Index: trunk/ppStack/src/ppStackLoop.c
===================================================================
--- trunk/ppStack/src/ppStackLoop.c	(revision 29552)
+++ trunk/ppStack/src/ppStackLoop.c	(revision 30620)
@@ -1,17 +1,219 @@
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include <pslib.h>
-#include <psmodules.h>
-
 #include "ppStack.h"
-#include "ppStackLoop.h"
+
+// static functions are defined below
+static int stackSummary(const ppStackOptions *options, const char *place);
+
+bool ppStackLoop(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");
+
+    // Preparation for stacking
+    psTrace("ppStack", 1, "Preparation for stacking: merging sources, determining target PSF....\n");
+
+    if (!ppStackPrepare(options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to prepare for stacking.");
+        return false;
+    }
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 1: Load Sources and Generate Target PSF: %f sec", psTimerClear("PPSTACK_STEPS"));
+    ppStackMemDump("prepare");
+    if (options->quality) return true; // Can't do anything else
+
+    // Convolve inputs
+    psTrace("ppStack", 1, "Convolving inputs to target PSF....\n");
+    if (!ppStackConvolve(options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to convolve images.");
+        return false;
+    }
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 2: Generate Convolutions and Save: %f sec", psTimerClear("PPSTACK_STEPS"));
+    ppStackMemDump("convolve");
+    if (options->quality) return true; // Can't do anything else
+
+    // Ensure sufficient inputs
+    {
+        int numGood = stackSummary(options, "initial combination");
+        psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe
+        bool safe = psMetadataLookupBool(NULL, recipe, "SAFE"); // Be safe when combining
+        if (safe && numGood <= 1) {
+            options->quality = PPSTACK_ERR_REJECTED;
+            psErrorStackPrint(stderr, "Insufficient inputs for combination with safety on");
+            psErrorClear();
+            psWarning("Insufficient inputs for combination with safety on");
+            return true;
+        }
+    }
+
+    // Start threading
+    ppStackThreadInit();
+    ppStackThreadData *stack = ppStackThreadDataSetup(options, config, true);
+    if (!stack) {
+        psError(psErrorCodeLast(), false, "Unable to initialise stack threads.");
+        return false;
+    }
+
+    // Prepare for combination
+    if (!ppStackCombinePrepare("PPSTACK.OUTPUT", "PPSTACK.OUTPUT.EXP", PPSTACK_FILES_STACK, stack, options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to prepare for combination.");
+        psFree(stack);
+        return false;
+    }
+
+    // Initial combination
+    psTrace("ppStack", 1, "Initial stack of convolved images....\n");
+    if (!ppStackCombineInitial(stack, options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to perform initial combination.");
+        psFree(stack);
+        return false;
+    }
+    ppStackMemDump("initial");
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 3: Make Initial Stack: %f sec", psTimerClear("PPSTACK_STEPS"));
+
+    // Done with stack inputs for now
+    // XXX is this where we are leaking??
+    for (int i = 0; i < options->num; i++) {
+        pmCellFreeData(options->cells->data[i]);
+    }
+    psFree(stack);
+
+    // Pixel rejection
+    psTrace("ppStack", 1, "Reject pixels....\n");
+    if (!ppStackReject(options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to reject pixels.");
+        psFree(stack);
+        return false;
+    }
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 4: Pixel Rejection: %f sec", psTimerClear("PPSTACK_STEPS"));
+
+    // Check inputs
+    {
+        int numGood = stackSummary(options, "final combination");
+        if (numGood <= 0) {
+            options->quality = PPSTACK_ERR_REJECTED;
+            psErrorStackPrint(stderr, "Insufficient inputs survived rejection stage");
+            psErrorClear();
+            psWarning("Insufficient inputs survived rejection stage");
+            return true;
+        }
+    }
+
+    stack = ppStackThreadDataSetup(options, config, true);
+    if (!stack) {
+        psError(psErrorCodeLast(), false, "Unable to initialise stack threads.");
+        return false;
+    }
+
+    // Final combination
+    psTrace("ppStack", 2, "Final stack of convolved images....\n");
+    if (!ppStackCombineFinal(stack, options->convCovars, options, config, false, false, true)) {
+        psError(psErrorCodeLast(), false, "Unable to perform final combination.");
+        psFree(stack);
+        return false;
+    }
+    psLogMsg("ppStack", PS_LOG_INFO, "Stage 5: Final Stack: %f sec", psTimerClear("PPSTACK_STEPS"));
+    ppStackMemDump("final");
+
+    // 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");
+
+    // Update Header
+    if (!ppStackUpdateHeader(stack, options, config)) {
+        psError(psErrorCodeLast(), false, "Unable to update header.");
+        psFree(stack);
+        return false;
+    }
+    // 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_STACK, PPSTACK_FILES_PHOT, true)) {
+        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", PPSTACK_FILES_UNCONV,
+                                   stack, options, config)) {
+            psError(psErrorCodeLast(), false, "Unable to prepare for combination.");
+            psFree(stack);
+            return false;
+        }
+
+	// generate the unconvolved stack
+        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");
+
+	// 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, // Stack options, with input mask
-                        const char *place              // Place in code
-    )
+static int stackSummary(const ppStackOptions *options, const char *place)
 {
     int numGood = 0;                // Number of good inputs
@@ -47,221 +249,2 @@
     return numGood;
 }
-
-
-
-bool ppStackLoop(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");
-
-
-    // Preparation for stacking
-    psTrace("ppStack", 1, "Preparation for stacking: merging sources, determining target PSF....\n");
-    if (!ppStackPrepare(options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to prepare for stacking.");
-        return false;
-    }
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 1: Load Sources and Generate Target PSF: %f sec",
-             psTimerClear("PPSTACK_STEPS"));
-    ppStackMemDump("prepare");
-    if (options->quality) {
-        // Can't do anything else
-        return true;
-    }
-
-    // Convolve inputs
-    psTrace("ppStack", 1, "Convolving inputs to target PSF....\n");
-    if (!ppStackConvolve(options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to convolve images.");
-        return false;
-    }
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 2: Generate Convolutions and Save: %f sec",
-             psTimerClear("PPSTACK_STEPS"));
-    ppStackMemDump("convolve");
-
-    if (options->quality) {
-        // Can't do anything else
-        return true;
-    }
-
-    // Ensure sufficient inputs
-    {
-        int numGood = stackSummary(options, "initial combination");
-        psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe
-        bool safe = psMetadataLookupBool(NULL, recipe, "SAFE"); // Be safe when combining
-        if (safe && numGood <= 1) {
-            options->quality = PPSTACK_ERR_REJECTED;
-            psErrorStackPrint(stderr, "Insufficient inputs for combination with safety on");
-            psErrorClear();
-            psWarning("Insufficient inputs for combination with safety on");
-            return true;
-        }
-    }
-
-    // Start threading
-    ppStackThreadInit();
-    ppStackThreadData *stack = ppStackThreadDataSetup(options, config, true);
-    if (!stack) {
-        psError(psErrorCodeLast(), false, "Unable to initialise stack threads.");
-        return false;
-    }
-
-    // Prepare for combination
-    if (!ppStackCombinePrepare("PPSTACK.OUTPUT", "PPSTACK.OUTPUT.EXP", PPSTACK_FILES_STACK,
-                               stack, options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to prepare for combination.");
-        psFree(stack);
-        return false;
-    }
-
-    // Initial combination
-    psTrace("ppStack", 1, "Initial stack of convolved images....\n");
-    if (!ppStackCombineInitial(stack, options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to perform initial combination.");
-        psFree(stack);
-        return false;
-    }
-    ppStackMemDump("initial");
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 3: Make Initial Stack: %f sec", psTimerClear("PPSTACK_STEPS"));
-
-    // Done with stack inputs for now
-    for (int i = 0; i < options->num; i++) {
-        pmCellFreeData(options->cells->data[i]);
-    }
-    psFree(stack);
-
-    // Pixel rejection
-    psTrace("ppStack", 1, "Reject pixels....\n");
-    if (!ppStackReject(options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to reject pixels.");
-        psFree(stack);
-        return false;
-    }
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 4: Pixel Rejection: %f sec", psTimerClear("PPSTACK_STEPS"));
-
-    // Check inputs
-    {
-        int numGood = stackSummary(options, "final combination");
-        if (numGood <= 0) {
-            options->quality = PPSTACK_ERR_REJECTED;
-            psErrorStackPrint(stderr, "Insufficient inputs survived rejection stage");
-            psErrorClear();
-            psWarning("Insufficient inputs survived rejection stage");
-            return true;
-        }
-    }
-
-    stack = ppStackThreadDataSetup(options, config, true);
-    if (!stack) {
-        psError(psErrorCodeLast(), false, "Unable to initialise stack threads.");
-        return false;
-    }
-
-    // Final combination
-    psTrace("ppStack", 2, "Final stack of convolved images....\n");
-    if (!ppStackCombineFinal(stack, options->convCovars, options, config, false, false, true)) {
-        psError(psErrorCodeLast(), false, "Unable to perform final combination.");
-        psFree(stack);
-        return false;
-    }
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 5: Final Stack: %f sec", psTimerClear("PPSTACK_STEPS"));
-    ppStackMemDump("final");
-
-    // 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");
-
-    // Clean up
-    psTrace("ppStack", 2, "Cleaning up after combination....\n");
-    if (!ppStackCleanup(stack, options, config)) {
-        psError(psErrorCodeLast(), false, "Unable to clean up.");
-        psFree(stack);
-        return false;
-    }
-    for (int i = 0; i < options->num; i++) {
-        pmCellFreeData(options->cells->data[i]);
-    }
-    psFree(stack);
-    psLogMsg("ppStack", PS_LOG_INFO, "Stage 7: Cleanup, WCS & JPEGS: %f sec", psTimerClear("PPSTACK_STEPS"));
-    ppStackMemDump("cleanup");
-
-#if 1
-    // 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", PPSTACK_FILES_UNCONV,
-                                   stack, options, config)) {
-            psError(psErrorCodeLast(), false, "Unable to prepare for combination.");
-            psFree(stack);
-            return false;
-        }
-
-        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");
-
-        if (!ppStackFilesIterateUp(config)) {
-            psError(psErrorCodeLast(), false, "Unable to close files.");
-            psFree(stack);
-            return false;
-        }
-        ppStackFileActivation(config, PPSTACK_FILES_UNCONV, false);
-        options->outRO->data_exists = false;
-        options->outRO->parent->data_exists = false;
-        options->outRO->parent->parent->data_exists = false;
-        psFree(options->outRO);
-        options->outRO = NULL;
-        options->expRO->data_exists = false;
-        options->expRO->parent->data_exists = false;
-        options->expRO->parent->parent->data_exists = false;
-        psFree(options->expRO);
-        options->expRO = NULL;
-
-        for (int i = 0; i < options->num; i++) {
-            pmCellFreeData(options->cells->data[i]);
-        }
-        psFree(stack);
-    }
-    psFree(options->cells); options->cells = NULL;
-#endif
-
-    // 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;
-}