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Timestamp:
Dec 15, 2016, 3:48:40 PM (10 years ago)
Author:
eugene
Message:

make makefile system a little more flexible; make tarballs automatically

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  • trunk/doc/release.2015/ps1.analysis/analysis.tex

    r39866 r39868  
    11\documentclass[iop,floatfix]{emulateapj}
    2 % \documentclass[iop,floatfix,onecolumn]{emulateapj}
     2
    33% \pdfoutput=1
    44
    5 % see latex.readme.txt for notes on using the PS1 template
    6 %\documentclass[12pt,preprint]{aastex}
    7 %\documentclass[manuscript]{aastex}
    8 %\documentclass[preprint2]{aastex}
    9 %\documentclass[preprint2,longabstract]{aastex}
    105\RequirePackage{color}
    116\RequirePackage{code}
    … …  
    1813%\def\plotext{pdf}
    1914\def\plotext{ps}
     15\def\plottype{eps}
    2016
    2117%\def\picdir{/home/eugene/chipresid.20140404}
    … …  
    3329% list and (2) re-order the list at the bottom (and comment-out as needed)
    3430\def\IfA{1}
     31\def\Princeton{2}
     32\def\DUR{3}
    3533\def\CfA{2}
    36 \def\MPIA{3}
    37 \def\Princeton{2}
    38 \def\USNO{4}
    39 \def\JHU{1}
    4034
    4135% This example has a first author from UH:
    4236\author{
    4337Eugene A. Magnier,\altaffilmark{\IfA}
    44 R. H. Lupton,\altaffilmark{\Princeton}
     38% R. H. Lupton,\altaffilmark{\Princeton}
    4539W.~E. Sweeney,\altaffilmark{\IfA}
    4640K.~C. Chambers,\altaffilmark{\IfA}
    … …  
    4943P.~A. Price,\altaffilmark{\Princeton}
    5044C. Z. Waters,\altaffilmark{\IfA}
    51 PS1 Builders
     45% PS1 Builders
     46L. Denneau,\altaffilmark{\IfA}
     47P. Draper,\altaffilmark{\DUR}
     48R. Jedicke,\altaffilmark{\IfA}
     49K. W. Hodapp,\altaffilmark{\IfA}
     50R.-P. Kudritzki,\altaffilmark{\IfA}
     51N. Metcalfe,\altaffilmark{\DUR}
     52C.~W. Stubbs,\altaffilmark{\CfA}
    5253% W.~S. Burgett,\altaffilmark{\IfA}
    53 % K.~C. Chambers,\altaffilmark{\IfA}
    54 % L. Denneau,\altaffilmark{\IfA}
    55 % P. Draper,\altaffilmark{\DUR}
    56 % H.~A. Flewelling,\altaffilmark{\IfA}
    5754% T. Grav,\altaffilmark{\IfA}
    5855% J. N. Heasley,\altaffilmark{\IfA}
    59 % K. W. Hodapp,\altaffilmark{\IfA}
    60 % M. E. Huber,\altaffilmark{\IfA}
    61 % R. Jedicke,\altaffilmark{\IfA}
    6256% N. Kaiser,\altaffilmark{\IfA}
    63 % R.-P. Kudritzki,\altaffilmark{\IfA}
    6457% G. A. Luppino,\altaffilmark{\IfA}
    6558% R. H. Lupton,\altaffilmark{\Princeton}
    6659% E. A. Magnier,\altaffilmark{\IfA}
    67 % N. Metcalfe,\altaffilmark{\DUH}
    6860% D. G. Monet,\altaffilmark{\USNO}
    6961% J.~S. Morgan,\altaffilmark{\IfA}
    7062% P. M. Onaka,\altaffilmark{\IfA}
    71 % P.~A. Price,\altaffilmark{\Princeton}
    72 % C.~W. Stubbs,\altaffilmark{\CfA}
    73 % W.~E. Sweeney,\altaffilmark{\IfA}
    7463% J.~L. Tonry, \altaffilmark{\IfA}
    75 % R. J. Wainscoat,\altaffilmark{\IfA} and
    76 % C. Z. Waters,\altaffilmark{\IfA}
     64R. J. Wainscoat\altaffilmark{\IfA}
    7765} % this bracket terminates author list
    7866
    7967% The ordering here should be sequential, matching the sequence in the list of authors:
    8068\altaffiltext{\IfA}{Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu HI 96822}
    81 % \altaffiltext{\CfA}{Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138}
    8269\altaffiltext{\Princeton}{Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544, USA}
     70\altaffiltext{\DUR}{Department of Physics, Durham University, South Road, Durham DH1 3LE, UK}
     71\altaffiltext{\CfA}{Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138}
    8372% \altaffiltext{\USNO}{US Naval Observatory, Flagstaff Station, Flagstaff, AZ 86001, USA}
    8473% \altaffiltext{\JHU}{Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA}
    … …  
    157146described in detail in \cite{2012ApJ...750...99T}.
    158147
     148{\color{red} {\em Note: These papers are being placed on arXiv.org to
     149    provide crucial support information at the time of the public
     150    release of Data Release 1 (DR1). We expect the arXiv versions to
     151    be updated prior to submission to the Astrophysical Journal in
     152    January 2017. Feedback and suggestions for additional information
     153    from early users of the data products are welcome during the
     154    submission and refereeing process.}}
     155
     156\section{Background}
     157
    159158The photometric and astrometric precision goals for the Pan-STARRS\,1
    160159surveys were quite stringent: photmetric accuracy of 10
    … …  
    183182astrometry.
    184183
    185 \subsection{Comparable Programs}
    186 
    187184A variety of astronomical software packages perform the basic object
    188185detection, measurement, and classification tasks needed by the
    … …  
    198195  pro: well-tested, stable code.  con: limited range of models,
    199196  algorithm converges slowly to a PSF model, limited tests of PSF
    200   validity, inflexible code base, fortran (P. Schechter)
     197  validity, inflexible code base, fortran \citep{1993PASP..105.1342S}.
    201198
    202199\item DAOPhot : Pixel-map PSF model with analytical component.  pro:
    203200  well-tested, high-quality photometry.  con: Difficult to use in an
    204   automated fashion, does it handle 2D variations well? (P. Stetson)
     201  automated fashion, does it handle 2D variations well? \citep{1987PASP...99..191S}.
    205202
    206203\item Sextractor : pure aperture measurement with rudimentary object
    207204  subtraction.  pro: fast, widely used, easy to automate.  con: poor
    208205  object separation in crowded regions, PSF-modeling was only in beta,
    209   not widely used at the time. (E. Bertin)
    210 
    211 \item apphot : IRAF-based aperture photometry.  pro: widely used.
    212   con: IRAF-based, aperture photometry. (???)
     206  not widely used at the time \citep{sextractor}.
    213207
    214208\item galfit : detailed galaxy modeling.  not a multi-object PSF
    215209  analysis tool.  con: does not provide a PSF model, not easily
    216210  automated.  very detailed results in very slow processing.  only a
    217   galaxy analysis program. (C. Impey)
     211  galaxy analysis program \citep{2002AJ....124..266P}.
    218212
    219213\item SDSS phot : con: tightly integrated into the SDSS software
    220   environment.  (R. Lupton)
     214  environment \citep{2001ASPC..238..269L}.
    221215
    222216\end{itemize}
    … …  
    425419subtracted might be useful for detection or even analysis of brighter
    426420sources.  Table~\ref{tab:mask_values} lists the 16 bit values used for
    427 PS1 mask images, along with their description (see \note{Waters et
    428   al. paper} for additional information).
     421PS1 mask images, along with their description \citep[see][for
     422  additional information]{waters2017}.
    429423
    430424\begin{table*}
    … …  
    495489which the values of \code{SKY} and \code{SKY_SIGMA} are calculated for
    496490each object in the output catalog.  See also the discussion in
    497 \note{Waters et al REF}.
     491\cite{waters2017}.
    498492
    499493\subsection{Initial Object Detection}
    … …  
    580574\begin{figure}[htbp]
    581575  \begin{center}
    582   \includegraphics[width=\hsize,angle=0,clip]{peaks.ps}
    583   \caption{Illustration of peak finding and culling peaks within a
     576%  \includegraphics[type=\plottype,ext=.\plotext,width=3.5in,height=2.5in,viewport=60 60 560 310]{peaks}
     577% \includegraphics[type=\plottype,ext=.\plotext,width=\hsize,height=1in,viewport=60 60 560 310,clip]{peaks}
     578  \includegraphics[type=\plottype,ext=.\plotext,width=\hsize,height=0.5\hsize,viewport=60 60 560 310,clip]{peaks}
     579  \caption{\label{fig:peaks} Illustration of peak finding and culling peaks within a
    584580    footprint.  Insignificant peaks within the footprint of a brighter
    585581    peak are ignored in further processing. }
    … …  
    608604\code{FOOTPRINT_CULL_NSIGMA_DELTA} (4.0) sigmas below the peak of
    609605interest, the peak is considered to be {\em locally insignificant} and
    610 removed from the list of possible detections.  In the vicinity of a
    611 saturated star, the rule is somewhat more agressive as the flat-topped
    612 or structured saturated top of a bright star may appear as multiple
    613 peaks with highly significant cols between them.  However, this is an
    614 artifact of the proximity to saturation.  In this regime, we require
    615 the col to also be a fixed fraction (5\%) of the saturation below the
    616 peak to avoid being marked as locally insignificant.
     606removed from the list of possible detections (see
     607Figure~\ref{fig:peaks}).  In the vicinity of a saturated star, the
     608rule is somewhat more agressive as the flat-topped or structured
     609saturated top of a bright star may appear as multiple peaks with
     610highly significant cols between them.  However, this is an artifact of
     611the proximity to saturation.  In this regime, we require the col to
     612also be a fixed fraction (5\%) of the saturation below the peak to
     613avoid being marked as locally insignificant.
    617614
    618615\subsubsection{Centroid and higher-order Moments}
     616\label{sec:moments}
    619617
    620618\begin{figure}[htbp]
    621619  \begin{center}
    622   \includegraphics[width=\hsize,angle=0,clip]{FWHM.smooth.trend.ps1.ps}
    623   \caption{Example of the biases encountered when measuring the second
     620  \includegraphics[type=\plottype,ext=.\plotext,width=\hsize,height=2.0\hsize,viewport=60 60 413 760]{FWHM.smooth.trend.ps1}
     621  \caption{\label{fig:moments.window} Example of the biases encountered when measuring the second
    624622    moments.  A simulated image was generated using the PS1 PSF
    625623    profile.  Each panel corresponds to a different value of
    … …  
    656654signal-to-noise of the object. 
    657655
    658 These effects are illustrated in Figure~\ref{fig:moment.window} using
     656These effects are illustrated in Figure~\ref{fig:moments.window} using
    659657simulated data.  An image was generated with a PSF model matching the
    660658radial profile of the PS1 PSF model with a FWHM of 1.4 arcseconds.  As
    … …  
    736734these moments.
    737735
    738 The Kron radius is defined the be 2.5$\times$ the first radial moment.
    739 The Kron flux is the sum of (sky-subtracted) pixel fluxes within the
    740 Kron radius.  We also calculate the flux in two related annular
    741 apertures: the Kron inner flux is the sum of pixel values for the
    742 annulus $R_1 < r < 2.5 R_1$, while the Kron outer flux is the sum of
    743 pixel values for $2.5 R_1 < r < 4 R_1$.  The first radial moment is
    744 limited at the low and high ends by $R_{\rm min} < M_r < R_{\rm max}$
    745 where $R_{\rm min}$ is the first radial moment of the PSF stars, or
    746 0.75$\times$ \code{MOMENTS_GAUSS_SIGMA} if that cannot be
    747 determined.  $R_{\rm max}$ is set to \code{PSF_MOMENTS_RADIUS}, the
    748 size of the moments aperture.
     736The Kron radius \citep{1980ApJS...43..305K} is defined the be
     7372.5$\times$ the first radial moment.  The Kron flux is the sum of
     738(sky-subtracted) pixel fluxes within the Kron radius.  We also
     739calculate the flux in two related annular apertures: the Kron inner
     740flux is the sum of pixel values for the annulus $R_1 < r < 2.5 R_1$,
     741while the Kron outer flux is the sum of pixel values for $2.5 R_1 < r
     742< 4 R_1$.  The first radial moment is limited at the low and high ends
     743by $R_{\rm min} < M_r < R_{\rm max}$ where $R_{\rm min}$ is the first
     744radial moment of the PSF stars, or 0.75$\times$
     745\code{MOMENTS_GAUSS_SIGMA} if that cannot be determined.  $R_{\rm
     746  max}$ is set to \code{PSF_MOMENTS_RADIUS}, the size of the moments
     747aperture.
    749748
    750749\subsection{PSF Determination}
    … …  
    906905\begin{figure}[htbp]
    907906  \begin{center}
    908   \includegraphics[width=\hsize,angle=0,clip]{moment.class.ps}
     907  \includegraphics[type=\plottype,ext=.\plotext,width=\hsize,height=\hsize,viewport=60 60 560 560]{moment.class}
    909908  \caption{\label{fig:moment.class} Illustration of PSF star selection using the FWHM derived
    910909    from the second moments in $X_{\rm ccd}$ and $Y_{\rm ccd}$
    … …  
    919918\subsubsection{PSF Candidate Object Model Fits}
    920919
     920% \note{link to psLibADD}
     921
    921922All candidate PSF objects are then fitted with the selected object
    922923model, allowing all of the parameters (PSF and independent) to vary in
    923924the fit.  PSPhot uses the Levenberg-Marquardt minimization technique
    924 \note{link to psLibADD} for the non-linear fitting.  Non-linear
     925for the non-linear fitting.  Non-linear
    925926fitting can be very computationally intensive, particularly for if the
    926927starting parameters are far from the minimization values.  PSPhot uses
    … …  
    10121013\subsubsection{PSF Model applied to detected objects}
    10131014
    1014 \note{review the discussion below}
     1015% \note{review the discussion below}
    10151016
    10161017Once a PSF model has been selected for an image, PSPhot attempts to
    10171018fit all of the detected objects, above a user-defined signal-to-noise
    1018 ratio (\note{KEYWORD}) with the PSF model.  For these fits, the
    1019 dependent parameters are fixed by the PSF model and only the 4
    1020 independent object model parameters are allowed to vary in the fit.
    1021 PSPhot again uses Levenberg-Marquardt minimization for the non-linear
    1022 fitting.  The objects are fitted in their S/N order, starting with the
    1023 brightest and working down to the user-specified limit.
     1019ratio with the PSF model.  For these fits, the dependent parameters
     1020are fixed by the PSF model and only the 4 independent object model
     1021parameters are allowed to vary in the fit.  PSPhot again uses
     1022Levenberg-Marquardt minimization for the non-linear fitting.  The
     1023objects are fitted in their S/N order, starting with the brightest and
     1024working down to the user-specified limit.
    10241025
    10251026Once a solution has been achieved for an object, PSPhot attempts to
    … …  
    11081109
    11091110\subsubsection{Source Size Assessment}
     1111\label{sec:source.size}
    11101112
    11111113After the PSF model has been fitted to all sources, and the Kron flux
    … …  
    12941296\frac{y^2}{2\sigma_y^2} + \sigma_{\rm xy} x y $).  The Pseudo-Gaussian
    12951297is a Taylor expansion of the Gaussian and is used by Dophot
    1296 \citep{dophot}.  The latter profiles are similar to the Moffat profile
    1297 form \citep{moffat,buonanno}, with small differences.  For the PS1
    1298 GPC1 analysis, we used the \code{PS1_V1} model, which we found by
    1299 experimentation to match well to the observed profiles generated by
    1300 PS1.  Using a fixed power-law exponent results in somewhat faster
    1301 profile fitting compared to the variable power-law exponent model.
     1298\citep{1993PASP..105.1342S}.  The latter profiles are similar to the
     1299Moffat profile form \citep{1969AA.....3..455M,1983AA...126..278B},
     1300with small differences.  For the PS1 GPC1 analysis, we used the
     1301\code{PS1_V1} model, which we found by experimentation to match well
     1302to the observed profiles generated by PS1.
     1303Figure~\ref{fig:radial.profiles} shows example radial profiles for
     1304moderately bright stars in fairly good (0.9 arcsec) and poor (2.2
     1305arcsec) seeing.  Using a fixed power-law exponent results in somewhat
     1306faster profile fitting compared to the variable power-law exponent
     1307model.
    13021308
    13031309% moffat : 1969A&A.....3..455M
    … …  
    13061312\begin{figure}[htbp]
    13071313  \begin{center}
    1308   \includegraphics[width=\hsize,angle=0,clip]{radial.profiles.ps}
    1309   \caption{Radial profiles of stellar images from PS1.  These two
     1314  \includegraphics[type=\plottype,ext=.\plotext,width=\hsize,height=\hsize,viewport=60 60 560 560]{radial.profiles}
     1315  \caption{\label{fig:radial.profiles} Radial profiles of stellar images from PS1.  These two
    13101316    profiles illustrate the radial trend of the PS1 PSFs for a star
    13111317    with FWHM 0.9 arcsec (red) and 2.2 arcsec (blue).  The black line
    … …  
    13721378\code{RMAX_NN}).
    13731379
    1374 \note{these profiles are not saved in PSPS}
     1380% \note{these profiles are not saved in PSPS}
    13751381
    13761382\subsection{Petrosian Radii and Magnitudes}
    13771383
    1378 Petrosian (REF) defined an adaptive aperture based on a ratio of
    1379 surface brightnesses.  The motivation is to define an aperture which
    1380 can be determined for galaxies without significant biases as a
    1381 function of distance.  Since surface brightness in a resolved object
    1382 is conserved, using a ratio of surface brightness to define a spatial
    1383 scale results in a spatial scale which is constant regardless of
    1384 galaxy distance. 
     1384\cite{1976ApJ...209L...1P} defined an adaptive aperture based on a
     1385ratio of surface brightnesses.  The motivation is to define an
     1386aperture which can be determined for galaxies without significant
     1387biases as a function of distance.  Since surface brightness in a
     1388resolved object is conserved, using a ratio of surface brightness to
     1389define a spatial scale results in a spatial scale which is constant
     1390regardless of galaxy distance.
    13851391
    13861392To measure the Petrosian radius and flux, we start by defining a
    … …  
    14281434median) flux in the annulus is within 1 $\sigma$ of the local sky
    14291435level.  If this limit is not reached before the slope of the flux from
    1430 one annulus to the next is less that \note{SOMETHING,
    1431   psphotRadialProfileWings.c}, then the annulus at which the slope
    1432 reaches this limit is used to define the sky radius.  These values are
    1433 saved in the output smf / cmf files, but not sent to the PSPS.  The
    1434 sky radius value is used below in the calculation of the kron magnitude.
     1436one annulus to the next is less than a user-defined limit, then the
     1437annulus at which the slope reaches this limit is used to define the
     1438sky radius.  These values are saved in the output smf / cmf files, but
     1439not sent to the PSPS.  The sky radius value is used below in the
     1440calculation of the kron magnitude.
    14351441
    14361442\subsection{Kron Magnitudes}
    14371443
    1438 Preliminary Kron radius and flux values are calculated soon after
    1439 sources are detected (\ref{sec:moments}).  However, these preliminary
    1440 values are not accurate due to the window-functions applied.  After
    1441 sources have been characterized and the PSF model is well-determined,
    1442 the Kron parameters are re-calculated more carefully.  In this version
    1443 of the calculation, the image is first smoothed by Gaussian kernel
    1444 with $\sigma = 1.7$ pixels, corresponding to a FWHM of 1.0\arcsec in
    1445 the PS1 stack images.  Next, the Kron radius is determined in an
    1446 iterative process: the first radial moment is measured using the pixels in an
    1447 aperture 6$\times$ the first radial moment from the previous
    1448 iteration.  On the first iteration, the sky radius is used in place of
    1449 the first radial moment.  By default, 2 iterations are performed.  The
    1450 Kron radius is defined the be 2.5$\times$ the first radial moment.
    1451 The Kron flux is the sum of pixel fluxes within the Kron radius.  We
    1452 also calculate the flux in two related annular apertures: the Kron
    1453 inner flux is the sum of pixel values for the annulus $R_1 < r < 2.5
    1454 R_1$, while the Kron outer flux is the sum of pixel values for $2.5
    1455 R_1 < r < 4 R_1$. 
     1444Preliminary Kron radius and flux values \citep{1980ApJS...43..305K}
     1445are calculated soon after sources are detected (Section~\ref{sec:moments}).
     1446However, these preliminary values are not accurate due to the
     1447window-functions applied.  After sources have been characterized and
     1448the PSF model is well-determined, the Kron parameters are
     1449re-calculated more carefully.  In this version of the calculation, the
     1450image is first smoothed by Gaussian kernel with $\sigma = 1.7$ pixels,
     1451corresponding to a FWHM of 1.0\arcsec\ in the PS1 stack images.  Next,
     1452the Kron radius is determined in an iterative process: the first
     1453radial moment is measured using the pixels in an aperture 6$\times$
     1454the first radial moment from the previous iteration.  On the first
     1455iteration, the sky radius is used in place of the first radial moment.
     1456By default, 2 iterations are performed.  The Kron radius is defined
     1457the be 2.5$\times$ the first radial moment.  The Kron flux is the sum
     1458of pixel fluxes within the Kron radius.  We also calculate the flux in
     1459two related annular apertures: the Kron inner flux is the sum of pixel
     1460values for the annulus $R_1 < r < 2.5 R_1$, while the Kron outer flux
     1461is the sum of pixel values for $2.5 R_1 < r < 4 R_1$.
    14561462
    14571463Two details in the calculation above should be noted.  First, for
    … …  
    14601466calculations.  The window used for the calculations is constrained to
    14611467be at least the size of the aperture based on the PSF stars
    1462 (\ref{sec:moments}).  At the other extreme, noise may make the radius
     1468(Section~\ref{sec:moments}).  At the other extreme, noise may make the radius
    14631469grow excessively, resulting in an unrealistically low effective
    14641470surface brightness.  The aperture is constrained to be less than a
    … …  
    14711477opposites sides of the central pixel are considered together.  The
    14721478geometric mean of the two fluxes is used to replace the flux values.
    1473 If the object has 180\degree symmetry, this operation has no impact.
     1479If the object has 180\degree\ symmetry, this operation has no impact.
    14741480However, if one of the two pixels is unusually high, the value will be
    14751481surpressed by the matched pixel on the other side.  This trick has the
    … …  
    14801486
    14811487In the galaxy model fittting stage, sources which meet certain
    1482 criteria are fitted with analytical models for galaxies.  The
    1483 three models used for the PV3 analysis have similar form:
     1488criteria are fitted with analytical models for galaxies.  Three
     1489traditional analytical galaxy models are implemented in \code{psphot}
     1490and used in the PV3 analysis:
    14841491\begin{itemize}
    14851492\item Exponential profile : $f = I_0 e^{-\rho}$
    1486 \item DeVaucouleur profile : $f = I_0 e^{-\rho^{1/4}}$
    1487 \item Sersic : $f = I_0 e^{-\rho^{1/n}}$
     1493\item DeVaucouleur profile \citep{1948AnAp...11..247D}: $f = I_0 e^{-\rho^{1/4}}$
     1494\item Sersic \citep{1963BAAA....6...41S} : $f = I_0 e^{-\rho^{1/n}}$
    14881495\end{itemize}
    14891496where $\rho$ is a normalized radial term: $\rho =
    … …  
    15001507our best guess for the PSF model at the location of the galaxy.  For
    15011508the PV3 analysis, all sources detected in the 'bright source' analysis
    1502 step ($S/N > 20 ?$) were fitted with all three galaxy models, unless
    1503 (a) the morphological test identified the source as a likely cosmic
    1504 ray (\ref{CR}) or (b) the peak of the PSF profile was above the
    1505 saturation limit for the chip \note{(link to the handling of
    1506   saturation in detrend paper)}.  Sources in the denser portions of
    1507 the Galactic plane and bulge were not included in the analysis.  This
    1508 restriction limited the total time spent on the galaxy modeling
    1509 analysis at the expense of galaxy photometry in the plane (though Kron
    1510 photometry is available for those objects).  The Galactic Plane region
    1511 was defined by $|b| > b_{\rm min}$ where $b_{\rm min} = b_0 + r_b
    1512 e^{\frac{-l^2}{2 \sigma_b^2}}$.  For the PV3 analysis, $b_0 = XX$,
    1513 $r_b = XX$, $\sigma_b = XX$.
     1509step ($S/N > 20$) were fitted with all three galaxy models, unless (a)
     1510the morphological test identified the source as a likely cosmic ray
     1511(Section~\ref{sec:source.size}) or (b) the peak of the PSF profile was
     1512above the saturation limit for the chip \citep[see the discussion in
     1513][ regarding the masking of saturated pixels]{waters2017}.  Sources in
     1514the denser portions of the Galactic plane and bulge were not included
     1515in the analysis.  This restriction limited the total time spent on the
     1516galaxy modeling analysis at the expense of galaxy photometry in the
     1517plane (though Kron photometry is available for those objects).  The
     1518Galactic Plane region was defined by $|b| > b_{\rm min}$ where $b_{\rm
     1519  min} = b_0 + r_b e^{\frac{-l^2}{2 \sigma_b^2}}$.  For the PV3
     1520analysis, $b_0 = $20\degree, $r_b = $15\degree, $\sigma_b = $50\degree.
     1521
     1522%  \note{need a discussion of the detector saturation behavior
     1523
     1524% \note{more detail below?} 
    15141525
    15151526Before the non-linear fitting may be performed, it is necessary to
    … …  
    15211532($R_{xx}$, $R_{yy}$ , $R_{xy}$) values; it was found that such a guess
    15221533tended to be too small and resulted in more iterations rather than
    1523 fewer. \note{more detail on that?}  The 1st radial moment (see
     1534fewer. The 1st radial moment (see
    15241535\ref{sec:moments}) is used to estimate the effective radius of the
    15251536model based on the results of Graham \& Driver (2005, Table 1).  They
    … …  
    16061617For the small size of the PSF model used to convolve the galaxy model
    16071618images, it was found that this direct convolution was faster than
    1608 using an FFT-based convolution \note{(examples?)}
     1619using an FFT-based convolution.
     1620
     1621% \note{(examples?)}
    16091622
    16101623For the Exponential and DeVaucouleur fits, all parameters are fitted
    … …  
    16561669for all 5 filters.  In this analysis, the best model for each object
    16571670is subtracted from the image pixels for all objects excluding the
    1658 object in consideration.  The 'best model' is \note{TBD}. 
     1671object in consideration.  The 'best model' is determined based on the
     1672minimum $\chi^2$ value for the model fits.
     1673
     1674% \note{more discussion of the selection of the best model}. 
    16591675
    16601676In addition to the raw radial apertures, the stack images are each
    … …  
    16671683procedure is then repeated with a target FWHM of 8\arcsec. 
    16681684
    1669 \note{is the first convolution done with the Alard-Lupton technique?}
     1685% \note{is the first convolution done with the Alard-Lupton technique?}
     1686
     1687\acknowledgments
     1688
     1689The Pan-STARRS1 Surveys (PS1) have been made possible through
     1690contributions of the Institute for Astronomy, the University of
     1691Hawaii, the Pan-STARRS Project Office, the Max-Planck Society and its
     1692participating institutes, the Max Planck Institute for Astronomy,
     1693Heidelberg and the Max Planck Institute for Extraterrestrial Physics,
     1694Garching, The Johns Hopkins University, Durham University, the
     1695University of Edinburgh, Queen's University Belfast, the
     1696Harvard-Smithsonian Center for Astrophysics, the Las Cumbres
     1697Observatory Global Telescope Network Incorporated, the National
     1698Central University of Taiwan, the Space Telescope Science Institute,
     1699the National Aeronautics and Space Administration under Grant
     1700No. NNX08AR22G issued through the Planetary Science Division of the
     1701NASA Science Mission Directorate, the National Science Foundation
     1702under Grant No. AST-1238877, the University of Maryland, and Eotvos
     1703Lorand University (ELTE) and the Los Alamos National Laboratory.
     1704
     1705\bibliographystyle{apj}
     1706% \bibliography{lib}{}
     1707\input{analysis.bbl}
     1708
     1709\end{document}
    16701710
    16711711\subsection{Forced Photometry : PSFs}
    … …  
    16751715\subsection{Output Options}
    16761716
    1677 \note{need to discuss tests}
    1678 
    1679 \note{need to discuss failings and holes}
     1717% \note{need to discuss tests}
     1718
     1719% \note{need to discuss failings and holes}
    16801720
    16811721\section{Alternative Scenarios}
    … …  
    17591799\end{verbatim}
    17601800
    1761 \bibliographystyle{apj}
    1762 \bibliography{lib}{}
    1763 
    1764 \end{document}
    1765 
    17661801Figures Needed for this document:
    17671802
    … …  
    17911826* put engineering docs (psLib, psModules) on public website
    17921827
    1793 % example of 2 image figure:
    1794 \begin{figure}
    1795   \centering
    1796   \begin{minipage}{0.45\hsize}
    1797     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_XY11_bt_trail.png}
    1798   \end{minipage}%
    1799   \begin{minipage}{0.45\hsize}
    1800     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0124o_XY11_bt_trail.png}
    1801   \end{minipage}
    1802   \caption{Example of a profile cut along the y-axis through a bright star on exposure o5677g0123o OTA11 in cell xy60 (left panel) and on the subsequent exposure o5677g0124o (right panel).  In both figures, the green points show the image corrected with all appropriate detrending steps, but without burntool applied, illustrating the amplitude of the persistence trails.  The red points show the same data after the burntool correction, which reduces the impact of these features.  Both exposures are in the \gps{} filter with exposure times of 43s}
    1803 \end{figure}
    1804 
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