kymo: allow calibrating upside down tether

lumicks/pylake/kymo.py

@@ -334,7 +334,7 @@ def duration(self):
     def pixelsize(self):
         """Returns a `List` of axes dimensions in calibrated units. The length of the
         list corresponds to the number of scan axes."""
-        return [self._calibration.value]
+        return [self._calibration.pixelsize]
 
     def plot(
         self,
@@ -386,7 +386,7 @@ def plot(
 
         image = self._get_plot_data(channel, adjustment)
 
-        size_calibrated = self._calibration.value * self._num_pixels[0]
+        size_calibrated = self._calibration.pixelsize * self._num_pixels[0]
 
         default_kwargs = dict(
             # With origin set to upper (default) bounds should be given as (0, n, n, 0)
@@ -1016,12 +1016,11 @@ def calibrate_to_kbp(self, length_kbp, *, start=None, end=None):
         if (start is None) ^ (end is None):
             raise ValueError("Both start and end points of the tether must be supplied.")
 
-        if start is not None:
-            if end < start:
-                raise ValueError("end must be larger than start.")
-            kbp_per_pixel = length_kbp / (end - start) * self.pixelsize_um[0]
-        else:
-            kbp_per_pixel = length_kbp / self._num_pixels[0]
+        kbp_per_pixel = (
+            length_kbp / (end - start) * self.pixelsize_um[0]
+            if start is not None
+            else length_kbp / self._num_pixels[0]
+        )
         pixel_origin = start / self.pixelsize_um[0] if start is not None else 0.0
 
         result = copy(self)
@@ -1123,7 +1122,7 @@ def label(self):
 @dataclass(frozen=True)
 class PositionCalibration:
     unit: PositionUnit = PositionUnit.pixel
-    value: float = 1.0
+    scale: float = 1.0
     origin: float = 0.0
 
     def __post_init__(self):
@@ -1132,11 +1131,15 @@ def __post_init__(self):
 
     def from_pixels(self, pixels):
         """Convert coordinates from pixel values to calibrated values"""
-        return self.value * (np.array(pixels) - self.origin)
+        return self.scale * (np.array(pixels) - self.origin)
 
     def to_pixels(self, calibrated):
         """Convert coordinates from calibrated values to pixel values"""
-        return np.array(calibrated) / self.value + self.origin
+        return np.array(calibrated) / self.scale + self.origin
+
+    @property
+    def pixelsize(self):
+        return np.abs(self.scale)
 
     @property
     def unit_label(self):
@@ -1146,7 +1149,7 @@ def downsample(self, factor):
         return (
             self
             if self.unit == PositionUnit.pixel
-            else PositionCalibration(self.unit, self.value * factor)
+            else PositionCalibration(self.unit, self.scale * factor)
         )
 
 

lumicks/pylake/kymotracker/tests/test_greedy_algorithm.py

@@ -171,3 +171,42 @@ def test_default_parameters(kymo_pixel_calibrations):
         with np.testing.assert_raises(AssertionError):
             for ref, track in zip(ref_tracks, tracks):
                 np.testing.assert_allclose(ref.position, track.position)
+
+
+@pytest.mark.parametrize("tether_len,start,end", [(10, 0.18, 0.62), (48.502, 0.03, 0.94)])
+def test_track_calibrated_flipped(tether_len, start, end):
+    """test that tracking a calibrated kymo with tether end < tether start yields the same
+    coordinates as tracking the flipped tether with end > start.
+    """
+
+    image = np.zeros((20, 25))
+
+    # ([time, position], ...)
+    ref_tracks = [
+        ([1, 5], [2, 6], [3, 7]),
+        ([5, 15], [6, 15], [7, 14], [8, 15], [9, 16]),
+    ]
+    for coords in ref_tracks:
+        for t, p in coords:
+            image[p, t] = 10
+
+    kymo = _kymo_from_array(image, "g", line_time_seconds=0.1, pixel_size_um=0.050)
+    kymo_flipped = kymo.flip()
+
+    # start, end = 0.18, 0.62
+    len_um = kymo._calibration.from_pixels(kymo._num_pixels[0] - 1)
+    end_flipped = len_um - end
+    start_flipped = len_um - start
+
+    # tether_len = 10
+    kymo = kymo.calibrate_to_kbp(tether_len, start=start, end=end)
+    kymo_flipped = kymo_flipped.calibrate_to_kbp(tether_len, start=start_flipped, end=end_flipped)
+
+    params = dict(pixel_threshold=5, window=3)
+    tracks = track_greedy(kymo, "green", track_width=3 * kymo._calibration.pixelsize, **params)
+    tracks_flipped = track_greedy(
+        kymo_flipped, "green", track_width=3 * kymo_flipped._calibration.pixelsize, **params
+    )
+
+    for track, track_flipped in zip(tracks, tracks_flipped):
+        np.testing.assert_allclose(track.position, track_flipped.position)

lumicks/pylake/tests/test_imaging_confocal/test_kymo_transforms.py

@@ -13,32 +13,29 @@ def test_calibrate_to_kbp(test_kymo):
 
     # test that default calibration is in microns
     assert kymo._calibration.unit == PositionUnit.um
-    assert kymo._calibration.value == 0.1
+    assert kymo._calibration.pixelsize == 0.1
 
     # test that calibration is stored as kilobase-pairs
     assert kymo_bp._calibration.unit == PositionUnit.kbp
-    np.testing.assert_allclose(kymo_bp._calibration.value, length_kbp / n_pixels)
+    np.testing.assert_allclose(kymo_bp._calibration.pixelsize, length_kbp / n_pixels)
 
     # test conversion from microns to calibration units
     np.testing.assert_allclose(
-        kymo._calibration.value * n_pixels,
+        kymo._calibration.pixelsize * n_pixels,
         ref.metadata.pixelsize_um[0] * n_pixels,
     )
     np.testing.assert_allclose(kymo.pixelsize, ref.metadata.pixelsize_um[0])
-    np.testing.assert_allclose(kymo_bp._calibration.value * n_pixels, length_kbp)
+    np.testing.assert_allclose(kymo_bp._calibration.pixelsize * n_pixels, length_kbp)
     np.testing.assert_allclose(kymo_bp.pixelsize, length_kbp / n_pixels)
 
     start = 0.12
     end = 0.33
     n_pixels_tether = (end - start) / ref.metadata.pixelsize_um[0]
 
     kymo_bp = kymo.calibrate_to_kbp(length_kbp, start=start, end=end)
-    np.testing.assert_allclose(kymo_bp._calibration.value * n_pixels_tether, length_kbp)
+    np.testing.assert_allclose(kymo_bp._calibration.pixelsize * n_pixels_tether, length_kbp)
     np.testing.assert_allclose(kymo_bp.pixelsize, length_kbp / n_pixels_tether)
 
-    with pytest.raises(ValueError, match="end must be larger than start."):
-        kymo.calibrate_to_kbp(length_kbp, start=end, end=start)
-
     with pytest.raises(RuntimeError, match="kymo is already calibrated in base pairs."):
         kymo_bp.calibrate_to_kbp(10)
 
@@ -87,8 +84,8 @@ def test_calibrate_sliced_cropped(test_kymo):
     np.testing.assert_allclose(kymo_bp.pixelsize[0], cropped_kymo_bp.pixelsize[0])
     # but will change total length
     np.testing.assert_allclose(
-        kymo_bp._calibration.value * n_cropped_pixels,
-        cropped_kymo_bp._calibration.value * cropped_kymo_bp._num_pixels[0],
+        kymo_bp._calibration.pixelsize * n_cropped_pixels,
+        cropped_kymo_bp._calibration.pixelsize * cropped_kymo_bp._num_pixels[0],
     )
 
 
@@ -143,23 +140,31 @@ def test_position_unit():
 
 def test_enum_in_calibration():
     with pytest.raises(TypeError, match="`unit` must be a PositionUnit instance"):
-        PositionCalibration("kbp", value=0.42)
+        PositionCalibration("kbp", scale=0.42)
 
-    c = PositionCalibration(PositionUnit.um, value=0.42)
+    c = PositionCalibration(PositionUnit.um, scale=0.42)
     assert c.unit_label == PositionUnit.um.label
 
 
 def test_coordinate_transforms():
     px_coord = [0, 1.2, 3.14, 85]
 
-    c = PositionCalibration(PositionUnit.kbp, value=0.42)
+    c = PositionCalibration(PositionUnit.kbp, scale=0.42)
     kbp_coord = [0, 0.504, 1.3188, 35.7]
     transformed = c.from_pixels(px_coord)
     np.testing.assert_allclose(kbp_coord, transformed)
     np.testing.assert_allclose(px_coord, c.to_pixels(transformed))
 
-    c = PositionCalibration(PositionUnit.kbp, value=0.42, origin=2.0)
-    kbp_coord = [-0.84, -0.336, 0.4788, 34.86]
+    c = PositionCalibration(PositionUnit.kbp, scale=0.42, origin=2.0)
+    kbp_coord = np.array([-0.84, -0.336, 0.4788, 34.86])
     transformed = c.from_pixels(px_coord)
     np.testing.assert_allclose(kbp_coord, transformed)
     np.testing.assert_allclose(px_coord, c.to_pixels(transformed))
+
+    c_flipped = PositionCalibration(PositionUnit.kbp, scale=-0.42, origin=2.0)
+    transformed = c_flipped.from_pixels(px_coord)
+    np.testing.assert_allclose(-kbp_coord, transformed)
+    np.testing.assert_allclose(px_coord, c_flipped.to_pixels(transformed))
+
+    assert c.scale == -c_flipped.scale
+    assert c.pixelsize == c_flipped.pixelsize