ephys-link 2.0.0b5__tar.gz → 2.0.0b6__tar.gz

{ephys_link-2.0.0b5 → ephys_link-2.0.0b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: ephys-link
-Version: 2.0.0b5
+Version: 2.0.0b6
 Summary: A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.
 Project-URL: Documentation, https://virtualbrainlab.org/ephys_link/installation_and_use.html
 Project-URL: Issues, https://github.com/VirtualBrainLab/ephys-link/issues
@@ -26,14 +26,14 @@ Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: <3.13,>=3.10
-Requires-Dist: aiohttp==3.9.5
+Requires-Dist: aiohttp==3.10.8
 Requires-Dist: colorama==0.4.6
-Requires-Dist: platformdirs==4.2.2
+Requires-Dist: platformdirs==4.3.6
 Requires-Dist: pyserial==3.5
-Requires-Dist: python-socketio[asyncio-client]==5.11.3
-Requires-Dist: pythonnet==3.0.3
+Requires-Dist: python-socketio[asyncio-client]==5.11.4
+Requires-Dist: pythonnet==3.0.4
 Requires-Dist: requests==2.32.3
-Requires-Dist: rich==13.7.1
+Requires-Dist: rich==13.8.1
 Requires-Dist: sensapex==1.400.1
 Requires-Dist: vbl-aquarium==0.0.22
 Description-Content-Type: text/markdown

{ephys_link-2.0.0b5 → ephys_link-2.0.0b6}/pyproject.toml

@@ -30,15 +30,15 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
 dependencies = [
-    "aiohttp==3.9.5",
+    "aiohttp==3.10.8",
     "colorama==0.4.6",
-    "platformdirs==4.2.2",
+    "platformdirs==4.3.6",
     "pyserial==3.5",
-    "python-socketio[asyncio_client]==5.11.3",
-    "pythonnet==3.0.3",
+    "python-socketio[asyncio_client]==5.11.4",
+    "pythonnet==3.0.4",
     "requests==2.32.3",
     "sensapex==1.400.1",
-    "rich==13.7.1",
+    "rich==13.8.1",
     "vbl-aquarium==0.0.22"
 ]
 

ephys_link-2.0.0b6/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "2.0.0b6"

{ephys_link-2.0.0b5 → ephys_link-2.0.0b6}/src/ephys_link/back_end/platform_handler.py

@@ -27,6 +27,7 @@ from vbl_aquarium.models.unity import Vector4
 from ephys_link.__about__ import __version__
 from ephys_link.bindings.fake_bindings import FakeBindings
 from ephys_link.bindings.mpm_bindings import MPMBinding
+from ephys_link.bindings.ump_3_bindings import Ump3Bindings
 from ephys_link.bindings.ump_4_bindings import Ump4Bindings
 from ephys_link.util.base_bindings import BaseBindings
 from ephys_link.util.common import vector4_to_array
@@ -69,6 +70,8 @@ class PlatformHandler:
         match options.type:
             case "ump-4":
                 return Ump4Bindings()
+            case "ump-3":
+                return Ump3Bindings()
             case "pathfinder-mpm":
                 return MPMBinding(options.mpm_port)
             case "fake":

ephys_link-2.0.0b6/src/ephys_link/bindings/ump_3_bindings.py

@@ -0,0 +1,138 @@
+"""Bindings for Sensapex uMp-3 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,
+    scalar_mm_to_um,
+    um_to_mm,
+    vector4_to_array,
+    vector_mm_to_um,
+)
+
+
+class Ump3Bindings(BaseBindings):
+    """Bindings for UMP-3 platform"""
+
+    def __init__(self) -> None:
+        """Initialize UMP-3 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"
+            raise ValueError(error_message)
+
+    async def get_manipulators(self) -> list[str]:
+        return list(map(str, self._ump.list_devices()))
+
+    async def get_axes_count(self) -> int:
+        return 3
+
+    def get_dimensions(self) -> Vector4:
+        return Vector4(x=20, y=20, z=20, w=20)
+
+    async def get_position(self, manipulator_id: str) -> Vector4:
+        manipulator_position = self._get_device(manipulator_id).get_pos(1)
+
+        # Add the depth axis to the end of the position.
+        manipulator_position.append(manipulator_position[0])
+
+        # Convert and return.
+        return um_to_mm(array_to_vector4(manipulator_position))
+
+    # noinspection PyTypeChecker
+    async def get_angles(self, _: str) -> Vector3:
+        """uMp-3 does not support getting angles so raise an error.
+
+        :raises: AttributeError
+        """
+        error_message = "UMP-3 does not support getting angles"
+        raise AttributeError(error_message)
+
+    # noinspection PyTypeChecker
+    async def get_shank_count(self, _: str) -> int:
+        """uMp-3 does not support getting shank count so raise an error.
+
+        :raises: AttributeError
+        """
+        error_message = "UMP-3 does not support getting shank count"
+        raise AttributeError(error_message)
+
+    def get_movement_tolerance(self) -> float:
+        return 0.001
+
+    # noinspection DuplicatedCode
+    async def set_position(self, manipulator_id: str, position: Vector4, speed: float) -> Vector4:
+        # Convert position to micrometers.
+        target_position_um = vector_mm_to_um(position)
+
+        # Request movement.
+        movement = self._get_device(manipulator_id).goto_pos(
+            vector4_to_array(target_position_um), scalar_mm_to_um(speed)
+        )
+
+        # Wait for movement to complete.
+        await get_running_loop().run_in_executor(None, movement.finished_event.wait, None)
+
+        # 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 set_depth(self, manipulator_id: str, depth: float, speed: float) -> float:
+        # Augment current position with depth.
+        current_position = await self.get_position(manipulator_id)
+        new_platform_position = current_position.model_copy(update={"x": depth})
+
+        # Make the movement.
+        final_platform_position = await self.set_position(manipulator_id, new_platform_position, speed)
+
+        # Return the final depth.
+        return float(final_platform_position.w)
+
+    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        <-  -x
+        # +z        <-  -z
+        # +d        <-  +d/x
+
+        return Vector4(
+            x=platform_space.y,
+            y=self.get_dimensions().x - platform_space.x,
+            z=self.get_dimensions().z - platform_space.z,
+            w=platform_space.w,
+        )
+
+    def unified_space_to_platform_space(self, unified_space: Vector4) -> Vector4:
+        # platform  <-  unified
+        # +x        <-  -y
+        # +y        <-  +x
+        # +z        <-  -z
+        # +d/x      <-  +d
+
+        return Vector4(
+            x=self.get_dimensions().y - unified_space.y,
+            y=unified_space.x,
+            z=self.get_dimensions().z - unified_space.z,
+            w=unified_space.w,
+        )
+
+    # Helper methods.
+    def _get_device(self, manipulator_id: str) -> SensapexDevice:
+        return self._ump.get_device(int(manipulator_id))

{ephys_link-2.0.0b5 → ephys_link-2.0.0b6}/src/ephys_link/bindings/ump_4_bindings.py

@@ -65,6 +65,7 @@ class Ump4Bindings(BaseBindings):
     def get_movement_tolerance(self) -> float:
         return 0.001
 
+    # noinspection DuplicatedCode
     async def set_position(self, manipulator_id: str, position: Vector4, speed: float) -> Vector4:
         # Convert position to micrometers.
         target_position_um = vector_mm_to_um(position)
@@ -75,7 +76,7 @@ class Ump4Bindings(BaseBindings):
         )
 
         # Wait for movement to finish.
-        await get_running_loop().run_in_executor(None, movement.finished_event.wait)
+        await get_running_loop().run_in_executor(None, movement.finished_event.wait, None)
 
         # Handle interrupted movement.
         if movement.interrupted:

ephys_link-2.0.0b5/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0b5"