Index: /branches/eam_branch_20081230/pswarp/src/pswarp.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarp.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarp.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarp.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.13.8.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
Index: /branches/eam_branch_20081230/pswarp/src/pswarp.h
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarp.h	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarp.h	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarp.h
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.16.8.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -14,12 +26,14 @@
 
 #include "pswarpErrorCodes.h"
-#define PSWARP_RECIPE  "PSWARP" // Name of the recipe to use
-#define PSASTRO_RECIPE "PSASTRO" // Name of the recipe to use
+#define PSWARP_RECIPE  "PSWARP" ///< Name of the recipe to use
+#define PSASTRO_RECIPE "PSASTRO" ///< Name of the recipe to use
 
-#define PSWARP_ANALYSIS_VARFACTOR "PSWARP.VARFACTOR" // Name for variance factor in analysis metadata
-#define PSWARP_ANALYSIS_GOODPIX   "PSWARP.GOODPIX" // Name for number of good pixels in analysis metadata
+#define PSWARP_ANALYSIS_VARFACTOR "PSWARP.VARFACTOR" ///< Name for variance factor in analysis metadata
+#define PSWARP_ANALYSIS_GOODPIX   "PSWARP.GOODPIX" ///< Name for number of good pixels in analysis metadata
 
-// a single pswarpMap converts coordinates from one image to a second image
-// the linear model is only valid over a limited range of pixels
+/**
+ * a single pswarpMap converts coordinates from one image to a second image
+ * the linear model is only valid over a limited range of pixels
+ */
 typedef struct {
     double Xo, Xx, Xy;
@@ -29,15 +43,16 @@
 } pswarpMap;
 
-// the pswarpMapGrid carries a collection of pswarpMag structures representing the
-// local value of the pswarpMap at different locations in the image.
+/* the pswarpMapGrid carries a collection of pswarpMag structures representing 
+ * the local value of the pswarpMap at different locations in the image.
+ */
 typedef struct {
     pswarpMap ***maps;
-    int nXpts, nYpts;                   // number of x,y samples in the grid
-    int nXpix, nYpix;                   // x,y spacing in src image pixels of grid samples
-    double xMin,  yMin;                 // coordinate of first grid sample
+    int nXpts, nYpts;                   ///< number of x,y samples in the grid
+    int nXpix, nYpix;                   ///< x,y spacing in src image pixels of grid samples
+    double xMin,  yMin;                 ///< coordinate of first grid sample
 } pswarpMapGrid;
 
 typedef struct {
-    // values which are common to all tiles
+    /** values which are common to all tilesa */
     pmReadout *input;
     pmReadout *output;
@@ -46,11 +61,11 @@
     psImage *region;
 
-    // input values for this tile
+    /** input values for this tile */
     int gridX;
     int gridY;
 
-    // output values for this tile
-    long goodPixels;                    // Number of good pixels
-    int xMin, xMax, yMin, yMax;         // Bounds of tile
+    /** output values for this tile */
+    long goodPixels;                    //< Number of good pixels
+    int xMin, xMax, yMin, yMax;         //< Bounds of tile
 } pswarpTransformTileArgs;
 
@@ -91,4 +106,6 @@
     );
 
-// define threads for this program
+/**
+ * define threads for this program
+ */
 bool pswarpSetThreads ();
Index: /branches/eam_branch_20081230/pswarp/src/pswarpArguments.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpArguments.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpArguments.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpArguments.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.22.8.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 # include <glob.h>
@@ -26,5 +38,5 @@
 
     {
-        int arg;                        // Argument Number
+        int arg;                        ///< Argument Number
         if ((arg = psArgumentGet(argc, argv, "-psphot-visual"))) {
             psArgumentRemove(arg, &argc, argv);
@@ -105,5 +117,7 @@
 }
 
-// Parse the recipe and format into the arguments
+/**
+ * Parse the recipe and format into the arguments
+ */
 bool pswarpOptions(pmConfig *config)
 {
@@ -116,5 +130,5 @@
 
     // Get grid size
-    bool status;                        // Status of MD lookup
+    bool status;                        ///< Status of MD lookup
     int nGridX = psMetadataLookupS32(&status, recipe, "GRID.NX");
     if (!status || nGridX <= 0) {
@@ -129,10 +143,10 @@
 
     // Get interpolation mode
-    const char *name = psMetadataLookupStr (&status, recipe, "INTERPOLATION.MODE"); // Name of interp mode
+    const char *name = psMetadataLookupStr (&status, recipe, "INTERPOLATION.MODE"); ///< Name of interp mode
     if (!name) {
         name = "BILINEAR";
         psLogMsg("pswarp", 3, "defaulting to %s interpolation", name);
     }
-    psImageInterpolateMode interpolationMode = psImageInterpolateModeFromString(name); // Mode for interp.
+    psImageInterpolateMode interpolationMode = psImageInterpolateModeFromString(name); ///< Mode for interp.
     if (interpolationMode == PS_INTERPOLATE_NONE) {
         interpolationMode = PS_INTERPOLATE_BILINEAR;
@@ -148,5 +162,5 @@
     }
 
-    float poorFrac = psMetadataLookupF32(&status, recipe, "POOR.FRAC"); // Frac of bad flux for a "poor"
+    float poorFrac = psMetadataLookupF32(&status, recipe, "POOR.FRAC"); ///< Frac of bad flux for a "poor"
     if (!status) {
         poorFrac = 0.0;
@@ -154,5 +168,5 @@
     }
 
-    float acceptFrac = psMetadataLookupF32(&status, recipe, "ACCEPT.FRAC"); // Min fraction of good pixels
+    float acceptFrac = psMetadataLookupF32(&status, recipe, "ACCEPT.FRAC"); ///< Min fraction of good pixels
     if (!status) {
         acceptFrac = 0.0;
@@ -194,5 +208,5 @@
     if (dump_file) {
         const char *skyCamera = psMetadataLookupStr(NULL, config->arguments,
-                                                    "SKYCELL.CAMERA");  // Name of camera for skycell
+                                                    "SKYCELL.CAMERA");  ///< Name of camera for skycell
         pmConfigCamerasCull(config, skyCamera);
         pmConfigRecipesCull(config, "PSWARP,PPSTATS,PSPHOT,MASKS");
Index: /branches/eam_branch_20081230/pswarp/src/pswarpCleanup.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpCleanup.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpCleanup.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpCleanup.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.7.20.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
Index: /branches/eam_branch_20081230/pswarp/src/pswarpDefine.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpDefine.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpDefine.c	(revision 21268)
@@ -1,5 +1,19 @@
+/** @file pswarpDefine.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.14.22.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
-// this function loads the skycell metadata
 
+/**
+ * loads the skycell metadata
+ */
 bool pswarpDefine (pmConfig *config) {
 
@@ -42,6 +56,6 @@
         view->cell = 0;
         view->readout = 0;
-        pmCell *source = pmFPAfileThisCell(config->files, view, "PSWARP.SKYCELL"); // Source cell
-        pmHDU *hdu = pmHDUFromCell(source); // HDU for source
+        pmCell *source = pmFPAfileThisCell(config->files, view, "PSWARP.SKYCELL"); ///< Source cell
+        pmHDU *hdu = pmHDUFromCell(source); ///< HDU for source
         if (!hdu || !hdu->header) {
             psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find header for sky cell.");
@@ -49,9 +63,9 @@
             return false;
         }
-        int numCols = psMetadataLookupS32(NULL, hdu->header, "NAXIS1"); // Number of columns
-        int numRows = psMetadataLookupS32(NULL, hdu->header, "NAXIS2"); // Number of rows
+        int numCols = psMetadataLookupS32(NULL, hdu->header, "NAXIS1"); ///< Number of columns
+        int numRows = psMetadataLookupS32(NULL, hdu->header, "NAXIS2"); ///< Number of rows
 
-        pmCell *target = pmFPAviewThisCell(view, output->fpa); // Target cell
-        pmReadout *readout = pmReadoutAlloc(target); // Target readout
+        pmCell *target = pmFPAviewThisCell(view, output->fpa); ///< Target cell
+        pmReadout *readout = pmReadoutAlloc(target); ///< Target readout
         readout->image = psImageAlloc(numCols, numRows, PS_TYPE_F32);
         psImageInit(readout->image, NAN);
@@ -72,6 +86,6 @@
     view->cell = 0;
     view->readout = -1;
-    pmHDU *phu = pmFPAviewThisPHU(view, skycell->fpa); // Skycell PHU
-    pmHDU *hdu = pmFPAviewThisHDU(view, skycell->fpa); // Skycell header
+    pmHDU *phu = pmFPAviewThisPHU(view, skycell->fpa); ///< Skycell PHU
+    pmHDU *hdu = pmFPAviewThisHDU(view, skycell->fpa); ///< Skycell header
     bool bilevelAstrometry = false;
     if (phu) {
@@ -83,5 +97,5 @@
 
     // We read from the skycell into the output.  i.e., the output receives the desired astrometry.
-    pmChip *outputChip = pmFPAviewThisChip(view, output->fpa); // Chip in the output
+    pmChip *outputChip = pmFPAviewThisChip(view, output->fpa); ///< Chip in the output
     if (bilevelAstrometry) {
         if (!pmAstromReadBilevelMosaic(output->fpa, phu->header)) {
@@ -104,5 +118,5 @@
     }
 
-    const char *name = psMetadataLookupStr(NULL, input->fpa->concepts, "FPA.OBS"); // Name of FPA
+    const char *name = psMetadataLookupStr(NULL, input->fpa->concepts, "FPA.OBS"); ///< Name of FPA
     view->chip = view->cell = view->readout = -1;
     pmFPAAddSourceFromView(output->fpa, name, view, output->format);
Index: /branches/eam_branch_20081230/pswarp/src/pswarpDefineSkycell.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpDefineSkycell.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpDefineSkycell.c	(revision 21268)
@@ -1,13 +1,27 @@
+/** @file pswarpDefineSkycell.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.10.6.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
-// XXX this function is based on pmFPAfileDefineFromArgs
-// a skycell consists of only one file
+/**
+ * \brief XXX this function is based on pmFPAfileDefineFromArgs
+ * a skycell consists of only one file
 
-// search for argname on the config->argument list
-// construct an FPA based on the files in this list (must represent a single FPA)
-// built the association between the FPA elements (CHIP/CELL) and the files
-// define the pmFPAfile filename and bind it to this FPA
-// save the pmFPAfile on config->files
-// return the pmFPAfile (a view to the one saved on config->files)
+ * search for argname on the config->argument list and construct
+ * an FPA based on the files in this list (must represent a single FPA)
+ * built the association between the FPA elements (CHIP/CELL) and the files
+ * define the pmFPAfile filename and bind it to this FPA
+ * save the pmFPAfile on config->files
+ * @return the pmFPAfile (a view to the one saved on config->files)
+ */
 bool pswarpDefineSkycell (pmFPAfile **outFile, pmConfig **outConfig, pmConfig *config, const char *filename, const char *argname)
 {
@@ -59,9 +73,8 @@
     psFitsClose(fits);
 
-    // XXX format needs to be equivalent to SIMPLE
-    // determine the current format from the header
-    // determine camera if not specified already
+    // We need to force the format for the skycell to be equivalent to SIMPLE.  Determine
+    // the current format from the header; Determine camera if not specified already
     // XXX EAM : this operation should be defined as a pmConfig function (pmConfigCopy?)
-    skyConfig = pmConfigAlloc(0, NULL);
+    skyConfig = pmConfigAlloc();
     skyConfig->user = psMemIncrRefCounter(config->user);
     skyConfig->system = psMemIncrRefCounter(config->system);
Index: /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.c.in
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.c.in	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.c.in	(revision 21268)
@@ -1,2 +1,17 @@
+/** @file pswarpErrorCodes.c.in
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.2.48.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+#include "pslib.h"
+#include "pswarpErrorCodes.h"
+
 /*
  * The line
@@ -5,7 +20,4 @@
  * will be replaced by values from errorCodes.dat
  */
-#include "pslib.h"
-#include "pswarpErrorCodes.h"
-
 void pswarpErrorRegister(void)
 {
@@ -14,5 +26,5 @@
        { PSWARP_ERR_${ErrorCode}, "${ErrorDescription}"},
     };
-    static int nerror = PSWARP_ERR_NERROR - PSWARP_ERR_BASE; // number of values in enum
+    static int nerror = PSWARP_ERR_NERROR - PSWARP_ERR_BASE; ///< number of values in enum
 
     for (int i = 0; i < nerror; i++) {
Index: /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.h.in
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.h.in	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpErrorCodes.h.in	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpErrorCodes.h.in
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.1.48.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #if !defined(PSWARP_ERROR_CODES_H)
 #define PSWARP_ERROR_CODES_H
Index: /branches/eam_branch_20081230/pswarp/src/pswarpFileNames.h
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpFileNames.h	(revision 21268)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpFileNames.h	(revision 21268)
@@ -0,0 +1,51 @@
+/** this file contains the lists of file rules used by pswarpLoop at different analysis steps
+    we use these lists to turn on or off different I/O files at different stages **/
+
+// Lists must end with a NULL
+
+// Lists of file rules for the detectors and skycells, and an independent list of everything else
+
+
+// Lists of file rules for the detectors
+static char *detectorFiles[] = { 
+  "PSWARP.INPUT", 
+  "PSWARP.MASK", 
+  "PSWARP.WEIGHT", 
+  NULL 
+};
+
+// Lists of file rules for the skycells
+static char *skycellFiles[] = { 
+  "PSWARP.OUTPUT", 
+  "PSWARP.OUTPUT.MASK", 
+  "PSWARP.OUTPUT.WEIGHT", 
+  NULL 
+};
+
+// Lists of file rules for photometry
+static char *photFiles[] = { 
+  "PSPHOT.INPUT", 
+  "PSPHOT.OUTPUT",
+#if PSPHOT_FIND_PSF
+  "PSPHOT.INPUT.CMF",
+#endif
+  "PSPHOT.RESID",
+  "PSPHOT.BACKMDL", 
+  "PSPHOT.BACKMDL.STDEV", 
+  "PSPHOT.BACKGND", 
+  "PSPHOT.BACKSUB",
+  "PSPHOT.PSF.SAVE", 
+  "SOURCE.PLOT.MOMENTS", 
+  "SOURCE.PLOT.PSFMODEL",
+  "SOURCE.PLOT.APRESID", 
+  NULL 
+};
+
+// Lists of file rules for the detectors and skycells, and an independent list of everything else
+static char *independentFiles[] = { 
+  "PSWARP.ASTROM", // Read independently from the input pixels
+  "PSWARP.SKYCELL", // Don't care about the skycell once we have its WCS
+  "PSWARP.OUTPUT.SOURCES", // Save these independently so we can do the PSF
+  NULL 
+};
+
Index: /branches/eam_branch_20081230/pswarp/src/pswarpHeadersLoad.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpHeadersLoad.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpHeadersLoad.c	(revision 21268)
@@ -1,12 +1,25 @@
+/** @file pswarpHeadersLoad.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.2.46.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
-// XXX this function should load all of the PSWARP.INPUT headers
-// it should examine the overlap between each chip in PSWARP.INPUT
-// and the output (pswarpMatchRange) and select/de-select the chips
-// and/or cell which contribute pixels.
-
-// pswarpDataLoad should then load the pixel of the needed chips
-
-// all of the different astrometry analysis modes use the same data load loop
+/** XXX this function should load all of the PSWARP.INPUT headers
+ * it should examine the overlap between each chip in PSWARP.INPUT
+ * and the output (pswarpMatchRange) and select/de-select the chips
+ * and/or cell which contribute pixels.
+ *
+ * pswarpDataLoad should then load the pixel of the needed chips
+ *
+ * all of the different astrometry analysis modes use the same data load loop
+ */
 bool pswarpHeadersLoad (pmConfig *config) {
 
Index: /branches/eam_branch_20081230/pswarp/src/pswarpLoop.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpLoop.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpLoop.c	(revision 21268)
@@ -1,30 +1,30 @@
+/** @file pswarpLoop.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.32.8.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #include "pswarp.h"
 #include <ppStats.h>
 
-#define WCS_NONLIN_TOL 0.001            // Non-linear tolerance for header WCS
-#define PSPHOT_FIND_PSF 0               // Use psphot's findPSF function?
-//#define TESTING 1                       // Testing output?
-
-// Lists of file rules for the detectors and skycells, and an independent list of everything else
-// Lists must end with a NULL
-static char *detectorFiles[] = { "PSWARP.INPUT", "PSWARP.MASK", "PSWARP.WEIGHT", NULL };
-static char *skycellFiles[] = { "PSWARP.OUTPUT", "PSWARP.OUTPUT.MASK", "PSWARP.OUTPUT.WEIGHT", NULL };
-static char *photFiles[] = { "PSPHOT.INPUT", "PSPHOT.OUTPUT",
-#if PSPHOT_FIND_PSF
-                             "PSPHOT.INPUT.CMF",
-#endif
-                             "PSPHOT.RESID",
-                             "PSPHOT.BACKMDL", "PSPHOT.BACKMDL.STDEV", "PSPHOT.BACKGND", "PSPHOT.BACKSUB",
-                             "PSPHOT.PSF.SAVE", "SOURCE.PLOT.MOMENTS", "SOURCE.PLOT.PSFMODEL",
-                             "SOURCE.PLOT.APRESID", NULL };
-static char *independentFiles[] = { "PSWARP.ASTROM", // Read independently from the input pixels
-                                    "PSWARP.SKYCELL", // Don't care about the skycell once we have its WCS
-                                    "PSWARP.OUTPUT.SOURCES", // Save these independently so we can do the PSF
-                                    NULL };
-
-// Activate a list of files
-static void fileActivation(pmConfig *config, // Configuration
-                           char **files, // Files to turn on/off
-                           bool state   // Activation state
+#define WCS_NONLIN_TOL 0.001            ///< Non-linear tolerance for header WCS
+#define PSPHOT_FIND_PSF 1               ///< Use psphot's findPSF function?
+#define TESTING 0                       ///< Testing output?
+
+#include "pswarpFileNames.h" ///< Lists of file rules used at different stages
+
+/**
+ * XXX these are generic functions which should be moved to psModules
+ * Activate a list of files
+ */
+static void fileActivation(pmConfig *config, ///< Configuration
+                           char **files, ///< Files to turn on/off
+                           bool state   ///< Activation state
     )
 {
@@ -35,10 +35,12 @@
 }
 
-// Run down the FPA hierarchy, checking files
-static bool ioChecksBefore(pmConfig *config // Configuration
+/**
+ * Run down the FPA hierarchy, checking files
+ */
+static bool ioChecksBefore(pmConfig *config ///< Configuration
                            )
 {
-    pmFPAview *view = pmFPAviewAlloc(0); // View for checking
-    bool status = true;                 // Status of checks
+    pmFPAview *view = pmFPAviewAlloc(0); ///< View for checking
+    bool status = true;                 ///< Status of checks
     status &= pmFPAfileIOChecks(config, view, PM_FPA_BEFORE);
     view->chip = 0;
@@ -50,11 +52,13 @@
 }
 
-// Run up the FPA hierarchy, checking files
-static bool ioChecksAfter(pmConfig *config // Configuration
+/**
+ * Run up the FPA hierarchy, checking files
+ */
+static bool ioChecksAfter(pmConfig *config ///< Configuration
                           )
 {
-    pmFPAview *view = pmFPAviewAlloc(0); // View for checking
+    pmFPAview *view = pmFPAviewAlloc(0); ///< View for checking
     view->chip = view->cell = 0;
-    bool status = true;                 // Status of checks
+    bool status = true;                 ///< Status of checks
     status &= pmFPAfileIOChecks(config, view, PM_FPA_AFTER);
     view->cell = -1;
@@ -67,5 +71,7 @@
 
 
-// Loop over the inputs, warp them to the output skycell and then write out the output.
+/**
+ * Loop over the inputs, warp them to the output skycell and then write out the output.
+ */
 bool pswarpLoop(pmConfig *config)
 {
@@ -113,8 +119,8 @@
     psFree (view);
 
-    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 (mdok && statsName && strlen(statsName) > 0) {
         psString resolved = pmConfigConvertFilename(statsName, config, true, true);
@@ -141,4 +147,5 @@
 
     // Read the input astrometry
+    // XXX rather than use the activations here, this should just explicitly loop over the desired filerule
     {
         pmFPAfileActivate(config->files, true, "PSWARP.ASTROM");
@@ -257,7 +264,7 @@
     }
 
-    pmCell *outCell = output->parent;   // Output cell
-    pmChip *outChip = outCell->parent;  // Output chip
-    pmFPA *outFPA = outChip->parent;    // Output FP
+    pmCell *outCell = output->parent;   ///< Output cell
+    pmChip *outChip = outCell->parent;  ///< Output chip
+    pmFPA *outFPA = outChip->parent;    ///< Output FP
 
     if (!pswarpPixelFraction(output, stats, config)) {
@@ -277,5 +284,5 @@
         varFactor /= goodPix;
 
-        psMetadataItem *vfItem = psMetadataLookup(outCell->concepts, "CELL.VARFACTOR"); // Item to update
+        psMetadataItem *vfItem = psMetadataLookup(outCell->concepts, "CELL.VARFACTOR"); ///< Item to update
         psAssert(vfItem && vfItem->type == PS_TYPE_F32, "Concept should be as specified.");
         if (!isfinite(vfItem->data.F32)) {
@@ -295,6 +302,6 @@
     psFree(cells);
 
-    psRegion *trimsec = psMetadataLookupPtr(NULL, outCell->concepts, "CELL.TRIMSEC"); // Trim section
-    trimsec->x0 = trimsec->x1 = trimsec->y0 = trimsec->y1 = 0; // All pixels
+    psRegion *trimsec = psMetadataLookupPtr(NULL, outCell->concepts, "CELL.TRIMSEC"); ///< Trim section
+    trimsec->x0 = trimsec->x1 = trimsec->y0 = trimsec->y1 = 0; ///< All pixels
 
     if (!psMetadataCopy(outFPA->concepts, input->fpa->concepts)) {
@@ -305,13 +312,13 @@
     }
 
-    pmHDU *hdu = outFPA->hdu;           // HDU for the output warped image
+    pmHDU *hdu = outFPA->hdu;           ///< HDU for the output warped image
 
     // Copy header from target
     {
-        pmFPAview *skyView = pmFPAviewAlloc(0); // View into skycell
+        pmFPAview *skyView = pmFPAviewAlloc(0); ///< View into skycell
         skyView->chip = skyView->cell = 0;
         pmCell *cell = pmFPAfileThisCell(config->files, skyView, "PSWARP.SKYCELL"); // Skycell cell
         psFree(skyView);
-        pmHDU *skyHDU = pmHDUFromCell(cell); // HDU
+        pmHDU *skyHDU = pmHDUFromCell(cell); ///< HDU
         if (!skyHDU) {
             psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find skycell HDU.");
@@ -364,5 +371,5 @@
         pmFPACopy(photFile->fpa, outFPA);
 
-        pmFPAview *view = pmFPAviewAlloc(0); // View into skycell
+        pmFPAview *view = pmFPAviewAlloc(0); ///< View into skycell
         view->chip = view->cell = view->readout = 0;
 
@@ -372,5 +379,5 @@
         // We can adjust the weight directly since this is a deep copy
         pmReadout *photRO = pmFPAviewThisReadout(view, photFile->fpa);
-        float vf = psMetadataLookupF32(NULL, photRO->parent->concepts, "CELL.VARFACTOR"); // Variance factor
+        float vf = psMetadataLookupF32(NULL, photRO->parent->concepts, "CELL.VARFACTOR"); ///< Variance factor
         psBinaryOp(photRO->weight, photRO->weight, "*", psScalarAlloc(vf, PS_TYPE_F32));
 
@@ -386,8 +393,8 @@
 #endif
 
-#ifdef TESTING
+#if (TESTING)
         {
-            #define PSF_SIZE 20         // Half-size of PSF
-            #define PSF_FLUX 10000      // Central flux for PSF
+            #define PSF_SIZE 20         ///< Half-size of PSF
+            #define PSF_FLUX 10000      ///< Central flux for PSF
             pmChip *photChip = pmFPAviewThisChip(view, photFile->fpa);
             pmPSF *psf = psMetadataLookupPtr(NULL, photChip->analysis, "PSPHOT.PSF");
@@ -419,8 +426,8 @@
     const char *chipName = psMetadataLookupStr(NULL, output->parent->parent->concepts, "CHIP.NAME");
     const char *cellName = psMetadataLookupStr(NULL, output->parent->concepts, "CELL.NAME");
-    psString headerName = NULL; // Header name for MD5
+    psString headerName = NULL; ///< Header name for MD5
     psStringAppend(&headerName, "MD5_%s_%s_%d", chipName, cellName, view->readout);
-    psVector *md5 = psImageMD5(output->image); // md5 hash
-    psString md5string = psMD5toString(md5); // String
+    psVector *md5 = psImageMD5(output->image); ///< md5 hash
+    psString md5string = psMD5toString(md5); ///< String
     psFree(md5);
     psMetadataAddStr(hdu->header, PS_LIST_TAIL, headerName, PS_META_REPLACE,
Index: /branches/eam_branch_20081230/pswarp/src/pswarpMapGrid.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpMapGrid.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpMapGrid.c	(revision 21268)
@@ -1,8 +1,22 @@
+/** @file pswarpMapGrid.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.6.20.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
-// pswarpMapGridFromImage builds a set (a grid) of locally-linear maps which convert the source
-// coordinates (src) to destination coordinates (dest).  we construct a grid with superpixel
-// spacing of nXpix, nYpix.  The transformation for each grid cell is valid for the superpixel.
-// The grid over-fills the source image so every source image pixel is guaranteed to have a map.
+/**
+ * pswarpMapGridFromImage builds a set (a grid) of locally-linear maps which convert the source
+ * coordinates (src) to destination coordinates (dest).  we construct a grid with superpixel
+ * spacing of nXpix, nYpix.  The transformation for each grid cell is valid for the superpixel.
+ * The grid over-fills the source image so every source image pixel is guaranteed to have a map.
+ */
 pswarpMapGrid *pswarpMapGridFromImage (pmReadout *dest, pmReadout *src, int nXpix, int nYpix) {
 
@@ -41,6 +55,8 @@
 }
 
-// set the grid coordinate (gridX,gridY) for the given source image coordinate (ix,iy)
-// XXX return true if the result is on the src image, false otherwise (???)
+/**
+ * set the grid coordinate (gridX,gridY) for the given source image coordinate (ix,iy)
+ * XXX return true if the result is on the src image, false otherwise (???)
+ */
 bool pswarpMapGridSetGrid (pswarpMapGrid *grid, int ix, int iy, int *gridX, int *gridY) {
 
@@ -51,5 +67,7 @@
 }
 
-// given the specified grid coordinate (gridX, gridY), return the min and max coordinates for the tile
+/**
+ * given the specified grid coordinate (gridX, gridY), return the min and max coordinates for the tile
+ */
 bool pswarpMapGridCoordRange (pswarpMapGrid *grid, int gridX, int gridY, psPlane *min, psPlane *max) {
 
@@ -63,6 +81,8 @@
 }
 
-// given the specified grid coordinate (gridX), return the x-coordinate for the source image
-// corresponding to the next grid cell
+/**
+ * given the specified grid coordinate (gridX), return the x-coordinate for the source image
+ * corresponding to the next grid cell
+ */
 int pswarpMapGridNextGrid_X (pswarpMapGrid *grid, int gridX) {
 
@@ -71,6 +91,8 @@
 }
 
-// given the specified grid coordinate (gridY), return the y-coordinate for the source image
-// corresponding to the next grid cell
+/**
+ * given the specified grid coordinate (gridY), return the y-coordinate for the source image
+ * corresponding to the next grid cell
+ */
 int pswarpMapGridNextGrid_Y (pswarpMapGrid *grid, int gridY) {
 
@@ -79,6 +101,8 @@
 }
 
-// measure the max error accumulated in applying one grid point to its neighbors
-// XXX double-check this
+/**
+ * measure the max error accumulated in applying one grid point to its neighbors
+ * XXX double-check this
+ */
 double pswarpMapGridMaxError (pswarpMapGrid *grid) {
 
@@ -102,5 +126,7 @@
 }
 
-// given the source coordinate (inX,inY), return the destination coordinate (outX,outY)
+/**
+ * given the source coordinate (inX,inY), return the destination coordinate (outX,outY)
+ */
 bool pswarpMapApply (double *outX, double *outY, pswarpMap *map, double inX, double inY) {
 
@@ -111,7 +137,9 @@
 }
 
-// determine the (linear) map for the given pixel (ix,iy) from source image (src) to the destination image (dest)
-// pixel is in src coords. input and output pixel coordinates are in the parent frame of the image (Note that the
-// astrometric transformations are supplied for the parent image coordinate frame.
+/**
+ * determine the (linear) map for the given pixel (ix,iy) from source image (src) to the destination image (dest)
+ * pixel is in src coords. input and output pixel coordinates are in the parent frame of the image (Note that the
+ * astrometric transformations are supplied for the parent image coordinate frame.
+ */
 bool pswarpMapSetLocalModel (pswarpMap *map, pmReadout *dest, pmReadout *src, int ix, int iy) {
 
@@ -139,5 +167,5 @@
     // XXX need to include readout->cell->chip offsets
 
-    // V(0,0) position
+    /** V(0,0) position */
     offset->x = ix;
     offset->y = iy;
@@ -149,5 +177,5 @@
     psPlaneTransformApply (V00, chipDest->fromFPA, FP);
     
-    // V(1,0) position
+    /** V(1,0) position */
     offset->x = ix + 1;
     offset->y = iy;
@@ -159,5 +187,5 @@
     psPlaneTransformApply (V10, chipDest->fromFPA, FP);
     
-    // V(0,1) position
+    /** V(0,1) position */
     offset->x = ix;
     offset->y = iy + 1;
Index: /branches/eam_branch_20081230/pswarp/src/pswarpMatchRange.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpMatchRange.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpMatchRange.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpMatchRange.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.4.46.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
@@ -13,7 +25,8 @@
     *maxY = PS_MAX (*maxY, srcPix->y);
 
-// we are warping from src to dest.  find the max overlapping pixels in the INPUT (src)
-// coordinate frame.  NOTE: these are in the parent pixel frame since the astrometric
-// transformation refers to the parent frame
+/** we are warping from src to dest.  find the max overlapping pixels in the INPUT (src)
+ * coordinate frame.  NOTE: these are in the parent pixel frame since the astrometric
+ * transformation refers to the parent frame
+ */
 bool pswarpMatchRange (int *minX, int *minY, int *maxX, int *maxY, pmReadout *dest, pmReadout *src) {
 
Index: /branches/eam_branch_20081230/pswarp/src/pswarpParseCamera.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpParseCamera.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpParseCamera.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpParseCamera.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.22.8.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
@@ -4,5 +16,5 @@
 {
     bool status;
-    bool mdok;                          // Status of MD lookup
+    bool mdok;                          ///< Status of MD lookup
     pmFPAfile *skycell = NULL;
     pmConfig *skyConfig = NULL;
Index: /branches/eam_branch_20081230/pswarp/src/pswarpPixelFraction.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpPixelFraction.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpPixelFraction.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpPixelFraction.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.4.28.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -30,5 +42,5 @@
     bool status; 
 
-    float minFrac = psMetadataLookupF32(NULL, config->arguments, "ACCEPT.FRAC"); // Minimum fraction
+    float minFrac = psMetadataLookupF32(NULL, config->arguments, "ACCEPT.FRAC"); ///< Minimum fraction
 
     // load the recipe
@@ -43,8 +55,8 @@
     psAssert (status, "MASK.OUTPUT was not defined");
 
-    psImage *image = readout->image;    // Image of interest
-    psImage *mask = readout->mask;      // Mask image
+    psImage *image = readout->image;    ///< Image of interest
+    psImage *mask = readout->mask;      ///< Mask image
 
-    int numCols = image->numCols, numRows = image->numRows; // Size of image
+    int numCols = image->numCols, numRows = image->numRows; ///< Size of image
     long numPix = numCols * numRows;
 
@@ -52,5 +64,5 @@
     int xMin = INT_MAX, xMax = -INT_MAX, yMin = INT_MAX, yMax = -INT_MAX;
 
-    long numBad = 0;                     // Number of bad pixels
+    long numBad = 0;                     ///< Number of bad pixels
     for (int y = 0; y < numRows; y++) {
         for (int x = 0; x < numCols; x++) {
@@ -74,6 +86,6 @@
     }
 
-    float goodFrac = (numPix - numBad) / (float)numPix; // Fraction of good pixels
-    bool accept = (goodFrac >= minFrac ? true : false); // Accept this readout?
+    float goodFrac = (numPix - numBad) / (float)numPix; ///< Fraction of good pixels
+    bool accept = (goodFrac >= minFrac ? true : false); ///< Accept this readout?
 
     if (stats) {
Index: /branches/eam_branch_20081230/pswarp/src/pswarpSetMaskBits.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpSetMaskBits.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpSetMaskBits.c	(revision 21268)
@@ -1,16 +1,28 @@
+/** @file pswarpSetMaskBits.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.2.28.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
-// This function is called by the stand-alone pswarp program to set the mask values in the
-// config file.  It sets the named mask values MASK.PSPHOT and MARK.PSPHOT in the PSPHOT
-// recipe.  Functions or programs which call psphotReadout as a library function must set these
-// named mask values in the PSPHOT recipe on their own.  This function should only be called
-// after the first header of the input mask image has been loaded and the named mask bits
-// updated in the config metadata.
-
+/** This function is called by the stand-alone pswarp program to set the mask values in the
+ * config file.  It sets the named mask values MASK.PSPHOT and MARK.PSPHOT in the PSPHOT
+ * recipe.  Functions or programs which call psphotReadout as a library function must set these
+ * named mask values in the PSPHOT recipe on their own.  This function should only be called
+ * after the first header of the input mask image has been loaded and the named mask bits
+ * updated in the config metadata.
+ */
 bool pswarpSetMaskBits (pmConfig *config) {
 
-    psImageMaskType maskIn = 0x00;			// mask for the input image
-    psImageMaskType markIn = 0x00;			// mark for the input image
-    psImageMaskType maskOut = 0x00;			// mask for the output image
+    psImageMaskType maskIn = 0x00;			///< mask for the input image
+    psImageMaskType markIn = 0x00;			///< mark for the input image
+    psImageMaskType maskOut = 0x00;			///< mask for the output image
 
     // this function sets the required single-image mask bits
Index: /branches/eam_branch_20081230/pswarp/src/pswarpSetThreads.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpSetThreads.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpSetThreads.c	(revision 21268)
@@ -1,6 +1,19 @@
+/** @file pswarpSetThreads.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.4.16.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
-// each thread runs this function, starting a new job when it finished with an old one
-// it is called with a (void *) pointer to its own thread pointer
+/** each thread runs this function, starting a new job when it finished with an old one
+ * it is called with a (void *) pointer to its own thread pointer
+ */
 bool pswarpThread_pswarpTransformTile(psThreadJob *job)
 {
Index: /branches/eam_branch_20081230/pswarp/src/pswarpThreads.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpThreads.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpThreads.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpThreads.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.2.20.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 # include "pswarp.h"
 
@@ -39,5 +51,7 @@
 }
 
-// create a pool of Nthreads
+/**
+ * create a pool of Nthreads
+ */
 bool pswarpThreadsCreate (int nThreads) {
 
Index: /branches/eam_branch_20081230/pswarp/src/pswarpTransformReadout.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpTransformReadout.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpTransformReadout.c	(revision 21268)
@@ -1,19 +1,33 @@
+/** @file pswarpTransformReadout.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.13.8.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #include "pswarp.h"
 
-// NOTE: in this function, the coordinates are transformed from the OUTPUT to the INPUT
+/**
+ * NOTE: in this function, the coordinates are transformed from the OUTPUT to the INPUT
+ */
 bool pswarpTransformReadout(pmReadout *output, pmReadout *input, pmConfig *config)
 {
     // XXX this implementation currently ignores the use of the region
-    psImage *region = NULL;             // Region to transform
+    psImage *region = NULL;             ///< Region to transform
 
     psTimerStart("warp");
 
     // Get warp parameters
-    bool mdok;                          // Status of MD lookup
-    int nGridX = psMetadataLookupS32(NULL, config->arguments, "GRID.NX"); // Number of grid points in x
-    int nGridY = psMetadataLookupS32(NULL, config->arguments, "GRID.NY"); // Number of grid points in y
+    bool mdok;                          ///< Status of MD lookup
+    int nGridX = psMetadataLookupS32(NULL, config->arguments, "GRID.NX"); ///< Number of grid points in x
+    int nGridY = psMetadataLookupS32(NULL, config->arguments, "GRID.NY"); ///< Number of grid points in y
     psImageInterpolateMode interpolationMode = psMetadataLookupS32(NULL, config->arguments,
-                                                                   "INTERPOLATION.MODE"); // Mode for interp
-    int numKernels = psMetadataLookupS32(NULL, config->arguments, "INTERPOLATION.NUM"); // Number of kernels
+                                                                   "INTERPOLATION.MODE"); ///< Mode for interp
+    int numKernels = psMetadataLookupS32(NULL, config->arguments, "INTERPOLATION.NUM"); ///< Number of kernels
 
     // load the recipe
@@ -27,9 +41,9 @@
     psAssert(mdok, "MASK.INPUT was not defined");
 
-    int nThreads = psMetadataLookupS32(&mdok, config->arguments, "NTHREADS"); // Number of threads
+    int nThreads = psMetadataLookupS32(&mdok, config->arguments, "NTHREADS"); ///< Number of threads
     if (!mdok) {
         nThreads = 0;
     }
-    float poorFrac = psMetadataLookupF32(NULL, config->arguments, "POOR.FRAC"); // Flux fraction for "poor"
+    float poorFrac = psMetadataLookupF32(NULL, config->arguments, "POOR.FRAC"); ///< Flux fraction for "poor"
 
     // pswarpMapGridFromImage builds a set of locally-linear maps which convert the
@@ -42,5 +56,5 @@
 
     // Get range of interest
-    int xOutMin, xOutMax, yOutMin, yOutMax; // Output pixel range
+    int xOutMin, xOutMax, yOutMin, yOutMax; ///< Output pixel range
     pswarpMatchRange(&xOutMin, &yOutMin, &xOutMax, &yOutMax, input, output);
 
@@ -53,6 +67,6 @@
     }
 
-    int xGridMin = nGridX, xGridMax = 0, yGridMin = nGridY, yGridMax = 0; // Grid range
-    int xGrid, yGrid;                   // Grid coordinates
+    int xGridMin = nGridX, xGridMax = 0, yGridMin = nGridY, yGridMax = 0; ///< Grid range
+    int xGrid, yGrid;                   ///< Grid coordinates
     pswarpMapGridSetGrid(grid, xOutMin, yOutMin, &xGrid, &yGrid);
     CHECK_GRID_RANGE();
@@ -121,5 +135,5 @@
     psThreadJob *job = NULL;
     int xMin = output->image->numCols, xMax = 0, yMin = output->image->numRows, yMax = 0; // Bounds
-    int goodPixels = 0;                 // total number of good pixels across all tiles
+    int goodPixels = 0;                 ///< total number of good pixels across all tiles
     while ((job = psThreadJobGetDone()) != NULL) {
         if (job->args->n < 1) {
Index: /branches/eam_branch_20081230/pswarp/src/pswarpTransformSources.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpTransformSources.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpTransformSources.c	(revision 21268)
@@ -1,7 +1,21 @@
+/** @file pswarpTransformSources.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.6.6.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #include "pswarp.h"
 
-#define SOURCE_ARRAY_BUFFER 100         // Size to grow the array of sources at a time
+#define SOURCE_ARRAY_BUFFER 100         ///< Size to grow the array of sources at a time
 
-// NOTE: in this function, the coordinates are transformed from the OUTPUT to the INPUT
+/**
+ * NOTE: in this function, the coordinates are transformed from the OUTPUT to the INPUT
+ */
 bool pswarpTransformSources(pmReadout *output, pmReadout *input, pmConfig *config)
 {
@@ -33,11 +47,11 @@
     // this does not cost us so much time.
     for (int i = 0; i < inSources->n; i++) {
-        pmSource *source = inSources->data[i]; // Source of interest
-        pmModel *model = source->modelPSF; // Model for this source
-        float xIn, yIn;             // Coordinates of source
+        pmSource *source = inSources->data[i]; ///< Source of interest
+        pmModel *model = source->modelPSF; ///< Model for this source
+        float xIn, yIn;             ///< Coordinates of source
         xIn = model->params->data.F32[PM_PAR_XPOS] - input->image->col0;
         yIn = model->params->data.F32[PM_PAR_YPOS] - input->image->row0;
 
-        int xGrid, yGrid;           // Grid coordinates for local map
+        int xGrid, yGrid;           ///< Grid coordinates for local map
         if (!pswarpMapGridSetGrid(sourceGrid, xIn + 0.5, yIn + 0.5, &xGrid, &yGrid)) {
             psError(PS_ERR_UNKNOWN, false, "Unable to get grid coordinates for source at %f,%f\n",
@@ -53,6 +67,6 @@
         }
 
-        pswarpMap *map = sourceGrid->maps[xGrid][yGrid]; // Locally linear transformation
-        double xOut, yOut;          // Output coordinates
+        pswarpMap *map = sourceGrid->maps[xGrid][yGrid]; ///< Locally linear transformation
+        double xOut, yOut;          ///< Output coordinates
         if (!pswarpMapApply(&xOut, &yOut, map, xIn + 0.5, yIn + 0.5)) {
             psError(PS_ERR_UNKNOWN, false, "Unable to transform coordinates for source at %f,%f\n",
@@ -73,5 +87,5 @@
         // Magnitudes will be off if there's any change in scale, but for our purposes (mainly x,y and
         // relative flux) that's OK.
-        pmSource *new = pmSourceAlloc(); // New source
+        pmSource *new = pmSourceAlloc(); ///< New source
         new->peak = pmPeakAlloc(xOut, yOut, source->peak->flux, PM_PEAK_LONE);
         new->peak->flux = source->peak->flux;
Index: /branches/eam_branch_20081230/pswarp/src/pswarpTransformTile.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpTransformTile.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpTransformTile.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpTransformTile.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.6.14.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #include "pswarp.h"
 
@@ -36,12 +48,12 @@
 bool pswarpTransformTile(pswarpTransformTileArgs *args)
 {
-    psImage *inImage = args->input->image; // Input image
-    psImage *outImage = args->output->image; // Output image
+    psImage *inImage = args->input->image; ///< Input image
+    psImage *outImage = args->output->image; ///< Output image
 
-    int inNumCols = inImage->numCols, inNumRows = inImage->numRows; // Size of input image
-    int outNumCols = outImage->numCols, outNumRows = outImage->numRows; // Size of output image
-    int outCol0 = outImage->col0, outRow0 = outImage->row0; // Offset of output image
+    int inNumCols = inImage->numCols, inNumRows = inImage->numRows; ///< Size of input image
+    int outNumCols = outImage->numCols, outNumRows = outImage->numRows; ///< Size of output image
+    int outCol0 = outImage->col0, outRow0 = outImage->row0; ///< Offset of output image
 
-    psPlane minPt, maxPt;               // Minimum and maximum points for this tile
+    psPlane minPt, maxPt;               ///< Minimum and maximum points for this tile
     pswarpMapGridCoordRange(args->grid, args->gridX, args->gridY, &minPt, &maxPt);
 
@@ -52,8 +64,8 @@
     psImageMaskType **inMaskData  = (args->input->mask)    ? args->input->mask->data.PS_TYPE_IMAGE_MASK_DATA : NULL;
 
-    pswarpMap *map = args->grid->maps[args->gridX][args->gridY]; // Map for this tile
-    psImage *region = args->region;     // Region to transform
+    pswarpMap *map = args->grid->maps[args->gridX][args->gridY]; ///< Map for this tile
+    psImage *region = args->region;     ///< Region to transform
 
-    // Bounds for iteration
+    /** Bounds for iteration */
     int xMin = PS_MAX(minPt.x, 0);
     int xMax = PS_MIN(maxPt.x, outNumCols);
@@ -62,5 +74,5 @@
 
     // Iterate over the output image pixels (parent frame)
-    long goodPixels = 0;                // Number of input pixels landing on the output image
+    long goodPixels = 0;                ///< Number of input pixels landing on the output image
     for (int y = yMin; y < yMax; y++) {
         for (int x = xMin; x < xMax; x++) {
@@ -81,6 +93,6 @@
 
             // psImagePixelInterpolate determines the value at pixel coordinate (x,y) in child coordinates
-            double imageValue, varValue; // Value of image and variance map
-            psImageMaskType maskValue = inMaskData ? inMaskData[(int)yIn][(int)xIn] : 0; // Value of mask
+            double imageValue, varValue; ///< Value of image and variance map
+            psImageMaskType maskValue = inMaskData ? inMaskData[(int)yIn][(int)xIn] : 0; ///< Value of mask
             if (!psImageInterpolate(&imageValue, &varValue, &maskValue, xIn, yIn, args->interp)) {
                 psError(PS_ERR_UNKNOWN, false, "Unable to interpolate image.");
@@ -88,5 +100,5 @@
             }
 
-            int xOut = x - outCol0, yOut = y - outRow0; // Position on output image
+            int xOut = x - outCol0, yOut = y - outRow0; ///< Position on output image
 
             if (outImageData) {
Index: /branches/eam_branch_20081230/pswarp/src/pswarpVersion.c
===================================================================
--- /branches/eam_branch_20081230/pswarp/src/pswarpVersion.c	(revision 21267)
+++ /branches/eam_branch_20081230/pswarp/src/pswarpVersion.c	(revision 21268)
@@ -1,2 +1,14 @@
+/** @file pswarpVersion.c
+ *
+ *  @brief
+ *
+ *  @ingroup pswarp
+ *
+ *  @author IfA
+ *  @version $Revision: 1.1.48.1 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-02 21:57:10 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -8,9 +20,9 @@
 #include "pswarp.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 pswarpVersion(void)
 {
-    psString version = NULL;            // Version, to return
+    psString version = NULL;            ///< Version, to return
     psStringAppend(&version, "%s-%s",PACKAGE_NAME,PACKAGE_VERSION);
     return version;
@@ -19,6 +31,6 @@
 psString pswarpVersionLong(void)
 {
-    psString version = pswarpVersion(); // Version, to return
-    psString tag = psStringStripCVS(cvsTag, "Name"); // CVS tag
+    psString version = pswarpVersion(); ///< Version, to return
+    psString tag = psStringStripCVS(cvsTag, "Name"); ///< CVS tag
     psStringAppend(&version, " (cvs tag %s) %s, %s", tag, __DATE__, __TIME__);
     psFree(tag);