Issue #28 added note re smoothing in docs and a test to check it's wo…

…rking
SciKit-Surgery · Oct 4, 2023 · 98ace2c · 98ace2c
1 parent 222ec6d
commit 98ace2c
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Showing 3 changed files with 162 additions and 9 deletions.
diff --git a/sksurgerynditracker/nditracker.py b/sksurgerynditracker/nditracker.py
@@ -116,7 +116,10 @@ def __init__(self, configuration):
 
             ports to probe:
 
-            use quaternions:
+            use quaternions: default is false
+
+            smoothing buffer: specify a buffer over which to average the
+                tracking, defaults to 1
 
         :raises Exception: IOError, KeyError, OSError
         """

diff --git a/tests/polaris_mocks.py b/tests/polaris_mocks.py
@@ -13,14 +13,13 @@
         "data/8700339.rom"]
     }
 
-SETTINGS_POLARIS_QUAT = {
-    "tracker type": "polaris",
-    "ports to probe": 20,
-    "romfiles" : [
-        "data/something_else.rom",
-        "data/8700339.rom"],
-    "use quaternions": "true"
-    }
+SETTINGS_POLARIS_QUAT = SETTINGS_POLARIS.copy()
+SETTINGS_POLARIS_QUAT["use quaternions"] = "true"
+
+SETTINGS_POLARIS_SMOOTH = SETTINGS_POLARIS.copy()
+SETTINGS_POLARIS_QUAT_SMOOTH = SETTINGS_POLARIS_QUAT.copy()
+SETTINGS_POLARIS_SMOOTH["smoothing buffer"] = 2
+SETTINGS_POLARIS_QUAT_SMOOTH["smoothing buffer"] = 2
 
 class MockPort:
     """A fake serial port for ndi"""

diff --git a/tests/test_sksurgerynditracker_mockndi_getframe.py b/tests/test_sksurgerynditracker_mockndi_getframe.py
@@ -6,6 +6,7 @@
 from sksurgerynditracker.nditracker import NDITracker
 
 from tests.polaris_mocks import SETTINGS_POLARIS, SETTINGS_POLARIS_QUAT, \
+        SETTINGS_POLARIS_SMOOTH, SETTINGS_POLARIS_QUAT_SMOOTH, \
         mockndiProbe, \
         mockndiOpen, mockndiGetError, mockComports, \
         mockndiGetPHSRHandle, mockndiVER, \
@@ -160,3 +161,153 @@ def test_getframe_missing(mocker):
     assert np.all(np.isnan(tracking_quality))
 
     del tracker
+
+def test_getframe_smooth_mock(mocker):
+    """
+    connects and configures, mocks ndicapy.ndiProbe to pass
+    reqs: 03, 04
+    """
+    tracker = None
+    bxsource = MockBXFrameSource()
+    ndidevice = MockNDIDevice()
+    mocker.patch('serial.tools.list_ports.comports', mockComports)
+    mocker.patch('ndicapy.ndiProbe', mockndiProbe)
+    mocker.patch('ndicapy.ndiOpen', mockndiOpen)
+    mocker.patch('ndicapy.ndiCommand', ndidevice.mockndiCommand)
+    mocker.patch('ndicapy.ndiGetError', mockndiGetError)
+    mocker.patch('ndicapy.ndiClose')
+    mocker.patch('ndicapy.ndiGetPHSRNumberOfHandles',
+            ndidevice.mockndiGetPHSRNumberOfHandles)
+    mocker.patch('ndicapy.ndiGetPHRQHandle', ndidevice.mockndiGetPHRQHandle)
+    mocker.patch('ndicapy.ndiPVWRFromFile')
+    mocker.patch('ndicapy.ndiGetPHSRHandle', mockndiGetPHSRHandle)
+    mocker.patch('ndicapy.ndiVER', mockndiVER)
+    mocker.patch('ndicapy.ndiGetBXFrame', bxsource.mockndiGetBXFrame)
+    mocker.patch('ndicapy.ndiGetBXTransform', bxsource.mockndiGetBXTransform)
+
+    tracker = NDITracker(SETTINGS_POLARIS_SMOOTH)
+
+    bxsource.setdevice(ndidevice)
+
+    (port_handles, time_stamps, frame_numbers, tracking,
+                tracking_quality ) = tracker.get_frame()
+
+    assert len(port_handles) == 2
+    assert len(time_stamps) == 2
+    assert frame_numbers.count(1) == 2
+    expected_tracking_0 = np.array([[1.,0.,0.,10.],
+                                 [0.,1.,0.,-20.],
+                                 [0.,0.,1.,5.],
+                                 [0.,0.,0.,1.]])
+    assert np.array_equal(expected_tracking_0, tracking[0])
+    expected_tracking_1 = np.array([[1.,0.,0.,0.],
+                                 [0.,1.,0.,0.],
+                                 [0.,0.,1.,0.],
+                                 [0.,0.,0.,1.]])
+    assert np.array_equal(expected_tracking_1, tracking[1])
+    assert tracking_quality.count(1.) == 2
+
+    (port_handles, time_stamps, frame_numbers, tracking,
+                tracking_quality ) = tracker.get_frame()
+
+    assert len(port_handles) == 2
+    assert len(time_stamps) == 2
+    assert frame_numbers.count(2) == 2
+    expected_tracking_0 = np.array([[1.,0.,0.,15.],
+                                 [0.,1.,0.,-30.],
+                                 [0.,0.,1.,7.5],
+                                 [0.,0.,0.,1.]])
+    assert np.array_equal(expected_tracking_0, tracking[0])
+    assert np.array_equal(expected_tracking_1, tracking[1])
+    assert tracking_quality.count(1.) == 2
+
+    del tracker
+
+def test_getframe_smooth_mock_quat(mocker):
+    """
+    Checks that get frame works with quaternions
+    """
+    tracker = None
+    bxsource = MockBXFrameSource()
+    ndidevice = MockNDIDevice()
+    mocker.patch('serial.tools.list_ports.comports', mockComports)
+    mocker.patch('ndicapy.ndiProbe', mockndiProbe)
+    mocker.patch('ndicapy.ndiOpen', mockndiOpen)
+    mocker.patch('ndicapy.ndiCommand', ndidevice.mockndiCommand)
+    mocker.patch('ndicapy.ndiGetError', mockndiGetError)
+    mocker.patch('ndicapy.ndiClose')
+    mocker.patch('ndicapy.ndiGetPHSRNumberOfHandles',
+            ndidevice.mockndiGetPHSRNumberOfHandles)
+    mocker.patch('ndicapy.ndiGetPHRQHandle', ndidevice.mockndiGetPHRQHandle)
+    mocker.patch('ndicapy.ndiPVWRFromFile')
+    mocker.patch('ndicapy.ndiGetPHSRHandle', mockndiGetPHSRHandle)
+    mocker.patch('ndicapy.ndiVER', mockndiVER)
+    mocker.patch('ndicapy.ndiGetBXFrame', bxsource.mockndiGetBXFrame)
+    mocker.patch('ndicapy.ndiGetBXTransform', bxsource.mockndiGetBXTransform)
+
+    tracker = NDITracker(SETTINGS_POLARIS_QUAT_SMOOTH)
+
+    bxsource.setdevice(ndidevice)
+
+    (port_handles, time_stamps, frame_numbers, tracking,
+                tracking_quality ) = tracker.get_frame()
+
+    assert len(port_handles) == 2
+    assert len(time_stamps) == 2
+    assert frame_numbers.count(1) == 2
+    expected_tracking_0 = np.array([[1.,0.,0.,0.,10.,-20,5.]])
+    assert np.array_equal(expected_tracking_0, tracking[0])
+    expected_tracking_1 = np.array([[1.,0.,0.,0.,0.,0.,0.]])
+    assert np.array_equal(expected_tracking_1, tracking[1])
+    assert tracking_quality.count(1.) == 2
+
+    (port_handles, time_stamps, frame_numbers, tracking,
+                tracking_quality ) = tracker.get_frame()
+
+    assert len(port_handles) == 2
+    assert len(time_stamps) == 2
+    assert frame_numbers.count(2) == 2
+    expected_tracking_0 = np.array([[1.,0.,0.,0.,15.,-30,7.5]])
+    assert np.array_equal(expected_tracking_0, tracking[0])
+    assert np.array_equal(expected_tracking_1, tracking[1])
+    assert tracking_quality.count(1.) == 2
+
+    del tracker
+
+def test_getframe_missing_smooth(mocker):
+    """
+    connects and configures, mocks ndicapy.ndiProbe to pass
+    reqs: 03, 04
+    """
+    tracker = None
+    bxsource = MockBXFrameSource()
+    ndidevice = MockNDIDevice()
+    mocker.patch('serial.tools.list_ports.comports', mockComports)
+    mocker.patch('ndicapy.ndiProbe', mockndiProbe)
+    mocker.patch('ndicapy.ndiOpen', mockndiOpen)
+    mocker.patch('ndicapy.ndiCommand', ndidevice.mockndiCommand)
+    mocker.patch('ndicapy.ndiGetError', mockndiGetError)
+    mocker.patch('ndicapy.ndiClose')
+    mocker.patch('ndicapy.ndiGetPHSRNumberOfHandles',
+            ndidevice.mockndiGetPHSRNumberOfHandles)
+    mocker.patch('ndicapy.ndiGetPHRQHandle', ndidevice.mockndiGetPHRQHandle)
+    mocker.patch('ndicapy.ndiPVWRFromFile')
+    mocker.patch('ndicapy.ndiGetPHSRHandle', mockndiGetPHSRHandle)
+    mocker.patch('ndicapy.ndiVER', mockndiVER)
+    mocker.patch('ndicapy.ndiGetBXFrame', bxsource.mockndiGetBXFrame)
+    mocker.patch('ndicapy.ndiGetBXTransform',
+            bxsource.mockndiGetBXTransformMissing)
+
+    tracker = NDITracker(SETTINGS_POLARIS_SMOOTH)
+
+    bxsource.setdevice(ndidevice)
+    (port_handles, time_stamps, frame_numbers, tracking,
+                tracking_quality ) = tracker.get_frame()
+
+    assert len(port_handles) == 2
+    assert len(time_stamps) == 2
+    assert frame_numbers.count(1) == 2
+    assert np.all(np.isnan(tracking))
+    assert np.all(np.isnan(tracking_quality))
+
+    del tracker