Index: /trunk/psModules/src/objects/pmSourceIO_PS1_DEV_1.c
===================================================================
--- /trunk/psModules/src/objects/pmSourceIO_PS1_DEV_1.c	(revision 16293)
+++ /trunk/psModules/src/objects/pmSourceIO_PS1_DEV_1.c	(revision 16294)
@@ -3,6 +3,6 @@
  *  @author EAM, IfA
  *
- *  @version $Revision: 1.7 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2008-01-02 20:39:04 $
+ *  @version $Revision: 1.8 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2008-02-03 22:04:47 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii
@@ -284,13 +284,24 @@
     // we write out all sources, regardless of quality.  the source flags tell us the state
     for (i = 0; i < sources->n; i++) {
-        pmSource *source = (pmSource *) sources->data[i];
-        source->seq = i;
+	// source->seq is set during the PSF output step, which must be called
+	// XXX test here if seq is set?
 
 	// skip source if it is not a ext sourc
-
-        // no difference between PSF and non-PSF model
-	// XXX the PSF output should report the value for the psf, not the ext, model
-        pmModel *model = source->modelEXT;
+	// XXX we have two places that extended source parameters are measured:
+	// psphotExtendedSources, which measures the aperture-like parameters and (potentially) the psf-convolved extended source models,
+	// psphotFitEXT, which does the simple extended source model fit (not psf-convolved)
+	// should we require both?
+
+	pmSource *source = sources->data[i];
+
+        // choose the convolved EXT model, if available, otherwise the simple one
+        pmModel *model = source->modelConv;
+        if (model == NULL) {
+	    model = source->modelEXT;
+	}
         if (model == NULL) continue;
+
+	// XXX do we need to do this?
+	if (source->extpars == NULL) continue;
 
 	PAR = model->params->data.F32;
@@ -306,19 +317,67 @@
         // XXX we are not writing out the mode (flags) or the type (psf, ext, etc)
         psMetadataAdd (row, PS_LIST_TAIL, "IPP_IDET",         PS_DATA_U32, "IPP detection identifier index",             source->seq);
-        psMetadataAdd (row, PS_LIST_TAIL, "X_EXT",            PS_DATA_F32, "PSF x coordinate",                           xPos);
-        psMetadataAdd (row, PS_LIST_TAIL, "Y_EXT",            PS_DATA_F32, "PSF y coordinate",                           yPos);
-        psMetadataAdd (row, PS_LIST_TAIL, "X_EXT_SIG",        PS_DATA_F32, "Sigma in PSF x coordinate",                  xErr);
-        psMetadataAdd (row, PS_LIST_TAIL, "Y_EXT_SIG",        PS_DATA_F32, "Sigma in PSF y coordinate",                  yErr);
-        psMetadataAdd (row, PS_LIST_TAIL, "EXT_INST_MAG",     PS_DATA_F32, "PSF fit instrumental magnitude",             PS_MIN (99.0, source->extMag));
-	// XXX need to calculate psfMag, psfMagErr, extMag, extMagErr...
-        psMetadataAdd (row, PS_LIST_TAIL, "EXT_INST_MAG_SIG", PS_DATA_F32, "Sigma of PSF instrumental magnitude",        PS_MIN (99.0, source->errMag));
+        psMetadataAdd (row, PS_LIST_TAIL, "X_EXT",            PS_DATA_F32, "EXT model x coordinate",                     xPos);
+        psMetadataAdd (row, PS_LIST_TAIL, "Y_EXT",            PS_DATA_F32, "EXT model y coordinate",                     yPos);
+        psMetadataAdd (row, PS_LIST_TAIL, "X_EXT_SIG",        PS_DATA_F32, "Sigma in EXT x coordinate",                  xErr);
+        psMetadataAdd (row, PS_LIST_TAIL, "Y_EXT_SIG",        PS_DATA_F32, "Sigma in EXT y coordinate",                  yErr);
+        psMetadataAdd (row, PS_LIST_TAIL, "EXT_INST_MAG",     PS_DATA_F32, "EXT fit instrumental magnitude",             source->extMag);
+        psMetadataAdd (row, PS_LIST_TAIL, "EXT_INST_MAG_SIG", PS_DATA_F32, "Sigma of PSF instrumental magnitude",        source->errMag);
 
         // XXX these should be major and minor, not 'x' and 'y'
-        psMetadataAdd (row, PS_LIST_TAIL, "EXT_WIDTH_X",      PS_DATA_F32, "PSF width in x coordinate",                  axes.major);
-        psMetadataAdd (row, PS_LIST_TAIL, "EXT_WIDTH_Y",      PS_DATA_F32, "PSF width in y coordinate",                  axes.minor);
-        psMetadataAdd (row, PS_LIST_TAIL, "EXT_THETA",        PS_DATA_F32, "PSF orientation angle",                      axes.theta);
+        psMetadataAdd (row, PS_LIST_TAIL, "EXT_WIDTH_MAJ",    PS_DATA_F32, "EXT width in x coordinate",                  axes.major);
+        psMetadataAdd (row, PS_LIST_TAIL, "EXT_WIDTH_MIN",    PS_DATA_F32, "EXT width in y coordinate",                  axes.minor);
+        psMetadataAdd (row, PS_LIST_TAIL, "EXT_THETA",        PS_DATA_F32, "EXT orientation angle",                      axes.theta);
+
+	// XXX at the moment, this will be a fixed size table, but perhaps have multiple output formats depending on what is measured?
 
 	// other values that I need to report:
 	// R, Mag Petrosian, .....
+	if (source->extpars) {
+
+	    // Petrosian measurements
+	    pmSourcePetrosianValues *petrosian = source->extpars->petrosian;
+	    if (petrosian) {
+		psMetadataAdd (row, PS_LIST_TAIL, "PETRO_MAG",        PS_DATA_F32, "Petrosian Magnitude",       petrosian->mag);
+		psMetadataAdd (row, PS_LIST_TAIL, "PETRO_MAG_ERR",    PS_DATA_F32, "Petrosian Magnitude Error", petrosian->magErr);
+		psMetadataAdd (row, PS_LIST_TAIL, "PETRO_RADIUS",     PS_DATA_F32, "Petrosian Radius",          petrosian->rad);
+		psMetadataAdd (row, PS_LIST_TAIL, "PETRO_RADIUS_ERR", PS_DATA_F32, "Petrosian Radius Error",    petrosian->radErr);
+	    }
+
+	    // Kron measurements
+	    pmSourceKronValues *kron = source->extpars->kron;
+	    if (kron) {
+		psMetadataAdd (row, PS_LIST_TAIL, "KRON_MAG",        PS_DATA_F32, "Kron Magnitude",       kron->mag);
+		psMetadataAdd (row, PS_LIST_TAIL, "KRON_MAG_ERR",    PS_DATA_F32, "Kron Magnitude Error", kron->magErr);
+		psMetadataAdd (row, PS_LIST_TAIL, "KRON_RADIUS",     PS_DATA_F32, "Kron Radius",          kron->rad);
+		psMetadataAdd (row, PS_LIST_TAIL, "KRON_RADIUS_ERR", PS_DATA_F32, "Kron Radius Error",    kron->radErr);
+	    }
+
+	    // Isophot measurements
+	    // XXX insert header data: isophotal level
+	    pmSourceIsophotalValues *isophot = source->extpars->isophot;
+	    if (isophot) {
+		psMetadataAdd (row, PS_LIST_TAIL, "ISOPHOT_MAG",        PS_DATA_F32, "Isophot Magnitude",       isophot->mag);
+		psMetadataAdd (row, PS_LIST_TAIL, "ISOPHOT_MAG_ERR",    PS_DATA_F32, "Isophot Magnitude Error", isophot->magErr);
+		psMetadataAdd (row, PS_LIST_TAIL, "ISOPHOT_RADIUS",     PS_DATA_F32, "Isophot Radius",          isophot->rad);
+		psMetadataAdd (row, PS_LIST_TAIL, "ISOPHOT_RADIUS_ERR", PS_DATA_F32, "Isophot Radius Error",    isophot->radErr);
+	    }
+
+	    pmSourceAnnuli *annuli = source->extpars->annuli;
+	    if (annuli) {
+		psVector *fluxVal = annuli->flux;
+		psVector *fluxErr = annuli->fluxErr;
+		psVector *fluxVar = annuli->fluxVar;
+
+		for (int j = 0; j < fluxVal->n; j++) {
+		    char name[32];
+		    sprintf (name, "FLUX_VAL_R_%02d", j);
+		    psMetadataAdd (row, PS_LIST_TAIL, name, PS_DATA_F32, "flux value in annulus", fluxVal->data.F32[j]);
+		    sprintf (name, "FLUX_ERR_R_%02d", j);
+		    psMetadataAdd (row, PS_LIST_TAIL, name, PS_DATA_F32, "flux error in annulus", fluxErr->data.F32[j]);
+		    sprintf (name, "FLUX_VAR_R_%02d", j);
+		    psMetadataAdd (row, PS_LIST_TAIL, name, PS_DATA_F32, "flux stdev in annulus", fluxVar->data.F32[j]);
+		}
+	    }
+	}
 
         psArrayAdd (table, 100, row);