Index: trunk/psModules/src/imcombine/pmStackReject.c
===================================================================
--- trunk/psModules/src/imcombine/pmStackReject.c	(revision 16479)
+++ trunk/psModules/src/imcombine/pmStackReject.c	(revision 16604)
@@ -25,5 +25,6 @@
     int numRegions = regions->n;        // Number of regions
     int numCols = 0, numRows = 0;       // Size of original image
-    int minCols = INT_MAX, minRows = INT_MAX; // Minimum coordinate for image --- should be 0,0
+    int minCols = INT_MAX, minRows = INT_MAX; // Minimum coordinate for image
+    int size = 0;                       // Size of kernel
     for (int i = 0; i < numRegions; i++) {
         psRegion *region = regions->data[i]; // Region of interest
@@ -46,4 +47,5 @@
         return NULL;
     }
+    psTrace("psModules.imcombine", 1, "Rejecting [%d:%d,%d:%d]\n", minCols, numCols, minRows, numRows);
 
     psImage *mask = psPixelsToMask(NULL, in, psRegionSet(0, numCols, 0, numRows), 0x01); // Mask image
@@ -56,6 +58,12 @@
     inRO->image = image;
     for (int i = 0; i < numRegions; i++) {
-        psRegion *region = regions->data[i]; // Region of interest
-        if (!pmSubtractionConvolve(convRO, NULL, inRO, NULL, NULL, 0, region, kernels, true)) {
+        psRegion *region = subRegions->data[i]; // Region of interest
+        if (valid && (region->x0 > valid->x1 || region->x1 < valid->x0 ||
+                      region->y0 > valid->y1 || region->y1 < valid->y0)) {
+            // Region is outside of our sub-image
+            continue;
+        }
+        pmSubtractionKernels *kernel = kernels->data[i]; // Kernel of interest
+        if (!pmSubtractionConvolve(convRO, NULL, inRO, NULL, NULL, 0, region, kernel, false, true)) {
             psError(PS_ERR_UNKNOWN, false, "Unable to convolve mask image in region %d.", i);
             psFree(convRO);
@@ -94,8 +102,9 @@
     // Threshold the convolved image
     psPixels *bad = psPixelsAllocEmpty(PIXEL_LIST_BUFFER); // List of pixels that should be masked
-    for (int y = 0; y < numRows; y++) {
-        for (int x = 0; x < numCols; x++) {
+    for (int y = size; y < convolved->numRows - size; y++) {
+        for (int x = size; x < convolved->numCols - size; x++) {
             if (convolved->data.F32[y][x] > threshold) {
-                bad = psPixelsAdd(bad, PIXEL_LIST_BUFFER, x, y);
+                // Pixel coordinates in "bad" correspond to the full image
+                bad = psPixelsAdd(bad, PIXEL_LIST_BUFFER, x + minCols, y + minRows);
             }
         }
@@ -103,14 +112,14 @@
     psFree(convolved);
 
-    // Now, we want to convolve the original pixels properly
-    mask = psPixelsToMask(NULL, bad, psRegionSet(0, numCols, 0, numRows), 0xff);
-    int size = kernels->size;           // Size of kernels
+    // Now, grow the mask to include everything that touches a bad pixel in the convolution
+    int x0 = minCols, y0 = minRows;     // Offset for mask image
+    mask = psPixelsToMask(NULL, bad, psRegionSet(x0, numCols - 1, y0, numRows - 1), 0xff);
     for (int i = 0; i < bad->n; i++) {
-        int xPix = bad->data[i].x, yPix = bad->data[i].y; // Coordinates of interest
+        int xPix = bad->data[i].x - x0, yPix = bad->data[i].y - y0; // Coordinates in frame of mask image
         // Convolution limits
         int xMin = PS_MAX(xPix - size, 0);
-        int xMax = PS_MIN(xPix + size, numCols - 1);
+        int xMax = PS_MIN(xPix + size, mask->numCols - 1);
         int yMin = PS_MAX(yPix - size, 0);
-        int yMax = PS_MIN(yPix + size, numRows - 1);
+        int yMax = PS_MIN(yPix + size, mask->numRows - 1);
         for (int y = yMin; y <= yMax; y++) {
             for (int x = xMin; x <= xMax; x++) {
@@ -119,8 +128,20 @@
         }
     }
-
     bad = psPixelsFromMask(bad, mask, 0xff);
     psFree(mask);
 
+    // Convert coordinates to frame of original image
+    for (int i = 0; i < bad->n; i++) {
+        int x = bad->data[i].x + x0;
+        int y = bad->data[i].y + y0;
+        if (x < 0 || x >= numCols || y < 0 || y >= numRows) {
+            psWarning("Bad pixel coordinate %d: %d,%d --- ignored.",
+                      i, x, y);
+            continue;
+        }
+        bad->data[i].x = x;
+        bad->data[i].y = y;
+    }
+
     return bad;
 }