PolSpice README

v03-08-01 (22 Dec 2023)

Installation
Standard Usage
List of Keywords
Important Note
Examples
Example of Options Input File



INSTALLATION :
  See the file named INSTALL in the top directory


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STANDARD USAGE :
  spice [-keyword(1) parameter(1) ... -keyword(N) parameter(N)]
     [-optinfile parameter_file]

  All keywords are optional

Format of parameter_file :
     keyword = parameter
     see example below


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LIST OF KEYWORDS : keyword [possible parameters](default)

-about
  prints copyright info and stops

-alm1fileout [name|YES|NO](NO)
  FITS file containing a_lm (Spherical Harmonics) coefficients of
  (masked and weighted) map1, (after optional application of -alm1weightin)
  NO desactivates output of the alm
  YES activates output of the alm into alm1.fits

-alm2fileout [name|YES|NO](NO)
  FITS file containing a_lm (Spherical Harmonics) coefficients of
  (masked and weighted) map2, (after optional application of -alm2weightin)
  NO desactivates output of the alm
  YES activates output of the alm into alm2.fits

-alm1weightin [name|YES|NO](NO)
  FITS file containing (l,m) weights applied to a_lm coefficients of map1
  (those absent are assumed to be 1.0)
  (the resulting weighted a_lm can be seen in -aml1fileout)
  NO desactivates the input of alm weights
  YES reads alm weights from almw1.fits
  Beware that applying arbitrary (l,m) weights will bias the final C(l) and C(theta)
  in ways that the code does NOT attempt to correct.

-alm2weightin [name|YES|NO](NO)
  FITS file containing (l,m) weights applied to a_lm coefficients of map2
  (those absent are assumed to be 1.0)
  (the resulting weighted a_lm can be seen in -aml2fileout)
  NO desactivates the input of alm weights
  YES reads alm weights from almw2.fits
  Beware that applying arbitrary (l,m) weights will bias the final C(l) and C(theta)
  in ways that the code does NOT attempt to correct.

-apodizesigma [dfloat|NO](NO)
  scale factor in DEGREES of the correlation function tappering,
  see option -apodizetype.
  For better results, -apodizesigma should be close to -thetamax.
  NO desactivates apodization.
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already apodized.

-apodizetype [int](0)
  type of apodization
  0: the correlation function is multiplied by a gaussian window
    (equal to 1 at theta=0,
     equal to 0.5 at theta= -apodizesigma/2,
     equal to 1/16 at theta= -apodizesigma).
  1: the correlation function is multiplied by a cosine window
    (equal to 1 at theta=0,
     equal to 0.5 at theta= -apodizesigma/2,
     equal to 0 at theta= -apodizesigma).

-beam [dfloat|NO](NO)
  gaussian beam FWHM (arcmin) for map 1.
  If specified, output c_l and c_theta are corrected for it
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already corrected
  for the beam

-beam_file [name|NO](NO)
  beam window function for map 1.
  If specified, output c_l and c_theta are corrected for it
  The file should be plain ASCII with 2 columns : l and B(l)
  or FITS (ASCII or BINARY) table containing B(l) starting at l=0
  (B(l) is sqrt of beam power spectrum).
  This over-rules the gaussian correction described by beam.
  NO will not read any beam_file (but a gaussian
    correction may be performed if -beam is set).
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already corrected
  for the beam.
  Starting with version 2.90 and if linked with HEALPix 3.10+
  file.fits[extname] means extension 'extname' of file.fits

-beam2 [dfloat|NO](NO)
  gaussian beam FWHM (arcmin) for map 2 (if applicable).
  (see beam)
Note: if the second beam is the same as the first one,
  then -beam2 should be explicitely given the same value as -beam

-beam_file2 [name|NO](NO)
  beam window function for map 2 (if applicable).
  If specified, output c_l and c_theta are corrected for it
  The file should be plain ASCII with 2 columns : l and B(l)
  or FITS (ASCII or BINARY) table containing B(l) starting at l=0
  (B(l) is sqrt of beam power spectrum).
  This over-rules the gaussian correction described by -beam2.
  NO will not read any -beam_file2 (but a gaussian
    correction may be performed if -beam2 is set.
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already corrected
  for the beam.
Note: if the second beam is the same as the first one,
  then -beam_file2 should be explicitely given the same value as -beam_file

-clfile [name|YES|NO](NO)
  name of output file for Cl
  YES activates Cl file output with name spice.cl
  NO desactivates output of Cl file
  NOTE : the current format of this file is a two columns array
  the first one corresponding to the value of l, the second one
  to the temperature Cl and, if polarization is activated, five
  additional spectra corresponding to EE, BB, TE, TB, EB
  and optionally ET, BT, BE are also written.

-cl_inmap_file [name|YES|NO](NO)
  name of input file containing the raw Cls of the map as obtained by
  running previously SpICE with the option -cl_outmap_file.
  If this option is active, it is not necessary anymore to read the input
  map file, and option -cl_outmap_file is of course inactive.
  YES reads the map raw Cls from file spice.clrawmap
  NO computes the raw Cl directly from the map.
  IMPORTANT NOTE : the cls computed that way can be affected by the nature
    of the masks and/or the weights. If the masks/weights are changed,
    the calculation will become inconsistent.

-cl_inmask_file [name|YES|NO](NO)
  name of input file containing the raw Cl of the weight/masks as
  obtained by running previously SpICE with the option -cl_outmask_file.
  If option -cl_inmask_file is active, the Cls of the masks are not computed,
  they are directly read in file specified by cl_inmask_file and option
  -cl_outmask_file is of course inactive.
  With option -cl_inmask_file active, it is in principle not necessary
  to read masks nor weights, but if masks/weights are not read, it means
  that the input map is supposed to have been processed prior to using spice,
  i.e. it has been multiplied by the masks/weights already.
  YES reads the weights/mask raw Cls from file spice.clrawmasks
  NO computes the raw Cl directly from the weights/masks.
  IMPORTANT NOTE : the cls computed for the map are affected by the nature
    of the masks and/or the weights. If the masks/weights are changed,
    the calculation will become inconsistent.

-cl_outmap_file [name|YES|NO](NO)
  name of output file containing the raw Cls of the map. This can be
  convenient in order to run SpICE with different parameters, without
  having to recompute these raw Cls.
  YES activates map raw Cls output with name spice.clrawmap
  NO desactivates output of map raw Cls file.

-cl_outmask_file [name|YES|NO](NO)
  name of output file containing the raw Cls of the weights/masks.
  This can be convenient in order to run SpICE with different parameters,
  without having to recompute these raw Cls.
  YES activates mask raw Cls output with name spice.clrawmasks
  NO desactivates output of mask raw Cls file.

-corfile [name|YES|NO](NO)
  name of output correlation file
  YES activates correlation file output with name spice.cor
  NO desactivates output of correlation file
  NOTE : the current format of this file is a three columns array
  the first one corresponding to the separation theta in radians
  the second one to cos(theta), the third one to the correlation
  function of the temperature and, if polarization is activated,
  five additional columns are written, corresponding respectively to
  QQ, UU, TQ, TU and QU in the coupled case and to EE, BB, TQ, TU and QU
  in the decoupled case (see option -decouple and -symmetric_cl).

-covfileout [name|YES|NO](NO)
  Computes and ouputs the TT C(l) covariance matrices
   These matrices are not needed by the code and are provided for
  eg, cosmological interpretation of the result.
  YES activates output of the cov. matrices in default
    FITS file spice.covariance
  NO desactivates output of the matrices

-decouple [YES|NO](NO)
  computes the decoupled correlation functions
  by an integral over QQ and UU correlation functions in angle space.
  NOTE : this option is active only if -polarization=YES,
  otherwise it is ignored (see also -tolerance).
  YES activates decoupling :
    Correlation functions computed are : TT, EE, BB, TQ, TU, QU, (QT, UT, UQ)
    Cls computed are : TT, EE, BB, TE, TB, EB, (ET, BT, BE)
    with no mixing between EE and BB
  NO desactivates decoupling :
    Correlation functions computed are : TT, QQ, UU, TQ, TU, QU, (QT, UT, UQ)
    Cls computed are : TT, EE, BB, TE, TB, EB, (ET, BT, BE)
    with coupling between EE and BB

   In both cases, the TE (and TB) estimators are unbiased using window functions (see
    options -tenormfilein, -tenormfileout, -windowfilein, -windowfileout).

-dry [YES|NO](NO)
  This unsafe option allows reading partly corrupted files, i.e. with
  incomplete headers. However the size of the fits file must be correct,
  i.e. it must correspond to a full sky map with 12*nside^2 pixels.

-extramapfile [name|NO](NO)
  name of the (optional) extra input map file (healpix SP fits file)
  to be added to mapfile before analysis.
  Must be in the some Coordinates, Nside and Units as mapfile
  (ordering can be different).

-extramapfile2 [name|NO](NO)
  name of the (optional) extra input map file (healpix SP fits file)
  to be added to mapfile2 before analysis.
  Must be in the some Coordinates, Nside and Units as mapfile2
  (ordering can be different).

-fits_out [YES|NO](NO)
  If set, the Cl and correlation (-clfile, -corfile, -cl_outmap_file, -cl_outmask_file)
  are written in FITS Ascii files, instead of plain text files.
  This does not affect the input Cl files (-cl_inmap_file and -cl_inmask_file),
  which will be read whatever is their format.

-help
  print this message and stop

-history
  print history of the program and stop

-kernelsfileout [name|YES|NO](NO)
  Compute and ouput the 4 kernels, each of size (lmax+1)*(2*lmax+1),
  relating the Spice (polarized) estimator to the 'true' underlying CMB spectra.
   These kernels are not needed by the code and are provided for
  eg, cosmological interpretation of the result.
   Note that these kernels depend on the choice
  of apodization (options -apodizetype and -apodizesigma)
  and on -thetamax and -nlmax.
   How to use them depends on the -decouple option
  (see the FITS file header for more information).
   This option is inactive if any of -windowfilein or -tenormfilein is active.
  YES activates output of the kernels in default
    FITS file spice.kernels
  NO desactivates output of the kernels

-listmapfiles1_K [name|NO](NO)
  with K integer in [1, 10]
  list of map files to be combined with weights -listmapweights1_K
  to form the first map to analyze.
  If this option is set, -mapfile (and -extramapfile) are ignored

-listmapfiles2_K [name|NO](NO)
  with K integer in [1, 10]
  list of map files to be combined with weights -listmapweights2_K
  to form the optional second map to cross-correlate with the first one.
  If this option is set, -mapfile2 (and -extramapfile2) are ignored

-listmapweights1_K [dfloat|NO](1.0)
  with K integer in [1, 10]
  list of weights to be applied to -listmapfiles1_K above
  to form the first map to analyze.
  m1 = w1(1) * m1(1) + w1(2) * m1(2) + ...

-listmapweights2_K [dfloat|NO](1.0)
  with K integer in [1, 10]
  list of weights to be applied to -listmapfiles2_K above
  to form the second optional map to analyze.
  m2 = w2(1) * m2(1) + w2(2) * m2(2) + ...

-mapfile [name|YES](YES)
  name of the input map file (healpix SP fits file)
  YES is equivalent to take input file map.fits
  Starting with version 2.90 and if linked with HEALPix 3.10+
  file.fits[extname] means extension 'extname' of file.fits

-mapfile2 [name|YES|NO](NO)
  name of the second (optional) input map file (healpix SP fits file)
  to cross-correlate with the first one (-mapfile)
  If provided, ONLY cross-correlation is performed (no auto-correlation)
  YES is equivalent to take input file map2.fits
  NO turns off map-map cross-correlation

-maskfile [name|YES|NO](NO)
  name of the input mask file (healpix SP fits file)
  A mask file is composed of zeros (masked) and ones (in)
  YES activates maskfile with name mask.fits
  NO desactivates -maskfile
  For non-binary masks, see -weightfile below
  Starting with version 2.90 and if linked with HEALPix 3.10+
  file.fits[extname] means extension 'extname' of file.fits

-maskfile2 [name|YES|NO](NO)
  name of the input mask file (healpix SP fits file)
  to be applied to the second map
  YES activates -maskfile2 with name mask2.fits
  NO desactivates -maskfile2
Notes:
1) if the you want the 2nd mask to be the same as the 1st one,
   set -maskfile2 to the same name as -maskfile
2) the 2 masks should overlap at least partially

-maskfilep [name|YES](YES)
  name of the input mask file (healpix SP fits file)
  to be applied to polarization.
  By default, it is the same as -maskfile
  Ignored if polarization is set to NO

-maskfilep2 [name|YES](YES)
  name of the input mask file (healpix SP fits file)
  to be applied to the second map polarization
  By default, it is the same as -maskfile2
  Ignored if polarization is set to NO

-nlmax [integer](3*Nside-1)
  value of the largest multipole used in the analysis.
  The default is 3*Nside-1, where Nside is the Healpix resolution parameter
  of the map being analyzed.
  Any value larger than 3*Nside-1 or ≤ 0 will be replaced by the default.

-noiseclfile [name|YES|NO](NO)
  name of input file for Cls of the noise
  if -noiseclfile is specified, noise subtraction is applied
  to both final Cls and correlation function (unless -noisecorfile is
  specified for the latter)
  YES activates noise subtraction from file noise.cl
  NO desactivates noise subtraction from a Cl noise file

-noisecorfile [name|YES|NO](NO)
  name of input file for correlation function of the noise
  if -noisecorfile is specified, noise subtraction is applied
  to both final correlation function and Cls (unless -noiseclfile is
  specified for the latter)
  YES activates noise subtraction from file noise.cor
  NO desactivates noise subtraction from a correlation noise file

-normfac [dfloat|NO](NO)
  normalization factor. If normfac is specified, the correlation
  function and the Cls are multiplied by normfac**2
  NO and -normfac=1.0 are equivalent : in that case
  normalization is inactive to save calculations.
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already
  normalized appropriately

-optinfile [name|YES|NO](NO)
  Read the options in an file (only those which are not specified
  interactively are taken into account).
  YES reads default input option file .spicerc
  NO desactivates the reading.
  NOTE 1 : The file containing the options is a 2-column file,
  the first column corresponds to the option (without the "-" at the
  beginning) and the second column to the parameter (see below for
  an example).
  NOTE 2 : It is not necessary to specify all the options in this
  file, and the order in which they appear does not matter. If an
  option is specified neither in the option file nor interactively,
  then the default value is assumed for this option.

-optoutfile [name|YES|NO](NO)
  Output the options in an file (read with option -optinfile or specified
  interactively. In that case, no calculation is performed, only the
  file containing the options is created.
  YES output option file with default name .spicerc
  NO desactivates the output
  NOTE : see note of -optinfile.

-overwrite [YES|NO](YES)
  Activates overwriting for all output files.
  YES overwrite all the output files generated previously.
  NO checks if any of the output files already exist. If it is the
  case, SpICE stops without mercy.
  To have more sophisticated handling of overwriting, the standard
  Healpix syntax can be used : file names in the form !name means
  that the name of the file to be used is name and the "!" explicitely allows
  overwriting.

-pixelfile [name|YES|NO](NO)
  name of input pixel correction file for 1st map
  YES activates pixel window correction with file
  ${HEALPIXDATA}/pixel_window_nxxxx.fits
  or
  ${HEALPIX}/data/pixel_window_nxxxx.fits
  where xxxx corresponds to the value of nside of input map file.
  NO desactivates pixel window correction.
  NOTE : if noise subtraction is active (options -noisecorfile or
  -noiseclfile), the input noise data are assumed to be already corrected
  for pixel window

-pixelfile2 [name|YES|NO](pixelfile)
  name of input pixel correction file for 2nd map (for cross-analysis)
Default value is the one chosen for -pixelfile.
If set to YES explicitly, or implicitly via -pixelfile,
the standard pixel window function adapted to the 2nd map Nside will be used.
It must be set to NO to prevent pixel correction of 2nd map.

-polarization [YES|NO](NO)
  to compute polarized power spectra/correlation functions
  in addition to standard temperature Cls/correlation
  function. The input map file is supposed to be in the standard
  polarized Healpix fits format, so it contains 3 maps (T,Q,U)
  instead of one.
  The polarized Cls and correlation functions computed depend on the
  choice of parameter decouple explained below (see option -decouple).

-subav [YES|NO](NO)
  in case the input map is expected to have an offset, its (weighted)
  average can be subtracted from it prior to the calculations,
  in order to insure zero average.
  When there are masks/weights, W(i), this average is computed
  simply as [sum_i W(i) map(i)]/[sum_i W(i)].
  See options -maskfile, -weightfile, -weightpower for more information
  on the masks/weights.
  It is important to notice that the estimator of the correlation function
  or the Cls is not expected anymore to be unbiased if option -subav
  is active. It would be the case only if the offset would be exactly
  known and not estimated directly from the data.
  YES activates average subtraction.
  NO desactivates average subtraction.

-subdipole [YES|NO](NO)
  the best fit monopole and dipole will regressed out from the
  (masked and weighted) data before spectral analysis.
  YES activates dipole and monopole subtraction.
  NO desactivates dipole and monopole subtraction.
  -subdipole=YES implies -subav=YES and has the same caveats.

-symmetric_cl [YES|NO](NO)
  by default, when 2 maps are provided, and -polarization is set,
  cross spectra such as TE are defined as T_map1 * E_map2
(in which case it is recommended to use the least noisy map as map2)
  and 9 spectra are produced.
  If -symmetric_cl is set to YES, then
  TE = (T_map1 * E_map2 + T_map2 * E_map1)/2
  and 6 spectra are produced.
In the single map case, TE=ET and only 6 spectra are produced.

-tenormfilein [name|YES|NO](NO)
  this option is ignored if -polarization is not active :
  reads the normalisation function needed to compute correctly the TE (and TB) spectra
  and correlation functions, instead of computing it.
  The calculation of this term depends on the apodization chosen
  (options -apodizetype and -apodizesigma).
  YES activates input of the normalisation function with default
    input file name spice.tenorm
    and desactivates the production of -kernelsfileout
  NO desactivates input of the normalisation function : it is computed
    on run time.

-tenormfileout [name|YES|NO](NO)
  Compute and ouput the normalisation function needed to compute the
  TE (and TB) spectra. Note that this function depends on the choice
   of apodization (options -apodizetype and -apodizesigma).
  This option is inactive, of course, if option -tenormfilein is active, or
  if option -polarization is inactive.
  YES activates output of the normalisation function in default
    file spice.tenorm
  NO desactivates output of the normalisation function (but it is
    computed if needed).

-tf_file [name|NO](NO)
  name of the input tranfer function file.
  The output C(l) will be divided by the transfer function(s) read
  from this file.
  The transfer function is defined as the ratio of 2 power spectra.
  The file should have the same format as the C(l) produced by this code.

-thetamax [dfloat|NO](NO)
  maximum value of angle theta used in the integrals to compute the
  power spectra from the correlation functions.
  NO desactivates upper bound (sets it to 180 degrees).

-tolerance [dfloat|NO](NO)
  relative tolerance on convergence of QQ and UU integrals (see -decouple)
  Active only when -decouple is set
  Smaller values give more accurate EE and BB spectra, in longer times.
  NO leaves it to its default value (1.e-5).

-usage
  print short usage reminder

-verbosity [0|1|2|YES|NO](1)
  verbose option :
  0 or NO : no verbose
  1 or YES : standard verbose
  2 : full verbose

-version
  prints version number and exits

-weightfile [name|YES|NO](NO)
  name of the input weight file (healpix SP fits file)
  Weights should be always positive or equal to zero.
  If masks are present, weights are multiplied by the masks.
  If masks are not present, weights are supposed to be already masked,
  i.e. are equal to zero for masked pixels
  YES activates -weightfile with name weight.fits
  NO desactivates -weightfile

-weightfile2 [name|YES|NO](NO)
  name of the input weight file (healpix SP fits file)
  to be applied to the second map
  YES activates -weightfile2 with name weight2.fits
  NO desactivates -weightfile2

-weightfilep [name|YES](YES)
  name of the input weight file (healpix SP fits file)
  to be applied to polarization (Q and U Stokes parameters).
  By default, it is the same as -weightfile
  Ignored if polarization is set to NO

-weightfilep2 [name|YES](YES)
  name of the input weight file (healpix SP fits file)
  to be applied to the second map polarization
  By default, it is the same as -weightfile2
  Ignored if polarization is set to NO

-weightpower [dfloat|NO](1.0)
  the weights are taken to this power.
  if -weightpower = 0.0, the weights are transformed into pure masks
  if -weightpower < 0.0, only the non zero values of the weights are
  modified.
  NO is equivalent to -weightpower=1.0.

-weightpower2 [dfloat|NO](1.0)
  the weights of the second map are taken to this power.
  NO is equivalent to -weightpower2=1.0.

-weightpowerp [dfloat|YES](YES)
  the weights applied to 1st map (Q,U) are taken to this power.
  Default: same as 1st Temperature weight power (see -weightpower)

-weightpowerp2 [dfloat|YES](YES)
  the weights applied to 2nd map (Q,U) are taken to this power.
  Default: same as 2nd Temperature weight power (see -weightpower2)

-windowfilein [name|YES|NO](NO)
  this option is ignored if polarization is not active :
  reads the kcross term needed to compute correctly the TE (and TB) spectra
  and correlation functions, instead of computing it.
  The calculation of this term depends on the apodization chosen
  (options -apodizetype and -apodizesigma).
  YES activates input of the window function with default
    input file name spice.window
  NO desactivates input of the window function : it is computed
    on run time.

-windowfileout [name|YES|NO](NO)
  Compute and ouput the kcross term needed to compute the
  TE (and TB) spectra. Note that this kcross term depends on the choice
   of apodization (options -apodizetype and -apodizesigma).
  This option is inactive, of course, if option -windowfilein is active, or
  if option -polarization is inactive.
  YES activates output of the window function in default
    file spice.window
  NO desactivates output of the window function (but it is
    computed if needed).



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IMPORTANT NOTE

The order of the operations is not the same whether mask/weights are present
or not.

If there is no mask/weight, spice is nearly equivalent to anafast, and
the order of operations is the following :
  (1a) map average subtraction, if required
  (2a) calculation of Cl
  (3a) pixel window correction, beam correction, transfer function correction,
     renormalization, if required
  (4a) calculation of the 2pt correlation function, xi, if needed
  (5a) apodization of xi and calculation of the final Cl, if needed
  (6a) subtraction of noise bias on Cl and/or xi, if applicable

If there is any mask/weight, the order of operations is the following
  (1b) multiplication of the map by the masks/weights
  (2b) subtraction of the (weighted) average
  (3b) calculation of the Cl of the map and of the masks/weights
  (4b) calculation of the correlation function of the map and of the
     masks/weights, and the corresponding ratio, xi
  (5b) decoupling if needed (polarization case)
  (6b) apodization of xi, if required
  (7b) renormalization, if required
  (8b) calculation of Cl from xi, if needed
  (9b) pixel window correction, beam correction, transfer function correction,
     if required, to obtain the final Cl
(10b) calculation of final xi, if needed
(11b) subtraction of noise bias on Cl and/or xi, if applicable

Note, therefore, that if there are masks/weights, beam correction and
pixel window correction are performed AFTER apodization, at variance with
the case without mask/weight. Such ordering in the procedure is expected
to introduce a small bias in the final results. Ideally, beam and pixel
window correction should be performed before apodization, but this is
possible only prior to masking/weighting on a FULL SKY map, i.e. before
operation (1b).

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EXAMPLES

spice
spice -mapfile YES -corfile YES -clfile YES
  reads default input map, computes correlation function
  and Cl and output them on default output files
  no masks/weights are taken into account

spice -mapfile mymap.fits -weightfile weights.fits -clfile NO
  reads input map mymap.fits, input file weights.fits for weights,
  output correlation functions only

spice -mapfile mymap.fits -maskfile mymasks.fits
    -weightfile myweights.fits -beam 18.d0
  reads input map mymap.fits, input mask file mymasks.fits,
  input weight file myweights.fits, computes Cl and
  correlation function with correction for a beam of
  18 arcmin, output them on default output files. If both
  mask and weight files are specified, the weights are
  multiplied by the masks, allowing one to read a full unmasked
  weight file

spice -mapfile mymap.fits -weightfile myweights.fits
    -noisecorfile mynoise.cor -noiseclfile mynoise.cl
  reads input map mymap.fits, input weight file myweights.fits,
  computes Cls and correlation function, subtracts from Cls
  the Cls of the noise from file mynoise.cl, subtracts from
  the correlation function the correlation function of the noise
  from mynoise.cor, output the results for the Cls and the
  correlation function on default output files.
  Since only the weights are specified, they are supposed
  to be appropriately masked.
  Even if only one noise file is specified, either from the
  option -noisecorfile or from the option -noiseclfile,
  noise correction is applied to both Cls and the the
  correlation function. But this latter way is less accurate
  because of the supplementary Legendre transform it involves.

spice -mapfile mymap.fits -polarization YES \
    -maskfile mymasks.fits
  reads multiple input mapfile mymap.fits (T,Q,U), computes
  the temperature and polarization Cls (TT, GG, CC, TG, TC and GC) and
  correlation functions (TT, QQ, UU, TQ, TU, QU), and writes the
  results in default output files. All the calculations use
  appropriate mask corrections.

spice -optinfile YES
spice -optinfile .spicerc
  Read options and parameters in default file .spicerc
  and run spice accordingly.

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EXAMPLE OF OPTIONS INPUT FILE (.spicerc) :
alm1fileout = NO
alm2fileout = NO
alm1weightin = NO
alm2weightin = NO
apodizesigma = NO
apodizetype = NO
beam = NO
beam_file = NO
beam2 = NO
beam_file2 = NO
clfile = NO
cl_outmap_file = NO
cl_inmap_file = NO
cl_outmask_file = NO
cl_inmask_file = NO
corfile = NO
covfileout = NO
decouple = NO
dry = NO
extramapfile = NO
extramapfile2 = NO
fits_out = NO
kernelsfileout = NO
listmapfiles1_1 = NO
listmapfiles1_2 = NO
listmapfiles1_3 = NO
listmapfiles1_4 = NO
listmapfiles1_5 = NO
listmapfiles1_6 = NO
listmapfiles1_7 = NO
listmapfiles1_8 = NO
listmapfiles1_9 = NO
listmapfiles1_10 = NO
listmapfiles2_1 = NO
listmapfiles2_2 = NO
listmapfiles2_3 = NO
listmapfiles2_4 = NO
listmapfiles2_5 = NO
listmapfiles2_6 = NO
listmapfiles2_7 = NO
listmapfiles2_8 = NO
listmapfiles2_9 = NO
listmapfiles2_10 = NO
listmapweights1_1 = 1.0000000000000000
listmapweights1_2 = 1.0000000000000000
listmapweights1_3 = 1.0000000000000000
listmapweights1_4 = 1.0000000000000000
listmapweights1_5 = 1.0000000000000000
listmapweights1_6 = 1.0000000000000000
listmapweights1_7 = 1.0000000000000000
listmapweights1_8 = 1.0000000000000000
listmapweights1_9 = 1.0000000000000000
listmapweights1_10 = 1.0000000000000000
listmapweights2_1 = 1.0000000000000000
listmapweights2_2 = 1.0000000000000000
listmapweights2_3 = 1.0000000000000000
listmapweights2_4 = 1.0000000000000000
listmapweights2_5 = 1.0000000000000000
listmapweights2_6 = 1.0000000000000000
listmapweights2_7 = 1.0000000000000000
listmapweights2_8 = 1.0000000000000000
listmapweights2_9 = 1.0000000000000000
listmapweights2_10 = 1.0000000000000000
mapfile = map.fits
mapfile2 = NO
maskfile = NO
maskfile2 = NO
maskfilep = YES
maskfilep2 = YES
nlmax = NO
normfac = NO
npairsthreshold = NO
noisecorfile = NO
noiseclfile = NO
overwrite = YES
pixelfile = NO
pixelfile2 = NO
polarization = NO
subav = NO
subdipole = NO
symmetric_cl = NO
tenormfilein = NO
tenormfileout = NO
tf_file = NO
thetamax = NO
tolerance = NO
verbosity = 1
weightfile = NO
weightfilep = YES
weightfile2 = NO
weightfilep2 = YES
weightpower = 1.0000000000000000
weightpower2 = 1.0000000000000000
weightpowerp = 1.0000000000000000
weightpowerp2 = 1.0000000000000000
windowfilein = NO
windowfileout = NO


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Installation
Standard Usage
List of Keywords
Important Note
Examples
Example of Options Input File

File generated automatically from README on Wed Mar 6 17:38:11 CET 2024