コード例 #1
0
ファイル: saltmosaic.py プロジェクト: dr-jpk/pysalt
def saltmosaic(images,outimages,outpref,geomfile,interp='linear',geotran=True, cleanup=True,clobber=False,logfile=None,verbose=True):

   #Start the logging
   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')



       # does CCD geometry definition file exist
       geomfilefile = geomfile.strip()
       saltio.fileexists(geomfile)

       gap = 0
       xshift = [0, 0]
       yshift = [0, 0]
       rotation = [0, 0]
       gap, xshift, yshift, rotation=saltio.readccdgeom(geomfile)

       # open each raw image file and apply the transformation to it
       for img, oimg in zip(infiles, outfiles):

           #open the structure
           struct = saltio.openfits(img)

           #create the mosaic
           ostruct=make_mosaic(struct, gap, xshift, yshift, rotation, interp_type=interp, geotran=geotran, cleanup=cleanup, log=log, verbose=verbose)

           #update the header information
           # housekeeping keywords
           fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
           saltkey.housekeeping(ostruct[0], 'SMOSAIC', 'Images have been mosaicked ', hist)

           #write the image out
           saltio.writefits(ostruct,oimg, clobber=clobber)
 
           #close the files
           saltio.closefits(struct)
           saltio.closefits(ostruct)
コード例 #2
0
ファイル: saltmosaic.py プロジェクト: swj1442291549/pysalt
def saltmosaic(images,
               outimages,
               outpref,
               geomfile,
               interp='linear',
               geotran=True,
               fill=False,
               cleanup=True,
               clobber=False,
               logfile=None,
               verbose=True):

    # Start the logging
    with logging(logfile, debug) as log:

        # Check the input images
        infiles = saltio.argunpack('Input', images)

        # create list of output files
        outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')

        # verify that the input and output lists are the same length
        saltio.comparelists(infiles, outfiles, 'Input', 'output')

        # does CCD geometry definition file exist
        geomfilefile = geomfile.strip()
        saltio.fileexists(geomfile)

        gap = 0
        xshift = [0, 0]
        yshift = [0, 0]
        rotation = [0, 0]
        gap, xshift, yshift, rotation = saltio.readccdgeom(geomfile)

        # open each raw image file and apply the transformation to it
        for img, oimg in zip(infiles, outfiles):

            # open the structure
            struct = saltio.openfits(img)

            # create the mosaic
            ostruct = make_mosaic(struct,
                                  gap,
                                  xshift,
                                  yshift,
                                  rotation,
                                  interp_type=interp,
                                  geotran=geotran,
                                  fill=fill,
                                  cleanup=cleanup,
                                  log=log,
                                  verbose=verbose)

            # update the header information
            # housekeeping keywords
            fname, hist = history(level=1,
                                  wrap=False,
                                  exclude=['images', 'outimages', 'outpref'])
            saltkey.housekeeping(ostruct[0], 'SMOSAIC',
                                 'Images have been mosaicked', hist)

            # write the image out
            ostruct.writeto(oimg, clobber=clobber, output_verify='ignore')

            # close the files
            struct.close()
            ostruct.close()
コード例 #3
0
def slotmerge(images, outimages, outpref, geomfile, clobber, logfile, verbose):

    with logging(logfile, debug) as log:
        # are the arguments defined
        saltsafeio.argdefined('images', images)
        saltsafeio.argdefined('geomfile', geomfile)
        saltsafeio.argdefined('logfile', logfile)

        # if the input file is a list, does it exist?
        if images[0] == '@':
            saltsafeio.listexists('Input', images)

        # parse list of input files
        infiles = saltsafeio.listparse('Raw image', images, '', '', '')

        # check input files exist
        saltsafeio.filesexist(infiles, '', 'r')

        # load output name list: @list, * and comma separated
        outimages = outimages.strip()
        outpref = outpref.strip()
        if len(outpref) == 0 and len(outimages) == 0:
            raise SaltIOError('Output file(s) not specified')

        # test output @filelist exists
        if len(outimages) > 0 and outimages[0] == '@':
            saltsafeio.listexists('Output', outimages)

        # parse list of output files
        outfiles = saltsafeio.listparse('Output image', outimages, outpref,
                                        infiles, '')

        # are input and output lists the same length?
        saltsafeio.comparelists(infiles, outfiles, 'Input', 'output')

        # do the output files already exist?
        if not clobber:
            saltsafeio.filesexist(outfiles, '', 'w')

        # does CCD geometry definition file exist
        geomfilefile = geomfile.strip()
        saltsafeio.fileexists(geomfile)

        # read geometry definition file
        gap = 0
        xshift = [0, 0]
        yshift = [0, 0]
        rotation = [0, 0]

        gap, xshift, yshift, rotation = saltsafeio.readccdgeom(geomfile)
        for ro in rotation:
            if ro != 0:
                log.warning('SLOTMERGE currently ignores CCD rotation')

        # Begin processes each file
        for infile, outfile in zip(infiles, outfiles):
            # determine the name for the output file
            outpath = outfile.rstrip(os.path.basename(outfile))
            if (len(outpath) == 0):
                outpath = '.'

            # open each raw image
            struct = saltsafeio.openfits(infile)

            # identify instrument
            instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltsafekey.instrumid(
                struct, infile)

            # how many amplifiers?
            nccds = saltsafekey.get('NCCDS', struct[0], infile)
            amplifiers = nccds * 2
            #if (nccds != 2):
            #    raise SaltError('Can not currently handle more than two CCDs')

            # CCD geometry coefficients
            if instrume == 'RSS' or instrume == 'PFIS':
                xsh = [xshift[0], 0., xshift[1]]
                ysh = [yshift[0], 0., yshift[1]]
                rot = [rotation[0], 0., rotation[1]]
                refid = 1
            if instrume == 'SALTICAM':
                xsh = [xshift[0], 0.]
                ysh = [yshift[0], 0.]
                rot = [rotation[0], 0]
                refid = 1

            # how many extensions?
            nextend = saltsafekey.get('NEXTEND', struct[0], infile)

            # how many exposures
            exposures = nextend / amplifiers

            # CCD on-chip binning
            xbin, ybin = saltsafekey.ccdbin(struct[0], infile)
            gp = int(gap / xbin)

            # create output hdu structure
            outstruct = [None] * int(exposures + 1)
            outstruct[0] = struct[0]

            # iterate over exposures, stitch them to produce file of CCD images
            for i in range(exposures):
                # Determine the total size of the image
                xsize = 0
                ysize = 0
                for j in range(amplifiers):
                    hdu = i * amplifiers + j + 1
                    try:
                        xsize += len(struct[hdu].data[0])
                        if ysize < len(struct[hdu].data):
                            ysize = len(struct[hdu].data)
                    except:
                        msg = 'Unable to access extension %i ' % hdu
                        raise SaltIOError(msg)
                xsize += gp * (nccds - 1)
                maxxsh, minxsh = determineshifts(xsh)
                maxysh, minysh = determineshifts(ysh)
                xsize += (maxxsh - minxsh)
                ysize += (maxysh - minysh)

                # Determine the x and y origins for each frame
                xdist = 0
                ydist = 0
                shid = 0
                x0 = np.zeros(amplifiers)
                y0 = np.zeros(amplifiers)
                for j in range(amplifiers):
                    x0[j] = xdist + xsh[shid] - minxsh
                    y0[j] = ysh[shid] - minysh
                    hdu = i * amplifiers + j + 1
                    darr = struct[hdu].data
                    xdist += len(darr[0])
                    if j % 2 == 1:
                        xdist += gp
                        shid += 1

                # make the out image
                outarr = np.zeros((ysize, xsize), np.float64)

                # Embed each frame into the output array
                for j in range(amplifiers):
                    hdu = i * amplifiers + j + 1
                    darr = struct[hdu].data
                    outarr = salttran.embed(darr, x0[j], y0[j], outarr)

                # Add the outimage to the output structure
                hdu = i * amplifiers + 1
                outhdu = i + 1
                outstruct[outhdu] = pyfits.ImageHDU(outarr)
                outstruct[outhdu].header = struct[hdu].header

                # Fix the headers in each extension
                datasec = '[1:%4i,1:%4i]' % (xsize, ysize)
                saltsafekey.put('DATASEC', datasec, outstruct[outhdu], outfile)
                saltsafekey.rem('DETSIZE', outstruct[outhdu], outfile)
                saltsafekey.rem('DETSEC', outstruct[outhdu], outfile)
                saltsafekey.rem('CCDSEC', outstruct[outhdu], outfile)
                saltsafekey.rem('AMPSEC', outstruct[outhdu], outfile)

                # add housekeeping key words
                outstruct[outhdu] = addhousekeeping(outstruct[outhdu], outhdu,
                                                    outfile)

            # close input FITS file
            saltsafeio.closefits(struct)

            # housekeeping keywords
            keymosaic = 'SLOTMERG'
            fname, hist = history(level=1, wrap=False)
            saltsafekey.housekeeping(struct[0], keymosaic,
                                     'Amplifiers have been mosaiced', hist)
            #saltsafekey.history(outstruct[0],hist)

            # this is added for later use by
            saltsafekey.put('NCCDS', 0.5, outstruct[0])
            saltsafekey.put('NSCIEXT', exposures, outstruct[0])
            saltsafekey.put('NEXTEND', exposures, outstruct[0])

            # write FITS file of mosaiced image
            outstruct = pyfits.HDUList(outstruct)
            saltsafeio.writefits(outstruct, outfile, clobber=clobber)
コード例 #4
0
ファイル: slotmerge.py プロジェクト: apodemus/pysalt3
def slotmerge(images,outimages,outpref,geomfile,clobber,logfile,verbose):

    with logging(logfile,debug) as log:
        # are the arguments defined
        saltsafeio.argdefined('images',images)
        saltsafeio.argdefined('geomfile',geomfile)
        saltsafeio.argdefined('logfile',logfile)

        # if the input file is a list, does it exist?
        if images[0] == '@':
            saltsafeio.listexists('Input',images)

        # parse list of input files
        infiles=saltsafeio.listparse('Raw image',images,'','','')

        # check input files exist
        saltsafeio.filesexist(infiles,'','r')

        # load output name list: @list, * and comma separated
        outimages = outimages.strip()
        outpref = outpref.strip()
        if len(outpref) == 0 and len(outimages) == 0:
            raise SaltIOError('Output file(s) not specified')

        # test output @filelist exists
        if len(outimages) > 0 and outimages[0] == '@':
            saltsafeio.listexists('Output',outimages)

        # parse list of output files
        outfiles=saltsafeio.listparse('Output image',outimages,outpref,infiles,'')

        # are input and output lists the same length?
        saltsafeio.comparelists(infiles,outfiles,'Input','output')

        # do the output files already exist?
        if not clobber:
            saltsafeio.filesexist(outfiles,'','w')

        # does CCD geometry definition file exist
        geomfilefile = geomfile.strip()
        saltsafeio.fileexists(geomfile)

        # read geometry definition file
        gap = 0
        xshift = [0, 0]
        yshift = [0, 0]
        rotation = [0, 0]

        gap, xshift, yshift, rotation=saltsafeio.readccdgeom(geomfile)
        for ro in rotation:
            if ro!=0:
                log.warning('SLOTMERGE currently ignores CCD rotation')

        # Begin processes each file
        for infile, outfile in zip(infiles, outfiles):
            # determine the name for the output file
            outpath = outfile.rstrip(os.path.basename(outfile))
            if (len(outpath) == 0):
                outpath = '.'

            # open each raw image
            struct=saltsafeio.openfits(infile)

            # identify instrument
            instrume,keyprep,keygain,keybias,keyxtalk,keyslot=saltsafekey.instrumid(struct,infile)

            # how many amplifiers?
            nccds=saltsafekey.get('NCCDS',struct[0],infile)
            amplifiers = nccds * 2
            #if (nccds != 2):
            #    raise SaltError('Can not currently handle more than two CCDs')

            # CCD geometry coefficients
            if instrume == 'RSS' or instrume == 'PFIS':
                xsh = [xshift[0], 0., xshift[1]]
                ysh = [yshift[0], 0., yshift[1]]
                rot = [rotation[0], 0., rotation[1]]
                refid = 1
            if instrume == 'SALTICAM':
                xsh = [xshift[0], 0.]
                ysh = [yshift[0], 0.]
                rot = [rotation[0], 0]
                refid = 1

            # how many extensions?
            nextend=saltsafekey.get('NEXTEND',struct[0],infile)

            # how many exposures
            exposures = nextend/amplifiers

            # CCD on-chip binning
            xbin, ybin=saltsafekey.ccdbin(struct[0],infile)
            gp = int(gap / xbin)

            # create output hdu structure
            outstruct = [None] * int(exposures+1)
            outstruct[0]=struct[0]

            # iterate over exposures, stitch them to produce file of CCD images
            for i in range(exposures):
                # Determine the total size of the image
                xsize=0
                ysize=0
                for j in range(amplifiers):
                    hdu=i*amplifiers+j+1
                    try:
                        xsize += len(struct[hdu].data[0])
                        if ysize < len(struct[hdu].data):
                            ysize=len(struct[hdu].data)
                    except:
                        msg='Unable to access extension %i ' % hdu
                        raise SaltIOError(msg)
                xsize += gp* (nccds-1)
                maxxsh, minxsh = determineshifts(xsh)
                maxysh, minysh = determineshifts(ysh)
                xsize += (maxxsh-minxsh)
                ysize += (maxysh-minysh)

                # Determine the x and y origins for each frame
                xdist=0
                ydist=0
                shid=0
                x0=np.zeros(amplifiers)
                y0=np.zeros(amplifiers)
                for j in range(amplifiers):
                    x0[j]=xdist+xsh[shid]-minxsh
                    y0[j]=ysh[shid]-minysh
                    hdu=i*amplifiers+j+1
                    darr=struct[hdu].data
                    xdist += len(darr[0])
                    if j%2==1:
                        xdist += gp
                        shid += 1

                # make the out image
                outarr=np.zeros((ysize, xsize), np.float64)

                # Embed each frame into the output array
                for j in range(amplifiers):
                    hdu=i*amplifiers+j+1
                    darr=struct[hdu].data
                    outarr=salttran.embed(darr, x0[j], y0[j], outarr)

                # Add the outimage to the output structure
                hdu=i*amplifiers+1
                outhdu=i+1
                outstruct[outhdu] = pyfits.ImageHDU(outarr)
                outstruct[outhdu].header=struct[hdu].header

                # Fix the headers in each extension
                datasec='[1:%4i,1:%4i]' % (xsize, ysize)
                saltsafekey.put('DATASEC',datasec, outstruct[outhdu], outfile)
                saltsafekey.rem('DETSIZE',outstruct[outhdu],outfile)
                saltsafekey.rem('DETSEC',outstruct[outhdu],outfile)
                saltsafekey.rem('CCDSEC',outstruct[outhdu],outfile)
                saltsafekey.rem('AMPSEC',outstruct[outhdu],outfile)

                # add housekeeping key words
                outstruct[outhdu]=addhousekeeping(outstruct[outhdu], outhdu, outfile)

            # close input FITS file
            saltsafeio.closefits(struct)

            # housekeeping keywords
            keymosaic='SLOTMERG'
            fname, hist=history(level=1, wrap=False)
            saltsafekey.housekeeping(struct[0],keymosaic,'Amplifiers have been mosaiced', hist)
            #saltsafekey.history(outstruct[0],hist)

            # this is added for later use by
            saltsafekey.put('NCCDS', 0.5, outstruct[0])
            saltsafekey.put('NSCIEXT', exposures, outstruct[0])
            saltsafekey.put('NEXTEND', exposures, outstruct[0])

            # write FITS file of mosaiced image
            outstruct=pyfits.HDUList(outstruct)
            saltsafeio.writefits(outstruct, outfile, clobber=clobber)