Index: trunk/ppSub/src/ppSubReadoutSubtract.c
===================================================================
--- trunk/ppSub/src/ppSubReadoutSubtract.c	(revision 31435)
+++ trunk/ppSub/src/ppSubReadoutSubtract.c	(revision 41382)
@@ -33,4 +33,5 @@
     bool noConvolve = psMetadataLookupBool(&mdok, recipe, "NOCONVOLVE"); // Do not use convolved images.
     bool addPair = psMetadataLookupBool(&mdok, recipe, "ADD.NOT.SUBTRACT"); // add instead of subtracting
+    bool doApplyMaskNaN = psMetadataLookupBool(&mdok, recipe, "APPLY.PIXELNAN"); // NaN the pixels underneath masks
 
     pmFPAview *view = ppSubViewReadout(); // View to readout
@@ -73,9 +74,11 @@
     // NAN the masked pixels in the diff image (pixels masked in A are not yet NAN'ed in B)
     psImageMaskType maskVal = pmConfigMaskGet("MASK.VALUE", config) | pmConfigMaskGet("BLANK", config); // Bits to mask in inputs
-    for (int iy = 0; iy < outRO->image->numRows; iy++) {
+    if(doApplyMaskNaN) {
+      for (int iy = 0; iy < outRO->image->numRows; iy++) {
 	for (int ix = 0; ix < outRO->image->numCols; ix++) {
 	    if ((outRO->mask->data.PS_TYPE_IMAGE_MASK_DATA[iy][ix] & maskVal) == 0) continue;
 	    outRO->image->data.F32[iy][ix] = NAN;
 	}
+      }
     }