fix(lee): exclude SSFP sequences and enhance T1c exclusion notes

Fiesta/CISS/SSFP are balanced-SSFP (T2-dominant) sequences whose
short TE fools the seq/TE fallback, causing T1c misclassification.
Add them to the exclusion regex and guard against empty candidates.

Expand write_excluded_notes to enumerate all series in a timepoint
(not just T1c candidates) and parse DICOM txt metadata for each
series' description and protocol, producing richer no-T1c reports.

scripts/03_scan_lee_t1c.py

@@ -19,7 +19,9 @@ from src.common import ROOT, DATA, save_jsonl, load_jsonl, is_head_series, path
 
 BASE = path("lee")
 T1_NAME_RE = re.compile(r"t1|tfl|spgr|mp2rage|tse3d|vfl|mpage", re.I)
-EXCL_RE = re.compile(r"\bt2\b|dwi|dti|mra|mrv|angi|swi|bold|\bpp2d|\bpp3d|perf|t2\*|t2star", re.I)
+# fiesta/ciss/ssfp: balanced-SSFP (fluid-bright, T2-dominant) — their short TE
+# fools the seq/TE fallback below, so they are excluded by name, not T1c
+EXCL_RE = re.compile(r"\bt2\b|dwi|dti|mra|mrv|angi|swi|bold|\bpp2d|\bpp3d|perf|t2\*|t2star|fiesta|ciss|ssfp", re.I)
 
 
 def parse_txt(p):
@@ -132,6 +134,8 @@ def scan_timepoint(sid, date, tpd):
     # timepoint has no thinner valid T1c; the others are flagged
     # thick_dropped: out of the selected manifest, but kept in raw so 04 can
     # fall back to them when every other T1c of the timepoint is lost
+    if not cand:
+        return []
     thin = [c for c in cand if c["max_sp"] <= MAX_SPACING]
     keep = thin if thin else [max(cand, key=lambda c: (c["acq"], c["n_slices"]))]
     dropped = [c for c in cand if c not in keep]

scripts/04_reconstruct_lee.py

@@ -286,27 +286,103 @@ def zero_tp_rows(uniq):
             and r["sid"] in sub_ok and (r["sid"], r["date"]) not in tp_ok]
 
 
+def scan_timepoint_series(sid, date, subj_dir):
+    """All series present in every <date>_MR_* timepoint dir of a subject.
+
+    Returns {ser: {"jpg": n_jpg_files, "txt": [(slice, path), ...]}} covering
+    not just the T1c candidates but every series the exam exported (T2 /
+    FLAIR / angio / ... that the scan never considered)."""
+    out = {}
+    if not subj_dir or not os.path.isdir(subj_dir):
+        return out
+    try:
+        tps = [d for d in os.listdir(subj_dir)
+               if d.startswith(date + "_MR_") and os.path.isdir(os.path.join(subj_dir, d))]
+    except OSError:
+        return out
+    pj = re.compile(rf"^{re.escape(sid)}_{date}_MR_(\d+)_(\d+)_(\d+)\.jpg$")
+    pt = re.compile(rf"^{re.escape(sid)}_{date}_MR_(\d+)_(\d+)\.txt$")
+    for tp in tps:
+        tpd = os.path.join(subj_dir, tp)
+        try:
+            entries = os.listdir(tpd)
+        except OSError:
+            continue
+        jpg_dir = next((os.path.join(tpd, e) for e in entries
+                        if os.path.isdir(os.path.join(tpd, e))), None)
+        jpg_files = []
+        if jpg_dir is not None:
+            try:
+                jpg_files = os.listdir(jpg_dir)
+            except OSError:
+                pass
+        for f in entries:
+            m = pt.match(f)
+            if m:
+                out.setdefault(m.group(1), {"jpg": 0, "txt": []})["txt"].append(
+                    (int(m.group(2)), os.path.join(tpd, f)))
+        for jf in jpg_files:
+            m = pj.match(jf)
+            if m:
+                out.setdefault(m.group(1), {"jpg": 0, "txt": []})["jpg"] += 1
+    return out
+
+
 def write_excluded_notes(zero_rows, all_rows, thick_rows, dyn_excl, reasons):
     """Write data/qa/<sid>/<date>_no_t1c.md for every timepoint with no
-    surviving T1c volume, listing each candidate series and its rejection reason."""
+    surviving T1c volume. Lists the study description and, for ALL series in
+    the timepoint (including ones the scan never considered as T1c), the
+    series description, protocol, and rejection reason (from the DICOM txt
+    metadata of each series' earliest slice sample)."""
     tps = {(r["sid"], r["date"]) for r in zero_rows}
     written = []
+
+    def esc(s):
+        return (s or "").strip().replace("|", "/").replace("\n", " ")
+
     for sid, date in sorted(tps):
         lst = [r for r in all_rows if (r["sid"], r["date"]) == (sid, date)]
         lst += [r for r in thick_rows if (r["sid"], r["date"]) == (sid, date)]
         lst.sort(key=lambda r: int(r["ser"]))
-        lines = [f"# {sid} {date}: no T1c volume", "",
+        rows_by_ser = {int(r["ser"]): r for r in lst}
-                 "This timepoint has no reconstructed T1c volume: every T1c "
+        cand = {r["key"] for r in lst}
-                 "candidate series was rejected.", "",
+        subj_dir = None
-                 "| series | slices | description | reason |",
-                 "|---|---|---|---|"]
         for r in lst:
-            if r["key"] in dyn_excl:
+            if r.get("jpg_dir"):
+                subj_dir = os.path.dirname(os.path.dirname(r["jpg_dir"]))
+                break
+        union = scan_timepoint_series(sid, date, subj_dir)
+        for r in lst:  # manifest series whose timepoint dir is gone
+            union.setdefault(str(int(r["ser"])), {"jpg": 0, "txt": []})
+        metas = {}
+        for ser, e in union.items():
+            r = rows_by_ser.get(int(ser))
+            src = min(e["txt"])[1] if e["txt"] else (r.get("txt_first") if r else "")
+            p = parse_txt(src) if src else None
+            metas[ser] = (p[5], p[6], p[7]) if p else ("", "", "")
+        study = next((m[0] for m in metas.values() if m[0]), "")
+        lines = [f"# {sid} {date}: no T1c volume", ""]
+        if study:
+            lines += [f"Study description: {study}", ""]
+        lines += [
+            "This timepoint has no reconstructed T1c volume: every T1c "
+            "candidate series was rejected. All series in this timepoint are "
+            "listed below.", "",
+            "| series | slices | series description | protocol | reason |",
+            "|---|---|---|---|---|"]
+        for ser in sorted(union, key=int):
+            e = union[ser]
+            r = rows_by_ser.get(int(ser))
+            key = f"lee_{sid}_{date}_s{ser}"
+            if key in dyn_excl:
                 why = "excluded: dynamic-frame series (other T1c in this timepoint)"
+            elif key in cand:
+                why = reasons.get(key, "no output")
             else:
-                why = reasons.get(r["key"], "no output")
+                why = "not a T1c candidate"
-            desc = (r.get("why") or "").strip().replace("|", "/")
+            n = e["jpg"] or (r.get("n_slices") if r else None) or "?"
-            lines.append(f"| s{r['ser']} | {r.get('n_slices', '?')} | {desc} | {why} |")
+            _, sdesc, sproto = metas[ser]
+            lines.append(f"| s{ser} | {n} | {esc(sdesc)} | {esc(sproto)} | {esc(why)} |")
         out = os.path.join(DATA, "qa", sid, f"{date}_no_t1c.md")
         os.makedirs(os.path.dirname(out), exist_ok=True)
         with open(out, "w") as f: