Index: /trunk/doc/modules/CameraImages.tex =================================================================== --- /trunk/doc/modules/CameraImages.tex (revision 4756) +++ /trunk/doc/modules/CameraImages.tex (revision 4757) @@ -108,9 +108,10 @@ A readout is the result of a single read of a cell (or a portion -thereof). It contains the offset from the lower-left corner of -the chip, in the case that the CCD was windowed, as well as the -binning factors and parity (if the binning value is negative, then -the parity is reversed). It also contains the pixel data, metadata -containers for the concepts and analysis, and a link to the parent. +thereof). It contains the offset from the lower-left corner of the +chip, in the case that the CCD was windowed, as well as the binning +factors and parity (if the binning value is negative, then the parity +is reversed). It also contains the pixel data (with corresponding +mask), metadata containers for the concepts and analysis, and a link +to the parent. \begin{verbatim} @@ -123,4 +124,5 @@ // Information psImage *image; // Imaging area of readout + psImage *mask; // Mask for image psList *bias; // List of bias section (sub-)images psMetadata *analysis; // Readout-level analysis metadata @@ -398,11 +400,4 @@ have \code{valid} set to \code{true}. -\begin{datatype} -typedef enum { - PM_FPA_MORPH_LEFTRIGHT, - PM_FPA_MORPH_IMAGEBIAS -} pmFPAMorphOption; -\end{datatype} - \begin{prototype} bool pmFPAMorph(pmFPA *toFPA, pmFPA *fromFPA, bool positionDependent, int chipNum, int cellNum); @@ -439,4 +434,12 @@ information with which to write the FITS images. +\begin{prototype} +pmFPAWriteMask(psFits *fits, pmFPA *fpa); +\end{prototype} + +\code{pmFPAWriteMask} is very similar to \code{pmFPAWrite}, but it +shall write the \code{mask} elements of the \code{pmReadout}s +comprinsing the \code{fpa}. + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Index: /trunk/doc/modules/ChangeLogSDRS.tex =================================================================== --- /trunk/doc/modules/ChangeLogSDRS.tex (revision 4756) +++ /trunk/doc/modules/ChangeLogSDRS.tex (revision 4757) @@ -1,3 +1,3 @@ -%%% $Id: ChangeLogSDRS.tex,v 1.28 2005-08-05 03:43:30 price Exp $ +%%% $Id: ChangeLogSDRS.tex,v 1.29 2005-08-11 03:05:26 price Exp $ \subsection{Changes from version 00 (16 August 2004) to version 01 (12 October 2004)} @@ -95,3 +95,10 @@ \item \code{pmConfigRead} shall call \code{psTimeInitialize}, \code{psLogSetLevel}, \code{psLogSetFormat}, \code{psTraceSetLevel}. +\item Added \code{pmConfigDB}. +\item Changed \code{pmNonLinearityLookup} to read a \code{psLookupTable}. +\item Changed input types for \code{pmMaskBadPixels}. +\item Added \code{pmFPAWriteMask}. +\item \code{pmMaskBadPixels} shall grow the mask for saturated by 1, in addition + to the explicit grow. +\item Added section on ``Paper Trail'' to Phase 2 functions. \end{itemize} Index: /trunk/doc/modules/ModulesSDRS.tex =================================================================== --- /trunk/doc/modules/ModulesSDRS.tex (revision 4756) +++ /trunk/doc/modules/ModulesSDRS.tex (revision 4757) @@ -1,3 +1,3 @@ -%%% $Id: ModulesSDRS.tex,v 1.52 2005-08-05 03:43:30 price Exp $ +%%% $Id: ModulesSDRS.tex,v 1.53 2005-08-11 03:05:26 price Exp $ \documentclass[panstarrs]{panstarrs} @@ -655,5 +655,4 @@ recipes contained in the \code{camera} configuration (details below). -We also specify an additional function: \begin{prototype} bool pmConfigValidateCamera(psMetadata *camera, psMetadata *header); @@ -664,4 +663,12 @@ the \code{camera} configuration (see \S\ref{sec:camerarule}); otherwise it shall return \code{false}. + +\begin{prototype} +psDB *pmConfigDB(psMetadata *site); +\end{prototype} + +\code{pmConfigDB} shall use the \code{site} configuration data to open +a database handle. \tbd{This is fairly straightforward at the moment, +but will change when we beef up security.} \subsubsection{Example usage} @@ -870,12 +877,14 @@ pmReadout *pmSubtractBias(pmReadout *in, void *fitSpec, const psList *overscans, pmOverscanAxis overscanAxis, const psStats *stat, - int nBin, pmFit fit, const pmReadout *bias); -\end{prototype} - -Two types of bias correction may optionally be performed on the input -image, \code{in}. The first is the subtraction of an overscan. + int nBin, pmFit fit, const pmReadout *bias, + const pmReadout *dark); +\end{prototype} + +Three types of bias correction may optionally be performed on the +input image, \code{in}. The first is the subtraction of an overscan. Multiple overscan regions may be specified and fit as a function of row (or column). The second is the subtraction of a full-frame bias -image (or a ``dark'' image). +image. The third is the subtraction of a suitably scaled full-frame +dark image. The input image, \code{in}, shall have the bias subtracted in-place. @@ -973,15 +982,17 @@ appropriate statistic applied to all the prescan/overscan pixels. -A bias (or dark) image shall be subtracted pixel-by-pixel from the -input image if \code{bias} is non-NULL. Note that the input image, -\code{in}, and the \code{bias} image need not be the same size, but -the function shall use the offsets in the image (\code{in->x0} and -\code{in->y0}) to determine the appropriate offsets to obtain the -correct pixel on the \code{bias}. In the event that the \code{bias} -image is too small (i.e., pixels on the input image refer to pixels -outside the range of the \code{bias} image), the function shall -generate an error. Any pixels masked in the \code{bias} shall also be -masked in the output. The bias image must be of the same type as the -input image. +A bias image shall be subtracted pixel-by-pixel from the input image +if \code{bias} is non-NULL. A dark image, multiplied by the +\code{darkTime}, shall be subtracted pixel-by-pixel from the input +image if \code{dark} is non-NULL. Note that the input image, +\code{in}, and the \code{bias} and \code{dark} frames need not be the +same size, but the function shall use the offsets in the image +(\code{in->x0} and \code{in->y0}) to determine the appropriate offsets +to obtain the correct pixel on the \code{bias}. In the event that the +\code{bias} image is too small (i.e., pixels on the input image refer +to pixels outside the range of the \code{bias} image), the function +shall generate an error. Any pixels masked in the \code{bias} or +\code{dark} shall also be masked in the output. The bias and dark +images may be copied to the same type as the input image if required. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -1009,29 +1020,13 @@ \begin{prototype} -pmReadout *pmNonLinearityLookup(pmReadout *in, const psVector *inFlux, const psVector *outFlux); -\end{prototype} - -For each pixel in the input image, the function shall find the flux -value in the \code{inFlux} vector, and replace the flux with the -corresponding value in the \code{outFlux} vector. If the sizes of the -\code{inFlux} and \code{outFlux} vectors differ, then the function -shall generate a warning, and the longer vector shall be truncated to -the length of the shorter. The \code{inFlux} vector may be assumed -to be pre-sorted and not contain duplicate values. - -If the particular value of a pixel is not found in the \code{inFlux} -vector, the corresponding \code{outFlux} shall be calculated through -linear interpolation. If the value of a pixel is beyond the range of -values specified in the \code{inFlux} vector, then the function shall -generate a warning (at most one warning of this type per call, -preferably mentioning the number of pixels out of bounds), and replace -that pixel value with the \code{outFlux} value corresponding to the -minimum or the maximum, depending on whether the pixel value is below -or above the range of \code{inFlux} values. - -In the event that the \code{inFlux} vector does not contain two or -more entries (being the lower limit required for linear -interpolation), then the function shall generate a warning, and make -no correction to any of the pixels. +pmReadout *pmNonLinearityLookup(pmReadout *in, const char *filename); +\end{prototype} + +For each pixel in the input image, the function shall replace the flux +with the corresponding value from the supplied lookup table, specified +by the \code{filename}. The lookup table file shall consist of two +columns of data, the first being the original flux value and the +second being the replaced flux value. The file shall be in a format +suitable for reading by \code{psLookupTableRead}. Both \code{pmNonLinearityPolynomial} and \code{pmNonLinearityLookup} @@ -1110,5 +1105,5 @@ shall be the following: \begin{prototype} -pmReadout *pmMaskBadPixels(pmReadout *in, const psImage *mask, unsigned int maskVal, +pmReadout *pmMaskBadPixels(pmReadout *in, const pmReadout *mask, unsigned int maskVal, float sat, unsigned int growVal, int grow); \end{prototype} @@ -1120,5 +1115,8 @@ pixels, along with all pixels within the \code{grow} radius masked. Pixels which have flux greater than \code{sat} shall also be masked, -but not grown. +and grown by a single pixel (in addition to the \code{grow} done on +the \code{growVal}). + +\tbd{In the future, may change grow to a convolution kernel}. Note that the input image, \code{in}, and the \code{mask} need not be @@ -1128,5 +1126,5 @@ the appropriate offsets to obtain the correct pixel on the mask. In the event that the \code{mask} image is too small (i.e., pixels on the -input image refer to pixels outside the range of the \code{mask} +input image correspond to pixels outside the range of the \code{mask} image), the function shall generate an error. @@ -1183,4 +1181,73 @@ The \code{mask} shall be of type U8, and the input image, \code{in}, must be of type F32. + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\subsection{Paper Trail} + +The elements of the focal plane hierarchy each contain an +\code{analysis} member, intended to log the results of the Phase 2 +tasks. The Phase 2 tasks shall add to the \code{analysis} members as +follows: + +\begin{itemize} +\item \code{pmMaskBadPixels}: + \begin{itemize} + \item \code{MASK.DONE} (STR): The time at which masking was + completed. + \item \code{MASK.SAT} (S32): The number of saturated pixels masked + in the image + \item \code{MASK.SAT.GROW} (S32): The number of additional pixels + masked by growing the saturated pixels. + \item \code{MASK.BAD} (S32): The number of pixels masked in the + image + \item \code{MASK.BAD.GROW} (S32): The number of additional pixels + masked by growing the specified bad pixels. + \end{itemize} +\item \code{pmNonLinearityPolynomial} and \code{pmNonLinearityLookup}: + \begin{itemize} + \item \code{NONLIN.DONE} (STR): The time at which the non-linearity + correction was completed. + \item \code{NONLIN.POLY} (STR): The polynomial coefficients used (if + applicable). + \item \code{NONLIN.LOOKUP} (STR): The filename for the lookup table + (if applicable). + \end{itemize} +\item \code{pmSubtractBias}: + \begin{itemize} + \item \code{BIAS.DONE} (STR): The time at which the bias-subtraction + was completed. + \item \code{BIAS.OVERSCAN.AXIS} (STR): Overscan axis used. + \item \code{BIAS.OVERSCAN.FIT.TYPE} (STR): Fit type applied to + overscan. + \item \code{BIAS.OVERSCAN.FIT.COEFF} (STR): Coefficients of overscan + fit. + \item \code{BIAS.OVERSCAN.REGION} (STR): Overscan regions (from + \code{x0,y0,numCols,numRows}). + \item \code{BIAS.OVERSCAN.BIN} (S32): Number of pixels per bin used + in overscan. + \item \code{BIAS.OVERSCAN.MEAN} (F32): The mean of the binned + overscan pixels after subtracting the fit. + \item \code{BIAS.OVERSCAN.SD} (F32): The standard deviation of the + binned overscan pixels after subtracting the fit. + \end{itemize} +\item \code{pmFlatField}: + \begin{itemize} + \item \code{FLAT.DONE} (STR): The time at which the flat-fielding + was completed. + \item \code{FLAT.BAD} (S32): Number of non-positive flat-field + pixels. + \end{itemize} +\end{itemize} + +To be added by higher-levels: +\begin{itemize} +\item \code{BIAS.NAME} (STR): Name of bias image +\item \code{DARK.NAME} (STR): Name of dark image +\item \code{FLAT.NAME} (STR): Name of flat image +\item \code{MASK.NAME} (STR): Name of mask image +\end{itemize} + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Calibration}