args()

    C = fits_table(args.ccds)
    print(len(C), 'CCDs in', args.ccds)
    C.camera = np.array([c.strip() for c in C.camera])
    
    survey = LegacySurveyData()
    bricks = survey.get_bricks_readonly()
    outbricks = bricks[np.array([n == args.brick for n in bricks.brickname])]
    assert(len(outbricks) == 1)
    
    outsurvey = LegacySurveyData(survey_dir = args.outdir)
    trymakedirs(args.outdir)
    outbricks.writeto(os.path.join(args.outdir, 'survey-bricks.fits.gz'))

    targetwcs = wcs_for_brick(outbricks[0])
    H,W = targetwcs.shape
    
    tycho = fits_table(os.path.join(survey.get_survey_dir(), 'tycho2.fits.gz'))
    print('Read', len(tycho), 'Tycho-2 stars')
    ok,tx,ty = targetwcs.radec2pixelxy(tycho.ra, tycho.dec)
    margin = 100
    tycho.cut(ok * (tx > -margin) * (tx < W+margin) *
              (ty > -margin) * (ty < H+margin))
    print('Cut to', len(tycho), 'Tycho-2 stars within brick')
    del ok,tx,ty
    tycho.writeto(os.path.join(args.outdir, 'tycho2.fits.gz'))
    
    outccds = C.copy()
    for c in ['ccd_x0', 'ccd_x1', 'ccd_y0', 'ccd_y1',
              'brick_x0', 'brick_x1', 'brick_y0', 'brick_y1',
              'plver', 'skyver', 'wcsver', 'psfver', 'skyplver', 'wcsplver',
              'psfplver' ]:
        outccds.delete_column(c)
    outccds.image_hdu[:] = 1

    # Convert to list to avoid truncating filenames
    outccds.image_filename = [fn for fn in outccds.image_filename]
    
    for iccd,ccd in enumerate(C):

        decam = (ccd.camera.strip() == 'decam')
        bok   = (ccd.camera.strip() == '90prime')

        im = survey.get_image_object(ccd)
        print('Got', im)
        slc = (slice(ccd.ccd_y0, ccd.ccd_y1), slice(ccd.ccd_x0, ccd.ccd_x1))
        tim = im.get_tractor_image(slc, pixPsf=True, splinesky=True,
                                   subsky=False, nanomaggies=False)
        print('Tim:', tim.shape)

        psf = tim.getPsf()
        print('PSF:', psf)
        psfex = psf.psfex
        print('PsfEx:', psfex)

        outim = outsurvey.get_image_object(ccd)
        print('Output image:', outim)

        print('Image filename:', outim.imgfn)
        trymakedirs(outim.imgfn, dir=True)

        imgdata = tim.getImage()
        dqdata = tim.dq
        if decam:
            # DECam-specific code remaps the DQ codes... re-read raw
            print('Reading data quality from', im.dqfn, 'hdu', im.hdu)
            dqdata = im._read_fits(im.dqfn, im.hdu, slice=tim.slice)
        ivdata = tim.getInvvar()

        if args.pad:
            # Create zero image of full size, copy in data.
            fullsize = np.zeros((ccd.height, ccd.width), imgdata.dtype)
            fullsize[slc] = imgdata
            imgdata = fullsize

            fullsize = np.zeros((ccd.height, ccd.width), dqdata.dtype)
            fullsize[slc] = dqdata
            dqdata = fullsize

            fullsize = np.zeros((ccd.height, ccd.width), ivdata.dtype)
            fullsize[slc] = ivdata
            ivdata = fullsize
            
        else:
            # Adjust the header WCS by x0,y0
            crpix1 = tim.hdr['CRPIX1']
            crpix2 = tim.hdr['CRPIX2']
            tim.hdr['CRPIX1'] = crpix1 - ccd.ccd_x0
            tim.hdr['CRPIX2'] = crpix2 - ccd.ccd_y0

        # Add image extension to filename
        # fitsio doesn't compress .fz by default, so drop .fz suffix
        
        outim.imgfn = outim.imgfn.replace('.fits', '-%s.fits' % im.ccdname)
        if not args.fpack:
            outim.imgfn = outim.imgfn.replace('.fits.fz', '.fits')

        # if bok:
        #     outim.whtfn  = outim.whtfn .replace('.wht.fits', '-%s.wht.fits' % im.ccdname)
        #     if not args.fpack:
        #         outim.whtfn  = outim.whtfn .replace('.fits.fz', '.fits')
        # else:
        if True:
            outim.wtfn  = outim.wtfn .replace('.fits', '-%s.fits' % im.ccdname)
            if not args.fpack:
                outim.wtfn  = outim.wtfn .replace('.fits.fz', '.fits')

        if outim.dqfn is not None:
            outim.dqfn  = outim.dqfn .replace('.fits', '-%s.fits' % im.ccdname)
            if not args.fpack:
                outim.dqfn  = outim.dqfn .replace('.fits.fz', '.fits')

        if bok:
            outim.psffn = outim.psffn.replace('.psf', '-%s.psf' % im.ccdname)

        ccdfn = outim.imgfn
        ccdfn = ccdfn.replace(outsurvey.get_image_dir(),'')
        if ccdfn.startswith('/'):
            ccdfn = ccdfn[1:]
        outccds.image_filename[iccd] = ccdfn

        print('Changed output filenames to:')
        print(outim.imgfn)
        print(outim.dqfn)

        ofn = outim.imgfn
        if args.fpack:
            f,ofn = tempfile.mkstemp(suffix='.fits')
            os.close(f)
        fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
        fitsio.write(ofn, imgdata, header=tim.hdr, extname=ccd.ccdname)

        if args.fpack:
            cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, outim.imgfn, ofn)
            print('Running:', cmd)
            rtn = os.system(cmd)
            assert(rtn == 0)

        h,w = tim.shape
        if not args.pad:
            outccds.width[iccd] = w
            outccds.height[iccd] = h
            outccds.crpix1[iccd] = crpix1 - ccd.ccd_x0
            outccds.crpix2[iccd] = crpix2 - ccd.ccd_y0

        wcs = Tan(*[float(x) for x in
                    [ccd.crval1, ccd.crval2, ccd.crpix1, ccd.crpix2,
                     ccd.cd1_1, ccd.cd1_2, ccd.cd2_1, ccd.cd2_2, ccd.width, ccd.height]])

        if args.pad:
            subwcs = wcs
        else:
            subwcs = wcs.get_subimage(ccd.ccd_x0, ccd.ccd_y0, w, h)
            outccds.ra[iccd],outccds.dec[iccd] = subwcs.radec_center()

        #if not bok:
        if True:
            print('Weight filename:', outim.wtfn)
            wfn = outim.wtfn
        # else:
        #     print('Weight filename:', outim.whtfn)
        #     wfn = outim.whtfn

        trymakedirs(wfn, dir=True)

        ofn = wfn
        if args.fpack:
            f,ofn = tempfile.mkstemp(suffix='.fits')
            os.close(f)

        fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
        fitsio.write(ofn, ivdata, header=tim.hdr, extname=ccd.ccdname)

        if args.fpack:
            cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, wfn, ofn)
            print('Running:', cmd)
            rtn = os.system(cmd)
            assert(rtn == 0)

        if outim.dqfn is not None:
            print('DQ filename', outim.dqfn)
            trymakedirs(outim.dqfn, dir=True)

            ofn = outim.dqfn
            if args.fpack:
                f,ofn = tempfile.mkstemp(suffix='.fits')
                os.close(f)

            fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
            fitsio.write(ofn, dqdata, header=tim.hdr, extname=ccd.ccdname)

            if args.fpack:
                cmd = 'fpack -g -q 0 -S %s > %s && rm %s' % (ofn, outim.dqfn, ofn)
                print('Running:', cmd)
                rtn = os.system(cmd)
                assert(rtn == 0)

        print('PSF filename:', outim.psffn)
        trymakedirs(outim.psffn, dir=True)
        psfex.writeto(outim.psffn)

        if not bok:
            print('Sky filename:', outim.splineskyfn)
            sky = tim.getSky()
            print('Sky:', sky)
            trymakedirs(outim.splineskyfn, dir=True)
            sky.write_fits(outim.splineskyfn)

    outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))

    # WISE
    if args.wise is not None:
        from wise.forcedphot import unwise_tiles_touching_wcs
        from wise.unwise import (unwise_tile_wcs, unwise_tiles_touching_wcs,
                                 get_unwise_tractor_image, get_unwise_tile_dir)
        # Read WCS...
        print('Reading TAN wcs header from', args.wise)
        targetwcs = Tan(args.wise)
        tiles = unwise_tiles_touching_wcs(targetwcs)
        print('Cut to', len(tiles), 'unWISE tiles')
        H,W = targetwcs.shape
        r,d = targetwcs.pixelxy2radec(np.array([1,   W,   W/2, W/2]),
                                      np.array([H/2, H/2, 1,   H  ]))
        roiradec = [r[0], r[1], d[2], d[3]]

        unwise_dir = os.environ['UNWISE_COADDS_DIR']
        wise_out = os.path.join(args.outdir, 'images', 'unwise')
        print('Will write WISE outputs to', wise_out)

        unwise_tr_dir = os.environ['UNWISE_COADDS_TIMERESOLVED_DIR']
        wise_tr_out = os.path.join(args.outdir, 'images', 'unwise-tr')
        print('Will write WISE time-resolved outputs to', wise_tr_out)

        W = fits_table(os.path.join(unwise_tr_dir, 'time_resolved_neo1-atlas.fits'))
        print('Read', len(W), 'time-resolved WISE coadd tiles')
        W.cut(np.array([t in tiles.coadd_id for t in W.coadd_id]))
        print('Cut to', len(W), 'time-resolved vs', len(tiles), 'full-depth')

        # Write the time-resolved index subset.
        W.writeto(os.path.join(wise_tr_out, 'time_resolved_neo1-atlas.fits'))

        # this ought to be enough for anyone =)
        Nepochs = 5

        wisedata = []

        # full depth
        for band in [1,2,3,4]:
            wisedata.append((unwise_dir, wise_out, tiles.coadd_id, band))

        # time-resolved
        for band in [1,2]:
            # W1 is bit 0 (value 0x1), W2 is bit 1 (value 0x2)
            bitmask = (1 << (band-1))
            for e in range(Nepochs):
                # Which tiles have images for this epoch?
                I = np.flatnonzero(W.epoch_bitmask[:,e] & bitmask)
                if len(I) == 0:
                    continue
                print('Epoch %i: %i tiles:' % (e, len(I)), W.coadd_id[I])
                edir = os.path.join(unwise_tr_dir, 'e%03i' % e)
                eoutdir = os.path.join(wise_tr_out, 'e%03i' % e)
                wisedata.append((edir, eoutdir, tiles.coadd_id[I], band))

        wrote_masks = set()

        for indir, outdir, tiles, band in wisedata:
            for tile in tiles:
                wanyband = 'w'
                tim = get_unwise_tractor_image(indir, tile, band,
                                               bandname=wanyband, roiradecbox=roiradec)
                print('Got unWISE tim', tim)
                print(tim.shape)
                
                thisdir = get_unwise_tile_dir(outdir, tile)
                print('Directory for this WISE tile:', thisdir)
                base = os.path.join(thisdir, 'unwise-%s-w%i-' % (tile, band))
                print('Base filename:', base)

                masked = True
                mu = 'm' if masked else 'u'

                imfn = base + 'img-%s.fits'       % mu
                ivfn = base + 'invvar-%s.fits.gz' % mu
                nifn = base + 'n-%s.fits.gz'      % mu
                nufn = base + 'n-u.fits.gz'

                #print('WISE image header:', tim.hdr)

                # Adjust the header WCS by x0,y0
                wcs = tim.wcs.wcs
                tim.hdr['CRPIX1'] = wcs.crpix[0]
                tim.hdr['CRPIX2'] = wcs.crpix[1]

                H,W = tim.shape
                tim.hdr['IMAGEW'] = W
                tim.hdr['IMAGEH'] = H

                print('WCS:', wcs)
                print('Header CRPIX', tim.hdr['CRPIX1'], tim.hdr['CRPIX2'])

                trymakedirs(imfn, dir=True)
                fitsio.write(imfn, tim.getImage(), header=tim.hdr, clobber=True)
                print('Wrote', imfn)
                fitsio.write(ivfn, tim.getInvvar(), header=tim.hdr, clobber=True)
                print('Wrote', ivfn)
                fitsio.write(nifn, tim.nims, header=tim.hdr, clobber=True)
                print('Wrote', nifn)
                fitsio.write(nufn, tim.nuims, header=tim.hdr, clobber=True)
                print('Wrote', nufn)

                if not (indir,tile) in wrote_masks:
                    print('Looking for mask file for', indir, tile)
                    # record that we tried this dir/tile combo
                    wrote_masks.add((indir,tile))
                    for idir in indir.split(':'):
                        tdir = get_unwise_tile_dir(idir, tile)
                        maskfn = 'unwise-%s-msk.fits.gz' % tile
                        fn = os.path.join(tdir, maskfn)
                        print('Mask file:', fn)
                        if os.path.exists(fn):
                            print('Reading', fn)
                            (x0,x1,y0,y1) = tim.roi
                            roislice = (slice(y0,y1), slice(x0,x1))
                            F = fitsio.FITS(fn)[0]
                            hdr = F.read_header()
                            M = F[roislice]
                            outfn = os.path.join(thisdir, maskfn)
                            fitsio.write(outfn, M, header=tim.hdr, clobber=True)
                            print('Wrote', outfn)
                            break

    outC = outsurvey.get_ccds_readonly()
    for iccd,ccd in enumerate(outC):
        outim = outsurvey.get_image_object(ccd)
        print('Got output image:', outim)
        otim = outim.get_tractor_image(pixPsf=True, splinesky=True)
        print('Got output tim:', otim)