Index: trunk/psphot/src/psphotFindDetections.c
===================================================================
--- trunk/psphot/src/psphotFindDetections.c	(revision 25755)
+++ trunk/psphot/src/psphotFindDetections.c	(revision 26894)
@@ -1,6 +1,30 @@
 # include "psphotInternal.h"
 
+// we store the detections on the readout->analysis for each readout this function finds new
+// peaks and new footprints.  any old peaks are saved on oldPeaks.  the resulting footprint set
+// contains all footprints (old and new)
+bool psphotFindDetections (pmConfig *config, const pmFPAview *view, bool firstPass)
+{
+    bool status = true;
+
+    // select the appropriate recipe information
+    psMetadata *recipe  = psMetadataLookupPtr (&status, config->recipes, PSPHOT_RECIPE);
+    psAssert (recipe, "missing recipe?");
+
+    int num = psMetadataLookupS32 (&status, config->arguments, "PSPHOT.INPUT.NUM");
+    psAssert (status, "programming error: must define PSPHOT.INPUT.NUM");
+
+    // loop over the available readouts
+    for (int i = 0; i < num; i++) {
+	if (!psphotFindDetectionsReadout (config, view, "PSPHOT.INPUT", i, recipe, firstPass)) {
+            psError (PSPHOT_ERR_CONFIG, false, "failed to find initial detections for PSPHOT.INPUT entry %d", i);
+	    return false;
+	}
+    }
+    return true;
+}
+
 // smooth the image, search for peaks, optionally define footprints based on the peaks
-pmDetections *psphotFindDetections (pmDetections *detections, pmReadout *readout, psMetadata *recipe) {
+bool psphotFindDetectionsReadout (pmConfig *config, const pmFPAview *view, const char *filename, int index, psMetadata *recipe, bool firstPass) {
 
     bool status;
@@ -9,14 +33,34 @@
     int NMAX = 0;
 
+    // find the currently selected readout
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, filename, index); // File of interest
+    psAssert (file, "missing file?");
+
+    pmReadout *readout = pmFPAviewThisReadout(view, file->fpa);
+    psAssert (readout, "missing readout?");
+
     // user-defined masks to test for good/bad pixels (build from recipe list if not yet set)
     psImageMaskType maskVal = psMetadataLookupImageMask(&status, recipe, "MASK.PSPHOT"); // Mask value for bad pixels
-    assert (maskVal);
+    psAssert (maskVal, "missing mask value?");
 
     // Use the new pmFootprints approach?
     const bool useFootprints = psMetadataLookupBool(NULL, recipe, "USE_FOOTPRINTS");
 
-    // on first pass, detections have not yet been allocated
+    pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS");
+    // on the initial pass, detections have not yet been allocated or saved on readout->analysis
     if (!detections) {
+	// create the container
         detections = pmDetectionsAlloc();
+	
+	// save detections on the readout->analysis
+	if (!psMetadataAddPtr (readout->analysis, PS_LIST_TAIL, "PSPHOT.DETECTIONS", PS_META_REPLACE | PS_DATA_UNKNOWN, "psphot detections", detections)) {
+	    psError (PSPHOT_ERR_CONFIG, false, "problem saving detections on readout");
+	    return false;
+	}
+    } else {
+	psMemIncrRefCounter(detections); // so we can free the detections below
+    }
+
+    if (firstPass) {
         pass = 1;
         NSIGMA_PEAK = psMetadataLookupF32 (&status, recipe, "PEAKS_NSIGMA_LIMIT"); PS_ASSERT (status, NULL);
@@ -30,6 +74,10 @@
     float threshold = PS_SQR(NSIGMA_PEAK);
 
-    // move the old peaks array (if it exists) to oldPeaks
-    // XXX generically, we should be able to call this function an arbitrary number of times
+    // move the old peaks array (if it exists) to oldPeaks XXX generically, we should be able
+    // to call this function an arbitrary number of times the old peaks are saved so they can
+    // be freed later -- the have to be freed after psphotFindFootprints is called below, since
+    // they are also owned by the oldFootprints, which are in turn merged into the new
+    // footprints.  (what about the source->peak entry?)
+    
     assert (detections->oldPeaks == NULL);
     detections->oldPeaks = detections->peaks;
@@ -39,18 +87,28 @@
     psImage *significance = psphotSignificanceImage (readout, recipe, pass, maskVal);
 
-    // display the backsub and backgnd images
-    psphotVisualShowSignificance (significance);
+    // display the significance image
+    psphotVisualShowSignificance (significance, -1.0, PS_SQR(3.0*NSIGMA_PEAK));
+
+    // XXX getting some strange results from significance image
+    if (0) {
+	psImage *lsig = (psImage *) psUnaryOp (NULL, significance, "log");
+	psphotVisualShowSignificance (lsig, 0.0, 4.0);
+	psFree (lsig);
+    }	
 
     // detect the peaks in the significance image
     detections->peaks = psphotFindPeaks (significance, readout, recipe, threshold, NMAX);
-    psMetadataAddF32  (recipe, PS_LIST_TAIL, "PEAK_THRESHOLD", PS_META_REPLACE, "Peak Detection Threshold", threshold);
+    psMetadataAddF32  (readout->analysis, PS_LIST_TAIL, "PEAK_THRESHOLD", PS_META_REPLACE, "Peak Detection Threshold", threshold);
     if (!detections->peaks) {
-        // No peaks found
-        return NULL;
+	// we only get a NULL peaks array due to a programming or config error. 
+	// this will result in a failure.
+	psFree (detections);
+	psError (PSPHOT_ERR_CONFIG, false, "failed on peak search");
+        return false;
     }
 
     // optionally merge peaks into footprints
     if (useFootprints) {
-        psphotFindFootprints (detections, significance, readout, recipe, threshold, pass, maskVal);
+	psphotFindFootprints (detections, significance, readout, recipe, threshold, pass, maskVal);
     }
 
@@ -61,5 +119,7 @@
     psphotVisualShowFootprints (detections);
 
-    return detections;
+    psFree (detections);
+
+    return true;
 }