Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImage.h
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImage.h	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImage.h	(revision 42167)
@@ -46,4 +46,5 @@
     bool doPatternContinuity;           // Cell continuity correction
     bool doBackgroundContinuity;        // Do mosaic continuity correction
+    bool doPatternDeadCells;            // match dead cell background patterns
     bool doFringe;                      // Fringe subtraction
     bool doPhotom;                      // Source identification and photometry
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageArguments.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageArguments.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageArguments.c	(revision 42167)
@@ -117,4 +117,5 @@
     pmConfigFileSetsMD (config->arguments, &argc, argv, "LINEARITY", "-linearity", "-linearlist");
     pmConfigFileSetsMD (config->arguments, &argc, argv, "PATTERN.ROW.AMP", "-pattern-row-amplitude", "-not-defined");
+    pmConfigFileSetsMD (config->arguments, &argc, argv, "PATTERN.DEAD.CELLS", "-pattern-dead-cells", "-not-defined");
 
     if ((argnum = psArgumentGet(argc, argv, "-burntool"))) {
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendFringe.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendFringe.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendFringe.c	(revision 42167)
@@ -327,7 +327,6 @@
     pmCell *cell = NULL;
 
-    // psTimerStart("apply.fringe");
-
-    assert (options->doFringe); // do not call if not needed
+    if (!options->doFringe) return true;
+
     assert (inputView->chip != -1);
     assert (inputView->cell == -1);
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendPattern.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendPattern.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendPattern.c	(revision 42167)
@@ -5,5 +5,5 @@
 #include "ppImage.h"
 
-#define ESCAPE(STATUS,...) {                    \
+#define ESCAPE(STATUS,...) {				\
         psError(PS_ERR_UNKNOWN, STATUS, __VA_ARGS__);   \
         psFree(view);                                   \
@@ -13,10 +13,38 @@
 static bool doPatternForView (bool *doit, const pmConfig *config, const pmChip *chip, const pmFPAview *view, const char *recipename, const char *recipevalue);
 
-bool ppImageDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView,
-                                ppImageOptions *options)
+bool ppImageDetrendPatternRowApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options);
+bool ppImageDetrendPatternContinuityApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options);
+bool ppImageDetrendPatternCellApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options);
+bool ppImageDetrendPatternDeadCellsApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options);
+
+// Apply the desired pattern corrections (if any).  This function is passed the chip for the
+// image being processed, but may interact with pmFPAfiles containing the pattern reference information
+bool ppImageDetrendPatternApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options)
 {
-    pmCell *cell = NULL;
-
-    assert(options->doPatternRow || options->doPatternCell || options->doPatternContinuity); // do not call if not needed
+    assert(inputView->chip != -1);
+    assert(inputView->cell == -1);
+    assert(inputView->readout == -1);
+
+    if (!ppImageDetrendPatternRowApply (config, chip, inputView, options)) {
+	return false;
+    }
+    if (!ppImageDetrendPatternContinuityApply (config, chip, inputView, options)) {
+	return false;
+    }
+    if (!ppImageDetrendPatternCellApply (config, chip, inputView, options)) {
+	return false;
+    }
+    if (!ppImageDetrendPatternDeadCellsApply (config, chip, inputView, options)) {
+	return false;
+    }
+    return(true);
+}
+
+bool ppImageDetrendPatternRowApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options)
+{
+    bool status;
+
+    if (!options->doPatternRow) return true;
+    
     assert(inputView->chip != -1);
     assert(inputView->cell == -1);
@@ -35,5 +63,5 @@
     // tables, one per chip.  Each table lists the typical bias-drift amplitude for cell,
     // measured from a collection of dark images.  These values are passed (via
-    // cell->analysis) to pmPatternRow which choosed to apply the correction based on the
+    // cell->analysis) to pmPatternRow which chooses to apply the correction based on the
     // ratio of the poisson noise due to the median background (+ read noise) and the
     // typical amplitude.  Tests show that if the amplitude / noise < 1/6, then the
@@ -44,215 +72,378 @@
     // chip.
 
-    // psTimerStart("apply.pattern");
-    if (options->doPatternRow) {
-
-        //psLogMsg("ppImage", PS_LOG_INFO, "Log: entering pattern.row routine");
-        //psWarning ("Entering pattern.row routine");
-
-        bool status;
-	pmHDU *hdu = pmHDUFromChip(chip);
-	if (psMetadataLookupBool(NULL,hdu->header,"PTRN_ROW")) {
-	  psLogMsg("ppImage", PS_LOG_INFO, "Not performing row pattern correction as it has already been done.");
-	  goto pattern_continuity;
-	}
-
-        const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME");
-        psLogMsg("ppImage", PS_LOG_INFO, "Performing row pattern correction for %s\n", chipName);
-
-	pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT");
-
-	// grab the PATTERN.ROW.AMP file
-	pmFPAfile *PRAfile = psMetadataLookupPtr (NULL, config->files, "PPIMAGE.PATTERN.ROW.AMP");
-	if (!PRAfile) {
-	  psLogMsg("ppImage", PS_LOG_INFO, "Pattern Row Amplitude file not found, applying to all (with limits from ROW.SUBSET) ");
-	}
-	
-	pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
-	*view = *inputView;
-	while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) {
-            //const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME");
-            //const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME");
-            //psWarning ("Looping through %s, %s\n", chipName, cellName);
-
-            if (!cell->process || !cell->file_exists) {
-		continue;
-            }
-            if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
-		ESCAPE(false, "load failure for Cell");
-            }
+    pmHDU *hdu = pmHDUFromChip(chip);
+    if (psMetadataLookupBool(&status, hdu->header, "PTRN_ROW")) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Not performing row pattern correction as it has already been done.");
+	return true;
+    }
+
+    const char *chipName = psMetadataLookupStr(&status, chip->concepts, "CHIP.NAME");
+    psLogMsg("ppImage", PS_LOG_INFO, "Performing row pattern correction for %s\n", chipName);
+
+    // XXX we use input->fpa below, but could we just use chip->parent?
+    pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT");
+
+    // grab the PATTERN.ROW.AMP file
+    pmFPAfile *PRAfile = psMetadataLookupPtr (&status, config->files, "PPIMAGE.PATTERN.ROW.AMP");
+    if (!PRAfile) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Pattern Row Amplitude file not found, applying to all (with limits from ROW.SUBSET) ");
+    }
+	
+    pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
+    *view = *inputView;
+
+    pmCell *cell = NULL;
+    while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) {
+	// const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME");
+	// const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME");
+	// psWarning ("Looping through %s, %s\n", chipName, cellName);
+
+	if (!cell->process || !cell->file_exists) {
+	    continue;
+	}
+
+	// this forces pmFPAfileRead of the PATTERN.ROW.AMP file (XXX but is this needed?)
+	if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+	    ESCAPE(false, "load failure for Cell");
+	}
 	    
-            if (!cell->data_exists) {
-                continue;
-            }
-
-            if (cell->readouts->n > 1) {
-                psWarning ("Skipping Video Cell for ppImageDetrendPatternApply");
-                continue;
-            }
-
-	    // grab the corresponding cell
-	    if (PRAfile) {
-	      pmCell *PRAcell = pmFPAviewThisCell (view, PRAfile->fpa);
-	      psAssert (PRAcell, "found Pattern Row Amplitude file, but not cell?");
-
-	      // find the nominal signal amplitude (check the ghost and/or crosstalk recipe file)
-	      float amplitude = psMetadataLookupF32 (&status, PRAcell->analysis, "PTN.ROW.AMP");
-	      if (!status) amplitude = NAN;
+	if (!cell->data_exists) {
+	    continue;
+	}
+
+	if (cell->readouts->n > 1) {
+	    psWarning ("Skipping Video Cell for ppImageDetrendPatternApply");
+	    continue;
+	}
+
+	// grab the corresponding cell
+	if (PRAfile) {
+	    pmCell *PRAcell = pmFPAviewThisCell (view, PRAfile->fpa);
+	    psAssert (PRAcell, "found Pattern Row Amplitude file, but not cell?");
+
+	    // find the nominal signal amplitude (check the ghost and/or crosstalk recipe file)
+	    float amplitude = psMetadataLookupF32 (&status, PRAcell->analysis, "PTN.ROW.AMP");
+	    if (!status) amplitude = NAN;
 	    
-	      // put the value on the science cell
-	      psMetadataAddF32 (cell->analysis, PS_LIST_TAIL, "PTN.ROW.AMP", PS_META_REPLACE, "", amplitude);
+	    // put the value on the science cell
+	    psMetadataAddF32 (cell->analysis, PS_LIST_TAIL, "PTN.ROW.AMP", PS_META_REPLACE, "", amplitude);
+	}
+
+	bool doPattern = false;
+	if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.ROW.SUBSET")) {
+	    ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
+	}
+	if (!doPattern) continue;
+
+	// switch to test threaded version
+	if (true) {
+	    // I need to allocate a view here to be freed by the
+	    // called function below.  
+	    pmFPAview *myView = pmFPAviewAlloc(0); // View for local processing
+	    *myView = *view;
+
+	    // allocate a job, construct the arguments for this job
+	    psThreadJob *job = psThreadJobAlloc("PPIMAGE_PATTERN_ROW_CELL");
+	    psArrayAdd(job->args, 1, config);
+	    psArrayAdd(job->args, 1, input->fpa);
+	    psArrayAdd(job->args, 1, chip);
+	    psArrayAdd(job->args, 1, cell);
+	    psArrayAdd(job->args, 1, myView);
+	    psArrayAdd(job->args, 1, options);
+	    if (!psThreadJobAddPending(job)) {
+		return false;
 	    }
-
-            bool doPattern = false;
-            if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.ROW.SUBSET")) {
-                ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
-            }
-            if (!doPattern) continue;
-
-	    // switch to test threaded version
-	    if (true) {
-		// I need to allocate a view here to be freed by the
-		// called function below.  
-		pmFPAview *myView = pmFPAviewAlloc(0); // View for local processing
-		*myView = *view;
-
-		// allocate a job, construct the arguments for this job
-		psThreadJob *job = psThreadJobAlloc("PPIMAGE_PATTERN_ROW_CELL");
-		psArrayAdd(job->args, 1, config);
-		psArrayAdd(job->args, 1, input->fpa);
-		psArrayAdd(job->args, 1, chip);
-		psArrayAdd(job->args, 1, cell);
-		psArrayAdd(job->args, 1, myView);
-		psArrayAdd(job->args, 1, options);
-		if (!psThreadJobAddPending(job)) {
-		    return false;
-		}
-	    } else {
-		// bump the counter since it must be freed by the function below.  
-		psMemIncrRefCounter (view); // View for local processing
-		if (!ppImageDetrendPatternApplyCell (config, input->fpa, chip, cell, view, options)) {
-		    return false;
-		}
+	} else {
+	    // bump the counter since it must be freed by the function below.  
+	    psMemIncrRefCounter (view); // View for local processing
+	    if (!ppImageDetrendPatternApplyCell (config, input->fpa, chip, cell, view, options)) {
+		return false;
 	    }
-
-	}
-
-        // wait here for the threaded jobs to finish
-	// if no threads are allocated, this 
-        if (!psThreadPoolWait(true, true)) {
-            psError(PS_ERR_UNKNOWN, false, "Unable to apply bias correction.");
-            return false;
-        }
-
-	psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_ROW",PS_META_REPLACE,"PATTERN.ROW correction applied",true);
-	psFree(view);
-    }
-
- pattern_continuity:
+	}
+    }
+
+    // wait here for the threaded jobs to finish
+    // if no threads are allocated, this 
+    if (!psThreadPoolWait(true, true)) {
+	psError(PS_ERR_UNKNOWN, false, "Unable to apply bias correction.");
+	return false;
+    }
+
+    psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_ROW",PS_META_REPLACE,"PATTERN.ROW correction applied",true);
+    psFree(view);
+   
+    return true;
+}
+
+bool ppImageDetrendPatternContinuityApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options)
+{
+    bool status;
+
+    if (!options->doPatternContinuity) return true;
+
+    assert(inputView->chip != -1);
+    assert(inputView->cell == -1);
+    assert(inputView->readout == -1);
 
     // see the comment for PATTERN.ROW; the same rules apply for PATTERN.CELL
 
-    if (options->doPatternContinuity) {
-        int numCells = chip->cells->n;       // Number of cells
-        psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell?
-        pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
-        *view = *inputView;
-
-	pmHDU *hdu = pmHDUFromChip(chip);
-	if (psMetadataLookupBool(NULL,hdu->header,"PTRN_CON")) {
-	  psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction as it has already been done.");
-	  goto pattern_cell;
-	}
-
-        const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME");
-        psLogMsg("ppImage", PS_LOG_INFO, "Performing pattern continuity correction for %s\n", chipName);
-
-	for (int i = 0; i < chip->cells->n; i++) {
-            view->cell = i;
-
-            pmCell *cell = chip->cells->data[i]; // Cell of interest
-
-            if (cell->readouts->n > 1) {
-                psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction on video cell.");
-                continue;
-            }
-
-            bool doPattern = false;
-            if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CONTINUITY.SUBSET")) {
-                ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
-            }
-
-            if (doPattern) {
-                tweak->data.U8[i] = 0xFF;
-            }
-	}
-
-	// Tweak the cells
-	if (!pmPatternContinuity(chip, tweak, options->patternCellBG, options->patternCellMean,
-				 options->maskValue, options->darkMask,options->patternContinuityEdgeWidth)) {
-	    psFree(tweak);
-	    psFree(view);
-	    return false;
-	}
+    int numCells = chip->cells->n;       // Number of cells
+    psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell?
+    pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
+    *view = *inputView;
+
+    pmHDU *hdu = pmHDUFromChip(chip);
+    if (psMetadataLookupBool(&status, hdu->header, "PTRN_CON")) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction as it has already been done.");
+	return true;
+    }
+
+    const char *chipName = psMetadataLookupStr(&status, chip->concepts, "CHIP.NAME");
+    psLogMsg("ppImage", PS_LOG_INFO, "Performing pattern continuity correction for %s\n", chipName);
+
+    for (int i = 0; i < chip->cells->n; i++) {
+	view->cell = i;
+
+	pmCell *cell = chip->cells->data[i]; // Cell of interest
+
+	if (cell->readouts->n > 1) {
+	    psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell continuity correction on video cell.");
+	    continue;
+	}
+
+	bool doPattern = false;
+	if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CONTINUITY.SUBSET")) {
+	    ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
+	}
+
+	if (doPattern) {
+	    tweak->data.U8[i] = 0xFF;
+	}
+    }
+
+    // Tweak the cells
+    if (!pmPatternContinuity(chip, tweak, options->patternCellBG, options->patternCellMean,
+			     options->maskValue, options->darkMask,options->patternContinuityEdgeWidth)) {
 	psFree(tweak);
 	psFree(view);
-
-	psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CON",PS_META_REPLACE,"PATTERN.CONTINUITY correction applied",true);
-    }
-
- pattern_cell:
-    
-    if (options->doPatternCell) {
-        int numCells = chip->cells->n;       // Number of cells
-        psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell?
-        pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
-        *view = *inputView;
-
-	pmHDU *hdu = pmHDUFromChip(chip);
-	if (psMetadataLookupBool(NULL,hdu->header,"PTRN_CEL")) {
-	  psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction as it has already been done.");
-	  goto pattern_done;
-	}
-
-        const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME");
-        psLogMsg("ppImage", PS_LOG_INFO, "Performing cell pattern correction for %s\n", chipName);
-
-	for (int i = 0; i < chip->cells->n; i++) {
-            view->cell = i;
-
-            pmCell *cell = chip->cells->data[i]; // Cell of interest
-
-            if (cell->readouts->n > 1) {
-                psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction on video cell.");
-                continue;
-            }
-
-            bool doPattern = false;
-            if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CELL.SUBSET")) {
-                ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
-            }
-            if (doPattern) {
-                tweak->data.U8[i] = 0xFF;
-            }
-	}
-
-	// Tweak the cells
-	if (!pmPatternCell(chip, tweak, options->patternCellBG, options->patternCellMean,
-			   options->maskValue, options->darkMask)) {
-	    psFree(tweak);
-	    psFree(view);
-	    return false;
-	}
+	return false;
+    }
+    psFree(tweak);
+    psFree(view);
+
+    psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CON",PS_META_REPLACE,"PATTERN.CONTINUITY correction applied",true);
+    return true;
+}
+
+bool ppImageDetrendPatternCellApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options)
+{
+    bool status;
+
+    if (!options->doPatternCell) return true;
+
+    assert(inputView->chip != -1);
+    assert(inputView->cell == -1);
+    assert(inputView->readout == -1);
+
+    int numCells = chip->cells->n;       // Number of cells
+    psVector *tweak = psVectorAlloc(numCells, PS_TYPE_U8); // Tweak cell?
+    pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
+    *view = *inputView;
+
+    pmHDU *hdu = pmHDUFromChip(chip);
+    if (psMetadataLookupBool(&status, hdu->header, "PTRN_CEL")) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction as it has already been done.");
+	return true;
+    }
+
+    const char *chipName = psMetadataLookupStr(&status, chip->concepts, "CHIP.NAME");
+    psLogMsg("ppImage", PS_LOG_INFO, "Performing cell pattern correction for %s\n", chipName);
+
+    for (int i = 0; i < chip->cells->n; i++) {
+	view->cell = i;
+
+	pmCell *cell = chip->cells->data[i]; // Cell of interest
+
+	if (cell->readouts->n > 1) {
+	    psLogMsg("ppImage", PS_LOG_INFO, "Not performing cell pattern correction on video cell.");
+	    continue;
+	}
+
+	bool doPattern = false;
+	if (!doPatternForView(&doPattern, config, chip, view, RECIPE_NAME, "PATTERN.CELL.SUBSET")) {
+	    ESCAPE(false, "Unable to determine whether row pattern matching should be applied.");
+	}
+	if (doPattern) {
+	    tweak->data.U8[i] = 0xFF;
+	}
+    }
+
+    // Tweak the cells
+    if (!pmPatternCell(chip, tweak, options->patternCellBG, options->patternCellMean,
+		       options->maskValue, options->darkMask)) {
 	psFree(tweak);
 	psFree(view);
-
-	psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CEL",PS_META_REPLACE,"PATTERN.CELL correction applied",true);
-    }
-
- pattern_done:
-
-    // psLogMsg ("ppImage", 5, "apply pattern: %f sec\n", psTimerMark ("apply.pattern"));
-
-    return(true);
+	return false;
+    }
+    psFree(tweak);
+    psFree(view);
+
+    psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_CEL",PS_META_REPLACE,"PATTERN.CELL correction applied",true);
+    return true;
+}
+
+bool ppImageDetrendPatternDeadCellsMask (pmChip *chip, psImageMaskType maskVal) {
+
+    int numCells = chip->cells->n;       // Number of cells
+
+    // now mask bad cells
+    for (int i = 0; i < numCells; i++) {
+        pmCell *cell = chip->cells->data[i]; // Cell of interest
+        pmReadout *ro = cell->readouts->data[0]; // Readout of interest
+
+	psImage *mask = ro->mask; // mask of interest
+	int numCols = mask->numCols, numRows = mask->numRows; // Size of image
+	
+	for (int y = 0; y < numRows; y++) {
+	    for (int x = 0; x < numCols; x++) {
+		mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= maskVal;
+	    }
+	}
+    }
+
+}
+
+bool ppImageDetrendPatternDeadCellsXY42 (pmChip *chip, psImageMaskType maskVal) {
+
+    bool status;
+
+    // extract the MEDIAN_CELL_BACKGROUND values to check for problems
+    int numCells = chip->cells->n;       // Number of cells
+    psVector *cellBackground = psVectorAllocEmpty (numCells, PS_DATA_F32);
+
+    for (int i = 0; i < numCells; i++) {
+	pmCell *cell = chip->cells->data[i];;
+
+	if (!cell->process || !cell->file_exists || !cell->data_exists) continue;
+	
+	// select the HDU for this cell
+	pmHDU *cellHDU = pmHDUFromCell(cell);  // HDU of interest
+	
+	psF32 BackValue = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL");
+	if (!status) continue;
+
+	psF32 BackError = psMetadataLookupF32(&status, cellHDU->header, "BACK_ERR");
+	if (!status) continue;
+
+	if (BackValue == 0.0) continue;
+	if (BackError == 0.0) continue;
+
+	psVectorAppend (cellBackground, BackValue / BackError);
+    }
+
+    if (cellBackground->n < 0.375*numCells) {
+	// Chip is bad, mask the whole thing
+	ppImageDetrendPatternDeadCellsMask (chip, maskVal);
+	psFree (cellBackground);
+	return true;
+    }
+
+    // Second, calculate the median
+    psVectorSortInPlace (cellBackground);
+    int midPt = cellBackground->n / 2.0;
+    float median = cellBackground->n % 2 ? cellBackground->data.F32[midPt] : 0.5*(cellBackground->data.F32[midPt] + cellBackground->data.F32[midPt-1]);
+    psFree (cellBackground);
+
+    if (median < 3.0) {
+	// Chip is bad, mask the whole thing
+	ppImageDetrendPatternDeadCellsMask (chip, maskVal);
+    }
+    psFree (cellBackground);
+    return true;
+}
+
+// to apply the dead cell pattern, we need to transfer the pattern for this chip from the
+// pmFPAfile for the pattern to the one for the image being processed.  
+bool ppImageDetrendPatternDeadCellsApply(pmConfig *config, pmChip *chip, const pmFPAview *inputView, ppImageOptions *options)
+{
+    bool status;
+
+    if (!options->doPatternDeadCells) return true;
+
+    assert(inputView->chip != -1);
+    assert(inputView->cell == -1);
+    assert(inputView->readout == -1);
+
+    const char *chipName = psMetadataLookupStr(&status, chip->concepts, "CHIP.NAME");
+    psLogMsg("ppImage", PS_LOG_INFO, "Performing cell pattern correction for %s\n", chipName);
+
+    pmHDU *hdu = pmHDUFromChip(chip);
+    if (psMetadataLookupBool(&status, hdu->header, "PTRN_DED")) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Not performing dead cell pattern correction as it has already been done.");
+	return true;
+    }
+
+    if (!strcmp (chipName, "XY40") || !strcmp (chipName, "XY42")) {
+	// special case : check for BACK_VAL / BACK_ERR > 3 or < 3
+	psLogMsg("ppImage", PS_LOG_INFO, "Using special case for XY40 and XY42");
+	ppImageDetrendPatternDeadCellsXY42 (chip, options->blankMask);
+	return true;
+    }
+
+    pmFPAfile *pattern = psMetadataLookupPtr(&status, config->files, "PPIMAGE.PATTERN.DEAD.CELLS");
+    if (!pattern) {
+	psLogMsg("ppImage", PS_LOG_INFO, "Pattern Dead Cells file not found, skipping");
+	return true;
+    }
+
+    pmFPAview *view = pmFPAviewAlloc(0); // View for local processing
+    *view = *inputView;
+
+    pmChip *patternChip = pmFPAviewThisChip (view, pattern->fpa);
+
+    // grab the pattern from the input pattern file chip
+    psImage *deadCellPattern = (psImage *) psMetadataLookupPtr (&status, patternChip->analysis, "PTN.DEAD.CELL");
+    if (!deadCellPattern) {
+        psLogMsg("psModules.detrend", PS_LOG_DETAIL, "No DEAD CELL pattern for chip, skipping\n");
+	psFree (view);
+	return true;
+    }
+
+    // copy the pattern pointer to the chip of the image being processed
+    psMetadataAddImage (chip->analysis, PS_LIST_TAIL, "PTN.DEAD.CELL", PS_META_REPLACE, "", deadCellPattern);
+
+    // extract the MEDIAN_CELL_BACKGROUND values to check for problems
+    int numCells = chip->cells->n;       // Number of cells
+    psVector *cellBackground = psVectorAllocEmpty (numCells, PS_DATA_F32);
+
+    pmCell *cell = NULL;
+    while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) {
+	if (!cell->process || !cell->file_exists || !cell->data_exists) {
+	    psVectorAppend (cellBackground, NAN);
+	    continue;
+	}
+	
+	// select the HDU for this cell
+	pmHDU *cellHDU = pmHDUFromCell(cell);  // HDU of interest
+	
+	psF32 value = psMetadataLookupF32(&status, cellHDU->header, "BACK_VAL");
+	if (!status) {
+	    psVectorAppend (cellBackground, NAN);
+	    continue;
+	}
+	psVectorAppend (cellBackground, value);
+    }
+
+    // match cellBackground pattern to registered patterns and mask as needed
+    if (!pmPatternDeadCells(chip, cellBackground, options->blankMask)) {
+	psFree(cellBackground);
+	psFree(view);
+	return false;
+    }
+    psFree(cellBackground);
+    psFree(view);
+
+    psMetadataAddBool(hdu->header, PS_LIST_TAIL, "PTRN_DED", PS_META_REPLACE, "PATTERN.DEADCELLS applied", true);
+    return true;
 }
 
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendReadout.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendReadout.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageDetrendReadout.c	(revision 42167)
@@ -126,6 +126,7 @@
 
     // measure the overscan-subtracted readoutBackground here (or subtract the overscan value?)
-    if (1) {
-	psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN);
+    // XXX this is the measurements and should be independent of the pattern masking
+    if (options->doPatternDeadCells) {
+	psStats *stats = psStatsAlloc (PS_STAT_ROBUST_MEDIAN | PS_STAT_ROBUST_STDEV);
 	psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS);
 	psImageBackground (stats, NULL, input->image, NULL, 0xffff, rng);
@@ -134,4 +135,5 @@
 	pmHDU *hdu = pmHDUFromReadout(input);  // HDU of interest
 	psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_VAL", PS_META_REPLACE, "Median cell background", stats->robustMedian);
+	psMetadataAddF32(hdu->header, PS_LIST_TAIL, "BACK_ERR", PS_META_REPLACE, "Stdev of cell background", stats->robustStdev);
 	psFree (stats);
 	psFree (rng);
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageLoop.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageLoop.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageLoop.c	(revision 42167)
@@ -171,17 +171,7 @@
         }
 
-        // Apply the pattern correction
-        // XX if (options->checkCellFailures) {
-        // XX   if (!ppImageDetrendPatternCellFailures(config,chip,view,options)) {
-        // XX     ESCAPE("Unable to apply pattern corrections");
-        // XX   }
-        // XX }
-
-
         // Apply the fringe correction
-        if (options->doFringe) {
-            if (!ppImageDetrendFringeApply(config, chip, view, options)) {
-                ESCAPE("Unable to defringe");
-            }
+	if (!ppImageDetrendFringeApply(config, chip, view, options)) {
+	    ESCAPE("Unable to defringe");
         }
 
@@ -191,9 +181,7 @@
         }
 
-        // Apply the pattern correction
-        if (options->doPatternRow || options->doPatternCell || options->doPatternContinuity) {
-          if (!ppImageDetrendPatternApply(config,chip,view,options)) {
-            ESCAPE("Unable to apply pattern corrections");
-          }
+        // Apply the pattern correction (only done if requested)
+	if (!ppImageDetrendPatternApply(config,chip,view,options)) {
+            ESCAPE("Problem applying pattern corrections");
         }
 
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageOptions.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageOptions.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageOptions.c	(revision 42167)
@@ -290,4 +290,5 @@
     options->doPatternCell = psMetadataLookupBool(NULL, recipe, "PATTERN.CELL");
     options->doPatternContinuity = psMetadataLookupBool(NULL, recipe, "PATTERN.CONTINUITY");
+    options->doPatternDeadCells = psMetadataLookupBool(NULL, recipe, "PATTERN.DEAD.CELLS");
 
     options->doMaskStats = psMetadataLookupBool(NULL, recipe, "MASK.STATS");
Index: /branches/eam_branches/ipp-20220316/ppImage/src/ppImageParseCamera.c
===================================================================
--- /branches/eam_branches/ipp-20220316/ppImage/src/ppImageParseCamera.c	(revision 42166)
+++ /branches/eam_branches/ipp-20220316/ppImage/src/ppImageParseCamera.c	(revision 42167)
@@ -190,4 +190,15 @@
 	    // an empty or invalid file may have been generated -- we want to skip, not raise an error
 	    pmFPAfile *PRAfile = psMetadataLookupPtr (NULL, config->files, "PPIMAGE.PATTERN.ROW.AMP");
+	    if (PRAfile) {
+	      PRAfile->state |= PM_FPA_STATE_INACTIVE;
+	    }
+        }
+    }
+    if (options->doPatternDeadCells) {
+        if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.PATTERN.DEAD.CELLS", "PATTERN.DEAD.CELLS",
+			       PM_FPA_FILE_PATTERN_DEAD_CELLS, PM_DETREND_TYPE_PATTERN_DEAD_CELLS)) {
+            psWarning ("Can't find a pattern dead cells source");
+	    // an empty or invalid file may have been generated -- we want to skip, not raise an error
+	    pmFPAfile *PRAfile = psMetadataLookupPtr (NULL, config->files, "PPIMAGE.PATTERN.DEAD.CELLS");
 	    if (PRAfile) {
 	      PRAfile->state |= PM_FPA_STATE_INACTIVE;