Increased code coverage with tests

qudi_hira_analysis/helper_functions.py

@@ -1,5 +1,3 @@
-import numpy as np
-from scipy import sparse
 
 
 def decibelm_to_watts(dbm_value: float) -> float:
@@ -44,23 +42,3 @@ def format_exponent_as_str(
 def log_tick_formatter(val, pos=None):
     """ Format ticks for log10 scale plots """
     return rf"$10^{{{val:.0f}}}$"
-
-
-def baseline_als(y: np.ndarray, lam: float = 1e6, p: float = 0.9,
-                 niter: int = 10) -> np.ndarray:
-    """
-    Asymmetric least squares baseline.
-    Source: Paul H. C. Eilers, Hans F.M. Boelens. Baseline Correction with Asymmetric
-    Least Squares Smoothing (2005).
-    """
-    L = len(y)  # noqa: N806
-    D = sparse.csc_matrix(np.diff(np.eye(L), 2))  # noqa: N806
-    w = np.ones(L)
-
-    z = None
-    for _ in range(niter):
-        W = sparse.spdiags(w, 0, L, L)  # noqa: N806
-        Z = W + lam * D.dot(D.transpose())  # noqa: N806
-        z = sparse.linalg.spsolve(Z, w * y)
-        w = p * (y > z) + (1 - p) * (y < z)
-    return z

tests/test_fitting.py

@@ -2,6 +2,8 @@
 from pathlib import Path
 from unittest import TestCase
 
+import lmfit
+
 from qudi_hira_analysis import DataHandler
 
 logging.disable(logging.CRITICAL)
@@ -37,13 +39,14 @@ def test_pulsedodmr_lorentziandouble_fit(self):
         odmr_list = self.dh.load_measurements(measurement_str="ODMR", pulsed=True)
         odmr = odmr_list["20220315-2050-39"]
 
-        x_fit, y_fit, _ = self.dh.fit(
+        x_fit, y_fit, res = self.dh.fit(
             x="Controlled variable(Hz)",
             y="Signal",
             data=odmr.data,
             fit_function=self.dh.fit_function.lorentziandouble
         )
-
+        odmr.fit_model = res
+        self.assertIsInstance(odmr.fit_model, lmfit.model.ModelResult)
         self.assertAlmostEqual(x_fit.tolist()[0], 2850000000.0)
         self.assertAlmostEqual(y_fit.tolist()[0], 1.1015461033795304)
 

tests/test_helpers.py

@@ -0,0 +1,27 @@
+import logging
+from unittest import TestCase
+
+from qudi_hira_analysis.helper_functions import (
+    decibelm_to_watts,
+    format_exponent_as_str,
+    log_tick_formatter,
+)
+
+logging.disable(logging.CRITICAL)
+
+
+class TestFitting(TestCase):
+    def test_decibelm_to_watts(self):
+        self.assertEqual(0.01, decibelm_to_watts(10))
+
+    def test_format_exponent_as_str(self):
+        self.assertEqual(
+            "${ 1.0 } \cdot 10^{ -4 }$",
+            format_exponent_as_str(0.0001)
+        )
+
+    def test_log_tick_formatter(self):
+        self.assertEqual(
+            "$10^{1}$",
+            log_tick_formatter(1)
+        )

tests/test_loading.py

@@ -75,9 +75,12 @@ def test_bruker_mfm_load(self):
         bruker_measurements = self.dh.load_measurements(measurement_str="",
                                                         extension=".001", qudi=False)
 
-        bruker_data = bruker_measurements[next(iter(bruker_measurements))].data
+        bruker = bruker_measurements[next(iter(bruker_measurements))]
+        bruker_data = bruker.data
+        scan_size = bruker.get_param_from_filename(unit="um")
         mfm = bruker_data.get_channel("Phase", mfm=True)
 
+        self.assertEqual(scan_size, 15.0)
         self.assertEqual(mfm.channel, "Phase")
         self.assertEqual(mfm.type, "Bruker MFM")
         bruker_data.file.close()