Index: trunk/doc/release.2015/systematics.20140411/diffusion.tex
===================================================================
--- trunk/doc/release.2015/systematics.20140411/diffusion.tex	(revision 40311)
+++ trunk/doc/release.2015/systematics.20140411/diffusion.tex	(revision 40321)
@@ -14,5 +14,6 @@
 % \RequirePackage{code}
 % \RequirePackage{pbox}
-\input{magnier.tex}
+% \input{magnier.tex}
+\input{astro.sty}
 
 %\newcommand\oldtext[1]{\color{red}#1}
@@ -32,11 +33,11 @@
 %\def\plotmode{bw}
 
-%\def\plotext{pdf}
-\def\plotext{eps}
+\def\plotext{pdf}
+%\def\plotext{eps}
 
 %\def\picdir{/home/eugene/chipresid.20140404}
 %\def\picdir{/data/kukui.2/eugene/chipresid.20140404}
-%\def\picdir{pics} %%% need to set this for local processing
-\def\picdir{.} %%% need to set this for the zip archive
+\def\picdir{pics} %%% need to set this for local processing
+%\def\picdir{.} %%% need to set this for the zip archive
 
 % Pick a terse version of the title here;
@@ -467,6 +468,5 @@
   the median deviation for measurements at the given chip pixel
   location compared with the average photometry for the given
-  object.  Fringing dominates the \yps-band signal, saturating the
-  color scale to black or white in areas.} \label{fig:psfmags.by.filter}}
+  object.  Fringing dominates the \yps-band signal.} \label{fig:psfmags.by.filter}}
 \end{center}
 \end{figure*}
@@ -575,7 +575,9 @@
 \oldtext{The per-pixel standard deviations of these plots are listed
   in Table~1.}  The signal-to-noise of these structures is again
-somewhat weak, but the pattern is clearly visible in \oldtext{these figures} \newtext{Figure~\ref{fig:all.effects.rband} (middle-left)}.
+somewhat weak, but the pattern is clearly visible in \oldtext{these
+  figures} \newtext{Figure~\ref{fig:all.effects.rband} (middle-left)}.
 
 \subsection{Flat-field Structures}
+\label{sec:flat-fields}
 
 % All Effects in r-band
@@ -613,15 +615,19 @@
 
 % 2012ApJ...750...99T = Tonry et al PS1 phot system
-\oldtext{Figure~4} \newtext{Figure~\ref{fig:all.effects.rband} (middle-right)}
-shows the high-spatial-frequency
-structures in the \newtext{\rps-band} flat-field\oldtext{ images}.  For this measurement, we have
-used a set of monochromatic flat-field images obtained with a tunable
-laser.  The laser is used to illuminate our flat-field screen which is
-then observed by the PS1 telescope.  These flat-field images were
-obtained 2011 Feb 09 as part of a campaign to study the PS1 system
-response \citep{2012ApJ...750...99T}.  Flats were obtain in a set of
-4nm steps sampling the spectral response curve of each filter.  To
-enhance the signal-to-noise, we have median-combined a set of 6 flats
-at the wavelength center of the corresponding filter.
+\oldtext{Figure~4} \newtext{Figure~\ref{fig:all.effects.rband}
+  (middle-right)} shows the high-spatial-frequency structures in the
+\newtext{\rps-band} flat-field\oldtext{ images}.  For this
+measurement, we have used a set of monochromatic flat-field images
+obtained with a tunable laser.  The laser is used to illuminate our
+flat-field screen which is then observed by the PS1 telescope.  These
+flat-field images were obtained 2011 Feb 09 as part of a campaign to
+study the PS1 system response \citep{2012ApJ...750...99T}.  Flats were
+obtain in a set of 4nm steps sampling the spectral response curve of
+each filter.  To enhance the signal-to-noise, we have median-combined
+a set of 6 flats at the wavelength center of the corresponding filter.
+\newtext{Note that the flat-field images used for the science analysis
+  are made from broad-band dome flat, not these monochromatic flats.
+  The monochromatic flats were used here to avoid smearing out any
+  effects which changed as a function of wavelength.}
 
 In order to mask pixels which do not flatten well, we generate a copy
@@ -632,19 +638,29 @@
 pixels associated with each superpixel.  
 
-\oldtext{Figure~\ref{fig:flats.by.filter} shows the superpixel images for the
-flat-fields in the five filters. These flat-field images are} \newtext{The flat-field image is}
-displayed as fractional deviations relative to the median of the flat-field
-image and can thus be compared to the magnitude residuals.  When
-flattening an image, \oldtext{these flat-fields} \newtext{the flat-field image} would be divided into the flux
-of the raw image.  The residuals are thus defined in the sense that a
-positive feature in \oldtext{these flats} \newtext{the flat} which does {\em not} represent a real
-quantum efficiency deviation would induce a {\em reduction} in the
-measured flux in those pixels, and thus a {\em negative} deviation in
-$\delta m_{psf}$ as defined above.  The dynamic range of the color
-scale in \oldtext{these plots} \newtext{this plot} is -0.01 to +0.01.  The tree-ring pattern is
-strong in the (\gps,\rps,\ips) images, but nearly swamped by fringing
-in \zps, and completely lost to fringing in \yps.  A diagonal banding
-pattern is also seen in \gps\ and \rps: this feature is thought to be due to
-the lithography process used to generate the CCD.  A blob can also
+\oldtext{Figure~\ref{fig:flats.by.filter} shows the superpixel images
+  for the flat-fields in the five filters. These flat-field images
+  are} \newtext{The flat-field image is} displayed as fractional
+deviations relative to the median of the flat-field image and can thus
+be compared to the magnitude residuals.  When flattening an image,
+\oldtext{these flat-fields} \newtext{the flat-field image} would be
+divided into the flux of the raw image.  The residuals are thus
+defined in the sense that a positive feature in \oldtext{these flats}
+\newtext{the flat} which does {\em not} represent a real quantum
+efficiency deviation would induce a {\em reduction} in the measured
+flux in those pixels, and thus a {\em negative} deviation in $\delta
+m_{psf}$ as defined above.  The dynamic range of the color scale in
+\oldtext{these plots} \newtext{this plot} is -0.01 to +0.01.  The
+tree-ring pattern is strong in the (\gps,\rps,\ips) images, but nearly
+swamped by fringing in \zps, and completely lost to fringing in \yps.
+\newtext{For the broad-band dome flats used for the science analysis,
+  the tree-ring patterns are apparent for all filters: the fringe
+  patterns seen in the \zps\ and \yps\ monochromatic flats are
+  apparently washed out by the range of wavelengths in the broad-band
+  flats.}
+
+A diagonal banding pattern is also apparent in \gps\ and \rps, though
+it is largely removed in Figure~\ref{fig:all.effects.rband} by the
+high-pass filtering mentioned above.  This feature is thought to be due
+to the lithography process used to generate the CCD.  A blob can also
 been seen covering 4 cells near the center of this chip; this is
 apparently a deposit of some kind on the detector.  Both of the latter
@@ -738,10 +754,20 @@
 PSF ellipticity from the $e_1$ term.
 
-\oldtext{Figure~5} \newtext{Figure~\ref{fig:all.effects.rband} (lower-left)}
-shows the spatial trend of the smear,
-$e_0$.  The dynamic range of \oldtext{these images} \newtext{this image} is -0.3 to +0.3 pixel$^2$. A
-tree-ring pattern is visible for all 5 filters, though \yps\ is
-dominated by the fringing pattern.  Structures with relatively low
-spatial frequencies can also be seen.
+\oldtext{Figure~5} \newtext{Figure~\ref{fig:all.effects.rband}
+  (lower-left)} shows the spatial trend of the smear, $e_0$.  The
+dynamic range of \oldtext{these images} \newtext{this image} is -0.3
+to +0.3 pixel$^2$. A tree-ring pattern is visible for all 5 filters,
+though \yps\ is dominated by the fringing pattern.  Structures with
+relatively low spatial frequencies can also be seen.
+
+% All Effects in r-band
+\begin{figure*}[htbp]
+\begin{center}
+\parbox[b]{\figwidth}{\includegraphics[width=5.0in]{\picdir/filter_trends.\plotext}}
+\caption{Amplitude of the 4 effects which follow the tree-rings as a
+  function of filter, relative to the amplitude in the \gps-band.}
+\label{fig:filter.trend}
+\end{center}
+\end{figure*}
 
 \oldtext{Figure~6} \newtext{Figure~\ref{fig:all.effects.rband} (lower-right)}
@@ -756,14 +782,4 @@
 variations are low-frequency and unrelated to the radial trend from
 the upper-left corner.
-
-% All Effects in r-band
-\begin{figure*}[htbp]
-\begin{center}
-\parbox[b]{\figwidth}{\includegraphics[width=5.0in]{\picdir/filter_trends.\plotext}}
-\caption{Amplitude of the 4 effects which follow the tree-rings as a
-  function of filter, relative to the amplitude in the \gps-band.}
-\label{fig:filter.trend}
-\end{center}
-\end{figure*}
 
 \subsection{Correlations Between Tree-Ring Patterns}
@@ -831,9 +847,10 @@
 For all four types of measurements, the \oldtext{slope of the fitted
   lines} \newtext{amplitudes relative to \gps} are \oldtext{listed in
-Table~2} \newtext{plotted in Figure~\ref{fig:filter.trend}}.  There is a consistency in
-the trend from \gps, with the strongest systematic tree-ring effects
-to \yps, with the weakest effects.  Note that the second moment smear
-and astrometry terms have different relative strength in
-\yps\ compared with \gps.
+  Table~2} \newtext{plotted in Figure~\ref{fig:filter.trend}}.  There
+is a consistency in the trend from \gps, with the strongest systematic
+tree-ring effects, to \yps, with the weakest effects.  Note that the
+relative strength of the second moment smear in the reddest bands
+compared to \gps\ is quite different from the relative strength of the
+astrometry and flat-field terms in the reddest bands.
 
 % smear trends by filter
@@ -1193,4 +1210,21 @@
 % http://adsabs.harvard.edu/abs/2006NIMPA.568...41K
 
+The origin of the fringing patterns observed in the \yps\ PSF and
+aperture photometry is uncertain.  The photometry fringe patterns are
+similar to the fringe patterns seen in the monochromatic flat-fields.
+However, since the broad-band flat-field images actually used for the
+science do not exhibit the fringes, the photometry fringes are not
+simply the result of having an inappropriate fringe term in the
+flat-field images.  One possible cause could be the interaction
+between spectral features in the (largely M and K) stars used for the
+photometry analysis interacting with the fringe effect -- in other
+words, a flat-field image generated with a uniform spectral density
+source may not be exactly right for sources with strong spectral
+features.  However, this explanation is clearly incomplete since it
+does not explain the difference in the amplitude of the fringes seen
+in the PSF vs the aperture photometry.  In any case, the presence of
+the fringe pattern does not affect our conclusions regarding the
+charge diffusion effect.
+
 \section{Conclusion}
 
@@ -1288,7 +1322,7 @@
 
 \bibliographystyle{apj}
-%\bibliography{lib}{}
+\bibliography{lib}{}
 %\input{diffusion.bbl}
-\input{magnier_bib.tex}
+%\input{magnier_bib.tex}
 
 \end{document}