Index: trunk/ppStack/src/ppStack.h
===================================================================
--- trunk/ppStack/src/ppStack.h	(revision 19214)
+++ trunk/ppStack/src/ppStack.h	(revision 19337)
@@ -5,5 +5,57 @@
 #define PPSTACK_INSPECT_PIXELS "PPSTACK.PIXELS" // Name of rejected pixels metadata items
 
+#include <pslib.h>
 #include <psmodules.h>
+
+// Mask values for inputs
+typedef enum {
+    PPSTACK_MASK_MATCH  = 0x01,         // PSF-matching failed
+    PPSTACK_MASK_REJECT = 0x02,         // Rejection failed
+    PPSTACK_MASK_BAD    = 0x04,         // Bad image (too many pixels rejected)
+    PPSTACK_MASK_ALL    = 0xff          // All errors
+} ppStackMask;
+
+// Thread for stacking chunks
+//
+// Each input file contributes a readout, into which is read a chunk from that file
+typedef struct {
+    psArray *readouts;                  // Input readouts to read and stack
+    bool read;                          // Has the scan been read?
+    bool busy;                          // Is the scan being processed?
+    int firstScan;                      // First row of the chunk to be read for this group
+    int lastScan;                       // Last row of the chunk to be read for this group
+} ppStackThread;
+
+// Allocator
+ppStackThread *ppStackThreadAlloc(psArray *readouts // Inputs readouts to read and stack
+    );
+
+// Data for threads
+typedef struct {
+    psArray *threads;                   // Threads doing stacking
+    int lastScan;                       // Last row that's been read
+    psArray *imageFits;                 // FITS file pointers for images
+    psArray *maskFits;                  // FITS file pointers for masks
+    psArray *weightFits;                // FITS file pointers for weights
+} ppStackThreadData;
+
+// Set up thread data
+ppStackThreadData *ppStackThreadDataSetup(const psArray *cells, // Array of input cells
+                                          const psArray *imageNames, // Names of images to read
+                                          const psArray *maskNames, // Names of masks to read
+                                          const psArray *weightNames, // Names of weight maps to read
+                                          const pmConfig *config // Configuration
+    );
+
+// Read chunk into the first available file thread
+ppStackThread *ppStackThreadRead(bool *status, // Status of read
+                                 ppStackThreadData *stack, // Stacks available for reading
+                                 pmConfig *config, // Configuration
+                                 int numChunk, // Chunk number (only for interest)
+                                 int overlap // Overlap between subsequent scans
+    );
+
+// Initialise the threads
+void ppStackThreadInit(void);
 
 // Setup command-line arguments
@@ -31,9 +83,15 @@
 
 // Perform stacking on a readout
-bool ppStackReadoutInitial(const pmConfig *config,   // Configuration
-                    pmReadout *outRO,   // Output readout
-                    const psArray *readouts, // Input readouts
-                    const psArray *regions, // Array with array of regions used in each PSF matching
-                    const psArray *kernels // Array with array of kernels used in each PSF matching
+//
+// Returns an array of pixels to inspect for each input image
+psArray *ppStackReadoutInitial(const pmConfig *config,   // Configuration
+                               pmReadout *outRO,   // Output readout
+                               const psArray *readouts, // Input readouts
+                               const psArray *regions, // Array with array of regions used in each PSF match
+                               const psArray *kernels // Array with array of kernels used in each PSF match
+    );
+
+// Thread entry point for ppStackReadoutInitial
+bool ppStackReadoutInitialThread(psThreadJob *job // Job to process
     );
 
@@ -43,4 +101,8 @@
                          const psArray *readouts, // Input readouts
                          const psArray *rejected // Array with pixels rejected in each image
+    );
+
+// Thread entry point for ppStackReadoutFinal
+bool ppStackReadoutFinalThread(psThreadJob *job // Job to process
     );
 
@@ -62,11 +124,11 @@
 
 /// Convolve image to match specified seeing
-bool ppStackMatch(pmReadout *readout, ///< Readout to be convolved; replaced with output
+bool ppStackMatch(pmReadout *readout, // Readout to be convolved; replaced with output
                   psArray **regions, // Array of regions used in each PSF matching, returned
                   psArray **kernels, // Array of kernels used in each PSF matching, returned
-                  const psArray *sources, ///< Array of sources
-                  const pmPSF *psf,     ///< Target PSF
-                  psRandom *rng,        ///< Random number generator
-                  const pmConfig *config ///< Configuration
+                  const psArray *sources, // Array of sources
+                  const pmPSF *psf,     // Target PSF
+                  psRandom *rng,        // Random number generator
+                  const pmConfig *config // Configuration
     );
 
@@ -75,7 +137,7 @@
 ///
 /// Corrects the sources to have consistent magnitudes.  Returns the source lists.
-psArray *ppStackSourceListAdd(psArray *lists, ///< List to which to add, or NULL
-                              psArray *sources, ///< Sources to add
-                              const pmConfig *config ///< Configuration
+psArray *ppStackSourceListAdd(psArray *lists, // List to which to add, or NULL
+                              psArray *sources, // Sources to add
+                              const pmConfig *config // Configuration
     );
 
@@ -83,10 +145,10 @@
 ///
 /// Corrects the sources to have consistent magnitudes where possible.  Returns the sources
-psArray *ppStackSourceListCombine(psArray *lists, ///< Source lists
-                                  const pmConfig *config ///< Configuration
+psArray *ppStackSourceListCombine(psArray *lists, // Source lists
+                                  const pmConfig *config // Configuration
     );
 
 /// Print sources into a ds9 regions file
-void ppStackSourcesPrint(const psArray *sources ///< Sources to print
+void ppStackSourcesPrint(const psArray *sources // Sources to print
     );