fix: spatial smoothing not working in some cases (close #15)

CHANGELOG

@@ -4,6 +4,10 @@
  - feat: contact point estimation methods now return detailed
    information about the procedure (currently plottable data to
    understand the process)
+ - fix: spatial smoothing not working in some cases (#15)
+ - ref: remove "...smoothed" column data (which was never used anyway);
+   instead, apply smoothing directly to AFMData subclass
+ - setup: bump afmformats from 0.16.0 to 0.16.3
 3.0.0
  - BREAKING CHANGE: The contact point estimation method "scheme_2020"
    has been removed, although it has been the default for some time.

nanite/indent.py

@@ -43,7 +43,7 @@ def __init__(self, data, metadata, diskcache=None):
 
     @property
     def data(self):
-        warnings.warn("Please use __getitem__ instead!")
+        warnings.warn("Please use __getitem__ instead!", DeprecationWarning)
         return self
 
     @property

nanite/preproc.py

@@ -276,38 +276,27 @@ def correct_split_approach_retract(apret):
 
     @staticmethod
     @preprocessing_step(identifier="smooth_height",
-                        name="spatial smoothing")
+                        name="monotonic height data")
     def smooth_height(apret):
-        """Smoothen height data
+        """Make height data monotonic
 
-        For the columns "height (measured)" and "tip position",
-        and for the approach and retract data separately, this
-        method adds the columns "height (measured, smoothed)" and
-        "tip position (smoothed)" to `apret`.
+        For the columns "height (measured)", "height (piezo), and
+        "tip position", this method ensures that the approach and
+        retract segments are monotonic.
         """
         orig = ["height (measured)",
+                "height (piezo)",
                 "tip position"]
-        dest = ["height (measured, smoothed)",
-                "tip position (smoothed)"]
-        for o, d in zip(orig, dest):
-            if o not in apret.columns:
+        for col in orig:
+            if col not in apret.columns:
                 continue
-            # Get approach and retract data
-            app_idx = apret["segment"] == 0
-            app = np.array(apret[o][app_idx])
-            ret_idx = apret["segment"] == np.max(apret["segment"])
-            ret = np.array(apret[o][ret_idx])
             # Apply smoothing
-            sm_app = smooth_axis_monotone(app)
-            sm_ret = smooth_axis_monotone(ret)
+            sm_app = smooth_axis_monotone(apret.appr[col])
+            sm_ret = smooth_axis_monotone(apret.retr[col])
 
-            # Make sure that approach always comes before retract
-            begin = np.where(app_idx)[0]
-            end = np.where(ret_idx)[0]
-            assert(np.all(end-begin > 0)), "Found retract before approach!"
-
-            # If everything is ok, we can add the new columns
-            apret[d] = np.concatenate((sm_app, sm_ret))
+            # Replace the column data
+            apret.appr[col] = sm_app
+            apret.retr[col] = sm_ret
 
 
 #: Available preprocessors

setup.py

@@ -31,7 +31,7 @@
     license="GPL v3",
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
-    install_requires=["afmformats>=0.16.0",
+    install_requires=["afmformats>=0.16.3",
                       "h5py>=2.8.0",
                       "lmfit>=1",
                       "numpy>=1.16.0",  # cython build

tests/test_indent2.py

@@ -16,13 +16,17 @@
 def test_app_ret():
     grp = IndentationGroup(jpkfile)
     idnt = grp[0]
+    idnt.apply_preprocessing(["compute_tip_position"])
+    height = np.array(idnt["height (measured)"], copy=True)
+    tip_position = np.array(idnt["tip position"], copy=True)
     idnt.apply_preprocessing(["smooth_height"])
-    hms = np.array(idnt["height (measured, smoothed)"])
+    hms = np.array(idnt["height (measured)"])
+    assert not np.all(height == hms)
     idnt.apply_preprocessing(["compute_tip_position",
                               "smooth_height"])
-    hms2 = np.array(idnt["height (measured, smoothed)"])
+    hms2 = np.array(idnt["height (measured)"])
     assert np.all(hms == hms2)
-    np.array(idnt["tip position (smoothed)"])
+    assert not np.all(idnt["tip position"] == tip_position)
 
 
 def test_tip_sample_separation():

tests/test_preproc.py

@@ -1,6 +1,7 @@
 """Test preprocessing"""
 import pathlib
 
+import numpy as np
 import pytest
 
 from nanite import IndentationGroup
@@ -57,6 +58,23 @@ def test_process_bad():
             idnt.fit_model()
 
 
+@pytest.mark.filterwarnings(
+    'ignore::nanite.smooth.DoubledSmoothingWindowWarning:')
+def test_smooth():
+    idnt = IndentationGroup(data_path / "spot3-0192.jpk-force")[0]
+    idnt.apply_preprocessing(["compute_tip_position",
+                              "correct_force_offset",
+                              "correct_tip_offset"])
+    orig = np.array(idnt["tip position"], copy=True)
+    # now apply smoothing filter
+    idnt.apply_preprocessing(["compute_tip_position",
+                              "correct_force_offset",
+                              "correct_tip_offset",
+                              "smooth_height"])
+    new = np.array(idnt["tip position"], copy=True)
+    assert not np.all(orig == new)
+
+
 def test_unknown_method():
     idnt = IndentationGroup(data_path / "spot3-0192.jpk-force")[0]
     with pytest.raises(KeyError, match="unknown_method"):