GA data model first version

datamodel.txt

@@ -673,6 +673,64 @@ The format will be identical to that of the pfsObject files.
 
 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 
+Physical parameter measurements for Galactic Archeology targets including flux-calibrated
+combined spectra and synthetic stellar template fits.
+
+    "pfsGAObject-%05d-%05d-%s-%016x-%03d-0x%016x.fits"
+         % (catId, tract, patch, objId, nVisit % 1000, pfsVisitHash)
+
+The format is similar to pfsObject files, but with additional HDUs and a different fluxTable format.
+
+HDU #j VELCORR         Velocity corrections used at each visit         [BINARY FITS TABLE]
+HDU #i STELLARPARAMS   Fundamental stellar parameter measurements      [BINARY FITS TABLE]
+HDU #l STELLARCOVAR    Covariance matrix of stellar parameters         [BINARY FITS TABLE] n*n
+HDU #k ABUND           Single element abundances                       [BINARY FITS TABLE]
+HDU #m ABUNDCOVAR      Covarinace matrix of single element abundances  [32-bit FLOAT]      n*n
+
+In the data tables outlined below, we allow for the possibility of multiple measurements of the same
+physical parameters indicated by the `method` field but we provide the full covariance matrix for
+the primary method only. The column `covarId` indicates the position of the parameter within the
+corresponding covariance matrix.
+
+The VELCORR table lists the velocity corrections used at each visit:
+
+    visit              visit identifier                                   32-bit int
+    JD                 Julian Date of the visit                           32-bit float
+    helio              Heliocentric correction at the visit [km s-1]      32-bit float
+    bary               Barycentric correction at the visit [km s-2]       32-bit float
+
+The STELLARPARAMS table lists the measured fundamental parameters
+
+    method             Method of measuring the parameters                 string
+    frame              Reference frame for measuring the velocity         string
+    param              Stellar parameter                                  string
+    covarId            Index of parameter within the covariance matrix    8-bit uint
+    unit               Physical unit of the parameter                     string
+    value              Measured value of the parameter                    32-bit float
+    valueErr           Uncertainty of the measured value                  32-bit float
+    flag               Measurement flag (true means bad)                  bool
+    status             Flags describing the quality of the measurement    string
+
+The ABUND table lists the measured single element abundances
+
+    method             Method of measuring the parameters                 string
+    element            Element name                                       string
+    covarId            Index of parameter within the covariance matrix    8-bit uint
+    value              Measured abundance                                 32-bit float
+    valueErr           Uncertainty of the measured abundance               32-bit float
+    flag               Measurement flag (true means bad)                  bool
+    status             Flags describing the quality of the measurement    string
+
+The FLUXTABLE of pfsGAObject files is extended and includes the following additional columns:
+
+    model              Best fit fluxed template model                     32-bit float
+    cont               Continuum model                                    32-bit float
+    norm_flux          Continuum-normalized flux                          32-bit float
+    norm_error         Error of continuum-normalized flux                 32-bit float
+    norm_model         Best fit continuum-normalized model                32-bit float
+
+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
+
 2D spectral line measurements
 
 The 2D pipeline measures the position and flux of sky and arc lines as part of the reduction process.

python/pfs/datamodel/__init__.py

@@ -15,3 +15,4 @@
 from .pfsTable import *
 from .pfsFocalPlaneFunction import *
 from .pfsFiberNorms import *
+from .ga import *

python/pfs/datamodel/fluxTable.py

@@ -38,11 +38,11 @@ class FluxTable:
     _hduName = "FLUX_TABLE"  # HDU name to use
 
     def __init__(self, wavelength, flux, error, mask, flags):
-        dims = np.array([len(wavelength.shape), len(flux.shape), len(error.shape), len(mask.shape)])
-        lengths = set([wavelength.shape, flux.shape, error.shape, mask.shape])
-        if np.any(dims != 1) or len(lengths) > 1:
-            raise RuntimeError("Bad shapes for wavelength,flux,error,mask: %s,%s,%s,%s" %
-                               (wavelength.shape, flux.shape, error.shape, mask.shape))
+        self.checkShapes(wavelength=wavelength,
+                         flux=flux,
+                         error=error,
+                         mask=mask)
+
         self.wavelength = wavelength
         self.flux = flux
         self.error = error
@@ -53,6 +53,17 @@ def __len__(self):
         """Return number of elements"""
         return len(self.wavelength)
 
+    def checkShapes(self, **kwargs):
+        keys = list(sorted(kwargs.keys()))
+        dims = np.array([len(kwargs[k].shape) for k in keys])
+        lengths = set([kwargs[k].shape for k in keys])
+
+        if np.any(dims != 1) or len(lengths) > 1:
+            names = ','.join(keys)
+            shapes = ','.join([str(kwargs[k].shape) for k in keys])
+            raise RuntimeError("Bad shapes for %s: %s" %
+                               (names, shapes))
+
     def toFits(self, fits):
         """Write to a FITS file