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FasToCh

Fast Topological Chase: Detection des filaments 2D :

by Colombi Stéphane (Sunday 16 April 2006)

Le code

GZ - 966.9 kb
fastoch
detecteur 2D de filaments

permet de detecter les structures filamentaires dans une carte rectangulaire 2D au format fits ou fortran 90 binaire dit "Totor".

Il a de nombreuses autres fonctionnalites, par exemple dessiner les isocontours, generer un champ 2D gaussien aleatoire et son mapping de Zeldovich, etc...

Resultat de la commande fastoch -help :



USAGE : fastoch -keyword(1) parameter(1) ... -keyword(N) parameter(N)

All keywords are optional


KEYWORDS : keyword [possible parameters](default)

-help
   print this message and stop

-about
   print copyright info and stop

-history
   print history of the program and stop

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

-mapfile [name|YES|NO](YES)
   name of the input map file (see option -format below for the format)
   YES is equivalent to take input file map
   NO desactivates reading of input map : the map is
   generated internally (see option -internal just below).

-maskfile [name|YES|NO](NO)
   name of the input mask file (see option -format below for the format)
   YES is equivalent to take input file mask
   NO desactivates reading of the input mask file.
   In that case no mask is assumed
   NOTE : we need an input map for the masks to be active
          masks are not read in -internal below is used

-internal {seed}[integer|YES](12321)
          {spectral_index}[dfloat|YES](0.)
          {output_file}[name|YES|NO](NO)
   For internal generation of the input map.
   A random Gaussian field with power-law power-spectrum,
   P(k)=k**spectral_index, is generated.
   An positive integer, seed, is needed for seeding the random
   numbers generator.
   If required, the corresponding map is writen in a file specified
   by output_file and the format is given by the option -format below.
   If option -internal is not specified, but that seed and spectral_index
   are still needed because input map was desactivated, default values are take
n.
   YES for seed is equivalent to default value,
      similarly for spectral_index.
   NO for output_file desactivates output (default).
   YES for output_file activates output with default name map
   NOTE : of course if internal generation of the map is not activated
     (i.e. if input map file is read), -internal parameters are ignored
     even if specified. In particular, no output map is generated even
     if output_file is activated properly.

-nx [integer](256)
   For internal generation of the map (-mapfile NO, dimension
   of the map along x axis.
   If not specified but still needed, nx=256 is the default.

-ny [integer](256)
   For internal generation of the map (-mapfile NO, dimension
   of the map along y axis.
   If not specified but still needed, ny=256 is the default.

-nz [integer](256)
   For internal generation of the map (-mapfile NO, dimension
   of the map along z axis (relevant only if the map is 3D).
   If not specified but still needed, nz=256 is the default.

-nside [integer](256)
   For internal generation of a healpix map.
   If not specified but still needed, nside=256 is the default.

-addseg {seed}[integer|YESNO](32123)
        {length}[integer|YESNO](nx/4)
        {ampfac}[dfloat|YESNO](10.d0)
        {nfilaments}[integer|YESNO](10)
        {output_file}[name|YESNO](NO)
   For superposing to the field (input one or internally generated)
   strong non gaussian features modelized as a set of segments
   put randomonly in the field, with random orientation and all with
   the same size length. The random field is locally amplified with
   a factor ampfac. If option -subaverage explained below is active
   amplification is done on a field with zero average, and average
   substraction is processed again after adding the filaments.
   seed : integer needed for seeding the random number generator.
      YES for seed is equivalent to default value.
   length : length of the segments in pixel size units.
      YES for length is equivalent to default value.
   ampfac : factor of amplification of the field inside the segments,
      which are one pixel width.
      YES for ampfac is equivalent to default value.
   nfilaments : number of segments drawn in the field (>= 1).
      YES for nfilaments is equivalent to default value.
   output_file : name of the output file for the modified field.
      YES for output_file activates output with default name
      fastoch.addsegmap
   If either one of the parameters seed, length, ampfac, or nfilaments is set
   to NO, the option addseg is desactivated.

-format [2D_BIN|2D_FITS|3D_BIN|HEALPIX|HEALDRY|YES](YES)
   Format of the file :
   2D_BIN : Fortran binary 2d file obtained by
         the following output :
         write(unit) nx,ny  [nx and ny are I4B integers]
         write(unit) map    [map is SP real]
   2D_FITS : standard 2d fits image (SP real)
   3D_BIN : Fortran binary 3d file obtained by
         the following output :
         write(unit) nx,ny,nz  [nx, ny and nz are I4B integers]
         write(unit) map       [map is SP real]
   HEALPIX : healpix fits file (on the sphere)
   HEALDRY : healpix fits file with lousy header
         This format is the same as HEALPIX but with
         less paranoiac checks on the header of the file
   YES : equivalent to 2D_BIN

-periodic [YES|NO](YES)
   Specifies if the input map has periodic boundaries
   This option is irrelevant for healpix maps

-subaverage [YES|NO](NO)
   Specifies if the input map has to be renormalized by subtracting
   the average (of unmasked pixels).
   This is important for the computation of the variance, which is done
   assuming that < map >=0.

-resamplingfactor [integer|NO](1)
   The map is resampled on a higher resolution map with resamplingfactor
   times more pixels in each direction, i.e. for e.g. a 2D map of dimension
   nx and ny, the resampled map is of dimensions nx*resamplingfactor and
   ny*resamplingfactor.
   For a healpix map, the resampling factor must be of course a power
   and will act on the value of nside.
   Note that resampling is done with the simplest "doner cell" method:
   it is necessary to (re)smooth the new map afterwards to regularize it,
   i.e. to make it non degenerate.
   NO corresponds to no resampling, resamplingfactor=1,
   which is the default.

-smoothinglength [dfloat|NO](NO)
   The map is convolved with a Gaussian window of size smoothinglength.
   Smoothinglength is expressed in pixel size units of the original
   (not resampled) map.
   NO corresponds to no smoothing.

-outputmap [name|YES|NO](NO)
   Name of the file corresponding to the map after resampling or/and
   smoothing if any.
   The format is the same as for the input map file (option -format).
   NO desactivates output (default).
   YES activates output with default name fastoch.smoothmap

-bicubic [YES|NO](NO)
   This option, which can be used only for flat two-dimensional maps,
   activates bicubic interpolation to do the calculations.
   Bicubic interpolation needs pre-computation of the gradient and
   the of diagonal term of the Hessian, which can be done either in
   Fourier space or with discrete scheme in real space (see option
   -fourier below for more details).
   Bicubic interpolation allows then a self-consistent (smooth)
   estimate of the diagonal terms of the Hessian. It is also used
   to compute accurate estimates of any quantity (density, gradient,
   hessian) at a specific position within the pixels, which is done
   by bilinear interpolation otherwise. Such accurate estimates
   are for example needed to draw correctly field lines.
   YES activates bicubic interpolation :
      - gradient and of diagonal terms of the hessian at the center of
      pixels are computed either in Fourier space or by discrete scheme
      differentiation.
      - diagonal terms of the hessian at the center of pixels are
      determined uniquely by the bicubic weights
      - field value, gradient and hessian of the field at any point
      within the map (e.g. of the center of a pixel) are calculated
      by bicubic interpolation weights and they all are smooth and
      self-consistent.
   NO desactivates bicubic interpolation.
      - gradient and hessian at the center of pixels are computed
      either in Fourier space or by discrete scheme differentiation.
      - field value, gradient and hessian of the field are calculated
      at any point within the map (off the center of a pixel) by bilinear
      interpolation, and are thus smooth but not necessarily self-consistent,
      for instance this method does not warranty that the gradient is
      curlfree
   In practice, bicubic interpolation and bilinear interpolation
   seem to give only tiny differences.

-fourier [YES|NO](NO)
   This option activates fourier space method to compute derivatives,
   otherwise discrete real space scheme is used. Fourier space method
   is probably not appropriate for maps with non periodic boundaries
   or with masks and, of course, cannot be used for healpix maps.
   YES activates fourier space method to compute
      derivatives. Example in 2D : if f(kx,ky) is the fourier transform
      of the field, its gradient will be given in fourier space by
      -i kx f(kx,ky), -i ky f(kx,fky), where i^2=-1 and its Hessian by
      -kx^2 f(kx,ky), -ky^2 f(kx,ky), -kx.ky f(kx,ky). Note that if
      bicubic interpolation is active, only gradient and off diagonal terms
      of the Hessian are computed in Fourier space, the diagonal terms of
      the Hessian being automatically given by the bicubic weights.
   NO desactivates fourier space method : discrete scheme
      in real space is used to compute the derivatives.
      Example in 2D : if f(i,j) is the value of the field at pixels
      (i,j), the gradient is computed as follows :
      grad_x(i,j)=0.5*(f(i+1,j)-f(i-1,j))
      grad_y(i,j)=0.5*(f(i,j+1)-f(i,j-1))
      and the Hessian as follows:
      hessian_xx(i,j)=f(i+1,j)-2*f(i,j)+f(i-1,j)
      hessian_yy(i,j)=f(i,j+1)-2*f(i,j)+f(i,j-1)
      hessian_xy(i,j)=0.25*[f(i+1,j+1)-f(i+1,j-1)-f(i-1,j+1)+f(i-1,j-1)]
      Note that if bicubic interpolation is active, only gradient and
      off diagonal terms [hessian_xy(i,j)] are computed with the discrete
      scheme, the diagonal terms of the Hessian being automatically given
      by the bicubic weights.
   In practice, Fourier or discrete calculations seem to give only tiny
   difference.

-skeleton [name|YES|NO](YES)
   Name of the output image for the skeleton.
   The skeleton is defined here as the points in the (smoothed) map where
   the gradient is aligned with the major axes of the Hessian, or in other
   where the gradient is eigenvector of the Hessian.
   The image is thus a file with same format as the input map file
   (option -format). A given pixel in the image has the value 0 if there
   is a filament belonging to the skeleton passing through, -1 otherwise.
   If option -critical explained below is active, the critical points are
   also displayed, with pixel values 1,2,3 corresponding respectively to minima
   saddle points and maxima for 2D and healpix maps, and with pixel values
   1,2,3,4 corresponding respectively to minima, saddle points of first and
   second kind and maxima for 3D maps.
   If option -unpolarized explained below is active, the unpolarized points
   are also displayed, with pixel value 4 in 2D and 5 in 3D. Furthermore,
   the skeleton is drawn in 2 colors, one corresponding to the case when
   the gradient is aligned with the major axis of the Hessian (value 6 in 2D
   and 7 in 3D), the other one corresponding to the case when the gradient
   is aligned with the minor axis of the Hessian (value 0).
   If option -smartske explained below is active, the skeleton is drawn
   in two colors, one corresponding to the part of the skeleton which
   would correspond to the real skeleton (value 6 in 2D and 7 in 3D),
   the other to the rest (value 0). The effects of this option overcome
   those of -unpolaized.
   Summary :
     default : skeleton(i,j)= 0 for skeleton present
                             -1 otherwise.
     -critical active : skeleton(i,j)=critical point value (ranging from
                        1 to 3 in 2D, from 1 to 4 in 3D) if critical point
                        present at (i,j)
     -unpolarized active : skeleton(i,j)=unpolarized point value (4 in 2D,
                        5 in 3D) if unpolarized point present at (i,j)
                        skeleton(i,j)=0 / 6 (2D) or 7 (3D) according to whether
                        gradient aligned with minor / major axis of Hessian.
     -smartske active : skeleton(i,j)=6 (2D) or 7 (3D)/0 according to whether
                        it would correspond to real skeleton or not.
   YES activates skeleton output with default name fastoch.skeleton
   NO desactivates skeleton output.

-skelength [name|YES|NO](YES)
   Name of the output file for skeleton length information.
   This file is a three column ascii file giving the skeleton length in
   pixel size units as a function of the density threshold.
   The first line of the file gives the value of nthreshold,
   then it is formatted as follows :
      first column : value of the density threshold
      second column : value of the density threshold in units of sigma
         where sigma^2 is the variance of the density field
      third column : length of the part of the skeleton which is above
         the density threshold, in units of pixel size of the original
         input map.
   Note that the first line of data correspond to the whole skeleton
   with a very negative density threshold.
   There are thus nthreshold+1 lines of data.
   YES activates skeleton length output with default name
   NO desactivates calculation and output of skeleton length file.
   NOTE 1 : to specify the number of thseshold values and the bounds in
      density for the measurements, use option -threshparm below.
   NOTE 2 : if option -smartske below is active, only the part of the skeleton
      that would be close to the real one contributes.

-smartske [YES|NO](NO)
   This option is relevant only if -skelength or -skeleton options above
   are active.
   YES activates "smart" selection of the local skeleton :
     the parts of the skeleton that would correspond to the real skeleton
     (options -voidborder or -voidborderlength) are painted in a different
     color, skeleton(i,j)=6 (2D) or 7 (3D), while the rest remains at the
     default value, skeleton(i,j)=0 as explained in option -skeleton.
     Note that this option overcomes the effects on -unpolarized.
     Furthermore, only the part of the skeleton which are "smart" are used
     for computing its length.
   NO desactivates smart skeleton selection. This is the default.

-critical [name|YES|NO](YES)
   Name of the output file for information on the critical points,
   i.e. points of space where the gradient of the field cancels.
   This file is a 4 or 5 column ascii file (depending if the input map is
   2D, healpix like, or 3D) formatted as follows :
   The first line gives the number of critical points, and then we have:
   1st column : kind of the critical point :
                healpix or 2D : 1 : minimum
                                2 : saddle
                                3 : maximum
                3D            : 1 : minimum
                                2 : "pancake" saddle
                                3 : "filament" saddle
                                4 : maximum
   2nd column : value of the field at this point, normalized by sigma,
                where sigma^2 is the variance of the density field.
   3rd column and more : position of the critical point on the map,
                in units of pixel size of the original input map.
   YES activates critical points output with default
   name fastoch.critical

-unpolarized [name|YES|NO](YES)
   Name of the output file for information on unpolarized points, i.e.
   points of space where the hessian is diagonal with equal eigenvalues,
   or equivalently in 2D, hessian_xx-hessian_yy=0 and 2*hessian_xy=0.
   This file is a 3 or 4 column ascii file (depending if the input map is
   2D, healpix like, or 3D) formatted as follows :
   The first line gives the number of unpolarized points, and then we have:
   1st column : value of the field at the point, normalized by sigma,
                where sigma^2 is the variance of the density field.
   2nd column and more : position of the unpolarized point on the map,
                in units of pixel size of the original input map.
   YES activates unpolarized points output with default
   name fastoch.unpolarized

-isocontour {nlevels}[integer|YES|NO](5)
            {nsigma}[dfloat|YES|NO](YES)
            {output file}[name|YES|NO](NO)
   isocontour image parameters :
   nlevels : specifies the number of isocontour lines considered.
      Each isocontour corresponds to a density value. The list of density
      values is symetric around zero.
      YES supposes for nlevels the default value.
   nsigma : specifies the min and max value of density isocontour considered
      in units of sigma, where sigma^2 is the variance of the density.
      example : for nsigma=2.5 and nthreshold=20, 20 values of density
      (contrast) will be considered, between -2.5 sigma and 2.5 sigma.
      YES takes by default the [-max(|rho|),+max(|rho|)]
      for the bounds.
   output file : name of the output file for the isocontour image.
      The image is a file with same format as the input map file
      (option -format). A given pixel in the image has the value 0 if it
      belongs to an isocontour, -1 otherwise.
      YES activates isocontour output with default name
      fastoch.isocontour
   If either of one of the parameters, nlevels, nsigma, output file is
   set to NO, the output isocontour file is
   desactivated.

-peakpatch [name|YES|NO](YES)
   Name of the output image for the peak patches.
   The peak patches are defined as regions of the map where one converges
   to the same peak while walking along the field lines (the field lines
   defined by the gradient of the map).
   The image is thus a file with same format as the input map file
   (option -format). A given pixel in the image has an integer value > 0
   if it is associated unambiguously with a peak, -1 otherwise.
   The drawing of the peak patches is controled by 2 parameters described
   more in detail below (option -fieldlineparameters).
   If some regions of the map are found to be undefined (usually because
   of an oscillation around a saddle point), a way to possibly solve
   that problem is to resample on a larger map. In practice, playing with the
   parameters given in -fieldlineparameters does not really improve the results
.
   YES activates peak patches output with default
   name fastoch.peakpatch

-voidpatch [name|YES|NO](YES)
   Name of the output image for the void patches.
   The void patches are exactly similar to the peak patches except that
   one walks along the field lines in the opposite direction from what
   was done for drawing the peak patches.
   YES activates void patches output with default
   name fastoch.voidpatch

-peakborder [name|YES|NO](YES)
   Name of the output image for the borders of the peak patches.
   The same rules of formatting apply as for -skeleton, except that
   unpolarized points are never drawn here.
   YES activates peak borders output with default
   name fastoch.peakborder

-voidborder [name|YES|NO](YES)
   Name of the output image for the borders of the void patches.
   The same rules of formatting apply as for -skeleton, except that
   unpolarized points are never drawn here.
   YES activates void borders output with default
   name fastoch.voidborder

-peakborderlength [name|YES|NO](NO)
   Name of the output file for the length of the peak patches borders as
   function of density threshold. It is formatted similarly as in option
   -skelength.
   YES activates peak patch border length output with default
   name fastoch.peakborderlength
   NO desactivates peak patch border length calculation and output.
   NOTE : to specify the number of thseshold values and the bounds in
      density for the measurements, use option -threshparm below.

-voidborderlength [name|YES|NO](NO)
   Name of the output file for the length of the peak patches borders as
   function of density threshold. It is formatted similarly as in option
   -skelength.
   YES activates void patch border length output with default
   name fastoch.voidborderlength
   NO desactivates void patch border length calculation and output.
   NOTE : to specify the number of thseshold values and the bounds in
      density for the measurements, use option -threshparm below.

-fieldlineparameters {dt}[dfloat|YES](1.0d0)
                     {second order}[YES|NO](NO)
   Parameters used to draw the field lines. The first one is a "time step" dt:
   Field lines are drawn with segments of length dt, in units of
   pixel size of the (resampled) map. The smaller is dt, the more accurate
   is the drawing of the field line, but the longer it takes.
   IMPORTANT : dt should be always smaller than unity.
   The second parameter specifies whether second order calculation is
   required (with correction from the Hessian): if activated, it augments
   slightly the cost of the field line drawing.

-sigmas [name|YES|NO](YES)
   Name of the output file for information on variances sigma0^2,
   sigma1^2 and sigma2^2, defined by
      sigma0^2 = < rho^2 >   (with < rho >=0), where rho is the
                             density of the smooth input map,
      sigma1^2 = < grad_x^2 > = < grad_y^2 >, where grad is the
                             gradient of rho,
      sigma2^2 = (8/3) < hessian_xx^2 > = (8/3) < hessian_yy^2 >
               = 8 < hessian_xy^2 >, where hessian is the Hessian
                             of rho.
   The values given in the ascii file are, in order
      sigma0, sigma1, sigma2
   YES activates sigmas output with default
   name fastoch.sigmas

-cumpdf [name|YES|NO](NO)
   Name of the output file for cumulated pdf information.
   This file is a three column ascii file giving the cumulated pdf in
   as a function of the density threshold.
   The first line of the file gives the value of nthreshold,
   then it is formatted as follows :
      first column : value of the density threshold
      second column : value of the density threshold in units of sigma
         where sigma^2 is the variance of the density field
      third column : cumulated pdf above the density threshold
   Note that the first line of data correspond to cumulated pdf=1
   (with a formally very negative density threshold)
   There are thus nthreshold+1 lines of data.
   YES activates cumulative pdf output with default name
   fastoch.cumpdf
   NO desactivates pdf calculation and output.
   NOTE : to specify the number of thseshold values and the bounds in
      density for the measurements, use option -threshparm below.

-threshparm {nthreshold}[integer|YES](100)
            {nsigma}[dfloat|YES](YES)
   Parameters for building the array of threshold values in density for
   selecting subsets of the map. These parameters are used when the following
   options are active :
      -skelength
      -peakborderlength
      -voidborderlength
      -cumpdf
   nthreshold : specifies the number of threshold values considered for the
      density.
      YES supposes for nthreshold the default value.
   nsigma : specifies the min and max value of density threshold considered.
      If nsigma is positive, the min and max values are supposed to be
      in units of sigma, where sigma^2 is the variance of the density.
      example : for nsigma=2.5 and nthreshold=20, 20 values of density
      (contrast) will be considered, between -2.5 sigma and 2.5 sigma.
      If nsigma is negative, the min and max values are on the density
      contrast itself (not renormalized by sigma).
      YES takes by default the [-max(|rho|),+max(|rho|)]
      for the bounds.

-zeldo {facnpar}[dfloat|YES](0.25d0)
       {amplit}[dfloat|YES](1.0d0)
       {output file}[name|YES|NO](NO)
   Zeldovich mover. If this option is active a Zeldovich mover is applied
   to the (smoothed) map on a set of particles as described below and
   output on a file. Note that the Zeldovich map is NOT USED for any other
   calculation. The other calculations are still performed on the
   original map (after resampling or/and smoothing if required).
   facnpar : The Zeldovich mover is processed on a set of npart=facnpar^2*nx*ny
,
      12*facnpar^2*nside^2, facnpar^3*nx*ny*nz respectively in 2D, healpix
      or 3D cases. For 2D and 3D case, periodic boundaries are assumed
      YES for facnpar is equivalent to taking the default value.
   amplit : amplitude of the displacement (equivalent to number of expansion
      factors with respect to initial conditions given by the density field.
      YES for amplit is equivalent to taking the default value.
   output file : name of the output file for the results. It is exactly in the
      same format as the input map, but a simple nearest grid point interpolati
on
      is used to compute the density at a grid point, each particle contributin
g
      to one.
      YES for the output file is equivalent to taking the default
        name fastoch.zeldomap
      NO for the output file desactivates Zeldovich mapping
        calculation which is the default.

-nonlinear [name|YES|NO](NO)
   Non linear transform of the map. If this option is active a new map is
   created, new map=exp(map/sigma) where sigma is the variance of the fluctuati
ons
   in the original map. This new map is output on the disk at the same
   format as the input map, but NOT USED for any other calculation. The
   other calculations are still performed on the original map (after resampling
   or/and smoothing if required).
   YES activates output of non linearly transformed field
      on the file fastoch.nonlinearmap
   NO desactivates output of non linearly transformed field which
      is the default.

-overwrite [YES|NO](YES)
   Specifies default status for output files:
   YES : FasToCh systematically overwrite the output files
      whether they already exist or not. This is the default.
   NO : FasToCh checks if the output files already exist prior
      to the calculations. An error occures if any of the output files
      already exists.

-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 .fastochrc
   NO desactivates the reading
   NOTE : the file containing the options is a 2 columns 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)

-optoutfile [name|YES|NO](NO)
   Output the options in an file (read with option -optinfile or specified
   interactively)
   YES output option file with default name .fastochrc
   NO desactivates the output
   NOTE : see note of -optinfile

EXAMPLE

fastoch -optinfile YES
fastoch -optinfile .fastochrc
   Read options and parameters in default file .fastochrc
   and run fastoch accordingly.

EXAMPLE OF OPTIONS INPUT FILE (.fastochrc) :
verbosity  1
mapfile  map
maskfile  NO
internal         12321  0.000000000000000E+000 NO
nx           256
ny           256
nz           256
nside           256
addseg  NO NO NO NO NO
format  2D_BIN
periodic  YES
subaverage  NO
resamplingfactor             1
smoothinglength  NO
outputmap  NO
bicubic  NO
fourier  NO
skeleton  fastoch.skeleton
skelength  fastoch.skelength
smartske  NO
critical  fastoch.critical
unpolarized  fastoch.unpolarized
isocontour             5 YES NO
peakpatch  fastoch.peakpatch
voidpatch  fastoch.voidpatch
voidborder  fastoch.voidborder
peakborder  fastoch.peakborder
peakborderlength  NO
voidborderlength  NO
fieldlineparameters     1.00000000000000 NO
sigmas  fastoch.sigmas
cumpdf  NO
zeldo    0.250000000000000        1.00000000000000 NO
nonlinear  NO
threshparm           100 YES
overwrite  YES