From: Kevin M. Rosenberg <kevin@rosenberg.net>
Date: Fri, 25 Aug 2000 15:59:13 +0000 (+0000)
Subject: r184: *** empty log message ***
X-Git-Tag: debian-4.5.3-3~833
X-Git-Url: http://git.kpe.io/?p=ctsim.git;a=commitdiff_plain;h=1e88cf0f7fa4f690ea9f110e8ed3f2b5338d0a10

r184: *** empty log message ***
---

diff --git a/ChangeLog b/ChangeLog
index 465d37e..9c6984f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+2.0.0-b10 - 8/31/00
+   ctsim: Added Auto Scaling for image windows
+   ctsim: Change title from "windowing" to "display scaling"
+   Added FieldOfView and FocalLength ratio parameters to projection collection
+   Changed name of Rowland Phantom to correct name of Shepp-Logan
+   Added data collection for equilinear scanner geometry
+   Fixed bug in backprojection selection
+   Improved projection collection animation
+	
 2.0.0-b9 - 8/22/00
    Added RCS Id strings to executable files
    Added RPM Spec file for RPM package creation
diff --git a/configure b/configure
index 79e9cb6..b46197c 100755
--- a/configure
+++ b/configure
@@ -712,7 +712,7 @@ fi
 
 PACKAGE=ctsim
 
-VERSION=2.0.0b9
+VERSION=2.0.0b10
 
 if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
   { echo "configure: error: source directory already configured; run "make distclean" there first" 1>&2; exit 1; }
diff --git a/configure.in b/configure.in
index 3998126..09d8ec9 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/ctsim.cpp)
-AM_INIT_AUTOMAKE(ctsim,2.0.0b9)
+AM_INIT_AUTOMAKE(ctsim,2.0.0b10)
 AM_CONFIG_HEADER(config.h)
 
 dnl Checks for programs.
diff --git a/include/backprojectors.h b/include/backprojectors.h
index ac609da..1781fe1 100644
--- a/include/backprojectors.h
+++ b/include/backprojectors.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: backprojectors.h,v 1.12 2000/07/22 15:45:33 kevin Exp $
+**  $Id: backprojectors.h,v 1.13 2000/08/25 15:59:13 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
@@ -143,7 +143,7 @@ class BackprojectTrig : public Backproject
 {
  public:
   BackprojectTrig (const Projections& proj, ImageFile& im, int interpID, const int interpFactor)
-      : Backproject::Backproject (proj, im, interpType, interpFactor)
+      : Backproject::Backproject (proj, im, interpID, interpFactor)
       {}
 
   void BackprojectView (const double* const t, double view_angle);
@@ -184,7 +184,7 @@ class BackprojectDiff2 : public BackprojectDiff
 {
  public:
   BackprojectDiff2 (const Projections& proj, ImageFile& im, int interpID, const int interpFactor)
-    :  BackprojectDiff::BackprojectDiff (proj, im, interpType, interpFactor)
+    :  BackprojectDiff::BackprojectDiff (proj, im, interpID, interpFactor)
     {}
 
   void BackprojectView (const double* const t, double view_angle);
@@ -194,7 +194,7 @@ class BackprojectIntDiff2 : public BackprojectDiff
 {
  public:
   BackprojectIntDiff2 (const Projections& proj, ImageFile& im, int interpID, const int interpFactor)
-    :  BackprojectDiff::BackprojectDiff (proj, im, interpType, interpFactor)
+    :  BackprojectDiff::BackprojectDiff (proj, im, interpID, interpFactor)
     {}
   
   void BackprojectView (const double* const t, double view_angle);
@@ -204,8 +204,8 @@ class BackprojectIntDiff2 : public BackprojectDiff
 class BackprojectIntDiff3 : public BackprojectDiff
 {
  public:
-  BackprojectIntDiff3 (const Projections& proj, ImageFile& im, int interpType, const int interpFactor)
-    :  BackprojectDiff::BackprojectDiff (proj, im, interpType, interpFactor)
+  BackprojectIntDiff3 (const Projections& proj, ImageFile& im, int interpID, const int interpFactor)
+    :  BackprojectDiff::BackprojectDiff (proj, im, interpID, interpFactor)
     {}
   
   void BackprojectView (const double* const t, double view_angle);
diff --git a/include/phantom.h b/include/phantom.h
index a4f29f2..56a8007 100644
--- a/include/phantom.h
+++ b/include/phantom.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: phantom.h,v 1.12 2000/07/31 14:48:35 kevin Exp $
+**  $Id: phantom.h,v 1.13 2000/08/25 15:59:13 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
@@ -134,9 +134,9 @@ class Phantom
  public:
     static const int PHM_INVALID;
     static const int PHM_HERMAN;
-    static const int PHM_BHERMAN;
-    static const int PHM_ROWLAND;
-    static const int PHM_BROWLAND;
+    static const int PHM_B_HERMAN;
+    static const int PHM_SHEPP_LOGAN;
+    static const int PHM_B_SHEPP_LOGAN;
     static const int PHM_UNITPULSE;
 
     Phantom ();
@@ -177,8 +177,8 @@ class Phantom
     
     void addStdHerman ();
     void addStdHermanBordered ();
-    void addStdRowland ();
-    void addStdRowlandBordered ();
+    void addStdSheppLogan ();
+    void addStdSheppLoganBordered ();
 
     void print () const;
 
diff --git a/include/scanner.h b/include/scanner.h
index 550573a..79eee68 100644
--- a/include/scanner.h
+++ b/include/scanner.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: scanner.h,v 1.11 2000/08/02 18:06:00 kevin Exp $
+**  $Id: scanner.h,v 1.12 2000/08/25 15:59:13 kevin Exp $
 **
 **
 **  This program is free software; you can redistribute it and/or modify
@@ -74,10 +74,12 @@ class Scanner
   static const int Scanner::GEOMETRY_EQUIANGULAR;
 
   
-  Scanner (const Phantom& phm, const char* const geometryName, int nDet, int nView, int nSample, const double rot_anglen);
+  Scanner (const Phantom& phm, const char* const geometryName, int nDet, int nView, int nSample, const double rot_anglen, double dFieldOfView, double dFocalLength);
   ~Scanner();
   
-  void collectProjections (Projections& proj, const Phantom& phm, const int start_view = 0, const int trace = TRACE_NONE, SGP* pSGP = NULL);
+  void collectProjections (Projections& proj, const Phantom& phm, const int trace = TRACE_NONE, SGP* pSGP = NULL);
+
+  void collectProjections (Projections& proj, const Phantom& phm, const int iStartView, const int iNumViews, bool bStoreAtViewPosition, const int trace = TRACE_NONE, SGP* pSGP = NULL);
 
   void setNView (int nView);
 
@@ -88,7 +90,7 @@ class Scanner
   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;}
+  const double detLen(void) const {return m_detLen;}
 
   static const int getGeometryCount() {return s_iGeometryCount;}
   static const char** getGeometryNameArray() {return s_aszGeometryName;}
@@ -104,12 +106,13 @@ class Scanner
   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 */
+  double m_dFieldOfView;        // Field of View
+  double m_dFocalLength;         // Focal Length
+  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_phmLen;              // Maximum Length of phantom or area of interest
   int m_trace;
   struct {
     double xd1,yd1,xd2,yd2;	/* Coordinates of detector endpoints */
@@ -120,7 +123,6 @@ class Scanner
   static const char* s_aszGeometryName[];
   static const char* s_aszGeometryTitle[];
   static const int s_iGeometryCount;
-  static const int N_EXTRA_DETECTORS=0;    // Number of extra detectors widths when calculating detlen 
 
   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, SGP* pSGP);
 
@@ -128,7 +130,7 @@ class Scanner
 
   double projectLineAgainstPElem (const PhantomElement& pelem, const double x1, const double y1, const double x2, const double y2, SGP* pSGP);
 
-  void traceShowParam (const char *label, const char *fmt, int row, int color, ...);
+  void traceShowParam (SGP* pSGP, const char *label, const char *fmt, int row, int color, ...);
 
 
 };
diff --git a/include/sgp.h b/include/sgp.h
index 7cda247..6240752 100644
--- a/include/sgp.h
+++ b/include/sgp.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: sgp.h,v 1.13 2000/08/02 18:06:00 kevin Exp $
+**  $Id: sgp.h,v 1.14 2000/08/25 15:59:13 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
@@ -137,6 +137,10 @@ private:
   static RGBColor s_aRGBColor[];
   static int s_iRGBColorCount;
 
+#if HAVE_WXWINDOWS
+  wxPen* m_pPen;
+#endif
+
 public:
   enum {                  // linestyles 
       LS_NOLINE = 0,
diff --git a/include/trace.h b/include/trace.h
index 88aa271..64826e9 100644
--- a/include/trace.h
+++ b/include/trace.h
@@ -1,15 +1,13 @@
 #ifndef TRACE_H
 #define TRACE_H
 
-enum TraceID {
-    TRACE_INVALID=-1,
-    TRACE_NONE=0, 		/* No tracing */
-    TRACE_TEXT,		/* Minimal status */
-    TRACE_PHM,		/* Show phantom */
-    TRACE_RAYS,		/* Show all rays */
-    TRACE_PLOT,		/* Plot raysums */
-    TRACE_CLIPPING	/* Plot clipping */
-};
+static const int TRACE_INVALID = 0xFFFF;
+static const int TRACE_NONE = 0x0000;
+static const int TRACE_TEXT = 0x0001;
+static const int TRACE_PHM = 0x0002;
+static const int TRACE_RAYS = 0x0004;
+static const int TRACE_PLOT = 0x0008;
+static const int TRACE_CLIPPING = 0x0010;
 
 class TraceLevel
 {
@@ -29,7 +27,7 @@ class TraceLevel
   
   int getTraceLevel(void) const { return m_traceLevel; }
   
-  static TraceID convertTraceNameToID (const char* traceName);
+  static int convertTraceNameToID (const char* traceName);
 
  private:
   
diff --git a/libctgraphics/sgp.cpp b/libctgraphics/sgp.cpp
index 9d3f1fc..6b826d7 100644
--- a/libctgraphics/sgp.cpp
+++ b/libctgraphics/sgp.cpp
@@ -7,7 +7,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: sgp.cpp,v 1.9 2000/08/02 18:06:00 kevin Exp $
+**  $Id: sgp.cpp,v 1.10 2000/08/25 15:59:13 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
@@ -81,6 +81,9 @@ SGPDriver::~SGPDriver ()
 
 SGP::SGP (const SGPDriver& driver)
     : m_driver (driver)
+#if HAVE_WXWINDOWS
+    , m_pPen(NULL)
+#endif
 {
   m_iPhysicalXSize = m_driver.getPhysicalXSize();
   m_iPhysicalYSize = m_driver.getPhysicalYSize();
@@ -225,8 +228,9 @@ SGP::setColor (int icol)
 #if HAVE_WXWINDOWS
     if (m_driver.isWX()) {
       wxColor colour (s_aRGBColor[icol].getRed(), s_aRGBColor[icol].getGreen(), s_aRGBColor[icol].getBlue());
-      wxPen pen (colour, 1, wxSOLID);
-      m_driver.idWX()->SetPen (pen);
+      delete m_pPen;
+      m_pPen = new wxPen (colour, 1, wxSOLID);
+      m_driver.idWX()->SetPen (*m_pPen);
     }
 #endif
   }
diff --git a/libctsim/backprojectors.cpp b/libctsim/backprojectors.cpp
index 7a1c55b..71aa8d4 100644
--- a/libctsim/backprojectors.cpp
+++ b/libctsim/backprojectors.cpp
@@ -8,7 +8,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: backprojectors.cpp,v 1.11 2000/07/23 01:49:03 kevin Exp $
+**  $Id: backprojectors.cpp,v 1.12 2000/08/25 15:59:13 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
@@ -286,18 +286,20 @@ Backproject::ScaleImageByRotIncrement ()
 
 void Backproject::errorIndexOutsideDetector (int ix, int iy, double theta, double r, double phi, double L, int iDetPos)
 {
-    printf ("r=%f, phi=%f\n", r, phi);
+    sys_error (ERR_WARNING, "r=%f, phi=%f", r, phi);
     errorIndexOutsideDetector (ix, iy, theta, L, iDetPos);
 }
 
 void Backproject::errorIndexOutsideDetector (int ix, int iy, double theta, double L, int iDetPos)
 {
-    printf ("ix=%d, iy=%d\n", ix, iy);
-    printf ("theta=%f, L=%f, detInc=%f\n", theta, L, detInc);
-    printf ("proj.ndet=%d, proj.detInc=%.4f, iDetCenter=%d\n", nDet, detInc, iDetCenter);
-    printf ("xMin=%15.8f, xMax=%15.8f, xInc=%15.8f\n", xMin, xMax, xInc);
-    printf ("yMin=%15.8f, yMax=%15.8f, yInc=%15.8f\n", yMin, yMax, yInc);
-    sys_error (ERR_WARNING, "iDetPos index outside bounds: %d [backprojector]", iDetPos);
+  ostringstream os;
+  os << "ix=" << ix << ", iy=" << iy << ", theta=" << theta << ", L=" << L << ", detinc=" << detInc << "\n";
+  os << "ndet=" << nDet << ", detInc=" << detInc << ", iDetCenter=" << iDetCenter << "\n";
+  os << "xMin=" << xMin << ", xMax=" << xMax << ", xInc=" << xInc << "\n";
+  os << "yMin=" << yMin << ", yMax=" << yMax << ", yInc=" << yInc << "\n";
+  os << "iDetPos index outside bounds: " << iDetPos << " [backprojector]";;
+
+  sys_error (ERR_WARNING, os.str().c_str());
 }
 
 
@@ -543,7 +545,7 @@ BackprojectIntDiff2::BackprojectView (const double* const filteredProj, const do
 	int detPosNearest = (curDetPos >= 0 ? ((curDetPos + halfScale) / scale) : ((curDetPos - halfScale) / scale));
 	int iDetPos = iDetCenter + detPosNearest;	// calc index in the filtered raysum vector 
 
-	if (iDetPos < 0 || iDetPos >= nDet)  // check for impossible: index outside of raysum pos 
+	if (iDetPos < 0 || iDetPos >= nDet)  // check for index outside of raysum pos 
 	    errorIndexOutsideDetector (ix, iy, theta, curDetPos, iDetPos);
 	else
 	  *pImCol++ += filteredProj[iDetPos];
@@ -588,12 +590,14 @@ BackprojectIntDiff3::BackprojectView (const double* const filteredProj, const do
   kint32 detPosColStart = nearest<kint32> ((start_r * cos (theta - start_phi) / detInc + iDetCenter) * scale);
 	
   // precalculate scaled difference for linear interpolation
-  double deltaFilteredProj [nDet - 1];
+  double deltaFilteredProj [nDet];
   if (interpType == Backprojector::INTERP_LINEAR) {
     for (int i = 0; i < nDet - 1; i++)
       deltaFilteredProj[i] = (filteredProj[i+1] - filteredProj[i]) * dInvScale;
   }
+  deltaFilteredProj[nDet - 1] = 0;  // last detector
 
+  int iLastDet = nDet - 1;
   for (int ix = 0; ix < nx; ix++, detPosColStart += det_dx) {
     kint32 curDetPos = detPosColStart;
     ImageFileColumn pImCol = v[ix];
@@ -601,21 +605,21 @@ BackprojectIntDiff3::BackprojectView (const double* const filteredProj, const do
     if (interpType == Backprojector::INTERP_NEAREST) {
       for (int iy = 0; iy < ny; iy++, curDetPos += det_dy) {
 	const int iDetPos = (curDetPos + halfScale) >> 16;
-	assert(iDetPos >= 0 && iDetPos < nDet);
-	*pImCol++ += filteredProj[iDetPos];
+	if (iDetPos >= 0 && iDetPos <= iLastDet)
+	  *pImCol++ += filteredProj[iDetPos];
       }	// end for iy
     } else if (interpType == Backprojector::INTERP_FREQ_PREINTERPOLATION) {
       for (int iy = 0; iy < ny; iy++, curDetPos += det_dy) {
 	const int iDetPos = ((curDetPos + halfScale) >> 16) * m_interpFactor;
-	assert(iDetPos >= 0 && iDetPos < nDet);
+	if (iDetPos >= 0 && iDetPos <= iLastDet)
 	*pImCol++ += filteredProj[iDetPos];
       }	// end for iy
     } else if (interpType == Backprojector::INTERP_LINEAR) {
       for (int iy = 0; iy < ny; iy++, curDetPos += det_dy) {
 	const kint32 iDetPos = curDetPos >> scaleShift;
 	const kint32 detRemainder = curDetPos & scaleBitmask;
-	assert(iDetPos >= 0 && iDetPos < nDet - 1);
-	*pImCol++ += filteredProj[iDetPos] + (detRemainder * deltaFilteredProj[iDetPos]);
+	if (iDetPos >= 0 && iDetPos <= iLastDet)
+	  *pImCol++ += filteredProj[iDetPos] + (detRemainder * deltaFilteredProj[iDetPos]);
       }	// end for iy
     } //end linear
   } // end for ix
diff --git a/libctsim/imagefile.cpp b/libctsim/imagefile.cpp
index 3f7c0be..9df4285 100644
--- a/libctsim/imagefile.cpp
+++ b/libctsim/imagefile.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: imagefile.cpp,v 1.10 2000/08/22 16:49:56 kevin Exp $
+**  $Id: imagefile.cpp,v 1.11 2000/08/25 15:59:13 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
@@ -66,7 +66,7 @@ ImageFile::displayScaling (const int scale, const ImageFileValue pmin, const Ima
       return 0;
 
 #if HAVE_G2_H
-    int pens [nx * ny * scale * scale ];
+    int* pPens = new int [nx * ny * scale * scale ];
 
     double view_scale = 255 / (pmax - pmin);
     int id_X11 = g2_open_X11 (nx * scale, ny * scale);
@@ -76,19 +76,23 @@ ImageFile::displayScaling (const int scale, const ImageFileValue pmin, const Ima
 	grayscale[i] = g2_ink (id_X11, cval, cval, cval);
     }
 
-    for (int i= 0, iy = ny - 1; iy >= 0; iy--) {
-	for (int ix = 0; ix < nx; ix++) {
-	    int cval = static_cast<int>((v[ix][iy] - pmin) * view_scale);
-	    if (cval < 0)  
-	      cval = 0;
-	    else if (cval > 255) 
-	      cval = 255;
-	    pens[i++] = grayscale[cval];
+    for (int iy = ny - 1; iy >= 0; iy--) {
+      int iRowPos = ((ny - 1 - iy) * scale) * (nx * scale);
+      for (int ix = 0; ix < nx; ix++) {
+	int cval = static_cast<int>((v[ix][iy] - pmin) * view_scale);
+	if (cval < 0)  
+	  cval = 0;
+	else if (cval > 255) 
+	  cval = 255;
+	for (int sy = 0; sy < scale; sy++)
+	  for (int sx = 0; sx < scale; sx++)
+	    pPens[iRowPos+(sy * nx * scale)+(sx + (ix * scale))] = grayscale[cval];
 	}
     }
 
-    g2_image (id_X11, 0., 0., nx, ny, pens);
+    g2_image (id_X11, 0., 0., nx * scale, ny * scale, pPens);
 
+    delete pPens;
     return (id_X11);
 
 #endif
diff --git a/libctsim/phantom.cpp b/libctsim/phantom.cpp
index 09245b2..c74c37a 100644
--- a/libctsim/phantom.cpp
+++ b/libctsim/phantom.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: phantom.cpp,v 1.15 2000/08/02 18:06:00 kevin Exp $
+**  $Id: phantom.cpp,v 1.16 2000/08/25 15:59:13 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
@@ -30,26 +30,26 @@
 
 const int Phantom::PHM_INVALID = -1;
 const int Phantom::PHM_HERMAN = 0;
-const int Phantom::PHM_BHERMAN = 1;
-const int Phantom::PHM_ROWLAND = 2;
-const int Phantom::PHM_BROWLAND = 3;
+const int Phantom::PHM_B_HERMAN = 1;
+const int Phantom::PHM_SHEPP_LOGAN = 2;
+const int Phantom::PHM_B_SHEPP_LOGAN = 3;
 const int Phantom::PHM_UNITPULSE = 4;
 
 const char* Phantom::s_aszPhantomName[] = 
 {
   {"herman"},
-  {"bherman"},
-  {"rowland"},
-  {"browland"},
+  {"herman-b"},
+  {"shepp-logan"},
+  {"shepp-logan-b"},
   {"unitpulse"},
 };
 
 const char* Phantom::s_aszPhantomTitle[] = 
 {
   {"Herman Head"},
-  {"Herman Head Bordered"},
-  {"Rowland Head"},
-  {"Rowland Head Bordered"},
+  {"Herman Head (Bordered)"},
+  {"Shepp-Logan"},
+  {"Shepp-Logan (Bordered)"},
   {"Unit Pulse"},
 };
 
@@ -155,14 +155,14 @@ Phantom::createFromPhantom (const int phmid)
     case PHM_HERMAN:
       addStdHerman();
       break;
-    case PHM_BHERMAN:
+    case PHM_B_HERMAN:
       addStdHermanBordered();
       break;
-    case PHM_ROWLAND:
-      addStdRowland();
+    case PHM_SHEPP_LOGAN:
+      addStdSheppLogan();
       break;
-    case PHM_BROWLAND:
-      addStdRowlandBordered ();
+    case PHM_B_SHEPP_LOGAN:
+      addStdSheppLoganBordered();
       break;
     case PHM_UNITPULSE:
       m_composition = P_UNIT_PULSE;
@@ -358,7 +358,7 @@ Phantom::draw (SGP& sgp) const
 
 
 /* NAME
- *   addStdRowland		Make head phantom of S.W. Rowland
+ *   addStdSheppLogan	Make head phantom of Shepp-Logan
  *
  * REFERENCES
  *   S. W. Rowland, "Computer Implementation of Image Reconstruction
@@ -367,7 +367,7 @@ Phantom::draw (SGP& sgp) const
  */
 
 void 
-Phantom::addStdRowland ()
+Phantom::addStdSheppLogan ()
 {
   addPElem ("ellipse",  0.0000,  0.0000, 0.6900,  0.9200,   0.0,  1.00);
   addPElem ("ellipse",  0.0000, -0.0184, 0.6624,  0.8740,   0.0, -0.98);
@@ -383,9 +383,9 @@ Phantom::addStdRowland ()
 }
 
 void 
-Phantom::addStdRowlandBordered ()
+Phantom::addStdSheppLoganBordered ()
 {
-  addStdRowland ();
+  addStdSheppLogan ();
   addPElem ("rectangle", 0.000, 0.0000, 0.7500, 1.000, 0.0, 0.00);
 }
 
@@ -421,7 +421,7 @@ void
 Phantom::addStdHermanBordered ()
 {
   addStdHerman();
-  addPElem ("rectangle",  0.000, 0.000, 8.650, 8.650,  0.00, 0.000);
+  addPElem ("rectangle",  0.000, 0.00, 9.000, 6.800,  0.00, 0.000);
 }
 
 
diff --git a/libctsim/procsignal.cpp b/libctsim/procsignal.cpp
index 70d759c..8156252 100644
--- a/libctsim/procsignal.cpp
+++ b/libctsim/procsignal.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: procsignal.cpp,v 1.2 2000/08/22 07:02:48 kevin Exp $
+**  $Id: procsignal.cpp,v 1.3 2000/08/25 15:59:13 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
@@ -77,7 +77,7 @@ const int ProcessSignal::s_iFilterGenerationCount = sizeof(s_aszFilterGeneration
 // CLASS IDENTIFICATION
 //   ProcessSignal
 //
-ProcessSignal::ProcessSignal (const char* szFilterName, const char* szFilterMethodName, double dBandwidth, double dSignalIncrement, int nSignalPoints, double dFilterParam, const char* szDomainName, const char* szFilterGenerationName, int iZeropad = 0, int iPreinterpolationFactor = 1, int iTraceLevel = TRACE_NONE)
+ProcessSignal::ProcessSignal (const char* szFilterName, const char* szFilterMethodName, double dBandwidth, double dSignalIncrement, int nSignalPoints, double dFilterParam, const char* szDomainName, const char* szFilterGenerationName, int iZeropad, int iPreinterpolationFactor, int iTraceLevel)
     : m_adFourierCosTable(NULL), m_adFourierSinTable(NULL), m_adFilter(NULL), m_fail(false)
 {
   m_idFilterMethod = convertFilterMethodNameToID (szFilterMethodName);
diff --git a/libctsim/projections.cpp b/libctsim/projections.cpp
index d6b496d..df7ccd2 100644
--- a/libctsim/projections.cpp
+++ b/libctsim/projections.cpp
@@ -8,7 +8,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: projections.cpp,v 1.21 2000/08/22 07:02:48 kevin Exp $
+**  $Id: projections.cpp,v 1.22 2000/08/25 15:59:13 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
@@ -81,8 +81,7 @@ Projections::initFromScanner (const Scanner& scanner)
   m_rotInc = scanner.rotInc();
   m_detInc = scanner.detInc();
   m_rotStart = 0;
-  m_detStart =  -scanner.radius() + (scanner.detInc() / 2);
-  m_phmLen = scanner.phmLen();
+  m_detStart =  -(scanner.detLen() / 2) + (scanner.detInc() / 2);
 }
 
 void
@@ -556,8 +555,6 @@ Projections::reconstruct (ImageFile& im, const char* const filterName, double fi
 
     processSignal.filterSignal (detval, filteredProj);
 
-
-
 #ifdef HAVE_BSPLINE_INTERP
     if (interp_type == I_BSPLINE) 
 	bspline (m_nDet, zoom_factor, spline_order, filteredProj, filteredProj);
diff --git a/libctsim/scanner.cpp b/libctsim/scanner.cpp
index 709dc0f..c4fc4d0 100644
--- a/libctsim/scanner.cpp
+++ b/libctsim/scanner.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: scanner.cpp,v 1.10 2000/08/03 09:21:12 kevin Exp $
+**  $Id: scanner.cpp,v 1.11 2000/08/25 15:59:13 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
@@ -82,7 +82,7 @@ DetectorArray::~DetectorArray (void)
  *   int nSample		Number of rays per detector
  */
 
-Scanner::Scanner (const Phantom& phm, const char* const geometryName, int nDet, int nView, int nSample, const double rot_anglen)
+Scanner::Scanner (const Phantom& phm, const char* const geometryName, int nDet, int nView, int nSample, const double rot_anglen, const double dFocalLengthRatio, const double dFieldOfViewRatio)
 {
   m_phmLen = phm.maxAxisLength();      // maximal length along an axis
 
@@ -101,29 +101,67 @@ Scanner::Scanner (const Phantom& phm, const char* const geometryName, int nDet,
     m_nSample = 1;
   if (nDet < 1)
     nDet = 1;
-  if ((nDet % 2) == 0)
-    ++nDet;		// ensure odd number of detectors
+  //  if ((nDet % 2) == 0)
+  //    ++nDet;		// ensure odd number of detectors
 
   m_nDet     = nDet;
   m_nView    = nView;
   m_nSample  = nSample;
-  m_detLen   = SQRT2 * m_phmLen * ((m_nDet + N_EXTRA_DETECTORS) / static_cast<double>(m_nDet));
-
-  m_rotLen   =  rot_anglen;
-
-  m_radius  = m_detLen / 2;
-  m_detInc  = m_detLen / m_nDet;
-  m_rotInc  = m_rotLen / m_nView;
-
-  m_initPos.xd1 = m_detLen / 2;
-  m_initPos.yd1 = -m_detLen / 2;
-  m_initPos.xd2 = m_detLen / 2;
-  m_initPos.yd2 = m_detLen / 2;
-  m_initPos.xs1 = -m_detLen / 2;
-  m_initPos.ys1 = -m_detLen / 2;
-  m_initPos.xs2 = -m_detLen / 2;
-  m_initPos.ys2 = m_detLen / 2;
-  m_initPos.angle = 0.0;
+  m_dFocalLength = (m_phmLen * SQRT2 / 2) * dFocalLengthRatio;
+  m_dFieldOfView = m_phmLen * SQRT2 * dFieldOfViewRatio;
+
+  if (m_idGeometry == GEOMETRY_PARALLEL) {
+    m_detLen   = m_dFieldOfView;
+    m_detInc  = m_detLen / m_nDet;
+    m_rotLen  = rot_anglen;
+    m_rotInc  = m_rotLen / m_nView;
+    
+    double dHalfDetLen = m_detLen / 2;
+    m_initPos.xs1 = -m_dFocalLength;
+    m_initPos.ys1 = -dHalfDetLen;
+    m_initPos.xs2 = -m_dFocalLength;
+    m_initPos.ys2 = dHalfDetLen;
+    m_initPos.xd1 = m_dFocalLength;
+    m_initPos.yd1 = -dHalfDetLen;
+    m_initPos.xd2 = m_dFocalLength;
+    m_initPos.yd2 = dHalfDetLen;
+    m_initPos.angle = 0.0;
+  } else if (m_idGeometry == GEOMETRY_EQUILINEAR) {
+    double dHalfSquare = m_phmLen / 2;
+    double dFocalPastPhm = m_dFocalLength - dHalfSquare;
+    if (dFocalPastPhm <= 0.) {
+      m_fail = true;
+      m_failMessage = "Focal Point inside of phantom";
+      return;
+    }
+    double dAngle = atan( dHalfSquare / dFocalPastPhm );
+    double dHalfDetLen = 2 * m_dFocalLength * tan (dAngle);
+
+    m_detLen = dHalfDetLen * 2;
+    m_detInc  = m_detLen / m_nDet;
+    m_rotLen  = rot_anglen;
+    m_rotInc  = m_rotLen / m_nView;
+    
+    m_initPos.xs1 = -m_dFocalLength;
+    m_initPos.ys1 = 0;
+    m_initPos.xs2 = -m_dFocalLength;
+    m_initPos.ys2 = 0;
+    m_initPos.xd1 = m_dFocalLength;
+    m_initPos.yd1 = -dHalfDetLen;
+    m_initPos.xd2 = m_dFocalLength;
+    m_initPos.yd2 = dHalfDetLen;
+    m_initPos.angle = 0.0;
+  } else if (m_idGeometry == GEOMETRY_EQUIANGULAR) {
+    double dHalfSquare = m_phmLen / 2;
+    double dFocalPastPhm = m_dFocalLength - dHalfSquare;
+    if (dFocalPastPhm <= 0.) {
+      m_fail = true;
+      m_failMessage = "Focal Point inside of phantom";
+      return;
+    }
+    double dAngle = atan( dHalfSquare / dFocalPastPhm );
+    m_detLen = dAngle * 2;
+  }
 }
 
 Scanner::~Scanner (void)
@@ -169,23 +207,30 @@ Scanner::convertGeometryNameToID (const char* const geomName)
   
 
 /* NAME
- *   raysum_collect				Calculate ray sums for a Phantom
+ *   collectProjections		Calculate projections for a Phantom
  *
  * SYNOPSIS
- *   rs = raysum_collect (det, phm, start_view, trace, unit_pulse)
- *   Scanner& det			Scanner specifications**
- *   RAYSUM *rs				Calculated ray sum matrix
- *   Phantom& phm			Phantom we are taking ray sums of
- *   int trace				Boolean flag to signal ray sum tracing
+ *   collectProjections (proj, phm, start_view, nView, bStoreViewPos, trace)
+ *   Projectrions& proj      Projection storage
+ *   Phantom& phm	     Phantom for which we collect projections
+ *   bool bStoreViewPos      TRUE then storage proj at normal view position
+ *   int trace		     Trace level
 */
 
+
 void
-Scanner::collectProjections (Projections& proj, const Phantom& phm, const int start_view = 0, const int trace = TRACE_NONE, SGP* pSGP = NULL)
+Scanner::collectProjections (Projections& proj, const Phantom& phm, const int trace, SGP* pSGP)
+{
+  collectProjections (proj, phm, 0, proj.nView(), true, trace, pSGP);
+}
+
+void
+Scanner::collectProjections (Projections& proj, const Phantom& phm, const int iStartView, const int iNumViews, bool bStoreAtViewPosition, const int trace, SGP* pSGP)
 {
   GRFMTX_2D rotmtx_initial, temp;
   GRFMTX_2D rotmtx_incr;
 
-  double start_angle = start_view * proj.rotInc();
+  double start_angle = iStartView * proj.rotInc();
   double xcent = phm.xmin() + (phm.xmax() - phm.xmin()) / 2;
   double ycent = phm.ymin() + (phm.ymax() - phm.ymin()) / 2;
 
@@ -200,38 +245,6 @@ Scanner::collectProjections (Projections& proj, const Phantom& phm, const int st
  
   m_trace = trace;
 
-#ifdef HAVE_SGP 
-  if (pSGP && m_trace >= TRACE_PHM) {
-    double halfPhmLen = m_phmLen / 2;
-    double wsize = SQRT2 * halfPhmLen;
-
-    pSGP->setRasterOp (RO_SET);
-    pSGP->eraseWindow ();
-    pSGP->setColor (C_LTBLUE);
-    pSGP->setWindow (xcent - wsize, ycent - wsize, xcent + wsize, ycent + wsize);
-    pSGP->setColor (C_BROWN);
-    pSGP->drawRect (xcent - halfPhmLen, ycent - halfPhmLen, xcent + halfPhmLen, ycent + halfPhmLen);
-    pSGP->setColor (C_BROWN);
-    pSGP->moveAbs (0., 0.);
-    pSGP->drawCircle (wsize);
-
-    traceShowParam ("X-Ray Simulator", "%s", RAYSUM_TRACE_ROW_TITLE, C_BLACK, " ");
-    traceShowParam ("---------------", "%s", RAYSUM_TRACE_ROW_TITLE2, C_BLACK, " ");
-    traceShowParam ("Phantom:",       "%s", RAYSUM_TRACE_ROW_PHANT_ID, C_YELLOW, " Herman");
-    traceShowParam ("Chomaticity  :", "%s", RAYSUM_TRACE_ROW_CHROMATIC, C_LTGREEN, "Mono");
-    traceShowParam ("Scatter      :", "%5.1f", RAYSUM_TRACE_ROW_SCATTER, C_LTGREEN, 0.);
-    traceShowParam ("Photon Uncert:", "%5.1f", RAYSUM_TRACE_ROW_PHOT_STAT, C_LTGREEN, 0.);
-    traceShowParam ("Num Detectors:", "%5d", RAYSUM_TRACE_ROW_NDET, C_LTRED, proj.nDet());
-    traceShowParam ("Num Views    :", "%5d", RAYSUM_TRACE_ROW_NVIEW, C_LTRED, proj.nView());
-    traceShowParam ("Samples / Ray:", "%5d", RAYSUM_TRACE_ROW_SAMPLES, C_LTRED, m_nSample);
-    
-    pSGP->setColor (C_LTGREEN);
-    phm.draw (*pSGP);
-    
-    pSGP->setMarker (SGP::MARK_BDIAMOND, C_LTGREEN);
-  }
-#endif
-
 /* Calculate initial rotation matrix */
   xlat_mtx2 (rotmtx_initial, -xcent, -ycent);
   rot_mtx2 (temp, start_angle);
@@ -253,8 +266,45 @@ Scanner::collectProjections (Projections& proj, const Phantom& phm, const int st
   
   int iview;
   double viewAngle;
-  for (iview = 0, viewAngle = start_angle;  iview < proj.nView(); iview++, viewAngle += proj.rotInc()) {
-      DetectorArray& detArray = proj.getDetectorArray( iview );
+  for (iview = 0, viewAngle = start_angle;  iview < iNumViews; iview++, viewAngle += proj.rotInc()) {
+    int iStoragePosition = iview;
+    if (bStoreAtViewPosition)
+      iStoragePosition += iStartView;
+
+    DetectorArray& detArray = proj.getDetectorArray( iStoragePosition );
+
+#ifdef HAVE_SGP 
+  if (pSGP && m_trace >= TRACE_PHM) {
+    pSGP->eraseWindow();
+    double dWindowSize = max(m_detLen, m_dFocalLength * 2) * SQRT2;
+    double dHalfWindowSize = dWindowSize / 2;
+    double dHalfPhmLen = m_phmLen /  2;
+
+    pSGP->setRasterOp (RO_SET);
+    pSGP->eraseWindow ();
+    pSGP->setWindow (xcent - dHalfWindowSize, ycent - dHalfWindowSize, xcent + dHalfWindowSize, ycent + dHalfWindowSize);
+    pSGP->setColor (C_BROWN);
+    pSGP->moveAbs (0., 0.);
+    pSGP->drawRect (xcent - dHalfPhmLen, ycent - dHalfPhmLen, xcent + dHalfPhmLen, ycent + dHalfPhmLen);
+
+#if 0    
+    traceShowParam (pSGP, "X-Ray Simulator", "%s", RAYSUM_TRACE_ROW_TITLE, C_BLACK, " ");
+    traceShowParam (pSGP, "---------------", "%s", RAYSUM_TRACE_ROW_TITLE2, C_BLACK, " ");
+    traceShowParam (pSGP, "Phantom:",       "%s", RAYSUM_TRACE_ROW_PHANT_ID, C_YELLOW, " Herman");
+    traceShowParam (pSGP, "Chomaticity  :", "%s", RAYSUM_TRACE_ROW_CHROMATIC, C_LTGREEN, "Mono");
+    traceShowParam (pSGP, "Scatter      :", "%5.1f", RAYSUM_TRACE_ROW_SCATTER, C_LTGREEN, 0.);
+    traceShowParam (pSGP, "Photon Uncert:", "%5.1f", RAYSUM_TRACE_ROW_PHOT_STAT, C_LTGREEN, 0.);
+    traceShowParam (pSGP, "Num Detectors:", "%5d", RAYSUM_TRACE_ROW_NDET, C_LTRED, proj.nDet());
+    traceShowParam (pSGP, "Num Views    :", "%5d", RAYSUM_TRACE_ROW_NVIEW, C_LTRED, proj.nViews());
+    traceShowParam (pSGP, "Samples / Ray:", "%5d", RAYSUM_TRACE_ROW_SAMPLES, C_LTRED, m_nSample);
+#endif
+    
+    pSGP->setColor (C_RED);
+    phm.draw (*pSGP);
+    
+    pSGP->setMarker (SGP::MARK_BDIAMOND, C_LTGREEN);
+  }
+#endif
 
 #ifdef HAVE_SGP
     if (pSGP && m_trace >= TRACE_PHM) {
@@ -264,9 +314,10 @@ Scanner::collectProjections (Projections& proj, const Phantom& phm, const int st
       pSGP->lineAbs (xd2, yd2);
       pSGP->moveAbs (xs1, ys1);
       pSGP->lineAbs (xs2, ys2);
+      pSGP->setRasterOp (RO_SET);
     }
-    if (m_trace)
-      traceShowParam ("Current View :", "%5d", RAYSUM_TRACE_ROW_CURR_VIEW, C_LTMAGENTA, iview);
+    if (m_trace >= TRACE_TEXT)
+      traceShowParam (pSGP, "Current View :", "%5d", RAYSUM_TRACE_ROW_CURR_VIEW, C_LTMAGENTA, iview);
 #endif
 	    
     projectSingleView (phm, detArray, xd1, yd1, xd2, yd2, xs1, ys1, xs2, ys2, pSGP);
@@ -276,10 +327,12 @@ Scanner::collectProjections (Projections& proj, const Phantom& phm, const int st
     if (pSGP && m_trace >= TRACE_PHM) {
       //	rs_plot (detArray, xd1, yd1, xcent, ycent, theta);
       pSGP->setColor (C_RED);
+      pSGP->setRasterOp (RO_XOR);
       pSGP->moveAbs (xd1, yd1);
       pSGP->lineAbs (xd2, yd2);
       pSGP->moveAbs (xs1, ys1);
       pSGP->lineAbs (xs2, ys2);
+      pSGP->setRasterOp (RO_SET);
     }
 #endif
     xform_mtx2 (rotmtx_incr, xd1, yd1);	 // rotate detector endpoints 
@@ -350,20 +403,25 @@ Scanner::projectSingleView (const Phantom& phm, DetectorArray& detArray, const d
 #ifdef HAVE_SGP
 	if (pSGP && m_trace >= TRACE_RAYS) {
 	  pSGP->setColor (C_LTBLUE);
+	  pSGP->setRasterOp (RO_XOR);
 	  pSGP->moveAbs (xs, ys);
 	  pSGP->lineAbs (xd, yd);
+	  pSGP->setRasterOp (RO_SET);
 	}
 #endif
 	sum += projectSingleLine (phm, xd, yd, xs, ys, pSGP);
 	      
 #ifdef HAVE_SGP
-	if (m_trace >= TRACE_RAYS)
-	  traceShowParam ("Attenuation  :", "%5.2f", RAYSUM_TRACE_ROW_ATTEN, C_LTMAGENTA, "sum");
+	if (m_trace >= TRACE_RAYS) {
+	  traceShowParam (pSGP, "Attenuation  :", "%5.2f", RAYSUM_TRACE_ROW_ATTEN, C_LTMAGENTA, sum);
+	}
 
 	if (pSGP && m_trace >= TRACE_RAYS) {
 	  pSGP->setColor (C_LTBLUE);
+	  pSGP->setRasterOp (RO_XOR);
 	  pSGP->moveAbs (xs, ys);
 	  pSGP->lineAbs (xd, yd);
+	  pSGP->setRasterOp (RO_SET);
 	}
 #endif
 	xd += ddx2;
@@ -381,20 +439,30 @@ Scanner::projectSingleView (const Phantom& phm, DetectorArray& detArray, const d
 
 
 void 
-Scanner::traceShowParam (const char *label, const char *fmt, int row, int color, ...)
+Scanner::traceShowParam (SGP* pSGP, const char *label, const char *fmt, int row, int color, ...)
 {  
-  char s[80];
+  char s[256];
   va_list arg;
 
   va_start(arg, color);
-  //  cio_set_cpos (raysum_trace_menu_column, row);
   snprintf (s, sizeof(s), label, "%s");
-  //  cio_set_text_clr (color - 8, 0);
-  cio_put_str (s);
+  string strOut(s);
   vsnprintf (s, sizeof(s), fmt, arg);
+  strOut += s;
+
+  //  cio_set_cpos (raysum_trace_menu_column, row);
+  //  cio_set_text_clr (color - 8, 0);
   //  cio_set_text_clr (color, 0);
-  cio_put_str (s);
-  cout << "\n";
+
+  if (pSGP) {
+      pSGP->moveAbs (0., row * 0.04);
+      pSGP->setTextColor (color, -1);
+      pSGP->drawText (strOut);
+  } else {
+    cio_put_str (strOut.c_str());
+    cio_put_str ("\n");
+  }
+
   va_end(arg);
 }
 
@@ -442,11 +510,13 @@ Scanner::projectLineAgainstPElem (const PhantomElement& pelem, double x1, double
 
 #ifdef HAVE_SGP
   if (pSGP && m_trace == TRACE_CLIPPING) {
+    pSGP->setRasterOp (RO_XOR);
     pSGP->moveAbs (x1, y1);
     pSGP->lineAbs (x2, y2);
     cio_tone (8000., 0.05);
     pSGP->moveAbs (x1, y1);
     pSGP->lineAbs (x2, y2);
+    pSGP->setRasterOp (RO_SET);
   }
 #endif
 
diff --git a/libctsim/trace.cpp b/libctsim/trace.cpp
index 3bb8ce8..dced2c6 100644
--- a/libctsim/trace.cpp
+++ b/libctsim/trace.cpp
@@ -8,7 +8,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: trace.cpp,v 1.1 2000/07/20 11:17:31 kevin Exp $
+**  $Id: trace.cpp,v 1.2 2000/08/25 15:59:13 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
@@ -34,10 +34,10 @@ const char TraceLevel::TRACE_PLOT_STR[]=     "plot";
 const char TraceLevel::TRACE_CLIPPING_STR[]= "clipping";
 
 
-TraceID
+int
 TraceLevel::convertTraceNameToID (const char *traceString)
 {
-  TraceID traceID = TRACE_INVALID;
+  int traceID = TRACE_INVALID;
 
   if (strcasecmp (traceString, TRACE_NONE_STR) == 0)
     traceID = TRACE_NONE;
diff --git a/libctsupport/syserror.cpp b/libctsupport/syserror.cpp
index 28ccba4..e59449f 100644
--- a/libctsupport/syserror.cpp
+++ b/libctsupport/syserror.cpp
@@ -2,7 +2,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: syserror.cpp,v 1.3 2000/06/19 19:04:05 kevin Exp $
+**  $Id: syserror.cpp,v 1.4 2000/08/25 15:59:13 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
@@ -58,7 +58,7 @@ const static int MAX_ERROR_COUNT = 20;
 void sys_verror (int severity, const char *msg, va_list arg)
 {
   if (severity < errorlevel)
-    return;			/* ignore error if less than max level */
+    return;	// ignore error if less than max level
 
   nErrorCount++;
   if (severity != ERR_FATAL) {
diff --git a/src/ctsim.h b/src/ctsim.h
index c013a34..6185d86 100644
--- a/src/ctsim.h
+++ b/src/ctsim.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: ctsim.h,v 1.4 2000/07/23 01:49:03 kevin Exp $
+**  $Id: ctsim.h,v 1.5 2000/08/25 15:59:13 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
@@ -98,8 +98,8 @@ enum {
     PJMENU_FILE_PROPERTIES,
     PHMMENU_FILE_PROPERTIES,
     PJMENU_PROCESS_RECONSTRUCT,
-    IFMENU_VIEW_WINDOW_AUTO,
-    IFMENU_VIEW_WINDOW_MINMAX,
+    IFMENU_VIEW_SCALE_AUTO,
+    IFMENU_VIEW_SCALE_MINMAX,
     PHMMENU_PROCESS_RASTERIZE,
     PHMMENU_PROCESS_PROJECTIONS,
 };
diff --git a/src/dialogs.cpp b/src/dialogs.cpp
index 4b2738f..ef5ece2 100644
--- a/src/dialogs.cpp
+++ b/src/dialogs.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: dialogs.cpp,v 1.8 2000/08/22 07:02:48 kevin Exp $
+**  $Id: dialogs.cpp,v 1.9 2000/08/25 15:59:13 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
@@ -280,11 +280,18 @@ DialogGetRasterParameters::getNSamples (void)
 /////////////////////////////////////////////////////////////////////
 
 
-DialogGetProjectionParameters::DialogGetProjectionParameters (wxFrame* pParent, int iDefaultNDet = 0, int iDefaultNView = 0, int iDefaultNSamples = 1, double dDefaultRotAngle = 1., int iDefaultGeometry = Scanner::GEOMETRY_PARALLEL)
-    : wxDialog (pParent, -1, "Set Projection Parameters", wxDefaultPosition, wxDefaultSize, wxDEFAULT_DIALOG_STYLE | wxCAPTION)
+DialogGetProjectionParameters::DialogGetProjectionParameters (wxFrame* pParent, int iDefaultNDet = 0, int iDefaultNView = 0, int iDefaultNSamples = 1, double dDefaultRotAngle = 1., double dDefaultFocalLength = 1, double dDefaultFieldOfView = 1., int iDefaultGeometry = Scanner::GEOMETRY_PARALLEL)
+  : wxDialog (pParent, -1, "Set Projection Parameters", wxDefaultPosition, wxDefaultSize, wxDEFAULT_DIALOG_STYLE | wxCAPTION)
 {
   wxBoxSizer* pTopSizer = new wxBoxSizer (wxVERTICAL);
 
+  m_dDefaultRotAngle = dDefaultRotAngle;
+  m_dDefaultFocalLength = dDefaultFocalLength;
+  m_dDefaultFieldOfView = dDefaultFieldOfView;
+  m_iDefaultNSamples = iDefaultNSamples;
+  m_iDefaultNView = iDefaultNView;
+  m_iDefaultNDet = iDefaultNDet;
+
   pTopSizer->Add (new wxStaticText (this, -1, "Set Projection Parameters"), 0, wxALIGN_CENTER | wxTOP | wxLEFT | wxRIGHT, 5);
 		   
   pTopSizer->Add (new wxStaticLine (this, -1, wxDefaultPosition, wxSize(3,3), wxHORIZONTAL), 0, wxEXPAND | wxALL, 5);
@@ -305,6 +312,12 @@ DialogGetProjectionParameters::DialogGetProjectionParameters (wxFrame* pParent,
   ostringstream osRotAngle;
   osRotAngle << dDefaultRotAngle;
   m_pTextCtrlRotAngle = new wxTextCtrl (this, -1, osRotAngle.str().c_str(), wxDefaultPosition, wxSize(100, 25), 0);
+  ostringstream osFocalLength;
+  osFocalLength << dDefaultFocalLength;
+  m_pTextCtrlFocalLength = new wxTextCtrl (this, -1, osFocalLength.str().c_str(), wxDefaultPosition, wxSize(100, 25), 0);
+  ostringstream osFieldOfView;
+  osFieldOfView << dDefaultFieldOfView;
+  m_pTextCtrlFieldOfView = new wxTextCtrl (this, -1, osFieldOfView.str().c_str(), wxDefaultPosition, wxSize(100, 25), 0);
 
   wxGridSizer *pGridSizer = new wxGridSizer (2, 4, 5);
   pGridSizer->Add (new wxStaticText (this, -1, "Detectors"), 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL);
@@ -315,6 +328,10 @@ DialogGetProjectionParameters::DialogGetProjectionParameters (wxFrame* pParent,
   pGridSizer->Add (m_pTextCtrlNSamples, 0, wxALIGN_CENTER_VERTICAL);
   pGridSizer->Add (new wxStaticText (this, -1, "Rotation Angle (PI units)"), 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL);
   pGridSizer->Add (m_pTextCtrlRotAngle, 0, wxALIGN_CENTER_VERTICAL);
+  pGridSizer->Add (new wxStaticText (this, -1, "Focal Length Ratio (phantom radius units)"), 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL);
+  pGridSizer->Add (m_pTextCtrlFocalLength, 0, wxALIGN_CENTER_VERTICAL);
+  pGridSizer->Add (new wxStaticText (this, -1, "Field of View (phantom diameter units)"), 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL);
+  pGridSizer->Add (m_pTextCtrlFieldOfView, 0, wxALIGN_CENTER_VERTICAL);
   pTopSizer->Add (pGridSizer, 1, wxALL, 10);
 
   pTopSizer->Add (new wxStaticLine (this, -1, wxDefaultPosition, wxSize(3,3), wxHORIZONTAL), 0, wxEXPAND | wxALL, 5);
@@ -383,6 +400,28 @@ DialogGetProjectionParameters::getRotAngle (void)
       return (m_dDefaultRotAngle);
 }
 
+double
+DialogGetProjectionParameters::getFocalLengthRatio (void)
+{
+    wxString strCtrl = m_pTextCtrlFocalLength->GetValue();
+    double dValue;
+    if (strCtrl.ToDouble (&dValue))
+	return (dValue);
+    else
+      return (m_dDefaultFocalLength);
+}
+
+double
+DialogGetProjectionParameters::getFieldOfViewRatio (void)
+{
+    wxString strCtrl = m_pTextCtrlFieldOfView->GetValue();
+    double dValue;
+    if (strCtrl.ToDouble (&dValue))
+	return (dValue);
+    else
+      return (m_dDefaultFieldOfView);
+}
+
 const char*
 DialogGetProjectionParameters::getGeometry (void)
 {
@@ -561,3 +600,69 @@ DialogGetReconstructionParameters::getFilterGenerationName (void)
 {
   return m_pListBoxFilterGeneration->getSelectionStringValue();
 }
+
+
+DialogAutoScaleParameters::DialogAutoScaleParameters (wxFrame *pParent, const ImageFile& rIF)
+  : wxDialog (pParent, -1, "Auto Scale Parameters", wxDefaultPosition, wxDefaultSize, wxDEFAULT_DIALOG_STYLE | wxCAPTION), m_rImageFile(rIF)
+{
+  wxBoxSizer* pTopSizer = new wxBoxSizer (wxVERTICAL);
+
+  pTopSizer->Add (new wxStaticText (this, -1, "Auto Scale Parameters"), 0, wxALIGN_CENTER | wxTOP | wxLEFT | wxRIGHT, 5);
+		   
+  pTopSizer->Add (new wxStaticLine (this, -1, wxDefaultPosition, wxSize(3,3), wxHORIZONTAL), 0, wxEXPAND | wxALL, 5);
+
+  wxString asTitle[3];
+  asTitle[0] = "Median";
+  asTitle[1] = "Mode";
+  asTitle[2] = "Mean";
+
+  m_pListBoxCenter = new wxListBox (this, -1, wxDefaultPosition, wxDefaultSize, 3, asTitle, wxLB_SINGLE | wxLB_NEEDED_SB);
+  m_pListBoxCenter->SetSelection (0);
+  pTopSizer->Add (m_pListBoxCenter, 0, wxALL | wxALIGN_CENTER | wxEXPAND);
+
+  wxGridSizer *pGridSizer = new wxGridSizer (2, 2, 5);
+  pGridSizer->Add (new wxStaticText (this, -1, "Standard Deviation Factor"), 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL);
+  m_pTextCtrlStdDevFactor = new wxTextCtrl (this, -1, "1.0", wxDefaultPosition, wxSize(100, 25), 0);
+  pGridSizer->Add (m_pTextCtrlStdDevFactor, 0, wxALIGN_CENTER_VERTICAL);
+  pTopSizer->Add (pGridSizer, 1, wxALL, 10);
+
+  pTopSizer->Add (new wxStaticLine (this, -1, wxDefaultPosition, wxSize(3,3), wxHORIZONTAL), 0, wxEXPAND | wxALL, 5);
+
+  wxBoxSizer* pButtonSizer = new wxBoxSizer (wxHORIZONTAL);
+  wxButton* pButtonOk = new wxButton (this, wxID_OK, "Okay");
+  wxButton* pButtonCancel = new wxButton (this, wxID_CANCEL, "Cancel");
+  pButtonSizer->Add (pButtonOk, 0, wxEXPAND | wxALL, 10);
+  pButtonSizer->Add (pButtonCancel, 0, wxEXPAND | wxALL, 10);
+
+  pTopSizer->Add (pButtonSizer, 0, wxALIGN_CENTER);
+
+  SetAutoLayout (true);
+  SetSizer (pTopSizer);
+  pTopSizer->Fit (this);
+  pTopSizer->SetSizeHints (this);
+}
+
+void 
+DialogAutoScaleParameters::getMinMax (double* pMin, double* pMax)
+{
+  int iCenter = m_pListBoxCenter->GetSelection();
+  double min, max, mean, mode, median, stddev;
+  m_rImageFile.statistics (min, max, mean, mode, median, stddev);
+  double dCenter = median;
+  if (iCenter == 1)
+    dCenter = mode;
+  else if (iCenter == 2)
+    dCenter = mean;
+  
+  wxString sStddevFactor = m_pTextCtrlStdDevFactor->GetValue();
+  double dValue;
+  if (! sStddevFactor.ToDouble (&dValue)) {
+    *theApp->getLog() << "Error: Non-numeric Standard Deviation Factor of " << sStddevFactor << "\n";
+    *pMin = min;
+    *pMax = max;
+  }
+  double dHalfWidth = dValue * stddev / 2;
+  *pMin = dCenter - dHalfWidth;
+  *pMax = dCenter + dHalfWidth;
+  *theApp->getLog() << "Setting minimum to " << *pMin << " and maximum to " << *pMax << "\n";
+}
diff --git a/src/dialogs.h b/src/dialogs.h
index e4f890c..7298348 100644
--- a/src/dialogs.h
+++ b/src/dialogs.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: dialogs.h,v 1.9 2000/08/22 07:02:48 kevin Exp $
+**  $Id: dialogs.h,v 1.10 2000/08/25 15:59:13 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
@@ -109,13 +109,15 @@ class DialogGetRasterParameters : public wxDialog
 class DialogGetProjectionParameters : public wxDialog
 {
  public:
-    DialogGetProjectionParameters (wxFrame* pParent, int iDefaultNDet = 0, int iDefaultNView = 0, int iDefaultNSamples = 1, double dDefaultRotAngle = 1., int iDefaultGeometry = Scanner::GEOMETRY_PARALLEL);
+    DialogGetProjectionParameters (wxFrame* pParent, int iDefaultNDet = 0, int iDefaultNView = 0, int iDefaultNSamples = 1, double dDefaultRotAngle = 1., double dDefaultFocalLength = 1, double dDefaultFieldOfView = 1., int iDefaultGeometry = Scanner::GEOMETRY_PARALLEL);
     ~DialogGetProjectionParameters (void);
 
     unsigned int getNDet (void);
     unsigned int getNView (void);
     unsigned int getNSamples (void);
     double getRotAngle (void);
+    double getFieldOfViewRatio (void);
+    double getFocalLengthRatio (void);
     const char* getGeometry(void);
 
  private:
@@ -123,6 +125,8 @@ class DialogGetProjectionParameters : public wxDialog
     wxTextCtrl* m_pTextCtrlNView;
     wxTextCtrl* m_pTextCtrlNSamples;
     wxTextCtrl* m_pTextCtrlRotAngle;
+    wxTextCtrl* m_pTextCtrlFocalLength;
+    wxTextCtrl* m_pTextCtrlFieldOfView;
 
     StringValueAndTitleListBox* m_pListBoxGeometry;
 
@@ -130,6 +134,8 @@ class DialogGetProjectionParameters : public wxDialog
     int m_iDefaultNView;
     int m_iDefaultNSamples;
     double m_dDefaultRotAngle;
+    double m_dDefaultFocalLength;
+    double m_dDefaultFieldOfView;
 };
 
 
@@ -171,5 +177,20 @@ class DialogGetReconstructionParameters : public wxDialog
     int m_iDefaultInterpParam;
 };
 
+class DialogAutoScaleParameters : public wxDialog
+{
+ public:
+    DialogAutoScaleParameters (wxFrame* pParent, const ImageFile& rImageFile);
+    virtual ~DialogAutoScaleParameters() {}
+
+    void getMinMax (double* pMin, double* pMax);
+
+ private:
+    const ImageFile& m_rImageFile;
+
+    wxTextCtrl* m_pTextCtrlStdDevFactor;
+    wxListBox* m_pListBoxCenter;
+};
+
 #endif
 
diff --git a/src/views.cpp b/src/views.cpp
index 4cb6f69..1cd730e 100644
--- a/src/views.cpp
+++ b/src/views.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: views.cpp,v 1.15 2000/08/22 16:49:56 kevin Exp $
+**  $Id: views.cpp,v 1.16 2000/08/25 15:59:13 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
@@ -108,8 +108,8 @@ IMPLEMENT_DYNAMIC_CLASS(ImageFileView, wxView)
 
 BEGIN_EVENT_TABLE(ImageFileView, wxView)
   EVT_MENU(IFMENU_FILE_PROPERTIES, ImageFileView::OnProperties)
-  EVT_MENU(IFMENU_VIEW_WINDOW_MINMAX, ImageFileView::OnWindowMinMax)
-  EVT_MENU(IFMENU_VIEW_WINDOW_AUTO, ImageFileView::OnWindowAuto)
+  EVT_MENU(IFMENU_VIEW_SCALE_MINMAX, ImageFileView::OnScaleMinMax)
+  EVT_MENU(IFMENU_VIEW_SCALE_AUTO, ImageFileView::OnScaleAuto)
 END_EVENT_TABLE()
 
 ImageFileView::ImageFileView(void) 
@@ -148,13 +148,24 @@ ImageFileView::OnProperties (wxCommandEvent& event)
 }
 
 void 
-ImageFileView::OnWindowAuto (wxCommandEvent& event)
+ImageFileView::OnScaleAuto (wxCommandEvent& event)
 {
-    *theApp->getLog() << "ImageFile: Window Auto\n";
+    const ImageFile& rIF = GetDocument()->getImageFile();
+    DialogAutoScaleParameters dialogAutoScale (m_frame, rIF);
+    int iRetVal = dialogAutoScale.ShowModal();
+    if (iRetVal == wxID_OK) {
+      m_bMinSpecified = true;
+      m_bMaxSpecified = true;
+      double dMin, dMax;
+      dialogAutoScale.getMinMax (&dMin, &dMax);
+      m_dMinPixel = dMin;
+      m_dMaxPixel = dMax;
+      OnUpdate (this, NULL);
+    }
 }
 
 void 
-ImageFileView::OnWindowMinMax (wxCommandEvent& event)
+ImageFileView::OnScaleMinMax (wxCommandEvent& event)
 {
     const ImageFile& rIF = GetDocument()->getImageFile();
     double min, max;
@@ -216,8 +227,8 @@ ImageFileView::CreateChildFrame(wxDocument *doc, wxView *view)
     file_menu->Append(wxID_PREVIEW, "Print Pre&view");
     
     wxMenu *view_menu = new wxMenu;
-    view_menu->Append(IFMENU_VIEW_WINDOW_MINMAX, "&Set Window Min/Max");
-    view_menu->Append(IFMENU_VIEW_WINDOW_AUTO, "&Auto Window...");
+    view_menu->Append(IFMENU_VIEW_SCALE_MINMAX, "Display Scale &Set...");
+    view_menu->Append(IFMENU_VIEW_SCALE_AUTO, "Display Scale &Auto...");
     
     wxMenu *help_menu = new wxMenu;
     help_menu->Append(MAINMENU_HELP_ABOUT, "&About");
@@ -391,19 +402,26 @@ PhantomView::OnProperties (wxCommandEvent& event)
 void
 PhantomView::OnProjections (wxCommandEvent& event)
 {
-  DialogGetProjectionParameters dialogProjection (m_frame, 367, 320, 1, 1., Scanner::GEOMETRY_PARALLEL);
+  DialogGetProjectionParameters dialogProjection (m_frame, 367, 320, 1, 1., 1., 1., Scanner::GEOMETRY_PARALLEL);
   int retVal = dialogProjection.ShowModal();
   if (retVal == wxID_OK) {
     int nDet = dialogProjection.getNDet();
     int nView = dialogProjection.getNView();
     int nSamples = dialogProjection.getNSamples();
     double dRotAngle = dialogProjection.getRotAngle();
+    double dFocalLengthRatio = dialogProjection.getFocalLengthRatio();
+    double dFieldOfViewRatio = dialogProjection.getFieldOfViewRatio();
+
     wxString sGeometry = dialogProjection.getGeometry();
     if (nDet > 0 && nView > 0 && sGeometry != "") {
       const Phantom& rPhantom = GetDocument()->getPhantom();
       ProjectionFileDocument* pProjectionDoc = dynamic_cast<ProjectionFileDocument*>(theApp->getDocManager()->CreateDocument("untitled.pj", wxDOC_SILENT));
       Projections& rProj = pProjectionDoc->getProjections();
-      Scanner theScanner (rPhantom, sGeometry.c_str(), nDet, nView, nSamples, dRotAngle);
+      Scanner theScanner (rPhantom, sGeometry.c_str(), nDet, nView, nSamples, dRotAngle, dFocalLengthRatio, dFieldOfViewRatio);
+      if (theScanner.fail()) {
+	*theApp->getLog() << "Failed making scanner: " << theScanner.failMessage().c_str() << "\n";
+	return;
+      }
       rProj.initFromScanner (theScanner);
 
 #if 1
@@ -414,7 +432,9 @@ PhantomView::OnProjections (wxCommandEvent& event)
       frame.GetClientSize(&x, &y);
       SGPDriver driver (dynamic_cast<wxDC*>(&dc), x, y);
       SGP sgp (driver);
-      theScanner.collectProjections (rProj, rPhantom, 0, TRACE_PHM, &sgp);
+      for (int iView = 0; iView < rProj.nView(); iView++) {
+	theScanner.collectProjections (rProj, rPhantom, iView, 1, true, TRACE_RAYS, &sgp);
+      }
 #else
       theScanner.collectProjections (rProj, rPhantom);
 #endif
@@ -422,7 +442,7 @@ PhantomView::OnProjections (wxCommandEvent& event)
       pProjectionDoc->Modify(true);
       pProjectionDoc->UpdateAllViews(this);
       ostringstream os;
-      os << "Projections for " << rPhantom.name() << ": nDet=" << nDet << ", nView=" << nView << ", nSamples=" << nSamples << ", RotAngle=" << dRotAngle << ", Geometry=" << sGeometry.c_str() << "\n";
+      os << "Projections for " << rPhantom.name() << ": nDet=" << nDet << ", nView=" << nView << ", nSamples=" << nSamples << ", RotAngle=" << dRotAngle << ", FocalLengthRatio=" << dFocalLengthRatio << ", FieldOfViewRatio=" << dFieldOfViewRatio << ", Geometry=" << sGeometry.c_str() << "\n";
       *theApp->getLog() << os.str().c_str();
     }
   }
diff --git a/src/views.h b/src/views.h
index 3c29c77..a11cfaf 100644
--- a/src/views.h
+++ b/src/views.h
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: views.h,v 1.6 2000/07/28 08:28:08 kevin Exp $
+**  $Id: views.h,v 1.7 2000/08/25 15:59:13 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
@@ -64,8 +64,8 @@ public:
     void OnUpdate(wxView *sender, wxObject *hint = NULL);
     bool OnClose (bool deleteWindow = true);
     void OnProperties (wxCommandEvent& event);
-    void OnWindowAuto (wxCommandEvent& event);
-    void OnWindowMinMax (wxCommandEvent& event);
+    void OnScaleAuto (wxCommandEvent& event);
+    void OnScaleMinMax (wxCommandEvent& event);
 
     ImageFileDocument* GetDocument(void) 
 	{ return dynamic_cast<ImageFileDocument*>(wxView::GetDocument()); }
diff --git a/tools/if2img.cpp b/tools/if2img.cpp
index d9e7004..d17409e 100644
--- a/tools/if2img.cpp
+++ b/tools/if2img.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: if2img.cpp,v 1.5 2000/08/22 17:03:54 kevin Exp $
+**  $Id: if2img.cpp,v 1.6 2000/08/25 15:59:13 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
@@ -48,7 +48,7 @@ static struct option my_options[] =
   {0, 0, 0, 0}
 };
 
-static const char* g_szIdStr = "$Id: if2img.cpp,v 1.5 2000/08/22 17:03:54 kevin Exp $";
+static const char* g_szIdStr = "$Id: if2img.cpp,v 1.6 2000/08/25 15:59:13 kevin Exp $";
 
 enum { O_AUTO_FULL, O_AUTO_STD0_1, O_AUTO_STD0_5, O_AUTO_STD1, O_AUTO_STD2, O_AUTO_STD3 };
 static const char O_AUTO_FULL_STR[]="full";
@@ -259,12 +259,16 @@ if2img_main (int argc, char *const argv[])
 	}
     }
 
+#if HAVE_SGP
+  if (optind + 1 == argc)
+    opt_format = O_FORMAT_DISP;  // display image if no options
+#endif
+
   if ((opt_format == O_FORMAT_DISP && optind + 1 != argc) 
-      || (opt_format != O_FORMAT_DISP && optind + 2 != argc))
-    {
-	if2img_usage(argv[0]);
-	return (1);
-    }
+      || (opt_format != O_FORMAT_DISP && optind + 2 != argc)) {
+    if2img_usage(argv[0]);
+    return (1);
+  }
   
   in_file = argv[optind];
 
diff --git a/tools/phm2if.cpp b/tools/phm2if.cpp
index b4338c9..9ff3b9a 100644
--- a/tools/phm2if.cpp
+++ b/tools/phm2if.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: phm2if.cpp,v 1.9 2000/08/03 09:57:29 kevin Exp $
+**  $Id: phm2if.cpp,v 1.10 2000/08/25 15:59:13 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
@@ -50,7 +50,7 @@ static struct option my_options[] =
   {0, 0, 0, 0}
 };
 
-static const char* g_szIdStr = "$Id: phm2if.cpp,v 1.9 2000/08/03 09:57:29 kevin Exp $";
+static const char* g_szIdStr = "$Id: phm2if.cpp,v 1.10 2000/08/25 15:59:13 kevin Exp $";
 
 void 
 phm2if_usage (const char *program)
@@ -63,9 +63,9 @@ phm2if_usage (const char *program)
   cout << "     ny              Number of pixels Y-axis" << endl;
   cout << "     --phantom       Phantom to use for projection" << endl;
   cout << "        herman       Herman head phantom" << endl;
-  cout << "        bherman      Bordered Herman head phantom" << endl;
-  cout << "        rowland      Rowland head phantom" << endl;
-  cout << "        browland     Bordered Rowland head phantom" << endl;
+  cout << "        herman-b     Herman head phantom (Bordered)" << endl;
+  cout << "        shepp-logan  Shepp-Logan head phantom" << endl;
+  cout << "        shepp-logan-b Shepp-Logan head phantom (Bordered)" << endl;
   cout << "        unitpulse    Unit pulse phantom" << endl;
   cout << "     --phmfile       Generate Phantom from phantom file" << endl;
   cout << "     --filter        Generate Phantom from a filter function" << endl;
diff --git a/tools/phm2pj.cpp b/tools/phm2pj.cpp
index 82cad2f..2bc4d98 100644
--- a/tools/phm2pj.cpp
+++ b/tools/phm2pj.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: phm2pj.cpp,v 1.9 2000/08/03 09:57:29 kevin Exp $
+**  $Id: phm2pj.cpp,v 1.10 2000/08/25 15:59:13 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
@@ -29,7 +29,7 @@
 #include "timer.h"
 
 
-enum { O_PHANTOM, O_DESC, O_NRAY, O_ROTANGLE, O_PHMFILE,
+enum { O_PHANTOM, O_DESC, O_NRAY, O_ROTANGLE, O_PHMFILE, O_GEOMETRY, O_FOCAL_LENGTH, O_FIELD_OF_VIEW,
        O_TRACE, O_VERBOSE, O_HELP, O_DEBUG, O_VERSION };
 
 static struct option phm2pj_options[] = 
@@ -39,6 +39,9 @@ static struct option phm2pj_options[] =
   {"desc", 1, 0, O_DESC},
   {"nray", 1, 0, O_NRAY},
   {"rotangle", 1, 0, O_ROTANGLE},
+  {"geometry", 1, 0, O_GEOMETRY},
+  {"focal-length", 1, 0, O_FOCAL_LENGTH},
+  {"field-of-view", 1, 0, O_FIELD_OF_VIEW},
   {"trace", 1, 0, O_TRACE},
   {"verbose", 0, 0, O_VERBOSE},
   {"help", 0, 0, O_HELP},
@@ -47,39 +50,43 @@ static struct option phm2pj_options[] =
   {0, 0, 0, 0}
 };
 
-static const char* g_szIdStr = "$Id: phm2pj.cpp,v 1.9 2000/08/03 09:57:29 kevin Exp $";
+static const char* g_szIdStr = "$Id: phm2pj.cpp,v 1.10 2000/08/25 15:59:13 kevin Exp $";
 
 
 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 << "        bherman   Bordered 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;
+  cout << "usage: " << fileBasename(program) << " outfile ndet nview [--phantom phantom-name] [--phmfile filename] [OPTIONS]\n";
+  cout << "Calculate (projections) through phantom object, either a predefined --phantom or a --phmfile\n\n";
+  cout << "     outfile          Name of output file for raysums\n";
+  cout << "     ndet             Number of detectors\n";
+  cout << "     nview            Number of rotated views\n";
+  cout << "     --phantom        Phantom to use for projection\n";
+  cout << "        herman        Herman head phantom\n";
+  cout << "        herman-b      Herman head phantom (Bordered)\n";
+  cout << "        shepp-logan   Shepp-Logan head phantom\n";
+  cout << "        shepp-logan-b Shepp-Logan head phantom (Bordered)\n";
+  cout << "        unitpulse     Unit pulse phantom\n";
+  cout << "     --phmfile        Get Phantom from phantom file\n";
+  cout << "     --desc           Description of raysum\n";
+  cout << "     --nray           Number of rays per detector (default = 1)\n";
+  cout << "     --rotangle       Degrees to rotate view through (multiple of PI)\n";
+  cout << "                      (default = 1)\n";
+  cout << "     --focal-length   Focal length ratio (ratio to radius of phantom)\n";
+  cout << "                      (default = 1)\n";
+  cout << "     --field-of-view  Field of view (ratio to diameter of phantom square)\n";
+  cout << "                      (default = 1)\n";
+  cout << "     --trace          Trace level to use\n";
+  cout << "        none          No tracing (default)\n";
+  cout << "        text          Trace text level\n";
+  cout << "        phm           Trace phantom image\n";
+  cout << "        rays          Trace rays\n";
+  cout << "        plot          Trace plot\n";
+  cout << "        clipping      Trace clipping\n";
+  cout << "     --verbose        Verbose mode\n";
+  cout << "     --debug          Debug mode\n";
+  cout << "     --version        Print version\n";
+  cout << "     --help           Print this help message\n";
 }
 
 #ifdef HAVE_MPI
@@ -97,6 +104,8 @@ phm2pj_main (int argc, char* argv[])
   int opt_ndet;
   int opt_nview;
   int opt_nray = 1;
+  double dOptFocalLength = 1.;
+  double dOptFieldOfView = 1.;
   int opt_trace = 0;
   string optPhmName (Phantom::convertPhantomIDToName(Phantom::PHM_HERMAN));
   int opt_verbose = 0;
@@ -152,6 +161,27 @@ phm2pj_main (int argc, char* argv[])
 	  return (1);
 	}
 	break;
+      case O_GEOMETRY:
+	optGeometryName = optarg;
+	break;
+      case O_FOCAL_LENGTH:
+	dOptFocalLength = strtod(optarg, &endptr);
+	endstr = optarg + strlen(optarg);
+	if (endptr != endstr) {
+	  cerr << "Error setting --focal-length to " << optarg << endl;
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	break;
+      case O_FIELD_OF_VIEW:
+	dOptFieldOfView = strtod(optarg, &endptr);
+	endstr = optarg + strlen(optarg);
+	if (endptr != endstr) {
+	  cerr << "Error setting --field-of-view to " << optarg << endl;
+	  phm2pj_usage(argv[0]);
+	  return (1);
+	}
+	break;
       case O_NRAY:
 	opt_nray = strtol(optarg, &endptr, 10);
 	endstr = optarg + strlen(optarg);
@@ -165,7 +195,7 @@ phm2pj_main (int argc, char* argv[])
 #ifdef VERSION
 	  cout << "Version: " << VERSION << endl << g_szIdStr << endl;
 #else
-          cout << "Unknown version number" << endl;
+          cout << "Unknown version number\n";
 #endif
 	  return (0);
       case O_HELP:
@@ -179,7 +209,7 @@ phm2pj_main (int argc, char* argv[])
     }
   
     if (optPhmName == "" && optPhmFileName == "") {
-      cerr << "No phantom defined" << endl << endl;
+      cerr << "No phantom defined\n" << endl;
       phm2pj_usage(argv[0]);
       return (1);
     }
@@ -227,7 +257,7 @@ phm2pj_main (int argc, char* argv[])
 
     if (optPhmFileName != "") {
 #ifdef HAVE_MPI
-      cerr << "Can not read phantom from file in MPI mode" << endl;
+      cerr << "Can not read phantom from file in MPI mode\n";
       return (1);
 #endif
       phm.createFromFile (optPhmFileName.c_str());
@@ -254,7 +284,7 @@ phm2pj_main (int argc, char* argv[])
 #endif
 
   opt_rotangle *= PI;
-  Scanner scanner (phm, optGeometryName.c_str(), opt_ndet, opt_nview, opt_nray, opt_rotangle);
+  Scanner scanner (phm, optGeometryName.c_str(), opt_ndet, opt_nview, opt_nray, opt_rotangle, dOptFocalLength, dOptFieldOfView);
   if (scanner.fail()) {
     cout << "Scanner Creation Error: " << scanner.failMessage() << endl;
     return (1);
@@ -273,10 +303,10 @@ phm2pj_main (int argc, char* argv[])
   pjLocal.setNView (mpiWorld.getMyLocalWorkUnits());
 
   if (opt_debug)
-    cout << "pjLocal->nview = " << pjLocal.nView() << " (process " << mpiWorld.getRank() << ")" << endl;;
+    cout << "pjLocal->nview = " << pjLocal.nView() << " (process " << mpiWorld.getRank() << ")\n";;
 
   TimerCollectiveMPI timerProject (mpiWorld.getComm());
-  scanner.collectProjections (pjLocal, phm, mpiWorld.getMyStartWorkUnit(), opt_trace);
+  scanner.collectProjections (pjLocal, phm, mpiWorld.getMyStartWorkUnit(), mpiWorld.getMyLocalWorkUnits(), false, opt_trace);
   if (opt_verbose)
     timerProject.timerEndAndReport ("Time to collect projections");
 
@@ -294,7 +324,7 @@ phm2pj_main (int argc, char* argv[])
     pSGPDriver = new SGPDriver ("phm2pj", 600, 600);
     pSGP = new SGP (*pSGPDriver);
   }
-  scanner.collectProjections (pjGlobal, phm, 0, opt_trace, pSGP);
+  scanner.collectProjections (pjGlobal, phm, opt_trace, pSGP);
   if (opt_trace >= TRACE_PHM) {
     cout << "Press enter to continue\n";
     cio_kb_getc();
@@ -303,7 +333,7 @@ phm2pj_main (int argc, char* argv[])
   }
 
 #else
-  scanner.collectProjections (pjGlobal, phm, 0, opt_trace);
+  scanner.collectProjections (pjGlobal, phm, opt_trace);
 #endif
 
 #endif
@@ -321,7 +351,7 @@ phm2pj_main (int argc, char* argv[])
 	pjGlobal.printScanInfo();
 	cout << endl;
 	cout << "  Remark: " << pjGlobal.remark() << endl;
-	cout << "Run time: " << pjGlobal.calcTime() << " seconds" << endl;
+	cout << "Run time: " << pjGlobal.calcTime() << " seconds\n";
       }
     }
 
@@ -384,7 +414,7 @@ main (int argc, char* argv[])
   } catch (exception e) {
     cerr << "Exception: " << e.what() << endl;
   } catch (...) {
-    cerr << "Unknown exception" << endl;
+    cerr << "Unknown exception\n";
   }
 
   return (retval);
diff --git a/tools/pjrec.cpp b/tools/pjrec.cpp
index 10adbff..19b9b86 100644
--- a/tools/pjrec.cpp
+++ b/tools/pjrec.cpp
@@ -9,7 +9,7 @@
 **  This is part of the CTSim program
 **  Copyright (C) 1983-2000 Kevin Rosenberg
 **
-**  $Id: pjrec.cpp,v 1.13 2000/08/22 07:02:48 kevin Exp $
+**  $Id: pjrec.cpp,v 1.14 2000/08/25 15:59:13 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
@@ -49,7 +49,7 @@ static struct option my_options[] =
   {0, 0, 0, 0}
 };
 
-static const char* g_szIdStr = "$Id: pjrec.cpp,v 1.13 2000/08/22 07:02:48 kevin Exp $";
+static const char* g_szIdStr = "$Id: pjrec.cpp,v 1.14 2000/08/25 15:59:13 kevin Exp $";
 
 void 
 pjrec_usage (const char *program)
@@ -92,7 +92,7 @@ pjrec_usage (const char *program)
   cout << "  --zeropad n   Set zeropad level (default = 0)\n";
   cout << "                set n to number of powers to two to pad\n";
   cout << "  --filter-generation  Filter Generation mode\n";
-  cout << "    direct       Use direct filter in spatial or frequency domain\n";
+  cout << "    direct       Use direct filter in spatial or frequency domain (default)\n";
   cout << "    inverse_fourier  Use inverse fourier transform of inverse filter\n";
   cout << "  --backproj    Backprojection Method" << endl;
   cout << "    trig        Trigometric functions at every point" << endl;
@@ -132,12 +132,12 @@ pjrec_main (int argc, char * argv[])
   string sRemark;
   bool bOptVerbose = false;
   bool bOptDebug = 1;
-  int iOptZeropad = 0;
+  int iOptZeropad = 1;
   int optTrace = TRACE_NONE;
   double dOptFilterParam = -1;
   string sOptFilterName (SignalFilter::convertFilterIDToName (SignalFilter::FILTER_ABS_BANDLIMIT));
   string sOptFilterMethodName (ProcessSignal::convertFilterMethodIDToName (ProcessSignal::FILTER_METHOD_CONVOLUTION));
-  string sOptFilterGenerationName (ProcessSignal::convertFilterGenerationIDToName (ProcessSignal::FILTER_GENERATION_INVERSE_FOURIER));
+  string sOptFilterGenerationName (ProcessSignal::convertFilterGenerationIDToName (ProcessSignal::FILTER_GENERATION_DIRECT));
   string sOptInterpName (Backprojector::convertInterpIDToName (Backprojector::INTERP_LINEAR));
   string sOptBackprojectName (Backprojector::convertBackprojectIDToName (Backprojector::BPROJ_IDIFF3));
   int iOptPreinterpolationFactor = 1;