Index: /branches/eam_branch_20081230/ppArith/src/ppArith.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArith.c	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArith.c	(revision 21229)
@@ -1,2 +1,14 @@
+/** @file ppArith.c
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.4.32.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:38:08 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -11,9 +23,9 @@
 int main(int argc, char *argv[])
 {
-    psExit exitValue = PS_EXIT_SUCCESS; // Exit value
+    psExit exitValue = PS_EXIT_SUCCESS; /** Exit value */
     psTimerStart("ppArith");
     psLibInit(NULL);
 
-    pmConfig *config = pmConfigRead(&argc, argv, PPARITH_RECIPE); // Configuration
+    pmConfig *config = pmConfigRead(&argc, argv, PPARITH_RECIPE); /** Configuration */
     if (!config) {
         psErrorStackPrint(stderr, "Error reading configuration.");
Index: /branches/eam_branch_20081230/ppArith/src/ppArith.h
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArith.h	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArith.h	(revision 21229)
@@ -1,32 +1,48 @@
+/** @file ppArith.h
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.3.32.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:37:55 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+
 #ifndef PP_ARITH_H
 #define PP_ARITH_H
 
-#define PPARITH_RECIPE "PPARITH"            /// Name of the recipe to use
+/// @addtogroup ppArith
+/// @{
+#define PPARITH_RECIPE "PPARITH"            /** Name of the recipe to use */
 
 /// Parse the arguments
-bool ppArithArguments(int argc, char *argv[], ///< Command-line arguments
-                      pmConfig *config    ///< Configuration
+bool ppArithArguments(int argc, char *argv[], /**< Command-line arguments */
+                      pmConfig *config    /**< Configuration */
     );
 
 /// Parse the camera input
-bool ppArithCamera(pmConfig *config       ///< Configuration
+bool ppArithCamera(pmConfig *config       /**< Configuration */
     );
 
 /// Loop over the FPA hierarchy
-bool ppArithLoop(pmConfig *config         ///< Configuration
+bool ppArithLoop(pmConfig *config         /**< Configuration */
     );
 
 /// Perform arithmetic on the readout
-bool ppArithReadout(pmReadout *output,  ///< Output readout
-                    const pmReadout *input1, ///< Input readout
-                    const pmReadout *input2, ///< Input readout
-                    const pmConfig *config, ///< Configuration
-                    const pmFPAview *view ///< View of readout on which to operate
+bool ppArithReadout(pmReadout *output,  /**< Output readout */
+                    const pmReadout *input1, /**< Input readout */
+                    const pmReadout *input2, /**< Input readout */
+                    const pmConfig *config, /**< Configuration */
+                    const pmFPAview *view /**< View of readout on which to operate */
     );
 
 /// Put the program version information into a metadata
-void ppArithVersionMetadata(psMetadata *metadata ///< Metadata to populate
+void ppArithVersionMetadata(psMetadata *metadata /**< Metadata to populate */
     );
 
+///@}
 
 #endif
Index: /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c	(revision 21229)
@@ -1,2 +1,14 @@
+/** @file ppArithArguments.c
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.4.30.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:38:25 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -35,5 +47,5 @@
                         )
 {
-    psString value = psMetadataLookupStr(NULL, arguments, argName); // Value of interest
+    psString value = psMetadataLookupStr(NULL, arguments, argName); /** Value of interest */
     if (value && strlen(value) > 0) {
         return psMetadataAddStr(target, PS_LIST_TAIL, mdName, 0, NULL, value);
@@ -42,5 +54,8 @@
 }
 
-// Add a single filename to the arguments as an array, so that it can be used with pmFPAfileBindFromArgs, etc
+/**
+ * \fn fileList
+ * Add a single filename to the arguments as an array, so that it can be used with pmFPAfileBindFromArgs, etc
+ */
 static void fileList(const char *file, // The symbolic name for the file
                      const char *name, // The name of the file
@@ -60,5 +75,5 @@
     assert(config);
 
-    psMetadata *arguments = psMetadataAlloc(); // Command-line arguments
+    psMetadata *arguments = psMetadataAlloc(); /** Command-line arguments */
     psMetadataAddStr(arguments, PS_LIST_TAIL, "-file1", 0, "First image", NULL);
     psMetadataAddStr(arguments, PS_LIST_TAIL, "-op", 0, "Operation to perform", NULL);
@@ -74,5 +89,5 @@
     psMetadataAddBool(config->arguments, PS_LIST_TAIL, "MASK", 0, "Produce a mask image?", isMask);
     const char *inFilerule = isMask ? "PPARITH.INPUT.MASK" : "PPARITH.INPUT.IMAGE"; // Input file rule
-    const char *outFilerule = isMask ? "PPARITH.OUTPUT.MASK" : "PPARITH.OUTPUT.IMAGE"; // Output file rule
+    const char *outFilerule = isMask ? "PPARITH.OUTPUT.MASK" : "PPARITH.OUTPUT.IMAGE"; /** Output file rule */
     psMetadataAddStr(config->arguments, PS_LIST_TAIL, "FILERULE.INPUT", 0,
                      "File rule for input", inFilerule);
@@ -80,8 +95,8 @@
                      "File rule for output", outFilerule);
 
-    bool status = false;                // Status for file definition
+    bool status = false;                /** Status for file definition */
 
     // First file
-    const char *name1 = psMetadataLookupStr(NULL, arguments, "-file1"); // Name of first image
+    const char *name1 = psMetadataLookupStr(NULL, arguments, "-file1"); /** Name of first image */
     if (!name1 || strlen(name1) == 0) {
         psError(PS_ERR_UNEXPECTED_NULL, true, "No input image specified.");
@@ -100,5 +115,5 @@
 
     // Second file is optional (won't be one for unary operations)
-    const char *name2 = psMetadataLookupStr(NULL, arguments, "-file2"); // Name of second image
+    const char *name2 = psMetadataLookupStr(NULL, arguments, "-file2"); /** Name of second image */
     if (name2 && strlen(name2) > 0) {
         fileList("INPUT2", name2, "Name of the second input image", config);
Index: /branches/eam_branch_20081230/ppArith/src/ppArithLoop.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithLoop.c	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithLoop.c	(revision 21229)
@@ -1,2 +1,14 @@
+/** @file ppArithLoop.c
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.6.28.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:39:11 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -16,10 +28,10 @@
     PS_ASSERT_PTR_NON_NULL(config, false);
 
-    bool mdok;                          // Status of MD lookup
+    bool mdok;                          /** Status of MD lookup */
     const char *statsName = psMetadataLookupStr(&mdok, config->arguments, "STATS"); // Filename for statistics
-    psMetadata *stats = NULL;           // Container for statistics
-    FILE *statsFile = NULL;             // File stream for statistics
+    psMetadata *stats = NULL;           /** Container for statistics */
+    FILE *statsFile = NULL;             /** File stream for statistics */
     if (statsName && strlen(statsName) > 0) {
-        psString resolved = pmConfigConvertFilename(statsName, config, true, true); // Resolved filename
+        psString resolved = pmConfigConvertFilename(statsName, config, true, true); /** Resolved filename */
         statsFile = fopen(resolved, "w");
         if (!statsFile) {
@@ -33,14 +45,14 @@
     }
 
-    const char *outName = psMetadataLookupStr(NULL, config->arguments, "FILERULE.OUTPUT"); // Output filerule
-    pmFPAfile *output = psMetadataLookupPtr(NULL, config->files, outName); // Output file
+    const char *outName = psMetadataLookupStr(NULL, config->arguments, "FILERULE.OUTPUT"); /** Output filerule */
+    pmFPAfile *output = psMetadataLookupPtr(NULL, config->files, outName); /** Output file */
     assert(output);                     // We added it earlier
 
-    const char *inName = psMetadataLookupStr(NULL, config->arguments, "FILERULE.INPUT"); // Input filerule
-    pmFPAfile *input1 = NULL, *input2 = NULL; // Input files
-    psString fileRegex = NULL;          // Regular expression to find input files
+    const char *inName = psMetadataLookupStr(NULL, config->arguments, "FILERULE.INPUT"); /** Input filerule */
+    pmFPAfile *input1 = NULL, *input2 = NULL; /** Input files */
+    psString fileRegex = NULL;   /** Regular expression to find input files */
     psStringAppend(&fileRegex, "^%s$", inName);
     psMetadataIterator *iter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, fileRegex); // Iterator
-    psMetadataItem *item = psMetadataGetAndIncrement(iter); // Item from iteration
+    psMetadataItem *item = psMetadataGetAndIncrement(iter); /** Item from iteration */
     input1 = item->data.V;
     assert(input1);                     // It should be there!
@@ -51,6 +63,6 @@
     psFree(iter);
 
-    pmFPAview *view = pmFPAviewAlloc(0); // Pointer into FPA hierarchy
-    pmHDU *lastHDU = NULL;              // Last HDU that was updated
+    pmFPAview *view = pmFPAviewAlloc(0); /** Pointer into FPA hierarchya */
+    pmHDU *lastHDU = NULL;              /** Last HDU that was updated */
 
     // Iterate over the FPA hierarchy
@@ -59,8 +71,8 @@
     }
 
-    pmChip *outChip;                    // Output chip of interest
+    pmChip *outChip;                    /** Output chip of interest */
     while ((outChip = pmFPAviewNextChip(view, output->fpa, 1)) != NULL) {
-        pmChip *inChip1 = pmFPAviewThisChip(view, input1->fpa); // Input chip of interest
-        pmChip *inChip2 = input2 ? pmFPAviewThisChip(view, input2->fpa) : NULL; // Input chip of interest
+        pmChip *inChip1 = pmFPAviewThisChip(view, input1->fpa); /** Input chip of interest */
+        pmChip *inChip2 = input2 ? pmFPAviewThisChip(view, input2->fpa) : NULL; /** Input chip of interest */
         if (inChip2 && ((!inChip1->file_exists && inChip2->file_exists) ||
                         (inChip1->file_exists && !inChip2->file_exists))) {
@@ -78,8 +90,8 @@
         }
 
-        pmCell *outCell;                // Cell of interest
+        pmCell *outCell;                /** Cell of interest */
         while ((outCell = pmFPAviewNextCell(view, output->fpa, 1)) != NULL) {
-            pmCell *inCell1 = pmFPAviewThisCell(view, input1->fpa); // Input cell of interest
-            pmCell *inCell2 = input2 ? pmFPAviewThisCell(view, input2->fpa) : NULL; // Input cell of interest
+            pmCell *inCell1 = pmFPAviewThisCell(view, input1->fpa); /** Input cell of interest */
+            pmCell *inCell2 = input2 ? pmFPAviewThisCell(view, input2->fpa) : NULL; /** Input cell of interest */
             if (inCell2 && ((!inCell1->file_exists && inCell2->file_exists) ||
                             (inCell1->file_exists && !inCell2->file_exists))) {
@@ -110,7 +122,7 @@
                     return false;
                 }
-                pmReadout *inRO1 = pmFPAviewThisReadout(view, input1->fpa);// Input readout of interest
+                pmReadout *inRO1 = pmFPAviewThisReadout(view, input1->fpa);/** Input readout of interest */
                 pmReadout *inRO2 = input2 ? pmFPAviewThisReadout(view, input2->fpa) :
-                    NULL;// Input readout of interest
+                    NULL;/** Input readout of interest */
 
                 if (inRO2 && ((!inRO1->data_exists && inRO2->data_exists) ||
Index: /branches/eam_branch_20081230/ppArith/src/ppArithReadout.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithReadout.c	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithReadout.c	(revision 21229)
@@ -1,2 +1,14 @@
+/** @file ppArithReadout.c
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.2.32.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:39:32 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -17,9 +29,9 @@
     PS_ASSERT_PTR_NON_NULL(view, false);
 
-    bool mdok;                          // Status of MD lookup
+    bool mdok;                          /** Status of MD lookup */
     bool isMask = psMetadataLookupBool(&mdok, config->arguments, "MASK");
 
-    psImage *inImage1;  // Input image 1
-    psImage *outImage;  // Output image
+    psImage *inImage1;  /** Input image 1 */
+    psImage *outImage;  /** Output image */
     if (isMask) {
         inImage1 = input1->mask;
@@ -42,5 +54,5 @@
     PS_ASSERT_IMAGE_NON_NULL(inImage1, false);
 
-    psImage *inImage2 = NULL;           // Input image 2
+    psImage *inImage2 = NULL;           /** Input image 2 */
     if (input2) {
         inImage2 = isMask ? input2->mask : input2->image;
Index: /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c	(revision 21228)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c	(revision 21229)
@@ -1,2 +1,14 @@
+/** @file ppArithVersion.c
+ *
+ *  @brief
+ *
+ *  @ingroup ppArith
+ *
+ *  @author IfA
+ *  @version $Revision: 1.1.32.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 01:39:49 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -10,9 +22,9 @@
 #include "ppArith.h"
 
-static const char *cvsTag = "$Name: not supported by cvs2svn $";// CVS tag name
+static const char *cvsTag = "$Name: not supported by cvs2svn $";/** CVS tag name */
 
 psString ppArithVersion(void)
 {
-    psString version = NULL;            // Version, to return
+    psString version = NULL;            /** Version, to return */
     psStringAppend(&version, "%s-%s",PACKAGE_NAME,PACKAGE_VERSION);
     return version;
@@ -21,5 +33,5 @@
 psString ppArithVersionLong(void)
 {
-    psString version = ppArithVersion(); // Version, to return
+    psString version = ppArithVersion(); /** Version, to return */
     psString tag = psStringStripCVS(cvsTag, "Name"); // CVS tag
     psStringAppend(&version, " (cvs tag %s) %s, %s", tag, __DATE__, __TIME__);
@@ -33,13 +45,13 @@
     PS_ASSERT_METADATA_NON_NULL(metadata,);
 
-    psString pslib = psLibVersionLong();// psLib version
-    psString psmodules = psModulesVersionLong(); // psModules version
-    psString ppStats = ppStatsVersionLong(); // ppStats version
-    psString ppArith = ppArithVersionLong(); // ppArith version
+    psString pslib = psLibVersionLong();/** psLib version */
+    psString psmodules = psModulesVersionLong(); /** psModules version */
+    psString ppStats = ppStatsVersionLong(); /** ppStats version */
+    psString ppArith = ppArithVersionLong(); /** ppArith version */
 
-    psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now
-    psString timeString = psTimeToISO(time); // The time in an ISO string
+    psTime *time = psTimeGetNow(PS_TIME_TAI); /** The time now */
+    psString timeString = psTimeToISO(time); /** The time in an ISO string */
     psFree(time);
-    psString head = NULL;               // Head string
+    psString head = NULL;               /** Head string */
     psStringAppend(&head, "ppArith processing at %s. Component information:", timeString);
     psFree(timeString);