move tests to unit/integration

jveitchmichaelis · Aug 12, 2023 · 4f52b53 · 4f52b53
1 parent 833d265
commit 4f52b53
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Showing 19 changed files with 103 additions and 84 deletions.
diff --git a/.gitignore b/.gitignore
@@ -131,11 +131,13 @@ dmypy.json
 iframe_figures/
 
 # test output
-test/*.json
+test*.json
 test/*.npy
 test/*.png
 
-test/test_output/*
+test/unit/test_output/*
+test/integration/test_output/*
+
 
 examples/output
 

diff --git a/test/test_effective_pixel.py → test/integration/test_effective_pixel.py b/test/test_effective_pixel.py → test/integration/test_effective_pixel.py
diff --git a/test/test_fitted_coefficients.py → test/integration/test_fitted_coefficients.py b/test/test_fitted_coefficients.py → test/integration/test_fitted_coefficients.py
diff --git a/test/test_lt_sprat_auto_atlas.py → test/integration/test_lt_sprat_auto_atlas.py b/test/test_lt_sprat_auto_atlas.py → test/integration/test_lt_sprat_auto_atlas.py
diff --git a/test/test_lt_sprat_manual_atlas.py → ...integration/test_lt_sprat_manual_atlas.py b/test/test_lt_sprat_manual_atlas.py → ...integration/test_lt_sprat_manual_atlas.py
@@ -80,23 +80,22 @@
     7967.34,
     8057.258,
 ]
-element = ["Xe"] * len(sprat_atlas_lines)
 
 user_atlas = Atlas(
     source="manual",
     wavelengths=sprat_atlas_lines,
     min_wavelength=3800.0,
     max_wavelength=8200.0,
     range_tolerance=200.0,
-    elements=element,
+    element="Xe",
     pressure=pressure,
     temperature=temperature,
     relative_humidity=relative_humidity,
 )
 
 config = {
     "log_level": "INFO",
-    "data": {
+    "detector": {
         "contiguous_range": None,
         "detector_min_wave": 3500.0,
         "detector_max_wave": 8200.0,
@@ -116,7 +115,6 @@
         "top_n_candidate": 5,
         "filter_close": True,
     },
-    "atlases": {...},
 }
 
 

diff --git a/test/test_matched_peaks.py → test/integration/test_matched_peaks.py b/test/test_matched_peaks.py → test/integration/test_matched_peaks.py
@@ -109,12 +109,11 @@ def calibrator(base_dir):
         7967.34,
         8057.258,
     ]
-    element = ["Xe"] * len(wavelengths)
 
     user_atlas = Atlas(
         source="manual",
         wavelengths=wavelengths,
-        elements=element,
+        element="Xe",
         min_wavelength=3500.0,
         max_wavelength=8100.0,
     )
@@ -139,7 +138,7 @@ def calibrator(base_dir):
 
     c.atlas.clear()
     assert len(a.atlas_lines) == 0
-    a.add_user_atlas(elements=elements, wavelengths=wavelengths)
+    a.add_user_atlas(element="Xe", wavelengths=wavelengths)
     c.set_atlas(a)
     c.atlas.remove_atlas_lines_range(9999.0)
     assert len(c.atlas.atlas_lines) == len(wavelengths) - 1

diff --git a/test/test_output/.gitignore b/test/test_output/.gitignore
diff --git a/test/test_atlas.py → test/unit/test_atlas.py b/test/test_atlas.py → test/unit/test_atlas.py
diff --git a/test/test_atlas_yaml_config.py → test/unit/test_atlas_yaml_config.py b/test/test_atlas_yaml_config.py → test/unit/test_atlas_yaml_config.py
diff --git a/test/test_config.yaml → test/unit/test_config.yaml b/test/test_config.yaml → test/unit/test_config.yaml
diff --git a/test/test_hough_transform.py → test/unit/test_hough_transform.py b/test/test_hough_transform.py → test/unit/test_hough_transform.py
diff --git a/test/test_init.py → test/unit/test_init.py b/test/test_init.py → test/unit/test_init.py
diff --git a/test/test_polynomial_fit.py → test/unit/test_polynomial_fit.py b/test/test_polynomial_fit.py → test/unit/test_polynomial_fit.py
@@ -12,31 +12,40 @@
 
 np.random.seed(0)
 
-peaks = np.sort(np.random.random(31) * 1000.0)
+num_pix = 1000
+peaks = np.sort(np.random.random(31) * float(num_pix))
 # Removed the closely spaced peaks
 distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
 distance_mask = np.insert(distance_mask, 0, False)
 peaks = peaks[~distance_mask]
 
 # Line list
-wavelengths_linear = 3000.0 + 5.0 * peaks
+linear_grad = 5
+min_wavelength = 3000
+max_wavelength = 3000 + linear_grad * num_pix
+
+wavelengths_linear = 3000.0 + linear_grad * peaks
 wavelengths_quadratic = 3000.0 + 4 * peaks + 1.0e-3 * peaks**2.0
 
-elements_linear = ["Linear"] * len(wavelengths_linear)
-elements_quadratic = ["Quadratic"] * len(wavelengths_quadratic)
+detector_config = {
+    "contiguous_range": None,
+    "num_pix": num_pix,
+    "detector_min_wave": min_wavelength,
+    "detector_max_wave": max_wavelength,
+}
 
 
 def test_linear_fit():
     atlas = Atlas(
         source="manual",
         wavelengths=wavelengths_linear,
-        min_wavelength=3500.0,
+        min_wavelength=3000.0,
         max_wavelength=8000.0,
-        elements=elements_linear,
+        element="linear",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 1000,
             "range_tolerance": 200.0,
@@ -46,6 +55,8 @@ def test_linear_fit():
         "ransac": {
             "minimum_matches": 20,
             "minimum_fit_error": 1e-25,
+            "max_tries": 500,
+            "degree": 1,
         },
     }
 
@@ -55,11 +66,10 @@ def test_linear_fit():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(max_tries=500, fit_deg=1)
-    print(res)
+    res = c.fit()
+
     # Refine solution
     res = c.match_peaks(res["fit_coeff"], refine=False, robust_refit=True)
-
     assert np.abs(res["fit_coeff"][1] - 5.0) / 5.0 < 0.001
     assert np.abs(res["fit_coeff"][0] - 3000.0) / 3000.0 < 0.001
     assert res["peak_utilisation"] > 0.8
@@ -73,11 +83,11 @@ def test_manual_refit():
         wavelengths=wavelengths_linear,
         min_wavelength=3500.0,
         max_wavelength=8000.0,
-        elements=elements_linear,
+        element="linear",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 1000,
             "range_tolerance": 500.0,
@@ -87,6 +97,8 @@ def test_manual_refit():
         "ransac": {
             "minimum_matches": 20,
             "minimum_fit_error": 1e-25,
+            "max_tries": 500,
+            "degree": 1,
         },
     }
 
@@ -96,7 +108,7 @@ def test_manual_refit():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(max_tries=500, fit_deg=1)
+    res = c.fit()
 
     # Refine solution
     res = c.match_peaks(res["fit_coeff"], refine=False, robust_refit=True)
@@ -109,13 +121,13 @@ def test_manual_refit_remove_points():
     atlas = Atlas(
         source="manual",
         wavelengths=wavelengths_linear,
-        min_wavelength=3500.0,
+        min_wavelength=3000.0,
         max_wavelength=8000.0,
-        elements=elements_linear,
+        element="linear",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 1000,
             "range_tolerance": 500.0,
@@ -125,6 +137,8 @@ def test_manual_refit_remove_points():
         "ransac": {
             "minimum_matches": 20,
             "minimum_fit_error": 1e-25,
+            "max_tries": 500,
+            "degree": 1,
         },
     }
 
@@ -134,7 +148,7 @@ def test_manual_refit_remove_points():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(max_tries=500, fit_deg=1)
+    res = c.fit()
 
     # Refine solution
     res = c.match_peaks(res["fit_coeff"], refine=False, robust_refit=True)
@@ -152,11 +166,11 @@ def test_manual_refit_add_points():
         wavelengths=wavelengths_linear,
         min_wavelength=3500.0,
         max_wavelength=8000.0,
-        elements=elements_linear,
+        element="linear",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 1000,
             "range_tolerance": 500.0,
@@ -166,6 +180,8 @@ def test_manual_refit_add_points():
         "ransac": {
             "minimum_matches": 20,
             "minimum_fit_error": 1e-25,
+            "max_tries": 500,
+            "degree": 1,
         },
     }
 
@@ -175,7 +191,7 @@ def test_manual_refit_add_points():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(max_tries=500, fit_deg=1)
+    res = c.fit()
 
     # Refine solution
     res = c.match_peaks(res["fit_coeff"], refine=False, robust_refit=True)
@@ -190,13 +206,13 @@ def test_quadratic_fit():
     atlas = Atlas(
         source="manual",
         wavelengths=wavelengths_quadratic,
-        min_wavelength=3500.0,
+        min_wavelength=3000.0,
         max_wavelength=8000.0,
-        elements=elements_quadratic,
+        element="quadratic",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 1000,
             "range_tolerance": 500.0,
@@ -206,6 +222,10 @@ def test_quadratic_fit():
         "ransac": {
             "minimum_matches": 20,
             "minimum_fit_error": 1e-25,
+            "max_tries": 2000,
+            "rms_tolerance": 5.0,
+            "inlier_tolerance": 2.0,
+            "degree": 2,
         },
     }
 
@@ -215,14 +235,12 @@ def test_quadratic_fit():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(
-        max_tries=2000, fit_tolerance=5.0, candidate_tolerance=2.0, fit_deg=2
-    )
+    res = c.fit()
     # Refine solution
     res_robust = c.match_peaks(
         res["fit_coeff"], refine=False, robust_refit=True
     )
-
+    print(res_robust["fit_coeff"])
     assert np.abs(res_robust["fit_coeff"][2] - 1e-3) / 1e-3 < 0.001
     assert np.abs(res_robust["fit_coeff"][1] - 4.0) / 4.0 < 0.001
     assert np.abs(res_robust["fit_coeff"][0] - 3000.0) / 3000.0 < 0.001
@@ -234,13 +252,13 @@ def test_quadratic_fit_legendre():
     atlas = Atlas(
         source="manual",
         wavelengths=wavelengths_quadratic,
-        min_wavelength=3500.0,
+        min_wavelength=3000.0,
         max_wavelength=8000.0,
-        elements=elements_quadratic,
+        element="quadratic",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 500,
             "range_tolerance": 200.0,
@@ -251,6 +269,11 @@ def test_quadratic_fit_legendre():
             "sample_size": 5,
             "minimum_matches": 10,
             "minimum_fit_error": 1e-25,
+            "max_tries": 10000,
+            "rms_tolerance": 5.0,
+            "inlier_tolerance": 2.0,
+            "degree": 2,
+            "fit_type": "legendre",
         },
     }
 
@@ -260,13 +283,7 @@ def test_quadratic_fit_legendre():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(
-        max_tries=10000,
-        fit_tolerance=5.0,
-        candidate_tolerance=2.0,
-        fit_deg=2,
-        fit_type="legendre",
-    )
+    res = c.fit()
 
     # Legendre 2nd order takes the form
     assert np.abs(res["fit_coeff"][1] - 4.0) / 4.0 < 0.001
@@ -279,13 +296,13 @@ def test_quadratic_fit_chebyshev():
     atlas = Atlas(
         source="manual",
         wavelengths=wavelengths_quadratic,
-        min_wavelength=3500.0,
+        min_wavelength=3000.0,
         max_wavelength=8000.0,
-        elements=elements_quadratic,
+        element="quadratic",
     )
 
     config = {
-        "data": {"contiguous_range": None, "num_pix": 1000},
+        "detector": detector_config,
         "hough": {
             "num_slopes": 500,
             "range_tolerance": 200.0,
@@ -296,6 +313,11 @@ def test_quadratic_fit_chebyshev():
             "sample_size": 5,
             "minimum_matches": 10,
             "minimum_fit_error": 1e-25,
+            "max_tries": 10000,
+            "rms_tolerance": 5.0,
+            "inlier_tolerance": 2.0,
+            "degree": 2,
+            "fit_type": "chebyshev",
         },
     }
 
@@ -305,13 +327,7 @@ def test_quadratic_fit_chebyshev():
     c.do_hough_transform(brute_force=False)
 
     # Run the wavelength calibration
-    res = c.fit(
-        max_tries=10000,
-        fit_tolerance=5.0,
-        candidate_tolerance=2.0,
-        fit_deg=2,
-        fit_type="chebyshev",
-    )
+    res = c.fit()
 
     assert np.abs(res["fit_coeff"][1] - 4.0) / 4.0 < 0.001
     assert np.abs(res["fit_coeff"][0] - 3000.0) / 3000.0 < 0.001

diff --git a/test/test_ransac.py → test/unit/test_ransac.py b/test/test_ransac.py → test/unit/test_ransac.py
@@ -2,11 +2,12 @@
 from functools import partialmethod
 
 import numpy as np
-from rascal.ransac import RansacSolver
 
 # Suppress tqdm output
 from tqdm import tqdm
 
+from rascal.ransac import RansacSolver
+
 tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)