{"id":16519738,"url":"https://github.com/zonca/polspice","last_synced_at":"2026-03-04T22:31:23.204Z","repository":{"id":138273248,"uuid":"306778755","full_name":"zonca/polspice","owner":"zonca","description":null,"archived":false,"fork":false,"pushed_at":"2020-10-24T01:05:57.000Z","size":156,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-13T09:23:26.187Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zonca.png","metadata":{"files":{"readme":"README","changelog":"HISTORY","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-10-24T01:00:42.000Z","updated_at":"2020-10-24T01:05:59.000Z","dependencies_parsed_at":null,"dependency_job_id":"7b467215-88df-4d6f-8640-bbf6e6f625b0","html_url":"https://github.com/zonca/polspice","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zonca%2Fpolspice","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zonca%2Fpolspice/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zonca%2Fpolspice/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zonca%2Fpolspice/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zonca","download_url":"https://codeload.github.com/zonca/polspice/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241580299,"owners_count":19985519,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-11T16:48:08.173Z","updated_at":"2026-03-04T22:31:23.166Z","avatar_url":"https://github.com/zonca.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"\nINSTALLATION : \n   See the file named INSTALL in the top directory \n  \nSTANDARD USAGE : \n   spice [-keyword(1) parameter(1) ... -keyword(N) parameter(N)] \n         [-optinfile parameter_file]\n  \n   All keywords are optional\n  \n Format of parameter_file :\n              keyword = parameter\n       see example below\n\nLIST OF KEYWORDS :     keyword [possible parameters](default)\n\n-about\n   print copyright info and stop\n\n-alm1fileout [name|YES|NO](NO)\n   FITS file containing a_lm coefficients of (masked and weighted) map1\n   NO desactivates output of the alm\n   YES activates output of the alm into alm1.fits\n\n-alm2fileout [name|YES|NO](NO)\n   FITS file containing a_lm coefficients of (masked and weighted) map2\n   NO desactivates output of the alm\n   YES activates output of the alm into alm1.fits\n\n-apodizesigma [dfloat|NO](NO)\n   scale factor in DEGREES of the correlation function tappering,\n   see option -apodizetype.\n   For better results, -apodizesigma should be close to -thetamax.\n   NO desactivates apodization.\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already apodized.\n\n-apodizetype [int](0)\n   type of apodization\n   0: the correlation function is multiplied by a gaussian window\n      (equal to 1    at theta=0,\n       equal to 0.5  at theta= -apodizesigma/2,\n       equal to 1/16 at theta= -apodizesigma).\n   1: the correlation function is multiplied by a cosine window \n      (equal to 1   at theta=0,\n       equal to 0.5 at theta= -apodizesigma/2,\n       equal to 0   at theta= -apodizesigma).\n\n-beam [dfloat|NO](NO)\n   gaussian beam FWHM (arcmin) for map 1.\n   If specified, output c_l and c_theta are corrected for it\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already corrected\n   for the beam\n\n-beam_file [name|NO](NO)\n   beam window function for map 1.\n   If specified, output c_l and c_theta are corrected for it\n   The file should be plain ASCII with 2 columns : l and B(l) \n   or FITS (ASCII or BINARY) table containing B(l) starting at l=0\n   (B(l) is sqrt of beam power spectrum).\n   This over-rules the gaussian correction described by beam.\n   NO will not read any beam_file (but a gaussian\n      correction may be performed if -beam is set).\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already corrected\n   for the beam.\n   Starting with version 2.90 and if linked with HEALPix 3.10+\n   file.fits[extname] means extension 'extname' of file.fits\n\n-beam2 [dfloat|NO](NO)\n   gaussian beam FWHM (arcmin) for map 2 (if applicable).\n   (see beam)\n  Note: if the second beam is the same as the first one,\n   then -beam2 should be explicitely given the same value as -beam\n\n-beam_file2 [name|NO](NO)\n   beam window function for map 2 (if applicable).\n   If specified, output c_l and c_theta are corrected for it\n   The file should be plain ASCII with 2 columns : l and B(l) \n   or FITS (ASCII or BINARY) table containing B(l) starting at l=0\n   (B(l) is sqrt of beam power spectrum).\n   This over-rules the gaussian correction described by -beam2.\n   NO will not read any -beam_file2 (but a gaussian\n      correction may be performed if -beam2 is set.\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already corrected\n   for the beam.\n  Note: if the second beam is the same as the first one,\n   then -beam_file2 should be explicitely given the same value as -beam_file\n\n-clfile [name|YES|NO](NO)\n   name of output file for Cl\n   YES activates Cl file output with name spice.cl\n   NO desactivates output of Cl file\n   NOTE : the current format of this file is a two columns array\n   the first one corresponding to the value of l, the second one\n   to the temperature Cl and, if polarization is activated, five\n   additional spectra corresponding to EE, BB, TE, TB, EB \n   and optionally ET, BT, BE are also written.\n\n-cl_inmap_file [name|YES|NO](NO)\n   name of input file containing the raw Cls of the map as obtained by\n   running previously SpICE with the option -cl_outmap_file.\n   If this option is active, it is not necessary anymore to read the input\n   map file, and option -cl_outmap_file is of course inactive.\n   YES reads the map raw Cls from file spice.clrawmap\n   NO computes the raw Cl directly from the map.\n   IMPORTANT NOTE : the cls computed that way can be affected by the nature\n      of the masks and/or the weights. If the masks/weights are changed,\n      the calculation will become inconsistent.\n\n-cl_inmask_file [name|YES|NO](NO)\n   name of input file containing the raw Cl of the weight/masks as\n   obtained by running previously SpICE with the option -cl_outmask_file.\n   If option -cl_inmask_file is active, the Cls of the masks are not computed,\n   they are directly read in file specified by cl_inmask_file and option\n   -cl_outmask_file is of course inactive.\n   With option -cl_inmask_file active, it is in principle not necessary\n   to read masks nor weights, but if masks/weights are not read, it means\n   that the input map is supposed to have been processed prior to using spice,\n   i.e. it has been multiplied by the masks/weights already.\n   YES reads the weights/mask raw Cls from file spice.clrawmasks\n   NO computes the raw Cl directly from the weights/masks.\n   IMPORTANT NOTE : the cls computed for the map are affected by the nature\n      of the masks and/or the weights. If the masks/weights are changed,\n      the calculation will become inconsistent.\n\n-cl_outmap_file [name|YES|NO](NO)\n   name of output file containing the raw Cls of the map. This can be\n   convenient in order to run SpICE with different parameters, without\n   having to recompute these raw Cls.\n   YES activates map raw Cls output with name spice.clrawmap\n   NO desactivates output of map raw Cls file.\n\n-cl_outmask_file [name|YES|NO](NO)\n   name of output file containing the raw Cls of the weights/masks.\n   This can be convenient in order to run SpICE with different parameters,\n   without having to recompute these raw Cls.\n   YES activates mask raw Cls output with name spice.clrawmasks\n   NO desactivates output of mask raw Cls file.\n\n-corfile [name|YES|NO](NO)\n   name of output correlation file\n   YES activates correlation file output with name spice.cor\n   NO desactivates output of correlation file\n   NOTE : the current format of this file is a three columns array\n   the first one corresponding to the separation theta in radians\n   the second one to cos(theta), the third one to the correlation\n   function of the temperature and, if polarization is activated,\n   five additional columns are written, corresponding respectively to\n   QQ, UU, TQ, TU and QU in the coupled case and to EE, BB, TQ, TU and QU\n   in the decoupled case (see option -decouple and -symmetric_cl).\n\n-covfileout [name|YES|NO](NO)\n   Computes and ouputs the TT C(l) covariance matrices \n     These matrices are not needed by the code and are provided for \n   eg, cosmological interpretation of the result.\n   YES activates output of the cov. matrices in default\n      FITS file spice.covariance\n   NO desactivates output of the matrices\n\n-decouple [YES|NO](NO)\n   computes the decoupled correlation functions\n   by an integral over QQ and UU correlation functions in angle space.\n   NOTE : this option is active only if -polarization=YES,\n   otherwise it is ignored (see also -tolerance).\n   YES activates decoupling :\n      Correlation functions computed are : TT, EE, BB, TQ, TU, QU, (QT, UT, UQ)\n      Cls computed are : TT, EE, BB, TE, TB, EB, (ET, BT, BE) \n      with no mixing between EE and BB\n   NO desactivates decoupling :\n      Correlation functions computed are : TT, QQ, UU, TQ, TU, QU, (QT, UT, UQ)\n      Cls computed are : TT, EE, BB, TE, TB, EB, (ET, BT, BE) \n      with coupling between EE and BB\n \n    In both cases, the TE (and TB) estimators are unbiased using window functions (see\n      options -tenormfilein, -tenormfileout, -windowfilein, -windowfileout).\n\n-dry [YES|NO](NO)\n   This unsafe option allows reading partly corrupted files, i.e. with\n   incomplete headers. However the size of the fits file must be correct,\n   i.e. it must correspond to a full sky map with 12*nside^2 pixels.\n\n-extramapfile [name|NO](NO)\n   name of the (optional) extra input map file (healpix SP fits file)\n   to be added to mapfile before analysis. \n   Must be in the some Coordinates, Nside and Units as mapfile\n   (ordering can be different).\n\n-extramapfile2 [name|NO](NO)\n   name of the (optional) extra input map file (healpix SP fits file)\n   to be added to mapfile2 before analysis. \n   Must be in the some Coordinates, Nside and Units as mapfile2\n   (ordering can be different).\n\n-fits_out [YES|NO](NO)\n   If set, the Cl and correlation (-clfile, -corfile, -cl_outmap_file, -cl_outmask_file)\n   are written in FITS Ascii files, instead of plain text files.\n   This does not affect the input Cl files (-cl_inmap_file and -cl_inmask_file),\n   which will be read whatever is their format.\n\n-help\n   print this message and stop\n\n-history\n   print history of the program and stop\n\n-kernelsfileout [name|YES|NO](NO)\n   Compute and ouput the 4 kernels, each of size (lmax+1)*(2*lmax+1),\n   relating the Spice (polarized) estimator to the 'true' underlying CMB spectra.\n     These kernels are not needed by the code and are provided for \n   eg, cosmological interpretation of the result.\n     Note that these kernels depend on the choice\n   of apodization (options -apodizetype and -apodizesigma) \n   and on -thetamax and -nlmax.\n     How to use them depends on the -decouple option \n   (see the FITS file header for more information).\n     This option is inactive if option -windowfilein is active.\n   YES activates output of the kernels in default\n      FITS file spice.kernels\n   NO desactivates output of the kernels\n\n-listmapfiles1_K [name|NO](NO)\n   with K integer in [1, 10]\n   list of map files to be combined with weights -listmapweights1_K\n   to form the first map to analyze.\n   If this option is set, -mapfile (and -extramapfile) are ignored\n\n-listmapfiles2_K [name|NO](NO)\n   with K integer in [1, 10]\n   list of map files to be combined with weights -listmapweights2_K\n   to form the optional second map to cross-correlate with the first one.\n   If this option is set, -mapfile2 (and -extramapfile2) are ignored\n\n-listmapweights1_K [dfloat|NO](1.0)\n   with K integer in [1, 10]\n   list of weights to be applied to -listmapfiles1_K above\n   to form the first map to analyze.\n   m1 = w1(1) * m1(1) + w1(2) * m1(2) + ... \n\n-listmapweights2_K [dfloat|NO](1.0)\n   with K integer in [1, 10]\n   list of weights to be applied to -listmapfiles2_K above\n   to form the second optional map to analyze.\n   m2 = w2(1) * m2(1) + w2(2) * m2(2) + ... \n\n-mapfile [name|YES](YES)\n   name of the input map file (healpix SP fits file)\n   YES is equivalent to take input file map.fits\n   Starting with version 2.90 and if linked with HEALPix 3.10+\n   file.fits[extname] means extension 'extname' of file.fits\n\n-mapfile2 [name|YES|NO](NO)\n   name of the second (optional) input map file (healpix SP fits file)\n   to cross-correlate with the first one (-mapfile)\n   If provided, ONLY cross-correlation is performed (no auto-correlation)\n   YES is equivalent to take input file map2.fits\n   NO turns off map-map cross-correlation\n\n-maskfile [name|YES|NO](NO)\n   name of the input mask file (healpix SP fits file)\n   A mask file is composed of zeros (masked) and ones (in)\n   YES activates maskfile with name mask.fits\n   NO desactivates -maskfile\n   Starting with version 2.90 and if linked with HEALPix 3.10+\n   file.fits[extname] means extension 'extname' of file.fits\n\n-maskfile2 [name|YES|NO](NO)\n   name of the input mask file (healpix SP fits file)\n   to be applied to the second map\n   YES activates -maskfile2 with name mask2.fits\n   NO desactivates -maskfile2\n Notes:\n  1) if the you want the 2nd mask to be the same as the 1st one, \n    set -maskfile2 to the same name as -maskfile\n  2) the 2 masks should overlap at least partially\n\n-maskfilep [name|YES](YES)\n   name of the input mask file (healpix SP fits file)\n   to be applied to polarization.\n   By default, it is the same as -maskfile\n   Ignored if polarization is set to NO\n\n-maskfilep2 [name|YES](YES)\n   name of the input mask file (healpix SP fits file)\n   to be applied to the second map polarization\n   By default, it is the same as -maskfile2\n   Ignored if polarization is set to NO\n\n-nlmax [integer](3*Nside-1)\n   value of the largest multipole used in the analysis.\n   The default is 3*Nside-1, where Nside is the Healpix resolution parameter \n   of the map being analyzed.\n   Any value larger than 3*Nside-1 or \u003c= 0 will be replaced by the default.\n\n-noiseclfile [name|YES|NO](NO)\n   name of input file for Cls of the noise\n   if -noiseclfile is specified, noise subtraction is applied\n   to both final Cls and correlation function (unless -noisecorfile is\n   specified for the latter)\n   YES activates noise subtraction from file noise.cl\n   NO desactivates noise subtraction from a Cl noise file\n\n-noisecorfile [name|YES|NO](NO)\n   name of input file for correlation function of the noise\n   if -noisecorfile is specified, noise subtraction is applied\n   to both final correlation function and Cls (unless -noiseclfile is\n   specified for the latter)\n   YES activates noise subtraction from file noise.cor\n   NO desactivates noise subtraction from a correlation noise file\n\n-normfac [dfloat|NO](NO)\n   normalization factor. If normfac is specified, the correlation\n   function and the Cls are multiplied by normfac**2\n   NO and -normfac=1.0 are equivalent : in that case\n   normalization is inactive to save calculations.\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already\n   normalized appropriately\n\n-optinfile [name|YES|NO](NO)\n   Read the options in an file (only those which are not specified\n   interactively are taken into account).\n   YES reads default input option file .spicerc\n   NO desactivates the reading.\n   NOTE 1 : The file containing the options is a 2-column file,\n   the first column corresponds to the option (without the \"-\" at the\n   beginning) and the second column to the parameter (see below for\n   an example).\n   NOTE 2 : It is not necessary to specify all the options in this\n   file, and the order in which they appear does not matter. If an\n   option is specified neither in the option file nor interactively,\n   then the default value is assumed for this option.\n\n-optoutfile [name|YES|NO](NO)\n   Output the options in an file (read with option -optinfile or specified\n   interactively. In that case, no calculation is performed, only the\n   file containing the options is created.\n   YES output option file with default name .spicerc\n   NO desactivates the output\n   NOTE : see note of -optinfile.\n\n-overwrite [YES|NO](YES)\n   Activates overwriting for all output files.\n   YES overwrite all the output files generated previously.\n   NO checks if any of the output files already exist. If it is the\n   case, SpICE stops without mercy.\n   To have more sophisticated handling of overwriting, the standard\n   Healpix syntax can be used : file names in the form !name means\n   that the name of the file to be used is name and the \"!\" explicitely allows\n   overwriting.\n\n-pixelfile [name|YES|NO](NO)\n   name of input pixel correction file for 1st map\n   YES activates pixel window correction with file \n   ${HEALPIXDATA}/pixel_window_nxxxx.fits\n   or\n   ${HEALPIX}/data/pixel_window_nxxxx.fits\n   where xxxx corresponds to the value of nside of input map file.\n   NO desactivates pixel window correction.\n   NOTE : if noise subtraction is active (options -noisecorfile or\n   -noiseclfile), the input noise data are assumed to be already corrected\n   for pixel window\n\n-pixelfile2 [name|YES|NO](pixelfile)\n   name of input pixel correction file for 2nd map (for cross-analysis)\n Default value is the one chosen for -pixelfile.\n If set to YES explicitly, or implicitly via -pixelfile, \n the standard pixel window function adapted to the 2nd map Nside will be used.\n It must be set to NO to prevent pixel correction of 2nd map.\n\n-polarization [YES|NO](NO)\n   to compute polarized power spectra/correlation functions\n   in addition to standard temperature Cls/correlation\n   function. The input map file is supposed to be in the standard\n   polarized Healpix fits format, so it contains 3 maps (T,Q,U)\n   instead of one.\n   The polarized Cls and correlation functions computed depend on the\n   choice of parameter decouple explained below (see option -decouple).\n\n-subav [YES|NO](NO)\n   in case the input map is expected to have an offset, its (weighted)\n   average can be subtracted from it prior to the calculations,\n   in order to insure zero average.\n   When there are masks/weights, W(i), this average is computed\n   simply as [sum_i W(i) map(i)]/[sum_i W(i)].\n   See options -maskfile, -weightfile, -weightpower for more information\n   on the masks/weights.\n   It is important to notice that the estimator of the correlation function\n   or the Cls is not expected anymore to be unbiased if option -subav\n   is active. It would be the case only if the offset would be exactly\n   known and not estimated directly from the data.\n   YES activates average subtraction.\n   NO desactivates average subtraction.\n\n-subdipole [YES|NO](NO)\n   the best fit monopole and dipole will regressed out from the\n   (masked and weighted) data before spectral analysis. \n   YES activates dipole and monopole subtraction.\n   NO desactivates dipole and monopole subtraction.\n   -subdipole=YES implies -subav=YES and has the same caveats.\n\n-symmetric_cl [YES|NO](NO)\n   by default, when 2 maps are provided, and -polarization is set,\n   cross spectra such as TE are defined as T_map1 * E_map2 \n  (in which case it is recommended to use the least noisy map as map2)\n   and 9 spectra are produced.\n   If -symmetric_cl is set to YES, then\n   TE = (T_map1 * E_map2 + T_map2 * E_map1)/2\n   and 6 spectra are produced.\n  In the single map case, TE=ET and only 6 spectra are produced.\n\n-tenormfilein [name|YES|NO](NO)\n   this option is ignored if -polarization is not active :\n   reads the normalisation function needed to compute correctly the TE (and TB) spectra\n   and correlation functions, instead of computing it. \n   The calculation of this term depends on the apodization chosen \n   (options -apodizetype and -apodizesigma).\n   YES activates input of the normalisation function with default\n      input file name spice.tenorm\n   NO desactivates input of the normalisation function : it is computed\n      on run time.\n\n-tenormfileout [name|YES|NO](NO)\n   Compute and ouput the normalisation function needed to compute the  \n   TE (and TB) spectra. Note that this function depends on the choice\n    of apodization (options -apodizetype and -apodizesigma).\n   This option is inactive, of course, if option -tenormfilein is active, or\n   if option -polarization is inactive.\n   YES activates output of the normalisation function in default\n      file spice.tenorm\n   NO desactivates output of the normalisation function (but it is\n      computed if needed).\n\n-tf_file [name|NO](NO)\n   name of the input tranfer function file.\n   The output C(l) will be divided by the transfer function(s) read\n   from this file.\n   The transfer function is defined as the ratio of 2 power spectra.\n   The file should have the same format as the C(l) produced by this code.\n\n-thetamax [dfloat|NO](NO)\n   maximum value of angle theta used in the integrals to compute the\n   power spectra from the correlation functions.\n   NO desactivates upper bound (sets it to 180 degrees).\n\n-tolerance [dfloat|NO](NO)\n   relative tolerance on convergence of QQ and UU integrals (see -decouple)\n   Active only when -decouple is set\n   Smaller values give more accurate EE and BB spectra, in longer times.\n   NO leaves it to its default value (1.e-5).\n\n-usage\n   print short usage reminder\n\n-verbosity [0|1|2|YES|NO](1)\n   verbose option :\n   0 or NO : no verbose\n   1 or YES : standard verbose\n   2 : full verbose\n\n-version\n   prints version number and exits\n\n-weightfile [name|YES|NO](NO)\n   name of the input weight file (healpix SP fits file)\n   Weights should be always positive or equal to zero.\n   If masks are present, weights are multiplied by the masks.\n   If masks are not present, weights are supposed to be already masked,\n   i.e. are equal to zero for masked pixels\n   YES activates -weightfile with name weight.fits\n   NO desactivates -weightfile\n\n-weightfile2 [name|YES|NO](NO)\n   name of the input weight file (healpix SP fits file)\n   to be applied to the second map\n   YES activates -weightfile2 with name weight2.fits\n   NO desactivates -weightfile2\n\n-weightfilep [name|YES](YES)\n   name of the input weight file (healpix SP fits file)\n   to be applied to polarization (Q and U Stokes parameters).\n   By default, it is the same as -weightfile\n   Ignored if polarization is set to NO\n\n-weightfilep2 [name|YES](YES)\n   name of the input weight file (healpix SP fits file)\n   to be applied to the second map polarization\n   By default, it is the same as -weightfile2\n   Ignored if polarization is set to NO\n\n-weightpower [dfloat|NO](1.0)\n   the weights are taken to this power.\n   if -weightpower = 0.0, the weights are transformed into pure masks\n   if -weightpower \u003c 0.0, only the non zero values of the weights are\n   modified.\n   NO is equivalent to -weightpower=1.0.\n\n-weightpower2 [dfloat|NO](1.0)\n   the weights of the second map are taken to this power.\n   NO is equivalent to -weightpower2=1.0.\n\n-weightpowerp [dfloat|YES](YES)\n   the weights applied to 1st map (Q,U) are taken to this power.\n   Default: same as 1st Temperature weight power (see -weightpower)\n\n-weightpowerp2 [dfloat|YES](YES)\n   the weights applied to 2nd map (Q,U) are taken to this power.\n   Default: same as 2nd Temperature weight power (see -weightpower2)\n\n-windowfilein [name|YES|NO](NO)\n   this option is ignored if polarization is not active :\n   reads the kcross term needed to compute correctly the TE (and TB) spectra\n   and correlation functions, instead of computing it. \n   The calculation of this term depends on the apodization chosen \n   (options -apodizetype and -apodizesigma).\n   YES activates input of the window function with default\n      input file name spice.window\n   NO desactivates input of the window function : it is computed\n      on run time.\n\n-windowfileout [name|YES|NO](NO)\n   Compute and ouput the kcross term needed to compute the  \n   TE (and TB) spectra. Note that this kcross term depends on the choice\n    of apodization (options -apodizetype and -apodizesigma).\n   This option is inactive, of course, if option -windowfilein is active, or\n   if option -polarization is inactive.\n   YES activates output of the window function in default\n      file spice.window\n   NO desactivates output of the window function (but it is\n      computed if needed).\n\n\nIMPORTANT NOTE\n\nThe order of the operations is not the same whether mask/weights are present\nor not.\n\nIf there is no mask/weight, spice is nearly equivalent to anafast, and\nthe order of operations is the following :\n   (1a) map average subtraction, if required\n   (2a) calculation of Cl\n   (3a) pixel window correction, beam correction, transfer function correction,\n       renormalization, if required\n   (4a) calculation of the 2pt correlation function, xi, if needed\n   (5a) apodization of xi and calculation of the final Cl, if  needed\n   (6a) subtraction of noise bias on Cl and/or xi, if applicable\n\nIf there is any mask/weight, the order of operations is the following\n   (1b) multiplication of the map by the masks/weights\n   (2b) subtraction of the (weighted) average\n   (3b) calculation of the Cl of the map and of the masks/weights\n   (4b) calculation of the correlation function of the map and of the\n       masks/weights, and the corresponding ratio, xi\n   (5b) decoupling if needed (polarization case)\n   (6b) apodization of xi, if required\n   (7b) renormalization, if required\n   (8b) calculation of Cl from xi, if needed\n   (9b) pixel window correction, beam correction, transfer function correction,\n       if required, to obtain the final Cl\n  (10b) calculation of final xi, if needed\n  (11b) subtraction of noise bias on Cl and/or xi, if applicable\n\nNote, therefore, that if there are masks/weights, beam correction and\npixel window correction are performed AFTER apodization, at variance with\nthe case without mask/weight. Such ordering in the procedure is expected\nto introduce a small bias in the final results. Ideally, beam and pixel\nwindow correction should be performed before apodization, but this is\npossible only prior to masking/weighting on a FULL SKY map, i.e. before\noperation (1b).\n\nEXAMPLES\n\nspice\nspice -mapfile YES -corfile YES -clfile YES\n   reads default input map, computes correlation function\n   and Cl and output them on default output files\n   no masks/weights are taken into account\n\nspice -mapfile mymap.fits -weightfile weights.fits -clfile NO\n   reads input map mymap.fits, input file weights.fits for weights,\n   output correlation functions only\n\nspice -mapfile mymap.fits -maskfile mymasks.fits \n      -weightfile myweights.fits -beam 18.d0\n   reads input map mymap.fits, input mask file mymasks.fits,\n   input weight file myweights.fits, computes Cl and\n   correlation function with correction for a beam of\n   18 arcmin, output them on default output files. If both\n   mask and weight files are specified, the weights are\n   multiplied by the masks, allowing one to read a full unmasked\n   weight file\n\nspice -mapfile mymap.fits -weightfile myweights.fits  \n      -noisecorfile mynoise.cor -noiseclfile mynoise.cl\n   reads input map mymap.fits, input weight file myweights.fits,\n   computes Cls and correlation function, subtracts from Cls\n   the Cls of the noise from file mynoise.cl, subtracts from\n   the correlation function the correlation function of the noise\n   from mynoise.cor, output the results for the Cls and the\n   correlation function on default output files.\n   Since only the weights are specified, they are supposed\n   to be appropriately masked.\n   Even if only one noise file is specified, either from the\n   option -noisecorfile or from the option -noiseclfile,\n   noise correction is applied to both Cls and the the\n   correlation function. But this latter way is less accurate\n   because of the supplementary Legendre transform it involves.\n\nspice -mapfile mymap.fits -polarization YES \\ \n      -maskfile mymasks.fits\n   reads multiple input mapfile mymap.fits (T,Q,U), computes\n   the temperature and polarization Cls (TT, GG, CC, TG, TC and GC) and\n   correlation functions (TT, QQ, UU, TQ, TU, QU), and writes the\n   results in default output files. All the calculations use\n   appropriate mask corrections.\n\nspice -optinfile YES\nspice -optinfile .spicerc\n   Read options and parameters in default file .spicerc\n   and run spice accordingly.\n\nEXAMPLE OF OPTIONS INPUT FILE (.spicerc) :\nalm1fileout = NO\nalm2fileout = NO\napodizesigma = NO\napodizetype = NO\nbeam = NO\nbeam_file = NO\nbeam2 = NO\nbeam_file2 = NO\nclfile = NO\ncl_outmap_file = NO\ncl_inmap_file = NO\ncl_outmask_file = NO\ncl_inmask_file = NO\ncorfile = NO\ncovfileout = NO\ndecouple = NO\ndry = NO\nextramapfile = NO\nextramapfile2 = NO\nfits_out = NO\nkernelsfileout = NO\nlistmapfiles1_1 = NO\nlistmapfiles1_2 = NO\nlistmapfiles1_3 = NO\nlistmapfiles1_4 = NO\nlistmapfiles1_5 = NO\nlistmapfiles1_6 = NO\nlistmapfiles1_7 = NO\nlistmapfiles1_8 = NO\nlistmapfiles1_9 = NO\nlistmapfiles1_10 = NO\nlistmapfiles2_1 = NO\nlistmapfiles2_2 = NO\nlistmapfiles2_3 = NO\nlistmapfiles2_4 = NO\nlistmapfiles2_5 = NO\nlistmapfiles2_6 = NO\nlistmapfiles2_7 = NO\nlistmapfiles2_8 = NO\nlistmapfiles2_9 = NO\nlistmapfiles2_10 = NO\nlistmapweights1_1 =    1.00000000000000\nlistmapweights1_2 =    1.00000000000000\nlistmapweights1_3 =    1.00000000000000\nlistmapweights1_4 =    1.00000000000000\nlistmapweights1_5 =    1.00000000000000\nlistmapweights1_6 =    1.00000000000000\nlistmapweights1_7 =    1.00000000000000\nlistmapweights1_8 =    1.00000000000000\nlistmapweights1_9 =    1.00000000000000\nlistmapweights1_10 =    1.00000000000000\nlistmapweights2_1 =    1.00000000000000\nlistmapweights2_2 =    1.00000000000000\nlistmapweights2_3 =    1.00000000000000\nlistmapweights2_4 =    1.00000000000000\nlistmapweights2_5 =    1.00000000000000\nlistmapweights2_6 =    1.00000000000000\nlistmapweights2_7 =    1.00000000000000\nlistmapweights2_8 =    1.00000000000000\nlistmapweights2_9 =    1.00000000000000\nlistmapweights2_10 =    1.00000000000000\nmapfile = map.fits\nmapfile2 = NO\nmaskfile = NO\nmaskfile2 = NO\nmaskfilep = YES\nmaskfilep2 = YES\nnlmax = NO\nnormfac = NO\nnpairsthreshold = NO\nnoisecorfile = NO\nnoiseclfile = NO\noverwrite = YES\npixelfile = NO\npixelfile2 = NO\npolarization = NO\nsubav = NO\nsubdipole = NO\nsymmetric_cl = NO\ntenormfilein = NO\ntenormfileout = NO\ntf_file = NO\nthetamax = NO\ntolerance = NO\nverbosity = 1\nweightfile = NO\nweightfilep = YES\nweightfile2 = NO\nweightfilep2 = YES\nweightpower =    1.00000000000000\nweightpower2 =    1.00000000000000\nweightpowerp =    1.00000000000000\nweightpowerp2 =    1.00000000000000\nwindowfilein = NO\nwindowfileout = NO\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzonca%2Fpolspice","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzonca%2Fpolspice","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzonca%2Fpolspice/lists"}