ephys-link 1.3.3__py3-none-any.whl → 2.0.0b1__py3-none-any.whl

ephys_link/util/common.py

@@ -0,0 +1,121 @@
+# 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__
+from ephys_link.util.console import Console
+
+# 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__):
+        Console.info_print("Update available", latest_version)
+        Console.info_print("", "Download at: https://github.com/VirtualBrainLab/ephys-link/releases/latest")
+
+
+# Unit conversions
+
+
+def mmps_to_umps(mmps: float) -> float:
+    """Convert millimeters per second to micrometers per second.
+
+    :param mmps: Speed in millimeters per second.
+    :type mmps: float
+    :returns: Speed in micrometers per second.
+    :rtype: float
+    """
+    return mmps * 1_000
+
+
+def mm_to_um(mm: Vector4) -> Vector4:
+    """Convert millimeters to micrometers.
+
+    :param mm: Length in millimeters.
+    :type mm: Vector4
+    :returns: Length 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/util/console.py

@@ -0,0 +1,112 @@
+# ruff: noqa: T201
+"""Console class for printing messages to the console.
+
+Configure the console to print error and debug messages.
+
+Usage: Create a Console object and call the appropriate method to print messages.
+"""
+
+from traceback import print_exc
+
+from colorama import Back, Fore, Style, init
+
+# Constants.
+TAB_BLOCK = "\t\t"
+
+
+class Console:
+    def __init__(self, *, enable_debug: bool) -> None:
+        """Initialize console properties.
+
+        :param enable_debug: Enable debug mode.
+        :type enable_debug: bool
+        """
+        self._enable_debug = enable_debug
+
+        # Repeat message fields.
+        self._last_message = ""
+        self._repeat_counter = 1
+
+        # Initialize colorama.
+        init(autoreset=True)
+
+    @staticmethod
+    def error_print(msg: str) -> None:
+        """Print an error message to the console.
+
+        :param msg: Error message to print.
+        :type msg: str
+        """
+        print(f"\n{Back.RED}{Style.BRIGHT} ERROR {Style.RESET_ALL}{TAB_BLOCK}{Fore.RED}{msg}")
+
+    @staticmethod
+    def labeled_error_print(label: str, msg: str) -> None:
+        """Print an error message with a label to the console.
+
+        :param label: Label for the error message.
+        :type label: str
+        :param msg: Error message to print.
+        :type msg: str
+        """
+        print(f"\n{Back.RED}{Style.BRIGHT} ERROR {label} {Style.RESET_ALL}{TAB_BLOCK}{Fore.RED}{msg}")
+
+    @staticmethod
+    def pretty_exception(exception: Exception) -> str:
+        """Pretty print an exception.
+
+        :param exception: Exception to pretty print.
+        :type exception: Exception
+        :return: Pretty printed exception.
+        :rtype: str
+        """
+        return f"{type(exception).__name__}: {exception}"
+
+    @staticmethod
+    def exception_error_print(label: str, exception: Exception) -> None:
+        """Print an error message with exception details to the console.
+
+        :param label: Label for the error message.
+        :type label: str
+        :param exception: Exception to print.
+        :type exception: Exception
+        """
+        Console.labeled_error_print(label, Console.pretty_exception(exception))
+        print_exc()
+
+    def debug_print(self, label: str, msg: str) -> None:
+        """Print a debug message to the console.
+
+        :param label: Label for the debug message.
+        :type label: str
+        :param msg: Debug message to print.
+        :type msg: str
+        """
+        if self._enable_debug:
+            self._repeat_print(f"{Back.BLUE}{Style.BRIGHT} DEBUG {label} {Style.RESET_ALL}{TAB_BLOCK}{Fore.BLUE}{msg}")
+
+    @staticmethod
+    def info_print(label: str, msg: str) -> None:
+        """Print info to console.
+
+        :param label: Label for the message.
+        :type label: str
+        :param msg: Message to print.
+        :type msg: str
+        """
+        print(f"\n{Back.GREEN}{Style.BRIGHT} {label} {Style.RESET_ALL}{TAB_BLOCK}{Fore.GREEN}{msg}")
+
+    # Helper methods.
+    def _repeat_print(self, msg: str) -> None:
+        """Print a message to the console with repeat counter.
+
+        :param msg: Message to print.
+        :type msg: str
+        """
+        if msg == self._last_message:
+            self._repeat_counter += 1
+        else:
+            self._repeat_counter = 1
+            self._last_message = msg
+            print()
+
+        print(f"\r{msg}{f" (x{self._repeat_counter})" if self._repeat_counter > 1 else ""}", end="")

{ephys_link-1.3.3.dist-info → ephys_link-2.0.0b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: ephys-link
-Version: 1.3.3
+Version: 2.0.0b1
 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
@@ -27,12 +27,14 @@ 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: colorama==0.4.6
 Requires-Dist: platformdirs==4.2.2
 Requires-Dist: pyserial==3.5
-Requires-Dist: python-socketio[asyncio-client]==5.11.2
+Requires-Dist: python-socketio[asyncio-client]==5.11.3
 Requires-Dist: pythonnet==3.0.3
-Requires-Dist: sensapex==1.400.0
-Requires-Dist: vbl-aquarium==0.0.15
+Requires-Dist: requests==2.32.3
+Requires-Dist: sensapex==1.400.1
+Requires-Dist: vbl-aquarium==0.0.19
 Description-Content-Type: text/markdown
 
 # Electrophysiology Manipulator Link

ephys_link-2.0.0b1.dist-info/RECORD

@@ -0,0 +1,25 @@
+ephys_link/__about__.py,sha256=QUUi7DnZ0lfA8ZZUdMrPNiqXewCSfYtIqTvB6q6NnGQ,25
+ephys_link/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ephys_link/__main__.py,sha256=pu7QLmS_30qWpgzeibMVD5FsVhICiK0wi7QkzX6F0qU,1373
+ephys_link/back_end/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ephys_link/back_end/platform_handler.py,sha256=5GfyLz8rX8VYypuT9JJokV12mnyUksriFOzRgp6H4W8,12939
+ephys_link/back_end/server.py,sha256=WP5NLJnIKtkVImdRgtZKxWEghd17FjsmpuczYpoFs3Q,7965
+ephys_link/bindings/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ephys_link/bindings/fake_bindings.py,sha256=_ZpXx4whztbO5jNGNqwoJFdqhIIbZ0VMx4mHkMge1r0,1726
+ephys_link/bindings/ump_4_bindings.py,sha256=1V_bQzq7xVX1qGxbK11nxX7X3L3cfh9RTdhbVJwBKg8,4651
+ephys_link/front_end/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ephys_link/front_end/cli.py,sha256=KJBSWqdz4T5z0Zor1tJSHTJKZeMcHAJf5gXXu38wQPU,3105
+ephys_link/front_end/gui.py,sha256=_gE6zFhFnzHPSyYd9MBvfK5xmDZHsUXcETDHzH66QzU,7518
+ephys_link/resources/CP210xManufacturing.dll,sha256=aM9k_XABjkq0TOMiIw8HeteB40zqEkUDNO8wo91EdYI,810232
+ephys_link/resources/NstMotorCtrl.dll,sha256=Xtpr3vBcxhcsOUGvgVEwYtGPvKEqDctIUGCK36GfU2Q,155136
+ephys_link/resources/SiUSBXp.dll,sha256=187zlclZNNezCkU1o1CbICRAmKWJxbh8ahP6L6wo-_Y,469752
+ephys_link/resources/libum.dll,sha256=YaD4dwiSNohx-XxHjx2eQWPOBEVvUIXARvx37e_yqNw,316316
+ephys_link/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ephys_link/util/base_bindings.py,sha256=FNqhB7kJf2n9g4wYHEBbQ2wEiZscR5sKCnIEZ6yujgE,4808
+ephys_link/util/common.py,sha256=IgmTpXRU2z7jfYV2zB4RGgjV34IaYa2s3TYpzKZkpao,3519
+ephys_link/util/console.py,sha256=kD4LLehdA1xLiGwdvjt5KxImDSyDkcoC2CQVOxTv8T4,3560
+ephys_link-2.0.0b1.dist-info/METADATA,sha256=j_XqMK_IK955IOE0ikj_JhqschZGCOKpgMiWdGzTrQQ,7975
+ephys_link-2.0.0b1.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+ephys_link-2.0.0b1.dist-info/entry_points.txt,sha256=o8wV3AdnJ9o47vg9ymKxPNVq9pMdPq8UZHE_iyAJx-k,124
+ephys_link-2.0.0b1.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+ephys_link-2.0.0b1.dist-info/RECORD,,

{ephys_link-1.3.3.dist-info → ephys_link-2.0.0b1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.24.2
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

ephys_link/common.py

@@ -1,49 +0,0 @@
-"""Commonly used functions and dictionaries
-
-Contains globally used helper functions and typed dictionaries (to be used as
-callback parameters)
-"""
-
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from vbl_aquarium.models.unity import Vector4
-
-# Debugging flag
-DEBUG = False
-
-# Ephys Link ASCII
-ASCII = r"""
-  ______       _                 _      _       _
- |  ____|     | |               | |    (_)     | |
- | |__   _ __ | |__  _   _ ___  | |     _ _ __ | | __
- |  __| | '_ \| '_ \| | | / __| | |    | | '_ \| |/ /
- | |____| |_) | | | | |_| \__ \ | |____| | | | |   <
- |______| .__/|_| |_|\__, |___/ |______|_|_| |_|_|\_\
-        | |           __/ |
-        |_|          |___/
-"""
-
-
-def dprint(message: str) -> None:
-    """Print message if debug is enabled.
-
-    :param message: Message to print.
-    :type message: str
-    :return: None
-    """
-    if DEBUG:
-        print(message)
-
-
-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]

ephys_link/emergency_stop.py

@@ -1,67 +0,0 @@
-from signal import SIGINT, SIGTERM, signal
-from threading import Event, Thread
-from time import sleep
-
-from serial import Serial
-from serial.tools import list_ports
-
-from ephys_link.common import dprint
-from ephys_link.server import Server
-
-
-class EmergencyStop:
-    """Serial system for emergency stop"""
-
-    def __init__(self, server: Server, serial_port: str) -> None:
-        """Setup serial port for emergency stop
-
-        :param server: The Ephys Link server instance
-        :type server: Server
-        :param serial_port: The serial port to poll
-        :type serial_port: str
-        :return: None
-        """
-        self._server = server
-        self._serial_port = serial_port
-        self._poll_rate = 0.05
-        self._kill_serial_event = Event()
-        self._poll_serial_thread = Thread(target=self._poll_serial, daemon=True)
-
-        # Register signals
-        signal(SIGTERM, self._close_serial)
-        signal(SIGINT, self._close_serial)
-
-    def watch(self) -> None:
-        """Start polling serial port for emergency stop"""
-        self._poll_serial_thread.start()
-
-    def _poll_serial(self) -> None:
-        """Continuously poll serial port for data
-
-        Close port on kill event
-        """
-        target_port = self._serial_port
-        if self._serial_port is None:
-            # Search for serial ports
-            for port, desc, _ in list_ports.comports():
-                if "Arduino" in desc or "USB Serial Device" in desc:
-                    target_port = port
-                    break
-
-        serial = Serial(target_port, 9600, timeout=self._poll_rate)
-        while not self._kill_serial_event.is_set():
-            if serial.in_waiting > 0:
-                serial.readline()
-                # Cause a break
-                dprint("[EMERGENCY STOP]\t\t Stopping all manipulators")
-                self._server.platform.stop()
-                serial.reset_input_buffer()
-            sleep(self._poll_rate)
-        print("Close poll")
-        serial.close()
-
-    def _close_serial(self, _, __) -> None:
-        """Close the serial connection"""
-        print("[INFO]\t\t Closing serial")
-        self._kill_serial_event.set()
-        self._poll_serial_thread.join()