deprecate _rlnAmplitude in favor of private __amplitude field.

Author: j-c-c

src/aspire/source/image.py

@@ -483,15 +483,21 @@ def offsets(self, values):
 
     @property
     def amplitudes(self):
-        return np.atleast_1d(
-            self.get_metadata(
-                "_rlnAmplitude", default_value=np.array(1.0, dtype=self.dtype)
+        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),
             )
-        )
+        return np.atleast_1d(np.asarray(values, dtype=np.float64))
 
     @amplitudes.setter
     def amplitudes(self, values):
-        return self.set_metadata("_rlnAmplitude", np.array(values, dtype=self.dtype))
+        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)
 
     @property
     def angles(self):

src/aspire/utils/relion_interop.py

@@ -12,6 +12,7 @@
 # of certain key fields used in the codebase,
 # which are originally read from Relion STAR files.
 relion_metadata_fields = {
+    "__amplitude": float,
     "_rlnVoltage": float,
     "_rlnDefocusU": float,
     "_rlnDefocusV": float,

tests/test_array_image_source.py

@@ -323,10 +323,10 @@ def test_dtype_passthrough(dtype):
     # Check dtypes
     np.testing.assert_equal(src.dtype, dtype)
     np.testing.assert_equal(src.images[:].dtype, dtype)
-    np.testing.assert_equal(src.amplitudes.dtype, dtype)
 
-    # offsets are always stored as doubles
+    # offsets and amplitudes are always stored as doubles
     np.testing.assert_equal(src.offsets.dtype, np.float64)
+    np.testing.assert_equal(src.amplitudes.dtype, np.float64)
 
 
 def test_stack_1d_only():

tests/test_simulation.py

@@ -882,6 +882,8 @@ 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: