feat: init

test/model/devices/remote_focus/test_rf_base.py

@@ -0,0 +1,106 @@
+# Copyright (c) 2021-2025  The University of Texas Southwestern Medical Center.
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted for academic and research use only (subject to the
+# limitations in the disclaimer below) provided that the following conditions are met:
+
+#      * Redistributions of source code must retain the above copyright notice,
+#      this list of conditions and the following disclaimer.
+
+#      * Redistributions in binary form must reproduce the above copyright
+#      notice, this list of conditions and the following disclaimer in the
+#      documentation and/or other materials provided with the distribution.
+
+#      * Neither the name of the copyright holders nor the names of its
+#      contributors may be used to endorse or promote products derived from this
+#      software without specific prior written permission.
+
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+
+# Standard Library Imports
+
+# Third Party Imports
+import pytest
+import numpy as np
+
+# Local Imports
+from navigate.model.devices.remote_focus.synthetic import SyntheticRemoteFocus
+from test.model.dummy import DummyModel
+
+
+def test_remote_focus_base_init():
+    model = DummyModel()
+    microscope_name = model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    SyntheticRemoteFocus(microscope_name, None, model.configuration)
+
+
+@pytest.mark.parametrize("smoothing", [0] + list(np.random.rand(5) * 100))
+def test_remote_focus_base_adjust(smoothing):
+    from test.model.dummy import DummyModel
+
+    model = DummyModel()
+    microscope_name = model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    microscope_state = model.configuration["experiment"]["MicroscopeState"]
+
+    waveform_constants = model.configuration["waveform_constants"]
+    imaging_mode = microscope_state["microscope_name"]
+    zoom = microscope_state["zoom"]
+    for channel_key in microscope_state["channels"].keys():
+        # channel includes 'is_selected', 'laser', 'filter', 'camera_exposure'...
+        channel = microscope_state["channels"][channel_key]
+
+        # Only proceed if it is enabled in the GUI
+        if channel["is_selected"] is True:
+            laser = channel["laser"]
+            waveform_constants["remote_focus_constants"][imaging_mode][zoom][laser][
+                "percent_smoothing"
+            ] = smoothing
+            channel["camera_exposure_time"] = np.random.rand() * 150 + 50
+
+    rf = SyntheticRemoteFocus(microscope_name, None, model.configuration)
+
+    # exposure_times = {
+    #     k: v["camera_exposure_time"] / 1000
+    #     for k, v in microscope_state["channels"].items()
+    # }
+    # sweep_times = {
+    #     k: 2 * v["camera_exposure_time"] / 1000
+    #     for k, v in microscope_state["channels"].items()
+    # }
+
+    (
+        exposure_times,
+        sweep_times,
+    ) = model.active_microscope.calculate_exposure_sweep_times()
+
+    waveform_dict = rf.adjust(exposure_times, sweep_times)
+
+    for k, v in waveform_dict.items():
+        try:
+            channel = microscope_state["channels"][k]
+            if not channel["is_selected"]:
+                continue
+            assert np.all(v <= rf.remote_focus_max_voltage)
+            assert np.all(v >= rf.remote_focus_min_voltage)
+            assert len(v) == int(sweep_times[k] * rf.sample_rate)
+        except KeyError:
+            # The channel doesn't exist. Points to an issue in how waveform dict
+            # is created.
+            continue

test/model/devices/remote_focus/test_rf_ni.py

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+import pytest
+
+
+@pytest.mark.hardware
+def test_remote_focus_ni_functions():
+    from navigate.model.devices.daq.ni import NIDAQ
+    from navigate.model.devices.remote_focus.ni import NIRemoteFocus
+    from test.model.dummy import DummyModel
+
+    model = DummyModel()
+    daq = NIDAQ(model.configuration)
+    microscope_name = model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    rf = NIRemoteFocus(microscope_name, daq, model.configuration)
+
+    funcs = ["adjust"]
+    args = [
+        [
+            {"channel_1": 0.2, "channel_2": 0.1, "channel_3": 0.15},
+            {"channel_1": 0.3, "channel_2": 0.2, "channel_3": 0.25},
+        ]
+    ]
+
+    for f, a in zip(funcs, args):
+        if a is not None:
+            getattr(rf, f)(*a)
+        else:
+            getattr(rf, f)()

test/model/devices/remote_focus/test_rf_synthetic.py

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+def test_remote_focus_synthetic_functions():
+    from navigate.model.devices.remote_focus.synthetic import (
+        SyntheticRemoteFocus,
+    )
+    from test.model.dummy import DummyModel
+
+    model = DummyModel()
+    microscope_name = model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    rf = SyntheticRemoteFocus(microscope_name, None, model.configuration)
+
+    funcs = ["move"]
+    args = [[0.1, None]]
+
+    for f, a in zip(funcs, args):
+        if a is not None:
+            getattr(rf, f)(*a)
+        else:
+            getattr(rf, f)()