optics group level not_ctf flag

Author: j-c-c

src/aspire/source/image.py

@@ -1330,9 +1330,6 @@ def _ensure_column(field, value):
         _ensure_column("_rlnVoltage", 0)
         _ensure_column("_rlnAmplitudeContrast", 0)
 
-        if missing_fields:
-            metadata["_aspireMetadata"] = np.full(n_rows, "no_ctf", dtype=object)
-
         # Restrict to the optics columns that are actually present on this source.
         optics_value_fields = [
             field for field in all_optics_fields if field in metadata
@@ -1359,6 +1356,10 @@ def _ensure_column(field, value):
             for field, value in zip(optics_value_fields, signature):
                 optics_block[field].append(value)
 
+        # Tag dummy optics if we had to synthesize any fields
+        if missing_fields:
+            optics_block["_aspireNoCTF"] = ["." for _ in range(len(group_lookup))]
+
         # Everything not lifted into the optics block stays with the particle metadata.
         particle_block = OrderedDict()
         if "_rlnOpticsGroup" in metadata:

src/aspire/source/relion.py

@@ -126,10 +126,7 @@ def __init__(
                 del self._metadata[key]
 
         # Detect ASPIRE-generated dummy variables
-        aspire_metadata = metadata.get("_aspireMetadata")
-        dummy_ctf = isinstance(aspire_metadata, (list, np.ndarray)) and np.all(
-            np.asarray(aspire_metadata) == "no_ctf"
-        )
+        no_ctf_flag = "_aspireNoCTF" in metadata
 
         # CTF estimation parameters coming from Relion
         CTF_params = [
@@ -169,7 +166,7 @@ def __init__(
             self.filter_indices = filter_indices
 
         # If we detect ASPIRE added dummy variables, log and initialize identity filter
-        elif dummy_ctf:
+        elif no_ctf_flag:
             logger.info(
                 "Detected ASPIRE-generated dummy optics; initializing identity filters."
             )

tests/test_coordinate_source.py

@@ -542,7 +542,6 @@ def testSave(self):
                 "_rlnImageName",
                 "_rlnCoordinateX",
                 "_rlnCoordinateY",
-                "_aspireMetadata",
             ],
         )
 
@@ -557,6 +556,7 @@ def testSave(self):
                 "_rlnAmplitudeContrast",
                 "_rlnImageSize",
                 "_rlnImageDimensionality",
+                "_aspireNoCTF",
             ],
         )
 

tests/test_simulation.py

@@ -926,18 +926,13 @@ def test_save_load_dummy_ctf_values(tmp_path, caplog):
 
     # STAR file should contain our fallback tag
     star = RelionStarFile(star_path)
-    particles_block = star.get_block_by_index(1)
-    np.testing.assert_array_equal(
-        particles_block["_aspireMetadata"], np.full(sim.n, "no_ctf", dtype=object)
-    )
+    optics_block = star.get_block_by_index(0)
+    assert "_aspireNoCTF" in optics_block
 
     # Tag should survive round-trip
     caplog.clear()
     reloaded = RelionSource(star_path)
-    np.testing.assert_array_equal(
-        reloaded._metadata["_aspireMetadata"],
-        np.full(reloaded.n, "no_ctf", dtype=object),
-    )
+    assert "_aspireNoCTF" in reloaded._metadata
 
     # Check message is logged about detecting dummy variables
     assert "Detected ASPIRE-generated dummy optics" in caplog.text