lowlevel: add make_continuous_slice

lumicks/pylake/lowlevel.py

@@ -1,8 +1,11 @@
+import numpy as np
+
 from lumicks.pylake.kymo import Kymo
 from lumicks.pylake.scan import Scan
-from lumicks.pylake.channel import empty_slice
+from lumicks.pylake.channel import Slice, Continuous, empty_slice
 from lumicks.pylake.point_scan import PointScan
 from lumicks.pylake.detail.confocal import ConfocalFile, ScanMetaData
+from lumicks.pylake.detail.imaging_mixins import _FIRST_TIMESTAMP
 
 
 def create_confocal_object(
@@ -30,3 +33,29 @@ def create_confocal_object(
     file = ConfocalFile(infowave, red_channel, green_channel, blue_channel)
     confocal_cls = {0: PointScan, 1: Kymo, 2: Scan}
     return confocal_cls[metadata.num_axes](name, file, infowave.start, infowave.stop, metadata)
+
+
+def make_continuous_slice(data, start, dt, y_label="y", name="") -> Slice:
+    """Make a continuous slice of data
+
+    Converts a raw `array_like` to a pylake `Slice`.
+
+    Parameters
+    ----------
+    data : array_like
+        Source of data
+    start : int
+        Start timestamp in nanoseconds since epoch
+    dt : int
+        Timestep in nanoseconds
+    y_label : str
+        Label to show on the y-axis.
+    name : str
+        Name of the slice (used on plot titles).
+    """
+    if start < _FIRST_TIMESTAMP:
+        raise ValueError(
+            f"Starting timestamp must be larger than {_FIRST_TIMESTAMP}. You provided: {start}."
+        )
+
+    return Slice(Continuous(np.asarray(data), start, dt), labels={"title": name, "y": y_label})

lumicks/pylake/tests/test_channels/test_channels.py

@@ -8,6 +8,7 @@
 import matplotlib as mpl
 
 from lumicks.pylake import channel
+from lumicks.pylake.lowlevel import make_continuous_slice
 from lumicks.pylake.calibration import ForceCalibrationList
 
 
@@ -66,7 +67,7 @@ def test_calibration_timeseries_channels():
     # This slices off everything
     nested_slice = nested_slice[120:]
     assert len(nested_slice.calibration) == 0
-    assert type(nested_slice.calibration) is list
+    assert isinstance(nested_slice.calibration, list)
 
 
 def test_calibration_continuous_channels():
@@ -981,3 +982,23 @@ def start(self):
 
     with pytest.raises(TypeError, match=invalid_range):
         s[BadType(0)]
+
+
+def test_low_level_construction():
+    start = 1388534400000000000
+    with pytest.raises(ValueError, match="Starting timestamp must be larger than"):
+        _ = make_continuous_slice(np.array([1, 2, 3]), start - 1, int(1e9 / 78125))
+
+    data = np.arange(200)
+    slc = make_continuous_slice(data, start, int(1e9 / 78125))
+    assert slc.start == start
+    assert slc._timesteps == int(1e9 / 78125)
+    assert slc.sample_rate == 78125
+    assert slc.labels["y"] == "y"
+    assert slc.labels["title"] == ""
+    np.testing.assert_equal(slc.data, data)
+    assert isinstance(slc._src, channel.Continuous)
+
+    slc = make_continuous_slice(data, start, int(1e9 / 78125), name="hi", y_label="there")
+    assert slc.labels["title"] == "hi"
+    assert slc.labels["y"] == "there"