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Dec 5, 2018, 6:15:07 AM (8 years ago)
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eugene
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final mods to figures and captions; nearly ready for submission

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

    r40563 r40567  
    177177in detail in \cite{2012ApJ...750...99T}.
    178178
    179 
    180179The Pan-STARRS 1 Science Survey uses the 1.4 gigapixel GPC1 camera
    181180with the PS1 telescope on Haleakala Maui to image the sky north of
    182181$-30^\circ$ declination.  The GPC1 camera is composed of 60 orthogonal
    183 transfer array (OTA) devices, each of which is an $8\times{}8$ grid of
    184 readout cells.  The large number of cells parallelizes the readout
    185 process, reducing the overhead in each exposure.  However, as a
    186 consequence, many calibration operations are needed to ensure the
    187 response is consistent across the entire seven square degree field of
    188 view.
     182transfer array (OTA) devices arranged in an $8\times{}8$ grid,
     183excluding the four corners.  Each of the 60 devices is itself an
     184$8\times{}8$ grid of readout cells.  The large number of cells
     185parallelizes the readout process, reducing the overhead in each
     186exposure.  However, as a consequence, many calibration operations are
     187needed to ensure the response is consistent across the entire seven
     188square degree field of view.
    189189
    190190\note{DS notes fonts are not consistent for keywords, etc}
    191 
    192 \note{DS: captions need to be clear re: illustrated effect}
    193 
    194 \note{need to define PV3 (and PV0-2) here.  see datasystem.tx}
    195191
    196192%The Processing Version 3 (PV3) reduction represents the third full
     
    262258section \ref{sec:discussion}.
    263259
    264 \note{describe gpc1 camera layout before the following paragraph}
     260As mentioned above, the GPC1 camera is composed of 60 orthogonal
     261transfer array (OTA) devices arranged in an $8\times{}8$ grid,
     262excluding the four corners.  Each of the 60 devices is itself an
     263$8\times{}8$ grid of readout cells consisting of $590 \times 598$
     264pixels.  We label the OTAs by their coordinate in the camera grid in
     265the form `OTAXY', where X and Y each range from 0 - 7, e.g., OTA12 would
     266be the chip in the $(1,2)$ position of the grid.  Similarly, we
     267identify the cells as `xyXY' where X and Y again each range from 0 -
     2687. 
    265269
    266270Image products presented in figures have been mosaicked to arrange
     
    277281and pixel $(590,1)$ to the top left of their position. For mosaics of
    278282the full field of view, the OTAs are arranged as they see the sky,
    279 with the cells arranged as in the single OTA images (Figure \ref{fig:optical ghosts}).  The lower left
    280 corner is the empty location where OTA70 would exist.  Toward the
    281 right, the OTA labels decrease in $X$ label, with the empty OTA00
    282 located in the lower right.  The OTA $Y$ labels increase upward in the
    283 mosaic.
     283with the cells arranged as in the single OTA images (Figure
     284\ref{fig:optical ghosts}).  The lower left corner is the empty
     285location where OTA70 would exist.  Toward the right, the OTA labels
     286decrease in $X$ label, with the empty OTA00 located in the lower
     287right.  The OTA $Y$ labels increase upward in the mosaic.
    284288
    285289%%\textit{Note: These papers are being placed on the arXiv.org to
     
    358362\label{sec:dark}
    359363
     364\begin{figure}
     365  \centering
     366  \begin{minipage}{0.45\hsize}
     367    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_M_OS_NL_XY23.png}
     368  \end{minipage}%
     369  \begin{minipage}{0.45\hsize}
     370    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_to_DARK_XY23.png}
     371  \end{minipage}
     372  \caption{{\bf Dark Correction:} An example of the dark model application to exposure o5677g0123o, OTA23 (2011-04-26, 43s \gps{} filter).  The left panel shows the image data mosaicked to the OTA level, and has had the static mask applied, the overscan subtracted, and the detector non-linearity corrected.  The right panel, shows the same exposure with the dark applied in addition to the processing shown on the left, removing the amplifier glows in the cell corners.}
     373  \label{fig:dark image}
     374\end{figure}
     375
    360376The dark current in the GPC1 detectors has significant variations
    361377across each cell.  The model we make to remove this signal considers
     
    381397\subsubsection{Time evolution}
    382398
     399\begin{figure}
     400  \centering
     401  \includegraphics[width=0.9\hsize,angle=0,clip]{images/B_profile_v1.pdf}
     402  \caption{Example showing a profile cut across exposure o5676g0195,
     403    OTA67 (2011-04-25, 43s \gps{} filter).  The entire first row of
     404    cells (xy00-xy07) have had a median calculated along each pixel
     405    column on the OTA mosaicked image.  Arbitrary offsets have been
     406    applied so the curves do not overlap.  The top curve (in purple)
     407    shows the initial raw profile, with no dark model applied.  The
     408    next curve (in green) shows the smoother profile after applying
     409    the appropriate B-mode dark model.  Applying the (incorrect)
     410    A-mode dark instead results in the third (blue) curve, which shows
     411    a significant increase in gradients across the cells.  The fourth
     412    (red) curve is the result of applying the PATTERN.CONTINUITY
     413    correction along with the B-mode dark model.  Although this
     414    creates a larger gradient across the mosaicked images, it
     415    decreases the cell-to-cell boundary offsets.  The bottom (black)
     416    curve shows the final image profile after all detrending and
     417    background subtraction (no offset applied).  The bright source at
     418    the cell xy00 to xy01 transition is a result of a large optical
     419    ghost which, due to the area covered, increases the median level
     420    more than the field stars.}
     421  \label{fig:dark switching}
     422\end{figure}
     423
    383424The dark model is not consistently stable over the full survey, with
    384425significant drift over the course of multiple months.  Some of the
     
    432473as it is correctable with a small number of dark models, this does not
    433474significantly impact detrending.
    434 
    435 \begin{figure}
    436   \centering
    437   \begin{minipage}{0.45\hsize}
    438     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_M_OS_NL_XY23.png}
    439   \end{minipage}%
    440   \begin{minipage}{0.45\hsize}
    441     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_to_DARK_XY23.png}
    442   \end{minipage}
    443   \caption{An example of the dark model application to exposure o5677g0123o, OTA23 (2011-04-26, 43s \gps{} filter).  The left panel shows the image data mosaicked to the OTA level, and has had the static mask applied, the overscan subtracted, and the detector non-linearity corrected.  The right panel, shows the same exposure with the dark applied in addition to the processing shown on the left, removing the amplifier glows in the cell corners.}
    444   \label{fig:dark image}
    445 \end{figure}
    446 
    447 \begin{figure}
    448   \centering
    449   \includegraphics[width=0.9\hsize,angle=0,clip]{images/B_profile_ex.png}
    450   \caption{Example showing a profile cut across exposure o5676g0195, OTA67 (2011-04-25, 43s \gps{} filter).  The entire first row of cells (xy00-xy07) have had a median calculated along each pixel column on the OTA mosaicked image.  Arbitrary offsets have been applied to shift the curves to not overlap.  The top curve (in purple) shows the initial raw profile, with no dark model applied.  The next curve (in green) shows the smoother profile after applying the appropriate B-mode dark model.  Applying the A-mode dark instead results in the blue curve, which shows a significant increase in gradients across the cells.  The orange curve shows the result of the PATTERN.CONTINUITY correction.  Although this creates a larger gradient across the mosaicked images, it decreases the cell-to-cell level changes.  The final yellow curve shows the final image profile after all detrending and background subtraction, and has not had an offset applied.  The bright source at the cell xy00 to xy01 transition is a result of a large optical ghost, which due to the area covered, increases the median level more than the field stars.}
    451   \label{fig:dark switching}
    452 \end{figure}
    453475
    454476\subsubsection{Video Dark}
     
    496518    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_VIDEODARK_VDim_VDdark_XY22.png}
    497519  \end{minipage}
    498   \caption{An example of the video dark model application to exposure o5677g0123o, OTA22 (2011-04-26, 43s \gps{} filter), which has a video cell located in cell xy16.  The left panel shows the image data mosaicked to the OTA level, and has had the static mask applied, the overscan subtracted, the detector non-linearity corrected, and a regular dark applied.  The right panel, shows the same exposure with a video dark applied instead of the standard dark.  The main impact of this change is the improved correction of the corner glows, which are over subtracted with the standard dark.}
     520  \caption{{\bf Video Dark:} An example of the video dark model application to exposure o5677g0123o, OTA22 (2011-04-26, 43s \gps{} filter), which has a video cell located in cell xy16.  The left panel shows the image data mosaicked to the OTA level, and has had the static mask applied, the overscan subtracted, the detector non-linearity corrected, and a regular dark applied.  The right panel, shows the same exposure with a video dark applied instead of the standard dark.  The main impact of this change is the improved correction of the corner glows, which are over subtracted with the standard dark.}
    499521  \label{fig:video_darks}
    500522\end{figure}
     
    627649measurements and the corresponding measurements on the science image
    628650provides the scale factor multiplied to the fringe before it is
    629 subtracted from the science image.
     651subtracted from the science image.  An example of the fringe correction can be seen in Figure~\ref{fig: fringe example}. 
    630652
    631653\begin{figure}
     
    637659    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5220g0025o_fringe_XY53.png}
    638660  \end{minipage}
    639   \caption{Example of the \yps{} filter fringe pattern on exposure o5220g0025o OTA53 (\yps{} filter 30s).  The left panel shows the OTA mosaic with all detrending except the fringe correction, while the right shows the same including the fringe correction.  Both images have been smoothed with a Gaussian with $\sigma = 3$ pixels to highlight the faint and large scale fringe patterns.
    640 }
     661  \caption{{\bf Fringing:} Example of the \yps{} filter fringe pattern
     662    on exposure o5220g0025o OTA53 (\yps{} filter 30s).  The left panel
     663    shows the OTA mosaic with all detrending except the fringe
     664    correction, while the right shows the same including the fringe
     665    correction.  Both images have been smoothed with a Gaussian with
     666    $\sigma = 3$ pixels to highlight the faint and large scale fringe
     667    patterns.  }
    641668  \label{fig: fringe example}
    642669\end{figure}
     
    725752    \colhead{Description (static values listed in bold)}}
    726753  \startdata
    727   {\bf DETECTOR & 0x0001 & A detector defect is present.} \\
    728   {\bf FLAT     & 0x0002 & The flat field model does not calibrate the pixel reliably.} \\
    729   {\bf DARK     & 0x0004 & The dark model does not calibrate the pixel reliably.} \\
    730   {\bf BLANK    & 0x0008 & The pixel does not contain valid data.} \\
    731   {\bf CTE      & 0x0010 & The pixel has poor charge transfer efficiency.} \\
     754  {\bf DETECTOR } & {\bf 0x0001}  & {\bf A detector defect is present.} \\
     755  {\bf FLAT     } & {\bf 0x0002}  & {\bf The flat field model does not calibrate the pixel reliably.} \\
     756  {\bf DARK     } & {\bf 0x0004}  & {\bf The dark model does not calibrate the pixel reliably.} \\
     757  {\bf BLANK    } & {\bf 0x0008}  & {\bf The pixel does not contain valid data.} \\
     758  {\bf CTE      } & {\bf 0x0010}  & {\bf The pixel has poor charge transfer efficiency.} \\
    732759  SAT      & 0x0020 & The pixel is saturated. \\
    733760  LOW      & 0x0040 & The pixel has a lower value than expected. \\
     
    840867corrector lens), and then back down onto the focal plane.  Due to the
    841868extra travel distance, the resulting source is out of focus and
    842 elongated along the radial direction of the camera focal plane. These
    843 optical ghosts can be modeled in the focal plane coordinates ($L,M$)
    844 which has its origin at the center of the focal plane.  In this
    845 system, a bright object at location ($L,M$) on the focal plane creates a
    846 reflection ghost on the opposite side of the optical axis near
    847 ($-L,-M$).  The exact location is fit as a third order polynomial in the
    848 focal plane $L$ and $M$ directions (as listed in Table
     869elongated along the radial direction of the camera focal
     870plane. Figure~\ref{fig:optical ghosts} shows an example exposure with
     871several prominent optical ghosts.
     872
     873These optical ghosts can be modeled in the focal plane coordinates
     874($L,M$) which has its origin at the center of the focal plane.  In
     875this system, a bright object at location ($L,M$) on the focal plane
     876creates a reflection ghost on the opposite side of the optical axis
     877near ($-L,-M$).  The exact location is fit as a third order polynomial
     878in the focal plane $L$ and $M$ directions (as listed in Table
    849879\ref{tab:ghost_centers}).  An elliptical annulus mask is constructed
    850880at the expected ghost location, with the major and minor axes defined
     
    887917\end{deluxetable}
    888918
    889 \begin{deluxetable}{lc}
    890   \tablecolumns{2}
     919\begin{deluxetable}{lrr}
     920  \tablecolumns{3}
    891921  \tablewidth{0pc}
    892922  \tablecaption{Optical Ghost Magnitude Limits}
    893   \tablehead{\colhead{Filter}&\colhead{$m_{inst}$}}
     923  \tablehead{\colhead{Filter} & \colhead{$m_{inst}$} & \colhead{Approx apparent mag ($3\pi$)}}
    894924  \startdata
    895   \gps{} & -16.5 \\
    896   \rps{} & -20.0 \\
    897   \ips{} & -25.0 \\
    898   \zps{} & -25.0 \\
    899   \yps{} & -25.0 \\
    900   \wps{} & -20.0 \\
     925  \gps{} & -16.5 & 12.2 \\
     926  \rps{} & -20.0 &  8.9 \\
     927  \ips{} & -25.0 &  3.7 \\
     928  \zps{} & -25.0 &  3.4 \\
     929  \yps{} & -25.0 &  2.5 \\
     930  \wps{} & -20.0 & 10.2 \\
    901931  \enddata
    902932  \label{tab:ghost_magnitudes}
     
    905935\begin{figure}
    906936  \centering
    907   \includegraphics[width=0.9\hsize,angle=0,clip]{images/full_fpa_ghosts.jpg}
    908   \caption{Example of the full GPC1 field of view illustrating the sources and destinations of optical ghosts on exposure o5677g0123o (2011-04-26, 43s \gps{} filter).  The bright stars on OTA33 and OTA44 result in nearly circular ghosts on the opposite OTA.  In contrast, the trio of stars on OTA11 result in very elongated ghosts on OTA66.}
     937% \includegraphics[width=0.9\hsize,angle=0,clip]{images/full_fpa_ghosts.jpg}
     938  \includegraphics[width=0.9\hsize,angle=0,clip]{images/full_fpa_ghosts.png}
     939  \caption{{\bf Ghosts:} Example of the full GPC1 field of view illustrating the sources and destinations of optical ghosts on exposure o5677g0123o (2011-04-26, 43s \gps{} filter).  The bright stars on OTA33 and OTA44 result in nearly circular ghosts on the opposite OTA.  In contrast, the trio of stars on OTA11 result in very elongated ghosts on OTA66.}
    909940  \label{fig:optical ghosts}
    910941\end{figure}
     
    917948telescope.  Sources brighter than $m_{inst} = -21$ ($\rps \lesssim
    9189497.5$) that fell on this reflective surface resulted in light being
    919 scattered across the detector surface in a long narrow glint.  This
    920 surface was physically masked on 2010-08-24, removing the possibility
    921 of glints in subsequent data, but images that were taken prior to this
    922 date have an advisory dynamic mask constructed when a reference source
    923 falls on the focal plane within one degree of the detector edge.  This
    924 mask is 150 pixels wide, with length $L = 2500 \left(-20 -
    925 m_{inst}\right)$ pixels.  These glint masks are constructed by
    926 selecting sufficiently bright sources in the reference catalog that
    927 fall within rectangular regions around each edge of the GPC1 camera.
    928 These regions are separated from the edge of the camera by 17
    929 arcminutes, and extend outwards an additional degree.
     950scattered across the detector surface in a long narrow glint. 
     951Figure~\ref{fig:optical glints} shows an example exposure with
     952a prominent optical glint.
     953
     954This reflective surface in the camera was physically masked on
     9552010-08-24, removing the possibility of glints in subsequent data, but
     956images that were taken prior to this date have an advisory dynamic
     957mask constructed when a reference source falls on the focal plane
     958within one degree of the detector edge.  This mask is 150 pixels wide,
     959with length $L = 2500 \left(-20 - m_{inst}\right)$ pixels.  These
     960glint masks are constructed by selecting sufficiently bright sources
     961in the reference catalog that fall within rectangular regions around
     962each edge of the GPC1 camera.  These regions are separated from the
     963edge of the camera by 17 arcminutes, and extend outwards an additional
     964degree.
    930965
    931966\begin{figure}
    932967  \centering
    933   \includegraphics[width=0.9\hsize,angle=0,clip]{images/glint_example_o5379g0103o.jpg}
    934   \caption{Example of a glint on exposure o5379g0103o (2010-07-02, 45s \ips{} filter).  The source star out of the field of view creates a long reflection that extends through OTA73 and OTA63.}
     968% \includegraphics[width=0.9\hsize,angle=0,clip]{images/glint_example_o5379g0103o.jpg}
     969  \includegraphics[width=0.9\hsize,angle=0,clip]{images/full_fpa_glints.png}
     970  \caption{{\bf Glints:}  Example of a glint on exposure o5379g0103o (2010-07-02, 45s \ips{} filter).  The source star out of the field of view creates a long reflection that extends through OTA73 and OTA63.}
    935971  \label{fig:optical glints}
    936972\end{figure}
     
    12191255    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0124o_wbt_XY11.png}
    12201256  \end{minipage}
    1221   \caption{Example of OTA11 cell xy50 on exposures o5677g0123o (left) and o5677g0124o (right).  The top panels show the image with all appropriate detrending steps, but without burntool, and the bottom show the same with burntool applied.  There is some slight over subtraction in fitting the initial trail, but the impact of the trail is greatly reduced in both exposures.}
     1257  \caption{{\bf Persistent Charge:}  Example of OTA11 cell xy50 on exposures o5677g0123o (left) and o5677g0124o (right).  The top panels show the image with all appropriate detrending steps, but without burntool, and the bottom show the same with burntool applied.  There is some slight over subtraction in fitting the initial trail, but the impact of the trail is greatly reduced in both exposures.}
    12221258  \label{fig:burntool images}
    12231259\end{figure}
     
    12261262\begin{figure}
    12271263  \centering
    1228   \begin{minipage}{0.45\hsize}
    1229     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123o_XY11_bt_trail.png}
    1230   \end{minipage}%
    1231   \begin{minipage}{0.45\hsize}
    1232     \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0124o_XY11_bt_trail.png}
    1233   \end{minipage}
    1234 
    1235   \caption{Example of a profile cut along the y-axis through a bright star on exposure o5677g0123o OTA11 in cell xy50 (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}
     1264  \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5677g0123n4o_XY11_bt_trail.pdf}
     1265
     1266  \caption{{\bf Burntool Correction:} Example of a profile cut along
     1267    the y-axis through a bright star on exposure o5677g0123o OTA11 in
     1268    cell xy50 (left panel) and on the subsequent exposure o5677g0124o
     1269    (right panel).  In both figures, the blue pluses show the image
     1270    corrected with all appropriate detrending steps, but without
     1271    burntool applied, illustrating the amplitude of the persistence
     1272    trails.  The red circles show the same data after the burntool
     1273    correction, which reduces the impact of these features.  Both
     1274    exposures are in the \gps{} filter with exposure times of 43s}
     1275
    12361276  \label{fig:burntool plot}
    12371277\end{figure}
     
    12611301effects.
    12621302
     1303% An example of this data is shown in Figure~\ref{fig: nonlinearity}. 
     1304
    12631305We store the average flux measurement and deviation from the linear
    12641306fit for each exposure time for each region on all detector cells in
    1265 the linearity detrend look-up tables.  An example of this data is
    1266 shown in Figure~\ref{fig: nonlinearity}.  When this correction is
     1307the linearity detrend look-up tables.  When this correction is
    12671308applied to science data, these lookup tables are loaded, and a linear
    12681309interpolation is performed to determine the correction needed for the
     
    12841325rejected.
    12851326
    1286 \begin{figure}
    1287   \centering
    1288   \includegraphics[width=0.9\hsize,angle=0,clip]{images/linearity_XY27_xy16.png}
    1289   \caption{Example of the linearity correction as a fraction of observed flux for OTA27, cell xy16.}
    1290   \label{fig: nonlinearity}
    1291 \end{figure}
     1327% this figure does not really clarify anything
     1328% \begin{figure}
     1329%   \centering
     1330%   \includegraphics[width=0.9\hsize,angle=0,clip]{images/linearity_XY27_xy16.png}
     1331%   \caption{Example of the linearity correction as a fraction of observed flux for OTA27, cell xy16.}
     1332%   \label{fig: nonlinearity}
     1333% \end{figure}
    12921334
    12931335\subsection{Pattern correction}
     
    13361378sky noise does not fully obscure the row-by-row noise.
    13371379
     1380%% GPC1 tuning describe in email from Peter Onaka 2009.11.30,
     1381%% with notes in GPC1TuningTestLog.pdf
     1382
    13381383This correction was required on all cells on all OTAs prior to
    1339 2009-12-01, at which point a modification of the camera electronics
    1340 reduced the scale of the row-by-row offsets for the majority of the
    1341 OTAs.  \czw{describe modification} As a result, we only apply this
    1342 correction to the cells where it is still necessary, as shown in
    1343 Figure \ref{fig: pattern row cells}.  A list of these cells is in
    1344 Table \ref{tab:pattern_row_cells}.
     13842009-12-01, at which point a modification of the camera clocking phase
     1385delays reduced the scale of the row-by-row offsets for the majority of
     1386the OTAs.  As a result, we only apply this correction to the cells
     1387where it is still necessary, as shown in Figure \ref{fig: pattern row
     1388  cells}.  A list of these cells is in Table
     1389\ref{tab:pattern_row_cells}.
    13451390
    13461391Although this correction largely resolves the row-by-row offset issue
     
    13911436    \includegraphics[width=0.9\hsize,angle=0,clip]{images/o5379g0103o_wpt_XY57.png}
    13921437  \end{minipage}
    1393   \caption{Example of the PATTERN.ROW correction on exposure o5379g0103o OTA57 cell xy01 (\ips{} filter 45s).  The left panel shows the cell with all appropriate detrending except the PATTERN.ROW, and the right shows the same cell with PATTERN.ROW applied.  The correction reduces the correlated noise on the right side, which is most distant from the read out amplifier.  There is a slight over subtraction along the rows near the bright star.}
     1438  \caption{{\bf Correlated Noise:} Example of the PATTERN.ROW correction on exposure o5379g0103o OTA57 cell xy01 (\ips{} filter 45s).  The left panel shows the cell with all appropriate detrending except the PATTERN.ROW, and the right shows the same cell with PATTERN.ROW applied.  The correction reduces the correlated noise on the right side, which is most distant from the read out amplifier.  There is a slight over subtraction along the rows near the bright star.}
    13941439  \label{fig: pattern row example}
    13951440\end{figure}
     
    16571702the input OTA images, with some reduction in accuracy.
    16581703
     1704Examples of a warped signal, variance, and mask image are illustrated
     1705in Figures~\ref{fig:warp image} through \ref{fig:warp mask}.
     1706
    16591707\begin{figure}
    16601708  \centering
    16611709  \includegraphics[width=0.9\hsize,angle=0,clip]{images/warp_2046019_sci.png}
    1662   \caption{Example of the warp image for skycell skycell.2047.005
    1663     centered at ($\alpha,\delta$) = (179.763, 32.1899) for exposure
    1664     o4985g0073o, (2009-06-03, 30s \zps{} filter).  The data from six
     1710  \caption{Example of the warp image for skycell skycell.1146.095
     1711    centered at ($\alpha,\delta$) = (11.934, -4.197) for exposure
     1712    o5104g0266o, (2009-09-30, 60s \rps{} filter).  The data from four
    16651713    OTAs contribute to this image, although they are all truncated by
    16661714    the skycell boundaries.  This skycell image is aligned such that
    16671715    north points to the top of the image, and east to the left.  The
    1668     contributing OTAs are from the right half of the detector, with
    1669     OTA24 contributing the most pixels, and originally have the
    1670     positive y axis pointing to the southwest in this warped image,
    1671     with the positive x axis to the northwest.}
     1716    contributing OTAs are OTA20, OTA21, OTA30, OTA31.}
    16721717  \label{fig:warp image}
    16731718\end{figure}
     
    16771722  \includegraphics[width=0.9\hsize,angle=0,clip]{images/warp_2046019_var.png}
    16781723  \caption{Example of the warp variance image for skycell
    1679     skycell.2047.005 of exposure o4985g0073o, the same as in Figure
     1724    skycell.1146.095 of exposure o5104g0266o, the same as in Figure
    16801725    \ref{fig:warp image}.  This variance map retains information about
    16811726    the higher flux levels that were found in burntool corrected
    16821727    persistence trails, which appear here as streaks along the
    1683     original OTA y axis.  The amplifier glows that are corrected in
    1684     the dark model are also more visible in the corners of the cells
    1685     in OTA24.  As both of these effects are corrected in the science
     1728    original OTA y axis.  The dark glows that are corrected in the
     1729    dark model are also more visible, especially on certain cell
     1730    edges.  As both of these effects are corrected in the science
    16861731    image, there are no significant features visible there.}
    16871732  \label{fig:warp variance}
     
    16911736  \centering
    16921737  \includegraphics[width=0.9\hsize,angle=0,clip]{images/warp_2046019_mask.png}
    1693   \caption{Example of the warp mask image for skycell skycell.2047.005
    1694     of exposure o4985g0073o, the same as in Figure \ref{fig:warp
     1738  \caption{Example of the warp mask image for skycell skycell.1146.095
     1739    of exposure o5104g0266o, the same as in Figure \ref{fig:warp
    16951740      image}.  This mask image shows the many small defects removed
    16961741    from the image, along with larger advisory trails on corrected
    16971742    burntool trails.  The saturated cores of the bright stars are also
    1698     masked, along with the diffraction spikes found on these stars.
    1699     In addition OTA24 shows the precautionary crosstalk bleed masks
    1700     for the two brightest stars applied to all cells within the same
    1701     row.}
     1743    masked, along with the diffraction spikes found on these stars.  A
     1744    ghost mask is visible just below the center as an elliptical
     1745    region.
     1746%    In addition OTA24 shows the precautionary crosstalk bleed masks
     1747%    for the two brightest stars applied to all cells within the same
     1748%    row.
     1749  \label{fig:warp mask}
     1750  }
    17021751\end{figure}
    17031752
     
    17161765sources.
    17171766
     1767As part of the stacking process, the collection of input pixels for a
     1768given output stack pixel are checked for consistency and outliers are
     1769rejected.  Varying image quality makes a pixel-by-pixel check for
     1770outliers challenging in the vicinity of brighter stars.  Pixels in the
     1771wings of bright stars are liable to be over-rejected as the image
     1772quality changes because the flux observed at a given position varies
     1773as its location on the stellar profile changes.  To avoid this effect,
     1774we convolve all input images to a common PSF before making the
     1775pixel-by-pixel comparison.  This PSF-matching technique allows us to
     1776detect inconsistent pixels even in the sensitive wings of bright objects.
     1777
    17181778For the $3\pi$ survey, the stacked image is comprised of all warp
    17191779frames for a given skycell in a single filter.  The source catalogs
    17201780and image components are loaded into the \IPPprog{ppStack} program to
    17211781prepare the inputs and stack the frames.
    1722 
    1723 \note{need to point out that we are convolving to a matched PSF}
    17241782
    17251783Once all files are ingested, the first step is to measure the size and
     
    17701828convolution kernels can be calculated for each image.  To calculate
    17711829the convolution kernels, we use the algorithm described by
    1772 \cite{1998ApJ...503..325A} and \cite{2000.alard} to perform optimal
    1773 image subtraction.  These `ISIS' kernels \citep[named after the
    1774   software package described by][]{1998ApJ...503..325A} are used with
    1775 FWHM values of 1.5, 3.0, and 6.0 pixels and polynomial orders of 6, 4,
    1776 and 2.  Regions around the sources identified in the input images are
    1777 extracted, convolved with the kernel, and the residual with the target
    1778 PSF used to update the parameters of the kernel via least squares
    1779 optimization.  Stamps that significantly deviate are rejected,
    1780 although the squared residual difference will increase with increasing
    1781 source flux.  To mitigate this effect, a parabola is fit to the
    1782 distribution of squared residuals as a function of source flux.
    1783 Stamps that deviate from this fit by more than $2.5\sigma$ are
    1784 rejected, and not used on further kernel fit iterations.  This process
    1785 is repeated twice, and the final convolution kernel is returned.
     1830\cite{1998ApJ...503..325A} and extended by \cite{2000A&AS..144..363A}
     1831to perform optimal image subtraction.  These `ISIS' kernels
     1832\citep[named after the software package described
     1833  by][]{1998ApJ...503..325A} are used with FWHM values of 1.5, 3.0,
     1834and 6.0 pixels and polynomial orders of 6, 4, and 2.  Regions around
     1835the sources identified in the input images are extracted, convolved
     1836with the kernel, and the residual with the target PSF used to update
     1837the parameters of the kernel via least squares optimization.  Stamps
     1838that significantly deviate are rejected, although the squared residual
     1839difference will increase with increasing source flux.  To mitigate
     1840this effect, a parabola is fit to the distribution of squared
     1841residuals as a function of source flux.  Stamps that deviate from this
     1842fit by more than $2.5\sigma$ are rejected, and not used on further
     1843kernel fit iterations.  This process is repeated twice, and the final
     1844convolution kernel is returned.
    17861845
    17871846This convolution may change the image flux scaling, so the kernel is
     
    18121871identify discrepant input values that should be excluded.
    18131872
    1814 \note{clarify 'should' below, e.g., with a histogram}
    1815 
    18161873If only a single input is available, the initial stack contains the
    18171874value from that single input.  If there are only two inputs, the
    1818 average of the two is used.  These cases should occur only rarely in
     1875average of the two is used.  These cases are expected to occur only rarely in
    18191876the $3\pi$ survey, as there are many input exposures that overlap each
    18201877point on the sky.  For the more common case of three or more inputs, a
     
    18791936distribution is likely to be unimodal), or if there are insufficient
    18801937inputs for this mixture model analysis, the input values are passed to
    1881 an Olympic \note{define} weighted mean calculation.  We reject $20\%$ of the number
    1882 of inputs through this process.  The number of bad inputs is set to
    1883 $N_\mathrm{bad} = 0.2 \times N_\mathrm{input} + 0.5$, with the 0.5 term
    1884 ensuring at least one input is rejected.  This number is further
    1885 separated into the number of low values to exclude, $N_\mathrm{low} =
    1886 N_\mathrm{bad} / 2$, which will default to zero if there are few
    1887 inputs, and $N_\mathrm{high} = N_\mathrm{low} - N_\mathrm{bad}$.
    1888 After sorting the input values to determine which values fall into the
    1889 low and high groups, the remaining input values are used in a weighted
    1890 mean using the image weights above.
     1938an ``Olympic'' weighted mean calculation (both the lowest and highest
     1939values are ignored in calculating the weighted mean).  We reject
     1940$20\%$ of the number of inputs through this process.  The number of
     1941bad inputs is set to $N_\mathrm{bad} = 0.2 \times N_\mathrm{input} +
     19420.5$, with the 0.5 term ensuring at least one input is rejected.  This
     1943number is further separated into the number of low values to exclude,
     1944$N_\mathrm{low} = N_\mathrm{bad} / 2$, which will default to zero if
     1945there are few inputs, and $N_\mathrm{high} = N_\mathrm{low} -
     1946N_\mathrm{bad}$.  After sorting the input values to determine which
     1947values fall into the low and high groups, the remaining input values
     1948are used in a weighted mean using the image weights above.
    18911949
    18921950A systematic variance term is necessary to correctly scale how
     
    19241982pixels.  The ISIS kernel used in the previous step is again used to
    19251983determine the largest square box that does not exceed the limit of
    1926 $0.25 \times \sum_{x,y} kernel^2$.  This square box is then convolved with
    1927 the rejected pixel mask to reject the neighboring pixels.  This final
    1928 list of rejected pixels is passed to the final combination, which
    1929 creates the final stack values from the weighted mean of the
     1984$0.25 \times \sum_{x,y} kernel^2$.  This square box is then convolved
     1985with the rejected pixel mask to reject the neighboring pixels.  This
     1986final list of rejected pixels is passed to the final combination,
     1987which creates the final stack values from the weighted mean of the
    19301988non-rejected pixels.  Six total images are constructed for this final
    19311989stack: the image, its variance, a mask, a map of the exposure time per
    19321990pixel, that exposure time map weighted by the input image weight, and
    1933 a map of the number of inputs per pixel.
    1934 
    1935 These convolved stack products are not retained, as the convolution is
     1991a map of the number of inputs per pixel.  Examples of each output
     1992image type for the stacking process are shown in
     1993Figures~\ref{fig:stack image} through \ref{fig:stack exp wtimage}.
     1994
     1995The convolved stack products are not retained, as the convolution is
    19361996used to ensure that the pixel rejection uses seeing-matched images.
    19371997This prevents any differences in the input PSF shape from skewing the
     
    19802040  \centering
    19812041  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_sci.png}
    1982   \caption{Example of the stack image for skycell skycell.2047.005
    1983     centered at ($\alpha,\delta$) = (179.763, 32.1899) in the \zps{}
    1984     filter, stack\_id 3775944.  This stack includes 25 input images,
    1985     including o4985g0073o the warp image in Figure \ref{fig:warp
    1986       image}, and has a combined exposure time of 870s.  Combining
     2042  \caption{Example of the stack image for skycell skycell.1146.095
     2043    centered at ($\alpha,\delta$) = (11.934, -4.197) in the \rps{}
     2044    filter, stack\_id 3956997.  This stack includes 39 input images
     2045    including o5104g0266o, the warp image in Figure \ref{fig:warp
     2046      image}, and has a combined exposure time of 1880s.  Combining
    19872047    such a large number of input images removes the inter-cell and
    19882048    inter-chip gaps, providing a fully populated image.  In addition,
     
    19972057  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_mask.png}
    19982058  \caption{Example of the stack mask image for skycell
    1999     skycell.2047.005 centered at ($\alpha,\delta$) = (179.763,
    2000     32.1899) in the \zps{} filter, stack\_id 3775944.  The entire
    2001     frame is largely unmasked after combining inputs, with the only
    2002     remaining masks falling on the cores of bright stars, and in small
    2003     regions around the brightest objects where the overlapping of
    2004     diffraction spike masks have removed all inputs.}
    2005 
     2059    skycell.1146.095 centered at ($\alpha,\delta$) = (11.934, -4.197)
     2060    in the \rps{} filter, stack\_id 3956997.  The entire frame is
     2061    largely unmasked after combining inputs, with the only remaining
     2062    masks falling on the cores of bright stars, and in small regions
     2063    around the brightest objects where the overlapping of diffraction
     2064    spike masks have removed all inputs.}
    20062065  \label{fig:stack mask image}
    20072066\end{figure}
     
    20102069  \centering
    20112070  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_var.png}
    2012   \caption{Example of the stack variance image for skycell
    2013     skycell.2047.005 centered at ($\alpha,\delta$) = (179.763,
    2014     32.1899) in the \zps{} filter, stack\_id 3775944.  The variance
     2071  \caption{Example of the stack variance image for skycell 
     2072    skycell.1146.095 centered at ($\alpha,\delta$) = (11.934, -4.197)
     2073    in the \rps{} filter, stack\_id 3956997.  The variance
    20152074    map for this stack is reasonably smooth, with the mottled pattern
    20162075    from the inter-chip and inter-cell gaps printing through.  Some
     
    20252084  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_num.png}
    20262085  \caption{Example of the stack number image for skycell
    2027     skycell.2047.005 centered at ($\alpha,\delta$) = (179.763,
    2028     32.1899) in the \zps{} filter, stack\_id 3775944.  This map shows
     2086    skycell.1146.095 centered at ($\alpha,\delta$) = (11.934, -4.197)
     2087    in the \rps{} filter, stack\_id 3956997.  This map shows
    20292088    the number of inputs contributing to each pixel of the output
    20302089    stack.  Again, the pattern of the inter-chip and inter-cell gaps
    2031     is visible, along with the mask pattern of regions with CTE
    2032     problems (visible in the upper right corner). }
     2090    is visible, along with other mask features. }
    20332091
    20342092  \label{fig:stack num image}
     
    20392097  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_exp.png}
    20402098  \caption{Example of the stack exposure time image for skycell
    2041     skycell.2047.005 centered at ($\alpha,\delta$) = (179.763,
    2042     32.1899) in the \zps{} filter, stack\_id 3775944.  As all input
    2043     warps had the same 30s exposure time, this map essentially
    2044     recreates the number map, with units of seconds of exposure
    2045     instead of number of inputs contributing to a given pixel.}
    2046 
     2099    skycell.1146.095 centered at ($\alpha,\delta$) = (11.934, -4.197)
     2100    in the \rps{} filter, stack\_id 3956997.  Since the input
     2101    exposures had exposures times of 40 and 60 seconds, the pattern
     2102    observed here similar to, but subtly different from the number
     2103    map.}
    20472104  \label{fig:stack exp image}
    20482105\end{figure}
     
    20522109  \includegraphics[width=0.9\hsize,angle=0,clip]{images/stack_3956997_expwt.png}
    20532110  \caption{Example of the stack weighted exposure image for skycell
    2054     skycell.2047.005 centered at ($\alpha,\delta$) = (179.763,
    2055     32.1899) in the \zps{} filter, stack\_id 3775944.  This map shows
     2111    skycell.1146.095 centered at ($\alpha,\delta$) = (11.934, -4.197)
     2112    in the \rps{} filter, stack\_id 3956997.  This map shows
    20562113    the weighted average exposure time, as described in the text.  It
    20572114    is similar to the simple exposure time map, but shows how some
    20582115    input exposures have their contributions weighted down due to the
    20592116    observed larger image variances.}
    2060 
    2061 
    20622117  \label{fig:stack exp wtimage}
    20632118\end{figure}
     
    22262281University (ELTE), and the Los Alamos National Laboratory.
    22272282
    2228 \note{ApJ, etc latex macros have an extra comma}
    2229 
    22302283\bibliography{lib}{}
    22312284\bibliographystyle{apj}
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