calibration: add application timestamp

changelog.md

@@ -7,6 +7,7 @@
 * Added parameter `allow_overwrite` to [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi) to allow re-downloading only those files where the checksum does not match.
 * Added force calibration information to channels accessed directly via the square bracket notation (e.g. `file["Force HF"]["Force 1x"].calibration`).
 * Calibration results and parameters are now accessible via properties which are listed when items are printed. See [calibration results](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html) and [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) API documentation for more information.
+* Added `applied_at` property to a [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) obtained from a force slice. This property returns the timestamp in nanoseconds at which the force calibration was applied.
 * Added improved printing of calibration items under `channel.calibration` providing a more convenient overview of the items associated with a `Slice`.
 * Added parameter `titles` to customize title of each subplot in `[`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
 

lumicks/pylake/calibration.py

@@ -27,6 +27,11 @@ def _get_parameter(self, _, bluelake_key):
         if bluelake_key in self:
             return self[bluelake_key]
 
+    @property
+    def applied_at(self):
+        """Time the calibration was applied in nanoseconds since epoch"""
+        return self.data.get("Timestamp (ns)")
+
     @property
     def _fitted_diode(self):
         """Diode parameters were fitted"""
@@ -354,8 +359,10 @@ def from_field(hdf5, force_channel, time_field="Stop time (ns)") -> "ForceCalibr
         items = []
         for calibration_item in hdf5["Calibration"].values():
             if force_channel in calibration_item:
-                attrs = calibration_item[force_channel].attrs
+                attrs = dict(calibration_item[force_channel].attrs)
                 if time_field in attrs.keys():
+                    # Copy the timestamp at which the calibration was applied into the item
+                    attrs["Timestamp (ns)"] = calibration_item.attrs.get("Timestamp (ns)")
                     items.append(ForceCalibrationItem(attrs))
 
         return ForceCalibration(time_field=time_field, items=items)

lumicks/pylake/tests/data/mock_file.py

@@ -53,7 +53,7 @@ class MockDataFile_v2(MockDataFile_v1):
     def get_file_format_version(self):
         return 2
 
-    def make_calibration_data(self, calibration_idx, group, attributes):
+    def make_calibration_data(self, calibration_idx, group, attributes, application_timestamp=None):
         if "Calibration" not in self.file:
             self.file.create_group("Calibration")
 
@@ -64,6 +64,9 @@ def make_calibration_data(self, calibration_idx, group, attributes):
         # e.g. Force 1x, Force 1y ... etc
         if group not in self.file["Calibration"][calibration_idx]:
             self.file["Calibration"][calibration_idx].create_group(group)
+            self.file["Calibration"][calibration_idx].attrs["Timestamp (ns)"] = (
+                application_timestamp if application_timestamp else attributes["Stop time (ns)"]
+            )
 
         # Attributes
         field = self.file["Calibration"][calibration_idx][group]

lumicks/pylake/tests/test_file/test_calibration_item.py

@@ -49,6 +49,7 @@
     "gamma_0 (kg/s)": 8.388052385084746e-09,
     "kappa (pN/nm)": 0.2421057076519628,
     "Bead center height (um)": 1.0,
+    "Timestamp (ns)": 1696171386701856700,
 }
 
 
@@ -168,6 +169,7 @@ def test_passive_item(compare_to_reference_dict, reference_data, calibration_dat
     assert item.diffusion_volts_std_err == ref_passive_fixed_diode_with_height["err_D (V^2/s)"]
     assert not item.diode_frequency_std_err
     assert not item.diode_relaxation_factor_std_err
+    assert item.applied_at is 1696171386701856700
 
     compare_to_reference_dict(item.power_spectrum_params(), test_name="power")
     compare_to_reference_dict(item._model_params(), test_name="model")

lumicks/pylake/tests/test_file/test_file_items.py

@@ -54,6 +54,7 @@ def test_calibration(h5_file):
 
         assert f["Force HF"]["Force 1x"].calibration == f.force1x.calibration
         assert f["Force HF"]["Force 2x"].calibration == f.force2x.calibration
+        assert f.force1x.calibration[2].applied_at == 10
 
 
 def test_marker(h5_file):