Index: trunk/doc/release.2015/ps1.analysis/analysis.tex
===================================================================
--- trunk/doc/release.2015/ps1.analysis/analysis.tex	(revision 40588)
+++ trunk/doc/release.2015/ps1.analysis/analysis.tex	(revision 40589)
@@ -794,5 +794,5 @@
 measurement of the moments.
 
-%% comfirmed: PSF_MOMENTS_RADIUS = 4 * MOMENTS_GAUSS_SIGMA (\sigma_w)
+%% confirmed: PSF_MOMENTS_RADIUS = 4 * MOMENTS_GAUSS_SIGMA (\sigma_w)
 %% factor of 4 is hard-wired in psphotSourceStats.c where MOMENTS_GAUSS_SIGMA is set.
 %% PSF_MOMENTS_RADIUS used for: moments analysis, Kron analysis (starting radius),
@@ -1548,6 +1548,75 @@
 After the initial, fast analysis of the image relying primarily on the
 PSF model, a complete analysis of the extended source properties may
-be performed.  For PS1 processing, this step is the nightly (PV0)
-analysis of individual exposures and only performed for the stacks.
+be performed.  For PS1 processing, this step is skipped in the nightly
+(PV0) analysis of individual exposures and only performed for the
+stacks in the major reprocessings.
+
+The extended souce analysis consists of the following types of
+measurements: 1) an analysis of the radial profile of the surface
+brightness of the source; 2) measurement of the Petrosian radius and
+magnitude; 3) convolved galaxy model fits; and 4) photometry in
+several fixed-sized apertures, both raw and convolved to a defined
+PSF size.
+
+%% NOTE: This is NOT true: extended source analysis applied to both
+%% PASS 1 and PASS 2 sources.  
+%%
+%% In order for a source to be included in the extended source
+%% analysis, it much have been detected in the 'bright source' analysis
+%% step ($S/N > 20$, Section~\ref{sec:xxxx}).  \note{is this restriction
+%% more or less severe than the mag limits?}  
+
+The extended source analysis is not applied to all object which may be
+galaxies.  Several restrictions are possible within the software.  For
+example, it is possible to limit which objects are processed by their
+aparent magnitudes, by their signal-to-noise, by an indication if they
+are in fact extended, by the local stellar density, or by the galactic
+latitude.  Some of these selections may be defined differently for the
+galaxy model fits and the Petrosian parameters.
+
+For the $3\pi$ PV3 processing, both an apparent magnitude cut and a
+Galactic latitude cut were applied.  The apparent magnitude limits for
+the galaxy model fits are applied to the measured Kron magnitude and
+depend on the filter as follows: (\grizy) = (21.5, 21.5, 21.5, 20.5,
+19.5).  These values were chosen to have roughly similar
+signal-to-noise in a typical stack image for neutral color objects.
+The magnitude limits for the Petrosian parameters were set to 25.0 for
+all filters, far below the detection limits and effectively not
+limiting the analysis based on apparent magnitude. For both galaxy
+model fits and Petrosian parameters, the Galactic latitude cut was
+defined by $|b| > b_{\rm min}$ where $b_{\rm min} = b_0 + r_b
+e^{\frac{-l^2}{2 \sigma_b^2}}$.  For the PV3 analysis, $b_0 =
+$20\degree, $r_b = $15\degree, $\sigma_b = $50\degree.  This contour
+avoids the denser portions of the Galactic plane and bulge, limiting
+the total time spent on the galaxy modeling analysis at the expense of
+galaxy photometry in the plane (though Kron photometry is available
+for those sources).  
+
+% galaxy model fits performed based on limits set in psphotChooseAnalysisOptions.c
+
+% petrosian analysis performed on same objects as galaxy model fits
+% if EXTENDED_SOURCE_PETROSIAN == TRUE (TRUE for PV3 stack - STACKPHOT)
+
+% galaxy model fits are performed on :
+% all if (PSPHOT.EXT.FIT.ALL.SOURCES == TRUE) (FALSE for PV3 stack)
+%   (even so, if density is higher than PSPHOT.EXT.FIT.ALL.THRESH, skip)
+
+% only extended sources (based on EXT.NSIGMA) if EXT.NSIGMA.LIMIT.USE
+% == TRUE (FALSE for PV3 stacks)
+
+% fit sources / measure petrosian to fixed flux limit if limits are
+% defined (they are for PV3)
+
+% mag limits by filter, e.g., : petro 25, extfit 21.5
+% are translated to flux in counts and compared to Kron flux
+
+% SN limit is used only if fixed flux limits are not set
+% SN limit set to EXTENDED_SOURCE_SN_LIM (10.0 for PV3)
+% S/N limit for Kron flux, 
+
+% S/N lim values set to 0.0 for all models in PV3
+
+% galaxy coordinate limits:
+% if |b| > 20.0 + 15.0 exp(-long^2 / (2 * 50^2))
 
 \subsubsection{Radial Profiles}
@@ -1675,21 +1744,14 @@
 local sky value, the Exponential and DeVaucouleur profiles have 7 free
 parameters and the Sersic profile has the additional free parameter of
-the Sersic index $n$.
-
-In this stage, the galaxy model is convolved with an approximation to
-our best guess for the PSF model at the location of the galaxy.  For
-the PV3 analysis, all sources detected in the 'bright source' analysis
-step ($S/N > 20$) were fitted with all three galaxy models, unless (a)
-the morphological test identified the source as a likely cosmic ray
+the Sersic index $n$.  In this stage, the galaxy model is convolved
+with an approximation to our best guess for the PSF model at the
+location of the galaxy.
+
+Sources which passed the extended source restrictions described above
+were fitted with all three galaxy models, unless (a) the morphological
+test identified the source as a likely cosmic ray
 (Section~\ref{sec:source.size}) or (b) the peak of the PSF profile was
-above the saturation limit for the chip \citep[see the discussion in
-][ regarding the masking of saturated pixels]{waters2017}.  Sources in
-the denser portions of the Galactic plane and bulge were not included
-in the analysis.  This restriction limited the total time spent on the
-galaxy modeling analysis at the expense of galaxy photometry in the
-plane (though Kron photometry is available for those sources).  The
-Galactic Plane region was defined by $|b| > b_{\rm min}$ where $b_{\rm
-  min} = b_0 + r_b e^{\frac{-l^2}{2 \sigma_b^2}}$.  For the PV3
-analysis, $b_0 = $20\degree, $r_b = $15\degree, $\sigma_b = $50\degree.
+above the saturation limit for the chip \citep[see the discussion
+  in][regarding the masking of saturated pixels]{waters2017}.  
 
 % \note{need a discussion of the detector saturation behavior
@@ -2185,29 +2247,4 @@
 catalog.
 
-% galaxy model fits performed based on limits set in psphotChooseAnalysisOptions.c
-
-% petrosian analysis performed on same objects as galaxy model fits
-% if EXTENDED_SOURCE_PETROSIAN == TRUE (TRUE for PV3 stack - STACKPHOT)
-
-% galaxy model fits are performed on :
-% all if (PSPHOT.EXT.FIT.ALL.SOURCES == TRUE) (FALSE for PV3 stack)
-%   (even so, if density is higher than PSPHOT.EXT.FIT.ALL.THRESH, skip)
-
-% only extended sources (based on EXT.NSIGMA) if EXT.NSIGMA.LIMIT.USE
-% == TRUE (FALSE for PV3 stacks)
-
-% fit sources / measure petrosian to fixed flux limit if limits are
-% defined (they are for PV3)
-
-% mag limits by filter, e.g., : petro 25, extfit 21.5
-% are translated to flux in counts and compared to Kron flux
-
-% SN limit is used only if fixed flux limits are not set
-% SN limit set to EXTENDED_SOURCE_SN_LIM (10.0 for PV3)
-% S/N limit for Kron flux, 
-
-% galaxy coordinate limits:
-% if |b| > 20.0 + 15.0 exp(-long^2 / (2 * 50^2))
-
 \section{Difference Image Photometry}