Index: branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl
===================================================================
--- branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl	(revision 34781)
+++ branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl	(revision 34785)
@@ -30,5 +30,6 @@
 	   'verbose'         => \$verbose,     # verbose commands
 	   'logfile=s'       => \$logfile,     # destination for stdout and stderr  
-	   'save_temps'      => \$save_temps   # save temporary files.
+	   'save_temps'      => \$save_temps,  # save temporary files.
+	   'dbname=s'        => \$dbname       # database name
     ) or pod2usage ( 2 );
 
Index: branches/czw_branch/20120906/ippTools/share/stacktool_tobkg.sql
===================================================================
--- branches/czw_branch/20120906/ippTools/share/stacktool_tobkg.sql	(revision 34785)
+++ branches/czw_branch/20120906/ippTools/share/stacktool_tobkg.sql	(revision 34785)
@@ -0,0 +1,29 @@
+SELECT
+    stackRun.stack_id,
+    stackRun.tess_id,
+    stackRun.skycell_id,
+    stackRun.workdir,
+    stackRun.reduction,
+    stackRun.label,
+    stackRun.state,
+    stackSumSkyfile.path_base,
+    rawExp.camera,
+    IFNULL(Label.priority, 10000) AS priority
+FROM stackRun
+JOIN stackInputSkyfile USING(stack_id)
+JOIN warpRun USING(warp_id)
+JOIN warpSkyfile USING(warp_id,skycell_id)
+JOIN fakeRun USING(fake_id)
+JOIN camRun USING(cam_id)
+JOIN chipRun USING(chip_id)
+JOIN rawExp USING(exp_id)
+LEFT JOIN stackSumSkyfile USING(stack_id)
+LEFT JOIN Label ON Label.label = stackRun.label
+WHERE
+    ((stackRun.state = 'full' AND stackSumSkyfile.fault = 0 AND stackSumSkyfile.quality = 0 AND stackSumSkyfile.background_model != 1))
+    AND (Label.active OR Label.active IS NULL)
+    -- WHERE hook %s
+GROUP BY stack_id
+HAVING (SUM(IF(warpRun.state = 'full', 1, 0)) = COUNT(stackInputSkyfile.warp_id) AND
+        SUM(IF(warpSkyfile.background_model = 1, 1, 0)) = COUNT(stackInputSkyfile.warp_id))
+
Index: branches/czw_branch/20120906/ppStack/src/ppStackCombineAlternate.c
===================================================================
--- branches/czw_branch/20120906/ppStack/src/ppStackCombineAlternate.c	(revision 34785)
+++ branches/czw_branch/20120906/ppStack/src/ppStackCombineAlternate.c	(revision 34785)
@@ -0,0 +1,115 @@
+#include "ppStack.h"
+
+// This is the doomsday switch.
+// #define TESTING                         // Enable test output
+bool ppStackCombineMedian(ppStackThreadData *stack, ppStackOptions *options, pmConfig *config)
+{
+  psAssert(stack, "Require stack");
+  psAssert(options, "Require options");
+  psAssert(config, "Require configuration");
+
+  psTimerStart("PPSTACK_BKGMED");
+
+
+  pmReadout *outRO = options->outRO;
+  
+  psArray *inputs  = psArrayAlloc(options->num);
+  for (int i = 0; i < options->num; i++) {
+    ppStackFileActivationSingle(config, PPSTACK_FILES_MEDIAN_IN, true, i);
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPSTACK.INPUT", i);
+    pmFPAview *view = ppStackFilesIterateDown(config);
+    pmReadout *ro = pmFPAviewThisReadout(view,file->fpa);
+    inputs->data[i] = ro;
+    pmFPAfileClose(file,view);
+  }
+  if (!pmStackSimpleMedianCombine(outRO,inputs)) {
+    psFree(inputs);
+    return(false);
+  }
+#if 0
+  if (!ppStackWriteImage("/tmp/test_forced.median.fits",
+			 outRO->parent->parent->parent->hdu->header,
+			 outRO->image,
+			 config)) {
+    fprintf(stderr,"Failed to write image because fail.\n");
+  }
+#endif
+  for (int i = 0; i < options->num; i++) {
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPSTACK.INPUT", i);
+    pmFPAview *view = ppStackFilesIterateDown(config);
+    bool success = pmFPAfileClose(file,view);
+    if (!success) {
+      psTrace("ppStack",5,"I failed at closing a file.\n");
+    }
+	      
+    psFitsClose(file->fits);
+    file->fits = NULL;
+    file->header = NULL;
+    file->state = PM_FPA_STATE_CLOSED;
+    file->wrote_phu = false;
+    ppStackFileActivationSingle(config, PPSTACK_FILES_MEDIAN_IN, false, i);
+  }
+  psFree(inputs);
+  outRO->data_exists = true;
+  outRO->parent->data_exists = true;
+  outRO->parent->parent->data_exists = true;
+  
+  return(true);
+}
+  
+
+bool ppStackCombineBackground(ppStackThreadData *stack, ppStackOptions *options, pmConfig *config)
+{
+  psAssert(stack, "Require stack");
+  psAssert(options, "Require options");
+  psAssert(config, "Require configuration");
+
+  psTimerStart("PPSTACK_BKGMED");
+
+
+  pmReadout *bkgRO = options->bkgRO;
+  
+  psArray *inputs  = psArrayAlloc(options->num);
+  for (int i = 0; i < options->num; i++) {
+    ppStackFileActivationSingle(config, PPSTACK_FILES_BKG, true, i);
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPSTACK.INPUT.BKGMODEL", i);
+    pmFPAview *view = ppStackFilesIterateDown(config);
+    pmReadout *ro = pmFPAviewThisReadout(view,file->fpa);
+    inputs->data[i] = ro;
+    pmFPAfileClose(file,view);
+  }
+  if (!pmStackSimpleMedianCombine(bkgRO,inputs)) {
+    psFree(inputs);
+    return(false);
+  }
+#if 0
+  if (!ppStackWriteImage("/tmp/test_forced.bkgmdl.fits",
+			 bkgRO->parent->parent->parent->hdu->header,
+			 bkgRO->image,
+			 config)) {
+    fprintf(stderr,"Failed to write image because fail.\n");
+  }
+#endif
+  for (int i = 0; i < options->num; i++) {
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPSTACK.INPUT.BKGMODEL", i);
+    pmFPAview *view = ppStackFilesIterateDown(config);
+    bool success = pmFPAfileClose(file,view);
+    if (!success) {
+      psTrace("ppStack",5,"I failed at closing a file.\n");
+    }
+	      
+    psFitsClose(file->fits);
+    file->fits = NULL;
+    file->header = NULL;
+    file->state = PM_FPA_STATE_CLOSED;
+    file->wrote_phu = false;
+    ppStackFileActivationSingle(config, PPSTACK_FILES_BKG, false, i);
+  }
+  psFree(inputs);
+  bkgRO->data_exists = true;
+  bkgRO->parent->data_exists = true;
+  bkgRO->parent->parent->data_exists = true;
+  
+  return(true);
+}
+  
Index: branches/czw_branch/20120906/ppStack/src/ppStackMedian.c
===================================================================
--- branches/czw_branch/20120906/ppStack/src/ppStackMedian.c	(revision 34785)
+++ branches/czw_branch/20120906/ppStack/src/ppStackMedian.c	(revision 34785)
@@ -0,0 +1,51 @@
+#include "ppStack.h"
+
+int main(int argc, char *argv[])
+{
+    psLibInit(NULL);
+    psTimerStart("PPSTACK");
+    psTimerStart("PPSTACK_STEPS");
+
+    pmErrorRegister();
+    ppStackErrorRegister();
+    psphotErrorRegister();
+
+    ppStackOptions *options = NULL;                               // Options for stacking
+
+    pmConfig *config = pmConfigRead(&argc, argv, PPSTACK_RECIPE); // Configuration
+    if (!config) {
+	ppStackCleanup(config, options);
+    }
+
+    ppStackVersionPrint();
+
+    if (!pmModelClassInit()) {
+        psError(PPSTACK_ERR_PROG, false, "Unable to initialise model classes.");
+	ppStackCleanup(config, options);
+    }
+
+    if (!psphotInit()) {
+        psError(PPSTACK_ERR_PROG, false, "Error initialising psphot.");
+	ppStackCleanup(config, options);
+    }
+
+    if (!ppStackArgumentsSetup(argc, argv, config)) {
+	ppStackCleanup(config, options);
+    }
+
+    if (!ppStackCamera(config)) {
+	ppStackCleanup(config, options);
+    }
+
+    if (!ppStackArgumentsParse(config)) {
+	ppStackCleanup(config, options);
+    }
+
+    options = ppStackOptionsAlloc();
+    if (!ppStackMedianLoop(config, options)) {
+	ppStackCleanup(config, options);
+    }
+
+    ppStackCleanup(config, options);
+}
+
Index: branches/czw_branch/20120906/ppStack/src/ppStackMedianLoop.c
===================================================================
--- branches/czw_branch/20120906/ppStack/src/ppStackMedianLoop.c	(revision 34785)
+++ branches/czw_branch/20120906/ppStack/src/ppStackMedianLoop.c	(revision 34785)
@@ -0,0 +1,204 @@
+#include "ppStack.h"
+
+// static functions are defined below
+/* static int stackSummary(const ppStackOptions *options, const char *place); */
+
+bool ppStackMedianLoop(pmConfig *config, ppStackOptions *options)
+{
+    assert(config);
+
+    psTimerStart("PPSTACK_TOTAL");
+    psTimerStart("PPSTACK_STEPS");
+
+    // Setup
+    psTrace("ppStack", 1, "Setup....\n");
+    if (!ppStackSetup(options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to setup.");
+        return false;
+    }
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 0: Setup: %f sec", psTimerClear("PPSTACK_STEPS"));
+    ppStackMemDump("setup");
+
+    // Duplicate code that is in ppStackConvolve
+    options->cells = psArrayAlloc(options->num); // Cells for convolved images --- a handle for reading again
+    pmFPAview *view = ppStackFilesIterateDown(config);
+    for (int i = 0; i < options->num; i++) {
+      ppStackFileActivationSingle(config, PPSTACK_FILES_MEDIAN_IN, true, i);
+      pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPSTACK.INPUT", i); // File of interest
+
+      //      pmFPAview *view = pmFPAviewAlloc(0);// Pointer into FPA hierarchy
+      if (!view) {
+	return false;
+      }
+      pmReadout *readout = pmFPAviewThisReadout(view, file->fpa); // Input readout
+      pmCell *inCell = readout->parent; // Input cell */
+      options->cells->data[i] = psMemIncrRefCounter(inCell);
+
+    }
+    psFree(view);
+    
+    ppStackThreadData *stack = ppStackThreadDataSetup(options, config, options->convolve);
+    if (!stack) {
+      psError(psErrorCodeLast(), false, "Unable to initialise stack threads.");
+      return false;
+    }
+    
+    // Preparation for stacking
+    if (!ppStackCombinePrepare("PPSTACK.OUTPUT",NULL,NULL,PPSTACK_FILES_MEDIAN_OUT,stack,options,config)) {
+      psError(psErrorCodeLast(), false, "Unabel to combine data.");
+      psFree(stack);
+      return false;
+    }
+      
+    if (!ppStackCombineMedian(stack, options, config)) {
+      psError(psErrorCodeLast(), false, "Unabel to combine data.");
+      psFree(stack);
+      return false;
+    }
+/*     for (int x = 0; x < options->outRO->image->numCols; x++) { */
+/*       for (int y = 0; y < options->outRO->image->numRows; y++) { */
+/* 	options->outRO->mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] = 0; */
+/*       } */
+/*     } */
+    psFree(options->outRO->mask);
+    // Do this before performing photometry so that the cmf header gets all of the information.
+    options->zpInput = NULL;
+    options->expTimeInput = NULL;
+    options->airmassInput = NULL;
+    if (!ppStackUpdateHeader(stack, options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to update header.");
+        psFree(stack);
+        return false;
+    }
+/*     // Generate median background stack here. */
+/*     if (!ppStackCombineBackground(stack, options, config)) { */
+/*       psError(psErrorCodeLast(), false, "Unable to generate median of background images."); */
+/*       psFree(stack); */
+/*       return false; */
+/*     } */
+//    ppStackFileActivation(config,PPSTACK_FILES_BKG ,false);    
+/*     // Photometry */
+/*     psTrace("ppStack", 1, "Photometering stacked image....\n"); */
+/*     if (!ppStackPhotometry(options, config)) { */
+/*         psError(psErrorCodeLast(), false, "Unable to perform photometry."); */
+/*         return false; */
+/*     } */
+/*     psLogMsg("ppStack", PS_LOG_INFO, "Stage 6: Photometry Analysis: %f sec", psTimerClear("PPSTACK_STEPS")); */
+/*     ppStackMemDump("photometry"); */
+
+    // Create JPEGS
+/*     if (!ppStackJPEGs(stack, options, config)) { */
+/*         psError(psErrorCodeLast(), false, "Unable to make jpegs."); */
+/*         psFree(stack); */
+/*         return false; */
+/*     } */
+/*     // Assemble Stats */
+/*     if (!ppStackStats(stack, options, config)) { */
+/*         psError(psErrorCodeLast(), false, "Unable to assemble statistics."); */
+/*         psFree(stack); */
+/*         return false; */
+/*     } */
+
+   // Clean up
+    
+    psTrace("ppStack", 2, "Cleaning up after combination....\n");
+    if (!ppStackCleanupFiles(stack, options, config, PPSTACK_FILES_MEDIAN_OUT, PPSTACK_FILES_MEDIAN_OUT, false)) {
+        psError(psErrorCodeLast(), false, "Unable to clean up.");
+        psFree(stack);
+        return false;
+    }
+    //    psFree(stack);
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 7: Cleanup, WCS & JPEGS: %f sec", psTimerClear("PPSTACK_STEPS"));
+    ppStackMemDump("cleanup");
+
+/*     // Unconvolved stack --- it's cheap to calculate, compared to everything else! */
+/*     // XXX unconvolved stack is currently using the convolved mask!  oops! */
+/*     if (options->convolve) { */
+/*         // Start threading */
+/*         ppStackThreadData *stack = ppStackThreadDataSetup(options, config, false); */
+/*         if (!stack) { */
+/*             psError(psErrorCodeLast(), false, "Unable to initialise stack threads."); */
+/*             return false; */
+/*         } */
+
+/*         // Prepare for combination */
+/*         if (!ppStackCombinePrepare("PPSTACK.UNCONV", "PPSTACK.UNCONV.EXP", NULL, PPSTACK_FILES_UNCONV, */
+/*                                    stack, options, config)) { */
+/*             psError(psErrorCodeLast(), false, "Unable to prepare for combination."); */
+/*             psFree(stack); */
+/*             return false; */
+/*         } */
+
+/* 	// generate the unconvolved stack. NOTE: this one must be normalized since the inputs have not been */
+/*         psTrace("ppStack", 2, "Stack of unconvolved images....\n"); */
+/*         if (!ppStackCombineFinal(stack, options->origCovars, options, config, false, true, false)) { */
+/*             psError(psErrorCodeLast(), false, "Unable to perform unconvolved combination."); */
+/*             psFree(stack); */
+/*             return false; */
+/*         } */
+/*         psLogMsg("ppStack", PS_LOG_INFO, "Stage 8: Unconvolved Stack: %f sec", psTimerClear("PPSTACK_STEPS")); */
+/*         ppStackMemDump("unconv"); */
+
+/* 	// Update Header */
+/* 	if (!ppStackUpdateHeader(stack, options, config)) { */
+/* 	    psError(psErrorCodeLast(), false, "Unable to update header."); */
+/* 	    psFree(stack); */
+/* 	    return false; */
+/* 	} */
+/* 	// Clean up unconvolved stack */
+/* 	psTrace("ppStack", 2, "Cleaning up after unconvolved stack....\n"); */
+/* 	if (!ppStackCleanupFiles(stack, options, config, PPSTACK_FILES_UNCONV, PPSTACK_FILES_NONE, false)) { */
+/* 	    psError(psErrorCodeLast(), false, "Unable to clean up."); */
+/* 	    psFree(stack); */
+/* 	    return false; */
+/* 	} */
+/* 	psFree(stack); */
+/*     } */
+    psFree(options->cells); options->cells = NULL;
+
+    // Finish up
+    psTrace("ppStack", 1, "Finishing up....\n");
+    if (!ppStackFinish(options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to finish up.");
+        return false;
+    }
+    ppStackMemDump("finish");
+
+    return true;
+}
+
+/* /// Print a summary of the inputs, and return the number of good inputs */
+/* static int stackSummary(const ppStackOptions *options, const char *place) */
+/* { */
+/*     int numGood = 0;                // Number of good inputs */
+/*     psString summary = NULL;        // Summary of images */
+/*     for (int i = 0; i < options->num; i++) { */
+/*         psString reason = NULL;         // Reason for rejecting */
+/*         if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] == 0) { */
+/*             psStringAppend(&reason, " Good."); */
+/*             numGood++; */
+/*         } else { */
+/*             if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PPSTACK_MASK_CAL) { */
+/*                 psStringAppend(&reason, " Calibration failed."); */
+/*             } */
+/*             if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PPSTACK_MASK_PSF) { */
+/*                 psStringAppend(&reason, " PSF measurement failed."); */
+/*             } */
+/*             if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PPSTACK_MASK_MATCH) { */
+/*                 psStringAppend(&reason, " PSF matching failed."); */
+/*             } */
+/*             if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PPSTACK_MASK_CHI2) { */
+/*                 psStringAppend(&reason, " PSF matching chi^2 deviant."); */
+/*             } */
+/*             if (options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PPSTACK_MASK_REJECT) { */
+/*                 psStringAppend(&reason, " Rejection exceeded threshold."); */
+/*             } */
+/*         } */
+/*         psStringAppend(&summary, "Image %d: %s\n", i, reason); */
+/*         psFree(reason); */
+/*     } */
+/*     psLogMsg("ppStack", PS_LOG_INFO, "Summary of images for %s:\n%s", place, summary); */
+/*     psFree(summary); */
+
+/*     return numGood; */
+/* } */