From: Kevin M. Rosenberg <kevin@rosenberg.net>
Date: Sat, 17 Jun 2000 20:12:15 +0000 (+0000)
Subject: r97: Converted Scanner and Projections to C++
X-Git-Tag: debian-4.5.3-3~920
X-Git-Url: http://git.kpe.io/?p=ctsim.git;a=commitdiff_plain;h=f4a23943110823118f35756dd41fbd6707f04511

r97: Converted Scanner and Projections to C++
---

diff --git a/ChangeLog b/ChangeLog
index 784dfb0..1fcd9b2 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+1.9.1 - 6/20/2000
+   Converted all file i/o to C++ library
+	
+1.9.0 - 6/15/2000
+   Skip versions to make version 2.0 the first C++ version
+   Renamed Raysums to Projections throughout files
+   Renamed Detector to Scanner
+   Converted Scanner and Projecions to full object-oriented
+	
 0.6.1 - 6/12/2000
    Converted Phantom and PhantomElements to Object-Oriented
    Converted Detector to Object-Oriented
diff --git a/cgi-bin/ctsim.cgi.in b/cgi-bin/ctsim.cgi.in
index 6b0da48..898aa89 100755
--- a/cgi-bin/ctsim.cgi.in
+++ b/cgi-bin/ctsim.cgi.in
@@ -22,7 +22,7 @@ CGI::ReadParse(\%in);
 
 # Incoming variables 
 #   Phantom_Name, Phantom_Nx, Phantom_Ny, Phantom_NSample
-#   RS_NDet, RS_NRot, RS_NRay, RS_RotAngle,
+#   PJ_NDet, PJ_NRot, PJ_NRay, PJ_RotAngle,
 #   IR_Nx, IR_Ny, IR_Filter, IR_Filter_Param
 
 my $error = "";
@@ -35,13 +35,13 @@ $error .= "Phantom name must not be blank<br>" if ($Phantom_Name eq "");
 $error .= "Phantom NX and NY must be between 5 and 1024<br>" if ($Phantom_Nx < 5 || $Phantom_Nx > 1024 || $Phantom_Ny < 5 || $Phantom_Ny > 1024);
 $error .= "Phantom NSample must be between 1 and 10<br>" if ($Phantom_NSample < 1 || $Phantom_NSample > 10);
 
-my $RS_NDet = FilterToNumber($in{'RS_NDet'});
-my $RS_NRot = FilterToNumber($in{'RS_NRot'});
-my $RS_NRay = FilterToNumber($in{'RS_NRay'});
-my $RS_RotAngle = FilterToNumber($in{'RS_RotAngle'});
-$error .= "Raysum NDet must be between 5 and 1800<br>" if ($RS_NDet < 5 || $RS_NDet > 1800);
-$error .= "Raysum NRot must be between 5 and 2048<br>" if ($RS_NRot < 5 || $RS_NRot > 2048);
-$error .= "Raysum RotAngle must be between 0.1 and 2<br>" if ($RS_RotAngle < 0.1 || $RS_RotAngle > 2);
+my $PJ_NDet = FilterToNumber($in{'PJ_NDet'});
+my $PJ_NRot = FilterToNumber($in{'PJ_NRot'});
+my $PJ_NRay = FilterToNumber($in{'PJ_NRay'});
+my $PJ_RotAngle = FilterToNumber($in{'PJ_RotAngle'});
+$error .= "Projection NDet must be between 5 and 1800<br>" if ($PJ_NDet < 5 || $PJ_NDet > 1800);
+$error .= "Projection NRot must be between 5 and 2048<br>" if ($PJ_NRot < 5 || $PJ_NRot > 2048);
+$error .= "Projection RotAngle must be between 0.1 and 2<br>" if ($PJ_RotAngle < 0.1 || $PJ_RotAngle > 2);
 
 #my $IR_Nx = FilterToNumber($in{'IR_Nx'});
 #my $IR_Ny = FilterToNumber($in{'IR_Ny'});
@@ -74,38 +74,38 @@ $error .= "IR Filter Parameter must be between 0 and 1<br>" if ($IR_Filter_Param
 my $tmpid = $$;
 my $auto_window_img = "std0.1";
 my $auto_window_diff = "std1";
-my $auto_window_rs = "full";
+my $auto_window_pj = "full";
 my $logfile = "$::jobdir/ctsim.log";
 
 my $result_fname = "$::datadir/result-$tmpid.html";
 my $phantom_fname = "$::datadir/phantom-$tmpid.if";
-my $rs_fname = "$::datadir/rs-$tmpid.rs";
+my $pj_fname = "$::datadir/pj-$tmpid.pj";
 my $ir_fname = "$::datadir/ir-$tmpid.if";
-my $rs_if_fname = "$::datadir/rs-$tmpid.if";
+my $pj_if_fname = "$::datadir/pj-$tmpid.if";
 my $diff_fname = "$::datadir/diff-$tmpid.if";
 my $phantom_png = "$::datadir/phantom-$tmpid.png";
 my $ir_png = "$::datadir/ir-$tmpid.png";
-my $rs_png = "$::datadir/rs-$tmpid.png";
+my $pj_png = "$::datadir/pj-$tmpid.png";
 my $diff_png = "$::datadir/diff-$tmpid.png";
 
 my $result_url = "$::url_datadir/result-$tmpid.html";
 my $phantom_png_url = "$::url_datadir/phantom-$tmpid.png";
 my $ir_png_url = "$::url_datadir/ir-$tmpid.png";
-my $rs_png_url = "$::url_datadir/rs-$tmpid.png";
+my $pj_png_url = "$::url_datadir/pj-$tmpid.png";
 my $diff_png_url = "$::url_datadir/diff-$tmpid.png";
 
 my $ctrec_ver = "$::bindir/ctrec";
-my $phm2rs_ver = "$::bindir/phm2rs";
+my $phm2pj_ver = "$::bindir/phm2pj";
 my $phm2if_ver = "$::bindir/phm2if";
 my $diff_ver = "$::bindir/if-2";
 $ctrec_ver = "/opt/lam/bin/mpirun N N $::lamrundir/ctrec-lam" if $MPI;
-$phm2rs_ver = "/opt/lam/bin/mpirun N N $::lamrundir/phm2rs-lam" if $MPI;
+$phm2pj_ver = "/opt/lam/bin/mpirun N N $::lamrundir/phm2pj-lam" if $MPI;
 $phm2if_ver = "/opt/lam/bin/mpirun N N $::lamrundir/phm2if-lam" if $MPI;
 
 my $gp_cmd = "$phm2if_ver $phantom_fname $Phantom_Nx $Phantom_Ny --phantom $Phantom_Name --nsample $Phantom_NSample";
-my $rs_cmd = "$phm2rs_ver $rs_fname $RS_NDet $RS_NRot --phantom $Phantom_Name --nray $RS_NRay --rotangle $RS_RotAngle";
-my $rs_if_cmd = "$::bindir/rs2if $rs_fname $rs_if_fname";
-my $ir_cmd = "$ctrec_ver $rs_fname $ir_fname $IR_Nx $IR_Ny --filter $IR_Filter --filter-param $IR_Filter_Param --interp $IR_Interp --backproj $IR_Backproj";
+my $pj_cmd = "$phm2pj_ver $pj_fname $PJ_NDet $PJ_NRot --phantom $Phantom_Name --nray $PJ_NRay --rotangle $PJ_RotAngle";
+my $pj_if_cmd = "$::bindir/pj2if $pj_fname $pj_if_fname";
+my $ir_cmd = "$ctrec_ver $pj_fname $ir_fname $IR_Nx $IR_Ny --filter $IR_Filter --filter-param $IR_Filter_Param --interp $IR_Interp --backproj $IR_Backproj";
 my $diff_cmd = "$diff_ver $phantom_fname $ir_fname $diff_fname --comp";
 
 my $window_options = "--auto $auto_window_img";
@@ -118,7 +118,7 @@ if ($Disp_Max ne 'auto') {
 
 my $png1_cmd = "$::bindir/if2img $phantom_fname $phantom_png $window_options --stats --format png";
 my $png2_cmd = "$::bindir/if2img $ir_fname $ir_png $window_options --stats --format png";
-my $png3_cmd = "$::bindir/if2img $rs_if_fname $rs_png --auto $auto_window_rs --stats --format png";
+my $png3_cmd = "$::bindir/if2img $pj_if_fname $pj_png --auto $auto_window_pj --stats --format png";
 my $png4_cmd = "$::bindir/if2img $diff_fname $diff_png --auto $auto_window_diff --stats --format png";
 
 my $title = "CT Simulation Results";
@@ -130,7 +130,7 @@ $out .= "<H1>$title</H1><HR>\n";
 
 if ($opt_d) {
     $out .= "<H2>Commands</H2>\n";
-    $out .= "$gp_cmd<br>\n$rs_cmd<br>\n$rs_if_cmd<br>\n$ir_cmd<br>\n$diff_cmd<br>\n$png1_cmd<br>\n$png2_cmd<br>\n" .
+    $out .= "$gp_cmd<br>\n$pj_cmd<br>\n$pj_if_cmd<br>\n$ir_cmd<br>\n$diff_cmd<br>\n$png1_cmd<br>\n$png2_cmd<br>\n" .
             "$png3_cmd<br>\n$png4_cmd<br>\n";
 }
 
@@ -141,21 +141,21 @@ if ($error ne "") {
     $out .= "<i>$error</i>";
 } else {
   my $gp_out;
-  my $rs_out;
-  my $rs_if_out;
+  my $pj_out;
+  my $pj_if_out;
   my $ir_out;
   my $diff_out;
   my $png_gp_out;
   my $png_ir_out;
-  my $png_rs_out;
+  my $png_pj_out;
   my $png_diff_out;
   $gp_out = `$gp_cmd`;
   if (-s $phantom_fname) {
-    $rs_out .= `$rs_cmd`;
+    $pj_out .= `$pj_cmd`;
     $png_gp_out .= `$png1_cmd`;
-    if (-s $rs_fname) {
-      $rs_if_out .= `$rs_if_cmd`;
-      $png_rs_out .= `$png3_cmd`;
+    if (-s $pj_fname) {
+      $pj_if_out .= `$pj_if_cmd`;
+      $png_pj_out .= `$png3_cmd`;
       $ir_out .= `$ir_cmd`;
       if (-s $ir_fname) {
 	$png_ir_out .= `$png2_cmd`;
@@ -165,7 +165,7 @@ if ($error ne "") {
     }
   }
 
-  $cmdout = "$gp_cmd\n $gp_out $rs_cmd\n $rs_out $rs_if_cmd\n $rs_if_out $ir_cmd\n $ir_out $diff_cmd\n $diff_out $png1_cmd\n $png_gp_out $png2_cmd\n $png_ir_out $png3_cmd\n $png_rs_out $png4_cmd\n $png_diff_out";
+  $cmdout = "$gp_cmd\n $gp_out $pj_cmd\n $pj_out $pj_if_cmd\n $pj_if_out $ir_cmd\n $ir_out $diff_cmd\n $diff_out $png1_cmd\n $png_gp_out $png2_cmd\n $png_ir_out $png3_cmd\n $png_pj_out $png4_cmd\n $png_diff_out";
   if (open(LOGFILE,">> $logfile")) {
     flock(LOGFILE,LOCK_EX);
     seek(LOGFILE, 0, 2);
@@ -182,17 +182,17 @@ if ($error ne "") {
   }
   my $png_gp_out_html = $png_gp_out;
   my $png_ir_out_html = $png_ir_out;
-  my $png_rs_out_html = $png_rs_out;
+  my $png_pj_out_html = $png_pj_out;
   my $png_diff_out_html = $png_diff_out;
   $png_gp_out_html =~ s/\n/<br>/gms;
   $png_ir_out_html =~ s/\n/<br>/gms;
-  $png_rs_out_html =~ s/\n/<br>/gms;
+  $png_pj_out_html =~ s/\n/<br>/gms;
   $png_diff_out_html =~ s/\n/<br>/gms;
   $out .= "<TABLE><TR><TD>Phantom Image</TD><TD>Reconstructed Image</TD></TR>\n";
   $out .= "<TR><TD><IMG SRC=\"$phantom_png_url\"><br><FONT SIZE=1>$png_gp_out</FONT></TD>\n";
   $out .= "<TD><IMG SRC=\"$ir_png_url\"><br><FONT SIZE=1>$png_ir_out</FONT></TD></TR>\n";
-  $out .= "<TR><TD>Raysum Sinusoid</TD><TD>Phantom/Reconst Error</TD></TR>\n";
-  $out .= "<TR><TD><IMG SRC=\"$rs_png_url\"><br><FONT SIZE=1>$png_rs_out</FONT></TD>\n";
+  $out .= "<TR><TD>Projection Sinusoid</TD><TD>Phantom/Reconst Error</TD></TR>\n";
+  $out .= "<TR><TD><IMG SRC=\"$pj_png_url\"><br><FONT SIZE=1>$png_pj_out</FONT></TD>\n";
   $out .= "<TD><IMG SRC=\"$diff_png_url\"><br><FONT SIZE=2>$diff_out</FONT><br><FONT SIZE=1>$png_diff_out</FONT></TD></TR>\n";
   $out .= "</TABLE>";
   $out .= "Execution time: $execution_time seconds\n";
@@ -227,10 +227,10 @@ if (open(JOBFILES,"> $::jobdir/$tmpid"))
     print JOBFILES "Phantom_Nx=$Phantom_Nx\n";
     print JOBFILES "Phantom_Ny=$Phantom_Nx\n";
     print JOBFILES "Phantom_NSample=$Phantom_NSample\n";
-    print JOBFILES "RS_NDet=$RS_NDet\n";
-    print JOBFILES "RS_NRot=$RS_NRot\n";
-    print JOBFILES "RS_NRay=$RS_NRay\n";
-    print JOBFILES "RS_RotAngle=$RS_RotAngle\n";
+    print JOBFILES "PJ_NDet=$PJ_NDet\n";
+    print JOBFILES "PJ_NRot=$PJ_NRot\n";
+    print JOBFILES "PJ_NRay=$PJ_NRay\n";
+    print JOBFILES "PJ_RotAngle=$PJ_RotAngle\n";
     print JOBFILES "IR_Nx=$IR_Nx\n";
     print JOBFILES "IR_Ny=$IR_Ny\n";
     print JOBFILES "IR_Interp=$IR_Interp\n";
@@ -240,7 +240,7 @@ if (open(JOBFILES,"> $::jobdir/$tmpid"))
     print JOBFILES "Disp_Min=$Disp_Min\n";
     print JOBFILES "Disp_Max=$Disp_Max\n";
     print JOBFILES "MPI=$MPI\n";
-    print JOBFILES "Files=$result_fname,$phantom_fname,$rs_fname,$ir_fname,$phantom_png,$ir_png,$rs_if_fname,$rs_png\n" if ($error eq "");
+    print JOBFILES "Files=$result_fname,$phantom_fname,$pj_fname,$ir_fname,$phantom_png,$ir_png,$pj_if_fname,$pj_png\n" if ($error eq "");
     printf JOBFILES "cmdout=$cmdout\n";
     flock(JOBFILES,LOCK_UN);
     close JOBFILES;
diff --git a/configure.in b/configure.in
index 9cc9819..7814d8e 100644
--- a/configure.in
+++ b/configure.in
@@ -4,7 +4,7 @@ dnl Must reset CDPATH so that bash's cd does not print to stdout
 dnl CDPATH=
 
 AC_INIT(src/ctrec.cpp)
-AM_INIT_AUTOMAKE(ctsim,0.6.1)
+AM_INIT_AUTOMAKE(ctsim,1.9.0)
 AM_CONFIG_HEADER(config.h)
 
 dnl Checks for programs.
@@ -310,7 +310,7 @@ ctlibs="$ctlibs_base -lir $ctlibs_graphics -lkmath -lk -lcio $ctlibs_tools"
 AC_SUBST(ctlibs)
 
 if test -n "$lamdir" ; then
-  lamprograms="ctrec-lam phm2if-lam phm2rs-lam"
+  lamprograms="ctrec-lam phm2if-lam phm2pj-lam"
   AC_SUBST(lamprograms)
 fi
 
diff --git a/html/simulate.html.in b/html/simulate.html.in
index 5424cbf..8b855a5 100644
--- a/html/simulate.html.in
+++ b/html/simulate.html.in
@@ -28,10 +28,10 @@ MPI Supercomputing:<br>
 <INPUT type="radio" name="MPI" value="no" checked>No (Single CPU)<br>
 </td><td valign="top">
 <h3>Simulate X-Ray acquistion</h3>
-Number of detectors: <input type="text" name="RS_NDet" size="4" value="367"><p>
-Number of Rotations: <input type="text" name="RS_NRot" size="4" value="320"><p>
-Number of Rays<br>(samples) per detector: <input type="text" name="RS_NRay" size="2" value="1"><p>
-Rotation Angle<br>as a multiple of PI: <input type="text" name="RS_RotAngle" size="3" value="1.0"><br>
+Number of detectors: <input type="text" name="PJ_NDet" size="4" value="367"><p>
+Number of Rotations: <input type="text" name="PJ_NRot" size="4" value="320"><p>
+Number of Rays<br>(samples) per detector: <input type="text" name="PJ_NRay" size="2" value="1"><p>
+Rotation Angle<br>as a multiple of PI: <input type="text" name="PJ_RotAngle" size="3" value="1.0"><br>
 </td><td valign="top">
 <H3>Image Reconstruction</H3>
 Interpolation:<br>
diff --git a/include/Makefile.am b/include/Makefile.am
index 74f7f81..901cad4 100644
--- a/include/Makefile.am
+++ b/include/Makefile.am
@@ -1,4 +1,5 @@
-noinst_HEADERS=ascii.h cio.h ct.h ezplot.h ir.h keyboard.h kmath.h kstddef.h pol.h sgp.h array2d.h imagefile.h backprojectors.h mpiworld.h byteorder.h phantom.h timer.h sstream
+noinst_HEADERS=ascii.h cio.h ct.h ezplot.h ir.h keyboard.h kmath.h kstddef.h pol.h sgp.h array2d.h imagefile.h backprojectors.h mpiworld.h byteorder.h phantom.h timer.h sstream scanner.h projections.h
+
 
 
 
diff --git a/include/backprojectors.h b/include/backprojectors.h
index ea0e85c..c28a11b 100644
--- a/include/backprojectors.h
+++ b/include/backprojectors.h
@@ -9,8 +9,11 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: backprojectors.h,v 1.2 2000/06/13 16:20:31 kevin Exp $
+**  $Id: backprojectors.h,v 1.3 2000/06/17 20:12:14 kevin Exp $
 **  $Log: backprojectors.h,v $
+**  Revision 1.3  2000/06/17 20:12:14  kevin
+**  Converted Scanner and Projections to C++
+**
 **  Revision 1.2  2000/06/13 16:20:31  kevin
 **  finished c++ conversions
 **
@@ -35,7 +38,7 @@
 class Backproject
 {
  public:
-    Backproject (const RAYSUM* rs, ImageFile& im, InterpolationType interpType);
+    Backproject (const Projections& proj, ImageFile& im, InterpolationType interpType);
 
     virtual ~Backproject ();
 
@@ -47,7 +50,7 @@ class Backproject
     void Backproject::errorIndexOutsideDetector (int ix, int iy, double theta, double L, int ni);
 
     InterpolationType interpType;
-    const RAYSUM* rs;
+    const Projections& proj;
     ImageFile& im;
     ImageFileArray v;
     kuint32 nx;
@@ -68,8 +71,8 @@ class Backproject
 class BackprojectTrig : public Backproject
 {
  public:
-  BackprojectTrig (const RAYSUM* rs, ImageFile& im, InterpolationType interpType)
-      : Backproject::Backproject (rs, im, interpType)
+  BackprojectTrig (const Projections& proj, ImageFile& im, InterpolationType interpType)
+      : Backproject::Backproject (proj, im, interpType)
       {}
 
   void BackprojectView (const double* const t, double view_angle);
@@ -79,7 +82,7 @@ class BackprojectTrig : public Backproject
 class BackprojectTable : public Backproject
 {
  public:
-  BackprojectTable (const RAYSUM* rs, ImageFile& im, InterpolationType interpType);
+  BackprojectTable (const Projections& proj, ImageFile& im, InterpolationType interpType);
   ~BackprojectTable ();
 
   void BackprojectView (const double* const t, double view_angle);
@@ -95,7 +98,7 @@ class BackprojectTable : public Backproject
 class BackprojectDiff : public Backproject
 {
  public:
-  BackprojectDiff (const RAYSUM* rs, ImageFile& im, InterpolationType interpType);
+  BackprojectDiff (const Projections& proj, ImageFile& im, InterpolationType interpType);
   ~BackprojectDiff ();
 
   void BackprojectView (const double* const t, double view_angle);
@@ -109,8 +112,8 @@ class BackprojectDiff : public Backproject
 class BackprojectDiff2 : public BackprojectDiff
 {
  public:
-  BackprojectDiff2 (const RAYSUM* rs, ImageFile& im, InterpolationType interpType)
-    :  BackprojectDiff::BackprojectDiff (rs, im, interpType)
+  BackprojectDiff2 (const Projections& proj, ImageFile& im, InterpolationType interpType)
+    :  BackprojectDiff::BackprojectDiff (proj, im, interpType)
     {}
 
   void BackprojectView (const double* const t, double view_angle);
@@ -119,12 +122,12 @@ class BackprojectDiff2 : public BackprojectDiff
 class BackprojectIntDiff2 : public BackprojectDiff
 {
  public:
-  BackprojectIntDiff2 (const RAYSUM* rs, ImageFile& im, InterpolationType interpType)
-    :  BackprojectDiff::BackprojectDiff (rs, im, interpType)
+  BackprojectIntDiff2 (const Projections& proj, ImageFile& im, InterpolationType interpType)
+    :  BackprojectDiff::BackprojectDiff (proj, im, interpType)
     {}
   
   void BackprojectView (const double* const t, double view_angle);
 };
 
 
-Backproject* selectBackprojector (BackprojType type, const RAYSUM*, ImageFile& im, InterpolationType interpType);
+Backproject* selectBackprojector (BackprojType type, const Projections& proj, ImageFile& im, InterpolationType interpType);
diff --git a/include/byteorder.h b/include/byteorder.h
index a3c51e8..187e4fb 100644
--- a/include/byteorder.h
+++ b/include/byteorder.h
@@ -4,14 +4,14 @@
 /* netorder.cpp */
 
 void *strreverse (void *dest, const void *src, size_t n);
-int read_nint16 (kuint16 *n, int fd);
-int write_nint16 (kuint16 const *n, int fd);
-int read_nint32 (kuint32 *n, int fd);
-int write_nint32 (kuint32 const *n, int fd);
-int read_nfloat32 (float *f, int fd);
-int write_nfloat32 (float const *f, int fd);
-int read_nfloat64 (double *d, int fd);
-int write_nfloat64 (double const *d, int fd);
+bool read_nint16 (kuint16 *n, int fd);
+bool write_nint16 (kuint16 const *n, int fd);
+bool read_nint32 (kuint32 *n, int fd);
+bool write_nint32 (kuint32 const *n, int fd);
+bool read_nfloat32 (float *f, int fd);
+bool write_nfloat32 (float const *f, int fd);
+bool read_nfloat64 (double *d, int fd);
+bool write_nfloat64 (double const *d, int fd);
 void ConvertNetworkOrder (void* buffer, size_t bytes);
 void ConvertReverseNetworkOrder (void* buffer, size_t bytes);
 
diff --git a/include/ct.h b/include/ct.h
index 0289653..4817fb3 100644
--- a/include/ct.h
+++ b/include/ct.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: ct.h,v 1.14 2000/06/15 19:07:10 kevin Exp $
+**  $Id: ct.h,v 1.15 2000/06/17 20:12:14 kevin Exp $
 **
 **  This program is free software; you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License (version 2) as
@@ -135,8 +135,10 @@ using namespace std;
 
 #include "array2d.h"
 #include "imagefile.h"
-#include "ir.h"
 #include "phantom.h"
+#include "projections.h"
+#include "scanner.h"
+#include "ir.h"
 #include "backprojectors.h"
 
 
diff --git a/include/imagefile.h b/include/imagefile.h
index 70c3fe4..ccf3769 100644
--- a/include/imagefile.h
+++ b/include/imagefile.h
@@ -17,15 +17,16 @@ private:
     Array2dFileLabel& operator= (const Array2dFileLabel&);
 
 public:
-    kfloat64 calc_time;
-    kuint16 label_type;
-    kuint16 year;
-    kuint16 month;
-    kuint16 day;
-    kuint16 hour;
-    kuint16 minute;
-    kuint16 second;
-    string label_str;
+    kfloat64 m_calcTime;
+    kuint16 m_labelType;
+    kuint16 m_year;
+    kuint16 m_month;
+    kuint16 m_day;
+    kuint16 m_hour;
+    kuint16 m_minute;
+    kuint16 m_second;
+    string m_strLabel;
+    mutable string m_strDate;
 
     static const int L_EMPTY = 0;
     static const int L_HISTORY = 1;
@@ -39,22 +40,22 @@ public:
 
     ~Array2dFileLabel();
 
-    string getLabelString (void) const
-	{ return label_str; }
+    const string& getLabelString (void) const
+	{ return m_strLabel; }
 
     kfloat64 getCalcTime (void) const
-	{ return calc_time; }
+	{ return m_calcTime; }
 
     kfloat64 getLabelType (void) const
-	{ return label_type; }
+	{ return m_labelType; }
 
     string& setLabelString (const char* const str)
-	{ label_str = str; return (label_str); }
+	{ m_strLabel = str; return (m_strLabel); }
 
     string& setLabelString (const string& str)
-	{ label_str = str; return (label_str); }
+	{ m_strLabel = str; return (m_strLabel); }
 
-    void getDateString (string& str) const;
+    const string& getDateString () const;
 };
 
 
@@ -118,9 +119,9 @@ public:
 
   void labelAdd (const Array2dFileLabel& label);
 
-  void labelAdd (const char* const label_str, double calc_time=0.);
+  void labelAdd (const char* const m_strLabel, double calc_time=0.);
 
-  void labelAdd (int type, const char* const label_str, double calc_time=0.);
+  void labelAdd (int type, const char* const m_strLabel, double calc_time=0.);
 
   void labelsCopy (Array2dFile& file, const char* const idStr = NULL);
 
@@ -524,20 +525,21 @@ Array2dFile<T>::labelRead (Array2dFileLabel& label, unsigned int label_num)
     return (false);
   }
 
-  read_nint16 (&label.label_type, file_id);
-  read_nint16 (&label.year, file_id);
-  read_nint16 (&label.month, file_id);
-  read_nint16 (&label.day, file_id);
-  read_nint16 (&label.hour, file_id);
-  read_nint16 (&label.minute, file_id);
-  read_nint16 (&label.second, file_id);
-  read_nfloat64 (&label.calc_time, file_id);
+  read_nint16 (&label.m_labelType, file_id);
+  read_nint16 (&label.m_year, file_id);
+  read_nint16 (&label.m_month, file_id);
+  read_nint16 (&label.m_day, file_id);
+  read_nint16 (&label.m_hour, file_id);
+  read_nint16 (&label.m_minute, file_id);
+  read_nint16 (&label.m_second, file_id);
+  read_nfloat64 (&label.m_calcTime, file_id);
 
   kuint16 strlength;
   read_nint16 (&strlength, file_id);
-  char *str = new char [strlength+1];
+  char str [strlength+1];
   read (file_id, str, strlength);
-  label.label_str = str;
+  str[strlength] = 0;
+  label.m_strLabel = str;
 
   return (true);
 }
@@ -565,17 +567,17 @@ Array2dFile<T>::labelAdd (const Array2dFileLabel& label)
 {
   labelSeek (num_labels);
   
-  write_nint16 (&label.label_type, file_id);
-  write_nint16 (&label.year, file_id);
-  write_nint16 (&label.month, file_id);
-  write_nint16 (&label.day, file_id);
-  write_nint16 (&label.hour, file_id);
-  write_nint16 (&label.minute, file_id);
-  write_nint16 (&label.second, file_id);
-  write_nfloat64 (&label.calc_time, file_id);
-  kuint16 strlength = label.label_str.length();
+  write_nint16 (&label.m_labelType, file_id);
+  write_nint16 (&label.m_year, file_id);
+  write_nint16 (&label.m_month, file_id);
+  write_nint16 (&label.m_day, file_id);
+  write_nint16 (&label.m_hour, file_id);
+  write_nint16 (&label.m_minute, file_id);
+  write_nint16 (&label.m_second, file_id);
+  write_nfloat64 (&label.m_calcTime, file_id);
+  kuint16 strlength = label.m_strLabel.length();
   write_nint16 (&strlength, file_id);
-  write (file_id, static_cast<const void*>(label.label_str.c_str()), strlength);
+  write (file_id, static_cast<const void*>(label.m_strLabel.c_str()), strlength);
 
   num_labels++;
 
diff --git a/include/ir.h b/include/ir.h
index c7b2f7b..8af8572 100644
--- a/include/ir.h
+++ b/include/ir.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: ir.h,v 1.27 2000/06/15 19:07:10 kevin Exp $
+**  $Id: ir.h,v 1.28 2000/06/17 20:12:14 kevin Exp $
 **
 **
 **  This program is free software; you can redistribute it and/or modify
@@ -31,82 +31,8 @@
 
 
 #include "phantom.h"
-
-
-/*----------------------------------------------------------------------*/
-/*				RAYSUM SYMBOLS				*/
-/*----------------------------------------------------------------------*/
-
-/* Ray sums are collected along an array of ndet detectors.  The data
- * for these detectors is stored in the structure DETECTARRAY
- */
-
-typedef float DETECT_TYPE;
-
-struct DetectorArray
-{
-  DETECT_TYPE *detval;	/* Pointer to array of values recorded by detector */
-  int ndet;		/* Number of detectors in array */
-  double view_angle;    /* View angle in radians */
-};
-typedef struct DetectorArray DETARRAY;
-
-
-typedef enum {
-    DETECTOR_PARALLEL,
-    DETECTOR_EQUIANGLE,
-    DETECTOR_EQUILINEAR
-} ScannerGeometry;
-  
-
-class Detector
-{
- public:
-  ScannerGeometry geometry;     /* Geometry of detectory */
-  int ndet;			/* Number of detectors in array */
-  int nview;			/* Number of rotated views */
-  int nsample;		        /* Number of rays per detector */
-  double detlen;		/* Total length of detector array */
-  double rotlen;		/* Rotation angle length in radians (norm 2PI) */
-  double det_inc;		/* Increment between centers of detectors */
-  double rot_inc;		/* Increment in rotation angle between views */
-  double radius;		/* Radius of rotation.  Distance from */
-				/*   center of phm to center of det */
-  double phmlen;                /* Maximum Length of phantom or area of interest */
-  struct {
-    double xd1,yd1,xd2,yd2;	/* Coordinates of detector endpoints */
-    double xs1,ys1,xs2,ys2;	/* Coordinates of source endpoints */
-    double angle;		/* Starting angle */
-  } init;
-
-  Detector (const Phantom& phm, const ScannerGeometry geometry, int ndet, int nview, int nsample, const double rot_anglen);
-  ~Detector();
-  
-};
-
-
-class Projections
-{
- public:
-  int fd;			/* Disk file descriptor */
-  int file_mode;		/* Current file mode (read or write) */
-  int header_size;		/* Size of disk file header */
-  int geometry;			/* Geometry of scanner */
-  struct DetectorArray **view;	/* Pointer to array of detarray_st pointers */
-
-  string remark;	        /* description of raysum data */
-  double calctime;		/* time required to calculate raysums */
-
-  int ndet;			/* number of detectors in array */
-  int nview;			/* number of rotated views */
-  double rot_start;		/* starting view rotation */
-  double rot_inc;		/* angle between rotations */
-  double det_start;		/* distance of beginning detector to center */
-				/*    of PHANTOM */
-  double det_inc;		/* increment between detectors */
-  double phmlen;		/* Length of PHANTOM edge (phm is square) */
-};
-typedef class Projections RAYSUM;
+#include "scanner.h"
+#include "projections.h"
 
 /*----------------------------------------------------------------------*/
 /*				USER SYMBOLS				*/
@@ -156,8 +82,6 @@ typedef enum {     /* Interpolation methods */
   I_LINEAR        /* Linear interpolation */
 } InterpolationType;
 
-static const int N_EXTRA_DETECTORS=4;           /* Number of extra detectors widths when calculating detlen */
-
 static const char O_TRACE_NONE_STR[]=     "none";
 static const char O_TRACE_TEXT_STR[]=     "text";
 static const char O_TRACE_PHM_STR[]=      "phm";
@@ -263,32 +187,6 @@ const char *name_of_filter_domain(const DomainType domain);
 BackprojType opt_set_backproj(const char *optarg);
 const char *name_of_backproj(const BackprojType backproj);
 
-/* raycollect.cpp */
-int raysum_collect (RAYSUM *rs, const Detector& det, const Phantom& phm, const int start_view, const int trace, const int unit_pulse);
-void rayview (const Phantom& phm, DETARRAY *darray, const Detector& det, const double xd1, const double yd1, const double xd2, const double yd2, const double xs1, const double ys1, const double xs2, const double ys2, const int unit_pulse);
-double phm_ray_attenuation (const Phantom& phm, const double x1, const double y1, const double x2, const double y2);
-double pelem_ray_attenuation (PhantomElement& pelem, const double x1, const double y1, const double x2, const double y2);
-void raysum_trace_show_param (const char *label, const char *fmt, int row, int color, ...);
-
-/* rayio.cpp */
-RAYSUM *raysum_create(const char *fname, const int nview, const int ndet);
-RAYSUM *raysum_create_from_det(const char *fname, const Detector& det);
-RAYSUM *raysum_open(const char *filename);
-void raysum_alloc_views(RAYSUM *rs);
-void raysum_free(RAYSUM *rs);
-int raysum_is_open(RAYSUM *rs);
-int raysum_close(RAYSUM *rs);
-int raysum_read_header(RAYSUM *rs);
-int raysum_write_header(RAYSUM *rs);
-int raysum_read(RAYSUM *rs);
-int raysum_write(RAYSUM *rs);
-void raysum_print(const RAYSUM *rs);
-void raysum_print_info(const RAYSUM *rs);
-DETARRAY *detarray_alloc(const int n);
-void detarray_free(DETARRAY *darray);
-int detarray_read(RAYSUM *rs, DETARRAY *darray, const int view_num);
-int detarray_write(RAYSUM *rs, const DETARRAY *darray, const int view_num);
-
 /* From phm2image.cpp */
 void phm_to_imagefile (const Phantom& phm, ImageFile& im, const int col_start, const int col_count, const int nsample, const int trace);
 
@@ -298,36 +196,6 @@ int image_display (const ImageFile& im);
 int image_display_scale (const ImageFile& im, const int scale, const double pmin, const double pmax);
 
 /* From reconstr.cpp */
-ImageFile& proj_reconst (ImageFile& im, RAYSUM *rs, const FilterType filt_type, double filt_param, InterpolationType interp_type, int interp_param, const BackprojType backproj_type, int const ir_trace);
-
-/* From bproj.cpp */
-void backproj_init (const RAYSUM *rs, ImageFile& im, const BackprojType bproj_method);
-int  backproj_calc (const RAYSUM *rs, ImageFile& im, const double *t, const double view_angle, const int interp_type, const int bproj_method);
-void backproj_term (const RAYSUM *rs, ImageFile& im, const int bproj_method);
-
-void backproj_init_trig (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_trig (const RAYSUM *rs, ImageFile& im, const double *t, 
-			 const double view_angle, const int interp_type);
-void backproj_term_trig (const RAYSUM *rs, ImageFile& im);
-void backproj_init_table (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_table (const RAYSUM *rs, ImageFile& im, const double *t, 
-			  const double view_angle, const int interp_type);
-void backproj_term_table (const RAYSUM *rs, ImageFile& im);
-void backproj_init_d (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_d (const RAYSUM *rs, ImageFile& im, const double *t, 
-		      const double view_angle, const int interp_type);
-void backproj_term_d (const RAYSUM *rs, ImageFile& im);
-void backproj_init_d2 (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_d2 (const RAYSUM *rs, ImageFile& im, const double *t, 
-		       const double view_angle, const int interp_type);
-void backproj_term_d2 (const RAYSUM *rs, ImageFile& im);
-void backproj_init_id (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_id (const RAYSUM *rs, ImageFile& im, const double *t, 
-		       const double view_angle, const int interp_type);
-void backproj_term_id (const RAYSUM *rs, ImageFile& im);
-void backproj_init_id2 (const RAYSUM *rs, ImageFile& im);
-int  backproj_calc_id2 (const RAYSUM *rs, ImageFile& im, const double *t, 
-			const double view_angle, const int interp_type);
-void backproj_term_id2 (const RAYSUM *rs, ImageFile& im);
+ImageFile& proj_reconst (ImageFile& im, Projections& rs, const FilterType filt_type, double filt_param, InterpolationType interp_type, int interp_param, const BackprojType backproj_type, int const ir_trace);
 
 #endif
diff --git a/include/kmath.h b/include/kmath.h
index 4837026..bb30f05 100644
--- a/include/kmath.h
+++ b/include/kmath.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: kmath.h,v 1.13 2000/06/15 19:07:10 kevin Exp $
+**  $Id: kmath.h,v 1.14 2000/06/17 20:12:14 kevin Exp $
 **
 **  This program is free software; you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License (version 2) as
@@ -64,6 +64,9 @@ template<class T>
 inline T clamp (T value, T lowerBounds, T upperBounds)
 { return (value >= upperBounds ? upperBounds : (value <= lowerBounds ? lowerBounds : value )); }
 
+template<class T>
+inline T lineLength (T x1, T y1, T x2, T y2)
+{ return static_cast<T>( sqrt ((x2-x1)*(x2-x1) + (y2-y1)*(y2-y1)) ); }
 
 /* clip.cpp */
 int clip_rect(double *x1, double *y1, double *x2, double *y2, const double rect[4]);
diff --git a/include/projections.h b/include/projections.h
new file mode 100644
index 0000000..bbf4305
--- /dev/null
+++ b/include/projections.h
@@ -0,0 +1,95 @@
+/*****************************************************************************
+** FILE IDENTIFICATION
+**
+**   Name:          projections.h
+**   Purpose:       Header file for Projections class
+**   Programmer:    Kevin Rosenberg
+**   Date Started:  July 1, 1984
+**
+**  This is part of the CTSim program
+**  Copyright (C) 1983-2000 Kevin Rosenberg
+**
+**  $Id: projections.h,v 1.1 2000/06/17 20:12:14 kevin Exp $
+**
+**
+**  This program is free software; you can redistribute it and/or modify
+**  it under the terms of the GNU General Public License (version 2) as
+**  published by the Free Software Foundation.
+**
+**  This program is distributed in the hope that it will be useful,
+**  but WITHOUT ANY WARRANTY; without even the implied warranty of
+**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+**  GNU General Public License for more details.
+**
+**  You should have received a copy of the GNU General Public License
+**  along with this program; if not, write to the Free Software
+**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+******************************************************************************/
+
+#ifndef PROJECTIONS_H
+#define PROJECTIONS_H
+
+class Scanner;
+class DetectorArray;
+
+// Projections
+class Projections
+{
+ public:
+  Projections (const int nView, const int nDet);
+  Projections (const Scanner& scanner);
+  Projections (void);
+  ~Projections (void);
+
+  void init (const int nView, const int nDet);
+
+  void printProjectionData (void);
+  void printScanInfo (void) const;
+
+  bool read (const char* fname);
+  bool write (const char* fname);
+  bool detarrayRead (DetectorArray& darray, const int view_num);
+  bool detarrayWrite (const DetectorArray& darray, const int view_num);
+
+  void setRotInc (double rotInc) { m_rotInc = rotInc;}
+  void setDetInc (double detInc) { m_detInc = detInc;}
+  void setPhmLen (double phmLen) { m_phmLen = phmLen;}
+  void setCalcTime (double calcTime) {m_calcTime = calcTime;}
+  void setRemark (const char* remark) {m_remark = remark;}
+  void setRemark (const string remark) {m_remark = remark;}
+
+  const double detStart(void) const {return m_detStart;}
+  const double rotStart(void) const {return m_rotStart;}
+  const double calcTime(void) const {return m_calcTime;}
+  const double phmLen(void) const {return m_phmLen;}
+  const char*  remark(void) const {return m_remark.c_str();}
+  const double detInc(void) const {return m_detInc;}
+  const double rotInc(void) const {return m_rotInc;}
+  const int nDet(void) const {return m_nDet;}
+  const int nView(void) const {return m_nView;}
+  DetectorArray& getDetectorArray (const int iview)
+      { return (*m_projData[iview]); }
+  
+ private:
+  int m_fd;			// Disk file descriptor 
+  int m_headerSize;		// Size of disk file header 
+  int m_geometry;		// Geometry of scanner 
+  struct DetectorArray **m_projData;	// Pointer to array of detarray_st pointers 
+  string m_remark;	        // description of raysum data 
+  int m_nDet;			// number of detectors in array 
+  int m_nView;			// number of rotated views 
+  double m_calcTime;		// time required to calculate raysums 
+  double m_rotStart;		// starting view rotation
+  double m_rotInc;		// angle between rotations 
+  double m_detStart;		// distance of beginning detector to center phantom
+  double m_detInc;		// increment between detectors 
+  double m_phmLen;		// Length of phantom edge (phm is square) 
+
+  bool headerRead (void);
+  bool headerWrite (void);
+  void newProjData (void);
+  void deleteProjData (void);
+};
+
+
+#endif
diff --git a/include/scanner.h b/include/scanner.h
new file mode 100644
index 0000000..8c5ab45
--- /dev/null
+++ b/include/scanner.h
@@ -0,0 +1,116 @@
+/*****************************************************************************
+** FILE IDENTIFICATION
+**
+**   Name:          scanner.h
+**   Purpose:       Scanner header file
+**   Programmer:    Kevin Rosenberg
+**   Date Started:  July 1, 1984
+**
+**  This is part of the CTSim program
+**  Copyright (C) 1983-2000 Kevin Rosenberg
+**
+**  $Id: scanner.h,v 1.1 2000/06/17 20:12:14 kevin Exp $
+**
+**
+**  This program is free software; you can redistribute it and/or modify
+**  it under the terms of the GNU General Public License (version 2) as
+**  published by the Free Software Foundation.
+**
+**  This program is distributed in the hope that it will be useful,
+**  but WITHOUT ANY WARRANTY; without even the implied warranty of
+**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+**  GNU General Public License for more details.
+**
+**  You should have received a copy of the GNU General Public License
+**  along with this program; if not, write to the Free Software
+**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+******************************************************************************/
+
+#ifndef SCANNER_H
+#define SCANNER_H
+
+#include "projections.h"
+
+// Projections are collected along an array of ndet detectors.  The data
+// for these detectors is stored in the class DetectorArray
+
+typedef float DetectorValue;
+
+class DetectorArray
+{
+ public:
+  DetectorArray (const int ndet);
+  ~DetectorArray (void);
+
+  const int nDet(void) const {return m_nDet;}
+  const double viewAngle(void) const {return m_viewAngle;}
+  DetectorValue* detValues(void) {return m_detValues;}
+  const DetectorValue* detValues(void) const {return m_detValues;}
+
+  void setViewAngle (double viewAngle)
+      { m_viewAngle = viewAngle; }
+
+ private:
+  DetectorValue* m_detValues;	/* Pointer to array of values recorded by detector */
+  int m_nDet;		/* Number of detectors in array */
+  double m_viewAngle;    /* View angle in radians */
+};
+
+typedef enum {
+    DETECTOR_PARALLEL,
+    DETECTOR_EQUIANGLE,
+    DETECTOR_EQUILINEAR
+} ScannerGeometry;
+  
+
+class Scanner
+{
+ public:
+  Scanner (const Phantom& phm, const ScannerGeometry geometry, int nDet, int nView, int nSample, const double rot_anglen);
+  ~Scanner();
+  
+  void collectProjections (Projections& proj, const Phantom& phm, const int start_view, const int trace);
+
+  const unsigned int nDet(void) const {return m_nDet;}
+  const unsigned int nView(void) const {return m_nView;}
+  const double phmLen(void) const {return m_phmLen;}
+  const double rotInc(void) const {return m_rotInc;}
+  const double detInc(void) const {return m_detInc;}
+  const double radius(void) const {return m_radius;}
+
+
+ private:
+  void projectSingleView (const Phantom& phm, DetectorArray& darray, const double xd1, const double yd1, const double xd2, const double yd2, const double xs1, const double ys1, const double xs2, const double ys2);
+
+  double projectSingleLine (const Phantom& phm, const double x1, const double y1, const double x2, const double y2);
+
+  double projectLineAgainstPElem (const PhantomElement& pelem, const double x1, const double y1, const double x2, const double y2);
+
+  void traceShowParam (const char *label, const char *fmt, int row, int color, ...);
+
+
+  ScannerGeometry m_geometry;     /* Geometry of detectory */
+  unsigned int m_nDet;			/* Number of detectors in array */
+  unsigned int m_nView;			/* Number of rotated views */
+  unsigned int m_nSample;		        /* Number of rays per detector */
+  double m_detLen;		/* Total length of detector array */
+  double m_rotLen;		/* Rotation angle length in radians (norm 2PI) */
+  double m_detInc;		/* Increment between centers of detectors */
+  double m_rotInc;		/* Increment in rotation angle between views */
+  double m_radius;		/* Radius of rotation.  Distance from */
+				/*   center of phm to center of det */
+  double m_phmLen;                /* Maximum Length of phantom or area of interest */
+
+  struct {
+    double xd1,yd1,xd2,yd2;	/* Coordinates of detector endpoints */
+    double xs1,ys1,xs2,ys2;	/* Coordinates of source endpoints */
+    double angle;		/* Starting angle */
+  } m_initPos;
+
+  static const int N_EXTRA_DETECTORS=4;           /* Number of extra detectors widths when calculating detlen */
+
+  int m_trace;
+
+};
+
+#endif
diff --git a/src/Makefile.am b/src/Makefile.am
index 7fda6a4..ec47a60 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,6 @@
-bin_PROGRAMS = ctsim ctrec phm2rs rs2if @lamprograms@  ifinfo phm2if if-1 if-2 if2img 
+bin_PROGRAMS = ctsim ctrec phm2pj pj2if @lamprograms@  ifinfo phm2if if-1 if-2 if2img 
 bin_SCRIPTS = sample-ctrec.sh
-EXTRA_PROGRAMS = ctrec-lam phm2rs-lam phm2if-lam
+EXTRA_PROGRAMS = ctrec-lam phm2pj-lam phm2if-lam
 INCLUDES=@my_includes@
 EXTRA_DIST=Makefile.nt mpiworld.cpp
 
@@ -8,14 +8,14 @@ ctsim_SOURCES = ctsim.cpp
 ctsim_LDADD = @ctlibs@
 ctrec_SOURCES = ctrec.cpp 
 ctrec_LDADD=@ctlibs@
-phm2rs_SOURCES=phm2rs.cpp
-phm2rs_LDADD=@ctlibs@
+phm2pj_SOURCES=phm2pj.cpp
+phm2pj_LDADD=@ctlibs@
 phm2if_SOURCES = phm2if.cpp
 phm2if_LDADD=@ctlibs@
 if2img_SOURCES = if2img.cpp
 if2img_LDADD=@ctlibs@
-rs2if_SOURCES = rs2if.cpp
-rs2if_LDADD=@ctlibs@
+pj2if_SOURCES = pj2if.cpp
+pj2if_LDADD=@ctlibs@
 if_1_SOURCES=if-1.cpp
 if_1_LDADD=@ctlibs@
 if_2_SOURCES=if-2.cpp
@@ -27,11 +27,11 @@ ctrec_lam_SOURCES=ctrec.cpp
 ctrec_lam_LDADD=@ctlamlibs@
 phm2if_lam_SOURCES=phm2if.cpp
 phm2if_lam_LDADD=@ctlamlibs@
-phm2rs_lam_SOURCES=phm2rs.cpp
-phm2rs_lam_LDADD=@ctlamlibs@
+phm2pj_lam_SOURCES=phm2pj.cpp
+phm2pj_lam_LDADD=@ctlamlibs@
 
 realclean:
-	rm -f *.pgm *.if *~ *.rs
+	rm -f *.pgm *.if *~ *.pj
 
 if USE_LAM
 CC_LAM = $(lamdir)/bin/balky
@@ -40,16 +40,16 @@ LAM_EXTRA_SRC = mpiworld.cpp
 ctrec-lam: ctrec.cpp mpiworld.cpp
 	$(CC_LAM) @DEFS@ $(CFLAGS) $(INCLUDES) -DHAVE_MPI ctrec.cpp -o ctrec-lam $(LDFLAGS) $(LAM_EXTRA_SRC) @ctlibs@
 
-phm2rs-lam: phm2rs.cpp mpiworld.cpp
-	$(CC_LAM) @DEFS@ $(CFLAGS) $(INCLUDES) -DHAVE_MPI phm2rs.cpp -o phm2rs-lam $(LDFLAGS) $(LAM_EXTRA_SRC) @ctlibs@
+phm2pj-lam: phm2pj.cpp mpiworld.cpp
+	$(CC_LAM) @DEFS@ $(CFLAGS) $(INCLUDES) -DHAVE_MPI phm2pj.cpp -o phm2pj-lam $(LDFLAGS) $(LAM_EXTRA_SRC) @ctlibs@
 
 phm2if-lam: phm2if.cpp mpiworld.cpp
 	$(CC_LAM) @DEFS@ $(CFLAGS) $(INCLUDES) -DHAVE_MPI phm2if.cpp -o phm2if-lam $(LDFLAGS) $(LAM_EXTRA_SRC) @ctlibs@
 
 endif
 
-shared: ctrec.cpp phm2rs.cpp 
-	$(CC) @DEFS@ $(CFLAGS) $(INCLUDES) -DNO_MAIN -shared phm2rs.cpp ctrec.cpp @ctlibs@ $(LDFLAGS) -o ir.so
+shared: ctrec.cpp phm2pj.cpp 
+	$(CC) @DEFS@ $(CFLAGS) $(INCLUDES) -DNO_MAIN -shared phm2pj.cpp ctrec.cpp @ctlibs@ $(LDFLAGS) -o ir.so
 
 
 
diff --git a/src/ctrec.cpp b/src/ctrec.cpp
index 586f2b6..0ec8402 100644
--- a/src/ctrec.cpp
+++ b/src/ctrec.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: ctrec.cpp,v 1.9 2000/06/15 19:07:10 kevin Exp $
+**  $Id: ctrec.cpp,v 1.10 2000/06/17 20:12:15 kevin Exp $
 **
 **  This program is free software; you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License (version 2) as
@@ -95,7 +95,7 @@ ctrec_usage (const char *program)
 
 
 #ifdef HAVE_MPI
-static void ScatterProjectionsMPI (MPIWorld& mpiWorld, RAYSUM *rsGlobal, RAYSUM *rsLocal, const int debug);
+static void ScatterProjectionsMPI (MPIWorld& mpiWorld, Projections& projGlobal, Projections& projLocal, const int debug);
 static void ReduceImageMPI (MPIWorld& mpiWorld, ImageFile* imLocal, ImageFile* imGlobal);
 #endif
 
@@ -104,8 +104,8 @@ int
 ctrec_main (int argc, char * argv[])
 {
   ImageFile *imGlobal = NULL;
-  RAYSUM *rsGlobal = NULL;
-  char *rs_name, *im_filename = NULL;
+  Projections projGlobal;
+  char *pj_name, *im_filename = NULL;
   string remark;
   char filt_name[80];
   char *endptr;
@@ -120,7 +120,6 @@ ctrec_main (int argc, char * argv[])
   int nx, ny;
 #ifdef HAVE_MPI
   ImageFile *imLocal;
-  RAYSUM *rsLocal;
   int mpi_nview, mpi_ndet;
   double mpi_detinc, mpi_rotinc, mpi_phmlen;
   MPIWorld mpiWorld (argc, argv);
@@ -198,7 +197,7 @@ ctrec_main (int argc, char * argv[])
       return (1);
     }
 
-    rs_name = argv[optind];
+    pj_name = argv[optind];
   
     im_filename = argv[optind + 1];
   
@@ -223,16 +222,15 @@ ctrec_main (int argc, char * argv[])
 
 #ifdef HAVE_MPI
   if (mpiWorld.getRank() == 0) {
-    rsGlobal = raysum_open (rs_name);
-    raysum_read (rsGlobal);
+    projGlobal.read (pj_name);
     if (opt_verbose)
-      raysum_print_info(rsGlobal);
+      projGlobal.printScanInfo();
 
-    mpi_ndet = rsGlobal->ndet;
-    mpi_nview = rsGlobal->nview;
-    mpi_detinc = rsGlobal->det_inc;
-    mpi_phmlen = rsGlobal->phmlen;
-    mpi_rotinc = rsGlobal->rot_inc;
+    mpi_ndet = projGlobal.nDet();
+    mpi_nview = projGlobal.nView();
+    mpi_detinc = projGlobal.detInc();
+    mpi_phmlen = projGlobal.phmLen();
+    mpi_rotinc = projGlobal.rotInc();
   }
 
   TimerCollectiveMPI timerBcast (mpiWorld.getComm());
@@ -256,15 +254,13 @@ ctrec_main (int argc, char * argv[])
 
   mpiWorld.setTotalWorkUnits (mpi_nview);
 
-  rsLocal = raysum_create (NULL, mpiWorld.getMyLocalWorkUnits(), mpi_ndet);
-  rsLocal->ndet = mpi_ndet;
-  rsLocal->nview = mpi_nview;
-  rsLocal->det_inc = mpi_detinc;
-  rsLocal->phmlen = mpi_phmlen;
-  rsLocal->rot_inc = mpi_rotinc;
+  Projections projLocal (mpiWorld.getMyLocalWorkUnits(), mpi_ndet);
+  projLocal.setDetInc (mpi_detinc);
+  projLocal.setPhmLen (mpi_phmlen);
+  projLocal.setRotInc (mpi_rotinc);
 
   TimerCollectiveMPI timerScatter (mpiWorld.getComm());
-  ScatterProjectionsMPI (mpiWorld, rsGlobal, rsLocal, opt_debug);
+  ScatterProjectionsMPI (mpiWorld, projGlobal, projLocal, opt_debug);
   if (opt_verbose)
       timerScatter.timerEndAndReport ("Time to scatter projections");
 
@@ -275,10 +271,9 @@ ctrec_main (int argc, char * argv[])
 
   imLocal = new ImageFile (nx, ny);
 #else
-  rsGlobal = raysum_open (rs_name);
-  raysum_read (rsGlobal);
+  projGlobal.read (pj_name);
   if (opt_verbose)
-    raysum_print_info(rsGlobal);
+    projGlobal.printScanInfo();
 
   imGlobal = new ImageFile (im_filename, nx, ny);
   imGlobal->fileCreate();
@@ -286,7 +281,7 @@ ctrec_main (int argc, char * argv[])
 
 #ifdef HAVE_MPI
   TimerCollectiveMPI timerReconstruct (mpiWorld.getComm());
-  proj_reconst (*imLocal, rsLocal, opt_filter, opt_filter_param, opt_interp, opt_interp_param, opt_backproj, opt_trace);
+  proj_reconst (*imLocal, projLocal, opt_filter, opt_filter_param, opt_interp, opt_interp_param, opt_backproj, opt_trace);
   if (opt_verbose)
       timerReconstruct.timerEndAndReport ("Time to reconstruct");
 
@@ -295,21 +290,20 @@ ctrec_main (int argc, char * argv[])
   if (opt_verbose)
       timerReduce.timerEndAndReport ("Time to reduce image");
 #else
-  proj_reconst (*imGlobal, rsGlobal, opt_filter, opt_filter_param, opt_interp, opt_interp_param, opt_backproj, opt_trace);
+  proj_reconst (*imGlobal, projGlobal, opt_filter, opt_filter_param, opt_interp, opt_interp_param, opt_backproj, opt_trace);
 #endif
 
 #ifdef HAVE_MPI
   if (mpiWorld.getRank() == 0)
 #endif
     {
-      raysum_close (rsGlobal);
-      double calctime = timerProgram.timerEnd();
+      double calcTime = timerProgram.timerEnd();
       imGlobal->arrayDataWrite ();
-      imGlobal->labelAdd (Array2dFileLabel::L_HISTORY, rsGlobal->remark.c_str(), rsGlobal->calctime);
-      imGlobal->labelAdd (Array2dFileLabel::L_HISTORY, remark.c_str(), calctime);
+      imGlobal->labelAdd (Array2dFileLabel::L_HISTORY, projGlobal.remark(), projGlobal.calcTime());
+      imGlobal->labelAdd (Array2dFileLabel::L_HISTORY, remark.c_str(), calcTime);
       imGlobal->fileClose ();
       if (opt_verbose)
-	cout << "Run time: " << calctime << " seconds" << endl;
+	cout << "Run time: " << calcTime << " seconds" << endl;
     }
 #ifdef HAVE_MPI
   MPI::Finalize();
@@ -325,25 +319,34 @@ ctrec_main (int argc, char * argv[])
 //////////////////////////////////////////////////////////////////////////////////////
 
 #ifdef HAVE_MPI
-static void ScatterProjectionsMPI (MPIWorld& mpiWorld, RAYSUM *rsGlobal, RAYSUM *rsLocal, const int opt_debug)
+static void ScatterProjectionsMPI (MPIWorld& mpiWorld, Projections& projGlobal, Projections& projLocal, const int opt_debug)
 {
   if (mpiWorld.getRank() == 0) {
     for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
       for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
-	mpiWorld.getComm().Send(&rsGlobal->view[iw]->ndet, 1, MPI::INT, iProc, 0);
-	mpiWorld.getComm().Send(&rsGlobal->view[iw]->view_angle, 1, MPI::DOUBLE, iProc, 0);
-	mpiWorld.getComm().Send(rsGlobal->view[iw]->detval, rsGlobal->ndet, MPI::FLOAT, iProc, 0);
+	DetectorArray& detarray = projGlobal.getDetectorArray( iw );
+	int nDet = detarray.nDet();
+	DetectorValue* detval = detarray.detValues();
+
+	double viewAngle = detarray.viewAngle();
+	mpiWorld.getComm().Send(&nDet, 1, MPI::INT, iProc, 0);
+	mpiWorld.getComm().Send(&viewAngle, 1, MPI::DOUBLE, iProc, 0);
+	mpiWorld.getComm().Send(detval, nDet, MPI::FLOAT, iProc, 0);
       }
     }
   }
 
   for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++) {
     MPI::Status status;
-    mpiWorld.getComm().Recv(&rsLocal->view[iw]->ndet, 1, MPI::INT, 0, 0, status);
-    mpiWorld.getComm().Recv(&rsLocal->view[iw]->view_angle, 1, MPI::DOUBLE, 0, 0, status);
-    mpiWorld.getComm().Recv(rsLocal->view[iw]->detval, rsLocal->ndet, MPI::FLOAT, 0, 0, status);
+    int nDet;
+    double viewAngle;
+    DetectorValue* detval = projLocal.getDetectorArray(iw).detValues();
+
+    mpiWorld.getComm().Recv(&nDet, 1, MPI::INT, 0, 0, status);
+    mpiWorld.getComm().Recv(&viewAngle, 1, MPI::DOUBLE, 0, 0, status);
+    mpiWorld.getComm().Recv(detval, nDet, MPI::FLOAT, 0, 0, status);
+    projLocal.getDetectorArray(iw).setViewAngle( viewAngle );
   }
-  rsLocal->nview = mpiWorld.getMyLocalWorkUnits();
 }
 
 static void
diff --git a/src/if2img.cpp b/src/if2img.cpp
index 6971fbb..85237a7 100644
--- a/src/if2img.cpp
+++ b/src/if2img.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: if2img.cpp,v 1.4 2000/06/13 16:20:31 kevin Exp $
+**  $Id: if2img.cpp,v 1.5 2000/06/17 20:12:15 kevin Exp $
 **
 **  This program is free software; you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License (version 2) as
@@ -292,16 +292,14 @@ if2img_main (int argc, char *const argv[])
     for (int i = 0; i < nlabels; i++) {
       Array2dFileLabel label;
       im.labelRead (label, i);
-      string str;
-      label.getDateString (str);
 
       if (label.getLabelType() == Array2dFileLabel::L_HISTORY) {
 	cout << "History: " << label.getLabelString() << endl;
 	cout << "  calc time = " << label.getCalcTime() << " secs" << endl;
-	cout << "  Timestamp = " << str << endl;
+	cout << "  Timestamp = " << label.getDateString() << endl;
       } else if (label.getLabelType() == Array2dFileLabel::L_USER) {
 	cout << "Note: " <<  label.getLabelString() << endl;
-	cout << "  Timestamp = %s" << str << endl;
+	cout << "  Timestamp = %s" << label.getDateString() << endl;
       }
     }
   }
diff --git a/src/ifinfo.cpp b/src/ifinfo.cpp
index 7c771f7..a054f2a 100644
--- a/src/ifinfo.cpp
+++ b/src/ifinfo.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: ifinfo.cpp,v 1.6 2000/06/13 16:20:31 kevin Exp $
+**  $Id: ifinfo.cpp,v 1.7 2000/06/17 20:12:15 kevin Exp $
 **
 **  This program is free software; you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License (version 2) as
@@ -142,17 +142,16 @@ ifinfo_main (int argc, char *const argv[])
 	    Array2dFileLabel label;
 	    im->labelRead (label, i);
 
-	    string str;
-	    label.getDateString (str);
-
 	    if (label.getLabelType() == Array2dFileLabel::L_HISTORY) {
-	      cout << "History: " << label.getLabelString() << endl;
+	      cout << "History: " << endl;
+	      cout << "  " << label.getLabelString() << endl;
 	      cout << "  calc time = " << label.getCalcTime() << " secs" << endl;
-	      cout << "  Timestamp = " << str << endl;
+	      cout << "  Timestamp = " << label.getDateString() << endl;
 	    } else if (label.getLabelType() == Array2dFileLabel::L_USER) {
 	      cout << "Note: " <<  label.getLabelString() << endl;
-	      cout << "  Timestamp = %s" << str << endl;
-	  }
+	      cout << "  Timestamp = %s" << label.getDateString() << endl;
+	    }
+	    cout << endl;
 	}
     }
 
@@ -221,13 +220,13 @@ ifinfo_main (int argc, char *const argv[])
 	    }
 	}
       stddev = sqrt(stddev / (nx * ny));
-      cout << "nx=" << nx << endl;
-      cout << "nx=" << ny << endl;
-      cout << "min=" << minfound << endl;
-      cout << "max=" << maxfound << endl;
-      cout << "mean=" << mean << endl;
-      cout << "mode=" << mode << endl;
-      cout << "stddef=" << stddev << endl;
+      cout << "    nx: " << nx << endl;
+      cout << "    nx: " << ny << endl;
+      cout << "   min: " << minfound << endl;
+      cout << "   max: " << maxfound << endl;
+      cout << "  mean: " << mean << endl;
+      cout << "  mode: " << mode << endl;
+      cout << "stddef: " << stddev << endl;
     }
   
   return (0);
diff --git a/src/phm2pj.cpp b/src/phm2pj.cpp
new file mode 100644
index 0000000..fe83154
--- /dev/null
+++ b/src/phm2pj.cpp
@@ -0,0 +1,342 @@
+/*****************************************************************************
+** FILE IDENTIFICATION
+**
+**   Name:          phm2pj.cpp
+**   Purpose:       Take projections of a phantom object
+**   Programmer:    Kevin Rosenberg
+**   Date Started:  1984
+**
+**  This is part of the CTSim program
+**  Copyright (C) 1983-2000 Kevin Rosenberg
+**
+**  $Id: phm2pj.cpp,v 1.1 2000/06/17 20:12:15 kevin Exp $
+**
+**  This program is free software; you can redistribute it and/or modify
+**  it under the terms of the GNU General Public License (version 2) as
+**  published by the Free Software Foundation.
+**
+**  This program is distributed in the hope that it will be useful,
+**  but WITHOUT ANY WARRANTY; without even the implied warranty of
+**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+**  GNU General Public License for more details.
+**
+**  You should have received a copy of the GNU General Public License
+**  along with this program; if not, write to the Free Software
+**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+******************************************************************************/
+
+#include "ct.h"
+#include "timer.h"
+
+
+enum { O_PHANTOM, O_DESC, O_NRAY, O_ROTANGLE, O_PHMFILE,
+       O_TRACE, O_VERBOSE, O_HELP, O_DEBUG, O_VERSION };
+
+static struct option phm2pj_options[] = 
+{
+  {"phantom", 1, 0, O_PHANTOM},
+  {"phmfile", 1, 0, O_PHMFILE},
+  {"desc", 1, 0, O_DESC},
+  {"nray", 1, 0, O_NRAY},
+  {"rotangle", 1, 0, O_ROTANGLE},
+  {"trace", 1, 0, O_TRACE},
+  {"verbose", 0, 0, O_VERBOSE},
+  {"help", 0, 0, O_HELP},
+  {"debug", 0, 0, O_DEBUG},
+  {"version", 0, 0, O_VERSION},
+  {0, 0, 0, 0}
+};
+
+
+void 
+phm2pj_usage (const char *program)
+{
+  cout << "usage: " << fileBasename(program) << " outfile ndet nview [--phantom phantom-name] [--phmfile filename] [OPTIONS]" << endl;
+  cout << "Calculate (projections) through phantom object, either a predefined --phantom or a --phmfile" << endl;
+  cout << "" << endl;
+  cout << "     outfile      Name of output file for raysums" << endl;
+  cout << "     ndet         Number of detectors" << endl;
+  cout << "     nview        Number of rotated views" << endl;
+  cout << "     --phantom    Phantom to use for projection" << endl;
+  cout << "        herman    Herman head phantom" << endl;
+  cout << "        rowland   Rowland head phantom" << endl;
+  cout << "        browland  Bordered Rowland head phantom" << endl;
+  cout << "        unitpulse Unit pulse phantom" << endl;
+  cout << "     --phmfile    Get Phantom from phantom file" << endl;
+  cout << "     --desc       Description of raysum" << endl;
+  cout << "     --nray       Number of rays per detector (default = 1)" << endl;
+  cout << "     --rotangle   Degrees to rotate view through, multiple of PI (default = 1)" << endl;
+  cout << "     --trace      Trace level to use" << endl;
+  cout << "        none      No tracing (default)" << endl;
+  cout << "        text      Trace text level" << endl;
+  cout << "        phm       Trace phantom image" << endl;
+  cout << "        rays      Trace rays" << endl;
+  cout << "        plot      Trace plot" << endl;
+  cout << "        clipping  Trace clipping" << endl;
+  cout << "     --verbose    Verbose mode" << endl;
+  cout << "     --debug      Debug mode" << endl;
+  cout << "     --version    Print version" << endl;
+  cout << "     --help       Print this help message" << endl;
+}
+
+#ifdef HAVE_MPI
+void GatherProjectionsMPI (MPIWorld& mpiWorld, Projections& pjGlobal, Projections& pjLocal, const int opt_debug);
+#endif
+
+int 
+phm2pj_main (int argc, char* argv[])
+{
+  Phantom phm;
+  ScannerGeometry opt_geometry = DETECTOR_PARALLEL;
+  char *opt_outfile = NULL;
+  string opt_desc;
+  string opt_phmfilename;
+  int opt_ndet, opt_nview;
+  int opt_nray = 1;
+  int opt_trace = 0;
+  int opt_phmnum = -1;
+  int opt_verbose = 0;
+  int opt_debug = 0;
+  double opt_rotangle = 1;
+  char* endptr = NULL;
+  char* endstr;
+
+#ifdef HAVE_MPI
+  MPIWorld mpiWorld (argc, argv);
+#endif
+
+  Timer timerProgram;
+
+#ifdef HAVE_MPI
+  if (mpiWorld.getRank() == 0) {
+#endif
+    while (1) {
+      int c = getopt_long(argc, argv, "", phm2pj_options, NULL);
+
+      if (c == -1)
+	break;
+      
+      switch (c) {
+      case O_PHANTOM:
+	if ((opt_phmnum = opt_set_phantom (optarg)) < 0) {
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	phm.create (opt_phmnum);
+	break;
+      case O_PHMFILE:
+#ifdef HAVE_MPI
+	if (mpiWorld.getRank() == 0)
+	  cerr << "Can not read phantom from file in MPI mode" << endl;
+	return (1);
+#endif
+	opt_phmfilename = optarg;
+	phm.createFromFile (opt_phmfilename.c_str());
+	break;
+      case O_VERBOSE:
+	opt_verbose = 1;
+	break;
+      case O_DEBUG:
+	opt_debug = 1;
+	break;
+	break;
+      case O_TRACE:
+	if ((opt_trace = opt_set_trace(optarg)) < 0) {
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	break;
+      case O_DESC:
+	opt_desc = optarg;
+	break;
+      case O_ROTANGLE:
+	opt_rotangle = strtod(optarg, &endptr);
+	endstr = optarg + strlen(optarg);
+	if (endptr != endstr) {
+	  cerr << "Error setting --rotangle to " << optarg << endl;
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	break;
+      case O_NRAY:
+	opt_nray = strtol(optarg, &endptr, 10);
+	endstr = optarg + strlen(optarg);
+	if (endptr != endstr) {
+	  cerr << "Error setting --nray to %s" << optarg << endl;
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	break;
+        case O_VERSION:
+#ifdef VERSION
+	cout << "Version: " << VERSION << endl;
+#else
+        cout << "Unknown version number" << endl;
+#endif
+	  exit(0);
+      case O_HELP:
+      case '?':
+	phm2pj_usage(argv[0]);
+	return (0);
+      default:
+	phm2pj_usage(argv[0]);
+	return (1);
+      }
+    }
+  
+    if (phm.nPElem() == 0) {
+      cerr << "No phantom defined" << endl;
+      phm2pj_usage(argv[0]);
+      return (1);
+    }
+    if (optind + 3 != argc) {
+      phm2pj_usage(argv[0]);
+      return (1);
+    }
+
+    opt_outfile = argv[optind];
+    opt_ndet = strtol(argv[optind+1], &endptr, 10);
+    endstr = argv[optind+1] + strlen(argv[optind+1]);
+    if (endptr != endstr) {
+      cerr << "Error setting --ndet to " << argv[optind+1] << endl;
+      phm2pj_usage(argv[0]);
+      return (1);
+    }
+    opt_nview = strtol(argv[optind+2], &endptr, 10);
+    endstr = argv[optind+2] + strlen(argv[optind+2]);
+    if (endptr != endstr) {
+      cerr << "Error setting --nview to " << argv[optind+2] << endl;
+      phm2pj_usage(argv[0]);
+      return (1);
+    }
+
+    ostringstream desc;
+    desc << "Raysum_Collect: NDet=" << opt_ndet << ", Nview=" << opt_nview << ", NRay=" << opt_nray << ", RotAngle=" << opt_rotangle << ", ";
+    if (opt_phmfilename.length()) {
+      desc << "PhantomFile=" << opt_phmfilename;
+    } else if (opt_phmnum != -1) {
+      desc << "Phantom=" << name_of_phantom(opt_phmnum);
+    }
+    if (opt_desc.length()) {
+      desc << ": " << opt_desc;
+    }
+    opt_desc = desc.str();
+#ifdef HAVE_MPI
+  }
+#endif
+
+#ifdef HAVE_MPI
+  mpiWorld.getComm().Bcast (&opt_rotangle, 1, MPI::DOUBLE, 0);
+  mpiWorld.getComm().Bcast (&opt_nview, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_ndet, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_nray, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_phmnum, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_verbose, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_debug, 1, MPI::INT, 0);
+  mpiWorld.getComm().Bcast (&opt_trace, 1, MPI::INT, 0);
+
+  if (mpiWorld.getRank() > 0 && opt_phmnum >= 0)
+    phm.create (opt_phmnum);
+#endif
+
+  opt_rotangle *= PI;
+  Scanner scanner (phm, opt_geometry, opt_ndet, opt_nview, opt_nray, opt_rotangle);
+
+#ifdef HAVE_MPI
+  mpiWorld.setTotalWorkUnits (opt_nview);
+
+  Projections pjGlobal;
+  if (mpiWorld.getRank() == 0) {
+    pjGlobal = Projections (scanner);
+  }
+  
+  Scanner localScanner (phm, opt_geometry, opt_ndet, mpiWorld.getMyLocalWorkUnits(), opt_nray, opt_rotangle);
+  Projections pjLocal (localScanner);
+  if (opt_debug)
+    cout << "pjLocal->nview = " << pjLocal.nView() << " (process " << mpiWorld.getRank() << ")" << endl;;
+
+  TimerMPI timerProject (mpiWorld.getComm());
+  localScanner.collectProjections (pjLocal, phm, mpiWorld.getMyStartWorkUnit(), opt_trace);
+  if (opt_verbose)
+    timerProject.timerEndAndReport ("Time to collect projections");
+
+  TimerMPI timerGather (mpiWorld.getComm());
+  GatherProjectionsMPI (mpiWorld, pjGlobal, pjLocal, opt_debug);
+  if (opt_verbose)
+    timerGather.timerEndAndReport ("Time to gather projections");
+#else
+  Projections pjGlobal (scanner);
+  scanner.collectProjections (pjGlobal, phm, 0, opt_trace);
+#endif
+  
+#ifdef HAVE_MPI
+  if (mpiWorld.getRank() == 0) 
+#endif
+    {
+      pjGlobal.setCalcTime (timerProgram.timerEnd());
+      pjGlobal.setRemark (opt_desc);
+      pjGlobal.write (opt_outfile);
+      if (opt_verbose) {
+	phm.print();
+	cout << endl;
+	pjGlobal.printScanInfo();
+	cout << endl;
+	cout << "Remark: " << pjGlobal.remark() << endl;
+	cout << "Run time: " << pjGlobal.calcTime() << " seconds" << endl;
+      }
+    }
+
+  return (0);
+}
+
+
+/* FUNCTION
+ *    GatherProjectionsMPI
+ *
+ * SYNOPSIS
+ *    Gather's raysums from all processes in pjLocal in pjGlobal in process 0
+ */
+
+#ifdef HAVE_MPI
+void GatherProjectionsMPI (MPIWorld& mpiWorld, Projections& pjGlobal, Projections& pjLocal, const int opt_debug)
+{
+  for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++) {
+    DetectorArray& detArray = pjLocal.getDetectorArray(iw);
+    double viewAngle = detArray.viewAngle();
+    int nDet = detArray.nDet();
+    DetectorValue* detval = detArray.detValues();
+
+    mpiWorld.getComm().Send(&viewAngle, 1, MPI::DOUBLE, 0, 0);
+    mpiWorld.getComm().Send(&nDet, 1, MPI::INT, 0, 0);
+    mpiWorld.getComm().Send(detval, nDet, MPI::FLOAT, 0, 0);
+  }
+
+  if (mpiWorld.getRank() == 0) {
+    for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
+      for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
+	MPI::Status status;
+	double viewAngle;
+	int nDet;
+	DetectorArray detArray = pjGlobal.getDetectorArray(iw);
+	DetectorValue* detval = detArray.detValues();
+
+	mpiWorld.getComm().Recv(&viewAngle, 1, MPI::DOUBLE, iProc, 0, status);
+	mpiWorld.getComm().Recv(&nDet, 1, MPI::INT, iProc, 0, status);
+	mpiWorld.getComm().Recv(detval, nDet, MPI::FLOAT, iProc, 0, status);
+	detArray.setViewAngle (viewAngle);
+      }
+    }
+  }
+
+}
+#endif
+
+
+#ifndef NO_MAIN
+int 
+main (int argc, char* argv[])
+{
+  return (phm2pj_main(argc, argv));
+}
+#endif
+
diff --git a/src/phm2rs.cpp b/src/phm2rs.cpp
deleted file mode 100644
index 0459349..0000000
--- a/src/phm2rs.cpp
+++ /dev/null
@@ -1,335 +0,0 @@
-/*****************************************************************************
-** FILE IDENTIFICATION
-**
-**   Name:          phm2rs.cpp
-**   Purpose:       Take projections of a phantom object
-**   Programmer:    Kevin Rosenberg
-**   Date Started:  1984
-**
-**  This is part of the CTSim program
-**  Copyright (C) 1983-2000 Kevin Rosenberg
-**
-**  $Id: phm2rs.cpp,v 1.6 2000/06/15 19:07:10 kevin Exp $
-**
-**  This program is free software; you can redistribute it and/or modify
-**  it under the terms of the GNU General Public License (version 2) as
-**  published by the Free Software Foundation.
-**
-**  This program is distributed in the hope that it will be useful,
-**  but WITHOUT ANY WARRANTY; without even the implied warranty of
-**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-**  GNU General Public License for more details.
-**
-**  You should have received a copy of the GNU General Public License
-**  along with this program; if not, write to the Free Software
-**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-******************************************************************************/
-
-#include "ct.h"
-#include "timer.h"
-
-
-enum { O_PHANTOM, O_DESC, O_NRAY, O_ROTANGLE, O_PHMFILE,
-       O_TRACE, O_VERBOSE, O_HELP, O_DEBUG, O_VERSION };
-
-static struct option phm2rs_options[] = 
-{
-  {"phantom", 1, 0, O_PHANTOM},
-  {"phmfile", 1, 0, O_PHMFILE},
-  {"desc", 1, 0, O_DESC},
-  {"nray", 1, 0, O_NRAY},
-  {"rotangle", 1, 0, O_ROTANGLE},
-  {"trace", 1, 0, O_TRACE},
-  {"verbose", 0, 0, O_VERBOSE},
-  {"help", 0, 0, O_HELP},
-  {"debug", 0, 0, O_DEBUG},
-  {"version", 0, 0, O_VERSION},
-  {0, 0, 0, 0}
-};
-
-
-void 
-phm2rs_usage (const char *program)
-{
-  cout << "usage: " << fileBasename(program) << " outfile ndet nview [--phantom phantom-name] [--phmfile filename] [OPTIONS]" << endl;
-  cout << "Calculate raysums (projections) through phantom object, either" << endl;
-  cout << "a predefined --phantom or a --phmfile" << endl;
-  cout << "" << endl;
-  cout << "     outfile      Name of output file for raysums" << endl;
-  cout << "     ndet         Number of detectors" << endl;
-  cout << "     nview        Number of rotated views" << endl;
-  cout << "     --phantom    Phantom to use for projection" << endl;
-  cout << "        herman    Herman head phantom" << endl;
-  cout << "        rowland   Rowland head phantom" << endl;
-  cout << "        browland  Bordered Rowland head phantom" << endl;
-  cout << "        unitpulse Unit pulse phantom" << endl;
-  cout << "     --phmfile    Get Phantom from phantom file" << endl;
-  cout << "     --desc       Description of raysum" << endl;
-  cout << "     --nray       Number of rays per detector (default = 1)" << endl;
-  cout << "     --rotangle   Degrees to rotate view through, multiple of PI (default = 1)" << endl;
-  cout << "     --trace      Trace level to use" << endl;
-  cout << "        none      No tracing (default)" << endl;
-  cout << "        text      Trace text level" << endl;
-  cout << "        phm       Trace phantom image" << endl;
-  cout << "        rays      Trace rays" << endl;
-  cout << "        plot      Trace plot" << endl;
-  cout << "        clipping  Trace clipping" << endl;
-  cout << "     --verbose    Verbose mode" << endl;
-  cout << "     --debug      Debug mode" << endl;
-  cout << "     --version    Print version" << endl;
-  cout << "     --help       Print this help message" << endl;
-}
-
-#ifdef HAVE_MPI
-void GatherProjectionsMPI (MPIWorld& mpiWorld, RAYSUM *rsGlobal, RAYSUM *rsLocal, const int opt_debug);
-#endif
-
-int 
-phm2rs_main (int argc, char* argv[])
-{
-  Detector *det;
-  Phantom phm;
-  RAYSUM *rsGlobal = NULL;
-  char *opt_outfile = NULL;
-  string opt_desc;
-  string opt_phmfilename;
-  char *endptr, *endstr;
-  int opt_ndet, opt_nview;
-  int opt_nray = 1;
-  int opt_trace = 0;
-  int opt_phmnum = -1;
-  int opt_verbose = 0;
-  int opt_debug = 0;
-  double opt_rotangle = 1;
-
-#ifdef HAVE_MPI
-  RAYSUM *rsLocal;
-  MPIWorld mpiWorld (argc, argv);
-#endif
-
-  Timer timerProgram;
-
-#ifdef HAVE_MPI
-  if (mpiWorld.getRank() == 0) {
-#endif
-    while (1) {
-      int c = getopt_long(argc, argv, "", phm2rs_options, NULL);
-      char *endptr = NULL;
-      char *endstr;
-      
-      if (c == -1)
-	break;
-      
-      switch (c) {
-      case O_PHANTOM:
-	if ((opt_phmnum = opt_set_phantom (optarg)) < 0) {
-	  phm2rs_usage(argv[0]);
-	  return (1);
-	}
-	phm.create (opt_phmnum);
-	break;
-      case O_PHMFILE:
-#ifdef HAVE_MPI
-	if (mpiWorld.getRank() == 0)
-	  cerr << "Can not read phantom from file in MPI mode" << endl;
-	return (1);
-#endif
-	opt_phmfilename = optarg;
-	phm.createFromFile (opt_phmfilename.c_str());
-	break;
-      case O_VERBOSE:
-	opt_verbose = 1;
-	break;
-      case O_DEBUG:
-	opt_debug = 1;
-	break;
-	break;
-      case O_TRACE:
-	if ((opt_trace = opt_set_trace(optarg)) < 0) {
-	  phm2rs_usage(argv[0]);
-	  return (1);
-	}
-	break;
-      case O_DESC:
-	opt_desc = optarg;
-	break;
-      case O_ROTANGLE:
-	opt_rotangle = strtod(optarg, &endptr);
-	endstr = optarg + strlen(optarg);
-	if (endptr != endstr) {
-	  cerr << "Error setting --rotangle to " << optarg << endl;
-	  phm2rs_usage(argv[0]);
-	  return (1);
-	}
-	break;
-      case O_NRAY:
-	opt_nray = strtol(optarg, &endptr, 10);
-	endstr = optarg + strlen(optarg);
-	if (endptr != endstr) {
-	  cerr << "Error setting --nray to %s" << optarg << endl;
-	  phm2rs_usage(argv[0]);
-	  return (1);
-	}
-	break;
-        case O_VERSION:
-#ifdef VERSION
-	cout << "Version: " << VERSION << endl;
-#else
-        cout << "Unknown version number" << endl;
-#endif
-	  exit(0);
-      case O_HELP:
-      case '?':
-	phm2rs_usage(argv[0]);
-	return (0);
-      default:
-	phm2rs_usage(argv[0]);
-	return (1);
-      }
-    }
-  
-    if (phm.nPElem() == 0) {
-      cerr << "No phantom defined" << endl;
-      phm2rs_usage(argv[0]);
-      return (1);
-    }
-    if (optind + 3 != argc) {
-      phm2rs_usage(argv[0]);
-      return (1);
-    }
-
-    opt_outfile = argv[optind];
-    opt_ndet = strtol(argv[optind+1], &endptr, 10);
-    endstr = argv[optind+1] + strlen(argv[optind+1]);
-    if (endptr != endstr) {
-      cerr << "Error setting --ndet to " << argv[optind+1] << endl;
-      phm2rs_usage(argv[0]);
-      return (1);
-    }
-    opt_nview = strtol(argv[optind+2], &endptr, 10);
-    endstr = argv[optind+2] + strlen(argv[optind+2]);
-    if (endptr != endstr) {
-      cerr << "Error setting --nview to " << argv[optind+2] << endl;
-      phm2rs_usage(argv[0]);
-      return (1);
-    }
-
-    ostringstream desc;
-    desc << "Raysum_Collect: NDet=" << opt_ndet << ", Nview=" << opt_nview << ", NRay=" << opt_nray << ", RotAngle=" << opt_rotangle << ", ";
-    if (opt_phmfilename.length()) {
-      desc << "PhantomFile=" << opt_phmfilename;
-    } else if (opt_phmnum != -1) {
-      desc << "Phantom=" << name_of_phantom(opt_phmnum);
-    }
-    if (opt_desc.length()) {
-      desc << ": " << opt_desc;
-    }
-    opt_desc = desc.str();
-#ifdef HAVE_MPI
-  }
-#endif
-
-#ifdef HAVE_MPI
-  mpiWorld.getComm().Bcast (&opt_rotangle, 1, MPI::DOUBLE, 0);
-  mpiWorld.getComm().Bcast (&opt_nview, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_ndet, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_nray, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_phmnum, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_verbose, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_debug, 1, MPI::INT, 0);
-  mpiWorld.getComm().Bcast (&opt_trace, 1, MPI::INT, 0);
-
-  if (mpiWorld.getRank() > 0 && opt_phmnum >= 0)
-    phm.create (opt_phmnum);
-#endif
-
-  opt_rotangle *= PI;
-  det = new Detector (phm, DETECTOR_PARALLEL, opt_ndet, opt_nview, opt_nray, opt_rotangle);
-
-#ifdef HAVE_MPI
-  mpiWorld.setTotalWorkUnits (opt_nview);
-
-  if (mpiWorld.getRank() == 0) {
-    rsGlobal = raysum_create_from_det (opt_outfile, *det);
-    raysum_alloc_views(rsGlobal);
-  }
-  
-  rsLocal = raysum_create_from_det (NULL, *det);
-  rsLocal->nview = mpiWorld.getMyLocalWorkUnits();
-  if (opt_debug)
-    cout << "rsLocal->nview = " << rsLocal->nview << " (process " << mpiWorld.getRank() << ")" << endl;;
-
-  TimerMPI timerProject (mpiWorld.getComm());
-  raysum_collect (rsLocal, *det, phm, mpiWorld.getMyStartWorkUnit(), opt_trace, FALSE);
-  if (opt_verbose)
-    timerProject.timerEndAndReport ("Time to collect projections");
-
-  TimerMPI timerGather (mpiWorld.getComm());
-  GatherProjectionsMPI (mpiWorld, rsGlobal, rsLocal, opt_debug);
-  if (opt_verbose)
-    timerGather.timerEndAndReport ("Time to gather projections");
-#else
-  rsGlobal = raysum_create_from_det (opt_outfile, *det);
-  raysum_collect (rsGlobal, *det, phm, 0, opt_trace, FALSE);
-#endif
-  
-#ifdef HAVE_MPI
-  if (mpiWorld.getRank() == 0) 
-#endif
-    {
-      rsGlobal->calctime = timerProgram.timerEnd();
-      rsGlobal->remark = opt_desc;
-      raysum_write (rsGlobal);
-      raysum_close (rsGlobal);
-      if (opt_verbose) {
-	cout << "Remark: " << rsGlobal->remark << endl;
-	cout << "Run time: " << rsGlobal->calctime << " seconds" << endl;
-      }
-    }
-
-  delete det;
-
-  return (0);
-}
-
-
-/* FUNCTION
- *    GatherProjectionsMPI
- *
- * SYNOPSIS
- *    Gather's raysums from all processes in rsLocal in rsGlobal in process 0
- */
-
-#ifdef HAVE_MPI
-void GatherProjectionsMPI (MPIWorld& mpiWorld, RAYSUM *rsGlobal, RAYSUM *rsLocal, const int opt_debug)
-{
-  for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++) {
-    mpiWorld.getComm().Send(&rsLocal->view[iw]->view_angle, 1, MPI::DOUBLE, 0, 0);
-    mpiWorld.getComm().Send(&rsLocal->view[iw]->ndet, 1, MPI::INT, 0, 0);
-    mpiWorld.getComm().Send(rsLocal->view[iw]->detval, rsLocal->ndet, MPI::FLOAT, 0, 0);
-  }
-
-  if (mpiWorld.getRank() == 0) {
-    for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
-      for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
-	MPI::Status status;
-
-	mpiWorld.getComm().Recv(&rsGlobal->view[iw]->view_angle, 1, MPI::DOUBLE, iProc, 0, status);
-	mpiWorld.getComm().Recv(&rsGlobal->view[iw]->ndet, 1, MPI::INT, iProc, 0, status);
-	mpiWorld.getComm().Recv(rsGlobal->view[iw]->detval, rsGlobal->ndet, MPI::FLOAT, iProc, 0, status);
-      }
-    }
-  }
-
-}
-#endif
-
-
-#ifndef NO_MAIN
-int 
-main (int argc, char* argv[])
-{
-  return (phm2rs_main(argc, argv));
-}
-#endif
-
diff --git a/src/pj2if.cpp b/src/pj2if.cpp
new file mode 100644
index 0000000..c77f901
--- /dev/null
+++ b/src/pj2if.cpp
@@ -0,0 +1,145 @@
+/*****************************************************************************
+** FILE IDENTIFICATION
+**
+**   Name:          proj2if.cpp
+**   Purpose:       Convert an projection data file to an image file
+**   Programmer:    Kevin Rosenberg
+**   Date Started:  April 2000
+**
+**  This is part of the CTSim program
+**  Copyright (C) 1983-2000 Kevin Rosenberg
+**
+**  $Id: pj2if.cpp,v 1.1 2000/06/17 20:12:15 kevin Exp $
+**
+**  This program is free software; you can redistribute it and/or modify
+**  it under the terms of the GNU General Public License (version 2) as
+**  published by the Free Software Foundation.
+**
+**  This program is distributed in the hope that it will be useful,
+**  but WITHOUT ANY WARRANTY; without even the implied warranty of
+**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+**  GNU General Public License for more details.
+**
+**  You should have received a copy of the GNU General Public License
+**  along with this program; if not, write to the Free Software
+**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+******************************************************************************/
+
+/* FILE
+ *   proj2if.c			Convert Raysum to image
+ *
+ * DATE
+ *   Apr 1999
+ */
+
+#include "ct.h"
+
+
+enum { O_VERBOSE, O_HELP, O_VERSION };
+
+static struct option my_options[] =
+{
+  {"verbose", 0, 0, O_VERBOSE},
+  {"help", 0, 0, O_HELP},
+  {"version", 0, 0, O_VERSION},
+  {0, 0, 0, 0}
+};
+
+
+void 
+proj2if_usage (const char *program)
+{
+  fprintf(stdout, "usage: %s in-proj-file out-if-file [OPTIONS]\n", fileBasename(program));
+  fprintf(stdout, "This program converts a projection file to a IF file\n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "   --verbose   Verbose mode\n");
+  fprintf(stdout, "   --version   Print version\n");
+  fprintf(stdout, "   --help      Print this help message\n");
+}
+
+	  
+
+int 
+proj2if_main (const int argc, char *const argv[])
+{
+  char *proj_name, *im_name;
+  int ix, iy;
+  bool opt_verbose = false;
+  extern int optind;
+  
+  while (1)
+    {
+      int c = getopt_long (argc, argv, "", my_options, NULL);
+      if (c == -1)
+	break;
+      
+      switch (c)
+	{
+	case O_VERBOSE:
+	  opt_verbose = true;
+	  break;
+        case O_VERSION:
+#ifdef VERSION
+	  fprintf(stdout, "Version %s\n", VERSION);
+#else
+	  fprintf(stderr, "Unknown version number");
+#endif
+	  exit(0);
+	case O_HELP:
+	case '?':
+	  proj2if_usage(argv[0]);
+	  return (0);
+	default:
+	  proj2if_usage(argv[0]);
+	  return (1);
+	}
+    }
+  
+  if (argc - optind != 2) {
+    proj2if_usage(argv[0]);
+    return (1);
+  }
+
+  proj_name = argv[optind];
+  im_name = argv[optind + 1];
+
+  Projections proj;
+  if (! proj.read (proj_name)) {
+    sys_error (ERR_SEVERE, "Can not open projection file %s", proj_name);
+    return (1);
+  }
+
+  if (opt_verbose)
+      proj.printScanInfo();
+  
+  ImageFile im (im_name, proj.nDet(), proj.nView());
+  
+  ImageFileArray v = im.getArray();
+
+  for (iy = 0; iy < proj.nView(); iy++)
+    {
+      DetectorArray& detarray = proj.getDetectorArray (iy);
+      const DetectorValue* detval = detarray.detValues();
+      for (ix = 0; ix < proj.nDet(); ix++)
+	{
+	  v[ix][iy] = detval[ix];
+	}
+    }
+
+  im.fileCreate ();
+  im.arrayDataWrite ();
+  im.labelAdd (Array2dFileLabel::L_HISTORY, proj.remark(), proj.calcTime());
+  im.labelAdd (Array2dFileLabel::L_HISTORY, "Conversion from .pj to .if");
+  im.fileClose ();
+  
+  return(0);
+}
+
+
+#ifndef NO_MAIN
+int 
+main (const int argc, char *const argv[])
+{
+  return (proj2if_main(argc, argv));
+}
+#endif
diff --git a/src/rs2if.cpp b/src/rs2if.cpp
deleted file mode 100644
index d82ee09..0000000
--- a/src/rs2if.cpp
+++ /dev/null
@@ -1,155 +0,0 @@
-/*****************************************************************************
-** FILE IDENTIFICATION
-**
-**   Name:          rs2if.cpp
-**   Purpose:       Convert an projection data file to an image file
-**   Programmer:    Kevin Rosenberg
-**   Date Started:  April 2000
-**
-**  This is part of the CTSim program
-**  Copyright (C) 1983-2000 Kevin Rosenberg
-**
-**  $Id: rs2if.cpp,v 1.6 2000/06/15 19:07:10 kevin Exp $
-**
-**  This program is free software; you can redistribute it and/or modify
-**  it under the terms of the GNU General Public License (version 2) as
-**  published by the Free Software Foundation.
-**
-**  This program is distributed in the hope that it will be useful,
-**  but WITHOUT ANY WARRANTY; without even the implied warranty of
-**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-**  GNU General Public License for more details.
-**
-**  You should have received a copy of the GNU General Public License
-**  along with this program; if not, write to the Free Software
-**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-******************************************************************************/
-
-/* FILE
- *   rs2if.c			Convert Raysum to image
- *
- * DATE
- *   Apr 1999
- */
-
-#include "ct.h"
-
-
-enum { O_VERBOSE, O_HELP, O_VERSION };
-
-static struct option my_options[] =
-{
-  {"verbose", 0, 0, O_VERBOSE},
-  {"help", 0, 0, O_HELP},
-  {"version", 0, 0, O_VERSION},
-  {0, 0, 0, 0}
-};
-
-
-void 
-rs2if_usage (const char *program)
-{
-  fprintf(stdout, "usage: %s in-rs-file out-if-file [OPTIONS]\n", fileBasename(program));
-  fprintf(stdout, "This program converts a raysum file to a IF file\n");
-  fprintf(stdout, "\n");
-  fprintf(stdout, "   --verbose   Verbose mode\n");
-  fprintf(stdout, "   --version   Print version\n");
-  fprintf(stdout, "   --help      Print this help message\n");
-}
-
-	  
-
-int 
-rs2if_main (const int argc, char *const argv[])
-{
-  ImageFile *im;
-  RAYSUM *rs;
-  DETARRAY *detarray;
-  char *rs_name, *im_name;
-  int ix, iy;
-  int opt_v = 0;
-  extern int optind;
-  
-  while (1)
-    {
-      int c = getopt_long (argc, argv, "", my_options, NULL);
-      if (c == -1)
-	break;
-      
-      switch (c)
-	{
-	case O_VERBOSE:
-	  opt_v = 1;
-	  break;
-        case O_VERSION:
-#ifdef VERSION
-	  fprintf(stdout, "Version %s\n", VERSION);
-#else
-	  fprintf(stderr, "Unknown version number");
-#endif
-	  exit(0);
-	case O_HELP:
-	case '?':
-	  rs2if_usage(argv[0]);
-	  return (0);
-	default:
-	  rs2if_usage(argv[0]);
-	  return (1);
-	}
-    }
-  
-  if (argc - optind != 2) {
-    rs2if_usage(argv[0]);
-    return (1);
-  }
-
-  rs_name = argv[optind];
-  im_name = argv[optind + 1];
-
-  if (file_exists(rs_name) == FALSE) {
-    fprintf (stderr, "Raysum file %s does not exist\n", rs_name);
-    return (1);
-  }
-  
-  rs = raysum_open (rs_name);
-
-  if (opt_v)
-    {
-      printf ("Number of detectors: %d\n", rs->ndet);
-      printf ("    Number of views: %d\n", rs->nview);
-      printf ("             Remark: %s\n", rs->remark.c_str());
-    }
-  
-  im = new ImageFile (im_name, rs->ndet, rs->nview);
-  
-  detarray = detarray_alloc (rs->ndet);
-  ImageFileArray v = im->getArray();
-
-  for (iy = 0; iy < rs->nview; iy++)
-    {
-      detarray_read (rs, detarray, iy);
-      for (ix = 0; ix < rs->ndet; ix++)
-	{
-	  v[ix][iy] = detarray->detval[ix];
-	}
-    }
-  detarray_free (detarray);
-  raysum_close (rs);
-
-  im->fileCreate ();
-  im->arrayDataWrite ();
-  im->labelAdd (Array2dFileLabel::L_HISTORY, rs->remark.c_str(), rs->calctime);
-  im->labelAdd (Array2dFileLabel::L_HISTORY, "Conversion from .rs to .idf");
-  im->fileClose ();
-  
-  return(0);
-}
-
-
-#ifndef NO_MAIN
-int 
-main (const int argc, char *const argv[])
-{
-  return (rs2if_main(argc, argv));
-}
-#endif
diff --git a/src/sample-ctrec.sh.in b/src/sample-ctrec.sh.in
index 3d2568c..11809a2 100755
--- a/src/sample-ctrec.sh.in
+++ b/src/sample-ctrec.sh.in
@@ -15,20 +15,20 @@ if [ -f sample-phm.if ] ; then
 fi
 
 # Simulate CT data collection and generate raysum sinugram for display
-${bin}phm2rs  sample-rs.rs 367 320 --nray 2  --phantom herman
-if [ -f sample-rs.rs ]; then
-  ${bin}rs2if  sample-rs.rs sample-rs.if
+${bin}phm2pj  sample-pj.pj 367 320 --nray 2  --phantom herman
+if [ -f sample-pj.pj ]; then
+  ${bin}pj2if  sample-pj.pj sample-pj.if
 fi
-if [ -f sample-rs.if ]; then
-  ${bin}if2img sample-rs.if sample-rs.png --format png
-  ${bin}if2img sample-rs.if sample-rs16.png --format png16
+if [ -f sample-pj.if ]; then
+  ${bin}if2img sample-pj.if sample-pj.png --format png
+  ${bin}if2img sample-pj.if sample-pj16.png --format png16
 fi
 
 # Reconstruct raysums and generate image for display
-${bin}ctrec   sample-rs.rs sample-rec.if 256 256 
+${bin}ctrec   sample-pj.pj sample-rec.if 256 256 
 if [ -f sample-rec.if ]; then 
   ${bin}if2img sample-rec.if sample-rec.png --format png
   ${bin}if2img sample-rec.if sample-rec16.png --format png16
 fi
 
-# Files sample-phm.png, sample-rs.png, and sample-rec.png are ready for display
+# Files sample-phm.png, sample-pj.png, and sample-rec.png are ready for display