362 new scale mpm bindings (#374)

* Read bindings, draft write, not real export yet

* Put TODO

* Version bump

* Move manipulator and handle system getting stuck

* WIP set depth

* Better movement code

* Fix some linting errors, update aquarium

* Switch to local coordinate system

* Merged depth binding and position

* Update python module launch instructions

* Version bump

* MPM echoing like other platforms. Need to limit HTTP debug

* Restrict debug log level to just ephys link

* Switch step mode

* Correct movement direction

* fixed position update and target coordinates for depth

* Progress with duplicated coordinate.

* Revert "Progress with duplicated coordinate."

This reverts commit 3eed59b.

* Dual axis movement does not work

* MPM movement working

* Apply poll limit to position

* Auto format code

---------

Co-authored-by: kjy5 <[email protected]>

README.md

@@ -80,13 +80,12 @@ window instead of `localhost`.
 pip install ephys-link
 ```
 
-Import the modules you need and launch the server.
+Import main and run (this will launch the setup GUI).
 
 ```python
-from ephys_link.server import Server
+from ephys_link.__main__ import main
 
-server = Server()
-server.launch("sensapex", args.proxy_address, 8081)
+main()
 ```
 
 ## Install for Development

pyproject.toml

@@ -61,6 +61,7 @@ exclude = ["/.github", "/.idea"]
 [tool.hatch.envs.default]
 python = "3.12"
 dependencies = [
+    "mypy",
     "coverage[toml]>=6.5",
     "pytest",
 ]

scripts/move_tester.py

@@ -1,15 +1,16 @@
 from asyncio import run
 
-from vbl_aquarium.models.ephys_link import SetPositionRequest
+from vbl_aquarium.models.ephys_link import EphysLinkOptions, SetDepthRequest
 from vbl_aquarium.models.unity import Vector4
 
 from ephys_link.back_end.platform_handler import PlatformHandler
 from ephys_link.util.console import Console
 
 c = Console(enable_debug=True)
-p = PlatformHandler("ump-4", c)
-target = Vector4()
-# target = Vector4(x=10, y=10, z=10, w=10)
+p = PlatformHandler(EphysLinkOptions(type="pathfinder-mpm"), c)
+# target = Vector4()
+target = Vector4(x=7.5, y=7.5, z=7.5, w=7.5)
 
-print(run(p.set_position(SetPositionRequest(manipulator_id="6", position=target, speed=5))).to_json_string())
+# print(run(p.set_position(SetPositionRequest(manipulator_id="A", position=target, speed=5))).to_json_string())
+print(run(p.set_depth(SetDepthRequest(manipulator_id="A", depth=7.5, speed=0.15))).to_json_string())
 print("Done!")

src/ephys_link/__about__.py

@@ -1 +1 @@
-__version__ = "2.0.0b3"
+__version__ = "2.0.0b5"

src/ephys_link/__main__.py

@@ -31,7 +31,7 @@ def main() -> None:
     console = Console(enable_debug=options.debug)
 
     # 3. Instantiate the Platform Handler with the appropriate platform bindings.
-    platform_handler = PlatformHandler(options.type, console)
+    platform_handler = PlatformHandler(options, console)
 
     # 4. Instantiate the Emergency Stop service.
 

src/ephys_link/back_end/platform_handler.py

@@ -12,6 +12,7 @@
 from vbl_aquarium.models.ephys_link import (
     AngularResponse,
     BooleanStateResponse,
+    EphysLinkOptions,
     GetManipulatorsResponse,
     PositionalResponse,
     SetDepthRequest,
@@ -25,6 +26,7 @@
 
 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_4_bindings import Ump4Bindings
 from ephys_link.util.base_bindings import BaseBindings
 from ephys_link.util.common import vector4_to_array
@@ -34,43 +36,45 @@
 class PlatformHandler:
     """Handler for platform commands."""
 
-    def __init__(self, platform_type: str, console: Console) -> None:
+    def __init__(self, options: EphysLinkOptions, console: Console) -> None:
         """Initialize platform handler.
 
-        :param platform_type: Platform type to initialize bindings from.
-        :type platform_type: str
+        :param options: CLI options.
+        :type options: EphysLinkOptions
         """
 
-        # Store the platform type.
-        self._platform_type = platform_type
+        # Store the CLI options.
+        self._options = options
 
         # Store the console.
         self._console = console
 
         # Define bindings based on platform type.
-        self._bindings = self._match_platform_type(platform_type)
+        self._bindings = self._match_platform_type(options)
 
         # Record which IDs are inside the brain.
         self._inside_brain: set[str] = set()
 
         # Generate a Pinpoint ID for proxy usage.
         self._pinpoint_id = str(uuid4())[:8]
 
-    def _match_platform_type(self, platform_type: str) -> BaseBindings:
+    def _match_platform_type(self, options: EphysLinkOptions) -> BaseBindings:
         """Match the platform type to the appropriate bindings.
 
-        :param platform_type: Platform type.
-        :type platform_type: str
+        :param options: CLI options.
+        :type options: EphysLinkOptions
         :returns: Bindings for the specified platform type.
         :rtype: :class:`ephys_link.util.base_bindings.BaseBindings`
         """
-        match platform_type:
+        match options.type:
             case "ump-4":
                 return Ump4Bindings()
+            case "pathfinder-mpm":
+                return MPMBinding(options.mpm_port)
             case "fake":
                 return FakeBindings()
             case _:
-                error_message = f'Platform type "{platform_type}" not recognized.'
+                error_message = f'Platform type "{options.type}" not recognized.'
                 self._console.critical_print(error_message)
                 raise ValueError(error_message)
 
@@ -99,7 +103,7 @@ def get_platform_type(self) -> str:
         :returns: Platform type config identifier (see CLI options for examples).
         :rtype: str
         """
-        return self._platform_type
+        return str(self._options.type)
 
     # Manipulator commands.
 
@@ -111,7 +115,7 @@ async def get_manipulators(self) -> GetManipulatorsResponse:
         """
         try:
             manipulators = await self._bindings.get_manipulators()
-            num_axes = await self._bindings.get_num_axes()
+            num_axes = await self._bindings.get_axes_count()
             dimensions = self._bindings.get_dimensions()
         except Exception as e:
             self._console.exception_error_print("Get Manipulators", e)
@@ -198,16 +202,16 @@ async def set_position(self, request: SetPositionRequest) -> PositionalResponse:
 
             # Return error if movement did not reach target within tolerance.
             for index, axis in enumerate(vector4_to_array(final_unified_position - request.position)):
-                # End once index is greater than the number of axes.
-                if index >= await self._bindings.get_num_axes():
+                # End once index is the number of axes.
+                if index == await self._bindings.get_axes_count():
                     break
 
                 # Check if the axis is within the movement tolerance.
-                if abs(axis) > await self._bindings.get_movement_tolerance():
+                if abs(axis) > self._bindings.get_movement_tolerance():
                     error_message = (
                         f"Manipulator {request.manipulator_id} did not reach target"
                         f" position on axis {list(Vector4.model_fields.keys())[index]}."
-                        f"Requested: {request.position}, got: {final_unified_position}."
+                        f" Requested: {request.position}, got: {final_unified_position}."
                     )
                     self._console.error_print("Set Position", error_message)
                     return PositionalResponse(error=error_message)
@@ -226,24 +230,27 @@ async def set_depth(self, request: SetDepthRequest) -> SetDepthResponse:
         :rtype: :class:`vbl_aquarium.models.ephys_link.DriveToDepthResponse`
         """
         try:
-            # Create a position based on the new depth.
-            current_platform_position = await self._bindings.get_position(request.manipulator_id)
-            current_unified_position = self._bindings.platform_space_to_unified_space(current_platform_position)
-            target_unified_position = current_unified_position.model_copy(update={"w": request.depth})
-            target_platform_position = self._bindings.unified_space_to_platform_space(target_unified_position)
-
             # Move to the new depth.
-            final_platform_position = await self._bindings.set_position(
+            final_platform_depth = await self._bindings.set_depth(
                 manipulator_id=request.manipulator_id,
-                position=target_platform_position,
+                depth=self._bindings.unified_space_to_platform_space(Vector4(w=request.depth)).w,
                 speed=request.speed,
             )
-            final_unified_position = self._bindings.platform_space_to_unified_space(final_platform_position)
+            final_unified_depth = self._bindings.platform_space_to_unified_space(Vector4(w=final_platform_depth)).w
+
+            # Return error if movement did not reach target within tolerance.
+            if abs(final_unified_depth - request.depth) > self._bindings.get_movement_tolerance():
+                error_message = (
+                    f"Manipulator {request.manipulator_id} did not reach target depth."
+                    f" Requested: {request.depth}, got: {final_unified_depth}."
+                )
+                self._console.error_print("Set Depth", error_message)
+                return SetDepthResponse(error=error_message)
         except Exception as e:
             self._console.exception_error_print("Set Depth", e)
             return SetDepthResponse(error=self._console.pretty_exception(e))
         else:
-            return SetDepthResponse(depth=final_unified_position.w)
+            return SetDepthResponse(depth=final_unified_depth)
 
     async def set_inside_brain(self, request: SetInsideBrainRequest) -> BooleanStateResponse:
         """Mark a manipulator as inside the brain or not.

src/ephys_link/back_end/server.py

@@ -12,7 +12,7 @@
     SetInsideBrainRequest,
     SetPositionRequest,
 )
-from vbl_aquarium.models.generic import VBLBaseModel
+from vbl_aquarium.utils.vbl_base_model import VBLBaseModel
 
 from ephys_link.back_end.platform_handler import PlatformHandler
 from ephys_link.util.common import PORT, check_for_updates, server_preamble

src/ephys_link/bindings/fake_bindings.py

@@ -1,6 +1,7 @@
 from vbl_aquarium.models.unity import Vector3, Vector4
 
 from ephys_link.util.base_bindings import BaseBindings
+from ephys_link.util.common import array_to_vector4
 
 
 class FakeBindings(BaseBindings):
@@ -22,11 +23,11 @@ def __init__(self) -> None:
     async def get_manipulators(self) -> list[str]:
         return list(map(str, range(8)))
 
-    async def get_num_axes(self) -> int:
+    async def get_axes_count(self) -> int:
         return 4
 
     def get_dimensions(self) -> Vector4:
-        return Vector4(x=20, y=20, z=20, w=20)
+        return array_to_vector4([20] * 4)
 
     async def get_position(self, manipulator_id: str) -> Vector4:
         return self._positions[int(manipulator_id)]
@@ -37,13 +38,17 @@ async def get_angles(self, manipulator_id: str) -> Vector3:
     async def get_shank_count(self, _: str) -> int:
         return 1
 
-    async def get_movement_tolerance(self) -> float:
+    def get_movement_tolerance(self) -> float:
         return 0.001
 
     async def set_position(self, manipulator_id: str, position: Vector4, _: float) -> Vector4:
         self._positions[int(manipulator_id)] = position
         return position
 
+    async def set_depth(self, manipulator_id: str, depth: float, _: float) -> float:
+        self._positions[int(manipulator_id)].w = depth
+        return depth
+
     async def stop(self, _: str) -> None:
         pass