fixups

lumicks/pylake/tests/test_imaging_confocal/test_kymo_slice_crop.py

@@ -13,6 +13,7 @@ def test_kymo_slicing(test_kymo):
     dead_time = (ref.timestamps.dt * ref.infowave.line_padding * 2) * 1e-9
     line_time = scan_time + dead_time
 
+    # need to start slicing from the first sample _after_ the dead time
     deadtime_slice_offset = (1 + ref.infowave.line_padding) * ref.timestamps.dt * 1e-9
 
     assert kymo.get_image("red").shape == (ref_pixels, ref_lines)
@@ -35,11 +36,11 @@ def test_kymo_slicing(test_kymo):
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :, 0])
 
-    factor = 2
-    sliced = kymo["0s":f"{factor * line_time}s"]
-    assert sliced.get_image("red").shape == (ref_pixels, factor)
-    assert sliced.shape == (ref_pixels, factor, 3)
-    np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :factor, 0])
+    num_lines = 2
+    sliced = kymo["0s":f"{num_lines * line_time}s"]
+    assert sliced.get_image("red").shape == (ref_pixels, num_lines)
+    assert sliced.shape == (ref_pixels, num_lines, 3)
+    np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :num_lines, 0])
 
     sliced = kymo["0s":f"-{line_time * 0.6}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines - 1)
@@ -65,12 +66,14 @@ def test_kymo_slicing(test_kymo):
     assert sliced.get_image("red").shape == (ref_pixels, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :3, 0])
 
-    sliced = kymo["3.5s":"14s"]
+    # slice from deadtime before first line until deadtime after first line
+    sliced = kymo[f"{scan_time + dead_time / 2}s":f"{2 * line_time - dead_time / 2}s"]
     assert sliced.get_image("red").shape == (ref_pixels, 1)
     assert sliced.shape == (ref_pixels, 1, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, 1:2, 0])
 
-    sliced = kymo["0s":"85s"]
+    # slice over entire kymo
+    sliced = kymo["0s":f"{line_time * (ref.metadata.lines_per_frame + 1)}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines)
     assert sliced.shape == (ref_pixels, ref_lines, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :, 0])
@@ -167,9 +170,12 @@ def test_kymo_crop(cropping_kymo):
         ref.image[2:3, :, 0],
     )
 
-    # Test cropping in base pairs
+def test_kymo_basepairs_crop(cropping_kymo):
+    """Test basic cropping functionality"""
+    kymo, ref = cropping_kymo
     kymo_bp = kymo.calibrate_to_kbp(1.000)
     px_size = kymo_bp.pixelsize[0]
+
     np.testing.assert_allclose(
         kymo_bp.crop_by_distance(px_size, 3 * px_size).get_image("red"), ref.image[1:3, :, 0]
     )
@@ -256,9 +262,6 @@ def test_incremental_offset(cropping_kymo):
     cropped = kymo.crop_by_distance(px_size, 4 * px_size)
     twice_cropped = cropped.crop_by_distance(px_size, 4 * px_size)
 
-    print(kymo.get_image("red"))
-    print(cropped.get_image("red"))
-    print(twice_cropped.get_image("red"))
     np.testing.assert_allclose(
         twice_cropped.get_image("red"),
         ref.image[2:4, :, 0],