ephys-link 2.2.1__tar.gz → 2.3.3__tar.gz

{ephys_link-2.2.1 → ephys_link-2.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ephys-link
-Version: 2.2.1
+Version: 2.3.3
 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
@@ -27,7 +27,7 @@ Requires-Dist: keyboard==0.13.5
 Requires-Dist: packaging==25.0
 Requires-Dist: platformdirs==4.5.1
 Requires-Dist: pyserial==3.5
-Requires-Dist: python-socketio==5.15.1
+Requires-Dist: python-socketio==5.16.0
 Requires-Dist: requests==2.32.5
 Requires-Dist: rich==14.2.0
 Requires-Dist: sensapex==1.504.1

{ephys_link-2.2.1 → ephys_link-2.3.3}/pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "packaging==25.0",
     "platformdirs==4.5.1",
     "pyserial==3.5",
-    "python-socketio==5.15.1",
+    "python-socketio==5.16.0",
     "requests==2.32.5",
     "sensapex==1.504.1",
     "rich==14.2.0",

{ephys_link-2.2.1 → ephys_link-2.3.3}/scripts/jackhammer.py

@@ -3,19 +3,25 @@ from ctypes import c_char, c_int
 from sensapex import UMP
 
 # Edit these parameters:
-DEVICE_ID = 3  # Manipulator ID.
+DEVICE_ID = 6  # Manipulator ID.
 AXIS = 3  # Axis (0=X, 1=Y, 2=Z, 3=D).
 
-NUMBER_OF_CYCLES = 20  # Number of time the first and second stage are repeated.
+NUMBER_OF_CYCLES = 120  # Number of time the first and second stage are repeated.
 
 NUMBER_OF_STEP_IN_FIRST_STAGE = 10
 FIRST_STAGE_THRUST_LENGTH = 15  # +/- 0 - 100
 
-NUMBER_OF_STEP_IN_SECOND_STAGE = 5
+NUMBER_OF_STEP_IN_SECOND_STAGE = 10
 SECOND_STAGE_THRUST_LENGTH = -15  # +/- 0 - 100
 
 # Do not edit below this line.
 um = UMP.get_ump()
+# test how much advancement is made after each iteration
+# test if looping thru each iteration is much slower than 20 in one call
+# Add delta variable and compare the advancement after each call until the manipulator either goes back or reaches the desired delta
+# Add get_position calls to monitor the position in the um.call
+# have a for loop or hard code number of iterations to compare the advancement after each call
+
 
 um.call(
     "um_take_jackhammer_step",

ephys_link-2.3.3/scripts/test_jackhammer.py

@@ -0,0 +1,14 @@
+from socketio import SimpleClient
+
+sio = SimpleClient()
+sio.connect("http://localhost:3000")
+result = sio.call("jackhammer", '''{
+    "manipulator_id": "6",
+    "iterations": 3,
+    "phase1_steps": 1,
+    "phase1_pulses": 80,
+    "phase2_steps": 1,
+    "phase2_pulses": -80
+}''')
+print(result)
+sio.disconnect()

ephys_link-2.3.3/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "2.3.3"

{ephys_link-2.2.1 → ephys_link-2.3.3}/src/ephys_link/back_end/platform_handler.py

@@ -6,7 +6,7 @@ Instantiates the appropriate bindings based on the platform type and uses them t
 Usage:
     Instantiate PlatformHandler with the platform type and call the desired command.
 """
-
+import asyncio
 from typing import final
 
 from vbl_aquarium.models.ephys_link import (
@@ -229,6 +229,44 @@ class PlatformHandler:
         else:
             self._inside_brain.discard(request.manipulator_id)
         return BooleanStateResponse(state=request.inside)
+    
+    async def jackhammer(
+        self,
+        manipulator_id: str,
+        axis: int,
+        iterations: int,
+        phase1_steps: int,
+        phase1_pulses: int,
+        phase2_steps: int,
+        phase2_pulses: int,
+    ) -> PositionalResponse:
+        """Perform jackhammer motion to break through dura.
+
+        Args:
+            manipulator_id: Manipulator ID.
+            axis: Axis to move (0=X, 1=Y, 2=Z, 3=W/Depth).
+            iterations: Number of jackhammer cycles.
+            phase1_steps: Number of steps in phase 1.
+            phase1_pulses: Pulse count for phase 1.
+            phase2_steps: Number of steps in phase 2.
+            phase2_pulses: Pulse count for phase 2.
+
+        Returns:
+            Final position of the manipulator after jackhammer and an error message if any.
+        """
+        try:
+            await self._bindings.jackhammer(
+                manipulator_id, axis, iterations, phase1_steps, phase1_pulses, phase2_steps, phase2_pulses
+            )
+            await asyncio.sleep(2)  # wait for movement to settle
+            final_position = self._bindings.platform_space_to_unified_space(
+                await self._bindings.get_position(manipulator_id)
+            )
+        except Exception as e:  # noqa: BLE001
+            self._console.exception_error_print("Jackhammer", e)
+            return PositionalResponse(error=self._console.pretty_exception(e))
+        else:
+            return PositionalResponse(position=final_position)
 
     async def stop(self, manipulator_id: str) -> str:
         """Stop a manipulator.

{ephys_link-2.2.1 → ephys_link-2.3.3}/src/ephys_link/back_end/server.py

@@ -242,6 +242,24 @@ class Server:
                 return await self._run_if_data_parses(
                     self._platform_handler.set_inside_brain, SetInsideBrainRequest, event, data
                 )
+            case "jackhammer":
+                if data:
+                    try:
+                        parsed = loads(str(data))
+                        return (
+                            await self._platform_handler.jackhammer(
+                                manipulator_id=parsed.get("manipulator_id", parsed.get("ManipulatorId", "")),
+                                axis=parsed.get("axis", parsed.get("Axis", 3)),
+                                iterations=parsed.get("iterations", parsed.get("Iterations", 10)),
+                                phase1_steps=parsed.get("phase1_steps", parsed.get("Phase1Steps", 10)),
+                                phase1_pulses=parsed.get("phase1_pulses", parsed.get("Phase1Pulses", 15)),
+                                phase2_steps=parsed.get("phase2_steps", parsed.get("Phase2Steps", 5)),
+                                phase2_pulses=parsed.get("phase2_pulses", parsed.get("Phase2Pulses", -15)),
+                            )
+                        ).to_json_string()
+                    except JSONDecodeError:
+                        return self._malformed_request_response(event, data)
+                return self._malformed_request_response(event, data)
             case "stop":
                 if data:
                     return await self._platform_handler.stop(str(data))  # pyright: ignore[reportAny]

{ephys_link-2.2.1 → ephys_link-2.3.3}/src/ephys_link/bindings/mpm_binding.py

@@ -206,6 +206,7 @@ class MPMBinding(BaseBinding):
         # Keep track of the previous depth to check if the manipulator stopped advancing unexpectedly.
         current_depth = (await self.get_position(manipulator_id)).w
         previous_depth = current_depth
+        depth = self.get_dimensions().w - depth
         unchanged_counter = 0
 
         # Send move request.
@@ -244,7 +245,7 @@ class MPMBinding(BaseBinding):
         self._movement_stopped = False
 
         # Return the final depth.
-        return float((await self.get_position(manipulator_id)).w)
+        return float(self.get_dimensions().w - (await self.get_position(manipulator_id)).w)
 
     @override
     async def stop(self, manipulator_id: str) -> None:

{ephys_link-2.2.1 → ephys_link-2.3.3}/src/ephys_link/bindings/ump_binding.py

@@ -10,6 +10,7 @@ from sensapex import UMP, SensapexDevice  # pyright: ignore [reportMissingTypeSt
 from vbl_aquarium.models.unity import Vector4
 
 from ephys_link.utils.base_binding import BaseBinding
+from ctypes import c_char, c_int
 from ephys_link.utils.converters import (
     list_to_vector4,
     scalar_mm_to_um,
@@ -144,6 +145,28 @@ class UmpBinding(BaseBinding):
     async def stop(self, manipulator_id: str) -> None:
         self._get_device(manipulator_id).stop()  # pyright: ignore [reportUnknownMemberType]
 
+    @override
+    async def jackhammer(
+        self,
+        manipulator_id: str,
+        axis: int,
+        iterations: int,
+        phase1_steps: int,
+        phase1_pulses: int,
+        phase2_steps: int,
+        phase2_pulses: int,
+    ) -> None:
+        self._ump.call(
+            "um_take_jackhammer_step",
+            c_int(int(manipulator_id)),
+            c_char(axis),
+            c_int(iterations),
+            c_int(phase1_steps),
+            c_int(phase1_pulses),
+            c_int(phase2_steps),
+            c_int(phase2_pulses),
+        )
+
     @override
     def platform_space_to_unified_space(self, platform_space: Vector4) -> Vector4:
         """

{ephys_link-2.2.1 → ephys_link-2.3.3}/src/ephys_link/utils/base_binding.py

@@ -147,6 +147,31 @@ class BaseBinding(ABC):
             manipulator_id: Manipulator ID.
         """
 
+
+    async def jackhammer(
+        self,
+        manipulator_id: str,
+        axis: int,
+        iterations: int,
+        phase1_steps: int,
+        phase1_pulses: int,
+        phase2_steps: int,
+        phase2_pulses: int,
+    ) -> None:
+        """Perform jackhammer motion to break through dura.
+
+        Args:
+            manipulator_id: Manipulator ID.
+            axis: Axis to move (0=X, 1=Y, 2=Z, 3=W/Depth).
+            iterations: Number of jackhammer cycles.
+            phase1_steps: Number of steps in phase 1.
+            phase1_pulses: Pulse count for phase 1 (positive=forward).
+            phase2_steps: Number of steps in phase 2.
+            phase2_pulses: Pulse count for phase 2 (negative=backward).
+        """
+        error_message = f"{self.get_display_name()} does not support jackhammer mode"
+        raise NotImplementedError(error_message)
+
     @abstractmethod
     def platform_space_to_unified_space(self, platform_space: Vector4) -> Vector4:
         """Convert platform space coordinates to unified space coordinates.

ephys_link-2.2.1/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "2.2.1"