use _aspireAmplitude to retain ampitudes for saved files

Author: j-c-c

src/aspire/source/image.py

@@ -483,21 +483,16 @@ def offsets(self, values):
 
     @property
     def amplitudes(self):
-        if self.has_metadata("__amplitude"):
-            values = self.get_metadata("__amplitude")
-        else:
-            values = self.get_metadata(
-                "_rlnAmplitude",
-                default_value=np.array(1.0, dtype=np.float64),
-            )
+        values = self.get_metadata(
+            "_aspireAmplitude",
+            default_value=np.array(1.0, dtype=np.float64),
+        )
         return np.atleast_1d(np.asarray(values, dtype=np.float64))
 
     @amplitudes.setter
     def amplitudes(self, values):
         values = np.asarray(values, dtype=np.float64)
-        self.set_metadata("__amplitude", values)
-        # Drop the legacy field if we encountered it while loading a STAR file.
-        self._metadata.pop("_rlnAmplitude", None)
+        self.set_metadata("_aspireAmplitude", values)
 
     @property
     def angles(self):

src/aspire/source/relion.py

@@ -195,6 +195,10 @@ def populate_metadata(self):
 
         metadata = RelionStarFile(self.filepath).get_merged_data_block()
 
+        # Promote legacy _rlnAmplitude column to the ASPIRE-specific name.
+        if "_rlnAmplitude" in metadata and "_aspireAmplitude" not in metadata:
+            metadata["_aspireAmplitude"] = metadata.pop("_rlnAmplitude")
+
         # particle locations are stored as e.g. '000001@first_micrograph.mrcs'
         # in the _rlnImageName column. here, we're splitting this information
         # so we can get the particle's index in the .mrcs stack as an int

src/aspire/utils/relion_interop.py

@@ -12,7 +12,8 @@
 # of certain key fields used in the codebase,
 # which are originally read from Relion STAR files.
 relion_metadata_fields = {
-    "__amplitude": float,
+    "_aspireAmplitude": float,
+    "_rlnAmplitude": float,
     "_rlnVoltage": float,
     "_rlnDefocusU": float,
     "_rlnDefocusV": float,

tests/test_simulation.py

@@ -882,8 +882,6 @@ def check_metadata(sim_src, relion_src):
     those in a RelionSource.
     """
     for k, v in sim_src._metadata.items():
-        if k.startswith("__"):
-            continue
         try:
             np.testing.assert_array_equal(v, relion_src._metadata[k])
         except AssertionError: