Move the processing code under pipeline/

Preparing to merge this repository into a combined astrophotography
repo. session-scripts/ becomes pipeline/ because the scripts import
layout.py from their own directory and must stay together, and because
'pipeline' says what it is rather than how it came about. observing/
stays at the top level: observing plans are not processing code.

pipeline/sb_common.py

@@ -0,0 +1,108 @@
+"""Shared constants and helpers for the NGC 5128 surface-photometry analysis."""
+import numpy as np, os, warnings
+warnings.filterwarnings('ignore')
+from astropy.io import fits
+from astropy.wcs import WCS
+
+import layout
+
+DATA = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+PIXSCALE = 0.5376                 # arcsec/px (verified from WCS)
+PIXAREA  = PIXSCALE**2            # arcsec^2 per pixel
+ZP5      = 27.942                 # sep.sum_circle r=5px zero point (verified)
+# curve of growth on 13 isolated field stars: F(r=25)/F(r=5) = 1.2158
+APCOR    = +2.5*np.log10(1.2158)  # = +0.2121 mag, r=5 -> r=25 ("total")
+ZPTOT    = ZP5 + APCOR            # 28.154, zero point for total flux
+MU0      = ZPTOT + 2.5*np.log10(PIXAREA)   # 26.807; mu = MU0 - 2.5*log10(I_ADU_per_px)
+X0, Y0   = 2397.88, 1592.09       # nucleus, from WCS + Gaia-verified astrometry
+DIST_MPC = 3.8
+KPC_PER_ARCSEC = DIST_MPC*1e3*np.pi/180/3600   # 0.01842 kpc/arcsec
+
+def path(*p): return layout.path(*p)
+
+def load(ch):
+    """Load one master as a contiguous native-endian float32 array."""
+    d = fits.getdata(path('master-%s.fit' % ch))
+    return np.ascontiguousarray(d.astype(np.float32))
+
+def wcs():
+    return WCS(fits.getheader(path('master-Luminance.fit')))
+
+def mu(I):
+    """Surface brightness (mag/arcsec^2) from intensity in ADU/pixel."""
+    I = np.asarray(I, float)
+    out = np.full(I.shape, np.nan)
+    m = I > 0
+    out[m] = MU0 - 2.5*np.log10(I[m])
+    return out
+
+def ell_radius(shape, x0, y0, eps, pa_rad):
+    """Semi-major-axis-equivalent radius map for a fixed ellipse geometry.
+    pa_rad measured counter-clockwise from the +x axis (photutils convention)."""
+    ny, nx = shape
+    y, x = np.mgrid[0:ny, 0:nx].astype(np.float32)
+    x -= np.float32(x0); y -= np.float32(y0)
+    c, s = np.float32(np.cos(pa_rad)), np.float32(np.sin(pa_rad))
+    xp = x*c + y*s
+    yp = -x*s + y*c
+    del x, y
+    return np.sqrt(xp*xp + (yp/np.float32(1.0-eps))**2)
+
+
+def sky_pa(pa_deg):
+    """Convert a photutils isophote PA (deg CCW from +x) to sky PA (deg E of N).
+
+    For this frame north lies 0.96 deg CCW of the +x axis and east lies along
+    -y, so the two conventions differ by very nearly 90 deg with a flip.
+    """
+    cd = wcs().pixel_scale_matrix
+    t = np.radians(np.asarray(pa_deg, float))
+    xi = cd[0, 0]*np.cos(t) + cd[0, 1]*np.sin(t)      # +east
+    eta = cd[1, 0]*np.cos(t) + cd[1, 1]*np.sin(t)     # +north
+    return np.degrees(np.arctan2(xi, eta)) % 180.
+
+
+def north_east_pixel():
+    """Unit vectors (dx, dy) pointing north and east in pixel coordinates."""
+    cd = wcs().pixel_scale_matrix
+    det = cd[0, 0]*cd[1, 1] - cd[0, 1]*cd[1, 0]
+    n = np.array([-cd[0, 1], cd[0, 0]])/det
+    e = np.array([cd[1, 1], -cd[1, 0]])/det
+    return n/np.hypot(*n), e/np.hypot(*e)
+
+
+ISO_HDR = ('sma_px,sma_arcsec,sma_arcmin,sma_kpc,intens_adu_px,intens_err,'
+           'rms_adu,mu_mag_arcsec2,mu_err,ellipticity,ellipticity_err,'
+           'pa_deg_ccw_from_x,pa_err_deg,pa_deg_east_of_north,ndata,nflag,'
+           'stop_code')
+
+
+def write_isophote_csv(tab, fn):
+    """Write an isophote table to CSV.
+
+    Rows with stop_code != 0 had too little unmasked azimuth for the geometry
+    to converge: photutils still measures a valid intensity along the held
+    ellipse, but its eps/PA are carried over from the previous isophote and its
+    formal errors are meaningless (they come back as values like 1169 and
+    24006).  Those five geometry columns are therefore blanked to NaN, so the
+    file cannot be read as if the geometry had been measured there.  The
+    intensity columns are kept, because they are real.
+    """
+    import os
+    a = tab['sma']*PIXSCALE
+    conv = tab['stop'] == 0
+    blank = lambda v: np.where(conv, v, np.nan)
+    with np.errstate(all='ignore'):
+        me = 2.5/np.log(10)*tab['int_err']/np.where(tab['intens'] > 0,
+                                                    tab['intens'], np.nan)
+    out = np.column_stack([tab['sma'], a, a/60., a*KPC_PER_ARCSEC,
+                           tab['intens'], tab['int_err'], tab['rms'],
+                           mu(tab['intens']), me,
+                           blank(tab['eps']), blank(tab['eps_err']),
+                           blank(tab['pa']), blank(tab['pa_err']),
+                           blank(sky_pa(tab['pa'])),
+                           tab['ndata'], tab['nflag'], tab['stop']])
+    np.savetxt(path(fn), out, delimiter=',', header=ISO_HDR, comments='',
+               fmt='%.5f')
+    print('wrote %s (%d rows, %d with converged geometry)'
+          % (fn, len(out), conv.sum()))