Index: trunk/ppImage/src/ppImageLoop_Threaded.c
===================================================================
--- trunk/ppImage/src/ppImageLoop_Threaded.c	(revision 23268)
+++ 	(revision )
@@ -1,141 +1,0 @@
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "ppImage.h"
-
-# define ESCAPE(MESSAGE) { \
-  psError(PS_ERR_UNKNOWN, false, MESSAGE); \
-  psFree (view); \
-  return false; \
-}
-
-bool ppImageLoop (pmConfig *config, ppImageOptions *options) {
-
-    bool status;
-    pmChip *chip;
-    pmCell *cell;
-    pmReadout *readout;
-
-    // measure the total elapsed time in ppImageLoop.
-    psTimerStart ("ppImageLoop");
-
-    pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT");
-    if (!status) {
-        psErrorStackPrint(stderr, "Can't find input data!\n");
-        ppImageCleanup(config, options);
-        exit(PS_EXIT_PROG_ERROR);
-    }
-
-    pmFPAview *view = pmFPAviewAlloc(0);// View for level of interest
-    pmHDU *lastHDU = NULL;              // Last HDU that was updated
-
-    // files associated with the science image
-    if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) ESCAPE ("load failure for FPA");
-
-    while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) {
-        psLogMsg ("ppImageLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process);
-        if (!chip->process || !chip->file_exists) {
-            continue;
-        }
-        if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) ESCAPE ("load failure for Chip");
-
-        while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) {
-            psLogMsg ("ppImageLoop", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process);
-            if (!cell->process || !cell->file_exists) {
-                continue;
-            }
-            if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) ESCAPE ("load failure for Cell");
-
-            // Put version information into the header
-            pmHDU *hdu = pmHDUFromCell(cell);
-            if (hdu && hdu != lastHDU) {
-                ppImageVersionMetadata(hdu->header);
-                lastHDU = hdu;
-            }
-
-            // process each of the readouts
-            while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) {
-                if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) ESCAPE ("load failure for Readout");
-                if (!readout->data_exists) {
-                    continue;
-                }
-
-		// XXX set the options->*Mask values here (after the mask images have been loaded
-		// and before any of the value are used)
-		if (!ppImageSetMaskBits (config, options)) ESCAPE ("Unable to set bit masks");
-		
-		if (!ppImageDetrendReadout(config, options, view)) ESCAPE ("Unable to detrend readout");
-            }
-        }
-
-        // Apply the fringe correction
-        if (options->doFringe) {
-	    if (!ppImageDetrendFringeApply (config, chip, view, options)) 
-		ESCAPE ("Unable to defringe");
-	}
-	
-	// measure various statistics for this image
-	if (!ppImagePixelStats (config, options, view)) 
-	    ESCAPE ("Unable to measures stats for image");
-
-        if (!ppImageMosaicChip(config, options, view, "PPIMAGE.CHIP", "PPIMAGE.OUTPUT"))
-            ESCAPE ("Unable to mosaic chip");
-
-        // we perform photometry on the readouts of this chip in the output
-        if (options->doPhotom) {
-            if (!ppImagePhotom(config, view)) ESCAPE ("error running photometry.");
-        }
-
-	// replace the masked pixels with the background level
-	if (options->replaceMasked) {
-	    if (!ppImageReplaceBackground (config, view, options)) 
-		ESCAPE ("Unable to replace masked pixels with background level");
-	}
-
-	// binning (used for display) must take place after the background is replaced, if desired
-        if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN1"))
-            ESCAPE ("Unable to bin chip (level 1).");
-
-        if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN2"))
-            ESCAPE ("Unable to bin chip (level 2).");
-
-        // Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?)
-        view->cell = -1;
-        while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) {
-            if (!cell->process || !cell->file_exists) {
-                continue;
-            }
-            if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) ESCAPE ("save failure for Cell");
-        }
-
-        // Close chip
-        if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) ESCAPE ("save failure for Chip");
-    }
-
-    // generate the full-scale FPA mosaic
-    if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA1", "PPIMAGE.BIN1")) ESCAPE ("failure in FPA Mosaic (level 1)");
-    if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA2", "PPIMAGE.BIN2")) ESCAPE ("failure in FPA Mosaic (level 2)");
-
-    // we perform astrometry on all chips after sources have been detected
-    // this also performs the psastro file IO
-    if (options->doAstromChip || options->doAstromMosaic) {
-        if (!ppImageAstrom(config)) ESCAPE ("error running astrometry.");
-    }
-
-    if (psTraceGetLevel("ppImage") >= 3) {
-	ppImageFileCheck (config);
-    }
-
-    // Write out summary statistics
-    if (!ppImageMetadataStats (config, options)) ESCAPE ("Unable to write statistics file.");
-
-    // Write out summary statistics
-    if (!ppImageStatsOutput (config, options)) ESCAPE ("Unable to write statistics file.");
-
-    // Output and Close FPA
-    if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) ESCAPE ("save failure for FPA");
-
-    psFree(view);
-    return true;
-}