Changeset 2520

Timestamp:

Nov 29, 2004, 10:18:55 AM (22 years ago)

Author:

eugene

Message:

new versions of phase2 scripts

Location:

trunk/archive/scripts

Files:

• phase2-alt.c (added)
• phase2.c (modified) (5 diffs)
• phase2.pl (modified) (3 diffs)

trunk/archive/scripts/phase2.c

@@ -17 +17 @@
   outroot = argv[2];
 
-  // define command-line options
-  cameraname = NULL;
-  cameraname = getargs ("-camera");  // pseudo-code, not a valid API
-  recipefile = NULL;
-  recipefile = getargs ("-recipe");  // pseudo-code, not a valid API
-
-  // base file needs to be hardwired, from environment, or based on program name
-  base   = psMetadataParseConfig (NULL, basefile, FALSE);  
-
-  // load site-specific information (such as database servers, etc)
-  sitefile = psMetadataLookup (base, "SITE");
-  site   = psMetadataParseConfig (NULL, sitefile, FALSE);  
-
-  // load only the headers from the given file input a list of headers
-  headers = psFITSReadHeaderSet (input);
+  fits = psFitsAlloc (input);
+
+  // load only the headers from the given file
+  headers = psFitsReadHeaderSet (fits);
  
   // identify camera (may be specified on command line)
   if (cameraname == NULL) {
-    cameraname = pmCameraFromHeader (headers.data[0]);
+    cameraname = pmCameraFromHeader (psListGet (headers->list, 0));
   }
   camerafile = psMetadataLookup (site, "CAMERA.%s", cameraname);
@@ -63 +52 @@
   // Is EXTNAME invarient?  (probably not; does not always exist)
 
+  /* This will work, but it is not efficient: 
+     we should work with the extensions in sequence */
   for (i = 0; i < FPA[0].chips.n; i++) {
     chip = FPA[0].chips.data[i];
 
+    if (Base == CELL) {
+      f = psFitsMoveExtName(f, extname);
+    }
+    
     for (j = 0; j < chip[0].cells.n; j++) {
       cell = chip[0].cells.data[j];
 
+      if (Base == CELL) {
+        f = psFitsMoveExtName(f, extname);
+      }
+
+      /* these need to work with the psFits pointer correctly 
       bias = load_bias_image (recipe, cell[0].metadata, cell[0].extname);
       dark = load_dark_image (recipe, cell[0].metadata, cell[0].extname);
@@ -74 +74 @@
       badpix = load_badpix_image (recipe, cell[0].metadata, cell[0].extname);
       fringe = load_fringe_image (recipe, cell[0].metadata, cell[0].extname);
+      */
 
       for (k = 0; k < cell[0].readouts.n; k++) {
@@ -79 +80 @@
 
         // load the specific readout pixels.  put this in a function?  
-        readout[0].image = psImageReadSection (NULL, 0, 0, 0, 0, 0, cell[0].extname, k, input);
+        status = pmReadoutLoad (fits, cell, k);
 
         kernel = make_kernel ();
@@ -299 +300 @@
 }
 
+
+bool pmConfigLoadBasic (psMetadata **site, psMetadata **base) {
+
+  // base file needs to be hardwired, from environment, or based on program name
+  base   = psMetadataParseConfig (NULL, basefile, FALSE);  
+
+  // load site-specific information (such as database servers, etc)
+  sitefile = psMetadataLookup (base, "SITE");
+  site   = psMetadataParseConfig (NULL, sitefile, FALSE);  
+
+}
+
+bool pmConfigLoadCamera (psMetadata **camera, psMetadata *site, psMetadata *header) {
+  
+  if (site == NULL) return (FALSE);
+
+  // identify camera (may be specified on command line)
+  cameraname = getargs ("-camera");  // pseudo-code, not a valid API
+
+  // if there is no source for camera info, fail
+  if ((cameraname == NULL) && (header == NULL)) {
+    return (FALSE);
+  }
+
+  // try to determine camera from header 
+  if (cameraname == NULL) {
+    cameraname = pmCameraFromHeader (header);
+  }
+
+  // find appropriate camera definition file
+  camerafile = psMetadataLookup (site, "CAMERA.%s", cameraname);
+
+  // load the camera details for the specific camera
+  *camera = psMetadataParseConfig (NULL, camerafile, FALSE);
+
+  return (TRUE);
+}
+
+bool pmConfigLoadRecipe (psMetadata **recipe, psMetadata *camera, char *script) {
+
+  char recipename[64];
+
+  if (site   == NULL) return (FALSE);
+  if (camera == NULL) return (FALSE);
+
+  // define command-line options
+  recipefile = getargs ("-recipe");  // pseudo-code, not a valid API
+
+  // recipefile is defined in the camera metadata, if not specified on command line
+  if (recipefile == NULL) {
+    sprintf (recipename, "RECIPE.%s", script);
+
+    // option 1: recipe is in the camera definition 
+    recipefile = psMetadataLookup (camera, recipename);
+
+    // option 2: recipe is in the metadata database (equiv to a detrend file)
+    // this option requires a different API (header data, etc)
+    recipefile = DetrendDatabaseLookup (recipename, site, camera, header);
+  }
+
+  *recipe = psMetadataParseConfig (NULL, recipefile, FALSE);  
+  return (TRUE);
+}

trunk/archive/scripts/phase2.pl

@@ -2 +2 @@
 
 sub usage {
-    print STDERR "USAGE: phase2.pl\n";
+    # input is foo.fits
+    # outputs are outroot.im.fits (image) outroot.ob.fits (object list), outroot.log, etc
+    print STDERR "USAGE: phase2 (input) (outroot)\n";
     exit 2;
 }
@@ -8 +10 @@
 if (@ARGV != 4) { &usage; }
 
-# phase2.pl has extensive intelligence about data sources
+# base file needs to be hardwired, from environment, or based on program name
+$base   = psMetadataParseConfig (NULL, basefile, FALSE);  
 
-# input: filename.fits
-# output: flattened image: filename.f.fits? filename.flt? (chosen externally?)
-# output: extracted stars: filename.p.tbl
-# output: constructed kernel: filename.k.fits
+# probably defined in the base file?
+$site   = psMetadataParseConfig (NULL, sitefile, FALSE);  
 
-# determine camera from image or externally?
+# this should be optionally specified as part of the command-line options
+# alternatively, this should be derived from the input file header data 
+$camera = psMetadataParseConfig (NULL, camerafile, FALSE);
 
-# load configuration information:
+# we need a way to define an optional alternative recipe
+$recipe = psMetadataParseConfig (NULL, recipefile, FALSE);  # defined in the camera file
 
-$config = psMetadataReadFile (NULL, $configfile);
+# load only the headers from the given file input a list of headers
+@headers = psFITSReadHeaderSet ($input);
 
-# check image:
-# is it a FITS image?
-# find camera
-# find mode:
-#  one cell per extension
-#  one chip per extension
-#  one FPA per extension
+# check the validity of the given set of headers based on expectactions for this camera
+# ** where does camera come from?
+# ** how do we do this if the camera is derived from the header info?
+$status = pmCameraValidateHeaders ($headers, $camera);
 
-@chips = getChips ($input);
-foreach $chip () {
-    @cells = getCells ($input, $chip);
-}
+# this gets a bit tenuous: what do we do with the collection?  
 
+# 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?
+$FPA = pmFPAfromHeader ($headers, $camera);
 
+### now we work on individual readouts:
 
-# construct kernel
+# we have the FPA, already validated
+# as part of the FPA, we have access to a specified READOUT and we know the corresponding EXTNAME
 
-# load bias
-# load dark 
-# apply bias and dark
+# load in the complete readout:
+$image    = psImageReadSection (NULL, 0, 0, 0, 0, 0, $extname, $Nreadout, $input);
 
-# all possible detrend operations
-#   - bias
-#   - dark
-#   - trim
-#   - mask bad pixels (astrometry independent)
-#   - mask artifacts (astrometry dependent)
-#   - flatten
-#   - fringe correct
+# load in the complete corresponding bias image (this should be done once per cell)
+# in this form, we are implying that the bias image is guaranteed to have the corresponding EXTNAME
+$bias     = psImageReadSection (NULL, 0, 0, 0, 0, 0, $extname, 0, $biasname);
 
-# convolution kernel is applied to:
-#   - flat
-#   - fringe
-#   - bias?
+# overscan options:
+# - overscan is defined by the recipe (BIAS.OVERSCAN has form [Xs,Xe:Ys:Ye])
+# - overscan is defined by the header (BIAS.OVERSCAN has value BIASSEC)
+# - overscan is not used (BIAS.OVERSCAN has value NONE)
 
-#
-
-
-$out = pmSubtractBias ($in, $fit);
-
-
-##### example: single chip, single cell, single readout:
-
-# input filename: $input
-
-# bias recipe:
-#   bias image: filename
-#   overscan: header BIASSE
-
-# bias subtraction options:
-# - use a bias image?
-# - 
-
-
-
-$image    = psImageReadSection (NULL, 0, 0, 0, 0, 0, $extname, -1, $input);
-$metadata = psMetadataReadHeader (NULL, $extname, -1, $input);
-
-$metaitem = psMetadataLookup ($metadata, "BIASSEC");
+# bias section from header:
+$ = psMetadataLookup ($readout->metadata, "BIASSEC");
 $overscan = psImageSubsection ($image, $metaitem->data.void);
 
@@ -88 +64 @@
 $image_b = pmSubtractBias ($image, NULL, $overlist, PM_OVERSCAN_COLUMNS, $stats, 0, PM_FIT_NONE, $bias);
 
-
-
-#######################
-