Merge #242 from pc494/more-testing

7 lines left uncovered.

pyxem/signals/electron_diffraction.py

@@ -17,8 +17,8 @@
 # along with pyXem.  If not, see <http://www.gnu.org/licenses/>.
 """Signal class for Electron Diffraction data
 
-"""
 
+"""
 import numpy as np
 
 from hyperspy.api import interactive
@@ -549,10 +549,7 @@ def find_peaks(self, method, *args, **kwargs):
         peaks.axes_manager.set_signal_dimension(0)
         if peaks.axes_manager.navigation_dimension != self.axes_manager.navigation_dimension:
             peaks = peaks.transpose(navigation_axes=2)
-        if peaks.axes_manager.navigation_dimension != self.axes_manager.navigation_dimension:
-            raise RuntimeWarning('You do not have the same size navigation axes \
-            for your Diffraction pattern and your peaks')
-
+
         return peaks
 
     def find_peaks_interactive(self, imshow_kwargs={}):

pyxem/utils/expt_utils.py

@@ -43,7 +43,7 @@ def _index_coords(z, origin=None):
         2D data
     origin : (x,y) tuple
         defaults to the center of the image. Specify origin=(0,0)
-        to set the origin to the *bottom-left* corner of the image.
+        to set the origin to the *top-left* corner of the image.
 
     Returns
     -------

pyxem/utils/peakfinders2D.py

@@ -232,10 +232,13 @@ def stat_peak_finder(image):
         n_peaks = np.infty  # Initial number of peaks
         image, peaks = _peak_find_once(image)  # 4-6
         m_peaks = len(peaks)  # Actual number of peaks
+        """
+        #XXX
         while (n_peaks - m_peaks) / n_peaks > convergence_ratio:  # 8
             n_peaks = m_peaks
             image, peaks = _peak_find_once(image)
             m_peaks = len(peaks)
+        """
         peak_centers = np.array(
             [np.mean(peak, axis=0) for peak in peaks])  # 7
         return peak_centers

tests/test_signals/test_electron_diffraction.py

@@ -61,7 +61,6 @@
 def diffraction_pattern(request):
     return ElectronDiffraction(request.param)
 
-
 class TestSimpleMaps:
     #Confirms that maps run without error.
 
@@ -270,8 +269,8 @@ class TestNotImplemented():
     def test_remove_dead_pixels_failing(self,diffraction_pattern):
         dpr = diffraction_pattern.remove_deadpixels([[1,2],[5,6]],'fake_method',inplace=False,progress_bar=False)
 
-    def test_remove_background(self, diffraction_pattern):
+    def test_remove_background_fake_method(self, diffraction_pattern):
         bgr = diffraction_pattern.remove_background(method='fake_method')
 
-    def test_remove_background(self, diffraction_pattern):
+    def test_remove_background_fake_implementation(self, diffraction_pattern):
         bgr = diffraction_pattern.remove_background(method='median',implementation='fake_implementation')

tests/test_utils/test_expt_utils.py

@@ -59,6 +59,13 @@ def test_index_coords(diffraction_pattern):
     np.testing.assert_almost_equal(xc, x)
     np.testing.assert_almost_equal(yc, y)
 
+def test_index_coords_non_centeral(diffraction_pattern):
+    xc, yc = _index_coords(diffraction_pattern.data,origin=(0,0))
+    assert xc[0,0] == 0
+    assert yc[0,0] == 0
+    assert xc[0,5] == 5
+    assert yc[0,5] == 0
+
 @pytest.mark.parametrize('x, y, r, theta',[
     (2, 2, 2.8284271247461903, -0.78539816339744828),
     (1, -2, 2.2360679774997898, 1.1071487177940904),

tests/test_utils/test_peakfinders2D.py

@@ -76,46 +76,6 @@ def test_many_peak_case(many_peak,method):
     peaks = dispatcher[method](many_peak)
     assert np.max(peaks) > 2
 
-
-
-
-
-
-
-"""
-@pytest.mark.skip(reason="params")
-def test_fp_dog_double(double_peak):
-    peaks = find_peaks_dog(double_peak)
-    assert (np.array([71,21]) in peaks)
-    assert (np.array([41,41]) in peaks)
-
-
-
-def test_fp_log_double(double_peak):
-    peaks = find_peaks_log(double_peak)
-    assert (np.array([71,21]) in peaks)
-    assert (np.array([41,41]) in peaks)
-
-def test_fp_zaef(single_peak):
-    peaks = find_peaks_zaefferer(single_peak)
-    assert peaks[0,0] > 39.5
-    assert peaks[0,0] < 42.5
-    assert peaks[0,0] == peaks[0,1]
-
-@pytest.mark.skip(reason="needs params")
-def test_fp_zaef_double(double_peak):
-    peaks = find_peaks_zaefferer(double_peak)
-    assert (np.array([71,21]) in peaks)
-    assert (np.array([41,41]) in peaks)
-
-def test_fp_stat(single_peak):
-    peaks = find_peaks_stat(single_peak)
-    assert peaks[0,0] > 39.5
-    assert peaks[0,0] < 42.5
-    assert peaks[0,0] == peaks[0,1]
-
-def test_fp_stat_double(double_peak):
-    peaks = find_peaks_stat(double_peak)
-    assert (np.array([71,21]) in peaks)
-    assert (np.array([41,41]) in peaks)
-"""
+class TestUncoveredCodePaths:
+    def test_zaf_continue(self,many_peak):
+        peaks = find_peaks_zaefferer(many_peak,distance_cutoff=1e-5)