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/mo_check.py

@@ -0,0 +1,85 @@
+"""Diagnostic: how good is the coordinate registration, and how many
+detections survive removal of the static sky?
+
+astroalign only reports a few dozen matched stars, which is enough to define a
+similarity transform but says nothing about how well it holds across a
+4788 x 3194 field. This refines each frame's transform by nearest-neighbour
+matching every detection against the reference frame's detections and refitting
+a full affine, then quotes the residual. It also counts, per frame, how many
+detections are left once everything coincident with a master-stack source is
+removed - that residual population is the input to the tracklet search.
+"""
+import os
+
+import numpy as np
+from astropy.io import fits
+from scipy.spatial import cKDTree
+from skimage.transform import AffineTransform
+
+import layout
+
+SRC = layout.SESSION
+OUT = layout.SESSION
+CACHE = layout.path("_mo_dets.npz")
+
+
+def load():
+    z = np.load(CACHE, allow_pickle=True)
+    meta = {r[0]: r for r in z["meta"]}
+    dets = {k: z[k] for k in meta}
+    return meta, dets
+
+
+def refine(dets, ref_key="Luminance_002", tol=3.0):
+    """Refit each frame's transform on all cross-matched detections."""
+    ref = dets[ref_key]
+    tree = cKDTree(ref[:, :2])
+    out = {}
+    for key, d in dets.items():
+        src = d[:, 2:4].astype(float)          # native coords
+        cur = d[:, :2].astype(float)           # astroalign-transformed
+        for t in (tol, 1.5):
+            dist, idx = tree.query(cur, distance_upper_bound=t)
+            ok = np.isfinite(dist)
+            if ok.sum() < 50:
+                break
+            tf = AffineTransform()
+            tf.estimate(src[ok], ref[idx[ok], :2].astype(float))
+            cur = tf(src)
+        dist, idx = tree.query(cur, distance_upper_bound=1.5)
+        ok = np.isfinite(dist)
+        out[key] = (cur, np.median(dist[ok]), np.percentile(dist[ok], 90),
+                    ok.sum())
+    return out
+
+
+def main():
+    meta, dets = load()
+    lum = [k for k in dets if k.startswith("Luminance")]
+    ref = refine(dets)
+
+    print("registration residual against reference frame (px):")
+    for k in sorted(dets):
+        _, med, p90, n = ref[k]
+        print(f"  {k:16s} n={n:5d}  median={med:.3f}  p90={p90:.3f}")
+
+    # Static sky = every source in the deep luminance master.
+    with fits.open(layout.path("master-Luminance.fit")) as hd:
+        master = hd[0].data.astype(np.float32)
+    import sep
+    bkg = sep.Background(master, bw=64, bh=64, fw=3, fh=3)
+    m = sep.extract(master - bkg.back(), 2.5, err=bkg.globalrms, minarea=4,
+                    deblend_cont=0.005)
+    print(f"\nmaster detections (static sky): {len(m)}")
+    mtree = cKDTree(np.column_stack([m["x"], m["y"]]))
+
+    print("\nresiduals after removing anything within 4 px of a master source:")
+    for k in sorted(lum):
+        cur = ref[k][0]
+        d, _ = mtree.query(cur, distance_upper_bound=4.0)
+        left = ~np.isfinite(d)
+        print(f"  {k:16s} {left.sum():5d} / {len(cur)}")
+
+
+if __name__ == "__main__":
+    main()