Merge pull request #340 from GSTT-CSC/release/2.1.0

Release/2.1.0

CITATION.cff

@@ -43,5 +43,5 @@ date-released: 2022-02-24
 message: "If you use hazen in your work, please cite it using these metadata."
 repository-code: "https://github.com/GSTT-CSC/hazen"
 title: hazen
-version: "1.1.4"
+version: "1.2.0"
 ...

hazenlib/__init__.py

@@ -85,7 +85,7 @@
 'Measured_slice_width' is an optional argument for the SNR function.
 'Log' is an optional argument that allows users to set the severity of the logs.
     <task>    snr | slice_position | slice_width | spatial_resolution | uniformity | ghosting | relaxometry | snr_map |
-    acr_ghosting | acr_uniformity |
+    acr_ghosting | acr_uniformity | acr_spatial_resolution | acr_slice_thickness | acr_snr | acr_slice_position | acr_geometric_accuracy
     <folder>
     --report
 

hazenlib/_version.py

@@ -1 +1 @@
-__version__ = '1.1.4'
+__version__ = '1.2.0'

tests/test_acr_geometric_accuracy.py

@@ -28,11 +28,20 @@ def test_object_centre(self):
     def test_geo_accuracy_slice1(self):
         slice1_vals = np.array(self.acr_geometric_accuracy_task.get_geometric_accuracy_slice1(self.dcm))
         slice1_vals = np.round(slice1_vals, 2)
+
+        print("\ntest_geo_accuracy.py::TestGeoAccuracy::test_geo_accuracy_slice1")
+        print("new_release:", slice1_vals)
+        print("fixed value:", self.L1)
+
         assert (slice1_vals == self.L1).all() == True
 
     def test_geo_accuracy_slice5(self):
         slice5_vals = np.array(self.acr_geometric_accuracy_task.get_geometric_accuracy_slice5(self.dcm2))
         slice5_vals = np.round(slice5_vals, 2)
+
+        print("\ntest_geo_accuracy.py::TestGeoAccuracy::test_geo_accuracy_slice1")
+        print("new_release:", slice5_vals)
+        print("fixed value:", self.L5)
         assert (slice5_vals == self.L5).all() == True
 
     def test_rotate_point(self):

tests/test_acr_ghosting.py

@@ -21,7 +21,13 @@ def test_object_centre(self):
         assert self.acr_ghosting_task.centroid_com(self.dcm.pixel_array)[1] == self.centre
 
     def test_ghosting(self):
-        assert round(self.acr_ghosting_task.get_signal_ghosting(self.dcm), 3) == self.psg
+        ghosting_val = round(self.acr_ghosting_task.get_signal_ghosting(self.dcm), 3)
+
+        print("\ntest_ghosting.py::TestGhosting::test_ghosting")
+        print("new_release_value:", ghosting_val)
+        print("fixed_value:", self.psg)
+
+        assert ghosting_val == self.psg
 
 
 class TestACRGhostingGE(unittest.TestCase):

tests/test_acr_slice_position.py

@@ -42,8 +42,15 @@ def test_wedge_find(self):
                 self.y_pts[1]).all() == True
 
     def test_slice_position(self):
-        assert round(self.acr_slice_position_task.get_slice_position(self.dcm_1), 2) == self.dL[0]
-        assert round(self.acr_slice_position_task.get_slice_position(self.dcm_11), 2) == self.dL[1]
+        slice_position_val_1 = round(self.acr_slice_position_task.get_slice_position(self.dcm_1), 2)
+        slice_position_val_11 = round(self.acr_slice_position_task.get_slice_position(self.dcm_11), 2)
+
+        print("\ntest_slice_position.py::TestSlicePosition::test_slice_position")
+        print("new_release_value:", slice_position_val_1)
+        print("fixed_value:", self.dL[0])
+
+        assert slice_position_val_1 == self.dL[0]
+        assert slice_position_val_11 == self.dL[1]
 
 
 class TestACRSlicePositionGE(unittest.TestCase):

tests/test_acr_slice_thickness.py

@@ -31,7 +31,13 @@ def test_ramp_find(self):
                 self.y_pts).all() == True
 
     def test_slice_thickness(self):
-        assert round(self.acr_slice_thickness_task.get_slice_thickness(self.dcm), 2) == self.dz
+        slice_thickness_val = round(self.acr_slice_thickness_task.get_slice_thickness(self.dcm), 2)
+
+        print("\ntest_slice_thickness.py::TestSliceThickness::test_slice_thickness")
+        print("new_release_value:", slice_thickness_val)
+        print("fixed_value:", self.dz)
+
+        assert slice_thickness_val == self.dz
 
 
 class TestACRSliceThicknessGE(unittest.TestCase):

tests/test_acr_snr.py

@@ -33,7 +33,13 @@ def test_snr_by_smoothing(self):
 
     def test_snr_by_subtraction(self):
         snr, _ = self.acr_snr_task.snr_by_subtraction(self.dcm, self.dcm2)
-        assert round(snr, 2) == self.sub_snr
+        rounded_snr = round(snr, 2)
+
+        print("\ntest_snr_by_subtraction.py::TestSnrBySubtraction::test_snr_by_subtraction")
+        print("new_release_value:", rounded_snr)
+        print("fixed_value:", self.sub_snr)
+
+        assert rounded_snr == self.sub_snr
 
 
 class TestACRSNRGE(unittest.TestCase):

tests/test_acr_spatial_resolution.py

@@ -51,8 +51,13 @@ def test_retrieve_slope(self):
                                                                              self.edge_type[1])[0], 3) == self.slope
 
     def test_get_MTF50(self):
-        assert self.acr_spatial_resolution_task.get_mtf50(self.dcm) == self.MTF50
+        mtf50_val = self.acr_spatial_resolution_task.get_mtf50(self.dcm)
+
+        print("\ntest_get_MTF50.py::TestGetMTF50::test_get_MTF50")
+        print("new_release_value:", mtf50_val)
+        print("fixed_value:", self.MTF50)
 
+        assert mtf50_val == self.MTF50
 
 class TestACRSpatialResolutionGE(unittest.TestCase):
     ACR_SPATIAL_RESOLUTION_DATA = pathlib.Path(TEST_DATA_DIR / 'acr')

tests/test_acr_uniformity.py

@@ -33,7 +33,13 @@ def test_circular_mask(self):
 
     def test_uniformity(self):
         results = self.acr_uniformity_task.get_integral_uniformity(self.dcm)
-        assert round(results, 2) == self.piu
+        rounded_results = round(results, 2)
+
+        print("\ntest_uniformity.py::TestUniformity::test_uniformity")
+        print("new_release_values:", rounded_results)
+        print("fixed_values:", self.piu)
+
+        assert rounded_results == self.piu
 
 
 # class TestACRUniformityPhilips(unittest.TestCase):

tests/test_ghosting.py

@@ -73,7 +73,13 @@ def test_get_ghost_slice(self):
         assert list(self.ghosting.get_ghost_slice(self.SIGNAL_BOUNDING_BOX, self.dcm)[1]) == list(self.GHOST_SLICE[1])
 
     def test_get_ghosting(self):
-        assert self.ghosting.get_ghosting(self.dcm) == self.GHOSTING
+        ghosting_val = self.ghosting.get_ghosting(self.dcm)
+
+        print("\ntest_get_ghosting.py::TestGetGhosting::test_get_ghosting")
+        print("new_release_value:", ghosting_val)
+        print("fixed_value:", self.GHOSTING)
+
+        assert ghosting_val == self.GHOSTING
 
 
 class TestCOLPEGhosting(TestGhosting):

tests/test_slice_position.py

@@ -45,9 +45,14 @@ def test_get_rods_coords(self):
 
     def test_slice_position(self):
         results = self.hazen_slice_position.run()
+        key = self.hazen_slice_position.key(self.hazen_slice_position.data[0])
+        slice_positions = results[key]['slice_positions']
 
-        assert results[self.hazen_slice_position.key(self.hazen_slice_position.data[0])][
-                   'slice_positions'] == self.SLICE_POSITION_OUTPUT
+        print("\ntest_slice_position.py::TestSlicePosition::test_slice_position")
+        print("new_release_value:", slice_positions)
+        print("fixed_value", self.SLICE_POSITION_OUTPUT)
+
+        assert slice_positions == self.SLICE_POSITION_OUTPUT
 
 
 # now test on canon data

tests/test_slice_width.py

@@ -236,12 +236,14 @@ def test_fit_trapezoid(self):
 
     def test_slice_width(self):
         results = self.slice_width.run()
-        self.slice_width.key(self.slice_width.data[0])
-        # key = f"{self.slice_width.data[0].SeriesDescription}_{self.slice_width.data[0].SeriesNumber}_{self.slice_width.data[0].InstanceNumber}"
-        # print("slice width")
-        # print(results[key]['slice_width_mm'])
-        # assert abs(results[key]['slice_width_mm'] - self.SW_MATLAB) < 0.1
-        assert abs(results[self.slice_width.key(self.slice_width.data[0])]['slice_width_mm'] - self.SW_MATLAB) < 0.1
+        key = self.slice_width.key(self.slice_width.data[0])
+        slice_width_mm = results[key]['slice_width_mm']
+
+        print("\ntest_slice_width.py::TestSliceWidth::test_slice_width")
+        print("new_release_value:", slice_width_mm)
+        print("fixed_value:", self.SW_MATLAB)
+
+        assert abs(slice_width_mm - self.SW_MATLAB) < 0.1
 
 
 class Test512Matrix(TestSliceWidth):

tests/test_snr.py

@@ -150,6 +150,9 @@ def test_get_object_centre(self):
 
     def test_image_snr(self):
         val = self.snr.run()
+        print("\ntest_snr.py::TestSnrThreshold::test_image_snr")
+        print("set values:", val)
+        print("new_release_values", self.snr.run())
         self.assertTrue(self.LOWER_SMOOTHED_SNR <= val[self.snr.key(self.snr.data[0])][
             f"snr_smoothing_normalised_{self.snr.key(self.snr.data[0])}"] <= self.UPPER_SMOOTHED_SNR)
         self.assertTrue(self.LOWER_SUBTRACT_SNR <= val[self.snr.key(self.snr.data[0])][

tests/test_snr_map.py

@@ -49,8 +49,13 @@ def test_calc_snr(self):
             self.snr_map.snr, 192.8818801790859)
 
     def test_calc_snr_map(self):
-        np.testing.assert_almost_equal(
-            self.snr_map.snr_map.cumsum().sum(), 128077116718.40483)
+        snr_map_cumsum = self.snr_map.snr_map.cumsum().sum()
+
+        print("\ntest_calc_snr_map.py::TestCalcSnrMap::test_calc_snr_map")
+        print("new_release_value:", snr_map_cumsum)
+        print("fixed_value:", 128077116718.40483)
+
+        np.testing.assert_almost_equal(snr_map_cumsum, 128077116718.40483)
 
     def test_plot_detailed(self):
         # Just check a valid figure handle is returned

tests/test_spatial_resolution.py

@@ -415,9 +415,16 @@ def test_mtf(self):
 
     def test_calculate_mtf(self):
         res = self.hazen_spatial_resolution.calculate_mtf(self.hazen_spatial_resolution.data[0])
-        assert res['frequency_encoding_direction'] == pytest.approx(self.MTF_FE)
-        assert res['phase_encoding_direction'] == pytest.approx(self.MTF_PE)
+        fe_res = res['frequency_encoding_direction']
+        pe_res = res['phase_encoding_direction']
 
+        print("\ntest_calculate_mtf.py::TestCalculateMtf::test_calculate_mtf")
+        print("new_release_value:", fe_res)
+        print("fixed_value:", self.MTF_FE)
+
+
+        assert fe_res == pytest.approx(self.MTF_FE)
+        assert pe_res == pytest.approx(self.MTF_PE)
 
 class TestPhilipsResolution(TestSpatialResolution):
     RESOLUTION_DATA = pathlib.Path(TEST_DATA_DIR / 'resolution')

tests/test_uniformity.py

@@ -17,10 +17,18 @@ def setUp(self):
 
     def test_uniformity(self):
         results = self.uniformity_task.run()
-        assert results[self.uniformity_task.key(self.uniformity_task.data[0])]['horizontal'][
-                   'IPEM'] == self.IPEM_HORIZONTAL
-        assert results[self.uniformity_task.key(self.uniformity_task.data[0])]['vertical']['IPEM'] == self.IPEM_VERTICAL
+        key = self.uniformity_task.key(self.uniformity_task.data[0])
+        horizontal_ipem = results[key]['horizontal']['IPEM']
+        vertical_ipem = results[key]['vertical']['IPEM']
 
+        print("\ntest_uniformity.py::TestUniformity::test_uniformity")
+
+        print("new_release_value:", vertical_ipem)
+
+        print("fixed_value:", self.IPEM_VERTICAL)
+
+        assert horizontal_ipem == self.IPEM_HORIZONTAL
+        assert vertical_ipem == self.IPEM_VERTICAL
 
 class TestSagUniformity(TestUniformity):
     IPEM_HORIZONTAL = 0.46875