Merge pull request #73 from UCL/72-delegate_compare_matrices

Issue #72 used compare matrices from aruco

.codeclimate.yml

@@ -0,0 +1,63 @@
+version: "2"         # required to adjust maintainability checks
+
+checks:
+  argument-count:
+    enabled: true
+    config:
+      threshold: 4
+  complex-logic:
+    enabled: true
+    config:
+      threshold: 4
+  file-lines:
+    enabled: true
+    config:
+      threshold: 250
+  method-complexity:
+    enabled: true
+    config:
+      threshold: 5
+  method-count:
+    enabled: true
+    config:
+      threshold: 20
+  method-lines:
+    enabled: true
+    config:
+      threshold: 25
+  nested-control-flow:
+    enabled: true
+    config:
+      threshold: 4
+  return-statements:
+    enabled: true
+    config:
+      threshold: 4
+  similar-code:
+    enabled: true
+    config:
+      threshold: #language-specific defaults. overrides affect all languages.
+  identical-code:
+    enabled: true
+    config:
+      threshold: #language-specific defaults. overrides affect all languages.
+
+# plugins:
+#   eslint:
+#     enabled: true
+#     channel: "eslint-6"
+#   rubocop:
+#     enabled: true
+#     channel: "rubocop-0-79"
+
+exclude_patterns:
+- "config/"
+- "db/"
+- "dist/"
+- "features/"
+- "**/test/"
+- "**/tests/"
+- "sksurgerybard/_version.py"
+- "versioneer.py"
+
+

requirements.txt

@@ -9,7 +9,7 @@ scikit-surgerycalibration>=0.1.9
 scikit-surgerycore>=0.6.8
 scikit-surgeryutils
 scikit-surgeryvtk
-scikit-surgeryarucotracker>=0.2.4
+scikit-surgeryarucotracker>=0.2.5
 opencv-contrib-python
 #scikit-surgeryspeech>=0.2.0 #uncomment this to use speech interface
 #PocketSphinx # uncomment this to use speech with sphinx

setup.py

@@ -62,7 +62,7 @@
         'scikit-surgerycalibration>=0.1.9',
         'scikit-surgeryutils',
         'scikit-surgeryvtk',
-        'scikit-surgeryarucotracker>=0.2.4',
+        'scikit-surgeryarucotracker>=0.2.5',
     ],
 
     entry_points={

tests/algorithms/test_pointer.py

@@ -5,7 +5,7 @@
 import pytest
 import numpy as np
 from sksurgerycore.transforms.transform_manager import TransformManager
-import sksurgerybard.algorithms.pointer as pointer
+from sksurgerybard.algorithms import pointer
 
 
 def test_write_pointer_invalid_tm():

tests/widgets/test_bard_overlay.py

@@ -5,6 +5,8 @@
 import copy
 import numpy as np
 import pytest
+from sksurgeryarucotracker.algorithms.compare_matrices \
+        import matrices_equivalent
 import sksurgerybard.widgets.bard_overlay_app as boa
 
 
@@ -41,53 +43,6 @@
 
 }
 
-def _matrices_equivalent(mat_a, mat_b, cube_length = 500.0, tolerance = 5.0):
-    """
-    Helper function to check the equivalence of 2 matrices.
-    Because the 3x3 rotation and the 1X3 translation can
-    have very different magnitudes we want something
-    a bit more nuances than just np.allclose for the
-    whole matrix.
-    np.allclose worked OK until opencv-contrib-python > 4.5.1
-    see Issue #69
-
-    Rather than comparing matrices let's look at what happens when we
-    apply them to point cooridinates. If we define an operating cube,
-    with the camera at the centre of the plane defined by the
-    x and y axes and z = 0, by testing the differences at the
-    extremities of that cube we can say that BARD is accurate to
-    within x mm over a volume of side length x mm. By default 5.0 mm and
-    500 mm.
-
-    This isn't very accurate but mainly seems to be due to
-    instability in opencv-contrib-python. If you wanted more
-    accuracy for a given application you could version
-    lock opencv-contrib-python
-    """
-    cube_points = np.array(
-                    [[-cube_length/2.0, -cube_length/2.0, cube_length, 1.],
-                     [-cube_length/2.0, cube_length/2.0, cube_length, 1.],
-                     [cube_length/2.0, cube_length/2.0, cube_length, 1.],
-                     [cube_length/2.0, -cube_length/2.0, cube_length, 1.],
-                     [-cube_length/2.0, -cube_length/2.0, 0., 1.],
-                     [-cube_length/2.0, cube_length/2.0, 0., 1.],
-                     [cube_length/2.0, cube_length/2.0, 0., 1.],
-                     [cube_length/2.0, -cube_length/2.0, 0., 1.]],
-                    dtype = np.float32)
-
-    trans_a = np.matmul(mat_a, cube_points.transpose())
-    trans_b = np.matmul(mat_b, cube_points.transpose())
-
-    equivalent = np.allclose(trans_a, trans_b, rtol = 0.0, atol = tolerance)
-
-    if not equivalent:
-        print ("trans a: " , trans_a.transpose())
-        print ("trans b: " , trans_b.transpose())
-        print ("diff: " , trans_a.transpose() - trans_b.transpose())
-
-    return equivalent
-
-
 def test_valid_config():
     """
     Loads a valid config file, and checks that we have retrieved the calibration
@@ -117,7 +72,7 @@ def test_valid_config():
        [ 0.0000e+00, 0.00000e+00, 0.00000e+00, 1.00000000e+00]],
        dtype=np.float32)
 
-    assert _matrices_equivalent(cam2model_regression,
+    assert matrices_equivalent(cam2model_regression,
                     bard_overlay.transform_manager.get("modelreference2camera"))
 
     pointer2camera_regression = np.array([
@@ -127,7 +82,7 @@ def test_valid_config():
         [ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00,  1.00000000e+00]],
         dtype=np.float32)
 
-    assert _matrices_equivalent(pointer2camera_regression,
+    assert matrices_equivalent(pointer2camera_regression,
                     bard_overlay.transform_manager.get("pointerref2camera"))
 
     pointer2model_regression = np.array([
@@ -137,7 +92,7 @@ def test_valid_config():
         [ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00,  1.00000000e+00]],
         dtype=np.float32)
 
-    assert _matrices_equivalent(pointer2model_regression,
+    assert matrices_equivalent(pointer2model_regression,
                 bard_overlay.transform_manager.get("pointerref2modelreference"))
 
     #skip 5 frames
@@ -151,7 +106,7 @@ def test_valid_config():
         [ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00,  1.00000000e+00]],
         dtype=np.float32)
 
-    assert _matrices_equivalent(cam2model_regression,
+    assert matrices_equivalent(cam2model_regression,
                     bard_overlay.transform_manager.get("modelreference2camera"))
 
     pointer2camera_regression = np.array([
@@ -161,7 +116,7 @@ def test_valid_config():
         [ 0.00000000e+00,  0.00000000e+00, 0.00000000e+00,  1.00000000e+00]],
         dtype=np.float32)
 
-    assert _matrices_equivalent(pointer2camera_regression,
+    assert matrices_equivalent(pointer2camera_regression,
                     bard_overlay.transform_manager.get("pointerref2camera"))
 
     pointer2model_regression = np.array([
@@ -171,7 +126,7 @@ def test_valid_config():
         [0.00000000e+00,  0.00000000e+00,  0.00000000e+00,  1.00000000e+00]],
         dtype=np.float32)
 
-    assert _matrices_equivalent(pointer2model_regression,
+    assert matrices_equivalent(pointer2model_regression,
                 bard_overlay.transform_manager.get("pointerref2modelreference"))
 
 
@@ -217,7 +172,7 @@ def test_with_no_pointer():
        [ 0.0000e+00, 0.00000e+00, 0.00000e+00, 1.00000000e+00]],
        dtype=np.float32)
 
-    assert _matrices_equivalent(cam2model_regression,
+    assert matrices_equivalent(cam2model_regression,
                     bard_overlay.transform_manager.get("modelreference2camera"))
 
     with pytest.raises(ValueError):