Add ND1000 open science project backend support

docs/_static/devices.json

@@ -1208,6 +1208,20 @@
     "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
     "oem": "https://lifesciences.tecan.com/multimode-plate-reader"
   },
+  {
+    "id": "thermo-fisher-nanodrop-1000",
+    "vendor": "Thermo Fisher",
+    "name": "NanoDrop 1000",
+    "kind": "plate reader",
+    "capabilities": [
+      "absorbance"
+    ],
+    "status": "basic",
+    "api": "pylabrobot.thermo_fisher.nanodrop_1000.ThermoFisherNanoDrop1000",
+    "api_version": "v1",
+    "code_slug": "thermo_fisher/nanodrop_1000",
+    "doc_slug": "thermo_fisher/nanodrop_1000/index"
+  },
   {
     "id": "thermo-fisher-alps-300",
     "vendor": "Thermo Fisher",

docs/user_guide/thermo_fisher/index.md

@@ -4,4 +4,5 @@
 :maxdepth: 1
 
 alps/index
+nanodrop_1000/index
 ```

docs/user_guide/thermo_fisher/nanodrop_1000/hello-world.ipynb

@@ -0,0 +1,79 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "nanodrop-intro",
+   "metadata": {},
+   "source": "# Thermo Fisher NanoDrop 1000\n\nThe NanoDrop 1000 measures absorbance spectra from small-volume samples. Complete the [NanoDrop 1000 setup guide](setup.md) before connecting with PyLabRobot."
+  },
+  {
+   "cell_type": "markdown",
+   "id": "nanodrop-connect-heading",
+   "metadata": {},
+   "source": "## Connect"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "nanodrop-connect",
+   "metadata": {},
+   "outputs": [],
+   "source": "from pylabrobot.thermo_fisher.nanodrop_1000 import ThermoFisherNanoDrop1000\n\nnanodrop = ThermoFisherNanoDrop1000()\nawait nanodrop.setup()"
+  },
+  {
+   "cell_type": "markdown",
+   "id": "nanodrop-blank-heading",
+   "metadata": {},
+   "source": "## Blank\n\nClean the pedestals, load the blank solution, lower the sampling arm, and acquire the blank."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "nanodrop-blank",
+   "metadata": {},
+   "outputs": [],
+   "source": "await nanodrop.take_blank(integration_ms=20)"
+  },
+  {
+   "cell_type": "markdown",
+   "id": "nanodrop-measure-heading",
+   "metadata": {},
+   "source": "## Measure a sample\n\nClean the pedestals, load the sample, lower the sampling arm, and measure absorbance. The result contains matching wavelength and absorbance lists."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "nanodrop-measure",
+   "metadata": {},
+   "outputs": [],
+   "source": "wavelengths, absorbance = await nanodrop.measure_absorbance(integration_ms=20)\n\npeak_index = max(range(len(absorbance)), key=absorbance.__getitem__)\nprint(f\"Peak absorbance: {absorbance[peak_index]:.3f} at {wavelengths[peak_index]:.1f} nm\")"
+  },
+  {
+   "cell_type": "markdown",
+   "id": "nanodrop-stop-heading",
+   "metadata": {},
+   "source": "## Disconnect"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "nanodrop-stop",
+   "metadata": {},
+   "outputs": [],
+   "source": "await nanodrop.stop()"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.11.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/user_guide/thermo_fisher/nanodrop_1000/index.md

@@ -0,0 +1,15 @@
+# Thermo Fisher NanoDrop 1000
+
+```{device-card} thermo-fisher-nanodrop-1000
+```
+
+The NanoDrop 1000 measures absorbance spectra from small-volume samples. Start with the setup guide
+to configure the USB connection, then follow the hello-world example to blank the instrument and
+measure a sample.
+
+```{toctree}
+:maxdepth: 1
+
+setup
+hello-world
+```

docs/user_guide/thermo_fisher/nanodrop_1000/setup.md

@@ -0,0 +1,49 @@
+# NanoDrop 1000 setup
+
+Install PyLabRobot with USB support:
+
+```bash
+pip install "pylabrobot[usb]"
+```
+
+## Windows USB driver
+
+The NanoDrop 1000 must use a libusb-compatible driver before PyLabRobot can communicate with it.
+Changing this driver prevents the official NanoDrop software from using the device until you switch
+the driver back.
+
+Some Windows 10 and 11 systems report the NanoDrop as an unknown USB device because its older USB
+controller does not provide a BOS descriptor. Only if Device Manager reports that problem, open an
+administrator Command Prompt and run:
+
+```bat
+reg add "HKLM\SYSTEM\CurrentControlSet\Control\usbflags\245710020002" /v SkipBOSDescriptorQuery /t REG_DWORD /d 1 /f
+```
+
+Unplug and reconnect the NanoDrop after changing the setting.
+
+Install the libusb driver with Zadig:
+
+1. Download and run [Zadig](https://zadig.akeo.ie/).
+2. Select **Options > List All Devices**.
+3. Select **NanoDrop 1000**.
+4. Select **libusb-win32** as the replacement driver.
+5. Click **Replace Driver** or **Install Driver**.
+
+## Restore the official driver
+
+To use the official NanoDrop software again:
+
+1. Open Device Manager.
+2. Find the NanoDrop 1000 under **libusb-win32 devices**.
+3. Select **Update driver > Browse my computer for drivers > Let me pick from a list**.
+4. Select the original NanoDrop or Cypress EZ-USB driver.
+
+If you added the BOS descriptor registry setting and want to remove it, run this from an
+administrator Command Prompt:
+
+```bat
+reg delete "HKLM\SYSTEM\CurrentControlSet\Control\usbflags\245710020002" /v SkipBOSDescriptorQuery /f
+```
+
+Continue with the [NanoDrop 1000 hello world](hello-world.md).

pylabrobot/io/usb.py

@@ -228,14 +228,20 @@ def _read_packet(
       # No data available (yet), this will give a timeout error. Don't reraise.
       return None
 
-  async def read(self, timeout: Optional[int] = None, size: Optional[int] = None) -> bytes:
+  async def read(
+    self,
+    timeout: Optional[int] = None,
+    size: Optional[int] = None,
+    endpoint: Optional[int] = None,
+  ) -> bytes:
     """Read a response from the device.
 
     Args:
       timeout: The timeout for reading from the device in seconds. If `None`, use the default
         timeout (specified by the `read_timeout` attribute).
       size: The maximum number of bytes to read. If `None`, read all available data until no
         more packets arrive.
+      endpoint: The endpoint address to read from. If `None`, use the configured read endpoint.
     """
 
     if self.dev is None or self.read_endpoint is None:
@@ -255,7 +261,7 @@ def read_or_timeout() -> bytes:
         last_packet: Optional[bytearray] = None
         while True:  # read while we have data, and while the last packet is the max size.
           remaining = size - len(resp) if size is not None else None
-          last_packet = self._read_packet(size=remaining)
+          last_packet = self._read_packet(size=remaining, endpoint=endpoint)
           if last_packet is not None:
             resp += last_packet
           if self.read_endpoint is None:
@@ -296,6 +302,29 @@ def read_or_timeout() -> bytes:
     )
     return response
 
+  async def drain(
+    self,
+    endpoint: Optional[int] = None,
+    timeout: float = 0.05,
+    size: int = 512,
+    max_duration: float = 1,
+  ) -> None:
+    """Discard queued input from an endpoint until no packet arrives before the timeout."""
+    if self.dev is None or self.read_endpoint is None:
+      raise RuntimeError(f"USB device for '{self.human_readable_device_name}' is not connected.")
+
+    deadline = time.monotonic() + max_duration
+    loop = asyncio.get_running_loop()
+    while time.monotonic() < deadline:
+      packet = await loop.run_in_executor(
+        self.read_executor,
+        lambda: self._read_packet(size=size, timeout=timeout, endpoint=endpoint),
+      )
+      if packet is None:
+        return
+
+    raise TimeoutError(f"Timed out draining USB device '{self.human_readable_device_name}'.")
+
   def get_available_devices(self) -> List["usb.core.Device"]:
     """Get a list of available devices that match the specified vendor and product IDs, and serial
     number and device_address if specified."""
@@ -561,7 +590,12 @@ async def write(self, data: bytes, timeout: Optional[float] = None):
       align_sequences(expected=next_command.data, actual=decoded)
       raise ValidationError("Data mismatch: difference was written to stdout.")
 
-  async def read(self, timeout: Optional[float] = None, size: Optional[int] = None) -> bytes:
+  async def read(
+    self,
+    timeout: Optional[float] = None,
+    size: Optional[int] = None,
+    endpoint: Optional[int] = None,
+  ) -> bytes:
     next_command = USBCommand(**self.cr.next_command())
     if not (
       next_command.module == "usb"
@@ -574,6 +608,15 @@ async def read(self, timeout: Optional[float] = None, size: Optional[int] = None
       data = data[:size]
     return data
 
+  async def drain(
+    self,
+    endpoint: Optional[int] = None,
+    timeout: float = 0.05,
+    size: int = 512,
+    max_duration: float = 1,
+  ) -> None:
+    pass
+
   def ctrl_transfer(
     self,
     bmRequestType: int,

pylabrobot/thermo_fisher/nanodrop_1000/__init__.py

@@ -0,0 +1,3 @@
+from .nanodrop_1000 import ThermoFisherNanoDrop1000
+
+__all__ = ["ThermoFisherNanoDrop1000"]