lowlevel: add low level api to create objects

Adds tested functions to directly create confocal objects and slices

lumicks/pylake/benchmark.py

@@ -2,6 +2,7 @@
 import timeit
 import tempfile
 import contextlib
+from copy import copy
 
 import numpy as np
 
@@ -41,14 +42,15 @@ def _generate_kymo_for_tracking(duration, line_count, samples_per_pixel=1):
 def _generate_blank_kymo_data(samples=1000000):
     """This is a different function since generating a junk data kymo is significantly faster than
     generating one with sensible image content."""
-    from lumicks.pylake.tests.data.mock_confocal import MockConfocalFile
+    from lumicks.pylake.tests.data.mock_confocal import mock_confocal_from_arrays
 
     counts = np.ones(samples)
     infowave = np.ones(samples)
     infowave[::2] = 0
     infowave[::10] = 2
 
-    return MockConfocalFile.from_streams(
+    return mock_confocal_from_arrays(
+        "kymo",
         start=0,
         dt=int(1e9),
         axes=[0],
@@ -86,17 +88,17 @@ class _KymoImage(_Benchmark):
     loops = 60
 
     def context(self):
-        confocal_file, metadata, stop = _generate_blank_kymo_data()
-        yield lambda: lk.kymo.Kymo("big_kymo", confocal_file, 0, stop, metadata).get_image("red")
+        kymo = _generate_blank_kymo_data()
+        yield lambda: copy(kymo).get_image("red")  # Copy to not use the cache!
 
 
 class _KymoTimestamps(_Benchmark):
     name = "Reconstructing kymo timestamps"
     loops = 45
 
     def context(self):
-        confocal_file, metadata, stop = _generate_blank_kymo_data()
-        yield lambda: lk.kymo.Kymo("big_kymo", confocal_file, 0, stop, metadata).timestamps
+        kymo = _generate_blank_kymo_data()
+        yield lambda: copy(kymo).timestamps  # Copy to not use the cache!
 
 
 class _Tracking(_Benchmark):

lumicks/pylake/detail/confocal.py

@@ -6,6 +6,8 @@
 import numpy as np
 from numpy import typing as npt
 
+from lumicks.pylake.channel import Slice, empty_slice
+
 from .image import reconstruct_image, reconstruct_image_sum
 from .mixin import PhotonCounts, ExcitationLaserPower
 from .plotting import parse_color_channel
@@ -157,7 +159,9 @@ def scan_order(self):
 
     @classmethod
     def from_json(cls, json_string):
-        json_dict = json.loads(json_string)["value0"]
+        json_dict = json.loads(json_string)
+        if "value0" in json_dict:
+            json_dict = json_dict["value0"]
 
         axes = [
             ScanAxis(ax["axis"], ax["num of pixels"], ax["pixel size (nm)"] / 1000)
@@ -167,14 +171,36 @@ def from_json(cls, json_string):
         return cls(axes, json_dict["scan volume"]["center point (um)"], json_dict["scan count"])
 
 
+class ConfocalFileProxy:
+    """Class with the minimal requirements to reconstruct confocal scans from photon streams"""
+
+    def __init__(
+        self,
+        infowave: Slice,
+        red_channel: Slice = empty_slice,
+        green_channel: Slice = empty_slice,
+        blue_channel: Slice = empty_slice,
+    ):
+        self.infowave = infowave
+        self.red_photon_count = red_channel
+        self.green_photon_count = green_channel
+        self.blue_photon_count = blue_channel
+
+    def __getitem__(self, key):
+        if key == "Info wave":
+            return {"Info wave": self.infowave}
+        else:
+            raise KeyError(f"Key {key} not found.")
+
+
 class BaseScan(PhotonCounts, ExcitationLaserPower):
     """Base class for confocal scans
 
     Parameters
     ----------
     name : str
         confocal scan name
-    file : lumicks.pylake.File
+    file : lumicks.pylake.File | lumicks.pylake.ConfocalFile
         Parent file. Contains the channel data.
     start : int
         Start point in the relevant info wave.

lumicks/pylake/detail/imaging_mixins.py

@@ -9,7 +9,7 @@
 from .timeindex import to_timestamp
 from ..adjustments import no_adjustment
 
-_FIRST_TIMESTAMP = 1388534400
+_FIRST_TIMESTAMP = 1388534400000000000
 
 
 class TiffExport:

lumicks/pylake/kymo.py

@@ -71,7 +71,7 @@ class Kymo(ConfocalImage):
     ----------
     name : str
         Kymograph name
-    file : lumicks.pylake.File
+    file : lumicks.pylake.File | lumicks.pylake.detail.confocal.ConfocalFile
         Parent file. Contains the channel data.
     start : int
         Start point in the relevant info wave.

lumicks/pylake/lowlevel.py

@@ -0,0 +1,61 @@
+import numpy as np
+
+from lumicks.pylake.kymo import Kymo
+from lumicks.pylake.scan import Scan
+from lumicks.pylake.channel import Slice, Continuous, empty_slice
+from lumicks.pylake.point_scan import PointScan
+from lumicks.pylake.detail.confocal import ScanMetaData, ConfocalFileProxy
+from lumicks.pylake.detail.imaging_mixins import _FIRST_TIMESTAMP
+
+
+def create_confocal_object(
+    name,
+    infowave,
+    json_metadata,
+    red_channel=empty_slice,
+    green_channel=empty_slice,
+    blue_channel=empty_slice,
+) -> Kymo | Scan | PointScan:
+    """Create a confocal object from slices and json metadata
+
+    Parameters
+    ----------
+    name : str
+        Name of this object
+    infowave : lumicks.pylake.Slice
+        Info wave that encodes how the photon counts should be assembled into an image.
+    json_metadata : str
+        json metadata generated by Bluelake.
+    red_channel, green_channel, blue_channel : lumicks.pylake.Slice
+        Photon counts
+    """
+    metadata = ScanMetaData.from_json(json_metadata)
+    file = ConfocalFileProxy(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/scan.py

@@ -18,7 +18,7 @@ class Scan(ConfocalImage, VideoExport, FrameIndex):
     ----------
     name : str
         Scan name
-    file : lumicks.pylake.File
+    file : lumicks.pylake.File | lumicks.pylake.detail.confocal.ConfocalFile
         Parent file. Contains the channel data.
     start : int
         Start point in the relevant info wave.