Index: /trunk/ppImage/test/gpc1_raw.config
===================================================================
--- /trunk/ppImage/test/gpc1_raw.config	(revision 6059)
+++ /trunk/ppImage/test/gpc1_raw.config	(revision 6059)
@@ -0,0 +1,172 @@
+# The raw GPC data comes off the telescope with each of the chips stored in separate files
+
+# How to identify this type
+RULE	METADATA
+#	TELESCOP	STR	PS1
+#	DETECTOR	STR	GPC1
+	EXTEND		BOOL	T
+	NEXTEND		S32	64
+	NAMPS		S32	64
+END
+
+# How to read this data
+PHU		STR	CHIP	# The FITS file represents a single chip
+EXTENSIONS	STR	CELL	# The extensions represent cells
+
+# What's in the FITS file?
+CONTENTS	METADATA
+	# Extension name, type
+	xy00	STR	pitch10u
+	xy01	STR	pitch10u
+	xy02	STR	pitch10u
+	xy03	STR	pitch10u
+	xy04	STR	pitch10u
+	xy05	STR	pitch10u
+	xy06	STR	pitch10u
+	xy07	STR	pitch10u
+	xy10	STR	pitch10u
+	xy11	STR	pitch10u
+	xy12	STR	pitch10u
+	xy13	STR	pitch10u
+	xy14	STR	pitch10u
+	xy15	STR	pitch10u
+	xy16	STR	pitch10u
+	xy17	STR	pitch10u
+	xy20	STR	pitch10u
+	xy21	STR	pitch10u
+	xy22	STR	pitch10u
+	xy23	STR	pitch10u
+	xy24	STR	pitch10u
+	xy25	STR	pitch10u
+	xy26	STR	pitch10u
+	xy27	STR	pitch10u
+	xy30	STR	pitch10u
+	xy31	STR	pitch10u
+	xy32	STR	pitch10u
+	xy33	STR	pitch10u
+	xy34	STR	pitch10u
+	xy35	STR	pitch10u
+	xy36	STR	pitch10u
+	xy37	STR	pitch10u
+	xy40	STR	pitch10u
+	xy41	STR	pitch10u
+	xy42	STR	pitch10u
+	xy43	STR	pitch10u
+	xy44	STR	pitch10u
+	xy45	STR	pitch10u
+	xy46	STR	pitch10u
+	xy47	STR	pitch10u
+	xy50	STR	pitch10u
+	xy51	STR	pitch10u
+	xy52	STR	pitch10u
+	xy53	STR	pitch10u
+	xy54	STR	pitch10u
+	xy55	STR	pitch10u
+	xy56	STR	pitch10u
+	xy57	STR	pitch10u
+	xy60	STR	pitch10u
+	xy61	STR	pitch10u
+	xy62	STR	pitch10u
+	xy63	STR	pitch10u
+	xy64	STR	pitch10u
+	xy65	STR	pitch10u
+	xy66	STR	pitch10u
+	xy67	STR	pitch10u
+	xy70	STR	pitch10u
+	xy71	STR	pitch10u
+	xy72	STR	pitch10u
+	xy73	STR	pitch10u
+	xy74	STR	pitch10u
+	xy75	STR	pitch10u
+	xy76	STR	pitch10u
+	xy77	STR	pitch10u
+END
+
+# Specify the cell data
+CELLS	METADATA
+	pitch10u	METADATA
+		CELL.BIASSEC.SOURCE	STR	VALUE
+		CELL.TRIMSEC.SOURCE	STR	VALUE
+		CELL.BIASSEC		STR	[575:606,1:594]
+		CELL.TRIMSEC		STR	[1:574,1:594]
+	#	CELL.BIASSEC		STR	BIASSEC
+	#	CELL.TRIMSEC		STR	DATASEC
+	END
+
+	# This is just in here for fun
+	pitch12u	METADATA
+		CELL.BIASSEC.SOURCE	STR	VALUE
+		CELL.TRIMSEC.SOURCE	STR	VALUE
+		CELL.BIASSEC		STR	[1:10,1:512];[523:574,1:512]
+		CELL.TRIMSEC		STR	[11:522,1:512]
+	#	CELL.BIASSEC		STR	BIASSEC
+	#	CELL.TRIMSEC		STR	TRIMSEC
+	END
+END
+
+
+# How to translate PS concepts into FITS headers
+TRANSLATION	METADATA
+	CELL.XBIN	STR	CCDSUM
+	CELL.YBIN	STR	CCDSUM
+	CELL.X0		STR	IMNPIX1
+	CELL.Y0		STR	IMNPIX2
+	CELL.XPARITY	STR	LTM1_1
+	CELL.YPARITY	STR	LTM2_2
+	CELL.SATURATION	STR	SATURATE
+END
+
+# Default PS concepts that may be specified by value
+DEFAULTS	METADATA
+	FPA.AIRMASS	F32	0.0
+	FPA.FILTER	STR	NONE
+	FPA.POSANGLE	F32	0.0
+	FPA.RA		STR	0:0:0
+	FPA.DEC		STR	0:0:0
+	FPA.RADECSYS	STR	ICRS
+	FPA.NAME	S32	12345
+	CELL.EXPOSURE	F32	0.0
+	CELL.DARKTIME	F32	0.0
+	CELL.GAIN	F32	1.0
+	CELL.READNOISE	F32	0.0
+	CELL.READDIR	S32	2
+	CELL.BAD	S32	0
+	CELL.TIMESYS	STR	UTC
+	CELL.TIME	STR	2005-11-23T12:34:56.78
+END
+
+# How to translation PS concepts into database lookups
+DATABASE	METADATA
+	TYPE		dbEntry		TABLE		COLUMN		GIVENDBCOL	GIVENPS
+#	CELL.GAIN	dbEntry		Camera		gain		chipId,cellId	CHIP,CELL
+#	CELL.READNOISE	dbEntry		Camera		readNoise	chipId,cellId	CHIP,CELL
+
+# A database entry refers to a particular column (COLUMN) in a
+# particular table (TABLE), given certain PS concepts (GIVENPS) that
+# match certain database columns (GIVENDBCOL).
+
+END
+
+
+# Where there might be some ambiguity, specify the format
+FORMATS		METADATA
+	FPA.RA		STR	HOURS
+	FPA.DEC		STR	DEGREES
+	CELL.TIME	STR	ISO
+	CELL.BINNING	STR	TOGETHER
+	CELL.X0		STR	FORTRAN
+	CELl.Y0		STR	FORTRAN
+END
+ 
+# Recipe options
+RECIPES		METADATA
+	PHASE2		STR	phase2.config		# Phase 2 recipe details
+END
+ 
+# How to get the supplementary stuff: mask and weight
+SUPPLEMENTARY	METADATA
+	MASK.SOURCE	STR	FILE		# Source type for mask: EXT | FILE
+	MASK.NAME	STR	%a_mask.fits	# Name for mask extension or filename
+	WEIGHT.SOURCE	STR	FILE		# Source type for weight: EXT | FILE
+	WEIGHT.NAME	STR	%a_weight.fits	# Name for weight extension or filename
+END
Index: /trunk/ppImage/test/ipprc.config
===================================================================
--- /trunk/ppImage/test/ipprc.config	(revision 6059)
+++ /trunk/ppImage/test/ipprc.config	(revision 6059)
@@ -0,0 +1,37 @@
+### Example .ipprc file
+
+### Database configuration
+DBSERVER	STR	ippdb.ifa.hawaii.edu	# Database host name (for psDBInit)
+DBUSER		STR	ipp			# Database user name (for psDBInit)
+DBPASSWORD	STR	password		# Database password (for psDBInit)
+
+### Setups for each camera system
+CAMERAS		METADATA
+	MEGACAM_RAW	STR	megacam_raw.config
+	GPC1_RAW	STR	gpc1_raw.config
+	MEGACAM_SPLICE	STR	megacam_splice.config
+#	LRIS_BLUE	STR	lris_blue.config
+#	LRIS_RED	STR	lris_red.config
+END
+
+### psLib setup
+#TIME		STR	/home/mithrandir/price/pan-starrs/jhroot/i686-pc-linux-gnu/etc/pslib/psTime.config	# Time configuration file
+LOGLEVEL	S32	9			# Logging level; 3=INFO
+LOGFORMAT	STR	THLNM			# Log format
+LOGDEST	STR	STDOUT				# Log destination
+TRACE		METADATA			# Trace levels
+	mosaicChip		S32	10
+	p_pmImageMosaic		S32	10
+	ppImageLoop		S32	10
+	ppImageLoadPixels	S32	10
+	pmSubtractBias		S32	10
+	pmFPAPrint		S32	10
+#	psModule.concepts	S32	10
+#	pmFPAWrite		S32	10
+#	pmConfigRead		S32	10
+#	pmFPAWriteMask		S32	10
+#	pmFPAWriteWeight	S32	10
+#	pmChipMosaic		S32	10
+#	pmFPAMorph		S32	10
+#	pap_psMetadataCopy	S32	9
+END
Index: /trunk/ppImage/test/megacam_raw.config
===================================================================
--- /trunk/ppImage/test/megacam_raw.config	(revision 6059)
+++ /trunk/ppImage/test/megacam_raw.config	(revision 6059)
@@ -0,0 +1,175 @@
+# The raw MegaCam data comes off the telescope with each of the chips stored in extensions of a MEF file.
+
+# How to identify this type
+RULE	METADATA
+	TELESCOP	STR	CFHT 3.6m
+	DETECTOR	STR	MegaCam
+	EXTEND		BOOL	T
+	NEXTEND		S32	72
+END
+
+# How to read this data
+PHU		STR	FPA	# The FITS file represents an entire FPA
+EXTENSIONS	STR	CELL	# The extensions represent cells
+
+# What's in the FITS file?
+CONTENTS	METADATA
+	# Extension name, chip name:type
+	amp00	STR	ccd00:left
+	amp01	STR	ccd00:right
+	amp02	STR	ccd01:left
+	amp03	STR	ccd01:right
+	amp04	STR	ccd02:left
+	amp05	STR	ccd02:right
+	amp06	STR	ccd03:left
+	amp07	STR	ccd03:right
+	amp08	STR	ccd04:left
+	amp09	STR	ccd04:right
+	amp10	STR	ccd05:left
+	amp11	STR	ccd05:right
+	amp12	STR	ccd06:left
+	amp13	STR	ccd06:right
+	amp14	STR	ccd07:left
+	amp15	STR	ccd07:right
+	amp16	STR	ccd08:left
+	amp17	STR	ccd08:right
+	amp18	STR	ccd09:left
+	amp19	STR	ccd09:right
+	amp20	STR	ccd10:left
+	amp21	STR	ccd10:right
+	amp22	STR	ccd11:left
+	amp23	STR	ccd11:right
+	amp24	STR	ccd12:left
+	amp25	STR	ccd12:right
+	amp26	STR	ccd13:left
+	amp27	STR	ccd13:right
+	amp28	STR	ccd14:left
+	amp29	STR	ccd14:right
+	amp30	STR	ccd15:left
+	amp31	STR	ccd15:right
+	amp32	STR	ccd16:left
+	amp33	STR	ccd16:right
+	amp34	STR	ccd17:left
+	amp35	STR	ccd17:right
+	amp36	STR	ccd18:left
+	amp37	STR	ccd18:right
+	amp38	STR	ccd19:left
+	amp39	STR	ccd19:right
+	amp40	STR	ccd20:left
+	amp41	STR	ccd20:right
+	amp42	STR	ccd21:left
+	amp43	STR	ccd21:right
+	amp44	STR	ccd22:left
+	amp45	STR	ccd22:right
+	amp46	STR	ccd23:left
+	amp47	STR	ccd23:right
+	amp48	STR	ccd24:left
+	amp49	STR	ccd24:right
+	amp50	STR	ccd25:left
+	amp51	STR	ccd25:right
+	amp52	STR	ccd26:left
+	amp53	STR	ccd26:right
+	amp54	STR	ccd27:left
+	amp55	STR	ccd27:right
+	amp56	STR	ccd28:left
+	amp57	STR	ccd28:right
+	amp58	STR	ccd29:left
+	amp59	STR	ccd29:right
+	amp60	STR	ccd30:left
+	amp61	STR	ccd30:right
+	amp62	STR	ccd31:left
+	amp63	STR	ccd31:right
+	amp64	STR	ccd32:left
+	amp65	STR	ccd32:right
+	amp66	STR	ccd33:left
+	amp67	STR	ccd33:right
+	amp68	STR	ccd34:left
+	amp69	STR	ccd34:right
+	amp70	STR	ccd35:left
+	amp71	STR	ccd35:right
+END
+
+# Specify the cell data
+CELLS	METADATA
+	left	METADATA	# Left amplifier
+		CELL.BIASSEC.SOURCE	STR	HEADER
+		CELL.TRIMSEC.SOURCE	STR	HEADER
+		CELL.BIASSEC		STR	BIASSEC
+		CELL.TRIMSEC		STR	DATASEC
+		CELL.XPARITY		S32	1 # We could have specified this as a DEFAULT, but this works
+		CELL.X0			S32	1
+		CELL.Y0			S32	1
+	END
+	right	METADATA	# Right amplifier
+		CELL.BIASSEC.SOURCE	STR	HEADER
+		CELL.TRIMSEC.SOURCE	STR	HEADER
+		CELL.BIASSEC		STR	BIASSEC
+		CELL.TRIMSEC		STR	DATASEC
+		CELL.XPARITY		S32	-1 # This cell is read out in the opposite direction
+		CELL.X0			S32	2048
+		CELL.Y0			S32	1
+	END
+END
+
+# How to translate PS concepts into FITS headers
+TRANSLATION	METADATA
+	FPA.NAME		STR	EXPNUM
+	FPA.AIRMASS		STR	AIRMASS
+	FPA.FILTER		STR	FILTER
+	FPA.POSANGLE		STR	ROTANGLE
+	FPA.RA			STR	RA
+	FPA.DEC			STR	DEC
+	FPA.RADECSYS		STR	RADECSYS
+	CELL.EXPOSURE		STR	EXPTIME
+	CELL.DARKTIME		STR	DARKTIME
+	CELL.GAIN		STR	GAIN
+	CELL.READNOISE		STR	RDNOISE
+	CELL.SATURATION		STR	SATURATE
+	CELL.TIME		STR	MJD-OBS
+	CELL.XBIN		STR	CCDBIN1
+	CELL.YBIN		STR	CCDBIN2
+END
+
+# Default PS concepts that may be specified by value
+DEFAULTS	METADATA
+	CELL.READDIR		S32	1		# Cell is read in x direction
+	CELL.BAD		S32	0
+	CELL.TIMESYS		STR	UTC
+	CELL.YPARITY		S32	1
+END
+
+# How to translation PS concepts into database lookups
+DATABASE	METADATA
+	TYPE		dbEntry		TABLE		COLUMN		GIVENDBCOL	GIVENPS
+#	CELL.GAIN	dbEntry		Camera		gain		chipId,cellId	CHIP.NAME,CELL.NAME
+#	CELL.READNOISE	dbEntry		Camera		readNoise	chipId,cellId	CHIP.NAME,CELL.NAME
+
+# A database entry refers to a particular column (COLUMN) in a
+# particular table (TABLE), given certain PS concepts (GIVENPS) that
+# match certain database columns (GIVENDBCOL).
+END
+
+
+# Where there might be some ambiguity, specify the format
+FORMATS		METADATA
+	FPA.RA		STR	HOURS
+	FPA.DEC		STR	DEGREES
+	CELL.TIME	STR	MJD
+#	CELL.BINNING	STR	SEPARATE
+	CELL.X0		STR	FORTRAN
+	CELL.Y0		STR	FORTRAN
+END
+
+# Recipe options
+RECIPES		METADATA
+	PHASE2		STR	phase2.config		# Phase 2 recipe details
+END
+
+
+# How to get the supplementary stuff: mask and weight
+SUPPLEMENTARY	METADATA
+	MASK.SOURCE	STR	FILE		# Source type for mask: EXT | FILE
+	MASK.NAME	STR	%a_mask.fits	# Name for mask extension or filename
+	WEIGHT.SOURCE	STR	FILE		# Source type for weight: EXT | FILE
+	WEIGHT.NAME	STR	%a_weight.fits	# Name for weight extension or filename
+END
Index: /trunk/ppImage/test/nonlin.dat
===================================================================
--- /trunk/ppImage/test/nonlin.dat	(revision 6059)
+++ /trunk/ppImage/test/nonlin.dat	(revision 6059)
@@ -0,0 +1,106 @@
+# Non-linearity correction lookup table
+# Col 1: Input value
+# Col 2: Corrected value
+0	0
+100	1
+200	2
+300	3
+400	4
+500	5
+600	6
+700	7
+800	8
+900	9
+1000	10
+1100	11
+1200	12
+1300	13
+1400	14
+1500	15
+1600	16
+1700	17
+1800	18
+1900	19
+2000	20
+2100	21
+2200	22
+2300	23
+2400	24
+2500	25
+2600	26
+2700	27
+2800	28
+2900	29
+3000	30
+3100	31
+3200	32
+3300	33
+3400	34
+3500	35
+3600	36
+3700	37
+3800	38
+3900	39
+4000	40
+4100	41
+4200	42
+4300	43
+4400	44
+4500	45
+4600	46
+4700	47
+4800	48
+4900	49
+5000	50
+5100	51
+5200	52
+5300	53
+5400	54
+5500	55
+5600	56
+5700	57
+5800	58
+5900	59
+6000	60
+6100	61
+6200	62
+6300	63
+6400	64
+6500	65
+6600	66
+6700	67
+6800	68
+6900	69
+7000	70
+7100	71
+7200	72
+7300	73
+7400	74
+7500	75
+7600	76
+7700	77
+7800	78
+7900	79
+8000	80
+8100	81
+8200	82
+8300	83
+8400	84
+8500	85
+8600	86
+8700	87
+8800	88
+8900	89
+9000	90
+9100	91
+9200	92
+9300	93
+9400	94
+9500	95
+9600	96
+9700	97
+9800	98
+9900	99
+10000	100
+10001	100
+1e6	100
Index: /trunk/ppImage/test/phase2.config
===================================================================
--- /trunk/ppImage/test/phase2.config	(revision 6059)
+++ /trunk/ppImage/test/phase2.config	(revision 6059)
@@ -0,0 +1,69 @@
+### Phase 2 recipe configuration file
+
+# List of tasks to perform
+MASK		BOOL	FALSE		# Mask bad pixels
+NONLIN		BOOL	FALSE		# Non-linearity correction
+BIAS		BOOL	FALSE		# Bias subtraction
+DARK		BOOL	FALSE		# Dark subtraction
+OVERSCAN	BOOL	TRUE		# Overscan subtraction
+FLAT		BOOL	TRUE		# Flat-field normalisation
+FRINGE		BOOL	FALSE		# Fringe subtraction
+SOURCE		BOOL	FALSE		# Source identification and photometry
+ASTROM		BOOL	FALSE		# Astrometry
+
+
+# Loading issues
+LOAD.DEPTH		STR	CHIP		# Depth at which to load pixels
+
+
+# Non-linearity correction
+NONLIN.SOURCE		STR	CHIP.NAME	# How to determine the source
+#@NONLIN.DATA		F32	0.0 1.001 0.001	# A polynomial
+NONLIN.DATA		STR	nonlin.dat	# Filename for lookup table
+#NONLIN.DATA		METADATA		# Source of non-linearity data
+#	ccd00		STR	nonlin00.dat	# A lookup table 
+#	@ccd01		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd02		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd03		F32	1.2345 		# A polynomial
+#	@ccd04		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd05		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd06		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd07		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd08		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd09		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd10		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd11		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd12		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd13		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd14		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd15		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd16		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd17		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd18		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd19		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd10		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd21		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd22		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd23		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd24		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd25		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd26		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd27		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd28		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd29		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd30		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd31		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd32		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd33		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd34		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd35		F32	0.0 1.001 0.001	# A polynomial
+#	@ccd36		F32	0.0 1.001 0.001	# A polynomial
+#END
+
+# Overscan subtraction
+OVERSCAN.SINGLE		BOOL	FALSE		# Reduce overscan to a single value?
+#OVERSCAN.FIT		STR	SPLINE		# NONE | POLYNOMIAL | SPLINE
+OVERSCAN.FIT		STR	POLYNOMIAL	# NONE | POLYNOMIAL | SPLINE
+OVERSCAN.ORDER		S32	5		# Order of polynomial fit
+OVERSCAN.STAT		STR	MEAN		# MEAN | MEDIAN
+