Index: trunk/ppBackground/src/ppBackgroundStackLoop.c
===================================================================
--- trunk/ppBackground/src/ppBackgroundStackLoop.c	(revision 36582)
+++ trunk/ppBackground/src/ppBackgroundStackLoop.c	(revision 36615)
@@ -20,4 +20,5 @@
       // If we didn't load the OTA solution from an external source, we need to build one.
       if (data->fit_OTAS) {
+	printf("Fitting OTAs!\n");
 	if (!ppBackgroundStackModelFitOTASolution(data)) {
 	  // Currently can't fail.
@@ -25,7 +26,50 @@
 	  return(false);
 	}
-      }
+
+	if (data->OTApath) {
+	  // This will write the solutions out.
+	  psMetadataIterator *iter = psMetadataIteratorAlloc(data->OTA_solutions, PS_LIST_HEAD, NULL); // Iterator
+	  psMetadataItem *item; // Item from iteration
+	  int i = 0;
+	  while ((item = psMetadataGetAndIncrement(iter))) {
+	    i++;
+	    if (item->type != PS_DATA_IMAGE) {
+	      psString chipName = item->name;
+	      psImage  *image    = item->data.V;
+	      psMetadata *header = psMetadataAlloc();
+	      psString solutionFileName = psStringCopy(data->OTApath);
+	      psStringAppend(&solutionFileName, ".%s.fits",chipName);
+	      psString resolved = pmConfigConvertFilename(solutionFileName,config,true,true);
+	      psFits *solutionFits = psFitsOpen(resolved,"w");
+	      if (!solutionFits) {
+		psError(2, false, "Unable to open FITS file %s to write model %s.", resolved, chipName);
+		psFitsClose(solutionFits);
+		psFree(resolved);
+		return(false);
+	      }
+	      if (!psFitsWriteImage(solutionFits, header, image, 0, NULL)) {
+		psError(2, false, "Unable to write FITS image %s.", resolved);
+		psFitsClose(solutionFits);
+		psFree(resolved);
+		return false;
+	      }
+	      if (!psFitsClose(solutionFits)) {
+		psError(2, false, "Unable to close FITS image %s.", resolved);
+		psFree(resolved);
+		return false;
+	      }
+	      psFree(resolved);
+	      psFree(solutionFileName);
+	    }
+	  }
+	  psFree(item);
+	  psFree(iter);
+	}
+	
+      }
+      
       
       // This seems wrong, but I need a blank modelMap object, so we fit the zero-data we've stored in the calib objects
+      printf("Determining blank modelMap!\n");
       if (!ppBackgroundStackModelFit(data)) {
 	psError(psErrorCodeLast(), false, "Error determining the blank modelMap object.");
@@ -34,4 +78,5 @@
       
       // Apply OTA solution
+      printf("Calib apply!\n");
       if (!ppBackgroundStackCalibApply(data)) {
 	psError(psErrorCodeLast(), false, "Error applying the calibration models.");
@@ -43,4 +88,5 @@
     {
       // Construct the offset information
+      printf("Model fit!\n");
       if (!ppBackgroundStackDataModelFit(data)) {
 	psError(psErrorCodeLast(), false, "Error determining the exposure/OTA scaling.");
@@ -49,4 +95,5 @@
       
       // Apply full correction
+      printf("Calib apply!\n");
       if (!ppBackgroundStackCalibApply(data)) {
 	psError(psErrorCodeLast(), false, "Error applying the calibration models.");
@@ -55,4 +102,5 @@
       
       // Fit the new model
+      printf("Determining model!\n");
       if (!ppBackgroundStackModelFit(data)) {
 	psError(psErrorCodeLast(), false, "Error determining the modelMap object.");
@@ -66,7 +114,12 @@
       pmFPAfile *stack = data->stack_data->data[i];
       pmFPAview *view = pmFPAviewAlloc(0);
-      // Define output image
-      pmFPAfile *stack_model = pmFPAfileDefineOutput(config,stack->fpa,"PPBACKGROUND.STACK.MODEL");
-
+
+      // Define output image.  Why is this always so hard to do?
+      pmFPA *tmp_fpa1,*tmp_fpa2;
+      tmp_fpa1 = pmFPAConstruct(config->camera,config->cameraName);
+      tmp_fpa2 = pmFPAConstruct(config->camera,config->cameraName);
+
+      pmFPAfile *stack_model = pmFPAfileDefineOutput(config,tmp_fpa1,"PPBACKGROUND.STACK.MODEL");
+      
       if (!stack_model) {
 	psError(psErrorCodeLast(), false, "Unable to generate output model");
@@ -74,5 +127,5 @@
       }
       
-      pmFPAfile *stack_corr  = pmFPAfileDefineOutput(config,stack->fpa,"PPBACKGROUND.STACK.OUTPUT");
+      pmFPAfile *stack_corr  = pmFPAfileDefineOutput(config,tmp_fpa2,"PPBACKGROUND.STACK.OUTPUT");
       if (!stack_corr) {
 	psError(psErrorCodeLast(), false, "Unable to generate output result");
@@ -82,5 +135,15 @@
       stack_corr->save = true;
 
+      printf("I'm about to loop over the parts of this stack: %d\n",i);
       // Iterate over the images.
+      pmFPAfileActivate(config->files,true,"PPBACKGROUND.STACK");
+      pmFPAfileActivate(config->files,true,"PPBACKGROUND.STACK.MODEL");
+      pmFPAfileActivate(config->files,true,"PPBACKGROUND.STACK.OUTPUT");
+      if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+	psError(psErrorCodeLast(), false, "load failure for Chip");
+	return(false);
+      }
+
+      
       pmChip *chip;
       while ((chip = pmFPAviewNextChip(view, stack->fpa, 1))) {
@@ -93,5 +156,5 @@
 	  return(false);
 	}
-
+	printf("  I'm in a chip\n");
 	pmCell *cell;
 	
@@ -109,4 +172,6 @@
 	    continue;
 	  }
+	  printf("    I'm in a cell\n");
+
 
 	  // process each of the readouts
@@ -120,8 +185,26 @@
 	      continue;
 	    }
-
-	    pmReadout *model = pmFPAfileThisReadout(config->files,view,"PPBACKGROUND.STACK.MODEL");
-	    pmReadout *corr  = pmFPAfileThisReadout(config->files,view,"PPBACKGROUND.STACK.OUTPUT");
-
+	    printf("      I'm in a readout\n");
+
+	    // Futz with things to get an acceptable output product.
+	    pmCell *model_cell = pmFPAviewThisCell(view,stack_model->fpa);
+	    pmCell *corr_cell  = pmFPAviewThisCell(view,stack_corr->fpa);
+	    
+	    pmReadout *model = pmReadoutAlloc(model_cell);
+	    pmReadout *corr  = pmReadoutAlloc(corr_cell);
+	    model->data_exists = true;
+	    corr->data_exists = true;
+	    model->parent->data_exists = true;
+	    corr->parent->data_exists = true;
+	    model->parent->parent->data_exists = true;
+	    corr->parent->parent->data_exists = true;
+	    model->image = psImageAlloc(readout->image->numCols,readout->image->numRows,PS_TYPE_F32);
+	    corr->image = psImageAlloc(readout->image->numCols,readout->image->numRows,PS_TYPE_F32);
+
+	    model_cell->concepts = psMemIncrRefCounter(cell->concepts);
+	    model_cell->conceptsRead = cell->conceptsRead;
+	    corr_cell->concepts = psMemIncrRefCounter(cell->concepts);
+	    corr_cell->conceptsRead = cell->conceptsRead;
+	    
 	    psPlane *pix = psPlaneAlloc();   // Pixel coordinates on chip
 	    psPlane *fp = psPlaneAlloc();    // Focal plane coordinates
@@ -130,11 +213,14 @@
 	    int x,y;
 	    for (y = 0; y < readout->image->numRows; y++) {
+	      pix->y = y;
 	      for (x = 0; x < readout->image->numCols; x++) {
+		pix->x = x;
 		// Calculate model for each pixel of output
-		psPlaneTransformApply(fp, chip->toFPA, pix);
-		psPlaneTransformApply(tp, stack->fpa->toTPA, fp);
+		//		psPlaneTransformApply(fp, chip->toFPA, pix);
+		psPlaneTransformApply(tp, stack->fpa->toTPA, pix);
 		
 		model->image->data.F32[y][x] = psImageMapEval(data->modelMap,tp->x,tp->y);
 		corr->image->data.F32[y][x] = readout->image->data.F32[y][x] + model->image->data.F32[y][x];
+		
 	      }
 	    }
@@ -143,19 +229,19 @@
 	    psFree(tp);
 	  } // Close readout
-
+	  printf("    I'm done with that readout\n");
 	  // Close output image
-	  // Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?)
-	  view->cell = -1;
-	  while ((cell = pmFPAviewNextCell(view, stack->fpa, 1)) != NULL) {
-	    if (!cell->process || !cell->file_exists) {
-	      continue;
-	    }
-	    if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {
-	      	psError(psErrorCodeLast(), false, "save failure for Cell");
-		return(false);
-	    }
-	  }
 	} // Close Cell
-	
+	// Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?)
+	view->cell = -1;
+	while ((cell = pmFPAviewNextCell(view, stack->fpa, 1)) != NULL) {
+	  if (!cell->process || !cell->file_exists) {
+	    continue;
+	  }
+	  if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {
+	    psError(psErrorCodeLast(), false, "save failure for Cell");
+	    return(false);
+	  }
+	}
+
         // Close chip
 	if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {