Python pyfits.open函数代码示例

def loadFiles(
    imName = None,
    maskName = None,
    satMaskName = None,
    invertMask = False,
):
    """Load a new image and/or mask and/or satMask from a fits file.

    Inputs:
    - imName: path to image FITS file; None to use current image
    - maskName: path to bad pixel mask; 0=good unless invertMask is true;
            None to use current mask, if any
    - satMaskName: path to saturated pixel mask; 0=good regardless of invertMask;
            None to use current mask, if any
    """
    global im, imFits, mask, maskFits, satMask, satMaskFits, isSat, sd
    if imName:
        imFits = pyfits.open(imName)
        print("Loading image %s into imFits and im" % (imName,))
        dataSec = parseDataSec(imFits[0].header.get("DATASEC"))
        dataShape = imFits[0].data.shape
        if dataSec is None:
            dataSec = [0, dataShape[0], 0, dataShape[1]]
        im = imFits[0].data[dataSec[0]:dataSec[1], dataSec[2]:dataSec[3]]
    if maskName:
        print("Loading bad pixel mask %s into maskFits and mask" % (maskName,))
        maskFits = pyfits.open(maskName)
        mask = maskFits[0].data[dataSec[0]:dataSec[1], dataSec[2]:dataSec[3]] > 0.1
    if satMaskName:
        print("Loading saturated pixel mask %s into satMaskFits and satMask" % (satMaskName,))
        satMaskFits = pyfits.open(satMaskName)
        satMask = satMaskFits[0].data[dataSec[0]:dataSec[1], dataSec[2]:dataSec[3]] > 0.1
    return im, mask, satMask

def plot_psi_weights(output,
                     modelfile='/d/monk/eigenbrot/WIYN/14B-0456/anal/models/allZ2_vardisp/allz2_vardisp_batch_interp.fits'):
    #Like the last page of all the fit plots, but for all pointings at once
    #cribbed from plot_bc_vardisp.py

    m = pyfits.open(modelfile)[1].data[0]
    numZ = np.unique(m['Z'][:,0]).size
    numAge = np.unique(m['AGE'][:,0]).size
    big_W = np.zeros((numZ,numAge))
    
    for p in range(6):
        coeffile = 'NGC_891_P{}_bin30_allz2.coef.fits'.format(p+1)
        print coeffile
        coef_arr = pyfits.open(coeffile)[1].data
        numap = coef_arr['VSYS'].size
        
        for i in range(numap):
            wdata = coef_arr[i]['LIGHT_FRAC'].reshape(numZ,numAge)
            big_W += wdata/np.max(wdata)

    bwax = plt.figure().add_subplot(111)
    bwax.imshow(big_W,origin='lower',cmap='Blues',interpolation='none')
    bwax.set_xlabel('SSP Age [Gyr]')
    bwax.set_xticks(range(numAge))
    bwax.set_xticklabels(m['AGE'][:numAge,0]/1e9)
    bwax.set_ylabel(r'$Z/Z_{\odot}$')
    bwax.set_yticks(range(numZ))
    bwax.set_yticklabels(m['Z'][::numAge,0])

    pp = PDF(output)
    pp.savefig(bwax.figure)
    pp.close()
    plt.close(bwax.figure)
    
    return

def combine_off_on(maskname, band, options, lampsOff=False):
    '''
    combine list of flats into a flat file'''


    file_off = os.path.join("combflat_lamps_off_2d_%s.fits" 
                    % (band))

    file_on = os.path.join("combflat_2d_%s.fits" 
                    % (band))

    file_on_save = os.path.join("combflat_lamps_on_2d_%s.fits" 
                    % (band))

    hdu_off  = pyfits.open(file_off)
    hdu_on   = pyfits.open(file_on)

    #save lamps On data set to new name
    hdu_on.writeto(file_on_save, clobber=True)

    hdu_on[0].data = hdu_on[0].data - hdu_off[0].data

    #Add comment that the difference was completed
    hdu_on[0].header.add_history("Differenced the Lamps on and Lamps off images ")
    #save lamps On data set to new name
    hdu_on.writeto(file_on, clobber=True)

    def test_parnames_round_trip(self):
        """
        Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/130

        Ensures that opening a random groups file in update mode or writing it
        to a new file does not cause any change to the parameter names.
        """

        # Because this test tries to update the random_groups.fits file, let's
        # make a copy of it first (so that the file doesn't actually get
        # modified in the off chance that the test fails
        self.copy_file('random_groups.fits')

        parameters = ['UU', 'VV', 'WW', 'BASELINE', 'DATE']
        with fits.open(self.temp('random_groups.fits'), mode='update') as h:
            assert h[0].parnames == parameters
            h.flush()
        # Open again just in read-only mode to ensure the parnames didn't
        # change
        with fits.open(self.temp('random_groups.fits')) as h:
            assert h[0].parnames == parameters
            h.writeto(self.temp('test.fits'))

        with fits.open(self.temp('test.fits')) as h:
            assert h[0].parnames == parameters

def fitstoarrays(ffile,fmask):

  fitsfile = pyfits.open(ffile)
  data = fitsfile[0].data

  header = pyfits.getheader(ffile)
  naxis1 = header['naxis1']
  naxis2 = header['naxis2']
  cdelt1 = header['cdelt1']
  cdelt2 = header['cdelt2']
  crpix1 = header['crpix1']
  crpix2 = header['crpix2']
  crval1 = header['crval1']
  crval2 = header['crval2']

  X = zeros(data.shape)
  Y = zeros(data.shape)

  for j in range(data.shape[0]):
    for i in range(data.shape[1]):
      X[j,i] = (1+i)*cdelt1
      Y[j,i] = (1+j)*cdelt2

  maskfile = pyfits.open(fmask)
  datam = maskfile[0].data

  mask = datam!=0
  #Z = (X**2+Y**2)

  return X[mask],Y[mask],data[mask]

def CoaddExposures(exposures, outnumber, datapath='/nfs/lsst2/photocalData/data/observer2/', verbose=False, normalise=False):
    import pyfits as pf
    import shutil
    import sys
    
    N_HDUS = 70
    print 'Coadding %s'%(exposures); sys.stdout.flush()
    n_exp = float(len(exposures))

    filenames = [datapath + 'DECam_00' + str(_) + '.fits.fz' for _ in exposures]
    outfilename = datapath + 'DECam_0' + str(9000000 + outnumber) + '.fits.fz' 
    
    shutil.copyfile(filenames[0],outfilename,)
    out_file = pf.open(outfilename, mode='update')
    
    primaryHeader = out_file[0].header
    total_EXPTIME  = primaryHeader['EXPTIME']
    total_EXPREQ   = primaryHeader['EXPREQ']
    total_DARKTIME = primaryHeader['DARKTIME']

    # convert all arrays to floats for summing and dividing purposes
    if verbose: print 'loading first file & converting dtype'
    for hdu in range(1, N_HDUS+1):
        out_file[hdu].data = out_file[hdu].data.astype(np.float32)
    
    # add other files to the original, collecting relevant metadata
    for i, filename in enumerate(filenames[1:]):
        this_file = pf.open(filename)
        total_EXPTIME  += this_file[0].header['EXPTIME']
        total_EXPREQ   += this_file[0].header['EXPREQ']
        total_DARKTIME += this_file[0].header['DARKTIME']

        for hdu in range(1, N_HDUS+1):
            if verbose: print 'adding hdu %s for file %s of %s'%(hdu,i+2,n_exp)
            out_file[hdu].data += this_file[hdu].data
    
    # Normalise
    if normalise:
        for hdu in range(1, N_HDUS+1):
            if verbose: print 'Normalising hdu %s'%hdu
            out_file[hdu].data /= n_exp

    # Update headers
    primaryHeader['nCOADDED'] = n_exp
    primaryHeader['filename'] = 'DECam_0' + str(9000000 + outnumber) + '.fits'
    primaryHeader['expnum']   = 9000000 + outnumber
    primaryHeader['COADD_OF'] = str(['DECam_00' + str(_) for _ in exposures]).translate(None, ''.join(['[',']',' ','\'']))
    primaryHeader['COADNUMS'] = (str(exposures).translate(None, ''.join(['[',']',' '])))
    if not normalise: n_exp = 1.
    primaryHeader['NORMED']   = str(normalise)
    primaryHeader['EXP_TOT']  = total_EXPTIME # always equal to the total exposure time
    primaryHeader['DARK_TOT'] = total_DARKTIME # always equal to the total darktime
    primaryHeader['EXP_T_EQ'] = total_EXPTIME / n_exp #equivalent expousre time, depending on noralisation
    primaryHeader['EXPREQ']   = total_EXPREQ / n_exp #equivalent EXPREQ time, depending on noralisation
    primaryHeader['DARKTIME'] = total_DARKTIME / n_exp #equivalent DARKTIME time, depending on noralisation

    if verbose: print 'Headers updated, writing to disk...'; sys.stdout.flush()
    out_file.flush()
    out_file.close()
    if verbose: print 'Fished coaddition of %s, written to %s'%(exposures, outfilename)

    def test_save_backup(self):
        """Test for https://trac.assembla.com/pyfits/ticket/121

        Save backup of file before flushing changes.
        """

        self.copy_file('scale.fits')

        with ignore_warnings():
            with fits.open(self.temp('scale.fits'), mode='update',
                           save_backup=True) as hdul:
                # Make some changes to the original file to force its header
                # and data to be rewritten
                hdul[0].header['TEST'] = 'TEST'
                hdul[0].data[0] = 0

        assert os.path.exists(self.temp('scale.fits.bak'))
        with fits.open(self.data('scale.fits'),
                       do_not_scale_image_data=True) as hdul1:
            with fits.open(self.temp('scale.fits.bak'),
                           do_not_scale_image_data=True) as hdul2:
                assert hdul1[0].header == hdul2[0].header
                assert (hdul1[0].data == hdul2[0].data).all()

        with ignore_warnings():
            with fits.open(self.temp('scale.fits'), mode='update',
                           save_backup=True) as hdul:
                # One more time to see if multiple backups are made
                hdul[0].header['TEST2'] = 'TEST'
                hdul[0].data[0] = 1

        assert os.path.exists(self.temp('scale.fits.bak'))
        assert os.path.exists(self.temp('scale.fits.bak.1'))

def compute_DC(pointing, folder, uw_chi):

    CI_file = glob('{}/*P{}*CI*.dat'.format(folder,pointing))[0]
    
    bestZ = np.loadtxt(CI_file, usecols=(5,), unpack=True, dtype=np.int)
    
    fzlist = ['0.005Z','0.02Z','0.2Z','0.4Z','1Z','2.5Z','allZ']

    hdu = pyfits.open('NGC_891_P{}_bin30.mso.fits'.format(pointing))[0]
    head = hdu.header
    data = hdu.data
    error = pyfits.open('NGC_891_P{}_bin30.meo.fits'.format(pointing))[0].data

    wave = (np.arange(data.shape[1]) - head['CRPIX1'] - 1)*head['CDELT1'] + head['CRVAL1']
    idx = np.where((wave >= 3800.) & (wave <= 6800.))[0]
    wave = wave[idx]
    data = data[:,idx]
    error = error[:,idx]    

    outarr = np.zeros(data.shape[0])

    for i, bz in enumerate(bestZ):
        best_file = '{}/{}/NGC_891_P{}_bin30_allz2.fit.fits'.\
                    format(folder,fzlist[bz],pointing)
        print i+1, fzlist[bz]
        models = pyfits.open(best_file)[0].data

        coef_file = '{}/{}/NGC_891_P{}_bin30_allz2.coef.fits'.\
                    format(folder,fzlist[bz],pointing)
        coefs = pyfits.open(coef_file)[1].data
        
        chisq = np.sum((data[i,:] - models[i,:])**2/error[i,:]**2)/coefs['TOTFREE'][i]
        outarr[i] = uw_chi[i] - chisq

    return outarr

def skyvar(wave, sky = 'kecksky.fits'):

    if False:
        sky = pyfits.open("kecksky.fits")
        crval = sky[0].header['CRVAL1']
        delta = sky[0].header['CDELT1']
        sky_flux = sky[0].data[0]
        print "Keck Sky used"
        
    else:
        sky = pyfits.open("licksky.fits")
        crval = sky[0].header['CRVAL1']
        delta = sky[0].header['CDELT1']        
        sky_flux = sky[0].data
        print "Lick sky used"

    start = crval - math.ceil(0.5*len(sky_flux)*delta)
    stop = crval + math.ceil(0.5*len(sky_flux)*delta)

    sky_wave = [(start+delta*i) for i in range(len(sky_flux))]

    plt.plot(sky_wave, sky_flux)
    plt.show()

    return new_sky

def fig11():
    hdulist1 = pf.open('/import/phy-pc1064_a/Documents/SiOJets_New/run4ALMA/imageShock_J2-1_45deg_molcool_dirty.fits.gz')
    hdulist2 = pf.open('/import/phy-pc1064_a/Documents/SiOJets_New/run4ALMA/imageShock_J5-4_45deg_molcool_dirty.fits.gz')
    hdulist3 = pf.open('/import/phy-pc1064_a/Documents/SiOJets_New/run4ALMA/imageShock_J8-7_45deg_molcool_dirty.fits.gz')
    
    
    A = hdulist1[0].header

    RAarr = [A['CRVAL1'] - i*A['CDELT1'] for i in range(A['NAXIS1']/2)] + [A['CRVAL1'] + i*A['CDELT1'] for i in range(A['NAXIS1']/2,A['NAXIS1'])]
    DECarr = [A['CRVAL2'] - i*A['CDELT2'] for i in range(A['NAXIS2']/2)] + [A['CRVAL2'] + i*A['CDELT2'] for i in range(A['NAXIS2']/2,A['NAXIS2'])]
    RAarr2 = RA2ICRS(RAarr)
    DECarr2 = DEC2ICRS(DECarr)
    VELarr2 = Velarr(pi/4.,100.0, A)
    print VELarr2[0]

    clevs1 = [0.0005, 0.001, 0.005, 0.025, 0.125]
    clevs2 = [0.01,0.05, 0.1, 0.2, 0.4,0.8,1.2] 
    # Get ALMA images
    f1 = plt.figure(figsize=[11,8])
    plt.subplots_adjust(wspace=0.05)
    ax1 = f1.add_subplot(121)
    
    im1 = imshow(hdulist1[0].data[:,:,:].sum(0),origin='image',vmin = 0.001, vmax = 0.25,cmap=cm.gist_heat)
    plt.colorbar(im1,ticks=clevs2)
    im2 = contour(hdulist3[0].data[:,:,:].sum(0),levels=clevs2,colors='b',linewidths=.70)
    im3 = contour(hdulist2[0].data[:,:,:].sum(0),levels=clevs2,colors='g',linewidths=.70)
    
    axis([100.0,250.0,0.0,320.0])
    ax1.xaxis.set_major_locator(MaxNLocator(4))
    ax1.yaxis.set_major_locator(MaxNLocator(4))
    locs,labels = plt.xticks()
    plt.xticks(locs,[RAarr2[int(i)] for i in locs],rotation=15)
    locs,labels = plt.yticks()
    plt.yticks(locs[1:-1],[DECarr2[int(i)] for i in locs[1:-1]],rotation=90)
    ax1.set_ylabel('Declination [J2000]')
    ax1.set_xlabel('Right Ascention [J2000]')
    plt.figtext(0.16,0.2,r'Image [Jy/beam] : 2-$>$1',color='r')
    plt.figtext(0.16,0.175,r'Green Contour : 5-$>$4',color='g')
    plt.figtext(0.16,0.15,r'Blue Contour : 8-$>$7',color='b')
    
    ax2 = f1.add_subplot(122)
    
    im1b = imshow(hdulist1[0].data[:,:,175].T,origin='image', vmax = 0.025,cmap=cm.gist_heat)
    plt.colorbar(im1b,ticks=clevs1)
    im2b = contour(hdulist3[0].data[:,:,175].T,levels=clevs1,colors='b',linewidths=.70)
    im3b = contour(hdulist2[0].data[:,:,175].T,levels=clevs1,colors='g',linewidths=.70)
    
    axis([0.0,150.0,0.0,320.0])
    ax2.xaxis.set_major_locator(MaxNLocator(4))
    #ax2.yaxis.set_major_locator(MaxNLocator(4))
    locs,labels = plt.xticks()
    plt.xticks(locs,[str('%.1f'%VELarr2[int(i)]) for i in locs])
    plt.setp(ax2,yticks=[])
    ax2.set_xlabel(r'Velocity [km s$^{-1}$]')
    
    plt.figtext(0.53,0.2,r'PV Diagram [Jy/beam] : 2-$>$1',color='r')
    plt.figtext(0.53,0.175,r'Green Contour : 5-$>$4',color='g')
    plt.figtext(0.53,0.15,r'Blue Contour : 8-$>$7',color='b')
    
    plt.show()

def FixTHINGS(imageIn, imageOut):
    
    print
    sys.stdout.write('Fixing file %s ... ' % imageIn)
    sys.stdout.flush()
    
    if imageOut != imageIn:
        hdu = pf.open(imageIn)
    else:
        hdu = pf.open(imageIn, mode='update')
        
    dataNew = hdu[0].data[0,0,:,:]
    
    del hdu[0].header['CTYPE3']; del hdu[0].header['CDELT3'];  del hdu[0].header['CRVAL3']
    del hdu[0].header['CRPIX3']; del hdu[0].header['CROTA3']
    del hdu[0].header['CTYPE4']; del hdu[0].header['CDELT4']; del hdu[0].header['CRVAL4']
    del hdu[0].header['CRPIX4']; del hdu[0].header['CROTA4']

    if imageOut != imageIn:
        if os.path.exists(imageOut): os.remove(imageOut)
        pf.writeto(imageOut, dataNew, hdu[0].header)
    else:
        hdu[0].data = dataNew
        hdu.flush()
    
    print 'Done'
    
    print
    return

    def test_hdu_fromstring(self):
        """
        Tests creating a fully-formed HDU object from a string containing the
        bytes of the HDU.
        """

        dat = open(self.data('test0.fits'), 'rb').read()

        offset = 0
        with fits.open(self.data('test0.fits')) as hdul:
            hdulen = hdul[0]._data_offset + hdul[0]._data_size
            hdu = fits.PrimaryHDU.fromstring(dat[:hdulen])
            assert isinstance(hdu, fits.PrimaryHDU)
            assert hdul[0].header == hdu.header
            assert hdu.data is None

        hdu.header['TEST'] = 'TEST'
        hdu.writeto(self.temp('test.fits'))
        with fits.open(self.temp('test.fits')) as hdul:
            assert isinstance(hdu, fits.PrimaryHDU)
            assert hdul[0].header[:-1] == hdu.header[:-1]
            assert hdul[0].header['TEST'] == 'TEST'
            assert hdu.data is None

        with fits.open(self.data('test0.fits'))as hdul:
            for ext_hdu in hdul[1:]:
                offset += hdulen
                hdulen = len(str(ext_hdu.header)) + ext_hdu._data_size
                hdu = fits.ImageHDU.fromstring(dat[offset:offset + hdulen])
                assert isinstance(hdu, fits.ImageHDU)
                assert ext_hdu.header == hdu.header
                assert (ext_hdu.data == hdu.data).all()

    def test_uint(self):
        hdulist_f = fits.open(self.data('o4sp040b0_raw.fits'))
        hdulist_i = fits.open(self.data('o4sp040b0_raw.fits'), uint=True)

        assert hdulist_f[1].data.dtype == np.float32
        assert hdulist_i[1].data.dtype == np.uint16
        assert np.all(hdulist_f[1].data == hdulist_i[1].data)

def plant(image,psf,outfile,list,dtime):
    import pyfits,os 
    import numarray as N
    psf_f=pyfits.open(psf)
    psf_flux=psf_f[0].data.sum()
    psf_x_size=psf_f[0].header.get('NAXIS1',0)
    psf_y_size=psf_f[0].header.get('NAXIS2',0)
    psf_x=psf_f[0].header.get('PSF_X',0)
    psf_y=psf_f[0].header.get('PSF_Y',0)
    psf_mag=psf_f[0].header.get('PSFMAG',26.0)
    image_f=pyfits.open(image)
    xmax=image_f[0].header.get('NAXIS1',0)
    ymax=image_f[0].header.get('NAXIS2',0)
    exptime=image_f[0].header.get('EXPTIME',1)
    zeropoint=image_f[0].header.get('PHOT_C',26.5)

    import mop_files
    ahdu=mop_files.read(list)
    import string,math,re
    from numarray.nd_image.interpolation import shift as shift

    from string import atof
    for i in range(len(ahdu['data']['x'])):
        x=float(ahdu['data']['x'][i])
        y=float(ahdu['data']['y'][i])
        mag=float(ahdu['data']['mag'][i])
        rate=float(ahdu['data']['pix_rate'][i])/3600.0
        angle=float(ahdu['data']['angle'][i])
        x_shift_rate=rate*math.cos(angle/57.3)
        y_shift_rate=rate*math.sin(angle/57.3)
        #flux=exptime*10**((zeropoint-mag)/2.5)
        #scale=flux/psf_flux
        scale=10**((psf_mag-mag)/2.5)*exptime
        #print scale
        niter=int(rate*exptime)+1
        scale=scale/niter
        dt = exptime/niter
        #print x,y,mag,niter
        for i in range(niter):
            curtime = dtime+dt*i
            x=x+x_shift_rate*curtime
            y=y+y_shift_rate*curtime
            x1=int(max(0,x-psf_x))
            x2=int(min(xmax,x+psf_x_size-psf_x))
            y1=int(max(0,y-psf_y))
            y2=int(min(ymax,y+psf_y_size-psf_y))
            #print x2,x1,y2,y1
            px1=int((psf_x-(x-x1)))
            px2=int(px1+(x2-x1))
            py1=int(psf_y-(y-y1))
            py2=int(py1+(y2-y1))
            sec = psf_f[0].data[py1:py2,px1:px2].copy()
            sec = shift(sec,(y-int(y),x-int(x)),order=3)
            #print sec.shape,y2-y1,x2-x1
            #print "Adding @ ",x,y,mag,scale," data=> ",y1,y2,x1,x2," PSF=> ",py1,py2,px1,px2
            
            image_f[0].data[y1:y2,x1:x2]+=scale*sec

    image_f.writeto(outfile)
    image_f.close()

def Select(dirin, filein , selfn, dirout,
           overwrite=False):
    "Select a subsample from ma table "

    """
    If overwrite is False, will skip existing files in destination
    directory.
    """

    mask=[ selfn(row) for row in pyfits.open(filein)[1].data ]
    mind=[ x for x,f in  enumerate (mask) if f]
    nrows=len(mind)

    print "Selected %i rows." % nrows
    
    fitsel=re.compile(".*fits?")
    flist = [ fnamein for fnamein in os.listdir(dirin) if fitsel.match(fnamein) ]
    
    for fnamein in flist:
        foutname=os.path.join(dirout,fnamein)

        if os.access(foutname, os.F_OK) and (not overwrite):
            print "Skipping %s as it already exists" % fnamein
        else:
            fin=pyfits.open(os.path.join(dirin,fnamein))

            newtab=pyfits.new_table( fin[1].columns , nrows= nrows)
            for cname in fin[1].columns.names:
                newtab.data.field(cname)._copyFrom( fin[1].data.field(cname)[ mind] )

        
            Write([pyfits.PrimaryHDU(), newtab],
                  foutname,
                  overwrite=1)