Index: /branches/eam_branch_20081230/ppArith/src/ppArith.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArith.c	(revision 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArith.c	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.4.32.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:38:08 $
+ *  @version $Revision: 1.4.32.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -23,9 +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 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArith.h	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.3.32.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:37:55 $
+ *  @version $Revision: 1.3.32.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -17,29 +17,39 @@
 /// @addtogroup ppArith
 /// @{
-#define PPARITH_RECIPE "PPARITH"            /** Name of the recipe to use */
+#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 */
+/**
+ * Parse the arguments
+ */
+bool ppArithArguments(int argc, char *argv[], ///< Command-line arguments 
+                      pmConfig *config    ///< Configuration 
     );
 
-/// Parse the camera input
-bool ppArithCamera(pmConfig *config       /**< Configuration */
+/**
+ * Parse the camera input
+ */
+bool ppArithCamera(pmConfig *config       ///< Configuration 
     );
 
-/// Loop over the FPA hierarchy
-bool ppArithLoop(pmConfig *config         /**< Configuration */
+/**
+ * Loop over the FPA hierarchy
+ */
+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 */
+/**
+ * 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 
     );
 
-/// Put the program version information into a metadata
-void ppArithVersionMetadata(psMetadata *metadata /**< Metadata to populate */
+/**
+ * Put the program version information into a metadata
+ */
+void ppArithVersionMetadata(psMetadata *metadata ///< Metadata to populate
     );
 
Index: /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c	(revision 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithArguments.c	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.4.30.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:38:25 $
+ *  @version $Revision: 1.4.30.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -22,8 +22,10 @@
 #include "ppArith.h"
 
-// Print usage information and die
-static void usage(const char *program,  // Name of the program
-                  psMetadata *arguments, // Command-line arguments
-                  pmConfig *config      // Configuration
+/**
+ * Print usage information and die
+ */
+static void usage(const char *program,  ///< Name of the program
+                  psMetadata *arguments, ///< Command-line arguments
+                  pmConfig *config      ///< Configuration
     )
 {
@@ -40,12 +42,14 @@
 }
 
-// Get a string value from the command-line and add it to the target
-static bool valueArgStr(psMetadata *arguments, // Command-line arguments
-                        const char *argName, // Argument name in the command-line arguments
-                        const char *mdName, // Name for value in the metadata
-                        psMetadata *target // Target metadata to which to add value
+/**
+ * Get a string value from the command-line and add it to the target
+ */
+static bool valueArgStr(psMetadata *arguments, ///< Command-line arguments
+                        const char *argName, ///< Argument name in the command-line arguments
+                        const char *mdName, ///< Name for value in the metadata
+                        psMetadata *target ///< Target metadata to which to add value
                         )
 {
-    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);
@@ -55,14 +59,13 @@
 
 /**
- * \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
-                     const char *comment, // Description of the file
-                     pmConfig *config // Configuration
+static void fileList(const char *file, ///< The symbolic name for the file
+                     const char *name, ///< The name of the file
+                     const char *comment, ///< Description of the file
+                     pmConfig *config ///< Configuration
     )
 {
-    psArray *files = psArrayAlloc(1); // Array with file names
+    psArray *files = psArrayAlloc(1); ///< Array with file names
     files->data[0] = psStringCopy(name);
     psMetadataAddArray(config->arguments, PS_LIST_TAIL, file, 0, comment, files);
@@ -75,5 +78,5 @@
     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);
@@ -88,6 +91,6 @@
     bool isMask = psMetadataLookupBool(NULL, arguments, "-mask"); // Are we dealing with masks?
     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 *inFilerule = isMask ? "PPARITH.INPUT.MASK" : "PPARITH.INPUT.IMAGE"; ///< Input 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);
@@ -95,8 +98,8 @@
                      "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.");
@@ -115,5 +118,5 @@
 
     // 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 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithLoop.c	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.6.28.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:39:11 $
+ *  @version $Revision: 1.6.28.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -28,10 +28,10 @@
     PS_ASSERT_PTR_NON_NULL(config, false);
 
-    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 */
+    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
     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) {
@@ -45,14 +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 */
+    psMetadataIterator *iter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, fileRegex); ///< Iterator
+    psMetadataItem *item = psMetadataGetAndIncrement(iter); ///< Item from iteration
     input1 = item->data.V;
     assert(input1);                     // It should be there!
@@ -63,6 +63,6 @@
     psFree(iter);
 
-    pmFPAview *view = pmFPAviewAlloc(0); /** Pointer into FPA hierarchya */
-    pmHDU *lastHDU = NULL;              /** Last HDU that was updated */
+    pmFPAview *view = pmFPAviewAlloc(0); ///< Pointer into FPA hierarchy
+    pmHDU *lastHDU = NULL;              ///< Last HDU that was updated
 
     // Iterate over the FPA hierarchy
@@ -71,8 +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))) {
@@ -90,8 +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))) {
@@ -117,12 +117,12 @@
             }
 
-            pmReadout *outRO;           // Readout of interest
+            pmReadout *outRO;           ///< Readout of interest
             while ((outRO = pmFPAviewNextReadout(view, output->fpa, 1))) {
                 if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
                     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 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithReadout.c	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.2.32.2 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:39:32 $
+ *  @version $Revision: 1.2.32.3 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -29,9 +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;
@@ -54,5 +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;
@@ -73,5 +73,5 @@
 
     // Look up appropriate values
-    const char *op = psMetadataLookupStr(NULL, config->arguments, "OPERATION"); // Operation to perform
+    const char *op = psMetadataLookupStr(NULL, config->arguments, "OPERATION"); ///< Operation to perform
 
     if (input2) {
Index: /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c
===================================================================
--- /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c	(revision 21238)
+++ /branches/eam_branch_20081230/ppArith/src/ppArithVersion.c	(revision 21239)
@@ -6,6 +6,6 @@
  *
  *  @author IfA
- *  @version $Revision: 1.1.32.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2009-01-30 01:39:49 $
+ *  @version $Revision: 1.1.32.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-01-30 22:00:45 $
  *  Copyright 2009 Institute for Astronomy, University of Hawaii
  */
@@ -22,9 +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;
@@ -33,6 +33,6 @@
 psString ppArithVersionLong(void)
 {
-    psString version = ppArithVersion(); /** Version, to return */
-    psString tag = psStringStripCVS(cvsTag, "Name"); // CVS tag
+    psString version = ppArithVersion(); ///< Version, to return
+    psString tag = psStringStripCVS(cvsTag, "Name"); ///< CVS tag
     psStringAppend(&version, " (cvs tag %s) %s, %s", tag, __DATE__, __TIME__);
     psFree(tag);
@@ -45,13 +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);
