Index: /trunk/psLib/swig/Makefile.am
===================================================================
--- /trunk/psLib/swig/Makefile.am	(revision 3167)
+++ /trunk/psLib/swig/Makefile.am	(revision 3168)
@@ -1,4 +1,4 @@
 
-EXTRA_DIST = pslib.i Makefile.PL 
+EXTRA_DIST = pslib.i Makefile.PL example/phase2.pl example/data/*
 
 clean-generic:
Index: unk/psLib/swig/phase2.pl
===================================================================
--- /trunk/psLib/swig/phase2.pl	(revision 3167)
+++ 	(revision )
@@ -1,484 +1,0 @@
-#!/usr/bin/perl -w
-package phase2;
-
-use strict;
-use pslib;
-#
-# Prototypes
-#
-sub DefineStats($);
-sub DirectionFromOverscan($);
-sub bias_subtract_readout($$$; @);
-sub dark_subtract_readout($$$);
-sub defringe_readout($$$$);
-sub getScalingFactor($$$);
-sub load_image($$$$);
-sub make_kernel();
-sub make_mask($$);
-sub mask_readout($$$$$);
-sub nonlinearity_correct_readout($$$$);
-sub phase2($$; @);
-sub pmCameraFromHeader($);
-sub pmCameraValidateHeaders($$);
-sub pmFPAfromHeader($$);
-sub pmFlatField($$$);
-sub pmRecipeDefineSection($$$);
-sub pmSectiontoRectangle($);
-sub pmSubtractBias($$$$$$$$);
-sub psFITSReadHeaderSet($);
-sub trim_readout($$$);
-
-###############################################################################
-#
-# Do the real work
-#
-sub phase2($$; @)
-{
-   my($input, $outroot, $cameraname, $recipefile, $basefile, $verbose) = @_;
-   $basefile ||= "base.config"; $verbose ||= 0;
-   my($nFail) = 0;
-   $outroot++;
-
-   pslib::psTraceSetLevel("ps.phase2", $verbose);
-
-   my($site);
-   if ($basefile) {
-      pslib::psTrace("ps.phase2", 2, "Basefile: $basefile\n");
-      
-      my($base) = pslib::psMetadataAlloc();
-      pslib::psMetadataParseConfig($base, $basefile, 1);
-      
-      my($sitefile) = pslib::psMetadataLookup($base, "SITE")->get_STR();
-      
-      $site = pslib::psMetadataAlloc();
-      pslib::psMetadataParseConfig($site, $sitefile, 1);
-   } else {
-      $site = undef;
-   }
-   
-   # load only the headers from the given file input a list of headers
-   my($headers) = psFITSReadHeaderSet($input);
-   
-   # identify camera (may be specified on command line)
-   my($camera);
-   if (!$cameraname) {
-      $cameraname = pmCameraFromHeader(pslib::psHashLookup($headers, "PHU"));
-      my($camerafile) = pslib::psMetadataLookup($site, ("CAMERA.$cameraname"))->get_STR();
-
-      # load the camera details for the specific camera
-      $camera = pslib::psMetadataAlloc();
-      pslib::psMetadataParseConfig($camera, $camerafile, 0);
-   }
-
-   # recipefile is defined in the camera metadata, if not specified on command line
-   if (!$recipefile) {
-      if (1) {			# 
-	 $recipefile = pslib::psMetadataLookup($camera, "RECIPE.PHASE2")->get_STR();
-      } else {                           # an alternative make this a database lookup & a function of date
-	 $recipefile = DetrendDatabaseLookup ("recipe", $camera, $headers);
-      }
-   }
-   
-   pslib::psTrace("ps.phase2", 2, "Reading recipe from $recipefile\n");
-   my($recipe) = pslib::psMetadataAlloc();
-   pslib::psMetadataParseConfig($recipe, $recipefile, 0);
-
-   # END CONFIG loading code
-
-   # check the validity of the given set of headers based on expectactions for this camera
-   pslib::psTrace("ps.phase2", 3, "Validating headers\n");
-   pmCameraValidateHeaders($headers, $camera);
-
-   # construct a complete, empty (ie, no pixel data) FPA structure for this camera / header set
-   # we need to construct the output container.  is it big enough to fit in memory?  assume so?
-   my($FPA) = pmFPAfromHeader($headers, $camera);
-   
-   # I\'m pretending the extname value for each cell in part of psCell
-   # Do we need to construct a list of the extname values associated with each readout?
-   # Is EXTNAME invarient?  (probably not; does not always exist)
-   #
-   # XXX Faked psCell->{extname} to exist and be NULL in pslib.i XXX
-   
-   my($i, $j, $k);
-   for ($i = 0; $i < $FPA->{chips}->{n}; $i++) {
-      my($chip) = $FPA->{chips}->get_chip($i);
-
-      pslib::psTrace("ps.phase2", 3, "Processing chip $i\n");
-      for ($j = 0; $j < $chip->{cells}->{n}; $j++) {
-	 my($cell) = $chip->{cells}->get_cell($j);
-	 
-	 pslib::psTrace("ps.phase2", 4, "Processing cell $j\n");
-	 my($bias) = load_image("BIAS", $recipe, $cell->{metadata}, $cell->{extname});
-	 my($dark) = load_image("DARK", $recipe, $cell->{metadata}, $cell->{extname});
-	 my($flat) = load_image("FLAT", $recipe, $cell->{metadata}, $cell->{extname});
-	 my($badpix) = load_image("BADPIX", $recipe, $cell->{metadata}, $cell->{extname});
-	 my($fringe) = load_image("FRINGE", $recipe, $cell->{metadata}, $cell->{extname});
-	 pslib::psTrace("ps.phase2", 5, "Read images for cell $j\n");
-	 
-	 for ($k = 0; $k < $cell->{readouts}->{n}; $k++) {
-	    pslib::psTrace("ps.phase2", 6, "Reading readout $k\n");
-	    
-	    my($readout) = $cell->{readouts}->get_readout($k);
-	    $readout->{image} = pslib::psImageReadSection(undef, 0, 0, 0, 0, 0, $cell->{extname}, $k, $input);
-
-	    if (!defined($readout->{metadata})) {
-	       pslib::psTrace("ps.phase2", 7, "Creating metadata\n");
-	       $readout->{metadata} = pslib::psMetadataAlloc();
-
-	       my($nbias) = 2;
-	       pslib::psMetadataAddStr($readout->{metadata}, $pslib::PS_LIST_TAIL,
-				       "BIASSEC", "Define bias section",
-				       sprintf("[0:%d,0:%d]",
-					       ($readout->{image}->{numRows} - 1, $nbias - 1)));
-	       pslib::psMetadataAddStr($readout->{metadata}, $pslib::PS_LIST_TAIL,
-				       "DATASEC", "Define datasection section",
-				       sprintf("[0:%d,%d:%d]",
-					       ($readout->{image}->{numRows} - 1, $nbias,
-						$readout->{image}->{numCols} - 1)));
-	    }
-	    
-	    my($kernel) = make_kernel();
-	    my($mask) = make_mask($readout->{image}->{numRows}, $readout->{image}->{numCols});
-	    
-	    pslib::psTrace("ps.phase2", 7, "Bias subtraction\n");
-	    bias_subtract_readout($readout, $bias, $recipe);
-	    
-	    pslib::psTrace("ps.phase2", 7, "Dark subtraction\n");
-	    dark_subtract_readout($readout, $dark, $recipe);
-	    nonlinearity_correct_readout($readout, $mask, $recipe, $camera);
-	    # 
-	    pslib::psTrace("ps.phase2", 7, "Trimming\n");
-	    trim_readout($readout, $mask, $recipe);
-	    mask_readout($readout, $mask, $badpix, $kernel, $recipe);
-	    # 
-	    # where do we convolve the flat with the kernel?
-	    #
-	    pmFlatField($readout, $mask, $flat);
-	    # 
-	    pslib::psTrace("ps.phase2", 7, "Defringing\n");
-	    defringe_readout($readout, $mask, $fringe, $recipe);
-
-	 }
-      }
-   }
-}
-
-sub bias_subtract_readout($$$; @)
-{
-   #"bias subtract the given readout according to the recipe (bias image may be None)
-   #no mask needed yet"
-   
-   my($readout, $bias, $recipe, $mask) = (undef, undef, undef, undef);
-   ($readout, $bias, $recipe, $mask) = @_;
-   #determine overscan option
-   my($biassec) = pmRecipeDefineSection($recipe, $readout->{metadata}, "BIAS.OVERSCAN");
-   my($overscan) = pslib::psImageSubsection($readout->{image}, $biassec);
-
-   # the type of statistic is defined by the recipe: BIAS.OVERSCAN.STATS
-   my($statname) = pslib::psMetadataLookup ($recipe, "BIAS.OVERSCAN.STATS")->get_STR();
-   my($stats) = DefineStats($statname);
-   
-   # identify the type of fit requested and relevant parameters
-   # the type of fit is defined by the recipe: BIAS.OVERSCAN.STATS
-   my($fitname) = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT")->get_STR();  # string defining overscan stats
-   
-   my($fitType, $fitSpec, $nBin, $nPts, $order);
-   if ($fitname eq "NONE") {
-      $fitType = "PM_FIT_NONE";
-      $fitSpec = undef;
-      $nBin = 0;
-   } elsif ($fitname eq "SPLINE") {
-      my($Npix) = "XXX";
-
-      $fitType = "PM_FIT_SPLINE";
-      $nBin = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.NBIN");
-      $nPts = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.NPTS");
-      $order = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.ORDER");
-      $fitSpec = psSpline1DAlloc($nPts, 3, 0, $Npix);                  # Npix is either NAXIS1 or NAXIS2 (Nx or Ny)
-   } elsif ($fitname eq "POLYNOMIAL") {
-      $fitType = "PM_FIT_POLYNOMIAL";
-      $nBin = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.NBIN");
-      $nPts = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.NPTS");
-      $order = pslib::psMetadataLookup($recipe, "BIAS.OVERSCAN.FIT.ORDER");
-      $fitSpec = psPolynomial1DAlloc($nPts, "PS_POLYNOMIAL_CHEB");
-   } else {
-      #raise pslib::PsUtilsError ("unknown fitname: %s" % fitname)
-   }
-   
-   my($overscanlist) = pslib::psListAlloc($overscan);
-   $readout->{image} = pmSubtractBias($readout->{image}, $fitSpec, $overscanlist,
-				      DirectionFromOverscan($biassec), $stats, $nBin, $fitType, $bias);
-
-   # add these to the readout->{metadata}? 
-   # or to the chip / cell metadata?
-}
-
-sub dark_subtract_readout($$$)
-{
-   #"subtract dark image using the appropriate scaling factor for this exposure time
-   #no mask needed yet"
-
-   my($readout, $dark, $recipe) = @_;
-
-   if (!defined($dark)) {
-      return;
-   }
-
-   # need to get a lookup table from the database, apply exptime for readout and dark
-   my($factor) = getScalingFactor($recipe, $readout, $dark);
-   
-   # $out = in - dark * factor
-   my($tmp) = pslib::psImageCopy(undef, $dark, $dark->{type}->{type});
-   pslib::psBinaryOp($tmp, $dark, "*", $factor);
-   pslib::psBinaryOp($readout->{image}, $readout->{image}, "-", $tmp);
-}
-
-sub nonlinearity_correct_readout($$$$)
-{
-   #"this corrects the non-linear response, but probably should use data determined at the cell level
-   #we need to set a mask value for pixels which have were out of range (TBD)"
-
-   my($readout, $mask, $recipe, $camera) = @_;
-   
-   my($method) = pslib::psMetadataLookup($recipe, "NONLINEAR.METHOD")->get_STR();
-   
-   # use a polynomial; get coeffs from recipe
-   if ($method eq "NONE") {
-      ;
-   } elsif ($method eq "POLYNOMIAL") {
-      my($correction);
-      $correction->{n} = pslib::psMetadataLookup($recipe, "NONLINEAR.ORDER")->{data}->{S32};
-      $correction->{coeffs} = pslib::psMetadataLookup($recipe, "NONLINEAR.COEFFS");
-      pslib::pmNonLinearityPolynomial($readout, $correction);
-   } elsif ($method eq "LOOKUP") {
-      my($time) = "XXX";
-      my($lookup_table) = DetrendDatabaseLookup($time, $camera, "etc?");
-      my($inFlux) = pslib::psFITSTableRead($lookup_table, "NONLINEAR.IN_FLUX");
-      my($outFlux) = pslib::psFITSTableRead($lookup_table, "NONLINEAR.OUT_FLUX");
-      pslib::pmNonLinearityLookup($readout, $inFlux, $outFlux);
-   } else {
-      #raise pslib::PsUtilsError ("unknown method: %s" % method);
-   }
-}
-
-sub trim_readout($$$)
-{
-   #"trim the image and mask based on the requested region"
-   my($readout, $mask, $recipe) = @_;
-   my($datasec) = pmRecipeDefineSection($recipe, $readout->{metadata}, "TRIM.DATASEC");
-   
-   my($r0, $r1, $c0, $c1) = ($datasec =~ /\[([0-9]+):([0-9]+),([0-9]+):([0-9]+)\]/);
-   
-   pslib::psImageTrim($readout->{image}, $c0, $r0, $c1, $r1);
-   $mask = pslib::psImageTrim($mask, $c0, $r0, $c1, $r1);
-}
-
-# apply the bad pixel mask to the image mask
-sub mask_readout($$$$$)
-{
-   my($readout, $mask, $badpix, $kernel, $recipe) = @_;
-}
-
-sub load_image($$$$)
-{
-   #"load in the complete corresponding image of proper type (this should be done once per cell)
-   #we are implying that the bias image is guaranteed to have the corresponding EXTNAME"
-
-   my($type, $recipe, $header, $extname) = @_;
-   my($source) = pslib::psMetadataLookup($recipe, $type . ".IMAGE")->get_STR();
-
-   my($name);
-   if (uc(substr($source, 0, 5)) eq "FILE:") {
-      $name = substr($source, 5);
-   } elsif (uc($source) eq "DB:BEST") {
-      $name = DetrendDatabaseLookup("best", $header);   # these APIs need to be seriously fleshed out!!
-   } elsif (uc($source) eq "DB:CLOSE") {
-      $name = DetrendDatabaseLookup("close", $header);   # these APIs need to be seriously fleshed out!!
-   } else {
-      #raise PsUtilsError ("Unknown source for $type: $source");
-   }
-
-   my($image);
-   if (defined($name)) {
-      $image = pslib::psImageReadSection (undef, 0, 0, 0, 0, 0, $extname, 0, $name);
-   } else {
-      $image = undef;
-   }
-
-   return $image;
-}
-
-sub pmRecipeDefineSection($$$)
-{
-   my($recipe, $header, $name) = @_;
-
-   my($source) = pslib::psMetadataLookup($recipe, $name)->get_STR();
-   
-   pslib::psTrace("ps.phase2.recipe", 10, "pmRecipeDefineSection (recipe, header, $name)\n");
-   
-   if (uc($source) eq "NONE") {
-      return psRectangleAlloc(0, 0, 0, 0); # the None section
-   } elsif (uc(substr($source, 0, 7)) eq "HEADER:") {
-      my($keyword) = substr($source,7);
-      my($section) = pslib::psMetadataLookup($header, $keyword)->get_STR();
-      return pmSectiontoRectangle($section);
-   } elsif (uc(substr($source, 0, 7)) eq "RECIPE:") {
-      my($section) = substr($source, 7);
-      return pmSectiontoRectangle($section);
-   }
-   
-   #raise pslib::PsUtilsError ("invalid section: $section");
-}
-
-#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
-
-sub DirectionFromOverscan($)
-{
-   #"The direction is implied by noting the long dimension of the biassec"
-   my($secstr) = @_;
-
-   return 1;
-}
-
-sub pmSectiontoRectangle($)
-{
-   #"Parse a specification of the form [col0:col1,row0:row1]
-   #For now, simply return it"
-   my($secstr) = @_;
-
-   return $secstr;
-}
-
-sub psFITSReadHeaderSet($)
-{
-   my($input) = @_;
-   
-   pslib::psTrace("ps.phase2", 2, "Reading headers: $input\n");
-
-   my($meta) = pslib::psMetadataAlloc();
-   pslib::psMetadataAddStr($meta, $pslib::PS_LIST_TAIL, "CAMERA", "Camera ID", "0");
-
-   my($headers) = pslib::psHashAlloc(64);
-   pslib::psHashAdd($headers, "PHU", $meta);
-   
-   return $headers;
-}
-
-sub pmCameraFromHeader($)
-{
-   #"Return a camera given the metadata read from a fits header"
-   my($meta) = @_;
-
-   return "0";
-}
-
-sub pmCameraValidateHeaders($$)
-{
-   my($headers, $camera) = @_;
-
-   if (0) {
-      #raise pslib::PsUtilsError ("Failed to validate $headers:$camera");
-   }
-}
-
-sub pmFPAfromHeader($$)
-{
-   my($headers, $camera) = @_;
-   
-   my($ra) = 1; my($dec) = 2; my($hourAngle) = 3; my($zenith) = 4; my($azimuth) = 5;
-   my($rotAngle) = 8;
-   my($temperature) = 9; my($pressure) = 10; my($humidity) = 11;
-   my($exposureTime) = 12;
-
-   my($nchips) = pslib::psMetadataLookup($camera, "NCHIPS")->{data}->{S32};
-   my($ncells) = pslib::psMetadataLookup($camera, "NCELLS")->{data}->{S32};
-   
-   my($obs) = pslib::psObservatoryAlloc("Haleakala", 21, 150, 3000, 0.1);
-   my($wavelength) = 5500e-10;
-   my($localTime) = pslib::psTimeGetTime($pslib::PS_TIME_TAI);
-
-   my($exposure) = pslib::psExposureAlloc($ra, $dec, $hourAngle, $zenith, $azimuth, $localTime,
-					  $rotAngle, $temperature, $pressure, $humidity, $exposureTime,
-					  $wavelength, $obs);
-   my($FPA) = pslib::psFPAAlloc($nchips, $exposure);
-   my($chips) = pslibc::psFPA_chips_get($FPA);
-   
-   my($i, $j, $k);
-   for ($i = 0; $i <$nchips; $i++) {
-      my($chip) = pslib::psChipAlloc($ncells, $FPA);
-      pslib::psArraySet($chips, $i, $chip);
-      my($cells) = pslibc::psChip_cells_get($chip);
-      for ($j = 0; $j <$ncells; $j++) {
-	 my($nReadouts) = pslib::psMetadataLookup($camera, "NREADOUTS.$i.$j")->{data}->{S32};
-
-	 my($cell) = pslib::psCellAlloc($nReadouts, $chip);
-	 
-	 pslib::psArraySet($cells, $j, $cell);
-	 
-	 my($readouts) = pslibc::psCell_readouts_get($cell);
-	 for ($k = 0; $k < $nReadouts; $k++) {
-	     pslib::psArraySet($readouts, $k, pslib::psReadoutAlloc());
-	 }
-      }
-   }
-
-   return $FPA;
-}
-
-sub make_kernel()
-{
-   my($nrow) = 5; my($ncol) = 5;
-   return pslib::psImageAlloc($ncol, $nrow, $pslib::PS_TYPE_F64);
-}
-
-sub make_mask($$)
-{
-   my($nrow, $ncol) = @_;
-
-   return pslib::psImageAlloc($ncol, $nrow, $pslib::PS_TYPE_F64);
-}
-
-sub DefineStats($)
-{
-   my($str) = @_;
-   return $str;
-}
-
-sub pmSubtractBias($$$$$$$$)
-{
-   #"Subtract the bias. Don't do a very good job..."
-   my($rawImage, $fitSpec, $overscanlist, $direction, $stats, $nBin, $type, $bias) = @_;
-   return pslib::psImageAlloc($rawImage->{numCols}, $rawImage->{numRows}, $pslib::PS_TYPE_F64);
-}
-
-sub getScalingFactor($$$)
-{
-   my($recipe, $readout, $dark) = @_;
-   my($source) = pslib::psMetadataLookup($recipe, "DARK.FACTOR")->get_STR();
-
-   if (uc(substr($source, 0, length("VALUE:"))) eq "VALUE:") {
-      return pslib::psScalarF32Alloc(substr($source, length("VALUE:")), $pslib::PS_TYPE_F64);
-   }
-
-   #raise pslib::PsUtilsError ("Unknown recipe for dark factor: $source");
-}
-
-sub pmFlatField($$$)
-{
-   my($readout, $mask, $flat) = @_;
-}
-
-sub defringe_readout($$$$)
-{
-   my($readout, $mask, $fringe, $recipe) = @_;
-}
-
-#(input, outroot, cameraname = None, recipefile = None, basefile = "base.config", verbose=0)
-if (1) {
-   phase2('data/data.fits', undef, undef, undef, "data/base.config", 4);
-   
-   if (pslib::psMemCheckLeaksToStderr(0,undef,0)) {
-      die "You leaked memory\n";
-   }
-}
-