Index: trunk/psastro/src/psastroMaskUpdates.c
===================================================================
--- trunk/psastro/src/psastroMaskUpdates.c	(revision 23665)
+++ trunk/psastro/src/psastroMaskUpdates.c	(revision 23810)
@@ -19,14 +19,4 @@
 }
 
-pmCell *pmCellInChip (pmChip *chip, float x, float y);
-bool pmCellCoordsForChip (float *xCell, float *yCell, pmCell *cell, float xChip, float yChip);
-bool pmChipCoordsForCell (float *xChip, float *yChip, pmCell *cell, float xCell, float yCell);
-
-bool psastroMaskCircle (psImage *mask, psImageMaskType value, float x0, float y0, float dX, float dY);
-bool psastroMaskBox (psImage *mask, psImageMaskType value, float x0, float y0, float dL, float dW, float theta);
-void psastroMaskLine (psImage *mask, psImageMaskType value, double x1, double y1, double x2, double y2, int dW);
-void psastroMaskLineBresen (psImage *mask, psImageMaskType value, int X1, int Y1, int X2, int Y2, int dW, int swapcoords);
-void psastroMaskRectangle (psImage *mask, psImageMaskType value, int x0, int y0, int x1, int y1);
-
 /**
  * create a mask or mask regions based on the collection of reference stars that * are in the vicinity of each chip
@@ -40,5 +30,7 @@
     float zeropt, exptime;
 
-    psImageMaskType maskValue  = pmConfigMaskGet("GHOST", config); // Mask value for ghost pixels
+    psImageMaskType ghostMaskValue = pmConfigMaskGet("GHOST", config); // Mask value for ghost pixels
+    psImageMaskType spikeMaskValue = pmConfigMaskGet("SPIKE", config); // Mask value for ghost pixels
+    psImageMaskType starMaskValue  = pmConfigMaskGet("STARCORE", config); // Mask value for ghost pixels
 
     // psImageMaskType maskBlank  = pmConfigMaskGet("BLANK", config); // Mask value for blank pixels
@@ -55,7 +47,12 @@
     if (!REFSTAR_MASK) return true;
 
+    // convert star positions to ghost positions and add to the readout->analysis data
+    if (!psastroLoadGhosts (config)) {
+        psError(PSASTRO_ERR_CONFIG, false, "Error loading ghosts");
+        return false;
+    }
+
     psLogMsg ("psastro", PS_LOG_INFO, "generating a bright-star mask");
 
-    bool REFSTAR_MASK_REGIONS              = psMetadataLookupBool (&status, recipe, "REFSTAR_MASK_REGIONS");
     bool REFSTAR_MASK_BLEED                = psMetadataLookupBool (&status, recipe, "REFSTAR_MASK_BLEED");
 
@@ -134,18 +131,4 @@
         if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
 
-        // text region files for testing
-        FILE *f = NULL;
-        if (REFSTAR_MASK_REGIONS) {
-          char *filename = NULL;
-          char *chipname = psMetadataLookupStr (&status, chip->concepts, "CHIP.NAME");
-          psStringAppend (&filename, "refstars.mask.%s.dat", chipname);
-          FILE *f = fopen (filename, "w");
-          if (!f) {
-            psWarning ("cannot create refstar mask file %s\n", filename);
-            continue;
-          }
-          psFree (filename);
-        }
-
         pmChip *refChip  = pmFPAviewThisChip (view, refMask->fpa);
 
@@ -173,9 +156,9 @@
 
             // we mask pixels on the input mask image (chip-mosaic)
-            pmCell *cellMask = pmFPAviewThisCell(view, outMask->fpa);
-            pmReadout *readoutMask = NULL;
-            if (cellMask->readouts->n) {
-                readoutMask = cellMask->readouts->data[0];
-            }
+            // pmCell *cellMask = pmFPAviewThisCell(view, outMask->fpa);
+            // pmReadout *readoutMask = NULL;
+            // if (cellMask->readouts->n) {
+            //     readoutMask = cellMask->readouts->data[0];
+            // }
 
             // process each of the readouts
@@ -184,7 +167,11 @@
                 if (! readout->data_exists) { continue; }
 
+		// XXX why not do this? 
+		pmReadout *readoutMask = pmFPAviewThisReadout (view, outMask->fpa);
+		if (!readoutMask) continue;
+
                 // select the raw objects for this readout
                 psArray *refstars = psMetadataLookupPtr (&status, readout->analysis, "PSASTRO.REFSTARS");
-                if (refstars == NULL) { continue; }
+                if (!refstars) continue;
 
                 // we need to generate the following masks regions:
@@ -204,46 +191,21 @@
                     float radius = REFSTAR_MASK_SATSTAR_MAG_SLOPE * (REFSTAR_MASK_SATSTAR_MAG_MAX - ref->Mag);
 
-                    if (REFSTAR_MASK_REGIONS) {
-                      fprintf (f, "CIRCLE %f %f  %f %f\n", ref->chip->x, ref->chip->y, radius, radius);
-                    }
-
                     // XXX for now, assume cell binning is 1x1 relative to chip
-                    if (readoutMask) {
-                        psastroMaskCircle (readoutMask->mask, maskValue, ref->chip->x, ref->chip->y, radius, radius);
-                    }
-
-                    // LINE for boundaries of the saturation spikes (scaled by magnitude)
-                    float spikeLength = REFSTAR_MASK_SATSPIKE_MAG_SLOPE * (REFSTAR_MASK_SATSPIKE_MAG_MAX - ref->Mag);
-                    float spikeWidth = 0.5*REFSTAR_MASK_SATSPIKE_WIDTH;
+		    psastroMaskCircle (readoutMask->mask, starMaskValue, ref->chip->x, ref->chip->y, radius, radius);
 
                     for (float theta = 0.0; theta < 2*M_PI; theta += M_PI / 2.0) {
-                        float x0, y0, x1, y1, dx, dy;
 
                         float Theta = theta - ROTANGLE - REFSTAR_MASK_SATSTAR_POS_ZERO;
 
-                        if (REFSTAR_MASK_REGIONS) {
-                          // lower side
-                          x0 = ref->chip->x + spikeWidth*sin(Theta);
-                          y0 = ref->chip->y - spikeWidth*cos(Theta);
-                          x1 = ref->chip->x + spikeLength*cos(Theta) + spikeWidth*sin(Theta);
-                          y1 = ref->chip->y + spikeLength*sin(Theta) - spikeWidth*cos(Theta);
-                          dx = x1 - x0;
-                          dy = y1 - y0;
-
-                          fprintf (f, "LINE %f %f  %f %f\n", x0, y0, dx, dy);
-
-                          // upper side
-                          x0 = ref->chip->x - spikeWidth*sin(Theta);
-                          y0 = ref->chip->y + spikeWidth*cos(Theta);
-                          x1 = ref->chip->x + spikeLength*cos(Theta) - spikeWidth*sin(Theta);
-                          y1 = ref->chip->y + spikeLength*sin(Theta) + spikeWidth*cos(Theta);
-                          dx = x1 - x0;
-                          dy = y1 - y0;
-                          fprintf (f, "LINE %f %f  %f %f\n", x0, y0, dx, dy);
-                        }
-
-                        if (readoutMask) {
-                            psastroMaskBox (readoutMask->mask, maskValue, ref->chip->x, ref->chip->y, spikeLength, spikeWidth, Theta);
-                        }
+			// LINE for boundaries of the saturation spikes (scaled by magnitude)
+			// float MAG_MAX = (theta == 0.0) || (theta == M_PI) ? REFSTAR_MASK_SATSPIKE_MAG_MAX1 : REFSTAR_MASK_SATSPIKE_MAG_MAX2;
+
+			float MAG_MAX = REFSTAR_MASK_SATSPIKE_MAG_MAX;
+			float spikeLength = REFSTAR_MASK_SATSPIKE_MAG_SLOPE * (MAG_MAX - ref->Mag);
+			float spikeWidth = 0.5*REFSTAR_MASK_SATSPIKE_WIDTH;
+			// XXX we can make the width depend on the spike as well...
+			// The length should also be a function of the image background level
+
+			psastroMaskBox (readoutMask->mask, spikeMaskValue, ref->chip->x, ref->chip->y, spikeLength, spikeWidth, Theta);
                     }
 
@@ -254,9 +216,5 @@
 
 			// LINE for boundaries of the bleed lines
-			if (REFSTAR_MASK_REGIONS) {
-			    fprintf (f, "LINE %f %f  %f %f\n", ref->chip->x, ref->chip->y, 0.0, -100.0);
-			}
-
-			if (readoutMask && refCell) {
+			if (refCell) {
 			    float xCell = 0.0;
 			    float yCell = 0.0;
@@ -271,12 +229,34 @@
 
 			    float width = REFSTAR_MASK_BLEED_MAG_SLOPE*(REFSTAR_MASK_BLEED_MAG_MAX - ref->Mag);
-			    psastroMaskRectangle (readoutMask->mask, maskValue, (int) ref->chip->x-0.5*width, (int) ref->chip->y, (int) ref->chip->x+0.5*width+1, yEnd);
+			    psastroMaskRectangle (readoutMask->mask, spikeMaskValue, (int) ref->chip->x-0.5*width, (int) ref->chip->y, (int) ref->chip->x+0.5*width+1, yEnd);
 			}
 		    }
                 }
+
+                // select the raw objects for this readout (loaded in psastroExtract.c)
+                psArray *ghosts = psMetadataLookupPtr (&status, readout->analysis, "PSASTRO.GHOSTS");
+                if (ghosts == NULL) { continue; }
+
+                // identify the bright stars of interest
+                for (int i = 0; i < ghosts->n; i++) {
+                    psastroGhost *ghost = ghosts->data[i];
+		    // XXX bright vs faint ghost bits? (OR with SUSPECT) 
+		    psastroMaskEllipticalAnnulus (readoutMask->mask, ghostMaskValue, ghost->chip->x, ghost->chip->y, ghost->inner, ghost->outer);
+                }
+
+		// select the raw objects for this readout, flag is they fall in a mask
+		psArray *rawstars = psMetadataLookupPtr (&status, readout->analysis, "PSASTRO.RAWSTARS");
+		if (rawstars == NULL) return false;
+		
+		// XXX finish this:
+		for (int i = 0; i < rawstars->n; i++) {
+		    pmAstromObj *raw = rawstars->data[i];
+		    psImageMaskType value = readoutMask->mask->data.PS_TYPE_IMAGE_MASK_DATA[(int)(raw->chip->x)][(int)(raw->chip->y)];
+		    if (value) continue;
+		}
             }
         }
 
-        // output sequence for mask corresponding to this chip
+        // output sequence for mask corresponding to this chip (XXX this may not be needed...)
         *viewMask = *view;
         while ((cell = pmFPAviewNextCell (viewMask, outMask->fpa, 1)) != NULL) {
@@ -290,9 +270,5 @@
             if (!pmFPAfileIOChecks (config, viewMask, PM_FPA_AFTER)) ESCAPE;
         }
-
         if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
-        if (REFSTAR_MASK_REGIONS) {
-          fclose (f);
-        }
     }
     if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
@@ -306,220 +282,2 @@
 }
 
-// XXX this is going to be very slow...
-pmCell *pmCellInChip (pmChip *chip, float x, float y) {
-
-# if (0)
-    int x0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.X0");
-    int y0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.Y0");
-    int xParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.XPARITY");
-    int yParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.YPARITY");
-
-    // XXX fix the binning : currently not selected from concepts
-    // int xBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.XBIN"); // Binning in x and y
-    // int yBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.YBIN"); // Binning in x and y
-    int xBin = 1;
-    int yBin = 1;
-
-    // Position on the cell
-    float xCell = PM_CHIP_TO_CELL(xChip, x0Cell, xParityCell, xBin);
-    float yCell = PM_CHIP_TO_CELL(yChip, y0Cell, yParityCell, yBin);
-# endif
-
-    for (int i = 0; i < chip->cells->n; i++) {
-
-        pmCell *cell = chip->cells->data[i];
-        psRegion *region = pmCellExtent (cell);
-
-        if (x < region->x0) goto skip;
-        if (x > region->x1) goto skip;
-        if (y < region->y0) goto skip;
-        if (y > region->y1) goto skip;
-
-        psFree (region);
-        return cell;
-
-    skip:
-        psFree (region);
-    }
-    return NULL;
-}
-
-/**
- * convert chip coords to cell coords, given known cell
- */
-bool pmCellCoordsForChip (float *xCell, float *yCell, pmCell *cell, float xChip, float yChip) {
-
-    int x0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.X0");
-    int y0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.Y0");
-    int xParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.XPARITY");
-    int yParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.YPARITY");
-
-    // XXX fix the binning : currently not selected from concepts
-    // int xBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.XBIN"); // Binning in x and y
-    // int yBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.YBIN"); // Binning in x and y
-    int xBin = 1;
-    int yBin = 1;
-
-    // Position on the cell
-    // ((pos)*(binning)*(cellParity) + (cell0))
-    // XXX this is probably totally wrong now....
-    // ((pos) - (cell0))*(cellParity)/(binning))
-    *xCell = (xChip - x0Cell)*xParityCell/xBin;
-    *yCell = (yChip - y0Cell)*yParityCell/yBin;
-
-    return true;
-}
-
-/**
- * convert chip coords to cell coords, given known cell
- */
-bool pmChipCoordsForCell (float *xChip, float *yChip, pmCell *cell, float xCell, float yCell) {
-
-    int x0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.X0");
-    int y0Cell = psMetadataLookupS32(NULL, cell->concepts, "CELL.Y0");
-    int xParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.XPARITY");
-    int yParityCell = psMetadataLookupS32(NULL, cell->concepts, "CELL.YPARITY");
-
-    // XXX fix the binning : currently not selected from concepts
-    // int xBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.XBIN"); // Binning in x and y
-    // int yBin = psMetadataLookupS32(NULL, cell->concepts, "CELL.YBIN"); // Binning in x and y
-    int xBin = 1;
-    int yBin = 1;
-
-    // Position on the cell
-    // ((pos)*(binning)*(cellParity) + (cell0))
-    // XXX this is probably totally wrong now....
-    // ((pos) - (cell0))*(cellParity)/(binning))
-    *xChip = xCell*xBin*xParityCell + x0Cell;
-    *yChip = yCell*yBin*yParityCell + y0Cell;
-
-    return true;
-}
-
-// XXX should be doing an OR
-bool psastroMaskCircle (psImage *mask, psImageMaskType value, float x0, float y0, float dX, float dY) {
-
-    // XXX need to worry about row0, col0
-    for (int ix = -dX; ix <= +dX; ix++) {
-        int jx = ix + x0;
-        if (jx < 0) continue;
-        if (jx >= mask->numCols) continue;
-        for (int iy = -dY; iy <= +dY; iy++) {
-            int jy = iy + y0;
-            if (jy < 0) continue;
-            if (jy >= mask->numRows) continue;
-
-            double r2 = PS_SQR(ix/dX) + PS_SQR(iy/dY);
-            if (r2 > 1.0) continue;
-
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[jy][jx] |= value;
-        }
-    }
-    return true;
-}
-
-// XXX should be doing an OR
-bool psastroMaskBox (psImage *mask, psImageMaskType value, float x0, float y0, float dL, float dW, float theta) {
-
-    // draw a series of lines (from -0.5*dW to +0.5*dW) of length dL, starting at x0, y0, angle theta
-
-    float xs = x0;
-    float ys = y0;
-
-    float xe = xs + dL*cos(theta);
-    float ye = ys + dL*sin(theta);
-
-    psastroMaskLine (mask, value, xs, ys, xe, ye, (int) dW);
-    return true;
-}
-
-/**
- * identify the quadrant and draw the correct line
- */
-void psastroMaskLine (psImage *mask, psImageMaskType value, double x1, double y1, double x2, double y2, int dW) {
-
-  int FlipDirect, FlipCoords;
-  int X1, Y1, X2, Y2, dX, dY;
-
-  /* rather than draw the line from float positions, we find the closest
-     integer end-points and draw the line between those pixels */
-
-  X1 = ROUND(x1);
-  Y1 = ROUND(y1);
-  X2 = ROUND(x2);
-  Y2 = ROUND(y2);
-
-  dX = X2 - X1;
-  dY = Y2 - Y1;
-
-  FlipCoords = (abs(dX) < abs(dY));
-  FlipDirect = FlipCoords ? (y1 > y2) : (x1 > x2);
-
-  if (!FlipDirect && !FlipCoords) psastroMaskLineBresen (mask, value, X1, Y1, X2, Y2, dW, FALSE);
-  if ( FlipDirect && !FlipCoords) psastroMaskLineBresen (mask, value, X2, Y2, X1, Y1, dW, FALSE);
-  if (!FlipDirect &&  FlipCoords) psastroMaskLineBresen (mask, value, Y1, X1, Y2, X2, dW, TRUE);
-  if ( FlipDirect &&  FlipCoords) psastroMaskLineBresen (mask, value, Y2, X2, Y1, X1, dW, TRUE);
-
-  return;
-}
-
-/**
- * use the Bresenham line drawing technique
- * integer-only Bresenham line-draw version which is fast
- */
-void psastroMaskLineBresen (psImage *mask, psImageMaskType value, int X1, int Y1, int X2, int Y2, int dW, int swapcoords) {
-
-    int X, Y, dX, dY;
-    int e, e2;
-
-    dX = X2 - X1;
-    dY = Y2 - Y1;
-
-    Y = Y1;
-    e = 0;
-    for (X = X1; X <= X2; X++) {
-        if (X > 0) {
-            if (swapcoords) {
-                if (X >= mask->numRows) continue;
-                for (int y = Y - dW; y <= Y + dW; y++) {
-                    if (y < 0) continue;
-                    if (y >= mask->numCols) continue;
-                    mask->data.PS_TYPE_IMAGE_MASK_DATA[X][y] |= value;
-                }
-            } else {
-                if (X >= mask->numCols) continue;
-                for (int y = Y - dW; y <= Y + dW; y++) {
-                    if (y < 0) continue;
-                    if (y >= mask->numRows) continue;
-                    mask->data.PS_TYPE_IMAGE_MASK_DATA[y][X] |= value;
-                }
-            }
-        }
-        e += dY;
-        e2 = 2 * e;
-        if (e2 > dX) {
-            Y++;
-            e -= dX;
-        }
-        if (e2 < -dX) {
-            Y--;
-            e += dX;
-        }
-    }
-    return;
-}
-
-void psastroMaskRectangle (psImage *mask, psImageMaskType value, int x0, int y0, int x1, int y1) {
-
-    int xs = PS_MAX (0, PS_MIN (mask->numCols, PS_MIN (x0, x1)));
-    int xe = PS_MAX (0, PS_MIN (mask->numCols, PS_MAX (x0, x1)));
-    int ys = PS_MAX (0, PS_MIN (mask->numRows, PS_MIN (y0, y1)));
-    int ye = PS_MAX (0, PS_MIN (mask->numRows, PS_MAX (y0, y1)));
-
-    for (int iy = ys; iy < ye; iy++) {
-        for (int ix = xs; ix < xe; ix++) {
-            mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] |= value;
-        }
-    }
-}
-