add files

tests/spectraVictor2/order0/known_to_fail.yaml

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tests/spectraVictor2/order0/known_value_large_tol.yaml

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tests/spectraVictor2/order1/known_to_fail.yaml

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tests/test_fft.py

@@ -0,0 +1,28 @@
+import os.path
+import numpy as np
+from numpy.testing import assert_allclose
+import pytest
+
+from optifik.fft import thickness_from_fft
+from optifik.analysis import smooth_intensities
+from optifik.io import load_spectrum
+
+
+def test_FFT():
+    FOLDER = os.path.join('tests', 'basic')
+    FILE_NAME = '003582.xy'
+    expected = 3524.51
+
+    spectrum_path = os.path.join(FOLDER, FILE_NAME)
+    lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
+    smoothed_intensities = smooth_intensities(raw_intensities)
+    r_index =  1.324188 + 3102.060378 / (lambdas**2)
+
+    thickness_FFT = thickness_from_fft(lambdas,
+                                       smoothed_intensities,
+                                       refractive_index=r_index)
+    result = thickness_FFT.thickness
+
+    assert_allclose(result, expected, rtol=1e-1)
+
+

tests/test_minmax.py

@@ -0,0 +1,54 @@
+import os.path
+import numpy as np
+from numpy.testing import assert_allclose
+import pytest
+
+from optifik.minmax import thickness_from_minmax
+from optifik.analysis import smooth_intensities
+from optifik.io import load_spectrum
+
+
+def test_minmax_ransac():
+    FOLDER = os.path.join('tests', 'basic')
+    FILE_NAME = '000004310.xy'
+    expected = 1338.35
+
+    spectrum_path = os.path.join(FOLDER, FILE_NAME)
+    lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
+    smoothed_intensities = smooth_intensities(raw_intensities)
+    r_index =  1.324188 + 3102.060378 / (lambdas**2)
+
+    prominence = 0.02
+
+    result = thickness_from_minmax(lambdas,
+                                   smoothed_intensities,
+                                   refractive_index=r_index,
+                                   min_peak_prominence=prominence,
+                                   method='ransac',
+                                   plot=False)
+
+    assert_allclose(result.thickness, expected, rtol=1e-1)
+
+
+def test_minmax_linreg():
+    FOLDER = os.path.join('tests', 'basic')
+    FILE_NAME = '000004310.xy'
+    expected = 1338.35
+
+    spectrum_path = os.path.join(FOLDER, FILE_NAME)
+    lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
+    smoothed_intensities = smooth_intensities(raw_intensities)
+    r_index =  1.324188 + 3102.060378 / (lambdas**2)
+
+    prominence = 0.02
+
+    result = thickness_from_minmax(lambdas,
+                                   smoothed_intensities,
+                                   refractive_index=r_index,
+                                   min_peak_prominence=prominence,
+                                   method='linreg',
+                                   plot=False)
+
+    assert_allclose(result.thickness, expected, rtol=1e-1)
+
+

tests/test_scheludko.py

@@ -3,55 +3,12 @@ import numpy as np
 from numpy.testing import assert_allclose
 import pytest
 
-from optifik.fft import thickness_from_fft
-from optifik.minmax import thickness_from_minmax
 from optifik.scheludko import thickness_from_scheludko
 from optifik.scheludko import get_default_start_stop_wavelengths
-from optifik.scheludko import thickness_for_order0
 from optifik.analysis import smooth_intensities
 from optifik.io import load_spectrum
 
 
-def test_FFT():
-    FOLDER = os.path.join('tests', 'basic')
-    FILE_NAME = '003582.xy'
-    expected = 3524.51
-
-    spectrum_path = os.path.join(FOLDER, FILE_NAME)
-    lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
-    smoothed_intensities = smooth_intensities(raw_intensities)
-    r_index =  1.324188 + 3102.060378 / (lambdas**2)
-
-    thickness_FFT = thickness_from_fft(lambdas,
-                                       smoothed_intensities,
-                                       refractive_index=r_index)
-    result = thickness_FFT.thickness
-
-    assert_allclose(result, expected, rtol=1e-1)
-
-
-def test_minmax_ransac():
-    FOLDER = os.path.join('tests', 'basic')
-    FILE_NAME = '000004310.xy'
-    expected = 1338.35
-
-    spectrum_path = os.path.join(FOLDER, FILE_NAME)
-    lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
-    smoothed_intensities = smooth_intensities(raw_intensities)
-    r_index =  1.324188 + 3102.060378 / (lambdas**2)
-
-    prominence = 0.02
-
-    result = thickness_from_minmax(lambdas,
-                                   smoothed_intensities,
-                                   refractive_index=r_index,
-                                   min_peak_prominence=prominence,
-                                   method='ransac',
-                                   plot=False)
-
-    assert_allclose(result.thickness, expected, rtol=1e-1)
-
-
 def test_scheludko_4peaks():
     FOLDER = os.path.join('tests', 'basic')
     FILE_NAME = '000005253.xy'
@@ -126,10 +83,15 @@ def test_order0():
     prominence = 0.03
 
 
-    result = thickness_for_order0(lambdas, smoothed_intensities,
-                                  refractive_index=r_index,
-                                             min_peak_prominence=prominence,
-                                             plot=False)
+    w_start, w_stop = None, None
+    result = thickness_from_scheludko(lambdas,
+                                      smoothed_intensities,
+                                      refractive_index=r_index,
+                                      wavelength_start=w_start,
+                                      wavelength_stop=w_stop,
+                                      interference_order=0,
+                                      plot=False)
+
 
     assert_allclose(result.thickness, expected, rtol=1e-1)