Index: trunk/ppMerge/src/ppMergeReadChunk.c
===================================================================
--- trunk/ppMerge/src/ppMergeReadChunk.c	(revision 18757)
+++ trunk/ppMerge/src/ppMergeReadChunk.c	(revision 18839)
@@ -1,11 +1,14 @@
 # include "ppMerge.h"
 
-ppMergeFileGroup *ppMergeReadChunk (psArray *fileGroups, pmConfig *config, int numChunk) {
+ppMergeFileGroup *ppMergeReadChunk (bool *status, psArray *fileGroups, pmConfig *config, int numChunk) {
+
+    *status = true;
+
+    bool mdok;
+    bool haveMasks = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.MASKS"); // Do we have masks?
+    bool haveWeights = psMetadataLookupBool(&mdok, config->arguments, "INPUTS.WEIGHTS"); // Do we have weights?
+    int rows = psMetadataLookupS32(NULL, config->arguments, "ROWS"); // Number of rows to read per chunk
 
     // select an available fileGroup
- 
-    bool haveMasks = psMetadataLookupBool(&mdok, arguments, "INPUTS.MASKS"); // Do we have masks?
-    bool haveWeights = psMetadataLookupBool(&mdok, arguments, "INPUTS.WEIGHTS"); // Do we have weights?
-
     while (1) {
 	// check for any fileGroups which can read data
@@ -14,5 +17,16 @@
 	    if (fileGroup->read) continue;
 
+	    // find max last scan so far
+	    int lastScan = 0;
+	    for (int i = 0; i < fileGroups->n; i++) {
+		ppMergeFileGroup *fileGroup = fileGroups->data[i];
+		lastScan = PS_MAX (fileGroup->lastScan, lastScan);
+	    }
+	    fileGroup->firstScan = lastScan;
+	    fileGroup->lastScan = lastScan + rows;
+
 	    psArray *readouts = fileGroup->readouts;
+
+	    psTimerStart ("ppMergeReadChunk");
 
 	    psTrace("ppStack", 2, "Reading data for chunk %d into fileGroup %d....n", numChunk, j);
@@ -20,27 +34,46 @@
 		pmReadout *inRO = readouts->data[i]; // Input readout
 
+		// override the recorded last scan
+		inRO->thisImageScan  = fileGroup->firstScan;
+		inRO->thisWeightScan = fileGroup->firstScan;
+		inRO->thisMaskScan   = fileGroup->firstScan;
+
 		// Read a chunk from a file
 		pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i); 
-		if (!pmReadoutReadChunk(inRO, file->fits, 0, rows, 0, config)) { 
-		    psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT %d", numChunk, i);
-		    return NULL;
-		}							
 
-		if (haveMasks) {
-		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.MASK", i); 
-		    if (!pmReadoutReadChunkMask(inRO, file->fits, 0, rows, 0, config)) { 
-			psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT.MASK %d", numChunk, NAME, i);
+		bool keepReading = false;
+		if (pmReadoutMore(inRO, file->fits, 0, rows, config)) {
+		    keepReading = true;
+		    if (!pmReadoutReadChunk(inRO, file->fits, 0, rows, 0, config)) { 
+			psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT %d", numChunk, i);
+			*status = false;
 			return NULL;
 		    }							
 		}
 
-		if (haveWeights) {
-		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", i); 
-		    if (!pmReadoutReadChunkWeight(inRO, file->fits, 0, rows, 0, config)) {
-			psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT.WEIGHT %d", numChunk, NAME, i);
+		if (haveMasks && pmReadoutMoreMask(inRO, file->fits, 0, rows, config)) {
+		    keepReading = true;
+		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.MASK", i); 
+		    if (!pmReadoutReadChunkMask(inRO, file->fits, 0, rows, 0, config)) { 
+			psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT.MASK %d", numChunk, i);
+			*status = false;
 			return NULL;
 		    }							
 		}
+
+		if (haveWeights && pmReadoutMoreWeight(inRO, file->fits, 0, rows, config)) {
+		    keepReading = true;
+		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", i); 
+		    if (!pmReadoutReadChunkWeight(inRO, file->fits, 0, rows, 0, config)) {
+			psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPMERGE.INPUT.WEIGHT %d", numChunk, i);
+			*status = false;
+			return NULL;
+		    }							
+		}
+		if (!keepReading) {
+		    return NULL;
+		}
 	    }
+
 	    fileGroup->read = fileGroup->busy = true;
 	    return fileGroup;
@@ -48,32 +81,11 @@
 
 	// check for any fileGroups which are done processing
-	bool wait = true;
-	bool more = true;
+	bool wait = false;
 	for (int j = 0; j < fileGroups->n; j++) {
 	    ppMergeFileGroup *fileGroup = fileGroups->data[j];
 	    if (!fileGroup->read || fileGroup->busy) continue;
-	    
-	    wait = false;
-	    psArray *readouts = fileGroup->readouts;
-	    // any more data to be read?
-	    for (int i = 0; i < readouts->n && more; i++) {
-		pmReadout *inRO = readouts->data[i];
-
-		pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i);
-		more &= pmReadoutMore(inRO, file->fits, 0, rows, config);
-
-		if (haveMasks) {
-		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.MASK", i);
-		    more &= pmReadoutMoreMask(inRO, file->fits, 0, rows, config);
-		}
-		if (haveWeights) {
-		    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT.WEIGHT", i);
-		    more &= pmReadoutMoreWeight(inRO, file->fits, 0, rows, config);
-		}
-	    }
 	    fileGroup->read = false;
+	    wait = true;
 	}
-	if (!more) return NULL;
-
 	if (wait) usleep (10000);
     }