Changeset 36680 for branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data

Timestamp:

Apr 21, 2014, 5:42:34 AM (12 years ago)

Author:

eugene

Message:

merge changes from trunk

Location:

branches/eam_branches/ps2-tc3-20130727

Files:

• . (modified) (1 prop)
• Ohana (modified) (1 prop)
• Ohana/src/opihi (modified) (1 prop)
• Ohana/src/opihi/cmd.data (modified) (1 prop)
• Ohana/src/opihi/cmd.data/Makefile (modified) (4 diffs)
• Ohana/src/opihi/cmd.data/cast.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/cast.c )
• Ohana/src/opihi/cmd.data/densify.c (modified) (5 diffs)
• Ohana/src/opihi/cmd.data/impeaks.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/impeaks.c )
• Ohana/src/opihi/cmd.data/imsmooth.2d.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/imsmooth.2d.c )
• Ohana/src/opihi/cmd.data/imsmooth.generic.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/imsmooth.generic.c )
• Ohana/src/opihi/cmd.data/init.c (modified) (8 diffs)
• Ohana/src/opihi/cmd.data/join.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/join.c )
• Ohana/src/opihi/cmd.data/match2d.c (modified) (3 diffs)
• Ohana/src/opihi/cmd.data/medimage.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/medimage.c )
• Ohana/src/opihi/cmd.data/medimage_commands.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/medimage_commands.c )
• Ohana/src/opihi/cmd.data/read_vectors.c (modified) (3 diffs)
• Ohana/src/opihi/cmd.data/rebin.c (modified) (1 diff)
• Ohana/src/opihi/cmd.data/test/join.sh (copied) (copied from trunk/Ohana/src/opihi/cmd.data/test/join.sh )
• Ohana/src/opihi/cmd.data/test/medimage.sh (copied) (copied from trunk/Ohana/src/opihi/cmd.data/test/medimage.sh )
• Ohana/src/opihi/cmd.data/vellipse.c (modified) (1 diff)
• Ohana/src/opihi/cmd.data/vgauss.c (modified) (2 diffs)
• Ohana/src/opihi/cmd.data/vlist.c (copied) (copied from trunk/Ohana/src/opihi/cmd.data/vlist.c )

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/Makefile

@@ -25 +25 @@
 $(SRC)/book.$(ARCH).o           \
 $(SRC)/book_commands.$(ARCH).o  \
+$(SRC)/cast.$(ARCH).o           \
 $(SRC)/center.$(ARCH).o \
 $(SRC)/clear.$(ARCH).o          \
@@ -63 +64 @@
 $(SRC)/imcut.$(ARCH).o          \
 $(SRC)/imhist.$(ARCH).o \
+$(SRC)/impeaks.$(ARCH).o        \
 $(SRC)/imsmooth.$(ARCH).o       \
+$(SRC)/imsmooth.generic.$(ARCH).o       \
+$(SRC)/imsmooth.2d.$(ARCH).o    \
 $(SRC)/integrate.$(ARCH).o      \
 $(SRC)/interpolate.$(ARCH).o    \
+$(SRC)/join.$(ARCH).o           \
 $(SRC)/jpeg.$(ARCH).o           \
 $(SRC)/kern.$(ARCH).o           \
@@ -84 +89 @@
 $(SRC)/mget.$(ARCH).o           \
 $(SRC)/minterpolate.$(ARCH).o   \
+$(SRC)/medimage.$(ARCH).o       \
+$(SRC)/medimage_commands.$(ARCH).o \
 $(SRC)/mset.$(ARCH).o           \
 $(SRC)/peak.$(ARCH).o           \
@@ -143 +150 @@
 $(SRC)/vmaxwell.$(ARCH).o          \
 $(SRC)/vgrid.$(ARCH).o             \
+$(SRC)/vlist.$(ARCH).o             \
 $(SRC)/vload.$(ARCH).o             \
 $(SRC)/vzload.$(ARCH).o            \

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/densify.c

@@ -2 +2 @@
 
 # define CHECKVAL(ARG) if (!isfinite(ARG)) { gprint (GP_ERR, "illegal value for %s: %f\n", #ARG, ARG); return (FALSE); }
+enum {IS_DOT, IS_SQUARE, IS_CIRCLE, IS_GAUSS};
 
 int densify (int argc, char **argv) {
 
-  int i, Nx, Ny, Xb, Yb, N, Xpix, Ypix, good, UseGraph;
+  int i, Nx, Ny, Xb, Yb, ix, iy, N, Xpix, Ypix, good, UseGraph;
   double Xmin, Xmax, dX, Ymin, Ymax, dY;
   float *val;
@@ -24 +25 @@
   }
 
+  float scale = 0.0;
+  if ((N = get_argument (argc, argv, "-scale"))) {
+    remove_argument (N, &argc, argv);
+    scale = atof(argv[N]);
+    remove_argument (N, &argc, argv);
+  }
+
+  int PSFTYPE = IS_DOT;
+  if ((N = get_argument (argc, argv, "-psf"))) {
+    remove_argument (N, &argc, argv);
+    if (!strcasecmp(argv[N], "dot"))    PSFTYPE = IS_DOT;
+    if (!strcasecmp(argv[N], "square")) PSFTYPE = IS_SQUARE;
+    if (!strcasecmp(argv[N], "circle")) PSFTYPE = IS_CIRCLE;
+    if (!strcasecmp(argv[N], "gauss"))  PSFTYPE = IS_GAUSS;
+    remove_argument (N, &argc, argv);
+  }
+
   good = UseGraph ? (argc == 4) : (argc == 10);
   if (!good) {
     gprint (GP_ERR, "USAGE: densify buffer x y Xmin Xmax dX Ymin Ymax dY\n");
     gprint (GP_ERR, "   OR: densify buffer x y -graph\n");
+    gprint (GP_ERR, " option: -psf [dot] (circle) (square) (gauss)\n");
     return (FALSE);
   }
@@ -69 +88 @@
   CHECKVAL(dY);
 
+  float scaleX = (scale > 0.0) ? scale / dX : 3.0;
+  float scaleY = (scale > 0.0) ? scale / dY : 3.0;
+
   Nx = (Xmax - Xmin) / dX + 1;
   Ny = (Ymax - Ymin) / dY + 1;
@@ -76 +98 @@
   CreateBuffer (bf, Nx, Ny, -32, 0.0, 1.0);
   strcpy (bf[0].file, "(empty)");
+  
+  float scale2 = (scaleX + 1.0) * (scaleY + 1.0);
+  float fSquare = 1.0 / scale2;
+  float fCircle = 1.0 / (3.141592 * scale2);
+  float fSigma  = 0.5 / scale2;
+  float fGauss  = 1.0 / (2.0 * 3.141592 * scale2);
 
   x = vx[0].elements.Flt;
@@ -83 +111 @@
     Xb = (*x - Xmin) / dX;
     Yb = (*y - Ymin) / dY;
-    if (Xb >= Nx) continue;
-    if (Yb >= Ny) continue;
-    if (Xb < 0) continue;
-    if (Yb < 0) continue;
-    val[Xb + Yb*Nx] ++;
+    switch (PSFTYPE) {
+      case IS_DOT:
+        if (Xb >= Nx) continue;
+        if (Yb >= Ny) continue;
+        if (Xb < 0) continue;
+        if (Yb < 0) continue;
+        val[Xb + Yb*Nx] ++;
+        break;
+      case IS_SQUARE:
+        for (ix = Xb - scaleX; ix <= Xb + scaleX; ix++) {
+          for (iy = Yb - scaleY; iy <= Yb + scaleY; iy++) {
+            if (ix >= Nx) continue;
+            if (iy >= Ny) continue;
+            if (ix < 0) continue;
+            if (iy < 0) continue;
+            val[ix + iy*Nx] += fSquare;
+          }
+        }
+        break;
+      case IS_CIRCLE:
+        for (ix = Xb - scaleX; ix <= Xb + scaleX; ix++) {
+          float dX = ix - Xb;
+          for (iy = Yb - scaleY; iy <= Yb + scaleY; iy++) {
+            float dY = iy - Yb;
+            float r2 = dX*dX + dY*dY;
+            if (r2 > 9) continue;
+            if (ix >= Nx) continue;
+            if (iy >= Ny) continue;
+            if (ix < 0) continue;
+            if (iy < 0) continue;
+            val[ix + iy*Nx] += fCircle;
+          }
+        }
+        break;
+      case IS_GAUSS:
+        for (ix = Xb - scaleX; ix <= Xb + scaleX; ix++) {
+          float dX = ix - Xb;
+          for (iy = Yb - scaleY; iy <= Yb + scaleY; iy++) {
+            float dY = iy - Yb;
+            float r2 = dX*dX + dY*dY;
+            if (ix >= Nx) continue;
+            if (iy >= Ny) continue;
+            if (ix < 0) continue;
+            if (iy < 0) continue;
+            val[ix + iy*Nx] += fGauss*exp(-fSigma*r2);
+          }
+        }
+        break;
+    }
   }
   return (TRUE);

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/init.c

@@ -10 +10 @@
 int center           PROTO((int, char **));
 int parity           PROTO((int, char **));
+int cast             PROTO((int, char **));
 int circstats        PROTO((int, char **));
 int clear            PROTO((int, char **));
@@ -52 +53 @@
 int imcut            PROTO((int, char **));
 int imhist           PROTO((int, char **));
+int impeaks          PROTO((int, char **));
 int imsmooth         PROTO((int, char **));
+int imsmooth_generic PROTO((int, char **));
+int imsmooth_2d      PROTO((int, char **));
 int integrate        PROTO((int, char **));
 int interpolate      PROTO((int, char **));
+int join             PROTO((int, char **));
 int jpeg             PROTO((int, char **));
 int kern             PROTO((int, char **));
@@ -74 +79 @@
 int mget             PROTO((int, char **));
 int minterp          PROTO((int, char **));
+int medimage_command PROTO((int, char **));
 int mset             PROTO((int, char **));
 int peak             PROTO((int, char **));
@@ -133 +139 @@
 int vmaxwell         PROTO((int, char **));
 int vload            PROTO((int, char **));
+int vlist            PROTO((int, char **));
 int vzload           PROTO((int, char **));
 int vstats           PROTO((int, char **));
@@ -160 +167 @@
   {1, "buffers",      list_buffers,     "list the currently allocated buffers (images)"},
   {1, "center",       center,           "center image on coords"},
+  {1, "cast",         cast,             "cast input vector to specified type"},
   {1, "circstats",    circstats,        "circular statistics"},
   {1, "clear",        clear,            "erase plot"},
@@ -205 +213 @@
   {1, "imcut",        imcut,            "linear image cut between arbitrary coords"},
   {1, "imhistogram",  imhist,           "histogram of an image region"},
+  {1, "impeaks",      impeaks,          "find peaks in an image (return vectors)"},
   {1, "imsmooth",     imsmooth,         "circular gaussian smoothing"},
+  {1, "imsmooth.generic", imsmooth_generic, "circular non-gaussian smoothing"},
+  {1, "imsmooth.2d",  imsmooth_2d,      "circular non-gaussian smoothing"},
   {1, "imstats",      imstats,          "statistics on a portion of an image"},
   {1, "integrate",    integrate,        "integrate a vector"},
   {1, "interpolate",  interpolate,      "interpolate between vector pairs"},
+  {1, "join",         join,             "find the join of two ID vectors"},
   {1, "jpeg",         jpeg,             "convert display image to JPEG"},
   {1, "kern",         kern,             "convolve with 3x3 kernel"},
@@ -224 +236 @@
   {1, "minterp",      minterp,          "interpolate image pixels"},
   {1, "iminterp",     minterp,          "interpolate image pixels"},
+  {1, "medimage",     medimage_command, "median image manipulation"},
   {1, "matrix",       matrix,           "matrix math operations"},
   {1, "match2d",      match2d,          "match 2 pairs of X,Y vectors and return matched indexes"},
@@ -290 +303 @@
   {1, "vgrid",        vgrid,            "generate an image from a triplet of vectors"},
   {1, "vhistogram",   histogram,        "generate histogram from vector"},
+  {1, "vlist",        vlist,            "append values to a vector from command line"},
   {1, "vload",        vload,            "load vectors as overlay on image display"},
   {1, "vmaxwell",     vmaxwell,         "fit a Maxwellian to a vector"},

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/match2d.c

@@ -14 +14 @@
   Vector *index1, *index2;
 
+  if ((N = get_argument (argc, argv, "-h"))) goto usage;
+  if ((N = get_argument (argc, argv, "--help"))) goto usage;
+
   CLOSEST = FALSE;
   if ((N = get_argument (argc, argv, "-closest"))) {
@@ -38 +41 @@
   if (argc != 6) {
     gprint (GP_ERR, "USAGE: match2d X1 Y1 X2 Y2 Radius [-index1 (index1)] [-index2 (index2)] [-closest]\n");
-    gprint (GP_ERR, "  if -closest is provided, index1 & index2 will have the same length as X1 and X2 (respectively)\n");
-    gprint (GP_ERR, "    with either the index of the match or a value of -1 for non-matches\n");
+    gprint (GP_ERR, "  use -h or --help for more detail\n");
     return (FALSE);
   }
@@ -90 +92 @@
 
   return (TRUE);
+
+usage:
+  gprint (GP_ERR, "we have two modes of operation:\n\n");
+
+  gprint (GP_ERR, "without -closest, we are finding all matched pairs within the match radius.  in this\n");
+  gprint (GP_ERR, "case, the two index vectors have the same length, one entry per matched pair.\n");
+  gprint (GP_ERR, "x1[index1],y1[index1] matches to x2[index2],y2[index2].\n\n");
+
+  gprint (GP_ERR, "with -closest selected, we are finding the closest element of set 1 to each of set 2\n");
+  gprint (GP_ERR, "and vice versa.  in this case, index1 is always the same length as x1,y1, while index2\n");
+  gprint (GP_ERR, "is the same lengths as x2,y2.  x2[index1],y2[index1] matches x1,y1 while\n");
+  gprint (GP_ERR, "x1[index2],y1[index2] matches x2,y2\n\n");
+
+  gprint (GP_ERR, "if -index1 or -index2 is not supplied, the vectors are created with names index1 or index2\n");
+  gprint (GP_ERR, "use 'reindex' to generate new vectors based on these index vectors\n");
+
+  return FALSE;
 }
 

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/read_vectors.c

@@ -23 +23 @@
 // vector types
 enum {COLTYPE_NONE, COLTYPE_FLT, COLTYPE_INT, COLTYPE_TIME, COLTYPE_CHAR};
+static int FITS_TRANSPOSE;
 
 int read_vectors (int argc, char **argv) {
@@ -34 +35 @@
 
   char *buffer = NULL;
+
+  FITS_TRANSPOSE = FALSE;
+  if ((Narg = get_argument (argc, argv, "-transpose"))) {
+    remove_argument (Narg, &argc, argv);
+    FITS_TRANSPOSE = TRUE;
+  }
 
   /* auto-sense table type */
@@ -410 +417 @@
     }
         
-    // define the multifield vector names
-    ALLOCATE (vec, Vector *, Nval);
-    for (j = 0; j < Nval; j++) {
-      if (Nval == 1) 
-        sprintf (name, "%s", argv[i]);
-      else
-        sprintf (name, "%s:%d", argv[i], j);
-      if ((vec[j] = SelectVector (name, ANYVECTOR, TRUE)) == NULL) ESCAPE ("bad vector name");
-      ResetVector (vec[j], vecType, Ny);
-    }
-
-    if (!strcmp (type, "char")) {
-      char *Ptr = data;
+    if (!FITS_TRANSPOSE) {
+      // define the multifield vector names (Nval vectors x Ny elements)
+      ALLOCATE (vec, Vector *, Nval);
+      for (j = 0; j < Nval; j++) {
+        if (Nval == 1) 
+          sprintf (name, "%s", argv[i]);
+        else
+          sprintf (name, "%s:%d", argv[i], j);
+        if ((vec[j] = SelectVector (name, ANYVECTOR, TRUE)) == NULL) ESCAPE ("bad vector name");
+        ResetVector (vec[j], vecType, Ny);
+      }
+
+      if (!strcmp (type, "char")) {
+        char *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Int[j] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "short")) {
+        short *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Int[j] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "int")) {
+        int *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Int[j] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "int64_t")) {
+        int64_t *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Int[j] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "float")) {
+        float *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Flt[j] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "double")) {
+        double *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[k][0].elements.Flt[j] = *Ptr;
+          }
+        }
+      }
+    } else {
+      // define the multifield vector names (Ny vectors x Nval elements)
+      ALLOCATE (vec, Vector *, Ny);
       for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Int[j] = *Ptr;
-        }
-      }
-    }
-    if (!strcmp (type, "short")) {
-      short *Ptr = data;
-      for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Int[j] = *Ptr;
-        }
-      }
-    }
-    if (!strcmp (type, "int")) {
-      int *Ptr = data;
-      for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Int[j] = *Ptr;
-        }
-      }
-    }
-    if (!strcmp (type, "int64_t")) {
-      int64_t *Ptr = data;
-      for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Int[j] = *Ptr;
-        }
-      }
-    }
-    if (!strcmp (type, "float")) {
-      float *Ptr = data;
-      for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Flt[j] = *Ptr;
-        }
-      }
-    }
-    if (!strcmp (type, "double")) {
-      double *Ptr = data;
-      for (j = 0; j < Ny; j++) {
-        for (k = 0; k < Nval; k++, Ptr++) {
-          vec[k][0].elements.Flt[j] = *Ptr;
+        if (Ny == 1) 
+          sprintf (name, "%s", argv[i]);
+        else
+          sprintf (name, "%s:%d", argv[i], j);
+        if ((vec[j] = SelectVector (name, ANYVECTOR, TRUE)) == NULL) ESCAPE ("bad vector name");
+        ResetVector (vec[j], vecType, Nval);
+      }
+
+      if (!strcmp (type, "char")) {
+        char *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Int[k] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "short")) {
+        short *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Int[k] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "int")) {
+        int *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Int[k] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "int64_t")) {
+        int64_t *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Int[k] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "float")) {
+        float *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Flt[k] = *Ptr;
+          }
+        }
+      }
+      if (!strcmp (type, "double")) {
+        double *Ptr = data;
+        for (j = 0; j < Ny; j++) {
+          for (k = 0; k < Nval; k++, Ptr++) {
+            vec[j][0].elements.Flt[k] = *Ptr;
+          }
         }
       }

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/rebin.c

@@ -133 +133 @@
               *Vout += *Vin;
               if (Normalize) {(*Vn) ++;}
+              // if ((i == 1) && (j == 1)) fprintf (stderr, "%d,%d : %d,%d : %f : %f : %d\n", i, j, x, y, *Vin, *Vout, *Vn);
             }
             if (Normalize) {Vn ++;}

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/vellipse.c

@@ -228 +228 @@
  */
 
+// XXX NOTE that PHI is defined with the wrong sign, should fix this...
 opihi_flt fellipseOD (opihi_flt alpha, opihi_flt *par, int Npar, opihi_flt *dpar) {
   

branches/eam_branches/ps2-tc3-20130727/Ohana/src/opihi/cmd.data/vgauss.c

@@ -48 +48 @@
   if ((ovec = SelectVector (argv[4], ANYVECTOR, TRUE)) == NULL) return (FALSE);
 
+  CastVector (xvec, OPIHI_FLT);
+  CastVector (yvec, OPIHI_FLT);
+
   int Nsvec = strlen(argv[3]);
 
@@ -69 +72 @@
   }
 
-  CastVector (xvec, OPIHI_FLT);
-  CastVector (yvec, OPIHI_FLT);
   CastVector (svec, OPIHI_FLT);
   // XXX Cast is failing.