kymo: add landmarks argument to calibrate_to_kbp

lumicks/pylake/kymo.py

@@ -998,7 +998,7 @@ def image_factory(_, channel):
 
         return result
 
-    def calibrate_to_kbp(self, length_kbp, *, start=None, end=None, length_um=None):
+    def calibrate_to_kbp(self, length_kbp, *, start=None, end=None, length_um=None, landmarks=None):
         """Calibrate from microns to other units.
 
         Parameters
@@ -1011,17 +1011,28 @@ def calibrate_to_kbp(self, length_kbp, *, start=None, end=None, length_um=None):
             End point of the tether in microns. Must also supply `start`.
         length_um: float | None
             Length of the tether in microns. Must also supply `start`.
+        landmarks: list | None
+            List of (micron, kbp) pairs of known positions. `start` must be `None`.
         """
         if self._calibration.unit == PositionUnit.kbp:
             raise RuntimeError("kymo is already calibrated in base pairs.")
 
         if start is None:
             if end is not None or length_um is not None:
-                raise ValueError("start must be supplied")
+                raise ValueError("Start must be supplied with end or length_um.")
+            elif landmarks is not None:
+                if len(landmarks) < 2:
+                    raise ValueError("At least 2 landmarks must be supplied.")
+                pixels = [self._calibration.to_pixels(landmark[0]) for landmark in landmarks]
+                kbp = [landmark[1] for landmark in landmarks]
+                kbp_per_pixel, intercept = np.polyfit(pixels, kbp, deg=1)
+                pixel_origin = -intercept / kbp_per_pixel
             else:
                 kbp_per_pixel = length_kbp / self._num_pixels[0]
                 pixel_origin = 0.0
         else:
+            if landmarks is not None:
+                raise ValueError("Cannot use landmarks with start.")
             if (end is None) and (length_um is None):
                 raise ValueError("Either end or length_um must be supplied with start.")
             if (end is not None) and (length_um is not None):

lumicks/pylake/tests/test_imaging_confocal/test_kymo_transforms.py

@@ -40,12 +40,31 @@ def test_calibrate_to_kbp(test_kymo):
         kymo_bp.calibrate_to_kbp(10)
 
 
-@pytest.mark.parametrize("start, end", [(None, 0.33), (0.12, None)])
-def test_calibrate_to_kbp_invalid_range(test_kymo, start, end):
+def test_calibrate_to_kbp_invalid(test_kymo):
     with pytest.raises(
-        ValueError, match="Both start and end points of the tether must be supplied."
+        ValueError, match="Start must be supplied with end or length_um."
     ):
-        test_kymo[0].calibrate_to_kbp(1, start=start, end=end)
+        test_kymo[0].calibrate_to_kbp(1, start=None, end=0.33)
+    with pytest.raises(
+        ValueError, match="Start must be supplied with end or length_um."
+    ):
+        test_kymo[0].calibrate_to_kbp(1, start=None, length_um=10.0)
+    with pytest.raises(
+        ValueError, match="Either end or length_um must be supplied with start."
+    ):
+        test_kymo[0].calibrate_to_kbp(1, start=0.33, end=None)
+    with pytest.raises(
+        ValueError, match="Either end or length_um must be supplied with start."
+    ):
+        test_kymo[0].calibrate_to_kbp(1, start=0.33, length_um=None)
+    with pytest.raises(
+        ValueError, match="Cannot use landmarks with start."
+    ):
+        test_kymo[0].calibrate_to_kbp(1, start=0.33, landmarks=([1, 2], [3, 4]))
+    with pytest.raises(
+        ValueError, match="At least 2 landmarks must be supplied."
+    ):
+        test_kymo[0].calibrate_to_kbp(1, landmarks=([1, 2], ))
 
 
 def check_factory_forwarding(kymo1, kymo2, check_timestamps):