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Guilhem Lavaux 2021-06-21 16:38:06 +02:00
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1
scripts/2df100k.sh Symbolic link
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../masks/2df100k/2df100k.sh

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scripts/2df230k.sh Symbolic link
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../masks/2df230k/2df230k.sh

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scripts/2qz.sh Symbolic link
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../masks/2qz10k/2qz.sh

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scripts/call Symbolic link
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../masks/healpix/healpix_conversion_scripts/call

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scripts/find_complement.sh Executable file
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#! /bin/sh
# © M E C Swanson 2008
#script to find the complement of a mangle mask
#USAGE: find_complement.sh <mask> <complement>
#EXAMPLE:find_complement.sh holes.pol complement.pol
#input mask can be pixelized beforehand to a fixed resolution
#if the mask is complicated, e.g. pixelize -Ps0,8 holes.pol holes_pixelized.pol
if [ "$MANGLEBINDIR" = "" ] ; then
MANGLEBINDIR="../../bin"
fi
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ "$MANGLEDATADIR" = "" ] ; then
MANGLEDATADIR="../../masks"
fi
mask=$1
complement=$2
dres=3
dscheme="s"
#check command line arguments
if [ "$mask" = "" ] || [ "$complement" = "" ] ; then
echo >&2 "ERROR: enter the input and output polygon files as command line arguments."
echo >&2 ""
echo >&2 "USAGE: find_complement.sh <mask> <complement>"
echo >&2 "EXAMPLE:find_complement.sh holes.pol complement.pol"
exit 1
fi
head -n 100 $mask > jmaskhead
#grab pixelization info from input files
awk '/pixelization/{print $0}' < jmaskhead > jpix
res=`awk '{print substr($2, 1, length($2)-1)}' < jpix`
scheme=`awk '{print substr($2, length($2))}' < jpix`
rm jpix jmaskhead
#if input file is unpixelized, pixelize it
#if input file is pixelized to a fixed resolution, use it as is.
if [ "$res" = "" ]; then
res=$dres
scheme=$dscheme
echo ""
echo "Pixelizing $1 ..."
$MANGLEBINDIR/pixelize -P${scheme}0,$res $mask jp || exit
echo ""
elif [ "$res" = -1 ] ; then
res=$dres
scheme=$dscheme
echo "WARNING: cannot take the complement of a mask pixelized adaptively."
echo "Pixelizing your mask using a fixed resolution:"
echo ""
echo "Pixelizing $1 ..."
$MANGLEBINDIR/pixelize -P${scheme}0,$res $mask jp || exit
echo ""
else
cp $mask jp
fi
#check for appropriate allsky file, and generate it if it's not there:
allsky=$MANGLEDATADIR/allsky/allsky$res$scheme.pol
if [ ! -e $allsky ] ; then
$MANGLESCRIPTSDIR/make_allsky.sh $res $scheme
fi
#check if input file is snapped
snapped=`awk '/snapped/{print $1}' < $mask`
#if input file isn't snapped, snap it
if [ ! "$snapped" = "snapped" ]; then
echo "Snapping $1 ..."
$MANGLEBINDIR/snap jp jps || exit
rm jp
else
mv jp jps
fi
#set weight of all polygons in mask to zero
echo 0 > jw0
echo "$MANGLEBINDIR/weight -zjw0 $mask jw"
$MANGLEBINDIR/weight -zjw0 jps jw || exit
rm jps
#balkanize the full sky with the zero-weighted mask to find the complement
echo "$MANGLEBINDIR/balkanize $allsky jw jb"
$MANGLEBINDIR/balkanize $allsky jw jb || exit
rm jw
#unify to get rid of zero weight polygons
echo "$MANGLEBINDIR/unify jb $complement"
$MANGLEBINDIR/unify jb $complement || exit
rm jb
echo "Complement of $mask written to ${complement}."

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scripts/graphmask.m Normal file
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function graphmask(infile,outfile,maprange,plottitle,outlines)
% © M E C Swanson 2008
%function for plotting MANGLE polygon files using the Matlab mapping toolbox.
%arguments:
%infile=polygon file to be plotted, in 'list' format, i.e.created with poly2poly -ol30 mypolys.pol mypolys.list
%outfile=name of eps file to output, or use 'none' if you want to, e.g., put the resulting figure into a subplot.
%maprange=[lonmin,lonmax,latmin,latmax] are optional latitude and longitude (Dec and RA)
%limits for the mask. If not provided, default is to plot full sky.
%title=optional title for the plot
%outlines=whether to draw black outlines around polygons. default is no outlines. Use outlines='on' to draw outlines.
%check if mapping toolbox is installed:
if ( ~exist('ispolycw') )
fprintf(2, 'To plot mangle masks in Matlab, you must have the mapping\ntoolbox (version 2.0.3 (R14SP1) or later) installed.\n');
exitval=1;
save('matlabexit.temp','exitval');
exit
end
%process input arguments
if(nargin<1)
error('graphmask requires at least one input argument: the name of the input data file to plot.');
end
if(nargin==1)
outfile='none';
maprange=[0 360 -90 90];
plottitle='';
outlines='';
lims=0;
end
if(nargin==2)
maprange=[0 360 -90 90];
plottitle='';
outlines='';
lims=0;
end
if(nargin==3)
plottitle='';
outlines='';
lims=1;
end
if(nargin==4)
outlines='';
lims=1;
end
if(nargin>=5)
lims=1;
end
if(all(maprange==0))
maprange=[0 360 -90 90];
lims=0;
end
%check if mapping toolbox is installed:
if (~isnumeric(maprange))
fprintf(2, 'ERROR: Non-numeric values used in maprange\n');
exitval=1;
save('matlabexit.temp','exitval');
exit
end
lonmin=maprange(1);
lonmax=maprange(2);
latmin=maprange(3);
latmax=maprange(4);
%set spacing for tickmarks
range=max(latmax-latmin, lonmax-lonmin);
avrange=mean([latmax-latmin, lonmax-lonmin]);
if(range<15)
sp=1;
else if (range<30)
sp=2;
else if (range<90)
sp=5;
else if (range<150)
sp=10;
else if (range<300)
sp=20;
else
sp=50;
end
end
end
end
end
%read in files
weightfile=[infile '.weight'];
xymat=load(infile);
wmat=load(weightfile);
fprintf(1,'Done reading files\n');
ra=xymat(1:end,1);
dec=xymat(1:end,2);
weight=wmat(1:end,2);
%set up map axes
axm=axesm('MapProjection', 'hammer','frame','on','FFaceColor','black','origin',180);
if (lims)
axesm('MapProjection','mercator','frame','on','maplatlimit',[latmin latmax], 'maplonlimit',[lonmin lonmax])
setm(gca,'ParallelLabel','on','PLabelLocation',sp,'LabelFormat','none','fontsize',10);
tightmap;
ax1=gca;
ax2=axes('Position',get(ax1,'Position'));
axesm('MapProjection','mercator','frame','on','maplatlimit',[latmin latmax], 'maplonlimit',[lonmin lonmax])
setm(gca,'FFaceColor','black')
else
axm=axesm('MapProjection', 'hammer','frame','on','FFaceColor','black','origin',180);
end
%plot polygons in list as patches
if (strcmp(outlines,'on'))
h=patchesm(dec,ra,'g','Edgecolor','black','Linewidth',0.3);
else
h=patchesm(dec,ra,'g','Edgecolor','none');
end
%normalize weights
minweight=min(weight);
maxweight=max(weight);
weight=(weight-minweight)./(maxweight-minweight);
%scale weight so that the minimum isn't black unless it's actually zero
if(minweight~=0)
minscale=.1;
zeroscale=minweight-minscale./(1-minscale).*(maxweight-minweight);
if(minscale>0 && zeroscale<=0)
zeroscale=0;
minscale=minweight./maxweight;
end
weight=(1-minscale).*weight+minscale;
else
zeroscale=minweight;
end
%set holes (polygons with points wound counterclockwise) to have weight 0
ccw=~ispolycw(dec,ra);
weight(ccw)=0;
%create cell array of colors with each element as grayscale weight
color=[weight weight weight];
cellcolor=num2cell(color,2);
%apply weight colors to patch objects
set(h,{'FaceColor'},cellcolor);
%tweak map display and add labels
if (lims)
set(gca,'XDir', 'reverse')
gridm on;
setm(gca,'MeridianLabel','on','MLabelLocation',sp,'MLineLocation',sp,'PLineLocation',sp,'MLabelParallel','south',...
'LabelFormat','none', 'MLineLimit',[latmin latmin+.01*avrange],'PLineLimit',[lonmax-.01*avrange, lonmax],...
'glinestyle','-','gcolor',[.5 .5 .5],'fontsize',10);
tightmap;
mlabelzero22pi
xlabel('\newline Right Ascension')
ylabel('Declination\newline ')
else
tightmap;
xlims=get(gca,'XLim');
ylims=get(gca,'YLim');
axis([1.01*xlims 1.01*ylims])
set(gca,'XDir', 'reverse','XColor',[1 1 1],'YColor',[1 1 1])
xlabel('-90^{\circ}','Color','k')
ylabel('360^{\circ}','Rotation',0.0,'Color','k','VerticalAlignment','Middle','HorizontalAlignment','Right')
ax1=gca;
ax2=copyobj(ax1,gcf);
set(ax2,'XAxisLocation','top', 'YAxisLocation','right','Color','none','XColor',[1 1 1],'YColor',[1 1 1]);
axes(ax2);
xlabel('+90^{\circ}','Color','k')
ylabel('0^{\circ}','Rotation',0.0,'Color','k','VerticalAlignment','Middle','HorizontalAlignment','Left')
end
title(plottitle);
%add colorbar
pb=pbaspect;
pos1=get(gca,'Position');
axes('Position',pos1)
axis off
colormap('gray')
caxis([zeroscale maxweight]);
pbaspect(pb);
pos1=get(gca,'Position');
cbar_handle=colorbar('EastOutside');
set(gca,'Position',pos1);
fprintf(1,'Done making mask image\n');
%export image as eps file
if(~strcmp(outfile,'none'))
set (gcf, 'Color', [1 1 1])
if(~lims)
set(gcf,'PaperPosition', [-1.75 .75 14 7])
end
print('-depsc','-r600',outfile);
fprintf(1,'Done writing mask image to %s\n',outfile);
exit
end

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scripts/graphmask.sh Executable file
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#!/bin/sh
# © M E C Swanson 2008
#plot the angular mask described by a polygon file in .list format
#using the matlab mapping toolbox
#
#optional 3rd-6th arguments give the RA and Dec range to plot the mask
#if no range is given, the full sky will be plotted
#To plot range that includes RA=0, use a negative number for the "low"
#end, e.g. for a 10 degree strip covering RA=355 degrees to RA=5 degrees,
#use a range of -5 5.
#Entering in "0 0 0 0" for the range will also give the default full sky behavior,
#which can be used if you also wish to, e.g., enter a title.
#
#optional 7th argument gives a title for the graph
#optional 8th argument turns on drawing black outlines around each polygon
#
#if specifying the full path to a file (rather than just running in the directory
#containing the file you want to plot), put the path in double-quotes as shown below.
#
#USAGE: graphmask.sh <infile> <outfile> [<ramin> <ramax> <decmin> <decmax>] [<title>] [<outlines>]
#EXAMPLES:
#fullsky, no outlines: graphmask.sh "dr4/safe0/sdss_dr4safe0_mask.list" "dr4/safe0/sdss_dr4safe0_mask.eps"
#defined range, title, no outlines: graphmask.sh sdss_slice.list sdss_slice.eps -45 35 8 21 "SDSS slice"
#defined range, no title, outlines: graphmask.sh sdss_slice.list sdss_slice.eps -45 35 8 21 "" on
#fullsky, no title, outlines: graphmask.sh sdss_slice.list sdss_slice.eps 0 0 0 0 "" on
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ $# -eq 2 ]; then
if [ -e $1 ]; then
if [ -e $2 ]; then
rm $2
fi
matlab -nodisplay -r addpath\(\'$MANGLESCRIPTSDIR\'\)\;graphmask\(\'$1\',\'$2\'\)
else
echo >&2 "ERROR: file $1 not found."
exit 1
fi
elif [ $# -ge 6 ]; then
if [ -e $1 ]; then
if [ -e $2 ]; then
rm $2
fi
echo "addpath('$MANGLESCRIPTSDIR'); graphmask('$1','$2',[$3,$4,$5,$6],'$7','$8')" > jgraphtemp.m
matlab -nodisplay < jgraphtemp.m
rm jgraphtemp.m
else
echo >&2 "ERROR: file $1 not found."
exit 1
fi
else
echo >&2 "USAGE: graphmask.sh <infile> <outfile> [<ramin> <ramax> <decmin> <decmax>] [<title>] [<outlines>]"
echo >&2 "EXAMPLES:"
echo >&2 "fullsky, no outlines: graphmask.sh \"dr4/safe0/sdss_dr4safe0_mask.list\" \"dr4/safe0/sdss_dr4safe0_mask.eps\""
echo >&2 "defined range, title, no outlines: graphmask.sh sdss_slice.list sdss_slice.eps -45 35 8 21 \"SDSS slice\""
echo >&2 "defined range, no title, outlines: graphmask.sh sdss_slice.list sdss_slice.eps -45 35 8 21 \"\" on"
echo >&2 "fullsky, no title, outlines: graphmask.sh sdss_slice.list sdss_slice.eps 0 0 0 0 \"\" on"
exit 1
fi
if [ -e matlabexit.temp ] || [ ! -e $2 ]; then
echo >&2 "ERROR: error in matlab plotting script."
if [ -e matlabexit.temp ]; then
rm matlabexit.temp
fi
exit 1
fi
echo all done!

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scripts/graphmask.sm Executable file
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graphmask 28 # © M E C Swanson 2008
#An sm script to plot mangle graphics files
#first argument: mangle graphics file to read: *.grph
#second argument: postscript file for output graph: *.eps
#third and fourth arguments: optional range for right ascension to plot
# (use 0 0 to plot using range from data)
#fifth and sixth arguments: optional range for declination to plot
# (use 0 0 to plot with dec range adjusted to give equal scaling on x and y axes,
# centered on the range of all the data.)
#seventh argument: title of graph: "I am a title"
#eighth argument: optional switch: 0 for outlines off, 1 for outlines on (default is 0)
#
#WARNINGS:
# -This script uses the opposite color scheme than the matlab script, i.e.,
# weight 1 = black, weight 0 = white
# -RA and Dec are treated as linear variables (no spherical projection). This means that
# ranges that span RA=0 won't plot properly.
# -SM can only plot square eps files, so if you define both RA and Dec range, they should
# have the same length, otherwise your plot will appear stretched.
# -SM has a line length limit of 1500 characters, which SDSS tends to have no trouble overloading.
# If you get an error reading the file, try making your graphics file with lower precision and
# fewer points per 2pi, i.e., use poly2poly -og12 -p3 instead of poly2poly -og30.
#
#USAGE: sm -m $MANGLESCRIPTSDIR/graphmask.sm <infile> <outfile> [<ramin> <ramax>] [<decmin> <decmax>] [<title>] [<outlines>]
#EXAMPLES:
#default range, no outlines: sm -m $MANGLESCRIPTSDIR/graphmask.sm sdss_slice.grph sdss_slice.eps
#defined RA range, outlines: sm -m $MANGLESCRIPTSDIR/graphmask.sm sdss_slice.grph sdss_slice.eps "SDSS slice" 0 35 0 0 1
#defined range, no outlines: sm -m $MANGLESCRIPTSDIR/graphmask.sm sdss_slice.grph sdss_slice.eps "SDSS slice" 10 20 10 20
#defined range, outlines: sm -m graphmask.sm sdss_slice.grph sdss_slice.eps "SDSS slice" 10 20 10 20 1
#
data $1
device postfilecolour $2
#location $gx1 $gx2 $gy1 $(.77*($gx2-$gx1))
if($?3) { define title $3 }
if($?3 && $?4) {
if(!($3==0 && $4==0)){
define azmin $3
define azmax $4
}
}
if($?5 && $?6) {
if(!($5==0 && $6==0)){
define elmin $5
define elmax $6
}
}
if($?7) { define title $7 }
if($?8) { define outlines $8 } else { define outlines 0 }
define i 0 # i = current line to read in file
define in_header 1 # in_header = 1 if reading header of file
#process header information
while{$in_header} {
define i ($i+1)
read row header $i.s
if (header[1]=='polygons'){
define npoly (ATOF((header[0])))
} else { if (header[0]=='unit'){
define unit (header[1])
} else { if (header[0]=='graphics'){
#we've reached the body of the data file, so move on
define in_header 0
} else {
write standard Unrecognized format in line $i of $1.
write standard Please fix the data file and try again.
write smerr.temp 1
quit
}}}
}
define i_start $i #i_start = first line of data
define polycount 0
define first_poly 1
#process polygon data
define numlines ($i_start+2*$npoly-1)
while { $i < $numlines } {
read row specs $i.s
if(specs[0]!='graphics' || dimen(specs)!=12){
write standard Formatting error in line $i of $1
write standard Your data file probably contains a line over 1500 characters long.
write standard Please try to make your data file with shorter lines:
write standard i.e., use poly2poly -og10 -p3 instead of poly2poly -og30.
write smerr.temp 1
quit
}
set id = ATOF(specs[1])
set n_tot = ATOF(specs[3])
set edges = ATOF(specs[5])
set w = ATOF(specs[7])
set midx = ATOF(specs[9])
set midy = ATOF(specs[10])
define numpoints (n_tot[0])
while{$numpoints>0}{
read row polypoints $($i+1)
set n = (dimen(polypoints)/2)
define numpoints ( $numpoints - n[0])
#if there are still points to read in for this polygon,
#we need to read in another line
if($numpoints>0){
write standard "extra line for disconnected polygon"
define numlines ($numlines+1)
}
#separate list of points in x y x y x y ... format into x and y vectors
set ix = 0,2*n[0]-2,2 #even numbers
set iy = 1,2*n[0]-1,2 #odd numbers
# x = numbers with even list indices (indices start at 0)
# y = numbers with odd list indices
# tack first point on at end to close the polygon
set x=polypoints[ix] CONCAT polypoints[0]
set y=polypoints[iy] CONCAT polypoints[1]
# if polygon is in range to be plotted, add it to plot list
if($first_poly){
#if this is the first polygon in list, start the list
set x_all = x
set y_all = y
set numpoints = n+1
set weight = w
define first_poly 0
} else {
#otherwise, tack this one on to the list
set x_all = x_all CONCAT x
set y_all = y_all CONCAT y
set numpoints = numpoints CONCAT (n+1)
set weight = weight CONCAT w
}
define i ($i+1)
define polycount ($polycount+1)
}
define i ($i+1)
}
limits x_all y_all
#adjust limits so the axes have equal scaling
if( ($fx2-$fx1)/$nx > ($fy2-$fy1)/$ny ) {
define ymid (($fy1+$fy2)/2)
define ymin ($ymid - .5*($fx2-$fx1)*$ny/$nx)
define ymax ($ymid + .5*($fx2-$fx1)*$ny/$nx)
define xmin $fx1
define xmax $fx2
} else { if( ($fx2-$fx1)/$nx < ($fy2-$fy1)/$ny ) {
define xmid (($fx1+$fx2)/2)
define xmin ($xmid - .5*($fy2-$fy1)*$nx/$ny)
define xmax ($xmid + .5*($fy2-$fy1)*$nx/$ny)
define ymin $fy1
define ymax $fy2
}}
limits $xmin $xmax $ymin $ymax
#if limits have been specified as arguments, use them
if($?azmin && $?azmax) {
write standard using user-defined limits for RA
define scale (($azmax-$azmin)/($xmax-$xmin))
define ymid (($fy1+$fy2)/2)
define ymin ($ymid - .5*($fy2-$fy1)*$scale)
define ymax ($ymid + .5*($fy2-$fy1)*$scale)
define xmin $azmin
define xmax $azmax
if($?elmin && $?elmax) {
write standard using user-defined limits for dec
define ymin $elmin
define ymax $elmax
}
}
limits $xmin $xmax $ymin $ymax
expand 1.00001
ANGLE 0
AXIS $fx2 $fx1 0 0 $gx1 $gy1 $($gx2-$gx1) 1 $(0)
AXIS $fx2 $fx1 0 0 $gx1 $gy2 $($gx2-$gx1) 0 $(1)
ANGLE 90
AXIS $fy1 $fy2 0 0 $gx1 $gy1 $($gy2-$gy1) 2 $(1)
AXIS $fy1 $fy2 0 0 $gx2 $gy1 $($gy2-$gy1) 0 $(0)
ANGLE 0
#box
xlabel Right Ascension ($unit)
ylabel Declination ($unit)
identification
if ($?title) {
define titlepos ($gy2+100)
relocate ($gx1 $titlepos)
putlabel 9 $title
}
define j 0
do i=0,$polycount-1 {
set k = $j, $j+numpoints[$i]-1
set x=x_all[k]
set y=y_all[k]
#flip so that RA increases from right to left
set x = $fx1+$fx2-x
define j ($j+numpoints[$i])
define gray (int(50+ 200*(1-weight[$i])))
ctype = <0 $gray 255> + 256*<0 $gray 255> + 256*256*<0 $gray 255>
#check if polygon is clockwise or counterclockwise
set ii=0,numpoints[$i]-2
set iplus=1,numpoints[$i]-1
set cross=((x[ii]*y[iplus])-(x[iplus]*y[ii]))
#ishole should be positive if polygon is a hole
set ishole=(.5*sum(cross))
if($outlines){
ctype 0
connect x y
} else {
ctype 1
connect x y
}
if (ishole > 0){
ctype 2
shade 0 x y
} else {
ctype 1
shade 0 x y
}
}
quit
#end

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scripts/graphmasksm.sh Executable file
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#!/bin/sh
# © M E C Swanson 2008
#plot the angular mask described by a polygon file in graphics format
#using sm
#
#optional 3rd-6th arguments give the RA and Dec range to plot the mask
#If no range is given, range will be calculated automatically from the data.
#If only an RA range is given, Dec range will be calculated automatically
#to give equal scaling on x and y axes, centered on the range of all the data.
#
#Entering in "0 0 0 0" for the range will also give an automatic range,
#which can be used if you also wish to, e.g., enter a title.
#Likewise entering "0 0" for the Dec range is equivalent to only specifying an RA range.
#
#optional 7th argument gives a title for the graph
#optional 8th argument turns on drawing black outlines around each polygon
#
#if specifying the full path to a file (rather than just running in the directory
#containing the file you want to plot), put the path in double-quotes as shown below.
#
#USAGE: graphmasksm.sh <infile> <outfile> [<ramin> <ramax>] [<decmin> <decmax>] [<title>] [<outlines>]
#EXAMPLES:
#default range, no outlines: graphmasksm.sh "dr4/safe0/sdss_dr4safe0_mask.grph" "dr4/safe0/sdss_dr4safe0_mask.eps"
#defined range, title, no outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps -45 35 8 21 "SDSS slice"
#defined range, no title, outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps -45 35 8 21 " " on
#default range, no title, outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps 0 0 0 0 " " on
#WARNINGS: (a.k.a., reasons to use the matlab plotting script instead!)
# -This script uses the opposite color scheme than the matlab script, i.e.,
# weight 1 = black, weight 0 = white
# -RA and Dec are treated as linear variables (no spherical projection). This means that
# ranges that span RA=0 won't plot properly.
# -SM can only plot square eps files, so if you define both RA and Dec range, they should
# have the same length, otherwise your plot will appear stretched.
# -SM has a line length limit of 1500 characters, which SDSS tends to have no trouble overloading.
# If you get an error reading the file, try making your graphics file with lower precision and
# fewer points per 2pi, i.e., use poly2poly -og12 -p3 instead of poly2poly -og30.
#
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ ! "$7" = "" ] ; then
title="\"$7\""
else
title=""
fi
if [ "$8" = "on" ] ; then
outlines=1
else
outlines=""
fi
if [ $# -ge 2 ]; then
if [ -e $1 ]; then
echo "Plotting $1 using sm ..."
if [ -e $2 ]; then
rm $2
fi
sm -m $MANGLESCRIPTSDIR/graphmask.sm $1 $2 $3 $4 $5 $6 $title $outlines > sm.temp
else
echo >&2 "ERROR: file $1 not found."
exit 1
fi
else
echo >&2 "USAGE: graphmasksm.sh <infile> <outfile> [<ramin> <ramax>] [<decmin> <decmax>] [<title>] [<outlines>]"
echo >&2 "EXAMPLES:"
echo >&2 "default range, no outlines: graphmasksm.sh \"dr4/safe0/sdss_dr4safe0_mask.grph\" \"dr4/safe0/sdss_dr4safe0_mask.eps\""
echo >&2 "defined range, title, no outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps -45 35 8 21 \"SDSS slice\""
echo >&2 "defined range, no title, outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps -45 35 8 21 \" \" on"
echo >&2 "default range, no title, outlines: graphmasksm.sh sdss_slice.grph sdss_slice.eps 0 0 0 0 \" \" on"
exit 1
fi
if [ -e smerr.temp ] || [ ! -e $2 ]; then
echo >&2 "ERROR: error in sm plotting script."
echo >&2 "See log in sm.temp for more details."
if [ -e smerr.temp ]; then
rm smerr.temp
fi
exit 1
fi
rm sm.temp
echo all done!

1
scripts/healpixpolys.sh Symbolic link
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../masks/healpix/healpixpolys.sh

1
scripts/healpixrast.sh Symbolic link
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../masks/healpix/healpixrast.sh

1
scripts/healpixrast2fits.sh Symbolic link
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../masks/healpix/healpixrast2fits.sh

1
scripts/make_allsky.sh Symbolic link
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../masks/allsky/make_allsky.sh

146
scripts/make_pixelmaps.sh Executable file
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#!/bin/sh
# © M E C Swanson 2008
#Script to make pixelmaps of a mask at several resolutions
#Pixelmaps give the average value of the mask's weight in each pixel,
#using one of mangle's pixelization schemes.
#pixelmaps are saved as $inputmask.$res$scheme, e.g. for
#the input mask sdss_dr7safe0_res6d.pol, pixelmap files will be
#sdss_dr7safe0_res6d.pol.1d, sdss_dr7safe0_res6d.pol.2d, etc.
#
#if a galaxy file is given, this script also uses polyid to find in which pixels
#each galaxy in the list lies. The input galaxy file can have any number of columns,
#but the first 2 columns should be the RA and dec.
#output galaxy files for each resolution will attach the pixel number to the end of
#each line in the galaxy file that lies within a pixel in the pixelmap. The naming
#scheme is the same as for the pixelmap files, e.g., for the input galaxy file
#sdss_dr7safe0_galdetails1.dat, the output galaxy files will be
#sdss_dr7safe0_galdetails1.dat.1d, sdss_dr7safe0_galdetails1.dat.2d, etc.
#
#By default, this script cuts out any pixels with average weights less than 0.5 for
#resolution 1 and average weights less than 0.8 for higher resolutions. To run
#the script without these cuts, enter a 0 for the final command line argument.
#
#USAGE: make_pixelmaps.sh <input mask file> [<input galaxy file>] [<0 to turn cuts off>]
#EXAMPLES:
#make_pixelmaps.sh sdss_dr7safe0_res6d.pol
#make_pixelmaps.sh sdss_dr7safe0_res6d.pol 0
#make_pixelmaps.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat
#make_pixelmaps.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat 0
if [ "$MANGLEBINDIR" = "" ] ; then
MANGLEBINDIR="../../bin"
fi
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ "$MANGLEDATADIR" = "" ] ; then
MANGLEDATADIR="../../masks"
fi
mask=$1
gals=$2
cutweights=$3
#check command line arguments
if [ "$mask" = "" ] ; then
echo >&2 "ERROR: enter the input polygon and galaxy files as command line arguments."
echo >&2 ""
echo >&2 "USAGE: make_pixelmaps.sh <input mask file> [<input galaxy file>] [<0 to turn cuts off>]"
echo >&2 "EXAMPLES:"
echo >&2 "make_pixelmaps.sh sdss_dr7safe0_res6d.pol"
echo >&2 "make_pixelmaps.sh sdss_dr7safe0_res6d.pol 0"
echo >&2 "make_pixelmaps.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat"
echo >&2 "make_pixelmaps.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat 0"
exit 1
fi
if [ "$gals" == 0 ] ; then
cutweights=0
gals=
fi
if [ "$cutweights" = "" ] ; then
cutweights=1
fi
dresmax=6
dscheme="d"
head -n 100 $mask > jmaskhead
#grab pixelization info from input file
awk '/pixelization/{print $0}' < jmaskhead > jpix
resmax=`awk '{print substr($2, 1, length($2)-1)}' < jpix`
scheme=`awk '{print substr($2, length($2))}' < jpix`
rm jpix
#check if input file is snapped and balkanized
snapped=`awk '/snapped/{print $1}' < jmaskhead`
balkanized=`awk '/balkanized/{print $1}' < jmaskhead`
rm jmaskhead
#if input file is not pixelized, snapped, and balkanized, exit.
#if input file is pixelized to a fixed resolution, use it as is.
if [ "$resmax" = "" ]; then
echo >&2 "ERROR: cannot make pixelmaps of an unpixelized mask."
echo >&2 "Pixelize your mask using the pixelize function first."
exit 1
elif [ "$resmax" = -1 ] ; then
resmax=$dresmax
echo "WARNING: making pixelmaps of a mask pixelized adaptively."
echo "Attempting to make pixelmaps up to resolution $resmax."
echo "To guarantee that pixelmaps can be made up to a given resolution,"
echo "Pixelize your mask using a fixed resolution <r> by using 'pixelize -P<scheme>0,<r>'."
fi
#if input file isn't snapped, exit
if [ ! "$snapped" = "snapped" ]; then
echo >&2 "ERROR: cannot make pixelmaps of an unsnapped mask."
echo >&2 "Run snap on your mask before running this script,"
echo >&2 "or add the 'snapped' keyword to your file if it is already snapped."
exit 1
fi
#if input file isn't balkanized, exit
if [ ! "$balkanized" = "balkanized" ]; then
echo >&2 "ERROR: cannot make pixelmaps of an unbalkanized mask."
echo >&2 "Run balkanize on your mask before running this script,"
echo >&2 "or add the 'balkanized' keyword to your file if it already consists"
echo >&2 "of only non-overlapping polygons."
exit 1
fi
for (( res=1; res<=$resmax; res++ ))
do
outmask=$mask.$res$scheme
echo "Generating pixelmap for resolution $res ..."
$MANGLEBINDIR/pixelmap -P${scheme}0,$res $mask $outmask || exit
#cut all pixels with weights less than 0.5 for resolution 1 or 0.8 for higher resolutions
if [ $cutweights -ne 0 ] ; then
if [ $res -le 1 ] ; then
weightcut=0.5
else
weightcut=0.8
fi
mv $outmask jp
$MANGLEBINDIR/poly2poly -j$weightcut jp $outmask || exit
echo "Pixels in $outmask have weights in the range defined in make_pixelmaps.sh."
echo "To run make_pixelmaps.sh without these cuts, enter a 0 for the last command line argument."
echo "EXAMPLE: make_pixelmaps.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat 0"
fi
if [ ! "$gals" == "" ] ; then
if [ -e "$gals" ] ; then
outgals=$gals.$res$scheme
$MANGLESCRIPTSDIR/polyid_gals.sh $outmask $gals $outgals
else
echo >&2 "ERROR: input galaxy file $gals not found!"
exit 1
fi
fi
done

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scripts/make_setup_script.sh Executable file
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#! /bin/sh
# © M E C Swanson 2008
#
#script called by wrapper script setup_mangle_environment to set
#mangle environment variables
#
#USAGE: type 'source setup_mangle_environment' in the base mangle directory
#If environment is setup correctly, typing
#'echo $MANGLEBINDIR; echo $MANGLESCRIPTSDIR; echo $MANGLEDATADIR'
#should print out the names of the appropriate directories.
#
#If the above command doesn't work, try 'source setup_mangle_environment $PWD/'
#
#
#You can also use 'source <MANGLEDIR>setup_mangle_environment <MANGLEDIR>'
#where <MANGLEDIR> is the path to the base mangle directory, e.g., /home/username/mangle2.1/
#
#To automatically set up the mangle environment variables when you start your shell,
#add the following line to your .bashrc (or .tcshrc, or .cshrc, or .login, or .profile)
#(replace <MANGLEDIR> with the path to your mangle installation):
#
#source <MANGLEDIR>setup_mangle_environment <MANGLEDIR>
#If no command line argument is given, assume we're running in the mangle directory
#
#arguments to make_setup_script.sh are:
# $1: 0 if export exists in the environment shell, nonzero otherwise
# $2: name of base mangle directory <MANGLEDIR>
if [ "$2" = "" ]; then
MANGLEDIR=$PWD/
#otherwise use the path in the first command-line argument as $MANGLEDIR
else
MANGLEDIR=$2
fi
MANGLEBINDIR="${MANGLEDIR}bin"
MANGLESCRIPTSDIR="${MANGLEDIR}scripts"
MANGLEDATADIR="${MANGLEDIR}masks"
#check to make sure directories exist
if [ ! -d $MANGLEBINDIR ]; then
echo >&2 "ERROR: The directory $MANGLEBINDIR does not exist"
fi
if [ ! -d $MANGLESCRIPTSDIR ]; then
echo >&2 "ERROR: The directory $MANGLESCRIPTSDIR does not exist"
fi
if [ ! -d $MANGLEDATADIR ]; then
echo >&2 "ERROR: The directory $MANGLEDATADIR does not exist"
fi
if [ ! -d $MANGLEBINDIR ] || [ ! -d $MANGLESCRIPTSDIR ] || [ ! -d $MANGLEDATADIR ]; then
echo >&2 ""
echo >&2 "USAGE: type 'source setup_mangle_environment' in the base mangle directory"
echo >&2 "Or use 'source <MANGLEDIR>setup_mangle_environment <MANGLEDIR>'"
echo >&2 "where <MANGLEDIR> is the path to the base mangle directory,"
echo >&2 "e.g., /home/username/mangle2.1/"
exit 1
fi
#export environment variables and put bin and scripts directories in the path
if [ "$1" = "0" ] ; then
cat <<EOF > setup_script
export MANGLEBINDIR=$MANGLEBINDIR
export MANGLESCRIPTSDIR=$MANGLESCRIPTSDIR
export MANGLEDATADIR=$MANGLEDATADIR
export PATH=$PATH:$MANGLEBINDIR:$MANGLESCRIPTSDIR
EOF
else
cat <<EOF > setup_script
setenv MANGLEBINDIR $MANGLEBINDIR
setenv MANGLESCRIPTSDIR $MANGLESCRIPTSDIR
setenv MANGLEDATADIR $MANGLEDATADIR
setenv PATH $PATH:$MANGLEBINDIR:$MANGLESCRIPTSDIR
EOF
fi

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scripts/mangle_sdss.sh Symbolic link
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../masks/sdss/mangle_sdss.sh

114
scripts/mangle_testsuite.sh Executable file
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#!/bin/sh
# © M E C Swanson 2008
#
#This script tests the mangle installation and creates a tarball of
#output files for further examination.
#
#USAGE: source run_mangle_testsuite > test.log
mkdir test
echo "mangle environment variables are:"
echo "MANGLEBINDIR=$MANGLEBINDIR"
echo "MANGLESCRIPTSDIR=$MANGLESCRIPTSDIR"
echo "MANGLEDATADIR=$MANGLEDATADIR"
echo "PATH=$PATH"
echo "Checking if unformatted fortran files are readable."
cd ../masks/2df100k
../../bin/weight -z2dF100k ngp_fields.dat jnf || exit
../../bin/weight -z2dF100k sgp_fields.dat jnf || exit
cd ../2df230k
../../bin/weight -z2dF230k ngp_fields.dat jnf || exit
../../bin/weight -z2dF230k sgp_fields.dat jnf || exit
rm jnf
echo "Running mangle on 2qz10k mask ..."
cd ../2qz10k/
./2qz.sh
if [ -e 2qz_res4s.eps ]; then
mv 2qz_res4s.eps ../../scripts/test
if [ -e 2qz_north_res4s.eps ]; then
mv 2qz_north_res4s.eps ../../scripts/test
fi
if [ -e 2qz_south_res4s.eps ]; then
mv 2qz_south_res4s.eps ../../scripts/test
fi
fi
mv 2qz_north_res4s.pol 2qz_south_res4s.pol ../../scripts/test
rm 2qz_*
samp=dr6
echo "Running mangle on slice of SDSS $samp mask ..."
cd ../sdss
./sdss_quickstart.sh
if [ -e sdss_${samp}safe0_slice.eps ]; then
mv sdss_${samp}safe0_slice.eps ../../scripts/test
elif [ -e sdss_${samp}safe0_slice1.eps ] && [ -e sdss_${samp}safe0_slice2.eps ]; then
mv sdss_${samp}safe0_slice1.eps sdss_${samp}safe0_slice2.eps ../../scripts/test
else
mv sdss_${samp}safe0_slice.pol ../../scripts/test
fi
rm sdss_${samp}safe0_slice.*
echo "Trimming 2qz north mask with an icosahedron polygon ..."
cd ../../scripts/test
cp ../../masks/icosahedron/icosahedron.pol .
../../bin/poly2poly -J7,7 icosahedron.pol ico7.pol
../../scripts/trim_mask.sh 2qz_north_res4s.pol ico7.pol trimmed_mask.pol
rm icosahedron.pol ico7.pol
echo "Rasterizing 2qz north mask ... "
rm ../../masks/healpix/healpix_polys/nside16_p5s.pol
../../scripts/healpixrast.sh 2qz_north_res4s.pol 16 rasterized_mask.pol
../../scripts/healpixrast2fits.sh 2qz_north_res4s.pol 16 rasterized_mask.fits 16 rasterized_mask.gif
../../scripts/call ../../bin/fits2dat_binary.x 1 16 rasterized_mask.fits j2
echo healpix_weight 3072 > j1
cat j1 j2 > rasterized_mask1.dat
rm j1 j2 args.dat
../../bin/poly2poly rasterized_mask1.dat rasterized_mask1.pol
echo "Making pixelmaps of 2qz north mask ..."
cp ../../masks/2qz10k/azel.dat jazel
tail +2 jazel > azel.dat
../../scripts/make_pixelmaps.sh 2qz_north_res4s.pol azel.dat 0
rm azel.dat jazel
if which matlab >/dev/null 2>&1 ; then
../../bin/poly2poly -ol30 trimmed_mask.pol trimmed_mask.list
../../scripts/graphmask.sh trimmed_mask.list trimmed_mask.eps
rm trimmed_mask.list*
../../bin/poly2poly -ol30 rasterized_mask.pol rasterized_mask.list
../../scripts/graphmask.sh rasterized_mask.list rasterized_mask.eps
rm rasterized_mask.list*
../../bin/poly2poly -ol30 rasterized_mask1.pol rasterized_mask1.list
../../scripts/graphmask.sh rasterized_mask1.list rasterized_mask1.eps
rm rasterized_mask1.list*
for(( i=1; i<=4; i++ ))
do
../../bin/poly2poly -ol30 2qz_north_res4s.pol.${i}s jpix.list
graphmask.sh jpix.list pixmap${i}.eps
rm jpix.list*
done
elif which sm >/dev/null 2>&1 ; then
../../bin/poly2poly -og30 trimmed_mask.pol trimmed_mask.grph
../../scripts/graphmasksm.sh trimmed_mask.grph trimmed_mask.eps
rm trimmed_mask.grph
../../bin/poly2poly -og30 rasterized_mask.pol rasterized_mask.grph
../../scripts/graphmasksm.sh rasterized_mask.grph rasterized_mask.eps
rm rasterized_mask.grph
../../bin/poly2poly -og30 rasterized_mask1.pol rasterized_mask1.grph
../../scripts/graphmasksm.sh rasterized_mask1.grph rasterized_mask1.eps
rm rasterized_mask1.grph
for(( i=1; i<=4; i++ ))
do
../../bin/poly2poly -og30 2qz_north_res4s.pol.${i}s jpix.grph
../../scripts/graphmasksm.sh jpix.grph pixmap${i}.eps
rm jpix.grph*
done
fi
cd ..
echo >&2 "mangle test suite complete! Output files are in test.tar.gz"
mv test.log test
tar cfz test.tar.gz test

1
scripts/plotmap.sh Symbolic link
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../masks/healpix/healpix_conversion_scripts/plotmap.sh

71
scripts/polyid_gals.sh Executable file
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#!/bin/sh
# © M E C Swanson 2008
#
#This script uses polyid to find in which polygons in the input mask
#each galaxy in the list lies. The input galaxy file can have any number of columns,
#but the first 2 columns should be the RA and dec.
#output galaxy files for each resolution will attach the polygon number to the end of
#each line in the galaxy file.
#
#By default, galaxies that are not in any polygon in the mask will be cut out of
#the output file. To keep all galaxies in the output file, enter a 0 for the final
#command line argument.
#
#USAGE: polyid_gals.sh <input mask file> <input galaxy file> <output galaxy file> [<0 to turn cuts off>]
#EXAMPLES:
#polyid_gals.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat sdss_dr7safe0_polyidgals_cut.dat
#polyid_gals.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat sdss_dr7safe0_polyidgals_uncut.dat 0
if [ "$MANGLEBINDIR" = "" ] ; then
MANGLEBINDIR="../../bin"
fi
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ "$MANGLEDATADIR" = "" ] ; then
MANGLEDATADIR="../../masks"
fi
mask=$1
gals=$2
outgals=$3
cut=$4
#check command line arguments
if [ "$mask" = "" ] || [ "$gals" = "" ] || [ "$outgals" = "" ]; then
echo >&2 "ERROR: enter the input polygon file and input and output galaxy files as command line arguments."
echo >&2 ""
echo >&2 "USAGE: polyid_gals.sh <input mask file> <input galaxy file> <output galaxy file> [<0 to turn cuts off>]"
echo >&2 "EXAMPLES:"
echo >&2 "polyid_gals.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat sdss_dr7safe0_polyidgals_cut.dat"
echo >&2 "polyid_gals.sh sdss_dr7safe0_res6d.pol sdss_dr7safe0_galdetails1.dat sdss_dr7safe0_polyidgals_uncut.dat 0"
exit 1
fi
if [ "$cut" = "" ] ; then
cut=1
fi
#count number of columns in input galaxy file
head -n 1 $gals > jgals
numfields=`awk '{print NF}' jgals`
rm jgals
#run polyid on galaxy file and assemble output galaxy files with polygon numbers
echo "Running polyid to find galaxies from $gals in $mask ... "
$MANGLEBINDIR/polyid $mask $gals j1 || exit
tail +2 j1 > j2
awk '{print $3}' j2 > j3
paste $gals j3 > j4
if [ $cut -ne 0 ] ; then
awk "NF == ($numfields+1) {print \$0}" j4 > $outgals
else
cp j4 $outgals
fi
rm j1 j2 j3 j4
count=`wc -l < $outgals`
echo ""
echo "wrote $count galaxies to $outgals."

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#USAGE: source run_mangle_testsuite > test.log
echo "Setting mangle environment variables"
cd ..
source setup_mangle_environment $PWD/
cd scripts
./mangle_testsuite.sh

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scripts/sdss_quickstart.sh Symbolic link
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../masks/sdss/sdss_quickstart.sh

140
scripts/trim_mask.sh Executable file
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#! /bin/sh
# © M E C Swanson 2008
#script to trim a mask so that it only includes polygons in a specified region
#USAGE: trim_mask.sh <mask> <trimmer> <outfile> [<pixelization arguments>]
#EXAMPLE:trim_mask.sh mask.pol trimmer.pol trimmed_mask.pol
# You can also optionally provide arguments to the pixelize function
# in the 4th argument:
#EXAMPLE: trim_mask.sh mask.pol trimmer.pol trimmed_mask.pol -Ps0,6
if [ "$MANGLEBINDIR" = "" ] ; then
MANGLEBINDIR="../../bin"
fi
if [ "$MANGLESCRIPTSDIR" = "" ] ; then
MANGLESCRIPTSDIR="../../scripts"
fi
if [ "$MANGLEDATADIR" = "" ] ; then
MANGLEDATADIR="../../masks"
fi
mask=$1
trimmer=$2
outfile=$3
pixargs=$4
#check command line arguments:
if [ "$mask" = "" ] || [ "$trimmer" = "" ] || [ "$outfile" = "" ] ; then
echo >&2 "ERROR: enter the input polygon file, a polygon defining the region you"
echo >&2 "want to trim to, and the output polygon file as command line arguments."
echo >&2 ""
echo >&2 "USAGE: trim_mask.sh <mask> <trimmer> <outfile> [<pixelization arguments>]"
echo >&2 "EXAMPLE: trim_mask.sh mask.pol trimmer.pol trimmed_mask.pol"
echo >&2 "EXAMPLE w/ optional argument to pixelize: trim_mask.sh mask.pol trimmer.pol trimmed_mask.pol -Ps0,6"
exit 1
fi
#if no argument for pixelize is given, pixelize to resolution 6 with the simple scheme:
if [ "$pixargs" = "" ] ; then
pixargs="-Ps0,6"
fi
head -n 100 $mask > jmaskhead
head -n 100 $trimmer > jtrimmerhead
#grab pixelization info from input files
awk '/pixelization/{print $0}' < jmaskhead > jpix
res1=`awk '{print substr($2, 1, length($2)-1)}' < jpix`
scheme1=`awk '{print substr($2, length($2))}' < jpix`
awk '/pixelization/{print $0}' < jtrimmerhead > jpix
res2=`awk '{print substr($2, 1, length($2)-1)}' < jpix`
scheme2=`awk '{print substr($2, length($2))}' < jpix`
rm jpix jmaskhead jtrimmerhead
#if input files are pixelized, make sure they are consistent:
if [ ! "$res1" = "" ] && [ ! "$res2" = "" ] ; then
if [ $res1 -eq -1 ] || [ $res2 -eq -1 ] ; then
echo >&2 "ERROR: cannot trim a mask pixelized adaptively."
echo >&2 "Pixelize both your mask and your trimmer polygon(s) using a fixed resolution,"
echo >&2 "e.g. -Ps0,8, and try again."
exit 1
fi
if [ $res1 -ne $res2 ] ; then
echo >&2 "ERROR: mask polygons and trimmer polygons must be pixelized to the same resolution."
echo >&2 "Pixelize both your mask and your trimmer polygon(s) using a fixed resolution,"
echo >&2 "e.g. -Ps0,8, and try again."
exit 1
fi
#if input files are unpixelized, pixelize them:
elif [ ! "$res1" = "" ] && [ "$res2" = "" ] ; then
if [ $res1 -eq -1 ] ; then
echo >&2 "ERROR: cannot trim a mask pixelized adaptively."
echo >&2 "Pixelize both your mask and your trimmer polygon(s) using a fixed resolution,"
echo >&2 "e.g. -Ps0,8, and try again."
exit 1
fi
echo "$MANGLEBINDIR/pixelize -P${scheme1}0,$res1 $trimmer trimmer_pix"
$MANGLEBINDIR/pixelize -P${scheme1}0,$res1 $trimmer trimmer_pix || exit
trimmer="trimmer_pix"
elif [ "$res1" = "" ] && [ ! "$res2" = "" ] ; then
if [ $res2 -eq -1 ] ; then
echo >&2 "ERROR: cannot trim a mask pixelized adaptively."
echo >&2 "Pixelize both your mask and your trimmer polygon(s) using a fixed resolution,"
echo >&2 "e.g. -Ps0,8, and try again."
exit 1
fi
echo "$MANGLEBINDIR/pixelize -P${scheme2}0,$res2 $mask mask_pix"
$MANGLEBINDIR/pixelize -P${scheme2}0,$res2 $mask mask_pix || exit
mask="mask_pix"
else
echo "$MANGLEBINDIR/pixelize $pixargs $trimmer trimmer_pix"
$MANGLEBINDIR/pixelize $pixargs $trimmer trimmer_pix || exit
echo "$MANGLEBINDIR/pixelize $pixargs $mask mask_pix"
$MANGLEBINDIR/pixelize $pixargs $mask mask_pix || exit
trimmer="trimmer_pix"
mask="mask_pix"
fi
#check if input file is snapped
snapped=`awk '/snapped/{print $1}' < $mask`
#if mask file isn't snapped, snap it
if [ ! "$snapped" = "snapped" ]; then
echo "Snapping $mask ..."
mv $mask jp
$MANGLEBINDIR/snap jp $mask || exit
rm jp
fi
#find the complement of the trimmer polygon
echo "$MANGLESCRIPTSDIR/find_complement.sh $trimmer trimmer_comp"
$MANGLESCRIPTSDIR/find_complement.sh $trimmer trimmer_comp || exit
#set the complement to have zero weight
echo 0 > jw0
echo "$MANGLEBINDIR/weight -zjw0 trimmer_comp jcomp0"
$MANGLEBINDIR/weight -zjw0 trimmer_comp jcomp0 || exit
rm jw0
#balkanize the mask with the zero-weight complement, thereby trimming off
#everything that does not lie within the trimmer polygon
echo "$MANGLEBINDIR/balkanize $mask jcomp0 jb"
$MANGLEBINDIR/balkanize $mask jcomp0 jb || exit
rm jcomp0
#unify to get rid of zero weight polygons
echo "$MANGLEBINDIR/unify jb $outfile"
$MANGLEBINDIR/unify jb $outfile || exit
rm jb
echo "Polygons of $1 trimmed by $2 written to ${outfile}."
#clean up
rm trimmer_comp
if [ -e trimmer_pix ] ; then
rm trimmer_pix
fi
if [ -e mask_pix ] ; then
rm mask_pix
fi