ephys-link 2.0.0b6__py3-none-any.whl → 2.0.0b10__py3-none-any.whl

ephys_link/bindings/ump_3_bindings.py

@@ -1,138 +0,0 @@
-"""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/util/common.py

@@ -1,120 +0,0 @@
-# ruff: noqa: T201
-"""Commonly used utility functions and constants."""
-
-from os.path import join
-from pathlib import Path
-
-from packaging.version import parse
-from requests import get
-from vbl_aquarium.models.unity import Vector4
-
-from ephys_link.__about__ import __version__
-
-# Ephys Link ASCII.
-ASCII = r"""
- ______       _                 _      _       _
-|  ____|     | |               | |    (_)     | |
-| |__   _ __ | |__  _   _ ___  | |     _ _ __ | | __
-|  __| | '_ \| '_ \| | | / __| | |    | | '_ \| |/ /
-| |____| |_) | | | | |_| \__ \ | |____| | | | |   <
-|______| .__/|_| |_|\__, |___/ |______|_|_| |_|_|\_\
-       | |           __/ |
-       |_|          |___/
-"""
-
-# Absolute path to the resource folder.
-RESOURCES_PATH = join(str(Path(__file__).parent.parent.absolute()), "resources")
-
-# Ephys Link Port
-PORT = 3000
-
-
-# Server startup.
-def server_preamble() -> None:
-    """Print the server startup preamble."""
-    print(ASCII)
-    print(__version__)
-    print()
-    print("This is the Ephys Link server window.")
-    print("You may safely leave it running in the background.")
-    print("To stop it, close this window or press CTRL + Pause/Break.")
-    print()
-
-
-def check_for_updates() -> None:
-    """Check for updates to the Ephys Link."""
-    response = get("https://api.github.com/repos/VirtualBrainLab/ephys-link/tags", timeout=10)
-    latest_version = response.json()[0]["name"]
-    if parse(latest_version) > parse(__version__):
-        print(f"Update available: {latest_version} !")
-        print("Download at: https://github.com/VirtualBrainLab/ephys-link/releases/latest")
-
-
-# Unit conversions
-
-
-def scalar_mm_to_um(mm: float) -> float:
-    """Convert scalar values of millimeters to micrometers.
-
-    :param mm: Scalar value in millimeters.
-    :type mm: float
-    :returns: Scalar value in micrometers.
-    :rtype: float
-    """
-    return mm * 1_000
-
-
-def vector_mm_to_um(mm: Vector4) -> Vector4:
-    """Convert vector values of millimeters to micrometers.
-
-    :param mm: Vector in millimeters.
-    :type mm: Vector4
-    :returns: Vector in micrometers.
-    :rtype: Vector4
-    """
-    return mm * 1_000
-
-
-def um_to_mm(um: Vector4) -> Vector4:
-    """Convert micrometers to millimeters.
-
-    :param um: Length in micrometers.
-    :type um: Vector4
-    :returns: Length in millimeters.
-    :rtype: Vector4
-    """
-    return um / 1_000
-
-
-def vector4_to_array(vector4: Vector4) -> list[float]:
-    """Convert a Vector4 to a list of floats.
-
-    :param vector4: Vector4 to convert.
-    :type vector4: :class:`vbl_aquarium.models.unity.Vector4`
-    :return: List of floats.
-    :rtype: list[float]
-    """
-    return [vector4.x, vector4.y, vector4.z, vector4.w]
-
-
-def array_to_vector4(array: list[float]) -> Vector4:
-    """Convert a list of floats to a Vector4.
-
-    :param array: List of floats.
-    :type array: list[float]
-    :return: First four elements of the list as a Vector4 padded with zeros if necessary.
-    :rtype: :class:`vbl_aquarium.models.unity.Vector4`
-    """
-
-    def get_element(this_array: list[float], index: int) -> float:
-        try:
-            return this_array[index]
-        except IndexError:
-            return 0.0
-
-    return Vector4(
-        x=get_element(array, 0),
-        y=get_element(array, 1),
-        z=get_element(array, 2),
-        w=get_element(array, 3),
-    )

ephys_link-2.0.0b6.dist-info/METADATA

@@ -1,166 +0,0 @@
-Metadata-Version: 2.3
-Name: ephys-link
-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
-Project-URL: Source, https://github.com/VirtualBrainLab/ephys-link
-Author-email: Kenneth Yang <kjy5@uw.edu>
-Maintainer-email: Kenneth Yang <kjy5@uw.edu>
-License-Expression: GPL-3.0-only
-License-File: LICENSE
-Keywords: electrophysiology,ephys,manipulator,neuroscience,neurotech,new-scale,sensapex,socket-io,virtualbrainlab
-Classifier: Intended Audience :: End Users/Desktop
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: Microsoft :: Windows
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-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==3.10.8
-Requires-Dist: colorama==0.4.6
-Requires-Dist: platformdirs==4.3.6
-Requires-Dist: pyserial==3.5
-Requires-Dist: python-socketio[asyncio-client]==5.11.4
-Requires-Dist: pythonnet==3.0.4
-Requires-Dist: requests==2.32.3
-Requires-Dist: rich==13.8.1
-Requires-Dist: sensapex==1.400.1
-Requires-Dist: vbl-aquarium==0.0.22
-Description-Content-Type: text/markdown
-
-# Electrophysiology Manipulator Link
-
-[![PyPI version](https://badge.fury.io/py/ephys-link.svg)](https://badge.fury.io/py/ephys-link)
-[![CodeQL](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml)
-[![Dependency Review](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml)
-[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
-[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-
-<!-- [![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml) -->
-
-<img width="100%" src="https://github.com/VirtualBrainLab/ephys-link/assets/82800265/0c7c60b1-0926-4697-a461-221554f82de1" alt="Manipulator and probe in pinpoint moving in sync">
-
-The [Electrophysiology Manipulator Link](https://github.com/VirtualBrainLab/ephys-link)
-(or Ephys Link for short) is a Python [Socket.IO](https://socket.io/docs/v4/#what-socketio-is) server that allows any
-Socket.IO-compliant application (such
-as [Pinpoint](https://github.com/VirtualBrainLab/Pinpoint))
-to communicate with manipulators used in electrophysiology experiments.
-
-**Supported Manipulators:**
-
-| Manufacturer | Model                                                                   |
-|--------------|-------------------------------------------------------------------------|
-| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                                |
-| New Scale    | <ul> <li>Pathfinder MPM Control v2.8+</li> <li>M3-USB-3:1-EP</li> </ul> |
-
-Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
-
-For more information regarding the server's implementation and how the code is organized, see
-the [package's development documentation](https://virtualbrainlab.org/ephys_link/development.html).
-
-For detailed descriptions of the server's API, see
-the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).
-
-# Installation
-
-## Prerequisites
-
-1. An **x86 Windows PC is required** to run the server.
-2. For Sensapex devices, the controller unit must be connected via an ethernet
-   cable and powered. A USB-to-ethernet adapter is acceptable. For New Scale manipulators,
-   the controller unit must be connected via USB and be powered by a 6V power
-   supply.
-3. To use the emergency stop feature, ensure an Arduino with
-   the [StopSignal](https://github.com/VirtualBrainLab/StopSignal) sketch is
-   connected to the computer. Follow the instructions on that repo for how to
-   set up the Arduino.
-
-**NOTE:** Ephys Link is an HTTP server without cross-origin support. The server
-is currently designed to interface with local/desktop instances of Pinpoint. It
-will not work with the web browser versions of Pinpoint at this time.
-
-## Launch from Pinpoint (Recommended)
-
-Pinpoint comes bundled with the correct version of Ephys Link. If you are using Pinpoint on the same computer your
-manipulators are connected to, you can launch the server from within Pinpoint. Follow the instructions in
-the [Pinpoint documentation](https://virtualbrainlab.org/pinpoint/tutorials/tutorial_ephys_link.html#configure-and-launch-ephys-link).
-
-## Install as Standalone Executable
-
-1. Download the latest executable from
-   the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
-2. Double-click the executable file to launch the configuration window.
-    1. Take note of the IP address and port. **Copy this information into Pinpoint to connect**.
-3. Select the desired configuration and click "Launch Server".
-
-The configuration window will close and the server will launch. Your configurations will be saved for future use.
-
-To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the
-same computer that Pinpoint is, use
-
-- Server: `localhost`
-- Port: `8081`
-
-If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup
-window instead of `localhost`.
-
-## Install as a Python package
-
-```bash
-pip install ephys-link
-```
-
-Import main and run (this will launch the setup GUI).
-
-```python
-from ephys_link.__main__ import main
-
-main()
-```
-
-## Install for Development
-
-1. Clone the repository.
-2. Install [Hatch](https://hatch.pypa.io/latest/install/)
-3. In a terminal, navigate to the repository's root directory and run
-
-   ```bash
-   hatch shell
-   ```
-
-This will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.
-
-If you encounter any dependency issues (particularly with `aiohttp`), try installing the latest Microsoft Visual C++
-(MSVC v143+ x86/64) and the Windows SDK (10/11)
-via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
-
-# Documentation and More Information
-
-Complete documentation including API usage and development installation can be
-found on the [Virtual Brain Lab Documentation page][docs] for Ephys Link.
-
-# Citing
-
-If this project is used as part of a research project you should cite
-the [Pinpoint repository][Pinpoint]. Please email
-Dan ([dbirman@uw.edu](mailto:dbirman@uw.edu)) if you have questions.
-
-Please reach out to Kenneth ([kjy5@uw.edu](mailto:kjy5@uw.edu)) for questions
-about the Electrophysiology Manipulator Link server. Bugs may be reported
-through the issues tab.
-
-[Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint
-
-[StopSignal]: https://github.com/VirtualBrainLab/StopSignal
-
-[docs]: https://virtualbrainlab.org/ephys_link/installation_and_use.html

ephys_link-2.0.0b6.dist-info/RECORD

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