write *correct* determineDistortion() tests

Author: chris-simpson

geminidr/f2/tests/longslit/test_determine_distortion.py

@@ -214,21 +214,25 @@ def test_regression_for_determine_distortion_using_wcs(
         distortion_determined_ad = p.writeOutputs().pop()
 
     ref_ad = ref_ad_factory(distortion_determined_ad.filename)
-    model = distortion_determined_ad[0].wcs.pipeline[
-        distortion_determined_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[2]
-    ref_model = ref_ad[0].wcs.pipeline[
-        ref_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[2]
+
+    # Confirm that the distortion model is placed after the rectification model
+    assert (distortion_determined_ad.wcs.avilable_frames.index("distortion_corrected") >
+            distortion_determined_ad.wcs.avilable_frames.index("rectified"))
+    assert (ref_ad.wcs.avilable_frames.index("distortion_corrected") >
+            ref_ad.wcs.avilable_frames.index("rectified"))
+
+    model = distortion_determined_ad[0].wcs.get_transform("pixels", "distortion_corrected")
+    ref_model = ref_ad[0].wcs.get_transform("pixels", "distortion_corrected")
 
     # Otherwise we're doing something wrong!
-    assert model.__class__.__name__ == ref_model.__class__.__name__ == "Chebyshev2D"
+    assert model[-1].__class__.__name__ == ref_model[-1].__class__.__name__ == "Chebyshev2D"
 
-    X, Y = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
+    Y, X = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
 
     # We only care about pixels in the illuminated region
     xx, yy = X[ad[0].mask == 0], Y[ad[0].mask == 0]
-    np.testing.assert_allclose(model(xx, yy), ref_model(xx, yy), atol=1)
+    diffs = model(xx, yy)[1] - ref_model(xx, yy)[1]  # 1 is y-axis in astropy
+    np.testing.assert_allclose(diffs, 0, atol=1)
 
 
 @pytest.mark.f2ls

geminidr/gnirs/tests/crossdispersed/test_determine_distortion.py

@@ -61,21 +61,25 @@ def test_regression_for_determine_distortion_using_wcs(
 
     ref_ad = ref_ad_factory(distortion_determined_ad.filename)
     for ext, ref_ext in zip(distortion_determined_ad, ref_ad):
-        model = ext.wcs.pipeline[
-            ext.wcs.available_frames.index(
-                "distortion_corrected") - 1].transform[2]
-        ref_model = ref_ext.wcs.pipeline[
-            ref_ext.wcs.available_frames.index(
-                "distortion_corrected") - 1].transform[2]
+        # Confirm that the distortion model is placed after the rectification model
+        assert (ext.wcs.avilable_frames.index("distortion_corrected") >
+                ext.wcs.avilable_frames.index("rectified"))
+        assert (ref_ext.wcs.avilable_frames.index("distortion_corrected") >
+                ref_ext.wcs.avilable_frames.index("rectified"))
+
+        model = ext.wcs.get_transform("pixels", "distortion_corrected")
+        ref_model = ref_ext.wcs.get_transform("pixels", "distortion_corrected")
 
         # Otherwise we're doing something wrong!
-        assert model.__class__.__name__ == ref_model.__class__.__name__ == "Chebyshev2D"
+        assert model[-1].__class__.__name__ == ref_model[-1].__class__.__name__ == "Chebyshev2D"
 
         Y, X = np.mgrid[:ext.shape[0], :ext.shape[1]]
 
         # We only care about pixels in the illuminated region
         xx, yy = X[ext.mask == 0], Y[ext.mask == 0]
-        np.testing.assert_allclose(model(xx, yy), ref_model(xx, yy), atol=1)
+        diffs = model(xx, yy)[1] - ref_model(xx, yy)[1]  # 1 is y-axis in astropy
+        np.testing.assert_allclose(diffs, 0, atol=1)
+
 
 # Local Fixtures and Helper Functions ------------------------------------------
 @pytest.fixture(scope='function')

geminidr/gnirs/tests/longslit/test_determine_distortion.py

@@ -115,22 +115,25 @@ def test_regression_for_determine_distortion_using_wcs(
         distortion_determined_ad = p.writeOutputs().pop()
 
     ref_ad = ref_ad_factory(distortion_determined_ad.filename)
-    model = distortion_determined_ad[0].wcs.pipeline[
-        distortion_determined_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[2]
-    ref_model = ref_ad[0].wcs.pipeline[
-        ref_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[2]
-    # do_plots(ad, ref_ad)
+
+    # Confirm that the distortion model is placed after the rectification model
+    assert (distortion_determined_ad.wcs.avilable_frames.index("distortion_corrected") >
+            distortion_determined_ad.wcs.avilable_frames.index("rectified"))
+    assert (ref_ad.wcs.avilable_frames.index("distortion_corrected") >
+            ref_ad.wcs.avilable_frames.index("rectified"))
+
+    model = distortion_determined_ad[0].wcs.get_transform("pixels", "distortion_corrected")
+    ref_model = ref_ad[0].wcs.get_transform("pixels", "distortion_corrected")
 
     # Otherwise we're doing something wrong!
-    assert model.__class__.__name__ == ref_model.__class__.__name__ == "Chebyshev2D"
+    assert model[-1].__class__.__name__ == ref_model[-1].__class__.__name__ == "Chebyshev2D"
 
-    X, Y = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
+    Y, X = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
 
     # We only care about pixels in the illuminated region
     xx, yy = X[ad[0].mask == 0], Y[ad[0].mask == 0]
-    np.testing.assert_allclose(model(xx, yy), ref_model(xx, yy), atol=1)
+    diffs = model(xx, yy)[1] - ref_model(xx, yy)[1]  # 1 is y-axis in astropy
+    np.testing.assert_allclose(diffs, 0, atol=1)
 
 
 @pytest.mark.gnirs

geminidr/niri/tests/longslit/test_determine_distortion.py

@@ -94,19 +94,26 @@ def test_regression_for_determine_distortion_using_wcs(
         distortion_determined_ad = p.writeOutputs().pop()
 
     ref_ad = ref_ad_factory(distortion_determined_ad.filename)
-    model = distortion_determined_ad[0].wcs.pipeline[
-        distortion_determined_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[1]
-    ref_model = ref_ad[0].wcs.pipeline[
-        ref_ad[0].wcs.available_frames.index(
-            "distortion_corrected")-1].transform[1]
+
+    # Confirm that the distortion model is placed after the rectification model
+    assert (distortion_determined_ad.wcs.avilable_frames.index("distortion_corrected") >
+            distortion_determined_ad.wcs.avilable_frames.index("rectified"))
+    assert (ref_ad.wcs.avilable_frames.index("distortion_corrected") >
+            ref_ad.wcs.avilable_frames.index("rectified"))
+
+    model = distortion_determined_ad[0].wcs.get_transform("pixels", "distortion_corrected")
+    ref_model = ref_ad[0].wcs.get_transform("pixels", "distortion_corrected")
 
     # Otherwise we're doing something wrong!
-    assert model.__class__.__name__ == ref_model.__class__.__name__ == "Chebyshev2D"
+    # This distortion model modifies x so an Identity(1) will be after it for y
+    assert model[-2].__class__.__name__ == ref_model[-2].__class__.__name__ == "Chebyshev2D"
 
-    X, Y = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
+    Y, X = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
 
-    np.testing.assert_allclose(model(X, Y), ref_model(X, Y), atol=1)
+    # We only care about pixels in the illuminated region
+    xx, yy = X[ad[0].mask == 0], Y[ad[0].mask == 0]
+    diffs = model(xx, yy)[0] - ref_model(xx, yy)[0]  # 0 is x-axis in astropy
+    np.testing.assert_allclose(diffs, 0, atol=1)
 
 
 @pytest.mark.nirils

gempy/library/peak_finding.py

@@ -681,7 +681,7 @@ def find_wavelet_peaks(data, widths=None, mask=None, variance=None, min_snr=1, m
     # the width and 1.0^ + 0.75^2 = 1.25^2).
     snr = np.divide(wavelet_transformed_data[0], np.sqrt(variance),
                     out=np.zeros_like(data, dtype=np.float32),
-                    where=variance > 0) * np.sqrt(2)
+                    where=variance > 0) * 1.25
 
     peaks = [x for x in peaks if snr[x] > min_snr]