feat: init

test/model/devices/galvo/test_galvo_base.py

@@ -0,0 +1,145 @@
+# 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.
+
+import unittest
+from unittest.mock import MagicMock
+from navigate.model.devices.galvo.synthetic import SyntheticGalvo
+from navigate.config import (
+    load_configs,
+    get_configuration_paths,
+    verify_configuration,
+    verify_waveform_constants,
+)
+from multiprocessing import Manager
+import numpy as np
+
+
+class TestGalvoBase(unittest.TestCase):
+    def setUp(self) -> None:
+        """Set up the configuration, experiment, etc."""
+        self.manager = Manager()
+        self.parent_dict = {}
+
+        (
+            configuration_path,
+            experiment_path,
+            waveform_constants_path,
+            rest_api_path,
+            waveform_templates_path,
+            gui_configuration_path,
+            multi_positions_path,
+        ) = get_configuration_paths()
+
+        self.configuration = load_configs(
+            self.manager,
+            configuration=configuration_path,
+            experiment=experiment_path,
+            waveform_constants=waveform_constants_path,
+            rest_api_config=rest_api_path,
+            waveform_templates=waveform_templates_path,
+            gui_configuration_path=gui_configuration_path,
+        )
+
+        verify_configuration(self.manager, self.configuration)
+        verify_waveform_constants(self.manager, self.configuration)
+        self.microscope_name = "Mesoscale"
+        self.device_connection = MagicMock()
+        galvo_id = 0
+
+        self.galvo = SyntheticGalvo(
+            microscope_name=self.microscope_name,
+            device_connection=self.device_connection,
+            configuration=self.configuration,
+            device_id=galvo_id,
+        )
+
+        self.exposure_times = {"channel_1": 0.11, "channel_2": 0.2, "channel_3": 0.3}
+        self.sweep_times = {"channel_1": 0.115, "channel_2": 0.2, "channel_3": 0.3}
+
+    def tearDown(self):
+        """Tear down the multiprocessing manager."""
+        self.manager.shutdown()
+
+    def test_galvo_base_initialization(self):
+        # Parent Class Super Init
+        assert self.galvo.microscope_name == "Mesoscale"
+        assert self.galvo.galvo_name == "Galvo 0"
+        assert self.galvo.sample_rate == 100000
+
+        assert (
+            self.galvo.camera_delay
+            == self.configuration["configuration"]["microscopes"][self.microscope_name][
+                "camera"
+            ]["delay"]
+            / 1000
+        )
+        assert self.galvo.galvo_max_voltage == 5
+        assert self.galvo.galvo_min_voltage == -5
+        assert self.galvo.galvo_waveform == "sawtooth" or "sine"
+        assert self.galvo.waveform_dict == {}
+
+    def test_adjust_with_valid_input(self):
+        # Test the method with valid input data
+        for waveform in ["sawtooth", "sine"]:
+            self.galvo.galvo_waveform = waveform
+            result = self.galvo.adjust(self.exposure_times, self.sweep_times)
+
+            # Assert that the result is a dictionary
+            self.assertIsInstance(result, dict)
+
+            # Assert that the keys in the result dictionary are the same as in the input
+            # dictionaries
+            self.assertSetEqual(set(result.keys()), set(self.exposure_times.keys()))
+
+            # Assert that the values in the result dictionary are not None
+            for value in result.values():
+                self.assertIsNotNone(value)
+
+    def test_adjust_with_invalid_input(self):
+        # Test the method with invalid input data
+        invalid_exposure_times = {"channel_1": 0.1}  # Missing channel 2 and 3 keys
+        invalid_sweep_times = {"channel_1": 0.1}  # Missing channel 2 and 3 keys
+
+        # Test if the method raises an exception or returns None with invalid input
+        with self.assertRaises(KeyError):
+            _ = self.galvo.adjust(invalid_exposure_times, invalid_sweep_times)
+
+    def test_with_improper_waveform(self):
+        self.galvo.galvo_waveform = "banana"
+        result = self.galvo.adjust(self.exposure_times, self.sweep_times)
+        assert result == self.galvo.waveform_dict
+
+    def test_waveform_clipping(self):
+        self.galvo.galvo_waveform = "sawtooth"
+        result = self.galvo.adjust(self.exposure_times, self.sweep_times)
+        for channel in "channel_1", "channel_2", "channel_3":
+            assert np.all(result[channel] <= self.galvo.galvo_max_voltage)
+            assert np.all(result[channel] >= self.galvo.galvo_min_voltage)

test/model/devices/galvo/test_galvo_ni.py

@@ -0,0 +1,133 @@
+# 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.
+
+import unittest
+from unittest.mock import MagicMock
+from navigate.model.devices.galvo.ni import NIGalvo
+from navigate.config import (
+    load_configs,
+    get_configuration_paths,
+    verify_configuration,
+    verify_waveform_constants,
+)
+from multiprocessing import Manager
+
+
+class TestNIGalvo(unittest.TestCase):
+    """Unit tests for the Galvo NI Device."""
+
+    def setUp(self) -> None:
+        """Set up the configuration, experiment, etc."""
+        self.manager = Manager()
+        self.parent_dict = {}
+
+        (
+            configuration_path,
+            experiment_path,
+            waveform_constants_path,
+            rest_api_path,
+            waveform_templates_path,
+            gui_configuration_path,
+            multi_positions_path,
+        ) = get_configuration_paths()
+
+        self.configuration = load_configs(
+            self.manager,
+            configuration=configuration_path,
+            experiment=experiment_path,
+            waveform_constants=waveform_constants_path,
+            rest_api_config=rest_api_path,
+            waveform_templates=waveform_templates_path,
+            gui_configuration_path=gui_configuration_path,
+        )
+        verify_configuration(self.manager, self.configuration)
+        verify_waveform_constants(self.manager, self.configuration)
+        self.microscope_name = "Mesoscale"
+        self.device_connection = MagicMock()
+        galvo_id = 0
+
+        self.galvo = NIGalvo(
+            microscope_name=self.microscope_name,
+            device_connection=self.device_connection,
+            configuration=self.configuration,
+            device_id=galvo_id,
+        )
+
+    def tearDown(self):
+        """Tear down the multiprocessing manager."""
+        self.manager.shutdown()
+
+    def test_galvo_ni_initialization(self):
+        # Parent Class Super Init
+        assert self.galvo.microscope_name == "Mesoscale"
+        assert self.galvo.galvo_name == "Galvo 0"
+        assert self.galvo.sample_rate == 100000
+        assert (
+            self.galvo.camera_delay
+            == self.configuration["configuration"]["microscopes"][self.microscope_name][
+                "camera"
+            ]["delay"]
+            / 1000
+        )
+        assert self.galvo.galvo_max_voltage == 5
+        assert self.galvo.galvo_min_voltage == -5
+        assert self.galvo.galvo_waveform == "sawtooth" or "sine"
+        assert self.galvo.waveform_dict == {}
+
+        # NIGalvo Init
+        assert self.galvo.trigger_source == "/PXI6259/PFI0"
+        assert hasattr(self.galvo, "daq")
+
+    def test_adjust(self):
+        sweep_times = {"channel_1": 0.3, "channel_2": 0.4, "channel_3": 0.5}
+
+        exposure_times = {"channel_1": 0.25, "channel_2": 0.35, "channel_3": 0.45}
+
+        waveforms = self.galvo.adjust(
+            exposure_times=exposure_times, sweep_times=sweep_times
+        )
+
+        assert type(waveforms) == dict
+        self.device_connection.assert_not_called()
+
+        for channel_key, channel_setting in self.configuration["experiment"][
+            "MicroscopeState"
+        ]["channels"].items():
+            if channel_setting["is_selected"]:
+                assert channel_key in waveforms.keys()
+
+        self.device_connection.analog_outputs.__setitem__.assert_called_with(
+            self.galvo.device_config["hardware"]["channel"],
+            {
+                "trigger_source": self.galvo.trigger_source,
+                "waveform": waveforms,
+            },
+        )

test/model/devices/galvo/test_galvo_synthetic.py

@@ -0,0 +1,86 @@
+# 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.
+
+import unittest
+from unittest.mock import MagicMock
+from navigate.model.devices.galvo.synthetic import SyntheticGalvo
+from navigate.config import (
+    load_configs,
+    get_configuration_paths,
+    verify_configuration,
+    verify_waveform_constants,
+)
+from multiprocessing import Manager
+
+
+class TestGalvoSynthetic(unittest.TestCase):
+    def setUp(self) -> None:
+        self.manager = Manager()
+        self.parent_dict = {}
+
+        (
+            configuration_path,
+            experiment_path,
+            waveform_constants_path,
+            rest_api_path,
+            waveform_templates_path,
+            gui_configuration_path,
+            multi_positions_path,
+        ) = get_configuration_paths()
+
+        self.configuration = load_configs(
+            self.manager,
+            configuration=configuration_path,
+            experiment=experiment_path,
+            waveform_constants=waveform_constants_path,
+            rest_api_config=rest_api_path,
+            waveform_templates=waveform_templates_path,
+            gui_configuration=gui_configuration_path,
+        )
+        verify_configuration(self.manager, self.configuration)
+        verify_waveform_constants(self.manager, self.configuration)
+        self.microscope_name = "Mesoscale"
+        self.device_connection = MagicMock()
+        galvo_id = 0
+
+        self.galvo = SyntheticGalvo(
+            microscope_name=self.microscope_name,
+            device_connection=self.device_connection,
+            configuration=self.configuration,
+            device_id=galvo_id,
+        )
+
+    def tearDown(self) -> None:
+        self.manager.shutdown()
+
+    def test_dunder_del(self):
+        """Test the __del__ method"""
+        self.galvo.__del__()