Updates from Overleaf

SITCOMTN-148.tex

@@ -1,6 +1,6 @@
 \documentclass[SE,lsstdraft,authoryear,toc]{lsstdoc}
 \input{meta}
-
+\usepackage{array}
 \usepackage{subcaption}
 \usepackage{longtable,booktabs,array}
 \usepackage{makecell}  %for multi-line cells in tables

acronyms.tex

@@ -5,13 +5,16 @@
 2D & Two-dimensional \\\hline
 3D & Three-dimensional \\\hline
 AC & Access Control \\\hline
+ADC & atmospheric dispersion corrector \\\hline
 ADU & Analogue-to-Digital Unit \\\hline
 B & Byte (8 bit) \\\hline
+BOT & Bench for Optical Testing \\\hline
 CCD & Charge-Coupled Device \\\hline
 CCOB & Camera Calibration Optical Bench \\\hline
 CCS & Camera Control System \\\hline
 CMB & Cosmic Microwave Background \\\hline
 CMOS & complementary metal-oxide semiconductor \\\hline
+CTI & Charge Transfer Inefficiency \\\hline
 DC & Data Center \\\hline
 EO & Electro Optical \\\hline
 FES & Filter Exchange System \\\hline
@@ -22,17 +25,23 @@
 LCA & Document handle LSST camera subsystem controlled documents \\\hline
 LED & Light-Emitting Diode \\\hline
 LSST & Legacy Survey of Space and Time (formerly Large Synoptic Survey Telescope) \\\hline
-LaTeX & (Leslie) Lamport TeX (document markup language and document preparation system) \\\hline
+MC & Monte-Carlo (simulation/process) \\\hline
 OCS & Observatory Control System \\\hline
-ORR & Operations Readiness Review \\\hline
 OpSim & Operations Simulation \\\hline
-PM & Project Manager \\\hline
+PCS & Pumped Coolant System \\\hline
+PCTI & Parallel Charge Transfer Inefficiency \\\hline
+PD & Program Development \\\hline
 PSF & Point Spread Function \\\hline
+PTC & Photon Transfer Curve \\\hline
+QE & quantum efficiency \\\hline
 REB & Readout Electronics Board \\\hline
+RTM & Raft Tower Module \\\hline
 S3 & (Amazon) Simple Storage Service \\\hline
+SCTI & Serial Charge Transfer Inefficiency \\\hline
 SE & System Engineering \\\hline
 SLAC & SLAC National Accelerator Laboratory \\\hline
 TMA & Telescope Mount Assembly \\\hline
 UCD & Unified Content Descriptor (IVOA standard) \\\hline
+UT & Universal Time \\\hline
 UTC & Coordinated Universal Time \\\hline
 \end{longtable}

meta.tex

@@ -1,5 +1,5 @@
 % GENERATED FILE -- edit this in the Makefile
 \newcommand{\lsstDocType}{SITCOMTN}
 \newcommand{\lsstDocNum}{148}
-\newcommand{\vcsRevision}{164cc1e-dirty}
-\newcommand{\vcsDate}{2024-12-18}
+\newcommand{\vcsRevision}{80cc9c9-dirty}
+\newcommand{\vcsDate}{2025-01-16}

phosphorescence_coffeestain_comparison_appendix.tex

@@ -1,4 +1,5 @@
 \section{Phosphorescence morphological comparisons with features seen in {\it blue} flat field response}
+\label{appendix:phos:coffeestains}
 
 Figures~\ref{fig:phos:stains:R01S00} through \ref{fig:phos:stains:R43S20} are an incomplete selection of ITL sensors with phosphorescence. They compare expressed phosphorescence (transient term) with the {\it blue} CCOB LED flat response. Inspection of these images would lead one to conclude that in certain cases, the phosphorescence patterns resemble the coffee stain patterns' regions of lower QE at short wavelength ({\it cf.} Fig.~\ref{fig:phos:stains}, Fig.~\ref{fig:phos:stains:R43S11}). In other cases, the opposite appears to be true ({\it cf.} Fig.~\ref{fig:phos:stains:R02S02}, Fig.~\ref{fig:phos:stains:R02S12}). In several cases, there appear to be no particular correlations. 
 

phosphorescence_identification_appendix.tex

@@ -1,5 +1,5 @@
 \section{Phosphorescence identification on ITL set of sensors}
-
+\label{appendix:phos:ident}
 \begin{figure}[!htbp]
 \centering
 \includegraphics[width=0.9\textwidth]{figures/phosphorescence-survey/itl_fluor_R00_0-19_rb1_log.png}

phosphorescence_kinetics.tex

@@ -1,5 +1,6 @@
 \section{Phosphorescence kinetics characterization}
-\label{sect:kinetics}
+\label{appendix:phos:kinetics}
+
 Figures~\ref{fig:phos:kinetics:R01S00} through \ref{fig:phos:kinetics:R43S20} quantify the expressed phosphorescence distributions in ROIs on seven of the problematic ITL sensors. Previously, we had captured the phosphorescence {\it transient term} across the ITL sensors ({\it cf.} Figs.~\ref{fig:phos:R00} thru \ref{fig:phos:R44}); here we track ROI pixel distribution parameters of individual median images constructed from the selection of specific images acquired across the 20 B-protocol datasets available (listed in Table~\ref{tab:phosphorescence:datasets}). 
 
 By fitting decay models to these persistence curves, it is immediately clear that there are multiple (>2) timescales at play for the pixels in each ROI. An example of such a fit is given in Figure~\ref{fig:phos:kinetics:fit:R20S20C13} where a 3-population relaxation model is used to characterize evolution of the 99\% quantile level of the distribution. In this case, there are three different exponential timescales determined: $(\tau_1,\tau_2,\tau_3) = (0.62,2.5,18.3)$ in image units (10.9, 43.8 \& 320 seconds, respectively). The corresponding ratio of these populations works out to 4.5\% (fast), 21.5\% (medium) and 74\% (slow), respectively. Inspection of the more detailed parameters plotted generally indicate skewed distributions from mismatches between medians and means; the choice of the 99\% quantile level to characterize was mainly to estimate the degree to which images would need to be phosphorescence-corrected (and/or the variance plane modified, given the asymmetric impact of the position specific, phosphorescence contribution in recorded images). 

phosphorescence_response.tex

@@ -1,20 +1,21 @@
 \section{Phosphorescence response characterization}
-\label{sect:response}
-Figures~\ref{fig:phos:resp:R01S00} through \ref{fig:phos:resp:R43S20} attempt to quantify the expressed phosphorescence response in ROIs on seven of the problematic ITL sensors. Previously, we had captured the phosphorescence {\it transient term} across the ITL sensors ({\it cf.} Figs.~\ref{fig:phos:R00} thru \ref{fig:phos:R44}); we also tracked ROI pixel distribution parameters of individual median images constructed from the selection of specific images acquired across the 20 B-protocol datasets available (listed in Table~\ref{tab:phosphorescence:datasets}). Here we analyze the signal level- and wavelength-dependences of the expressed phosphorescence captured in the first dark image following flat exposure. Table~XX provides the image numbers.. 
+\label{appendix:phos:response}
 
-Because these runs were performed to sample a two dimensional parameter space,  that would lead to 
+Figures~\ref{fig:phos:resp:R01S00} through \ref{fig:phos:resp:R43S20} attempt to quantify the expressed phosphorescence response in ROIs on seven of the problematic ITL sensors. Previously, we had captured the phosphorescence {\it transient term} across the ITL sensors ({\it cf.} Figs.~\ref{fig:phos:R00} thru \ref{fig:phos:R44}); we also tracked ROI pixel distribution parameters of individual median images constructed from the selection of specific images acquired across the 20 B-protocol datasets available (listed in Table~\ref{tab:phosphorescence:datasets}). Here we analyze the signal level- and wavelength-dependences of the expressed phosphorescence captured in the first dark image following flat exposure. Table~\ref{tab:phos:sens:datasets} provides the dataset IDs and SeqIDs used for this analysis. 
 
-By fitting decay models to these persistence curves, it is immediately clear that there are multiple (>2) timescales at play for the pixels in each ROI. An example of such a fit is given in Figure~\ref{fig:phos:kinetics:fit:R20S20C13} where a 3-population relaxation model is used to characterize evolution of the 99\% quantile level of the distribution. In this case, there are three different exponential timescales determined: $(\tau_1,\tau_2,\tau_3) = (0.62,2.5,18.3)$ in image units (10.9, 43.8 \& 320 seconds, respectively). The corresponding ratio of these populations works out to 4.5\% (fast), 21.5\% (medium) and 74\% (slow), respectively. Inspection of the more detailed parameters plotted generally indicate skewed distributions from mismatches between medians and means; the choice of the 99\% quantile level to characterize was mainly to estimate the degree to which images would need to be phosphorescence-corrected (and/or the variance plane modified, given the asymmetric impact of the position specific, phosphorescence contribution in recorded images). 
+\input{phosphorescence_response_datasets_table}
 
-%\begin{figure}[!htbp]
-%\centering
-%\begin{subfigure}{0.8\textwidth}    
-%  \centering
-%  \includegraphics[width=\textwidth]{figures/phosphorescence-%survey/phos_kinetics/R20_S20_sel_1820-1920_535-635_phos_decay_fit.png}    
-%\end{subfigure}
-%\caption{A three-population fit of the phosphorescence expressed by the %vapire pixel region of R20\_S20\_C13. The fit was performed on the 99\% %quantile level where signal levels are well above the $3\sigma$ level of %the noise distribution. Here, image numbers are parasitically used as %time units, with roughly 17.5 seconds per image.}
-%\label{fig:phos:resp:fit:R20S20C13}
-%\end{figure}
+These runs were performed to sample a two-dimensional, rectangular parameter space, and each measurement was executed only once. The resulting sampling was completed incrementally, over 3 separate days. Using only one image for each data point, we were not able to median multiple images acquired under identical conditions (as we had done for Sections~\ref{appendix:phos:ident}, \ref{appendix:phos:coffeestains} and \ref{appendix:phos:kinetics}). 
+
+Because there is significant variation in morphological characteristics of the phosphorescence, we adopted the following strategy to quantify phosphorescence expression in each: Once the image is processed through ISR, each of the sensor specific ROIs are used to filter the pixels, and the signal distribution parameters are evaluated. The 99\% quantile signal level was used as a bright end proxy for the expressed phosphorescence for each ROI. A consequence of this is that when there is insignificant or undetectable phosphorescence, this proxy choice would be artificially high, which would be pegged at about 4$\sigma$ above the noise distribution mean. 
+
+The figures provide dashed lines that represent constant {\it phosphorescence efficiency ratios} to guide the eye (at 10\%, 1\% and 0.1\%), while different color LED illumination are represented by different plotting symbols and line colors. The only CCOB LED used across the entire range of trigger flat signal levels is the {\it blue} one. The 400k$e^-$ {\it blue} LED trigger flat induced phosphorescence levels are the only ones described thus far in Sections~\ref{appendix:phos:ident}, \ref{appendix:phos:coffeestains} and \ref{appendix:phos:kinetics}.  
+
+Two of the sensors exhibiting distributed and structured phosphorescence expression (R02\_S02 \& R43\_S20) appear to have phosphorescence yields below $3\times 10^{-3}$ for {\it uv} and {\it blue} LED illumination. Given the kinetics studied for these ROIs for {\it blue} LED illumination ({\it cf.} Figs~\ref{fig:phos:kinetics:R02S02} and \ref{fig:phos:kinetics:R43S20}), the worst case contribution may be 55~$e^-$/pix/15s ({\it uv} LED, $30{\mathrm k}e^{-} \times e^{+0.62} \times 10^{-3}$). The $e^{+0.62}$ scaling factor comes from the fact that the LED flash occurs (and ends) at the beginning of the trigger flat illumination and typically lasts for just a fraction of the image time of $\sim17.5$ seconds.
+
+One other sensor with distributed, coffee stain-like phosphorescence (R02\_S12) shows significantly more signal in one of the ROIs ({\it uv} and {\it blue} LEDs for 30k$e^-$ and 400k$e^-$, respectively). Upon applying the $e^{+0.62}$ factor, the worst case phosphorescence here would scale to 560$e^-$/pix/15s and 1800$e^-$/pix/15s, respectively.
+
+The remaining four sensors (R01\_S00, R03\_S10, R20\_S20 \& R43\_S11) show even more phosphorescence. The first three of these are due to {\it vampire pixels} (with or without central hot spots), while the last one showed the diffuse glow along the edges which ``shuts off'' with HV Bias. The phosphorescent yield high-end proxy limits for these ROIs fall within the $10^{-2}$ to $10^{-1}$ range. There are even a few data points that approach or exceed $10^{-1}$ (R03\_S10 \& R20\_S20) and such phosphorescence levels might be hard to believe, especially if the LED flash timing correction factor of $e^{+0.62}$ is also applied. One thing to keep in mind is that {\it vampire pixels} are known to bend drift field lines to produce regions with (apparently) $>100\%$ QE. For example, the {\it vampire pixel} on R03\_S10\_C15 contains a group of pixels that can receive up to 15$\times$ the target level in a flat exposure, so such large yields as we've seen here are perhaps not so mysterious after all.
 
 \begin{figure}[!htbp]
 \centering

phosphorescence_response_datasets_table.tex

@@ -0,0 +1,77 @@
+\begin{center}
+\begin{longtable}{lll}
+\caption{Zephyr Scale E-numbers and corresponding SeqIDs analyzed to estimate signal level and wavelength dependence of the phosphorescence response.} \label{tab:phos:sens:datasets} \\
+%\hline 
+\toprule\noalign{}
+%\multicolumn{1}{c}{\textbf{Run Type}} & 
+\multicolumn{3}{c}{\textbf{Run numbers and SeqIDs of first dark following trigger}} \\
+%\multicolumn{3}{c}{\textbf{(arranged by CCOB LED and trigger flat target signal)}} \\
+%\multicolumn{1}{c}{\textbf{Third column}} \\ 
+%\hline 
+\midrule\noalign{}
+\endfirsthead
+
+\multicolumn{3}{c}%
+{{\tablename\ \thetable{} -- continued from previous page}} \\
+%\hline 
+\toprule\noalign{}
+%\multicolumn{1}{c}{\textbf{Run Type}} & 
+\multicolumn{3}{c}{\textbf{Run numbers and SeqIDs of first dark following trigger}} \\
+%\multicolumn{3}{c}{\textbf{(arranged by CCOB LED and trigger flat target signal)}} \\
+%\hline 
+\midrule\noalign{}
+\endhead
+
+%\hline 
+\midrule\noalign{}
+\multicolumn{3}{r}{{Continued on next page}} \\ 
+%\hline
+\bottomrule\noalign{}
+\endfoot
+
+\hline \hline
+\endlastfoot
+\midrule\noalign{}
+CCOB LED & trigger flat target signal & runID \& SeqID \\
+\midrule\noalign{}
+uv &   500 & E1770:20241028\_000010 \\
+uv &  1000 & E1503:20241020\_000489 \\
+uv &  1500 & E1771:20241028\_000039 \\
+uv &  3000 & E1504:20241020\_000533 \\
+uv &  4500 & E1772:20241028\_000068 \\
+uv &  5000 & E1505:20241020\_000577 \\
+uv & 10000 & E1506:20241020\_000621 \\
+uv & 13500 & E1773:20241028\_000097 \\
+uv & 30000 & E1507:20241020\_000665 \\
+\midrule\noalign{}
+blue &   500 & E1774:20241028\_000126 \\
+blue &  1000 & E1502:20241020\_000445 \\
+blue &  1500 & E1775:20241028\_000155 \\
+blue &  3000 & E1501:20241020\_000401 \\
+blue &  4500 & E1776:20241028\_000184 \\
+blue &  5000 & E1500:20241020\_000357 \\
+blue & 10000 & E1499:20241020\_000313 \\
+blue & 13500 & E1777:20241028\_000213 \\
+blue & 30000 & E1498:20241020\_000269 \\
+blue & 50000 & E1491:20241018\_000989 \\
+blue &150000 & E1485:20241018\_000725 \\
+blue &400000 & E1484:20241018\_000678 \\
+\midrule\noalign{}
+red & 50000 & E1490:20241018\_000945 \\
+red &150000 & E1486:20241018\_000769 \\
+red &400000 & E1483:20241018\_000634 \\
+\midrule\noalign{}
+nm750 & 50000 & E1492:20241018\_001033 \\
+nm750 &150000 & E1487:20241018\_000813 \\
+nm750 &400000 & E1479:20241018\_000543 \\
+\midrule\noalign{}
+nm850 & 50000 & E1493:20241018\_001077 \\
+nm850 &150000 & E1488:20241018\_000857 \\
+nm850 &400000 & E1477:20241018\_000455 \\
+\midrule\noalign{}
+nm960 & 50000 & E1494:20241018\_001121 \\
+nm960 &150000 & E1489:20241018\_000901 \\
+nm960 &400000 & E1478:20241018\_000499 \\
+\bottomrule\noalign{}
+\end{longtable}
+\end{center}