fix: do not modify preprocessing options when applying them

CHANGELOG

@@ -1,3 +1,7 @@
+3.1.1
+ - fix: do not modify preprocessing options when applying them (create
+   a copy of the dictionary)
+ - ref: remove `Indentation.reset` in favor of `AFMData.reset_data`
 3.1.0
  - feat: new contact point estimation method "fit_constant_polynomial"
    which applies a piece-wise constant and polynomial fit

nanite/indent.py

@@ -1,6 +1,5 @@
 from collections import OrderedDict
 import copy
-import inspect
 import warnings
 
 import afmformats
@@ -33,14 +32,6 @@ def __init__(self, data, metadata, diskcache=None):
         # Curve rating (see `self.rate_quality`)
         self._rating = None
 
-        # Store initial parameters for reset (see `self.reset`)
-        frame = inspect.currentframe()
-        iargs, _, _, values = inspect.getargvalues(frame)
-        self._init_kwargs = {
-            "data": copy.deepcopy(data),
-            "metadata": copy.deepcopy(metadata)
-        }
-
     @property
     def data(self):
         warnings.warn("Please use __getitem__ instead!", DeprecationWarning)
@@ -91,9 +82,10 @@ def apply_preprocessing(self, preprocessing=None, options=None,
             fp = self.fit_properties
             fp["preprocessing"] = preprocessing
             fp["preprocessing_options"] = options
-            # Reset all data
-            self.reset()
+            # Reset rating
+            self._rating = None
             # Apply preprocessing
+            # (This will call `AFMData.reset_data` on self)
             details = IndentationPreprocessor.apply(apret=self,
                                                     identifiers=preprocessing,
                                                     options=options,
@@ -380,7 +372,3 @@ def rate_quality(self, regressor="Extra Trees", training_set="zef18",
             # Use cached rating
             rt = self._rating[-1]
         return rt
-
-    def reset(self):
-        """Resets all data operations"""
-        self.__init__(**self._init_kwargs)

nanite/preproc.py

@@ -75,13 +75,6 @@ def apply(apret, identifiers=None, options=None, ret_details=False,
             Return preprocessing details dictionary
         preproc_names: list
             Deprecated - use `identifiers` instead
-
-        Notes
-        -----
-        This method is usually called from within the `Indentation`
-        class instance. If you are using this class directly and
-        apply it more than once, you might need to call
-        `apret.reset()` before preprocessing a second time.
         """
         if preproc_names is not None:
             identifiers = preproc_names
@@ -103,7 +96,9 @@ class instance. If you are using this class directly and
                 if req is not None and ((set(req) & set(act)) != set(req)):
                     raise ValueError(f"The preprocessing step '{pid}' requires"
                                      f" the steps {meth.steps_required}!")
-                kwargs = options.get(pid, {})  # empty dict if not defined
+                # create a copy of the dictionary (if it exists) so that
+                # `ret_details` is not written to it
+                kwargs = copy.deepcopy(options.get(pid, {}))
                 if "ret_details" in inspect.signature(meth).parameters:
                     # only set `ret_details` if method accepts it
                     kwargs["ret_details"] = ret_details

tests/test_indent.py

@@ -173,6 +173,63 @@ def test_get_model():
     assert md2 is md
 
 
+def test_preprocessing_reset():
+    fd = nanite.IndentationGroup(jpkfile)[0]
+    fd.apply_preprocessing(["compute_tip_position",
+                            "correct_force_offset",
+                            "correct_tip_offset"],
+                           options={"correct_tip_offset": {
+                               "method": "fit_constant_line"}})
+
+    inparams = nanite.model.model_hertz_paraboloidal.get_parameter_defaults()
+    inparams["baseline"].vary = True
+    inparams["contact_point"].set(1.8e-5)
+
+    # Perform fit and make sure that all properties are set
+    fd.fit_model(model_key="hertz_para",
+                 params_initial=inparams,
+                 range_x=(0, 0),
+                 range_type="absolute",
+                 x_axis="tip position",
+                 y_axis="force",
+                 segment="approach",
+                 weight_cp=False)
+    fd.rate_quality(training_set="zef18",
+                    regressor="Extra Trees")
+    assert fd._rating is not None
+    assert fd.preprocessing == ["compute_tip_position",
+                                "correct_force_offset",
+                                "correct_tip_offset"]
+    assert fd.preprocessing_options == {"correct_tip_offset": {
+                                        "method": "fit_constant_line"}}
+    assert not fd._preprocessing_details
+    assert np.allclose(
+        fd._fit_properties["params_fitted"]["contact_point"].value,
+        -3.5147555568064786e-06,
+        atol=0)
+    assert "tip position" in fd
+
+    # Change preprocessing and make sure properties are reset
+    fd.apply_preprocessing(["compute_tip_position",
+                            "correct_force_offset",
+                            "correct_tip_offset"],
+                           options={"correct_tip_offset": {
+                               "method": "fit_constant_polynomial"}})
+    assert fd._rating is None
+    assert fd.preprocessing == ["compute_tip_position",
+                                "correct_force_offset",
+                                "correct_tip_offset"]
+    assert fd.preprocessing_options == {"correct_tip_offset": {
+                                        "method": "fit_constant_polynomial"}}
+    assert not fd._preprocessing_details
+    assert "params_fitted" not in fd._fit_properties
+    assert "tip position" in fd
+
+    # Change preprocessing, removing tip position
+    fd.apply_preprocessing(["correct_force_offset"])
+    assert "tip position" not in fd
+
+
 def test_rate_quality_cache():
     ds1 = nanite.IndentationGroup(jpkfile)
     idnt = ds1[0]