ephys-link 2.0.0__py3-none-any.whl → 2.0.0b1__py3-none-any.whl

ephys_link/bindings/ump_4_bindings.py

@@ -0,0 +1,127 @@
+"""Bindings for Sensapex uMp-4 platform.
+
+Usage: Instantiate Ump4Bindings to interact with the Sensapex uMp-4 platform.
+"""
+
+from asyncio import get_running_loop
+
+from sensapex import UMP, SensapexDevice
+from vbl_aquarium.models.unity import Vector3, Vector4
+
+from ephys_link.util.base_bindings import BaseBindings
+from ephys_link.util.common import RESOURCES_PATH, array_to_vector4, mm_to_um, mmps_to_umps, um_to_mm, vector4_to_array
+from ephys_link.util.console import Console
+
+
+class Ump4Bindings(BaseBindings):
+    """Bindings for UMP-4 platform"""
+
+    def __init__(self) -> None:
+        """Initialize UMP-4 bindings."""
+
+        # Establish connection to Sensapex API (exit if connection fails).
+        UMP.set_library_path(RESOURCES_PATH)
+        self._ump = UMP.get_ump()
+        if self._ump is None:
+            error_message = "Unable to connect to uMp"
+            Console.error_print(error_message)
+            raise ValueError(error_message)
+
+    async def get_manipulators(self) -> list[str]:
+        return list(map(str, self._ump.list_devices()))
+
+    async def get_num_axes(self) -> int:
+        return 4
+
+    def get_dimensions(self) -> Vector4:
+        return Vector4(x=20, y=20, z=20, w=20)
+
+    async def get_position(self, manipulator_id: str) -> Vector4:
+        return um_to_mm(array_to_vector4(self._get_device(manipulator_id).get_pos(1)))
+
+    # noinspection PyTypeChecker
+    async def get_angles(self, _: str) -> Vector3:
+        """uMp-4 does not support getting angles so raise an error.
+
+        :raises: AttributeError
+        """
+        error_message = "UMP-4 does not support getting angles"
+        raise AttributeError(error_message)
+
+    # noinspection PyTypeChecker
+    async def get_shank_count(self, _: str) -> int:
+        """uMp-4 does not support getting shank count so raise an error.
+
+        :raises: AttributeError
+        """
+        error_message = "UMP-4 does not support getting shank count"
+        raise AttributeError(error_message)
+
+    async def get_movement_tolerance(self) -> float:
+        return 0.001
+
+    async def set_position(self, manipulator_id: str, position: Vector4, speed: float) -> Vector4:
+        """Set the position of the manipulator.
+
+        Waits using Asyncio until the movement is finished. This assumes the application is running in an event loop.
+
+        :param manipulator_id: Manipulator ID.
+        :type manipulator_id: str
+        :param position: Platform space position to set the manipulator to (mm).
+        :type position: Vector4
+        :param speed: Speed to move the manipulator to the position (mm/s).
+        :type speed: float
+        :returns: Final position of the manipulator in platform space (mm).
+        :rtype: Vector4
+        :raises RuntimeError: If the movement is interrupted.
+        """
+        # Convert position to micrometers.
+        target_position_um = mm_to_um(position)
+
+        # Request movement.
+        movement = self._get_device(manipulator_id).goto_pos(vector4_to_array(target_position_um), mmps_to_umps(speed))
+
+        # Wait for movement to finish.
+        await get_running_loop().run_in_executor(None, movement.finished_event.wait)
+
+        # Handle interrupted movement.
+        if movement.interrupted:
+            error_message = f"Manipulator {manipulator_id} interrupted: {movement.interrupt_reason}"
+            raise RuntimeError(error_message)
+
+        return um_to_mm(array_to_vector4(movement.last_pos))
+
+    async def stop(self, manipulator_id: str) -> None:
+        self._get_device(manipulator_id).stop()
+
+    def platform_space_to_unified_space(self, platform_space: Vector4) -> Vector4:
+        # unified   <-  platform
+        # +x        <-  +y
+        # +y        <-  -z
+        # +z        <-  +x
+        # +d        <-  +d
+
+        return Vector4(
+            x=platform_space.y,
+            y=self.get_dimensions().z - platform_space.z,
+            z=platform_space.x,
+            w=platform_space.w,
+        )
+
+    def unified_space_to_platform_space(self, unified_space: Vector4) -> Vector4:
+        # platform  <-  unified
+        # +x        <-  +z
+        # +y        <-  +x
+        # +z        <-  -y
+        # +d        <-  +d
+
+        return Vector4(
+            x=unified_space.z,
+            y=unified_space.x,
+            z=self.get_dimensions().z - unified_space.y,
+            w=unified_space.w,
+        )
+
+    # Helper methods.
+    def _get_device(self, manipulator_id: str) -> SensapexDevice:
+        return self._ump.get_device(int(manipulator_id))

ephys_link/front_end/cli.py

@@ -1,104 +1,98 @@
-"""Command-line interface for the Electrophysiology Manipulator Link.
-
-Usage:
-    Instantiate CLI and call `parse_args()` to get the parsed arguments.
-
-    ```python
-    CLI().parse_args()
-    ```
-"""
-
-from argparse import ArgumentParser
-from typing import final
-
-from vbl_aquarium.models.ephys_link import EphysLinkOptions
-
-from ephys_link.__about__ import __version__ as version
-
-
-@final
-class CLI:
-    """Command-line interface for the Electrophysiology Manipulator Link.
-
-    Configures the CLI parser and options.
-    """
-
-    def __init__(self) -> None:
-        """Initialize CLI parser."""
-
-        self._parser = ArgumentParser(
-            description="Electrophysiology Manipulator Link: a Socket.IO interface for manipulators in electrophysiology experiments.",
-            prog="python -m ephys-link",
-        )
-
-        _ = self._parser.add_argument(
-            "-b", "--background", dest="background", action="store_true", help="Skip configuration window."
-        )
-        _ = self._parser.add_argument(
-            "-i",
-            "--ignore-updates",
-            dest="ignore_updates",
-            action="store_true",
-            help="Skip (ignore) checking for updates.",
-        )
-        _ = self._parser.add_argument(
-            "-t",
-            "--type",
-            type=str,
-            dest="type",
-            default="ump-4",
-            help='Manipulator type (i.e. "ump-4", "pathfinder-mpm", "fake"). Default: "ump-4".',
-        )
-        _ = self._parser.add_argument(
-            "-d",
-            "--debug",
-            dest="debug",
-            action="store_true",
-            help="Enable debug mode.",
-        )
-        _ = self._parser.add_argument(
-            "-p",
-            "--use-proxy",
-            dest="use_proxy",
-            action="store_true",
-            help="Enable proxy mode.",
-        )
-        _ = self._parser.add_argument(
-            "-a",
-            "--proxy-address",
-            type=str,
-            default="proxy2.virtualbrainlab.org",
-            dest="proxy_address",
-            help="Proxy IP address.",
-        )
-        _ = self._parser.add_argument(
-            "--mpm-port",
-            type=int,
-            default=8080,
-            dest="mpm_port",
-            help="Port New Scale Pathfinder MPM's server is on. Default: 8080.",
-        )
-        _ = self._parser.add_argument(
-            "-s",
-            "--serial",
-            type=str,
-            default="no-e-stop",
-            dest="serial",
-            nargs="?",
-            help="Emergency stop serial port (i.e. COM3). Default: disables emergency stop.",
-        )
-        _ = self._parser.add_argument(
-            "-v",
-            "--version",
-            action="version",
-            version=f"Electrophysiology Manipulator Link v{version}",
-            help="Print version and exit.",
-        )
-
-    def parse_args(self) -> EphysLinkOptions:
-        """Parse arguments and return them
-
-        Returns:
-            Parsed arguments
-        """
-        return EphysLinkOptions(**vars(self._parser.parse_args()))  # pyright: ignore [reportAny]
+"""Command-line interface for the Electrophysiology Manipulator Link.
+
+Usage: instantiate CLI and call parse_args() to get the parsed arguments.
+"""
+
+from argparse import ArgumentParser
+
+from vbl_aquarium.models.ephys_link import EphysLinkOptions
+
+from ephys_link.__about__ import __version__ as version
+
+
+class CLI:
+    """Command-line interface for the Electrophysiology Manipulator Link.
+
+    Configures the CLI parser and options.
+    """
+
+    def __init__(self) -> None:
+        """Initialize CLI parser."""
+
+        self._parser = ArgumentParser(
+            description="Electrophysiology Manipulator Link:"
+            " a Socket.IO interface for manipulators in electrophysiology experiments.",
+            prog="python -m ephys-link",
+        )
+
+        self._parser.add_argument(
+            "-b", "--background", dest="background", action="store_true", help="Skip configuration window."
+        )
+        self._parser.add_argument(
+            "-i",
+            "--ignore-updates",
+            dest="ignore_updates",
+            action="store_true",
+            help="Skip (ignore) checking for updates.",
+        )
+        self._parser.add_argument(
+            "-t",
+            "--type",
+            type=str,
+            dest="type",
+            default="ump-4",
+            help='Manipulator type (i.e. "ump-4", "ump-3", "pathfinder-mpm", "new-scale", "fake"). Default: "ump-4".',
+        )
+        self._parser.add_argument(
+            "-d",
+            "--debug",
+            dest="debug",
+            action="store_true",
+            help="Enable debug mode.",
+        )
+        self._parser.add_argument(
+            "-p",
+            "--use-proxy",
+            dest="use_proxy",
+            action="store_true",
+            help="Enable proxy mode.",
+        )
+        self._parser.add_argument(
+            "-a",
+            "--proxy-address",
+            type=str,
+            default="proxy2.virtualbrainlab.org",
+            dest="proxy_address",
+            help="Proxy IP address.",
+        )
+        self._parser.add_argument(
+            "--mpm-port",
+            type=int,
+            default=8080,
+            dest="mpm_port",
+            help="Port New Scale Pathfinder MPM's server is on. Default: 8080.",
+        )
+        self._parser.add_argument(
+            "-s",
+            "--serial",
+            type=str,
+            default="no-e-stop",
+            dest="serial",
+            nargs="?",
+            help="Emergency stop serial port (i.e. COM3). Default: disables emergency stop.",
+        )
+        self._parser.add_argument(
+            "-v",
+            "--version",
+            action="version",
+            version=f"Electrophysiology Manipulator Link v{version}",
+            help="Print version and exit.",
+        )
+
+    def parse_args(self) -> EphysLinkOptions:
+        """Parse arguments and return them
+
+        :returns: Parsed arguments
+        :rtype: EphysLinkOptions
+        """
+        return EphysLinkOptions(**vars(self._parser.parse_args()))