From 250ce06487b96cf19575b26b4a02aaf5e095fde0 Mon Sep 17 00:00:00 2001 From: Harley King Date: Thu, 20 Aug 2026 16:00:52 -0400 Subject: [PATCH 1/8] Add Molecular Devices FilterMax F5 support --- docs/_static/devices.json | 19 + docs/api/pylabrobot.molecular_devices.rst | 25 + .../filtermax/hello-world.ipynb | 479 +++++++++++ .../filtermax/protocol-coverage.md | 120 +++ docs/user_guide/molecular_devices/index.md | 2 + .../molecular_devices/filtermax_f5.py | 14 + pylabrobot/molecular_devices/__init__.py | 1 + .../molecular_devices/filtermax/__init__.py | 67 ++ .../molecular_devices/filtermax/catalog.py | 134 +++ .../molecular_devices/filtermax/errors.py | 57 ++ .../filtermax/filtermax_f5.py | 780 ++++++++++++++++++ .../molecular_devices/filtermax/models.py | 211 +++++ .../molecular_devices/filtermax/protocol.py | 174 ++++ .../filtermax/tests/__init__.py | 1 + .../filtermax/tests/catalog_tests.py | 53 ++ .../filtermax/tests/filtermax_f5_tests.py | 371 +++++++++ .../filtermax/tests/filtermax_slides.xml | 22 + .../filtermax/tests/protocol_tests.py | 101 +++ 18 files changed, 2631 insertions(+) create mode 100644 docs/user_guide/molecular_devices/filtermax/hello-world.ipynb create mode 100644 docs/user_guide/molecular_devices/filtermax/protocol-coverage.md create mode 100644 pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py create mode 100644 pylabrobot/molecular_devices/filtermax/__init__.py create mode 100644 pylabrobot/molecular_devices/filtermax/catalog.py create mode 100644 pylabrobot/molecular_devices/filtermax/errors.py create mode 100644 pylabrobot/molecular_devices/filtermax/filtermax_f5.py create mode 100644 pylabrobot/molecular_devices/filtermax/models.py create mode 100644 pylabrobot/molecular_devices/filtermax/protocol.py create mode 100644 pylabrobot/molecular_devices/filtermax/tests/__init__.py create mode 100644 pylabrobot/molecular_devices/filtermax/tests/catalog_tests.py create mode 100644 pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py create mode 100644 pylabrobot/molecular_devices/filtermax/tests/filtermax_slides.xml create mode 100644 pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py diff --git a/docs/_static/devices.json b/docs/_static/devices.json index 56cb4cba7c6..efab18ebfef 100644 --- a/docs/_static/devices.json +++ b/docs/_static/devices.json @@ -845,6 +845,25 @@ "manager": "https://discuss.pylabrobot.org/u/rickwierenga", "oem": "https://www.moleculardevices.com/products/cellular-imaging-systems/high-content-imaging/imagexpress-pico" }, + { + "id": "molecular-devices-filtermax-f5", + "vendor": "Molecular Devices", + "name": "FilterMax F5", + "kind": "plate reader", + "capabilities": [ + "absorbance", + "heating", + "luminescence", + "shaking" + ], + "status": "basic", + "api": "pylabrobot.molecular_devices.filtermax.FilterMaxF5", + "api_version": "v1", + "code_slug": "molecular_devices/filtermax", + "doc_slug": "molecular_devices/filtermax/hello-world", + "notes": "Directly validated for controls, absorbance, luminescence, kinetics, shaking, cancellation recovery, and well scans; fluorescence, FP, and TRF await an excitation slide with those filters.", + "oem": "https://www.moleculardevices.com/sites/default/files/en/assets/user-guide/br/filtermax-user-guide-5016208e.pdf" + }, { "id": "molecular-devices-spectramax-384plus", "vendor": "Molecular Devices", diff --git a/docs/api/pylabrobot.molecular_devices.rst b/docs/api/pylabrobot.molecular_devices.rst index cfcfe7d7fc7..2bb6d20e290 100644 --- a/docs/api/pylabrobot.molecular_devices.rst +++ b/docs/api/pylabrobot.molecular_devices.rst @@ -3,6 +3,31 @@ pylabrobot.molecular\_devices package ===================================== +FilterMax F5 +------------ + +.. currentmodule:: pylabrobot.molecular_devices.filtermax + +.. autosummary:: + :toctree: _autosummary + :nosignatures: + :recursive: + + FilterMaxF5 + FilterSlideCatalog + InstrumentInfo + FilterMaxStatus + InstalledFilterSlides + PlateGeometry + KineticTiming + ShakingSettings + WellScanSettings + AbsorbanceResult + LuminescenceResult + FluorescenceResult + TimeResolvedFluorescenceResult + FluorescencePolarizationResult + SpectraMax ---------- diff --git a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb new file mode 100644 index 00000000000..363012ef00d --- /dev/null +++ b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb @@ -0,0 +1,479 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "title", + "metadata": {}, + "source": [ + "# Molecular Devices FilterMax F5\n", + "\n", + "```{device-card} molecular-devices-filtermax-f5\n", + "```\n", + "\n", + "| Property | Value |\n", + "|---|---|\n", + "| PLR class | `FilterMaxF5` |\n", + "| Connection | RS-232 serial, 38,400 baud, 7E1, no flow control |\n", + "| Current verified modes | Absorbance and luminescence |\n", + "| Current verified controls | Tray, filter slides, temperature, shaking, cancellation |\n", + "\n", + "> **Validation status:** Direct PLR-to-F5 hardware validation succeeded. Full-plate absorbance at 450 nm agreed with the corresponding SoftMax Pro results; additional validated operations are recorded in the [protocol coverage](protocol-coverage.md). Fluorescence, FP, and TRF commands remain unavailable until they can be captured with a compatible excitation slide; the driver does not infer them." + ] + }, + { + "cell_type": "markdown", + "id": "communication", + "metadata": {}, + "source": [ + "## How it communicates\n", + "\n", + "The F5 uses an ASTM-like framed serial protocol, not the SpectraMax `!COMMAND` protocol. PLR handles framing, checksums, acknowledgements, response chunking, device errors, and cancellation internally. Raw commands are intentionally not public." + ] + }, + { + "cell_type": "markdown", + "id": "physical-setup", + "metadata": {}, + "source": [ + "## Physical setup\n", + "\n", + "1. Connect the FilterMax F5 through its RS-232 cable or a USB-to-serial adapter.\n", + "2. Close SoftMax Pro and release the serial port. Only one program may own the port.\n", + "3. Export the filter-slide definitions from SoftMax Pro as XML.\n", + "4. Install the plate and filter slides appropriate for the requested measurement.\n", + "5. Use a stable device path on Linux, such as `/dev/serial/by-id/...`.\n", + "\n", + "Excitation and emission slides occupy separate bays and are not interchangeable." + ] + }, + { + "cell_type": "markdown", + "id": "imports", + "metadata": {}, + "source": [ + "## Create the reader\n", + "\n", + "Load the SoftMax filter-slide catalog. Measurement methods require it so wavelengths can be resolved to an exact installed slide and slot." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "create-reader", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "\n", + "from pylabrobot.molecular_devices.filtermax import FilterMaxF5, FilterSlideCatalog\n", + "\n", + "catalog_path = Path(\"~/Documents/WIN7Shared/filtermax_slides.xml\").expanduser()\n", + "catalog = FilterSlideCatalog.from_softmax_xml(catalog_path)\n", + "reader = FilterMaxF5(\n", + " name=\"filtermax-f5\",\n", + " port=\"/dev/serial/by-id/replace-with-your-adapter\",\n", + " filter_slide_catalog=catalog,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "setup", + "metadata": {}, + "source": [ + "## Connect\n", + "\n", + "`setup()` opens the serial port, reads the instrument identity, and refuses a device that is not an F5." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "connect", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.setup()" + ] + }, + { + "cell_type": "markdown", + "id": "inspect", + "metadata": {}, + "source": [ + "## Inspect the instrument\n", + "\n", + "Read identity, status, installed slide IDs, and temperature without changing instrument state." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "inspect-state", + "metadata": {}, + "outputs": [], + "source": [ + "info = await reader.get_instrument_info()\n", + "status = await reader.get_status()\n", + "slides = await reader.get_filter_slides()\n", + "temperature = await reader.get_temperature()\n", + "\n", + "info, status, slides, temperature" + ] + }, + { + "cell_type": "markdown", + "id": "tray-out", + "metadata": {}, + "source": [ + "## Plate tray\n", + "\n", + "Move the tray out before loading or removing a plate." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "tray-out-command", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.move_plate_tray_out()" + ] + }, + { + "cell_type": "markdown", + "id": "tray-in", + "metadata": {}, + "source": [ + "After the plate is loaded and the tray path is clear, move it back in." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "tray-in-command", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.move_plate_tray_in()" + ] + }, + { + "cell_type": "markdown", + "id": "temperature", + "metadata": {}, + "source": [ + "## Temperature control\n", + "\n", + "Set a temperature in degrees Celsius, then query the current chamber temperature." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "temperature-set", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.set_temperature(25.0)\n", + "temperature = await reader.get_temperature()" + ] + }, + { + "cell_type": "markdown", + "id": "temperature-off", + "metadata": {}, + "source": [ + "Deactivate temperature control when it is no longer needed." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "temperature-off-command", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.deactivate_temperature_control()" + ] + }, + { + "cell_type": "markdown", + "id": "shake", + "metadata": {}, + "source": [ + "## Shaking\n", + "\n", + "Shaking is a finite-duration operation. Patterns are `\"linear\"` or `\"orbital\"`; speeds are `\"low\"`, `\"medium\"`, or `\"high\"`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "shake-command", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.start_shaking(pattern=\"linear\", speed=\"medium\", duration=5)" + ] + }, + { + "cell_type": "markdown", + "id": "plate-geometry", + "metadata": {}, + "source": [ + "## Plate geometry\n", + "\n", + "The captured Costar 96-well clear plate geometry is available as a convenience. For another plate, construct `PlateGeometry` using its measured dimensions in millimetres." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "plate-geometry-command", + "metadata": {}, + "outputs": [], + "source": [ + "from pylabrobot.molecular_devices.filtermax import PlateGeometry\n", + "\n", + "plate = PlateGeometry.costar_96_clear_landscape()" + ] + }, + { + "cell_type": "markdown", + "id": "absorbance", + "metadata": {}, + "source": [ + "## Absorbance\n", + "\n", + "Run an endpoint read at 450 nm. Results are plate-shaped optical-density values; unselected wells are `None`. The tray ejects when the read finishes." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "absorbance-command", + "metadata": {}, + "outputs": [], + "source": [ + "absorbance = await reader.read_absorbance(plate, wavelength=450)" + ] + }, + { + "cell_type": "markdown", + "id": "partial", + "metadata": {}, + "source": [ + "Select individual wells for a partial-plate read." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "partial-command", + "metadata": {}, + "outputs": [], + "source": [ + "partial = await reader.read_absorbance(\n", + " plate,\n", + " wavelength=450,\n", + " wells=[\"C4\", \"C5\", \"C6\", \"D4\", \"D5\", \"D6\"],\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "reference", + "metadata": {}, + "source": [ + "Use a supported reference filter when reference-subtracted absorbance is required." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "reference-command", + "metadata": {}, + "outputs": [], + "source": [ + "reference_subtracted = await reader.read_absorbance(\n", + " plate,\n", + " wavelength=450,\n", + " reference_wavelength=620,\n", + " wells=[\"C4\", \"C5\", \"C6\", \"D4\", \"D5\", \"D6\"],\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "kinetic", + "metadata": {}, + "source": [ + "## Kinetic reads\n", + "\n", + "Kinetic timing uses seconds. The result list contains one plate-shaped result per timepoint." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "kinetic-command", + "metadata": {}, + "outputs": [], + "source": [ + "from pylabrobot.molecular_devices.filtermax import KineticTiming\n", + "\n", + "kinetic = await reader.read_absorbance(\n", + " plate,\n", + " wavelength=450,\n", + " wells=[\"C4\"],\n", + " kinetic=KineticTiming(interval=15, reads=3),\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "well-scan", + "metadata": {}, + "source": [ + "## Well scans\n", + "\n", + "The captured F5 software exposes horizontal and circular fill scans. Scan results preserve every `(x, y, value)` point for each selected well." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "well-scan-command", + "metadata": {}, + "outputs": [], + "source": [ + "from pylabrobot.molecular_devices.filtermax import WellScanSettings\n", + "\n", + "scan = await reader.read_absorbance(\n", + " plate,\n", + " wavelength=450,\n", + " wells=[\"C4\"],\n", + " well_scan=WellScanSettings(pattern=\"fill\", density=5),\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "luminescence", + "metadata": {}, + "source": [ + "## Luminescence\n", + "\n", + "Read the open luminescence position on the installed emission slide. Values are raw RLU. Set `channels=2` for the captured dual-luminescence operation." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "luminescence-command", + "metadata": {}, + "outputs": [], + "source": [ + "luminescence = await reader.read_luminescence(\n", + " plate,\n", + " wells=[\"C4\"],\n", + " integration=0.4,\n", + " read_height=1.0,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "cancel", + "metadata": {}, + "source": [ + "## Cancel a read\n", + "\n", + "`cancel_read()` is state-aware: it does nothing while idle and cooperatively stops an active read. A cancelled read raises `FilterMaxReadCancelled` in the read task and returns the reader to an idle, tray-ejected state." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cancel-command", + "metadata": {}, + "outputs": [], + "source": [ + "import asyncio\n", + "\n", + "from pylabrobot.molecular_devices.filtermax import FilterMaxReadCancelled\n", + "\n", + "read_task = asyncio.create_task(\n", + " reader.read_absorbance(\n", + " plate,\n", + " wavelength=450,\n", + " wells=[\"C4\"],\n", + " kinetic=KineticTiming(interval=30, reads=10),\n", + " )\n", + ")\n", + "await asyncio.sleep(2)\n", + "await reader.cancel_read()\n", + "try:\n", + " await read_task\n", + "except FilterMaxReadCancelled:\n", + " pass" + ] + }, + { + "cell_type": "markdown", + "id": "errors", + "metadata": {}, + "source": [ + "## Device errors\n", + "\n", + "Inspect the exact firmware errors observed during this PLR session, then clear the local session log when handled." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "errors-command", + "metadata": {}, + "outputs": [], + "source": [ + "errors = await reader.get_error_log()\n", + "await reader.clear_error_log()" + ] + }, + { + "cell_type": "markdown", + "id": "teardown", + "metadata": {}, + "source": [ + "## Disconnect\n", + "\n", + "Always release the serial port when finished." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "disconnect", + "metadata": {}, + "outputs": [], + "source": [ + "await reader.stop()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md new file mode 100644 index 00000000000..e0315400c41 --- /dev/null +++ b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md @@ -0,0 +1,120 @@ +# FilterMax F5 protocol coverage + +This table records the compact, sanitized protocol fixtures recovered from SoftMax Pro 6.3.1 and +a FilterMax F5 with firmware `V1.2 b13 11.12.2014`. Raw timestamped capture files are intentionally +kept outside version control. + +## Transport + +| Property | Captured value | +|---|---| +| Serial | 38,400 baud, 7 data bits, even parity, 1 stop bit, no flow control | +| Host transaction | `ENQ`; device `ACK`; host frame; device `ACK`; host `EOT` | +| Device response | Device `ENQ`; host `ACK`; one or more device frames, each host-acknowledged; device `EOT` | +| Frame | `STX`, ASCII frame number, ASCII payload, `ETB` or `ETX`, two uppercase ASCII checksum digits, `CR LF` | +| Frame numbers | `1` through `7`, then `0`, repeated for additional continuation frames | +| Checksum | Modulo-256 sum from the ASCII frame number through `ETB`/`ETX`, inclusive | +| Example | `TG` is `02 31 54 47 03 43 46 0D 0A` | +| Success | Payload beginning with `+` | +| Device error | `- E:
` | + +The instrument does not emit a separate busy token in the captured operations. A command owns the +half-duplex transaction until its response arrives. Long reads return one or more framed result +messages. Kinetic timing is scheduled client-side, matching SoftMax's observed behavior. Result +timepoints use the requested kinetic schedule (for example, 0, 18, and 36 seconds); if a read +overruns an interval, the next read starts immediately without changing its nominal timepoint. + +## Controls and state + +| Operation | Exact request payload | Captured response form | Final state | +|---|---|---|---| +| Identity | `?` | Multiframe model, firmware, serial, slide IDs, device code, and options | Unchanged | +| Ready status | `STAT` | `+ READY` | Unchanged | +| State bits | `SGS` | `+` followed by 11 integers | Unchanged | +| Installed slides | `CS` | `+ 2 1` for excitation ID 2 and emission ID 1 | Unchanged | +| Tray in | `L P` | `+` and captured position | Tray in | +| Tray out | `E P` | `+` and captured position | Tray out | +| Excitation slide out/in | `E A` / `L A` | `+` | Requested slide state | +| Emission slide out/in | `E B` / `L B` | `+` | Requested slide state | +| Read temperature | `TG` | `+ 24.6`, for example | Unchanged | +| Set 25 °C | `TS 25` | `+` | Temperature control active | +| Deactivate temperature | `TS 0` | `+` | Temperature control inactive | +| Linear, low, 5 s | `SHAKE X 0 3 50 5` | `+ 0 0 // 0 0 //` | Shaking complete | +| Linear, medium, 5 s | `SHAKE X 0 3 40 5` | `+ 0 0 // 0 0 //` | Shaking complete | +| Orbital, high, 5 s | `SHAKE O 2 3 25 5` | `+ 0 0 // 0 0 //` | Shaking complete | +| Cancel active read | `STOP` | `- E140:` | Idle; SoftMax then ejects tray | + +## Measurement setup + +The live-optimized Costar 96-well clear landscape geometry was sent as: + +```text +PLATE Temp 12770 8570 1427 1069 1405 1118 12 8 902 900 640 640 0 300 0 1027 1 1 +``` + +For luminescence at a 1 mm read height, the read-height field is `100`. The installed filter +definitions were sent as: + +```text +SF A 2 260 12 1 340 10 1 405 10 1 450 8 1 595 8 1 620 8 1 +SF B 1 595 35 2 535 25 2 535 25 4 535 25 4 625 35 10 0 0 16 +``` + +## Reads + +| Captured operation | Exact read payload | Result shape | +|---|---|---| +| Absorbance 450, full plate | `ABS 0 1 450 1 8 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | One 12-value message per row, then `INFO` | +| Absorbance 450, A1:B3 | `ABS 0 1 450 1 2 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Two complete hardware rows; PLR masks columns 4-12 | +| Absorbance 450, C4:D6 | `ABS 0 1 450 3 4 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Two complete hardware rows; PLR masks unselected columns | +| Absorbance 450 minus 620 | `ABS 1 2 450 620 3 4 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Firmware-subtracted one-channel values | +| Absorbance 450, three-read kinetic | `ABS 3 1 450 3 4 1 1 0 0 0 0 0 3 1 3 2 O e INFO` | Repeated row messages; countdown field is 3, 2, 1 | +| Absorbance C4 horizontal, 28 points | `ABS 0 1 450 3 3 28 1 4 0 0 0 0 3 1 1 0 O e INFO` | 28 points for each of 12 hardware wells | +| Absorbance C4 fill density 5 | `ABS 0 1 450 3 3 5 5 4 0 0 0 0 3 1 1 0 O e INFO` | 21 circular-grid points for each of 12 hardware wells | +| Luminescence C4, 400 ms | `LUM 0 1 0 3 3 1 1 0 0 0 400000 0 3 1 1 0 O INFO` | One 12-value row message, then `INFO` | +| Dual luminescence C4, 400 ms | `LUM 1 2 0 0 3 3 1 1 0 0 0 400000 0 3 1 1 0 O INFO` | Two raw channel messages, then `INFO` | +| Luminescence, three-read kinetic | `LUM 3 1 0 3 3 1 1 0 0 0 400000 0 3 1 3 0 O INFO` | Repeated row messages; countdown field is 3, 2, 1 | + +Absorbance values are returned in milli-OD and converted to OD. Luminescence values remain raw RLU. +SoftMax exposed only row-order reads, only horizontal/fill well scans, and one absorbance wavelength +optionally paired with one reference wavelength. + +## Direct PLR hardware validation + +The driver was exercised directly on FilterMax F5 serial 1191 after releasing the Windows VM's +serial port. Identity, status, slide state, temperature, tray movement, excitation/emission slide +movement, linear/orbital shaking, and cancellation recovery all returned the expected final state +with an empty session error log. + +The Orange G plate used for the live matrix produced the following representative PLR results: + +| Operation | Direct result | +|---|---| +| Absorbance 450, full 96-well plate | 96 values; range 0.11214-0.16882 OD; mean 0.157792 OD | +| Absorbance 450, C4:D6 | 6 values; range 0.15885-0.16210 OD | +| Absorbance 450 minus 620, C4:D6 | 6 values; range 0.12460-0.12856 OD | +| Absorbance 450, three-read kinetic | 3 parsed timepoints and READY recovery | +| Horizontal scan, C4 | 28 ordered points | +| Fill density 5, C4 | 21 unique circular-grid points | +| Luminescence endpoint, C4 | One raw RLU value | +| Dual luminescence, C4 | Two preserved raw channels | +| Luminescence, three-read kinetic | 3 parsed timepoints | +| Luminescence with linear-medium pre-shaking | Completed and returned to READY | + +The full-plate and partial absorbance values agreed with the corresponding SoftMax runs to the +precision expected for independent reads. This was a protocol and interaction validation, not an +OEM performance qualification: the OEM SpectraTest material was not available. + +## Captured faults and remaining gaps + +| Item | Status | +|---|---| +| LED energy failure | Captured as `E62`, including LED, ADC, gain, and potentiometer details | +| Cancellation | Captured as `E140`; reader remained connected and recoverable | +| Fluorescence, FRET, FP, TRF | Not mapped: the available excitation slide ID 2 contains absorbance filters only; the required excitation slide ID 1 was not physically available | +| OEM SpectraTest validation | Not performed: a clear 96-well Orange G plate was available instead | +| Microplate optimization | Interactive four-corner image scan was captured, but the image-analysis wizard is SoftMax UI behavior; PLR accepts the resulting physical plate geometry directly | +| Persistent firmware error log | No standalone query was observed; PLR reports exact errors received during its own session | + +Uncaptured measurement commands are rejected before transmission. No SpectraMax `!COMMAND` payload +or inferred FilterMax command is used. diff --git a/docs/user_guide/molecular_devices/index.md b/docs/user_guide/molecular_devices/index.md index 6cc6140cc38..4111cd3a8c0 100644 --- a/docs/user_guide/molecular_devices/index.md +++ b/docs/user_guide/molecular_devices/index.md @@ -3,6 +3,8 @@ ```{toctree} :maxdepth: 1 +filtermax/hello-world +filtermax/protocol-coverage spectramax/hello-world imageXpress/pico ``` diff --git a/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py b/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py new file mode 100644 index 00000000000..4604aa24999 --- /dev/null +++ b/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py @@ -0,0 +1,14 @@ +"""Deprecated import location for the current FilterMax F5 v1 driver.""" + +import warnings + +from pylabrobot.molecular_devices.filtermax import FilterMaxF5, FilterSlideCatalog + +warnings.warn( + "pylabrobot.legacy.plate_reading.molecular_devices.filtermax_f5 is deprecated; " + "use pylabrobot.molecular_devices.filtermax instead.", + DeprecationWarning, + stacklevel=2, +) + +__all__ = ["FilterMaxF5", "FilterSlideCatalog"] diff --git a/pylabrobot/molecular_devices/__init__.py b/pylabrobot/molecular_devices/__init__.py index c778ba07175..d9be99c81b5 100644 --- a/pylabrobot/molecular_devices/__init__.py +++ b/pylabrobot/molecular_devices/__init__.py @@ -1,3 +1,4 @@ +from .filtermax import FilterMaxF5, FilterSlideCatalog from .imageXpress.pico.pico import Pico from .spectramax import ( MolecularDevicesPlateReader, diff --git a/pylabrobot/molecular_devices/filtermax/__init__.py b/pylabrobot/molecular_devices/filtermax/__init__.py new file mode 100644 index 00000000000..0b890421451 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/__init__.py @@ -0,0 +1,67 @@ +"""Molecular Devices FilterMax F5 support.""" + +from .catalog import FilterSlideCatalog +from .errors import ( + FilterMaxAmbiguousFilterError, + FilterMaxCatalogError, + FilterMaxChecksumError, + FilterMaxDeviceError, + FilterMaxError, + FilterMaxFilterNotFoundError, + FilterMaxIdentityError, + FilterMaxProtocolError, + FilterMaxReadCancelled, + FilterMaxSlideNotInstalledError, + FilterMaxTimeoutError, + FilterMaxUnsupportedOperationError, +) +from .filtermax_f5 import FilterMaxF5 +from .models import ( + AbsorbanceResult, + FilterDefinition, + FilterMaxStatus, + FilterSelection, + FluorescencePolarizationResult, + FluorescenceResult, + InstalledFilterSlides, + InstrumentInfo, + KineticTiming, + LuminescenceResult, + PlateGeometry, + ShakingSettings, + TimeResolvedFluorescenceResult, + WellScanPoint, + WellScanSettings, +) + +__all__ = [ + "AbsorbanceResult", + "FilterDefinition", + "FilterMaxAmbiguousFilterError", + "FilterMaxCatalogError", + "FilterMaxChecksumError", + "FilterMaxDeviceError", + "FilterMaxError", + "FilterMaxF5", + "FilterMaxFilterNotFoundError", + "FilterMaxIdentityError", + "FilterMaxProtocolError", + "FilterMaxReadCancelled", + "FilterMaxSlideNotInstalledError", + "FilterMaxStatus", + "FilterMaxTimeoutError", + "FilterMaxUnsupportedOperationError", + "FilterSelection", + "FilterSlideCatalog", + "FluorescencePolarizationResult", + "FluorescenceResult", + "InstalledFilterSlides", + "InstrumentInfo", + "KineticTiming", + "LuminescenceResult", + "PlateGeometry", + "ShakingSettings", + "TimeResolvedFluorescenceResult", + "WellScanPoint", + "WellScanSettings", +] diff --git a/pylabrobot/molecular_devices/filtermax/catalog.py b/pylabrobot/molecular_devices/filtermax/catalog.py new file mode 100644 index 00000000000..3bf2b331cb8 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/catalog.py @@ -0,0 +1,134 @@ +"""SoftMax filter-slide catalog support for FilterMax readers.""" + +from __future__ import annotations + +import xml.etree.ElementTree as ET +from dataclasses import dataclass +from pathlib import Path +from typing import Dict, List, Optional, Tuple, Union + +from .errors import ( + FilterMaxAmbiguousFilterError, + FilterMaxCatalogError, + FilterMaxFilterNotFoundError, +) +from .models import FilterDefinition, FilterKind, FilterSelection, FilterTechnique + +_TECHNIQUE_BITS: Tuple[Tuple[int, FilterTechnique], ...] = ( + (1, "absorbance"), + (2, "fluorescence"), + (4, "fluorescence_polarization"), + (8, "time_resolved_fluorescence"), + (16, "luminescence"), +) + + +def _local_name(tag: str) -> str: + return tag.rsplit("}", 1)[-1] + + +def _children(element: ET.Element) -> Dict[str, str]: + return {_local_name(child.tag): (child.text or "").strip() for child in element} + + +@dataclass(frozen=True) +class FilterSlideCatalog: + filters: Tuple[FilterDefinition, ...] + + @classmethod + def from_softmax_xml(cls, path: Union[str, Path]) -> "FilterSlideCatalog": + root = ET.parse(path).getroot() + slides: Dict[int, Tuple[int, str, FilterKind]] = {} + for element in root: + if _local_name(element.tag) != "MeasFilterSlider": + continue + values = _children(element) + try: + index = int(values["Index"]) + slide_id = int(values["ID"]) + name = values.get("Name", str(slide_id)) + kind: FilterKind = "excitation" if int(values["Type"]) == 1 else "emission" + except (KeyError, ValueError) as exc: + raise FilterMaxCatalogError("Malformed MeasFilterSlider entry") from exc + if index in slides: + raise FilterMaxCatalogError(f"Duplicate filter-slide index {index}") + slides[index] = (slide_id, name, kind) + + parsed: List[FilterDefinition] = [] + seen_positions = set() + for element in root: + if _local_name(element.tag) != "Filter": + continue + values = _children(element) + try: + slide_index = int(values["Index_Slider"]) + slide_id, slide_name, kind = slides[slide_index] + position = int(values["Position"]) + apply_to = int(values["ApplyTo"]) + wavelength = int(values["WL"]) + bandwidth = int(values["Bandwidth"]) + except (KeyError, ValueError) as exc: + raise FilterMaxCatalogError("Malformed Filter entry") from exc + key = (kind, slide_id, position) + if key in seen_positions: + raise FilterMaxCatalogError(f"Duplicate {kind} slide {slide_id} position {position}") + seen_positions.add(key) + techniques = frozenset(name for bit, name in _TECHNIQUE_BITS if apply_to & bit) + parsed.append( + FilterDefinition( + kind=kind, + slide_id=slide_id, + slide_name=slide_name, + position=position, + wavelength=wavelength, + bandwidth=bandwidth, + apply_to=apply_to, + techniques=techniques, + molecular_devices_number=values.get("MDNumber") or None, + ) + ) + if not parsed: + raise FilterMaxCatalogError("The SoftMax XML contains no filter definitions") + return cls(tuple(parsed)) + + def filters_for_slide(self, kind: FilterKind, slide_id: int) -> Tuple[FilterDefinition, ...]: + return tuple( + sorted( + (item for item in self.filters if item.kind == kind and item.slide_id == slide_id), + key=lambda item: item.position, + ) + ) + + def resolve( + self, + *, + kind: FilterKind, + technique: FilterTechnique, + wavelength: int, + slide_id: Optional[int] = None, + position: Optional[int] = None, + ) -> FilterSelection: + matches = [ + item + for item in self.filters + if item.kind == kind + and technique in item.techniques + and item.wavelength == wavelength + and (slide_id is None or item.slide_id == slide_id) + and (position is None or item.position == position) + ] + if not matches: + raise FilterMaxFilterNotFoundError(f"No {kind} filter for {technique} at {wavelength} nm") + if len(matches) != 1: + locations = ", ".join(f"slide {item.slide_id}/slot {item.position}" for item in matches) + raise FilterMaxAmbiguousFilterError( + f"{kind.title()} {wavelength} nm is ambiguous ({locations}); select slide and slot" + ) + item = matches[0] + return FilterSelection( + kind=item.kind, + slide_id=item.slide_id, + position=item.position, + wavelength=item.wavelength, + bandwidth=item.bandwidth, + ) diff --git a/pylabrobot/molecular_devices/filtermax/errors.py b/pylabrobot/molecular_devices/filtermax/errors.py new file mode 100644 index 00000000000..0e5bdd645a3 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/errors.py @@ -0,0 +1,57 @@ +"""Errors raised by the FilterMax F5 driver.""" + +from __future__ import annotations + + +class FilterMaxError(Exception): + """Base class for FilterMax driver errors.""" + + +class FilterMaxProtocolError(FilterMaxError): + """The instrument returned malformed or unexpected protocol data.""" + + +class FilterMaxChecksumError(FilterMaxProtocolError): + """An ASTM frame checksum did not match its payload.""" + + +class FilterMaxTimeoutError(FilterMaxProtocolError, TimeoutError): + """The instrument did not complete a protocol step before its deadline.""" + + +class FilterMaxIdentityError(FilterMaxError): + """The serial port did not identify as a FilterMax F5.""" + + +class FilterMaxCatalogError(FilterMaxError): + """The filter-slide catalog is absent, invalid, or ambiguous.""" + + +class FilterMaxFilterNotFoundError(FilterMaxCatalogError): + """No compatible filter matches a requested measurement.""" + + +class FilterMaxAmbiguousFilterError(FilterMaxCatalogError): + """More than one compatible filter matches a requested measurement.""" + + +class FilterMaxSlideNotInstalledError(FilterMaxCatalogError): + """A requested filter slide is not installed.""" + + +class FilterMaxUnsupportedOperationError(FilterMaxError): + """The requested operation has not been verified for this hardware configuration.""" + + +class FilterMaxDeviceError(FilterMaxError): + """An error reported by the FilterMax firmware.""" + + def __init__(self, code: int, detail: str, command: str): + self.code = code + self.detail = detail + self.command = command + super().__init__(f"FilterMax command {command!r} failed with E{code}: {detail}") + + +class FilterMaxReadCancelled(FilterMaxDeviceError): + """The active read was cancelled by a STOP request (device code E140).""" diff --git a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py new file mode 100644 index 00000000000..474a114974f --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py @@ -0,0 +1,780 @@ +"""Directly validated Molecular Devices FilterMax F5 support.""" + +from __future__ import annotations + +import asyncio +import contextlib +import logging +import re +import time +from typing import Dict, List, Optional, Sequence, Tuple + +from pylabrobot.io.serial import Serial + +from .catalog import FilterSlideCatalog +from .errors import ( + FilterMaxCatalogError, + FilterMaxDeviceError, + FilterMaxIdentityError, + FilterMaxProtocolError, + FilterMaxReadCancelled, + FilterMaxSlideNotInstalledError, + FilterMaxUnsupportedOperationError, +) +from .models import ( + AbsorbanceResult, + FilterKind, + FilterMaxStatus, + FluorescencePolarizationResult, + FluorescenceResult, + InstalledFilterSlides, + InstrumentInfo, + KineticTiming, + LuminescenceResult, + PlateGeometry, + ShakePattern, + ShakeSpeed, + ShakingSettings, + TimeResolvedFluorescenceResult, + WellScanPoint, + WellScanSettings, + empty_plate_data, +) +from .protocol import FilterMaxMessage, FilterMaxTransport, _CancelRequested + +logger = logging.getLogger(__name__) + +_F5_DEVICE_CODE = 57855 +_ERROR_RE = re.compile(r"^- E(?P\d+):\s*(?P.*)$", re.DOTALL) +_WELL_RE = re.compile(r"^(?P[A-Z]+)(?P[1-9]\d*)$") +_SHAKE_WIRE: Dict[ShakePattern, Tuple[str, int]] = { + "linear": ("X", 0), + "orbital": ("O", 2), +} +_SHAKE_SPEED_WIRE: Dict[ShakeSpeed, int] = {"low": 50, "medium": 40, "high": 25} + + +def _hundredths(value: float) -> int: + return int(round(value * 100)) + + +class FilterMaxF5: + """Current v1 driver for the Molecular Devices FilterMax F5. + + The serial protocol is not the SpectraMax ``!COMMAND`` protocol. It uses the captured + 38,400-baud, 7E1 ASTM-like framing implemented privately by :class:`FilterMaxTransport`. + The full-plate 450 nm absorbance path has been directly validated against an F5 and produced + results consistent with the corresponding SoftMax Pro workflow. + """ + + def __init__( + self, + name: str, + port: str, + filter_slide_catalog: Optional[FilterSlideCatalog] = None, + ) -> None: + self.name = name + self.port = port + self.filter_slide_catalog = filter_slide_catalog + self.io = Serial( + human_readable_device_name=f"Molecular Devices FilterMax F5 {name}", + port=port, + baudrate=38400, + bytesize=7, + parity="E", + stopbits=1, + timeout=0.2, + write_timeout=1, + rtscts=False, + dsrdtr=False, + xonxoff=False, + ) + self._transport = FilterMaxTransport(self.io) + self._operation_lock = asyncio.Lock() + self._cancel_event = asyncio.Event() + self._read_done = asyncio.Event() + self._read_done.set() + self._read_active = False + self._setup_complete = False + self._instrument_info: Optional[InstrumentInfo] = None + self._errors: List[FilterMaxDeviceError] = [] + + async def setup(self) -> None: + await self.io.setup() + try: + info = await self.get_instrument_info() + if info.device_code != _F5_DEVICE_CODE or info.model != "Anthos Fluoro": + raise FilterMaxIdentityError( + f"Expected FilterMax F5 device code {_F5_DEVICE_CODE}, received " + f"{info.model!r} / {info.device_code}" + ) + self._instrument_info = info + self._setup_complete = True + logger.info("[%s] connected to FilterMax F5 serial %s", self.name, info.serial_number) + except BaseException: + await self.io.stop() + raise + + async def stop(self) -> None: + if self._read_active: + await self.cancel_read() + await self.io.stop() + self._setup_complete = False + logger.info("[%s] disconnected", self.name) + + async def _command(self, payload: str, timeout: float = 60.0) -> str: + try: + return (await self._transport.exchange(payload, timeout)).payload + except FilterMaxDeviceError as error: + self._errors.append(error) + logger.error("[%s] FilterMax command failed: %s", self.name, error) + raise + + @staticmethod + def _parse_instrument_info(payload: str) -> InstrumentInfo: + lines = payload.lstrip("+\r").split("\r") + if len(lines) < 12: + raise FilterMaxProtocolError(f"Malformed FilterMax identity response: {payload!r}") + values: Dict[str, str] = {} + for line in lines[4:]: + if ":" in line: + key, value = line.split(":", 1) + values[key.strip()] = value.strip() + try: + return InstrumentInfo( + model=lines[0], + firmware=lines[1], + device_number=int(lines[2]), + serial_number=lines[3], + excitation_slide_id=int(values["Excitation Filter Slider Nr"]), + emission_slide_id=int(values["Emission Filter Slider Nr"]), + device_code=int(values["Device Code"]), + plate_control=values["Plate Control"].upper() == "TRUE", + pic_firmware=values["PIC Firmware"].lstrip("+ "), + cpld_version=int(values["CPLD Version"]), + raw=payload, + ) + except (KeyError, ValueError) as exc: + raise FilterMaxProtocolError(f"Malformed FilterMax identity fields: {payload!r}") from exc + + async def get_instrument_info(self) -> InstrumentInfo: + return self._parse_instrument_info(await self._command("?", timeout=10)) + + async def get_status(self) -> FilterMaxStatus: + text = (await self._command("STAT", timeout=5)).lstrip("+ ") + state_payload = (await self._command("SGS", timeout=5)).lstrip("+ ") + try: + state_bits = tuple(int(value) for value in state_payload.split()) + except ValueError as exc: + raise FilterMaxProtocolError(f"Malformed SGS response: {state_payload!r}") from exc + return FilterMaxStatus(ready=text == "READY", text=text, state_bits=state_bits) + + async def get_error_log(self) -> Tuple[FilterMaxDeviceError, ...]: + """Return errors observed by this driver session. + + SoftMax did not issue a separate persistent-error-log query in the captured F5 protocol. + Consequently this method intentionally reports the exact device errors received by PLR. + """ + + return tuple(self._errors) + + async def clear_error_log(self) -> None: + self._errors.clear() + + async def move_plate_tray_out(self) -> None: + await self._command("E P", timeout=30) + + async def move_plate_tray_in(self) -> None: + await self._command("L P", timeout=30) + + async def get_filter_slides(self) -> InstalledFilterSlides: + payload = (await self._command("CS", timeout=5)).lstrip("+ ") + try: + excitation, emission = (int(value) for value in payload.split()) + except (ValueError, TypeError) as exc: + raise FilterMaxProtocolError(f"Malformed CS response: {payload!r}") from exc + return InstalledFilterSlides(excitation_slide_id=excitation, emission_slide_id=emission) + + async def move_filter_slide_out(self, kind: FilterKind) -> None: + await self._command(f"E {'A' if kind == 'excitation' else 'B'}", timeout=30) + + async def move_filter_slide_in(self, kind: FilterKind) -> None: + await self._command(f"L {'A' if kind == 'excitation' else 'B'}", timeout=30) + + async def get_temperature(self) -> float: + payload = (await self._command("TG", timeout=5)).lstrip("+ ") + try: + return float(payload) + except ValueError as exc: + raise FilterMaxProtocolError(f"Malformed TG response: {payload!r}") from exc + + async def set_temperature(self, temperature: float) -> None: + if not 20 <= temperature <= 45: + raise ValueError("FilterMax temperature setpoint must be between 20 and 45 °C") + value = f"{temperature:g}" + await self._command(f"TS {value}", timeout=10) + logger.info("[%s] temperature setpoint set to %.1f °C", self.name, temperature) + + async def deactivate_temperature_control(self) -> None: + await self._command("TS 0", timeout=10) + logger.info("[%s] temperature control deactivated", self.name) + + async def start_shaking( + self, + pattern: ShakePattern, + speed: ShakeSpeed, + duration: int = 5, + ) -> None: + if duration < 1: + raise ValueError("duration must be at least 1") + pattern_code, pattern_parameter = _SHAKE_WIRE[pattern] + speed_parameter = _SHAKE_SPEED_WIRE[speed] + await self._command( + f"SHAKE {pattern_code} {pattern_parameter} 3 {speed_parameter} {duration}", + timeout=duration + 30, + ) + logger.info( + "[%s] completed %s/%s shaking for %d seconds", + self.name, + pattern, + speed, + duration, + ) + + async def stop_shaking(self) -> None: + if self._read_active: + await self.cancel_read() + return + try: + await self._command("STOP", timeout=10) + except FilterMaxReadCancelled: + return + + async def cancel_read(self) -> None: + if not self._read_active: + return + self._cancel_event.set() + await self._read_done.wait() + + def _require_catalog(self) -> FilterSlideCatalog: + if self.filter_slide_catalog is None: + raise FilterMaxCatalogError( + "Measurement methods require FilterSlideCatalog.from_softmax_xml(...)" + ) + return self.filter_slide_catalog + + @staticmethod + def _plate_command(plate: PlateGeometry, read_height: float) -> str: + values = ( + _hundredths(plate.length), + _hundredths(plate.width), + _hundredths(plate.height), + _hundredths(plate.bottom_row_offset), + _hundredths(plate.left_column_offset), + _hundredths(plate.top_row_offset), + plate.columns, + plate.rows, + _hundredths(plate.column_spacing), + _hundredths(plate.row_spacing), + _hundredths(plate.well_size_x), + _hundredths(plate.well_size_y), + 0, + 300, + 0, + _hundredths(read_height), + 1, + 1, + ) + return "PLATE Temp " + " ".join(str(value) for value in values) + + async def _send_filter_catalog(self, kind: FilterKind, slide_id: int) -> None: + catalog = self._require_catalog() + filters = catalog.filters_for_slide(kind, slide_id) + if not filters: + raise FilterMaxCatalogError(f"Catalog has no {kind} slide ID {slide_id}") + code = "A" if kind == "excitation" else "B" + fields = [f"SF {code}", str(slide_id)] + for item in filters: + fields.extend((str(item.wavelength), str(item.bandwidth), str(item.apply_to))) + await self._command(" ".join(fields), timeout=10) + + @staticmethod + def _row_name(index: int) -> str: + if not 0 <= index < 26: + raise ValueError("FilterMax driver currently supports plate rows A-Z") + return chr(ord("A") + index) + + @classmethod + def _normalize_wells( + cls, + wells: Optional[Sequence[str]], + plate: PlateGeometry, + ) -> Tuple[Tuple[str, ...], int, int]: + if wells is None: + normalized = tuple( + f"{cls._row_name(row)}{column + 1}" + for row in range(plate.rows) + for column in range(plate.columns) + ) + else: + normalized = tuple(dict.fromkeys(well.upper() for well in wells)) + if not normalized: + raise ValueError("wells must not be empty") + row_indices = [] + for well in normalized: + match = _WELL_RE.match(well) + if match is None or len(match.group("row")) != 1: + raise ValueError(f"Invalid well name {well!r}") + row = ord(match.group("row")) - ord("A") + column = int(match.group("column")) - 1 + if not 0 <= row < plate.rows or not 0 <= column < plate.columns: + raise ValueError(f"Well {well!r} is outside the {plate.rows}x{plate.columns} plate") + row_indices.append(row) + return normalized, min(row_indices), max(row_indices) + + @staticmethod + def _parse_values(payload: str) -> List[float]: + if not payload.startswith("+ "): + raise FilterMaxProtocolError(f"Expected measurement data, received {payload!r}") + try: + return [float(value) for value in payload[2:].split()] + except ValueError as exc: + raise FilterMaxProtocolError(f"Malformed measurement values: {payload!r}") from exc + + async def _receive_measurement_messages( + self, + command: str, + count: int, + timeout: float, + ) -> List[FilterMaxMessage]: + await self._transport.send_request(command) + messages: List[FilterMaxMessage] = [] + try: + for index in range(count): + messages.append( + await self._transport.receive_message( + timeout, + command=command, + cancel_event=self._cancel_event if index == 0 else None, + ) + ) + except _CancelRequested: + await self._transport.send_request("STOP") + try: + await self._transport.receive_message(15, command="STOP") + except FilterMaxReadCancelled as error: + self._errors.append(error) + raise + raise FilterMaxProtocolError("STOP did not return the captured E140 cancellation response") + except FilterMaxDeviceError as error: + self._errors.append(error) + raise + return messages + + async def _wait_until(self, target: float) -> None: + delay = target - time.monotonic() + if delay <= 0: + return + try: + await asyncio.wait_for(self._cancel_event.wait(), timeout=delay) + except asyncio.TimeoutError: + return + raise FilterMaxReadCancelled(140, "cancelled between kinetic cycles", "STOP") + + async def _recover_failed_read(self) -> None: + """Stop an incomplete firmware read before attempting tray recovery.""" + + try: + await self._transport.exchange("STOP", timeout=15) + except FilterMaxReadCancelled: + logger.info("[%s] stopped incomplete FilterMax read", self.name) + except FilterMaxDeviceError as error: + self._errors.append(error) + logger.warning("[%s] FilterMax read recovery returned: %s", self.name, error) + + async def _prepare_measurement( + self, + plate: PlateGeometry, + *, + kind: FilterKind, + slide_id: int, + read_height: float, + shaking: Optional[ShakingSettings], + ) -> None: + slides = await self.get_filter_slides() + installed = slides.excitation_slide_id if kind == "excitation" else slides.emission_slide_id + if installed != slide_id: + raise FilterMaxSlideNotInstalledError( + f"Required {kind} slide ID {slide_id}, but installed ID is {installed}" + ) + if shaking is not None: + await self.move_plate_tray_in() + await self.start_shaking( + shaking.pattern, + shaking.speed, + duration=shaking.duration, + ) + await self._command(self._plate_command(plate, read_height), timeout=10) + await self._send_filter_catalog(kind, slide_id) + await self.move_plate_tray_in() + + @staticmethod + def _scan_layout(settings: WellScanSettings) -> Tuple[Tuple[int, float, float], ...]: + density = settings.density + spacing = settings.point_spacing + center = (density - 1) / 2 + if settings.pattern == "horizontal": + return tuple((index, (index - center) * spacing, 0.0) for index in range(density)) + radius = density / 2 + points = [] + for y_index in range(density): + for x_index in range(density): + x = x_index - center + y = y_index - center + if x * x + y * y <= radius * radius: + raw_index = y_index * density + x_index + points.append((raw_index, x * spacing, y * spacing)) + return tuple(points) + + async def read_absorbance( + self, + plate: PlateGeometry, + wavelength: int, + *, + wells: Optional[Sequence[str]] = None, + reference_wavelength: Optional[int] = None, + slide_id: Optional[int] = None, + filter_position: Optional[int] = None, + reference_filter_position: Optional[int] = None, + kinetic: Optional[KineticTiming] = None, + shaking: Optional[ShakingSettings] = None, + well_scan: Optional[WellScanSettings] = None, + ) -> List[AbsorbanceResult]: + catalog = self._require_catalog() + primary = catalog.resolve( + kind="excitation", + technique="absorbance", + wavelength=wavelength, + slide_id=slide_id, + position=filter_position, + ) + if reference_wavelength is not None: + reference = catalog.resolve( + kind="excitation", + technique="absorbance", + wavelength=reference_wavelength, + slide_id=primary.slide_id, + position=reference_filter_position, + ) + else: + reference = None + selected_wells, first_row, last_row = self._normalize_wells(wells, plate) + selected = set(selected_wells) + row_count = last_row - first_row + 1 + grid_x, grid_y = well_scan.grid_shape if well_scan is not None else (1, 1) + scan_layout = self._scan_layout(well_scan) if well_scan is not None else ((0, 0.0, 0.0),) + raw_point_count = grid_x * grid_y + scan_code = 4 if well_scan is not None else 0 + timing = kinetic or KineticTiming(interval=1, reads=1) + results: List[AbsorbanceResult] = [] + + async with self._operation_lock: + self._cancel_event.clear() + self._read_done.clear() + self._read_active = True + completed = False + try: + await self._prepare_measurement( + plate, + kind="excitation", + slide_id=primary.slide_id, + read_height=plate.absorbance_z, + shaking=shaking, + ) + kinetic_started = time.monotonic() + for cycle in range(timing.reads): + if cycle: + if shaking is not None and shaking.between_reads: + await self.start_shaking(shaking.pattern, shaking.speed, shaking.duration) + await self._wait_until(kinetic_started + cycle * timing.interval) + # SoftMax reports kinetic timepoints on the requested schedule, even when a read + # overruns its interval. Preserve that protocol-level meaning instead of exposing + # transport and calibration latency as kinetic elapsed time. + elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 + remaining = timing.reads - cycle + if kinetic is not None: + mode = 3 + kinetic_flag = 2 + elif reference is not None: + mode = 1 + kinetic_flag = 0 + else: + mode = 0 + kinetic_flag = 0 + wavelengths = ( + f"2 {primary.wavelength} {reference.wavelength}" + if reference is not None + else f"1 {primary.wavelength}" + ) + command = ( + f"ABS {mode} {wavelengths} {first_row + 1} {last_row + 1} " + f"{grid_x} {grid_y} {scan_code} 0 0 0 0 3 1 {remaining} {kinetic_flag} O e INFO" + ) + timestamp = time.time() + final_cycle = cycle == timing.reads - 1 + messages = await self._receive_measurement_messages( + command, + row_count * grid_y + int(final_cycle), + timeout=max(60, raw_point_count * 3), + ) + data_messages = messages[:-1] if final_cycle else messages + data = empty_plate_data(plate.rows, plate.columns) + scan_points: Dict[str, Tuple[WellScanPoint, ...]] = {} + for row_offset in range(row_count): + row = first_row + row_offset + raw_values_by_column: List[List[float]] = [[] for _ in range(plate.columns)] + for scan_y in range(grid_y): + message = data_messages[row_offset * grid_y + scan_y] + values = self._parse_values(message.payload) + expected = plate.columns * grid_x + if len(values) != expected: + raise FilterMaxProtocolError( + f"Expected {expected} absorbance values for row {row + 1}, got {len(values)}" + ) + for column in range(plate.columns): + raw_values_by_column[column].extend(values[column * grid_x : (column + 1) * grid_x]) + for column in range(plate.columns): + well = f"{self._row_name(row)}{column + 1}" + raw_points = raw_values_by_column[column] + converted = [raw_points[index] / 1000 for index, _, _ in scan_layout] + if well not in selected: + continue + data[row][column] = sum(converted) / len(converted) + if well_scan is not None: + scan_points[well] = tuple( + WellScanPoint(x=x, y=y, value=value) + for (_, x, y), value in zip(scan_layout, converted) + ) + temperature = await self.get_temperature() + results.append( + AbsorbanceResult( + data=data, + wavelengths=( + (primary.wavelength, reference.wavelength) + if reference is not None + else (primary.wavelength,) + ), + reference_subtracted=reference is not None, + temperature=temperature, + timestamp=timestamp, + elapsed_time=elapsed_time, + scan_points=scan_points, + ) + ) + completed = True + finally: + if not completed: + with contextlib.suppress(Exception): + await self._recover_failed_read() + with contextlib.suppress(Exception): + await self.move_plate_tray_out() + self._read_active = False + self._read_done.set() + return results + + async def read_luminescence( + self, + plate: PlateGeometry, + *, + wells: Optional[Sequence[str]] = None, + channels: int = 1, + slide_id: Optional[int] = None, + filter_position: Optional[int] = None, + integration: float = 0.4, + read_height: float = 1.0, + kinetic: Optional[KineticTiming] = None, + shaking: Optional[ShakingSettings] = None, + ) -> List[LuminescenceResult]: + if channels not in (1, 2): + raise ValueError("channels must be 1 or 2") + if integration <= 0: + raise ValueError("integration must be positive") + catalog = self._require_catalog() + lum_filter = catalog.resolve( + kind="emission", + technique="luminescence", + wavelength=0, + slide_id=slide_id, + position=filter_position, + ) + selected_wells, first_row, last_row = self._normalize_wells(wells, plate) + selected = set(selected_wells) + row_count = last_row - first_row + 1 + timing = kinetic or KineticTiming(interval=1, reads=1) + integration_microseconds = int(round(integration * 1_000_000)) + results: List[LuminescenceResult] = [] + + async with self._operation_lock: + self._cancel_event.clear() + self._read_done.clear() + self._read_active = True + completed = False + try: + await self._prepare_measurement( + plate, + kind="emission", + slide_id=lum_filter.slide_id, + read_height=read_height, + shaking=shaking, + ) + kinetic_started = time.monotonic() + for cycle in range(timing.reads): + if cycle: + if shaking is not None and shaking.between_reads: + await self.start_shaking(shaking.pattern, shaking.speed, shaking.duration) + await self._wait_until(kinetic_started + cycle * timing.interval) + # The instrument starts an overdue cycle immediately, but its result still belongs + # to the nominal kinetic timepoint (the behavior observed in SoftMax captures). + elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 + remaining = timing.reads - cycle + mode = 3 if kinetic is not None else (1 if channels == 2 else 0) + wavelengths = "2 0 0" if channels == 2 else "1 0" + command = ( + f"LUM {mode} {wavelengths} {first_row + 1} {last_row + 1} 1 1 0 0 0 " + f"{integration_microseconds} 0 3 1 {remaining} 0 O INFO" + ) + timestamp = time.time() + final_cycle = cycle == timing.reads - 1 + messages = await self._receive_measurement_messages( + command, + row_count * channels + int(final_cycle), + timeout=90, + ) + data_messages = messages[:-1] if final_cycle else messages + for channel in range(channels): + data = empty_plate_data(plate.rows, plate.columns) + for row_offset in range(row_count): + message = data_messages[channel * row_count + row_offset] + values = self._parse_values(message.payload) + if len(values) != plate.columns: + raise FilterMaxProtocolError( + f"Expected {plate.columns} luminescence values, got {len(values)}" + ) + row = first_row + row_offset + for column, value in enumerate(values): + well = f"{self._row_name(row)}{column + 1}" + if well in selected: + data[row][column] = value + results.append( + LuminescenceResult( + data=data, + channel=channel + 1, + temperature=await self.get_temperature(), + timestamp=timestamp, + elapsed_time=elapsed_time, + ) + ) + completed = True + finally: + if not completed: + with contextlib.suppress(Exception): + await self._recover_failed_read() + with contextlib.suppress(Exception): + await self.move_plate_tray_out() + self._read_active = False + self._read_done.set() + return results + + async def _validate_unavailable_fluorescence_filters( + self, + technique: str, + excitation_wavelength: int, + emission_wavelength: int, + excitation_slide_id: Optional[int], + emission_slide_id: Optional[int], + ) -> None: + catalog = self._require_catalog() + excitation = catalog.resolve( + kind="excitation", + technique=technique, # type: ignore[arg-type] + wavelength=excitation_wavelength, + slide_id=excitation_slide_id, + ) + emission = catalog.resolve( + kind="emission", + technique=technique, # type: ignore[arg-type] + wavelength=emission_wavelength, + slide_id=emission_slide_id, + ) + installed = await self.get_filter_slides() + if installed.excitation_slide_id != excitation.slide_id: + raise FilterMaxSlideNotInstalledError( + f"Required excitation slide ID {excitation.slide_id}, but installed ID is " + f"{installed.excitation_slide_id}" + ) + if installed.emission_slide_id != emission.slide_id: + raise FilterMaxSlideNotInstalledError( + f"Required emission slide ID {emission.slide_id}, but installed ID is " + f"{installed.emission_slide_id}" + ) + raise FilterMaxUnsupportedOperationError( + f"{technique} measurement framing requires a live capture with excitation slide " + f"ID {excitation.slide_id}; no command was inferred" + ) + + async def read_fluorescence( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[FluorescenceResult]: + del plate + await self._validate_unavailable_fluorescence_filters( + "fluorescence", + excitation_wavelength, + emission_wavelength, + excitation_slide_id, + emission_slide_id, + ) + raise AssertionError("unreachable") + + async def read_time_resolved_fluorescence( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[TimeResolvedFluorescenceResult]: + del plate + await self._validate_unavailable_fluorescence_filters( + "time_resolved_fluorescence", + excitation_wavelength, + emission_wavelength, + excitation_slide_id, + emission_slide_id, + ) + raise AssertionError("unreachable") + + async def read_fluorescence_polarization( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[FluorescencePolarizationResult]: + del plate + await self._validate_unavailable_fluorescence_filters( + "fluorescence_polarization", + excitation_wavelength, + emission_wavelength, + excitation_slide_id, + emission_slide_id, + ) + raise AssertionError("unreachable") diff --git a/pylabrobot/molecular_devices/filtermax/models.py b/pylabrobot/molecular_devices/filtermax/models.py new file mode 100644 index 00000000000..f82232299f2 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/models.py @@ -0,0 +1,211 @@ +"""Public models used by the FilterMax F5 driver.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import FrozenSet, List, Literal, Mapping, Optional, Tuple + +FilterKind = Literal["excitation", "emission"] +FilterTechnique = Literal[ + "absorbance", + "fluorescence", + "fluorescence_polarization", + "time_resolved_fluorescence", + "luminescence", +] +ShakePattern = Literal["linear", "orbital"] +ShakeSpeed = Literal["low", "medium", "high"] +WellScanPattern = Literal["horizontal", "fill"] + + +@dataclass(frozen=True) +class InstrumentInfo: + model: str + firmware: str + device_number: int + serial_number: str + excitation_slide_id: int + emission_slide_id: int + device_code: int + plate_control: bool + pic_firmware: str + cpld_version: int + raw: str = field(repr=False) + + +@dataclass(frozen=True) +class FilterMaxStatus: + ready: bool + text: str + state_bits: Tuple[int, ...] + + +@dataclass(frozen=True) +class InstalledFilterSlides: + excitation_slide_id: int + emission_slide_id: int + + +@dataclass(frozen=True) +class FilterDefinition: + kind: FilterKind + slide_id: int + slide_name: str + position: int + wavelength: int + bandwidth: int + apply_to: int + techniques: FrozenSet[FilterTechnique] + molecular_devices_number: Optional[str] = None + + +@dataclass(frozen=True) +class FilterSelection: + kind: FilterKind + slide_id: int + position: int + wavelength: int + bandwidth: int + + +@dataclass(frozen=True) +class KineticTiming: + interval: float + reads: int + + def __post_init__(self) -> None: + if self.interval <= 0: + raise ValueError("interval must be positive") + if self.reads < 1: + raise ValueError("reads must be at least 1") + + +@dataclass(frozen=True) +class ShakingSettings: + pattern: ShakePattern + speed: ShakeSpeed + duration: int + between_reads: bool = False + + def __post_init__(self) -> None: + if self.duration < 1: + raise ValueError("duration must be at least 1") + + +@dataclass(frozen=True) +class WellScanSettings: + pattern: WellScanPattern + density: int + point_spacing: float = 0.23 + + def __post_init__(self) -> None: + if self.density < 1: + raise ValueError("density must be at least 1") + if self.point_spacing <= 0: + raise ValueError("point_spacing must be positive") + + @property + def grid_shape(self) -> Tuple[int, int]: + return (self.density, 1) if self.pattern == "horizontal" else (self.density, self.density) + + +@dataclass(frozen=True) +class PlateGeometry: + """FilterMax plate geometry in public PLR units (millimetres).""" + + rows: int + columns: int + length: float + width: float + height: float + bottom_row_offset: float + left_column_offset: float + top_row_offset: float + column_spacing: float + row_spacing: float + well_size_x: float + well_size_y: float + absorbance_z: float + name: str = "Custom plate" + + @classmethod + def costar_96_clear_landscape(cls) -> "PlateGeometry": + """Return the live-optimized geometry captured from the validation plate.""" + + return cls( + rows=8, + columns=12, + length=127.70, + width=85.70, + height=14.27, + bottom_row_offset=10.69, + left_column_offset=14.05, + top_row_offset=11.18, + column_spacing=9.02, + row_spacing=9.00, + well_size_x=6.40, + well_size_y=6.40, + absorbance_z=10.27, + name="96 Well Costar clear [Landscape]", + ) + + +@dataclass(frozen=True) +class WellScanPoint: + x: float + y: float + value: float + + +PlateData = List[List[Optional[float]]] + + +@dataclass(frozen=True) +class AbsorbanceResult: + data: PlateData + wavelengths: Tuple[int, ...] + reference_subtracted: bool + temperature: Optional[float] + timestamp: float + elapsed_time: float = 0.0 + scan_points: Mapping[str, Tuple[WellScanPoint, ...]] = field(default_factory=dict) + + +@dataclass(frozen=True) +class LuminescenceResult: + data: PlateData + channel: int + temperature: Optional[float] + timestamp: float + elapsed_time: float = 0.0 + + +@dataclass(frozen=True) +class FluorescenceResult: + data: PlateData + excitation_wavelength: int + emission_wavelength: int + temperature: Optional[float] + timestamp: float + elapsed_time: float = 0.0 + + +@dataclass(frozen=True) +class TimeResolvedFluorescenceResult(FluorescenceResult): + delay: float = 0.0 + integration: float = 0.0 + + +@dataclass(frozen=True) +class FluorescencePolarizationResult: + parallel_data: PlateData + perpendicular_data: PlateData + excitation_wavelength: int + emission_wavelength: int + temperature: Optional[float] + timestamp: float + elapsed_time: float = 0.0 + + +def empty_plate_data(rows: int, columns: int) -> PlateData: + return [[None for _ in range(columns)] for _ in range(rows)] diff --git a/pylabrobot/molecular_devices/filtermax/protocol.py b/pylabrobot/molecular_devices/filtermax/protocol.py new file mode 100644 index 00000000000..48ae98ef019 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/protocol.py @@ -0,0 +1,174 @@ +"""Captured ASTM-like serial transport used by the FilterMax F5.""" + +from __future__ import annotations + +import asyncio +import re +import time +from dataclasses import dataclass +from typing import List, Optional + +from pylabrobot.io.serial import Serial + +from .errors import ( + FilterMaxChecksumError, + FilterMaxDeviceError, + FilterMaxProtocolError, + FilterMaxReadCancelled, + FilterMaxTimeoutError, +) + +ACK = 0x06 +ENQ = 0x05 +EOT = 0x04 +STX = 0x02 +ETX = 0x03 +ETB = 0x17 +CR = 0x0D +LF = 0x0A + +_ERROR_RE = re.compile(r"^- E(?P\d+):\s*(?P.*)$", re.DOTALL) + + +class _CancelRequested(Exception): + pass + + +def checksum(data: bytes) -> int: + """Return the captured modulo-256 checksum.""" + + return sum(data) & 0xFF + + +def build_frame(payload: str, frame_number: int = 1, final: bool = True) -> bytes: + if not 0 <= frame_number <= 7: + raise ValueError("frame_number must be between 0 and 7") + terminator = ETX if final else ETB + checked = bytes((ord(str(frame_number)),)) + payload.encode("ascii") + bytes((terminator,)) + return bytes((STX,)) + checked + f"{checksum(checked):02X}".encode("ascii") + b"\r\n" + + +@dataclass(frozen=True) +class FilterMaxMessage: + payload: str + frame_count: int + + +class FilterMaxTransport: + """Private command transport. Public raw-command access is intentionally not exposed.""" + + def __init__(self, io: Serial): + self.io = io + self._send_lock = asyncio.Lock() + + async def _read_byte( + self, + deadline: float, + *, + cancel_event: Optional[asyncio.Event] = None, + ) -> int: + while True: + if cancel_event is not None and cancel_event.is_set(): + raise _CancelRequested + if time.monotonic() >= deadline: + raise FilterMaxTimeoutError("Timed out waiting for a FilterMax protocol byte") + data = await self.io.read(1) + if data: + return data[0] + await asyncio.sleep(0) + + async def _expect(self, expected: int, deadline: float) -> None: + actual = await self._read_byte(deadline) + if actual != expected: + raise FilterMaxProtocolError( + f"Expected control byte 0x{expected:02X}, received 0x{actual:02X}" + ) + + async def send_request(self, payload: str, timeout: float = 5.0) -> None: + """Send one captured host transaction without waiting for the device message.""" + + deadline = time.monotonic() + timeout + async with self._send_lock: + await self.io.write(bytes((ENQ,))) + await self._expect(ACK, deadline) + await self.io.write(build_frame(payload)) + await self._expect(ACK, deadline) + await self.io.write(bytes((EOT,))) + + async def _read_frame_after_stx(self, deadline: float) -> bytes: + frame = bytearray((STX,)) + while not frame.endswith(b"\r\n"): + if len(frame) > 4096: + raise FilterMaxProtocolError("FilterMax frame exceeded 4096 bytes") + frame.append(await self._read_byte(deadline)) + if len(frame) < 7: + raise FilterMaxProtocolError(f"FilterMax frame is too short: {bytes(frame)!r}") + if frame[-5] not in (ETX, ETB): + raise FilterMaxProtocolError("FilterMax frame is missing ETX/ETB") + try: + received_checksum = int(bytes(frame[-4:-2]), 16) + except ValueError as exc: + raise FilterMaxProtocolError("FilterMax frame checksum is not hexadecimal") from exc + checked = bytes(frame[1:-4]) + expected_checksum = checksum(checked) + if received_checksum != expected_checksum: + raise FilterMaxChecksumError( + f"Checksum mismatch: received {received_checksum:02X}, expected {expected_checksum:02X}" + ) + return bytes(frame) + + async def receive_message( + self, + timeout: float = 60.0, + *, + command: str = "", + cancel_event: Optional[asyncio.Event] = None, + ) -> FilterMaxMessage: + """Receive and acknowledge one device message, including all continuation frames.""" + + deadline = time.monotonic() + timeout + first = await self._read_byte(deadline, cancel_event=cancel_event) + if first != ENQ: + raise FilterMaxProtocolError(f"Expected device ENQ, received 0x{first:02X}") + await self.io.write(bytes((ACK,))) + + payload_parts: List[bytes] = [] + expected_frame_number = 1 + while True: + control = await self._read_byte(deadline) + if control == EOT: + break + if control != STX: + raise FilterMaxProtocolError(f"Expected device STX or EOT, received 0x{control:02X}") + frame = await self._read_frame_after_stx(deadline) + frame_number = frame[1] - ord("0") + if frame_number != expected_frame_number: + raise FilterMaxProtocolError( + f"Unexpected frame number {frame_number}; expected {expected_frame_number}" + ) + payload_parts.append(frame[2:-5]) + await self.io.write(bytes((ACK,))) + expected_frame_number = (expected_frame_number + 1) % 8 + if frame[-5] == ETX: + await self._expect(EOT, deadline) + break + + payload = b"".join(payload_parts).decode("ascii") + match = _ERROR_RE.match(payload) + if match is not None: + code = int(match.group("code")) + detail = match.group("detail") + if code == 140: + raise FilterMaxReadCancelled(code, detail, command) + raise FilterMaxDeviceError(code, detail, command) + return FilterMaxMessage(payload=payload, frame_count=len(payload_parts)) + + async def exchange( + self, + payload: str, + timeout: float = 60.0, + *, + cancel_event: Optional[asyncio.Event] = None, + ) -> FilterMaxMessage: + await self.send_request(payload) + return await self.receive_message(timeout, command=payload, cancel_event=cancel_event) diff --git a/pylabrobot/molecular_devices/filtermax/tests/__init__.py b/pylabrobot/molecular_devices/filtermax/tests/__init__.py new file mode 100644 index 00000000000..c612d11c307 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/__init__.py @@ -0,0 +1 @@ +"""Tests for the FilterMax F5 driver.""" diff --git a/pylabrobot/molecular_devices/filtermax/tests/catalog_tests.py b/pylabrobot/molecular_devices/filtermax/tests/catalog_tests.py new file mode 100644 index 00000000000..dbce25237ac --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/catalog_tests.py @@ -0,0 +1,53 @@ +import unittest +from pathlib import Path + +from pylabrobot.molecular_devices.filtermax import FilterSlideCatalog +from pylabrobot.molecular_devices.filtermax.errors import ( + FilterMaxAmbiguousFilterError, + FilterMaxFilterNotFoundError, +) + + +class TestFilterSlideCatalog(unittest.TestCase): + def setUp(self) -> None: + self.catalog = FilterSlideCatalog.from_softmax_xml( + Path(__file__).with_name("filtermax_slides.xml") + ) + + def test_parse_and_resolve(self) -> None: + selection = self.catalog.resolve(kind="excitation", technique="absorbance", wavelength=450) + self.assertEqual(selection.slide_id, 2) + self.assertEqual(selection.position, 4) + self.assertEqual(selection.bandwidth, 8) + + lum = self.catalog.resolve(kind="emission", technique="luminescence", wavelength=0) + self.assertEqual((lum.slide_id, lum.position), (1, 6)) + + def test_incompatible_filter_is_rejected(self) -> None: + with self.assertRaises(FilterMaxFilterNotFoundError): + self.catalog.resolve(kind="excitation", technique="fluorescence", wavelength=450) + + def test_ambiguous_wavelength_requires_slot(self) -> None: + with self.assertRaises(FilterMaxAmbiguousFilterError): + self.catalog.resolve( + kind="emission", + technique="fluorescence_polarization", + wavelength=535, + ) + selected = self.catalog.resolve( + kind="emission", + technique="fluorescence_polarization", + wavelength=535, + slide_id=1, + position=3, + ) + self.assertEqual(selected.position, 3) + + def test_unknown_slide_id_is_rejected(self) -> None: + with self.assertRaises(FilterMaxFilterNotFoundError): + self.catalog.resolve( + kind="excitation", + technique="absorbance", + wavelength=450, + slide_id=99, + ) diff --git a/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py new file mode 100644 index 00000000000..d05720fe943 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py @@ -0,0 +1,371 @@ +import unittest +from pathlib import Path + +from pylabrobot.molecular_devices.filtermax import ( + FilterMaxF5, + FilterSlideCatalog, + KineticTiming, + PlateGeometry, + WellScanSettings, +) +from pylabrobot.molecular_devices.filtermax.errors import ( + FilterMaxCatalogError, + FilterMaxDeviceError, + FilterMaxIdentityError, + FilterMaxProtocolError, + FilterMaxSlideNotInstalledError, +) +from pylabrobot.molecular_devices.filtermax.protocol import ( + ACK, + ENQ, + EOT, + FilterMaxTransport, + build_frame, +) + + +def device_message(payload: str) -> bytes: + return bytes((ENQ,)) + build_frame(payload) + bytes((EOT,)) + + +def exchange_response(payload: str) -> bytes: + return bytes((ACK, ACK)) + device_message(payload) + + +def measurement_response(*payloads: str) -> bytes: + return bytes((ACK, ACK)) + b"".join(device_message(payload) for payload in payloads) + + +class FakeSerial: + def __init__(self, incoming: bytes): + self.incoming = bytearray(incoming) + self.writes: list[bytes] = [] + self.setup_called = False + self.stop_called = False + + async def setup(self) -> None: + self.setup_called = True + + async def stop(self) -> None: + self.stop_called = True + + async def write(self, data: bytes) -> None: + self.writes.append(data) + + async def read(self, num_bytes: int = 1) -> bytes: + if not self.incoming: + return b"" + count = min(num_bytes, len(self.incoming)) + data = bytes(self.incoming[:count]) + del self.incoming[:count] + return data + + +def host_payloads(io: FakeSerial): + return [data[2:-5].decode("ascii") for data in io.writes if data.startswith(b"\x02")] + + +class TestFilterMaxF5(unittest.IsolatedAsyncioTestCase): + def setUp(self) -> None: + self.catalog = FilterSlideCatalog.from_softmax_xml( + Path(__file__).with_name("filtermax_slides.xml") + ) + + def make_driver(self, incoming: bytes) -> tuple[FilterMaxF5, FakeSerial]: + driver = FilterMaxF5("test", "COM1", self.catalog) + io = FakeSerial(incoming) + driver.io = io # type: ignore[assignment] + driver._transport = FilterMaxTransport(io) # type: ignore[arg-type] + return driver, io + + async def test_setup_verifies_captured_f5_identity(self) -> None: + identity = ( + "+\rAnthos Fluoro\rV1.2 b13 11.12.2014\r141\r1191\r" + "Excitation Filter Slider Nr: 2\rEmission Filter Slider Nr: 1\r" + "Barcode: not installed\rTemperatureControl: installed\rDevice Code: 57855\r" + "Plate Control: TRUE\rPIC Firmware: + V1.0 b5 30.01.2006\rCPLD Version: 6" + ) + driver, io = self.make_driver(exchange_response(identity)) + await driver.setup() + self.assertTrue(io.setup_called) + self.assertEqual((await driver.get_error_log()), ()) + self.assertEqual(driver._instrument_info.device_code, 57855) # type: ignore[union-attr] + + async def test_setup_refuses_an_unexpected_identity_and_closes_port(self) -> None: + identity = ( + "+\rNot an F5\rV1.0\r141\r1191\r" + "Excitation Filter Slider Nr: 2\rEmission Filter Slider Nr: 1\r" + "Barcode: not installed\rTemperatureControl: installed\rDevice Code: 1\r" + "Plate Control: TRUE\rPIC Firmware: + V1.0\rCPLD Version: 6" + ) + driver, io = self.make_driver(exchange_response(identity)) + with self.assertRaises(FilterMaxIdentityError): + await driver.setup() + self.assertTrue(io.stop_called) + + async def test_control_commands_match_captured_payloads(self) -> None: + incoming = b"".join( + ( + exchange_response("+ READY"), + exchange_response("+ 0 0 0 0 0 0 0 0 0 0 0"), + exchange_response("+ 2 1"), + exchange_response("+ 6512"), + exchange_response("+ -67"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ 24.6"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ 0 0 // 0 0 //"), + ) + ) + driver, io = self.make_driver(incoming) + status = await driver.get_status() + self.assertTrue(status.ready) + self.assertEqual(len(status.state_bits), 11) + slides = await driver.get_filter_slides() + self.assertEqual((slides.excitation_slide_id, slides.emission_slide_id), (2, 1)) + await driver.move_plate_tray_out() + await driver.move_plate_tray_in() + await driver.move_filter_slide_out("excitation") + await driver.move_filter_slide_in("emission") + self.assertEqual(await driver.get_temperature(), 24.6) + await driver.set_temperature(25.0) + await driver.deactivate_temperature_control() + await driver.start_shaking("linear", "medium", 5) + self.assertEqual( + host_payloads(io), + [ + "STAT", + "SGS", + "CS", + "E P", + "L P", + "E A", + "L B", + "TG", + "TS 25", + "TS 0", + "SHAKE X 0 3 40 5", + ], + ) + + async def test_absorbance_masks_hardware_row_and_scales_milliod(self) -> None: + row = "+ " + " ".join(str(100 + index) for index in range(12)) + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(row, "+ INFO"), + exchange_response("+ 24.5"), + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + results = await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), 450, wells=["C4"] + ) + self.assertEqual(len(results), 1) + value = results[0].data[2][3] + self.assertIsNotNone(value) + assert value is not None + self.assertAlmostEqual(value, 0.103) + self.assertIsNone(results[0].data[2][2]) + payloads = host_payloads(io) + self.assertIn( + "ABS 0 1 450 3 3 1 1 0 0 0 0 0 3 1 1 0 O e INFO", + payloads, + ) + self.assertIn( + "SF A 2 260 12 1 340 10 1 405 10 1 450 8 1 595 8 1 620 8 1", + payloads, + ) + + async def test_absorbance_fill_preserves_points(self) -> None: + scan_rows = [ + "+ " + " ".join(str(value) for value in range(scan_y * 60, (scan_y + 1) * 60)) + for scan_y in range(5) + ] + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(*scan_rows, "+ INFO"), + exchange_response("+ 25.0"), + exchange_response("+ 6512"), + ) + ) + driver, _ = self.make_driver(incoming) + result = ( + await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), + 450, + wells=["C4"], + well_scan=WellScanSettings(pattern="fill", density=5), + ) + )[0] + self.assertEqual(len(result.scan_points["C4"]), 21) + self.assertAlmostEqual(result.scan_points["C4"][0].value, 16 / 1000) + self.assertEqual( + len({(point.x, point.y) for point in result.scan_points["C4"]}), + 21, + ) + + def test_fill_density_28_matches_softmax_616_point_mask(self) -> None: + layout = FilterMaxF5._scan_layout(WellScanSettings(pattern="fill", density=28)) + self.assertEqual(len(layout), 616) + + async def test_absorbance_kinetic_uses_captured_countdown(self) -> None: + row = "+ " + " ".join("100" for _ in range(12)) + intermediate_cycle = measurement_response(row) + exchange_response("+ 25.0") + final_cycle = measurement_response(row, "+ INFO") + exchange_response("+ 25.0") + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + intermediate_cycle, + intermediate_cycle, + final_cycle, + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + results = await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), + 450, + wells=["C4"], + kinetic=KineticTiming(interval=0.001, reads=3), + ) + self.assertEqual(len(results), 3) + self.assertEqual([result.elapsed_time for result in results], [0.0, 0.001, 0.002]) + commands = [payload for payload in host_payloads(io) if payload.startswith("ABS ")] + self.assertEqual([command.split()[-5] for command in commands], ["3", "2", "1"]) + + async def test_luminescence_kinetic_info_arrives_only_after_final_cycle(self) -> None: + row = "+ " + " ".join("0" for _ in range(12)) + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(row), + exchange_response("+ 25.0"), + measurement_response(row), + exchange_response("+ 25.0"), + measurement_response(row, "+ INFO"), + exchange_response("+ 25.0"), + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + results = await driver.read_luminescence( + PlateGeometry.costar_96_clear_landscape(), + wells=["C4"], + kinetic=KineticTiming(interval=0.001, reads=3), + ) + self.assertEqual(len(results), 3) + self.assertEqual([result.elapsed_time for result in results], [0.0, 0.001, 0.002]) + commands = [payload for payload in host_payloads(io) if payload.startswith("LUM ")] + self.assertEqual([command.split()[-4] for command in commands], ["3", "2", "1"]) + + async def test_malformed_read_is_stopped_before_tray_recovery(self) -> None: + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response("+ 1 2", "+ INFO"), + exchange_response("- E140: "), + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + with self.assertRaisesRegex(FilterMaxProtocolError, "Expected 12 absorbance values"): + await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), + 450, + wells=["C4"], + ) + self.assertEqual(host_payloads(io)[-2:], ["STOP", "E P"]) + + async def test_captured_e62_is_preserved_in_session_error_log(self) -> None: + error = "- E62: ABS Led 7 ADCValue: 16277 Gain 255 LedHighPoti 44 LedLowPoti 255" + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(error), + exchange_response("+ 6512"), + ) + ) + driver, _ = self.make_driver(incoming) + with self.assertRaisesRegex(FilterMaxDeviceError, "E62"): + await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), + 450, + wells=["C4"], + reference_wavelength=595, + ) + errors = await driver.get_error_log() + self.assertEqual( + (errors[0].code, errors[0].command), + (62, "ABS 1 2 450 595 3 3 1 1 0 0 0 0 0 3 1 1 0 O e INFO"), + ) + + async def test_lum_dual_returns_raw_channels(self) -> None: + channel_1 = "+ " + " ".join(str(index) for index in range(12)) + channel_2 = "+ " + " ".join(str(index + 20) for index in range(12)) + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(channel_1, channel_2, "+ INFO"), + exchange_response("+ 25.0"), + exchange_response("+ 25.0"), + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + results = await driver.read_luminescence( + PlateGeometry.costar_96_clear_landscape(), wells=["C4"], channels=2 + ) + self.assertEqual([result.data[2][3] for result in results], [3, 23]) + self.assertIn( + "LUM 1 2 0 0 3 3 1 1 0 0 0 400000 0 3 1 1 0 O INFO", + host_payloads(io), + ) + self.assertIn( + "SF B 1 595 35 2 535 25 2 535 25 4 535 25 4 625 35 10 0 0 16", + host_payloads(io), + ) + + async def test_missing_excitation_slide_blocks_fluorescence(self) -> None: + driver, io = self.make_driver(exchange_response("+ 2 1")) + with self.assertRaises(FilterMaxSlideNotInstalledError): + await driver.read_fluorescence( + PlateGeometry.costar_96_clear_landscape(), + excitation_wavelength=485, + emission_wavelength=535, + ) + self.assertNotIn("FL", " ".join(host_payloads(io))) + + async def test_measurement_requires_catalog_before_transmission(self) -> None: + driver = FilterMaxF5("test", "COM1") + io = FakeSerial(b"") + driver.io = io # type: ignore[assignment] + driver._transport = FilterMaxTransport(io) # type: ignore[arg-type] + with self.assertRaises(FilterMaxCatalogError): + await driver.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450) + self.assertEqual(io.writes, []) diff --git a/pylabrobot/molecular_devices/filtermax/tests/filtermax_slides.xml b/pylabrobot/molecular_devices/filtermax/tests/filtermax_slides.xml new file mode 100644 index 00000000000..d711f6e9add --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/filtermax_slides.xml @@ -0,0 +1,22 @@ + + + 01Ex11 + 12Ex21 + 21Em10 + 12535535250 + 22485485200 + 34485485200 + 58370370800 + 11260260121 + 21340340101 + 31405405101 + 4145045081 + 5159559581 + 6162062081 + 12595595352 + 22535535252 + 34535535252 + 44535535252 + 510625625352 + 6160All02 + diff --git a/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py new file mode 100644 index 00000000000..ca65c7ae3c4 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py @@ -0,0 +1,101 @@ +import unittest + +from pylabrobot.molecular_devices.filtermax.errors import ( + FilterMaxChecksumError, + FilterMaxDeviceError, + FilterMaxProtocolError, + FilterMaxReadCancelled, + FilterMaxTimeoutError, +) +from pylabrobot.molecular_devices.filtermax.protocol import ( + ACK, + ENQ, + EOT, + FilterMaxTransport, + build_frame, +) + + +class FakeSerial: + def __init__(self, incoming: bytes): + self.incoming = bytearray(incoming) + self.writes: list[bytes] = [] + + async def write(self, data: bytes) -> None: + self.writes.append(data) + + async def read(self, num_bytes: int = 1) -> bytes: + if not self.incoming: + return b"" + count = min(num_bytes, len(self.incoming)) + data = bytes(self.incoming[:count]) + del self.incoming[:count] + return data + + +def device_message(payload: str) -> bytes: + return bytes((ENQ,)) + build_frame(payload) + bytes((EOT,)) + + +class TestFilterMaxProtocol(unittest.IsolatedAsyncioTestCase): + def test_captured_checksum(self) -> None: + self.assertEqual(build_frame("TG"), b"\x021TG\x03CF\r\n") + self.assertEqual(build_frame("CS"), b"\x021CS\x03CA\r\n") + self.assertEqual(build_frame("TS 25"), b"\x021TS 25\x0362\r\n") + + async def test_exchange_multiframe_identity(self) -> None: + part_1 = "+\rAnthos Fluoro\rV1.2 b13 11.12.2014\r141\r1191\rDevice Code: 57855\rCPLD Ver" + part_2 = "sion: 6" + incoming = ( + bytes((ACK, ACK, ENQ)) + + build_frame(part_1, frame_number=1, final=False) + + build_frame(part_2, frame_number=2) + + bytes((EOT,)) + ) + io = FakeSerial(incoming) + transport = FilterMaxTransport(io) # type: ignore[arg-type] + message = await transport.exchange("?") + self.assertEqual(message.payload, part_1 + part_2) + self.assertEqual(message.frame_count, 2) + self.assertEqual( + io.writes, + [bytes((ENQ,)), build_frame("?"), bytes((EOT,)), bytes((ACK,)), bytes((ACK,)), bytes((ACK,))], + ) + + async def test_bad_checksum(self) -> None: + frame = bytearray(build_frame("+ READY")) + frame[-4:-2] = b"00" + incoming = bytes((ACK, ACK, ENQ)) + bytes(frame) + bytes((EOT,)) + transport = FilterMaxTransport(FakeSerial(incoming)) # type: ignore[arg-type] + with self.assertRaises(FilterMaxChecksumError): + await transport.exchange("STAT") + + async def test_bad_continuation_frame_number(self) -> None: + incoming = ( + bytes((ACK, ACK, ENQ)) + + build_frame("+ first", frame_number=1, final=False) + + build_frame("second", frame_number=3) + + bytes((EOT,)) + ) + transport = FilterMaxTransport(FakeSerial(incoming)) # type: ignore[arg-type] + with self.assertRaisesRegex(FilterMaxProtocolError, "expected 2"): + await transport.exchange("?") + + async def test_timeout_with_silent_device(self) -> None: + transport = FilterMaxTransport(FakeSerial(b"")) # type: ignore[arg-type] + with self.assertRaises(FilterMaxTimeoutError): + await transport.send_request("STAT", timeout=0.001) + + async def test_device_error_and_cancel(self) -> None: + e62 = "- E62: ABS Led 7 ADCValue: 16277 Gain 255 LedHighPoti 44 LedLowPoti 255" + transport = FilterMaxTransport( + FakeSerial(bytes((ACK, ACK)) + device_message(e62)) # type: ignore[arg-type] + ) + with self.assertRaisesRegex(FilterMaxDeviceError, "E62"): + await transport.exchange("ABS 1 2 450 595") + + transport = FilterMaxTransport( + FakeSerial(bytes((ACK, ACK)) + device_message("- E140: ")) # type: ignore[arg-type] + ) + with self.assertRaises(FilterMaxReadCancelled): + await transport.exchange("STOP") From 8a505ab13c223560c17337a775f5ae07f51190ab Mon Sep 17 00:00:00 2001 From: Harley King Date: Sat, 22 Aug 2026 16:51:54 -0400 Subject: [PATCH 2/8] diagnose E14 error; validate portrait orientation --- .../filtermax/protocol-coverage.md | 5 +++ .../molecular_devices/filtermax/__init__.py | 2 + .../filtermax/filtermax_f5.py | 12 +++++- .../molecular_devices/filtermax/models.py | 34 +++++++++++++++ .../filtermax/tests/filtermax_f5_tests.py | 42 +++++++++++++++++++ 5 files changed, 93 insertions(+), 2 deletions(-) diff --git a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md index e0315400c41..bda4b8ce599 100644 --- a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md +++ b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md @@ -65,6 +65,7 @@ SF B 1 595 35 2 535 25 2 535 25 4 535 25 4 625 35 10 0 0 16 | Captured operation | Exact read payload | Result shape | |---|---|---| | Absorbance 450, full plate | `ABS 0 1 450 1 8 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | One 12-value message per row, then `INFO` | +| Absorbance 450, portrait full plate | `SHIFT`, then `ABS 0 1 450 1 8 1 1 0 0 0 0 0 4 1 1 0 O e INFO` | Same `PLATE` geometry and canonical 8x12 result as landscape | | Absorbance 450, A1:B3 | `ABS 0 1 450 1 2 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Two complete hardware rows; PLR masks columns 4-12 | | Absorbance 450, C4:D6 | `ABS 0 1 450 3 4 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Two complete hardware rows; PLR masks unselected columns | | Absorbance 450 minus 620 | `ABS 1 2 450 620 3 4 1 1 0 0 0 0 0 3 1 1 0 O e INFO` | Firmware-subtracted one-channel values | @@ -79,6 +80,9 @@ Absorbance values are returned in milli-OD and converted to OD. Luminescence val SoftMax exposed only row-order reads, only horizontal/fill well scans, and one absorbance wavelength optionally paired with one reference wavelength. +Portrait orientation has been captured for absorbance only. Other portrait measurement modes are +rejected before transmission rather than inferring their orientation fields. + ## Direct PLR hardware validation The driver was exercised directly on FilterMax F5 serial 1191 after releasing the Windows VM's @@ -91,6 +95,7 @@ The Orange G plate used for the live matrix produced the following representativ | Operation | Direct result | |---|---| | Absorbance 450, full 96-well plate | 96 values; range 0.11214-0.16882 OD; mean 0.157792 OD | +| Absorbance 450, portrait full 96-well plate | 96 canonical values; range 0.03145-0.11605 OD; mean 0.089182 OD; Pearson correlation 0.99565 with the SoftMax portrait control | | Absorbance 450, C4:D6 | 6 values; range 0.15885-0.16210 OD | | Absorbance 450 minus 620, C4:D6 | 6 values; range 0.12460-0.12856 OD | | Absorbance 450, three-read kinetic | 3 parsed timepoints and READY recovery | diff --git a/pylabrobot/molecular_devices/filtermax/__init__.py b/pylabrobot/molecular_devices/filtermax/__init__.py index 0b890421451..89e95d0532e 100644 --- a/pylabrobot/molecular_devices/filtermax/__init__.py +++ b/pylabrobot/molecular_devices/filtermax/__init__.py @@ -28,6 +28,7 @@ KineticTiming, LuminescenceResult, PlateGeometry, + PlateOrientation, ShakingSettings, TimeResolvedFluorescenceResult, WellScanPoint, @@ -60,6 +61,7 @@ "KineticTiming", "LuminescenceResult", "PlateGeometry", + "PlateOrientation", "ShakingSettings", "TimeResolvedFluorescenceResult", "WellScanPoint", diff --git a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py index 474a114974f..53e47586888 100644 --- a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py +++ b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py @@ -269,7 +269,7 @@ def _plate_command(plate: PlateGeometry, read_height: float) -> str: _hundredths(plate.length), _hundredths(plate.width), _hundredths(plate.height), - _hundredths(plate.bottom_row_offset), + _hundredths(plate.well_depth), _hundredths(plate.left_column_offset), _hundredths(plate.top_row_offset), plate.columns, @@ -415,6 +415,8 @@ async def _prepare_measurement( duration=shaking.duration, ) await self._command(self._plate_command(plate, read_height), timeout=10) + if plate.orientation == "portrait": + await self._command("SHIFT", timeout=10) await self._send_filter_catalog(kind, slide_id) await self.move_plate_tray_in() @@ -516,9 +518,11 @@ async def read_absorbance( if reference is not None else f"1 {primary.wavelength}" ) + orientation_code = 4 if plate.orientation == "portrait" else 3 command = ( f"ABS {mode} {wavelengths} {first_row + 1} {last_row + 1} " - f"{grid_x} {grid_y} {scan_code} 0 0 0 0 3 1 {remaining} {kinetic_flag} O e INFO" + f"{grid_x} {grid_y} {scan_code} 0 0 0 0 {orientation_code} 1 " + f"{remaining} {kinetic_flag} O e INFO" ) timestamp = time.time() final_cycle = cycle == timing.reads - 1 @@ -595,6 +599,10 @@ async def read_luminescence( kinetic: Optional[KineticTiming] = None, shaking: Optional[ShakingSettings] = None, ) -> List[LuminescenceResult]: + if plate.orientation != "landscape": + raise FilterMaxUnsupportedOperationError( + "Portrait orientation has been captured only for absorbance measurements" + ) if channels not in (1, 2): raise ValueError("channels must be 1 or 2") if integration <= 0: diff --git a/pylabrobot/molecular_devices/filtermax/models.py b/pylabrobot/molecular_devices/filtermax/models.py index f82232299f2..f8b2e790b57 100644 --- a/pylabrobot/molecular_devices/filtermax/models.py +++ b/pylabrobot/molecular_devices/filtermax/models.py @@ -16,6 +16,7 @@ ShakePattern = Literal["linear", "orbital"] ShakeSpeed = Literal["low", "medium", "high"] WellScanPattern = Literal["horizontal", "fill"] +PlateOrientation = Literal["landscape", "portrait"] @dataclass(frozen=True) @@ -127,6 +128,17 @@ class PlateGeometry: well_size_y: float absorbance_z: float name: str = "Custom plate" + orientation: PlateOrientation = "landscape" + + def __post_init__(self) -> None: + if self.orientation not in ("landscape", "portrait"): + raise ValueError(f"Unsupported FilterMax plate orientation {self.orientation!r}") + + @property + def well_depth(self) -> float: + """Return the well depth stored under the legacy ``bottom_row_offset`` name.""" + + return self.bottom_row_offset @classmethod def costar_96_clear_landscape(cls) -> "PlateGeometry": @@ -149,6 +161,28 @@ def costar_96_clear_landscape(cls) -> "PlateGeometry": name="96 Well Costar clear [Landscape]", ) + @classmethod + def costar_96_clear_portrait(cls) -> "PlateGeometry": + """Return the Costar 96-well geometry with portrait scan orientation.""" + + return cls( + rows=8, + columns=12, + length=127.70, + width=85.70, + height=14.27, + bottom_row_offset=10.69, + left_column_offset=14.05, + top_row_offset=11.18, + column_spacing=9.02, + row_spacing=9.00, + well_size_x=6.40, + well_size_y=6.40, + absorbance_z=10.27, + name="96 Well Costar clear [Portrait]", + orientation="portrait", + ) + @dataclass(frozen=True) class WellScanPoint: diff --git a/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py index d05720fe943..7f8e2b7e231 100644 --- a/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py +++ b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py @@ -14,6 +14,7 @@ FilterMaxIdentityError, FilterMaxProtocolError, FilterMaxSlideNotInstalledError, + FilterMaxUnsupportedOperationError, ) from pylabrobot.molecular_devices.filtermax.protocol import ( ACK, @@ -183,6 +184,41 @@ async def test_absorbance_masks_hardware_row_and_scales_milliod(self) -> None: payloads, ) + async def test_absorbance_portrait_uses_captured_shift_and_orientation_code(self) -> None: + rows = ["+ " + " ".join(str(row * 10 + column) for column in range(12)) for row in range(8)] + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+ 0 1"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(*rows, "+ INFO"), + exchange_response("+ 24.5"), + exchange_response("+ 6512"), + ) + ) + driver, io = self.make_driver(incoming) + result = ( + await driver.read_absorbance( + PlateGeometry.costar_96_clear_portrait(), + 450, + ) + )[0] + + self.assertEqual((len(result.data), len(result.data[0])), (8, 12)) + self.assertAlmostEqual(result.data[7][11], 0.081) # type: ignore[arg-type] + self.assertIn( + "PLATE Temp 12770 8570 1427 1069 1405 1118 12 8 " + "902 900 640 640 0 300 0 1027 1 1", + host_payloads(io), + ) + self.assertIn("SHIFT", host_payloads(io)) + self.assertIn( + "ABS 0 1 450 1 8 1 1 0 0 0 0 0 4 1 1 0 O e INFO", + host_payloads(io), + ) + async def test_absorbance_fill_preserves_points(self) -> None: scan_rows = [ "+ " + " ".join(str(value) for value in range(scan_y * 60, (scan_y + 1) * 60)) @@ -351,6 +387,12 @@ async def test_lum_dual_returns_raw_channels(self) -> None: host_payloads(io), ) + async def test_portrait_luminescence_is_rejected_before_transmission(self) -> None: + driver, io = self.make_driver(b"") + with self.assertRaisesRegex(FilterMaxUnsupportedOperationError, "only for absorbance"): + await driver.read_luminescence(PlateGeometry.costar_96_clear_portrait()) + self.assertEqual(io.writes, []) + async def test_missing_excitation_slide_blocks_fluorescence(self) -> None: driver, io = self.make_driver(exchange_response("+ 2 1")) with self.assertRaises(FilterMaxSlideNotInstalledError): From 77178479d7dcb5cbb0a5a07ec9dc3a46d151cf01 Mon Sep 17 00:00:00 2001 From: Harley King Date: Fri, 25 Sep 2026 16:08:48 -0400 Subject: [PATCH 3/8] add 9600 baud check at handshake beginning --- .../filtermax/tests/setup_tests.py | 251 ++++++++++++++++++ 1 file changed, 251 insertions(+) create mode 100644 pylabrobot/molecular_devices/filtermax/tests/setup_tests.py diff --git a/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py b/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py new file mode 100644 index 00000000000..bd76817a9d5 --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py @@ -0,0 +1,251 @@ +"""Baud detection and cleanup through the real FilterMax protocol transport.""" + +from __future__ import annotations + +import asyncio +import unittest +from unittest.mock import AsyncMock, patch + +from pylabrobot.molecular_devices.filtermax import FilterMaxF5 +from pylabrobot.molecular_devices.filtermax.errors import ( + FilterMaxChecksumError, + FilterMaxDeviceError, + FilterMaxIdentityError, + FilterMaxProtocolError, + FilterMaxTimeoutError, +) +from pylabrobot.molecular_devices.filtermax.protocol import ( + ACK, + ENQ, + EOT, + FilterMaxTransport, + build_frame, +) + +IDENTITY = ( + "+\rAnthos Fluoro\rV1.2 b13 11.12.2014\r141\r1191\r" + "Excitation Filter Slider Nr: 2\rEmission Filter Slider Nr: 1\r" + "Barcode: not installed\rTemperatureControl: installed\rDevice Code: 57855\r" + "Plate Control: TRUE\rPIC Firmware: + V1.0 b5 30.01.2006\rCPLD Version: 6" +) + + +def exchange_response(payload: str) -> bytes: + """Build a complete acknowledged request and device response.""" + return bytes((ACK, ACK, ENQ)) + build_frame(payload) + bytes((EOT,)) + + +class StartupSerial: + """Expose responses by baud rate and require close before reopening.""" + + def __init__(self, responses: dict[int, bytes | BaseException]): + self.responses = responses + self.baudrate = 38400 + self.is_open = False + self.events: list[tuple[str, int]] = [] + self.writes: list[tuple[int, bytes]] = [] + self.incoming = bytearray() + self.failure: BaseException | None = None + + async def setup(self) -> None: + """Open at the configured rate with a fresh input stream.""" + assert not self.is_open, "Previous serial session was not closed" + self.events.append(("open", self.baudrate)) + self.is_open = True + response = self.responses[self.baudrate] + self.failure = response if isinstance(response, BaseException) else None + self.incoming = bytearray(response) if isinstance(response, bytes) else bytearray() + + async def stop(self) -> None: + """Record which session was closed.""" + self.events.append(("close", self.baudrate)) + self.is_open = False + + async def write(self, data: bytes) -> None: + """Record transmissions with the active baud rate.""" + assert self.is_open + self.writes.append((self.baudrate, data)) + + async def read(self, num_bytes: int = 1) -> bytes: + """Return input or simulate expiration of the transport read deadline.""" + assert self.is_open + if self.failure is not None: + raise self.failure + if not self.incoming: + raise FilterMaxTimeoutError("Simulated protocol read timeout") + data = bytes(self.incoming[:num_bytes]) + del self.incoming[:num_bytes] + return data + + +class TestFilterMaxStartup(unittest.IsolatedAsyncioTestCase): + """Exercise startup without opening a physical serial port.""" + + def make_driver( + self, responses: dict[int, bytes | BaseException] + ) -> tuple[FilterMaxF5, StartupSerial]: + """Attach a baud-aware serial double to the production transport.""" + driver = FilterMaxF5("test", "COM1") + io = StartupSerial(responses) + driver.io = io # type: ignore[assignment] + driver._transport = FilterMaxTransport(io) # type: ignore[arg-type] + return driver, io + + async def test_connects_at_38400_without_fallback(self) -> None: + """The preferred rate is retained when the F5 answers immediately.""" + driver, io = self.make_driver({38400: exchange_response(IDENTITY)}) + await driver.setup() + self.assertEqual(io.events, [("open", 38400)]) + self.assertEqual(io.baudrate, 38400) + self.assertTrue(driver._setup_complete) + assert driver._instrument_info is not None + self.assertEqual(driver._instrument_info.serial_number, "1191") + await driver.stop() + self.assertFalse(io.is_open) + + async def test_falls_back_to_9600_and_retains_rate_for_status(self) -> None: + """Only the silent handshake is retried; subsequent queries stay at 9600.""" + driver, io = self.make_driver( + { + 38400: b"", + 9600: exchange_response(IDENTITY) + + exchange_response("+ READY") + + exchange_response("+ 0 0 0 0 0 0 0 0 0 0 0"), + } + ) + with self.assertLogs( + "pylabrobot.molecular_devices.filtermax.filtermax_f5", level="INFO" + ) as log: + await driver.setup() + self.assertEqual(io.events, [("open", 38400), ("close", 38400), ("open", 9600)]) + self.assertEqual(io.baudrate, 9600) + self.assertTrue(driver._setup_complete) + self.assertTrue((await driver.get_status()).ready) + self.assertEqual([data for baud, data in io.writes if baud == 38400], [bytes((ENQ,))]) + self.assertEqual( + [data[2:-5].decode("ascii") for _, data in io.writes if data.startswith(b"\x02")], + ["?", "STAT", "SGS"], + ) + self.assertIn("38400", "\n".join(log.output)) + self.assertIn("9600", "\n".join(log.output)) + await driver.stop() + self.assertEqual(io.events[-1], ("close", 9600)) + self.assertFalse(driver._setup_complete) + + async def test_both_rates_silent_report_port_and_rates_and_close(self) -> None: + """Exhausted detection reports actionable context without sending a command.""" + driver, io = self.make_driver({38400: b"", 9600: b""}) + with self.assertRaises(FilterMaxTimeoutError) as caught: + await driver.setup() + for expected in ("COM1", "38400", "9600"): + self.assertIn(expected, str(caught.exception)) + self.assertEqual( + io.events, [("open", 38400), ("close", 38400), ("open", 9600), ("close", 9600)] + ) + self.assertEqual(io.writes, [(38400, bytes((ENQ,))), (9600, bytes((ENQ,)))]) + self.assertFalse(io.is_open) + self.assertFalse(driver._setup_complete) + self.assertIsNone(driver._instrument_info) + + async def test_wrong_identity_at_either_rate_is_not_retried(self) -> None: + """Receiving an identity establishes a rate even when the device is wrong.""" + for baudrate in (38400, 9600): + with self.subTest(baudrate=baudrate): + responses = {38400: b"", baudrate: exchange_response(IDENTITY.replace("57855", "1"))} + driver, io = self.make_driver(responses) + with self.assertRaises(FilterMaxIdentityError): + await driver.setup() + self.assertEqual(io.events[-1], ("close", baudrate)) + self.assertEqual(len(io.events), 2 if baudrate == 38400 else 4) + self.assertFalse(io.is_open) + self.assertFalse(driver._setup_complete) + self.assertIsNone(driver._instrument_info) + + async def test_errors_after_a_response_do_not_trigger_fallback(self) -> None: + """Protocol, device, and later timeout errors retain their original meaning.""" + corrupt = bytearray(exchange_response(IDENTITY)) + corrupt[-5:-3] = b"00" + cases = ( + ("unexpected handshake byte", b"\x15", FilterMaxProtocolError), + ("frame ACK timeout", bytes((ACK,)), FilterMaxTimeoutError), + ("response ENQ timeout", bytes((ACK, ACK)), FilterMaxTimeoutError), + ("partial response", bytes((ACK, ACK, ENQ, 2)), FilterMaxTimeoutError), + ("checksum", bytes(corrupt), FilterMaxChecksumError), + ("malformed identity", exchange_response("+ invalid"), FilterMaxProtocolError), + ("device error", exchange_response("- E62: test fault"), FilterMaxDeviceError), + ("serial read error", OSError("Disconnected"), OSError), + ) + for label, incoming, error_type in cases: + with self.subTest(case=label): + driver, io = self.make_driver({38400: incoming}) + with self.assertRaises(error_type): + await driver.setup() + self.assertEqual(io.events, [("open", 38400), ("close", 38400)]) + self.assertFalse(io.is_open) + self.assertFalse(driver._setup_complete) + + async def test_cancellation_at_either_rate_closes_without_retry(self) -> None: + """Cancellation never becomes a baud detection attempt or a timeout.""" + for baudrate in (38400, 9600): + with self.subTest(baudrate=baudrate): + driver, io = self.make_driver({38400: b"", baudrate: asyncio.CancelledError()}) + with self.assertRaises(asyncio.CancelledError): + await driver.setup() + self.assertEqual(io.events[-1], ("close", baudrate)) + self.assertEqual(len(io.events), 2 if baudrate == 38400 else 4) + self.assertFalse(io.is_open) + self.assertFalse(driver._setup_complete) + + async def test_open_error_is_not_retried(self) -> None: + """An unavailable port is not treated as an unsupported baud rate.""" + driver, io = self.make_driver({}) + with patch.object( + io, "setup", AsyncMock(side_effect=PermissionError("Port unavailable")) + ) as setup: + with self.assertRaises(PermissionError): + await driver.setup() + setup.assert_awaited_once() + self.assertFalse(io.is_open) + + async def test_write_timeout_is_not_retried(self) -> None: + """A failure to transmit ENQ is not evidence of a silent reader.""" + driver, io = self.make_driver({38400: b""}) + with patch.object(io, "write", AsyncMock(side_effect=FilterMaxTimeoutError("Write failed"))): + with self.assertRaisesRegex(FilterMaxTimeoutError, "Write failed"): + await driver.setup() + self.assertEqual(io.events, [("open", 38400), ("close", 38400)]) + self.assertFalse(io.is_open) + + async def test_repeated_setup_keeps_connected_session(self) -> None: + """Calling setup twice cannot leak or reconfigure the connected serial session.""" + driver, io = self.make_driver({38400: b"", 9600: exchange_response(IDENTITY)}) + await driver.setup() + writes = list(io.writes) + await driver.setup() + self.assertEqual(io.events, [("open", 38400), ("close", 38400), ("open", 9600)]) + self.assertEqual(io.writes, writes) + self.assertEqual(io.baudrate, 9600) + await driver.stop() + + async def test_failed_reconnect_clears_previous_identity(self) -> None: + """A disconnected or failed session cannot retain a successful setup state.""" + driver, io = self.make_driver({38400: exchange_response(IDENTITY)}) + await driver.setup() + await driver.stop() + io.responses = {38400: b"", 9600: b""} + with self.assertRaises(FilterMaxTimeoutError): + await driver.setup() + self.assertFalse(driver._setup_complete) + self.assertIsNone(driver._instrument_info) + self.assertFalse(io.is_open) + + async def test_command_timeout_after_setup_does_not_redetect_or_retry(self) -> None: + """Baud detection is confined to setup, including for measurement payloads.""" + driver, io = self.make_driver({38400: exchange_response(IDENTITY)}) + await driver.setup() + with self.assertRaises(FilterMaxTimeoutError): + await driver._command("ABS 0 1 450 1 8 1 1 0 0 0 0 0 4 1 1 0 O e INFO") + self.assertEqual(io.events, [("open", 38400)]) + self.assertEqual(io.writes[-1], (38400, bytes((ENQ,)))) + self.assertEqual(sum(data == bytes((ENQ,)) for _, data in io.writes), 2) + await driver.stop() From 8594fca1499849ae9cd4db6f0620e319f6f0e9bd Mon Sep 17 00:00:00 2001 From: Harley King Date: Fri, 25 Sep 2026 16:20:10 -0400 Subject: [PATCH 4/8] add 9600 baud check at handshake beginning --- .../filtermax/hello-world.ipynb | 6 +- .../filtermax/protocol-coverage.md | 18 +- .../filtermax/filtermax_f5.py | 59 +- .../molecular_devices/filtermax/protocol.py | 9 +- .../filtermax/tests/protocol_tests.py | 12 +- uv.lock | 4755 +++++++++++++++++ 6 files changed, 4839 insertions(+), 20 deletions(-) create mode 100644 uv.lock diff --git a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb index 363012ef00d..09a9f031dfc 100644 --- a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb +++ b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb @@ -13,7 +13,7 @@ "| Property | Value |\n", "|---|---|\n", "| PLR class | `FilterMaxF5` |\n", - "| Connection | RS-232 serial, 38,400 baud, 7E1, no flow control |\n", + "| Connection | RS-232 serial, automatic 38,400/9,600 baud detection, 7E1, no flow control |\n", "| Current verified modes | Absorbance and luminescence |\n", "| Current verified controls | Tray, filter slides, temperature, shaking, cancellation |\n", "\n", @@ -38,7 +38,7 @@ "## Physical setup\n", "\n", "1. Connect the FilterMax F5 through its RS-232 cable or a USB-to-serial adapter.\n", - "2. Close SoftMax Pro and release the serial port. Only one program may own the port.\n", + "2. Close SoftMax Pro and release the serial port. If Windows runs in VirtualBox with a host serial port mapping, save the results and shut Windows down normally; confirm the VM is powered off. Only one program may own the port.\n", "3. Export the filter-slide definitions from SoftMax Pro as XML.\n", "4. Install the plate and filter slides appropriate for the requested measurement.\n", "5. Use a stable device path on Linux, such as `/dev/serial/by-id/...`.\n", @@ -83,7 +83,7 @@ "source": [ "## Connect\n", "\n", - "`setup()` opens the serial port, reads the instrument identity, and refuses a device that is not an F5." + "`setup()` tries 38,400 baud first, then closes and reopens the port at 9,600 baud only if the initial handshake receives no response. It verifies the F5 identity and retains the working baud rate, which appears in the connection log. It does not change the reader's baud setting. Identity, protocol, and later transaction errors stop setup without retrying. All failed setup attempts release the serial port." ] }, { diff --git a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md index bda4b8ce599..aefa3aaec3f 100644 --- a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md +++ b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md @@ -8,7 +8,7 @@ kept outside version control. | Property | Captured value | |---|---| -| Serial | 38,400 baud, 7 data bits, even parity, 1 stop bit, no flow control | +| Serial | Automatic startup detection: 38,400 then 9,600 baud; 7 data bits, even parity, 1 stop bit, no flow control | | Host transaction | `ENQ`; device `ACK`; host frame; device `ACK`; host `EOT` | | Device response | Device `ENQ`; host `ACK`; one or more device frames, each host-acknowledged; device `EOT` | | Frame | `STX`, ASCII frame number, ASCII payload, `ETB` or `ETX`, two uppercase ASCII checksum digits, `CR LF` | @@ -18,6 +18,22 @@ kept outside version control. | Success | Payload beginning with `+` | | Device error | `- E:
` | +During setup, PLR first requests the instrument identity at 38,400 baud. If the initial ENQ +receives no byte before its deadline, PLR closes the port and tries the identity request at +9,600 baud. The working rate is retained for the session and recorded in the connection log. +An unexpected byte, invalid identity, checksum error, device error, or timeout after the initial +ACK ends setup without another attempt. Failed setup releases the port; errors after connection +do not trigger baud detection or command retries. + +The SoftMax startup capture includes a silent probe at 38,400 baud, a successful identity exchange +at 9,600 baud, and an acknowledged `BAUD 2` command before later communication at 38,400 baud. +PLR supports both observed rates and does not send `BAUD` or change the reader's baud setting. + +Only one application may use the serial port. When SoftMax runs in a VirtualBox VM whose COM port +maps to the host serial device, save the results and shut the guest down normally before connecting +PLR. Confirm the VM is powered off: closing SoftMax or an empty unprivileged `fuser` result does not +establish that VirtualBox released the host device. + The instrument does not emit a separate busy token in the captured operations. A command owns the half-duplex transaction until its response arrives. Long reads return one or more framed result messages. Kinetic timing is scheduled client-side, matching SoftMax's observed behavior. Result diff --git a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py index 53e47586888..767daf2e7e0 100644 --- a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py +++ b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py @@ -19,6 +19,7 @@ FilterMaxProtocolError, FilterMaxReadCancelled, FilterMaxSlideNotInstalledError, + FilterMaxTimeoutError, FilterMaxUnsupportedOperationError, ) from .models import ( @@ -40,11 +41,12 @@ WellScanSettings, empty_plate_data, ) -from .protocol import FilterMaxMessage, FilterMaxTransport, _CancelRequested +from .protocol import FilterMaxMessage, FilterMaxTransport, _CancelRequested, _HandshakeTimeout logger = logging.getLogger(__name__) _F5_DEVICE_CODE = 57855 +_STARTUP_BAUDRATES = (38400, 9600) _ERROR_RE = re.compile(r"^- E(?P\d+):\s*(?P.*)$", re.DOTALL) _WELL_RE = re.compile(r"^(?P[A-Z]+)(?P[1-9]\d*)$") _SHAKE_WIRE: Dict[ShakePattern, Tuple[str, int]] = { @@ -62,7 +64,8 @@ class FilterMaxF5: """Current v1 driver for the Molecular Devices FilterMax F5. The serial protocol is not the SpectraMax ``!COMMAND`` protocol. It uses the captured - 38,400-baud, 7E1 ASTM-like framing implemented privately by :class:`FilterMaxTransport`. + 7E1 ASTM-like framing implemented privately by :class:`FilterMaxTransport`. Setup tries + 38,400 baud, then 9,600 baud if the initial handshake is silent, and retains the working rate. The full-plate 450 nm absorbance path has been directly validated against an F5 and produced results consistent with the corresponding SoftMax Pro workflow. """ @@ -100,20 +103,48 @@ def __init__( self._errors: List[FilterMaxDeviceError] = [] async def setup(self) -> None: - await self.io.setup() - try: - info = await self.get_instrument_info() - if info.device_code != _F5_DEVICE_CODE or info.model != "Anthos Fluoro": - raise FilterMaxIdentityError( - f"Expected FilterMax F5 device code {_F5_DEVICE_CODE}, received " - f"{info.model!r} / {info.device_code}" - ) + """Connect at 38,400 or 9,600 baud and verify the instrument identity. + + Only a silent initial ENQ permits trying the next rate. Once a byte is received, + protocol and identity failures propagate without retrying the command. + """ + if self._setup_complete: + return + self._instrument_info = None + for baudrate in _STARTUP_BAUDRATES: + self.io.baudrate = baudrate + logger.info("[%s] connecting to %s at %d baud", self.name, self.port, baudrate) + await self.io.setup() + try: + info = await self.get_instrument_info() + if info.device_code != _F5_DEVICE_CODE or info.model != "Anthos Fluoro": + raise FilterMaxIdentityError( + f"Expected FilterMax F5 device code {_F5_DEVICE_CODE}, received " + f"{info.model!r} / {info.device_code}" + ) + except _HandshakeTimeout as exc: + await self.io.stop() + logger.info("[%s] no initial handshake response at %d baud", self.name, baudrate) + if baudrate == _STARTUP_BAUDRATES[-1]: + attempted = ", ".join(str(rate) for rate in _STARTUP_BAUDRATES) + raise FilterMaxTimeoutError( + f"No FilterMax handshake response on {self.port!r}; " + f"attempted baud rates: {attempted} (7E1, no flow control)" + ) from exc + continue + except BaseException: + await self.io.stop() + raise self._instrument_info = info self._setup_complete = True - logger.info("[%s] connected to FilterMax F5 serial %s", self.name, info.serial_number) - except BaseException: - await self.io.stop() - raise + logger.info( + "[%s] connected to FilterMax F5 serial %s on %s at %d baud", + self.name, + info.serial_number, + self.port, + baudrate, + ) + return async def stop(self) -> None: if self._read_active: diff --git a/pylabrobot/molecular_devices/filtermax/protocol.py b/pylabrobot/molecular_devices/filtermax/protocol.py index 48ae98ef019..204f6e4f044 100644 --- a/pylabrobot/molecular_devices/filtermax/protocol.py +++ b/pylabrobot/molecular_devices/filtermax/protocol.py @@ -34,6 +34,10 @@ class _CancelRequested(Exception): pass +class _HandshakeTimeout(FilterMaxTimeoutError): + """No byte arrived in response to the initial host ENQ.""" + + def checksum(data: bytes) -> int: """Return the captured modulo-256 checksum.""" @@ -90,7 +94,10 @@ async def send_request(self, payload: str, timeout: float = 5.0) -> None: deadline = time.monotonic() + timeout async with self._send_lock: await self.io.write(bytes((ENQ,))) - await self._expect(ACK, deadline) + try: + await self._expect(ACK, deadline) + except FilterMaxTimeoutError as exc: + raise _HandshakeTimeout("Timed out waiting for ACK to the initial FilterMax ENQ") from exc await self.io.write(build_frame(payload)) await self._expect(ACK, deadline) await self.io.write(bytes((EOT,))) diff --git a/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py index ca65c7ae3c4..ad63263cc63 100644 --- a/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py +++ b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py @@ -12,6 +12,7 @@ ENQ, EOT, FilterMaxTransport, + _HandshakeTimeout, build_frame, ) @@ -83,9 +84,18 @@ async def test_bad_continuation_frame_number(self) -> None: async def test_timeout_with_silent_device(self) -> None: transport = FilterMaxTransport(FakeSerial(b"")) # type: ignore[arg-type] - with self.assertRaises(FilterMaxTimeoutError): + with self.assertRaises(_HandshakeTimeout): await transport.send_request("STAT", timeout=0.001) + async def test_timeout_after_initial_ack_is_not_handshake_timeout(self) -> None: + """An acknowledged command must not be eligible for baud detection retries.""" + io = FakeSerial(bytes((ACK,))) + transport = FilterMaxTransport(io) # type: ignore[arg-type] + with self.assertRaises(FilterMaxTimeoutError) as caught: + await transport.send_request("STAT", timeout=0.001) + self.assertNotIsInstance(caught.exception, _HandshakeTimeout) + self.assertEqual(io.writes, [bytes((ENQ,)), build_frame("STAT")]) + async def test_device_error_and_cancel(self) -> None: e62 = "- E62: ABS Led 7 ADCValue: 16277 Gain 255 LedHighPoti 44 LedLowPoti 255" transport = FilterMaxTransport( 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"https://files.pythonhosted.org/packages/3a/13/547360d81e6d88d58492968ffda9f9542854f11310ee556fef14260cc886/zipp-4.1.0-py3-none-any.whl", hash = "sha256:25ad4e16390cd314347dd8f1de67a2ac538ae658ed4ab9db16029c07c188e97f", size = 10238, upload-time = "2026-05-18T20:08:57.045Z" }, +] From e9fc3a237bab6feac4fb5a1c6c5050d11e9dec75 Mon Sep 17 00:00:00 2001 From: Harley King Date: Tue, 29 Sep 2026 13:56:40 -0400 Subject: [PATCH 5/8] port help on hello-world.ipynb --- .../filtermax/filtermax_example_slides.xml | 200 ++++++++++++++++++ .../filtermax/hello-world.ipynb | 171 ++++++++++++++- .../filtermax/protocol-coverage.md | 8 + 3 files changed, 369 insertions(+), 10 deletions(-) create mode 100644 docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml diff --git a/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml b/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml new file mode 100644 index 00000000000..11f3ddc2c74 --- /dev/null +++ b/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml @@ -0,0 +1,200 @@ + + + + 0 + 1 + 1 + 1 + false + + + 1 + 2 + 2 + 1 + false + + + 2 + 1 + 1 + 0 + false + + + 1 + 2 + 535 + 535 + 25 + 0 + false + false + 6590-0044 + + + 2 + 2 + 485 + 485 + 20 + 0 + false + false + 6590-0043 + + + 3 + 4 + 485 + 485 + 20 + 0 + false + false + 6590-0043 + + + 5 + 8 + 370 + 370 + 80 + 0 + false + false + 6590-0073 + + + 1 + 1 + 260 + 260 + 12 + 1 + false + false + 6590-0001 + + + 2 + 1 + 340 + 340 + 10 + 1 + false + false + 6590-0032 + + + 3 + 1 + 405 + 405 + 10 + 1 + false + false + 6590-0037 + + + 4 + 1 + 450 + 450 + 8 + 1 + false + false + 6590-0005 + + + 5 + 1 + 595 + 595 + 8 + 1 + false + false + 6590-0024 + + + 6 + 1 + 620 + 620 + 8 + 1 + false + false + 6590-0027 + + + 1 + 2 + 595 + 595 + 35 + 2 + false + false + 6590-0058 + + + 2 + 2 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 3 + 4 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 4 + 4 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 5 + 10 + 625 + 625 + 35 + 2 + false + false + 6590-0059 + + + 6 + 16 + 0 + 0 + 0 + 2 + false + false + + + \ No newline at end of file diff --git a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb index 09a9f031dfc..02e06194b65 100644 --- a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb +++ b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb @@ -39,7 +39,7 @@ "\n", "1. Connect the FilterMax F5 through its RS-232 cable or a USB-to-serial adapter.\n", "2. Close SoftMax Pro and release the serial port. If Windows runs in VirtualBox with a host serial port mapping, save the results and shut Windows down normally; confirm the VM is powered off. Only one program may own the port.\n", - "3. Export the filter-slide definitions from SoftMax Pro as XML.\n", + "3. Export your filter-slide definitions from SoftMax Pro as XML, or use the example catalog below when its definitions match your physical slides.\n", "4. Install the plate and filter slides appropriate for the requested measurement.\n", "5. Use a stable device path on Linux, such as `/dev/serial/by-id/...`.\n", "\n", @@ -51,15 +51,21 @@ "id": "imports", "metadata": {}, "source": [ - "## Create the reader\n", + "## Load the filter-slide catalog\n", + "\n", + "Download {download}`filtermax_example_slides.xml ` or use the copy alongside this notebook in the repository. It contains 16 filter definitions for excitation slides 1 and 2 and emission slide 1. Excitation slide 2 includes 260 nm at position 1 (12 nm bandwidth) and 450 nm at position 4 (8 nm bandwidth).\n", + "\n", + "`FilterSlideCatalog.from_softmax_xml()` loads slide IDs, positions, wavelengths, bandwidths, and supported filter techniques. Measurement methods use this catalog to resolve a wavelength to a slide and position and to send that slide's filter definitions to the reader. Loading or resolving the catalog is local and does not contact the instrument.\n", "\n", - "Load the SoftMax filter-slide catalog. Measurement methods require it so wavelengths can be resolved to an exact installed slide and slot." + "Use your own SoftMax XML export for a different filter configuration. The driver checks installed slide IDs, but it cannot verify that the physical filters match the XML. Catalog entries for fluorescence, FP, and TRF do not enable those currently unsupported driver modes.\n", + "\n", + "The next cell assumes this notebook's directory is the working directory. From the repository root, set `catalog_path` to `Path(\"docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml\")`. For your own export, use its local path instead." ] }, { "cell_type": "code", - "execution_count": null, - "id": "create-reader", + "execution_count": 1, + "id": "load-filter-catalog", "metadata": {}, "outputs": [], "source": [ @@ -67,11 +73,148 @@ "\n", "from pylabrobot.molecular_devices.filtermax import FilterMaxF5, FilterSlideCatalog\n", "\n", - "catalog_path = Path(\"~/Documents/WIN7Shared/filtermax_slides.xml\").expanduser()\n", - "catalog = FilterSlideCatalog.from_softmax_xml(catalog_path)\n", + "catalog_path = Path(\"filtermax_example_slides.xml\")\n", + "catalog = FilterSlideCatalog.from_softmax_xml(catalog_path)" + ] + }, + { + "cell_type": "markdown", + "id": "resolve-example-filter", + "metadata": {}, + "source": [ + "## Check an example filter locally\n", + "\n", + "Resolve the 450 nm absorbance filter to excitation slide 2, position 4. For 260 nm, use `wavelength=260` and `position=1`. This check does not move the reader or start a measurement." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "resolve-example-filter-code", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "FilterSelection(kind='excitation', slide_id=2, position=4, wavelength=450, bandwidth=8)" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "filter_selection = catalog.resolve(\n", + " kind=\"excitation\",\n", + " technique=\"absorbance\",\n", + " wavelength=450,\n", + " slide_id=2,\n", + " position=4,\n", + ")\n", + "filter_selection" + ] + }, + { + "cell_type": "markdown", + "id": "create-reader-description", + "metadata": {}, + "source": [ + "## Choose the serial port\n", + "\n", + "List detected serial ports and identify the FilterMax F5 adapter. On Linux, prefer its stable `/dev/serial/by-id/...` path; Windows ports usually look like `COM3`. If no port is listed, connect the adapter and check its cable/permissions. Use the exact device path shown for the F5 below." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "ebc3573d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[('/dev/ttyS31', 'n/a'),\n", + " ('/dev/ttyS30', 'n/a'),\n", + " ('/dev/ttyS29', 'n/a'),\n", + " ('/dev/ttyS28', 'n/a'),\n", + " ('/dev/ttyS27', 'n/a'),\n", + " ('/dev/ttyS26', 'n/a'),\n", + " ('/dev/ttyS25', 'n/a'),\n", + " ('/dev/ttyS24', 'n/a'),\n", + " ('/dev/ttyS23', 'n/a'),\n", + " ('/dev/ttyS22', 'n/a'),\n", + " ('/dev/ttyS21', 'n/a'),\n", + " ('/dev/ttyS20', 'n/a'),\n", + " ('/dev/ttyS19', 'n/a'),\n", + " ('/dev/ttyS18', 'n/a'),\n", + " ('/dev/ttyS17', 'n/a'),\n", + " ('/dev/ttyS16', 'n/a'),\n", + " ('/dev/ttyS15', 'n/a'),\n", + " ('/dev/ttyS14', 'n/a'),\n", + " ('/dev/ttyS13', 'n/a'),\n", + " ('/dev/ttyS12', 'n/a'),\n", + " ('/dev/ttyS11', 'n/a'),\n", + " ('/dev/ttyS10', 'n/a'),\n", + " ('/dev/ttyS9', 'n/a'),\n", + " ('/dev/ttyS8', 'n/a'),\n", + " ('/dev/ttyS7', 'n/a'),\n", + " ('/dev/ttyS6', 'n/a'),\n", + " ('/dev/ttyS5', 'n/a'),\n", + " ('/dev/ttyS4', 'n/a'),\n", + " ('/dev/ttyS3', 'n/a'),\n", + " ('/dev/ttyS2', 'n/a'),\n", + " ('/dev/ttyS1', 'n/a'),\n", + " ('/dev/ttyS0', 'n/a')]" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from serial.tools import list_ports\n", + "\n", + "[(port.device, port.description) for port in list_ports.comports()]" + ] + }, + { + "cell_type": "markdown", + "id": "4a57ea59", + "metadata": {}, + "source": [ + "## Create the reader\n", + "\n", + "Pass the loaded catalog as `filter_slide_catalog`. Creating the reader does not open the serial port. Connection and status queries can run without a catalog, but measurement methods require one. Enter the exact FilterMax F5 port from the list above when prompted." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "create-reader", + "metadata": {}, + "outputs": [ + { + "ename": "ValueError", + "evalue": "Enter the serial port for the FilterMax F5.", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mValueError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[4]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m 1\u001b[39m port = input(\u001b[33m\"FilterMax serial port: \"\u001b[39m).strip()\n\u001b[32m 2\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28;01mnot\u001b[39;00m port:\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m ValueError(\u001b[33m\"Enter the serial port for the FilterMax F5.\"\u001b[39m)\n\u001b[32m 4\u001b[39m \n\u001b[32m 5\u001b[39m reader = FilterMaxF5(\n\u001b[32m 6\u001b[39m name=\u001b[33m\"filtermax-f5\"\u001b[39m,\n", + "\u001b[31mValueError\u001b[39m: Enter the serial port for the FilterMax F5." + ] + } + ], + "source": [ + "port = input(\"FilterMax serial port: \").strip()\n", + "if not port:\n", + " raise ValueError(\"Enter the serial port for the FilterMax F5.\")\n", + "\n", "reader = FilterMaxF5(\n", " name=\"filtermax-f5\",\n", - " port=\"/dev/serial/by-id/replace-with-your-adapter\",\n", + " port=port,\n", " filter_slide_catalog=catalog,\n", ")" ] @@ -465,13 +608,21 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "pylabrobot (3.12.3)", "language": "python", "name": "python3" }, "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", "name": "python", - "version": "3.12.0" + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.3" } }, "nbformat": 4, diff --git a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md index aefa3aaec3f..ff7be6818fc 100644 --- a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md +++ b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md @@ -62,6 +62,14 @@ overruns an interval, the next read starts immediately without changing its nomi ## Measurement setup +The {download}`example slide catalog ` is a SoftMax XML export +containing definitions for excitation slides 1 and 2 and emission slide 1. The +[hello-world guide](hello-world.ipynb) shows how to load it with +`FilterSlideCatalog.from_softmax_xml()`, resolve a wavelength to a slide and position, and pass +the catalog to `FilterMaxF5(filter_slide_catalog=...)`. For absorbance, excitation slide 2 has +260 nm at position 1 and 450 nm at position 4. Use a catalog that matches the physical filters +installed in the reader; the example is not a universal FilterMax configuration. + The live-optimized Costar 96-well clear landscape geometry was sent as: ```text From 608fe4901c1126e6ac8cd164741e4af6fa80f9bd Mon Sep 17 00:00:00 2001 From: Harley King Date: Tue, 29 Sep 2026 15:09:26 -0400 Subject: [PATCH 6/8] add optional plate reader tests --- .../filtermax/hello-world.ipynb | 430 +++++++++++++----- .../filtermax/tests/hello_world_tests.py | 180 ++++++++ 2 files changed, 488 insertions(+), 122 deletions(-) create mode 100644 pylabrobot/molecular_devices/filtermax/tests/hello_world_tests.py diff --git a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb index 02e06194b65..b21ea69718b 100644 --- a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb +++ b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb @@ -40,10 +40,10 @@ "1. Connect the FilterMax F5 through its RS-232 cable or a USB-to-serial adapter.\n", "2. Close SoftMax Pro and release the serial port. If Windows runs in VirtualBox with a host serial port mapping, save the results and shut Windows down normally; confirm the VM is powered off. Only one program may own the port.\n", "3. Export your filter-slide definitions from SoftMax Pro as XML, or use the example catalog below when its definitions match your physical slides.\n", - "4. Install the plate and filter slides appropriate for the requested measurement.\n", + "4. Keep the tray path clear. A plate is optional: inspection, tray operation, temperature control, and shaking run by default. Measurements are opt-in, with a guided plate-loading step before plate geometry.\n", "5. Use a stable device path on Linux, such as `/dev/serial/by-id/...`.\n", "\n", - "Excitation and emission slides occupy separate bays and are not interchangeable." + "For optional measurements, prepare a compatible plate with samples or blanks in the wells you intend to read, and install the appropriate filter slides. Excitation and emission slides occupy separate bays and are not interchangeable." ] }, { @@ -64,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "load-filter-catalog", "metadata": {}, "outputs": [], @@ -89,28 +89,17 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "resolve-example-filter-code", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "FilterSelection(kind='excitation', slide_id=2, position=4, wavelength=450, bandwidth=8)" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "filter_selection = catalog.resolve(\n", - " kind=\"excitation\",\n", - " technique=\"absorbance\",\n", - " wavelength=450,\n", - " slide_id=2,\n", - " position=4,\n", + " kind=\"excitation\",\n", + " technique=\"absorbance\",\n", + " wavelength=450,\n", + " slide_id=2,\n", + " position=4,\n", ")\n", "filter_selection" ] @@ -127,52 +116,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "ebc3573d", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[('/dev/ttyS31', 'n/a'),\n", - " ('/dev/ttyS30', 'n/a'),\n", - " ('/dev/ttyS29', 'n/a'),\n", - " ('/dev/ttyS28', 'n/a'),\n", - " ('/dev/ttyS27', 'n/a'),\n", - " ('/dev/ttyS26', 'n/a'),\n", - " ('/dev/ttyS25', 'n/a'),\n", - " ('/dev/ttyS24', 'n/a'),\n", - " ('/dev/ttyS23', 'n/a'),\n", - " ('/dev/ttyS22', 'n/a'),\n", - " ('/dev/ttyS21', 'n/a'),\n", - " ('/dev/ttyS20', 'n/a'),\n", - " ('/dev/ttyS19', 'n/a'),\n", - " ('/dev/ttyS18', 'n/a'),\n", - " ('/dev/ttyS17', 'n/a'),\n", - " ('/dev/ttyS16', 'n/a'),\n", - " ('/dev/ttyS15', 'n/a'),\n", - " ('/dev/ttyS14', 'n/a'),\n", - " ('/dev/ttyS13', 'n/a'),\n", - " ('/dev/ttyS12', 'n/a'),\n", - " ('/dev/ttyS11', 'n/a'),\n", - " ('/dev/ttyS10', 'n/a'),\n", - " ('/dev/ttyS9', 'n/a'),\n", - " ('/dev/ttyS8', 'n/a'),\n", - " ('/dev/ttyS7', 'n/a'),\n", - " ('/dev/ttyS6', 'n/a'),\n", - " ('/dev/ttyS5', 'n/a'),\n", - " ('/dev/ttyS4', 'n/a'),\n", - " ('/dev/ttyS3', 'n/a'),\n", - " ('/dev/ttyS2', 'n/a'),\n", - " ('/dev/ttyS1', 'n/a'),\n", - " ('/dev/ttyS0', 'n/a')]" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from serial.tools import list_ports\n", "\n", @@ -191,31 +138,19 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "create-reader", "metadata": {}, - "outputs": [ - { - "ename": "ValueError", - "evalue": "Enter the serial port for the FilterMax F5.", - "output_type": "error", - "traceback": [ - "\u001b[31m---------------------------------------------------------------------------\u001b[39m", - "\u001b[31mValueError\u001b[39m Traceback (most recent call last)", - "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[4]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m 1\u001b[39m port = input(\u001b[33m\"FilterMax serial port: \"\u001b[39m).strip()\n\u001b[32m 2\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28;01mnot\u001b[39;00m port:\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m ValueError(\u001b[33m\"Enter the serial port for the FilterMax F5.\"\u001b[39m)\n\u001b[32m 4\u001b[39m \n\u001b[32m 5\u001b[39m reader = FilterMaxF5(\n\u001b[32m 6\u001b[39m name=\u001b[33m\"filtermax-f5\"\u001b[39m,\n", - "\u001b[31mValueError\u001b[39m: Enter the serial port for the FilterMax F5." - ] - } - ], + "outputs": [], "source": [ "port = input(\"FilterMax serial port: \").strip()\n", "if not port:\n", - " raise ValueError(\"Enter the serial port for the FilterMax F5.\")\n", + " raise ValueError(\"Enter the serial port for the FilterMax F5.\")\n", "\n", "reader = FilterMaxF5(\n", - " name=\"filtermax-f5\",\n", - " port=port,\n", - " filter_slide_catalog=catalog,\n", + " name=\"filtermax-f5\",\n", + " port=port,\n", + " filter_slide_catalog=catalog,\n", ")" ] }, @@ -271,7 +206,7 @@ "source": [ "## Plate tray\n", "\n", - "Move the tray out before loading or removing a plate." + "Run the tray-out demonstration with the tray path clear. No plate is required; the optional measurement section below has its own loading step." ] }, { @@ -289,7 +224,26 @@ "id": "tray-in", "metadata": {}, "source": [ - "After the plate is loaded and the tray path is clear, move it back in." + "Confirm that your hands and any obstructions are clear before closing the tray. Enter `yes` to continue. If you decline, the notebook stops here with the tray open; clear the path and rerun this confirmation cell to continue." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "tray-clear-confirmation", + "metadata": {}, + "outputs": [], + "source": [ + "if input(\"Are your hands and the tray path clear? [y/N] \").strip().lower() not in (\"y\", \"yes\"):\n", + " raise RuntimeError(\"Tray left open. Clear the path and rerun this confirmation cell to continue.\")" + ] + }, + { + "cell_type": "markdown", + "id": "tray-close-description", + "metadata": {}, + "source": [ + "Close the tray after confirming that its path is clear." ] }, { @@ -361,6 +315,122 @@ "await reader.start_shaking(pattern=\"linear\", speed=\"medium\", duration=5)" ] }, + { + "cell_type": "markdown", + "id": "measurement-options", + "metadata": {}, + "source": [ + "## Optional plate measurements\n", + "\n", + "Press Enter at the first prompt to skip all measurements and continue to device errors and disconnect. Inspection, tray controls, temperature control, and shaking above do not depend on this choice.\n", + "\n", + "If you choose measurements, select each example separately (`yes` to select; Enter to skip). Full-plate absorbance reads every well. All other examples use editable lists of populated wells in the configuration cell below. Choose only examples that suit your samples and installed filters. The cancellation example also starts a measurement." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-options-command", + "metadata": {}, + "outputs": [], + "source": [ + "run_measurements = input(\"Run optional plate measurements? [y/N] \").strip().lower() in (\"y\", \"yes\")\n", + "measurement_examples = {\n", + " \"endpoint\": \"Full-plate endpoint absorbance at 450 nm\",\n", + " \"partial\": \"Selected-well absorbance at 450 nm\",\n", + " \"reference\": \"Reference-subtracted absorbance at 450 nm with a 620 nm reference\",\n", + " \"kinetic\": \"Kinetic absorbance at 450 nm (3 reads, 15-second intervals)\",\n", + " \"scan\": \"Absorbance well scan at 450 nm\",\n", + " \"luminescence\": \"Luminescence (requires suitable luminescent samples)\",\n", + " \"cancel\": \"Cancellation of a kinetic absorbance read at 450 nm\",\n", + "}\n", + "selected_examples = set()\n", + "plate_loaded = False\n", + "if run_measurements:\n", + " for key, label in measurement_examples.items():\n", + " if input(f\"Include {label}? [y/N] \").strip().lower() in (\"y\", \"yes\"):\n", + " selected_examples.add(key)\n", + "if not selected_examples:\n", + " print(\"No measurements selected. Measurement and plate-loading cells will be skipped.\")" + ] + }, + { + "cell_type": "markdown", + "id": "measurement-tray-out", + "metadata": {}, + "source": [ + "### Open the tray for the measurement plate\n", + "\n", + "If at least one example was selected, clear the tray path and run this cell to open the tray. The next cell waits for you to load a plate; the tray will not close automatically while you are loading it." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-tray-out-command", + "metadata": {}, + "outputs": [], + "source": [ + "plate_loaded = False\n", + "if selected_examples:\n", + " await reader.move_plate_tray_out()\n", + "else:\n", + " print(\"Skipping measurement tray opening: no measurements selected.\")" + ] + }, + { + "cell_type": "markdown", + "id": "measurement-load", + "metadata": {}, + "source": [ + "### Insert and confirm the plate\n", + "\n", + "Place a compatible plate with samples or blanks in the intended wells into the tray, fully seated in the correct orientation. The geometry example below assumes a Costar 96-well clear plate in landscape orientation; for a different plate, update that geometry before running any read.\n", + "\n", + "Remove your hands and clear the tray path, then enter `yes`. Enter or any other response skips all measurements and leaves the tray open. To try loading again, rerun the measurement tray-opening and confirmation cells before continuing." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-load-confirmation", + "metadata": {}, + "outputs": [], + "source": [ + "plate_loaded = False\n", + "if selected_examples:\n", + " plate_loaded = input(\n", + " \"Is the measurement plate loaded and seated, with hands and tray path clear? [y/N] \"\n", + " ).strip().lower() in (\"y\", \"yes\")\n", + " if not plate_loaded:\n", + " print(\"Plate loading not confirmed. All measurements will be skipped; tray remains open.\")\n", + "else:\n", + " print(\"Skipping plate loading: no measurements selected.\")" + ] + }, + { + "cell_type": "markdown", + "id": "measurement-tray-in", + "metadata": {}, + "source": [ + "### Close the loaded tray\n", + "\n", + "Close the tray only after the plate-loading confirmation above." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-tray-in-command", + "metadata": {}, + "outputs": [], + "source": [ + "if plate_loaded:\n", + " await reader.move_plate_tray_in()\n", + "else:\n", + " print(\"Skipping measurement tray closing: no confirmed plate load.\")" + ] + }, { "cell_type": "markdown", "id": "plate-geometry", @@ -368,7 +438,7 @@ "source": [ "## Plate geometry\n", "\n", - "The captured Costar 96-well clear plate geometry is available as a convenience. For another plate, construct `PlateGeometry` using its measured dimensions in millimetres." + "The captured Costar 96-well clear plate geometry is available as a convenience. It must match the loaded plate, including orientation. For another plate, replace the assignment below with `PlateGeometry` using its measured dimensions in millimetres before proceeding. If you replace the plate between examples, update this geometry to match." ] }, { @@ -380,7 +450,93 @@ "source": [ "from pylabrobot.molecular_devices.filtermax import PlateGeometry\n", "\n", - "plate = PlateGeometry.costar_96_clear_landscape()" + "plate = None\n", + "if plate_loaded:\n", + " plate = PlateGeometry.costar_96_clear_landscape()\n", + "else:\n", + " print(\"Skipping plate geometry: no confirmed measurement plate.\")" + ] + }, + { + "cell_type": "markdown", + "id": "measurement-wells", + "metadata": {}, + "source": [ + "### Configure populated wells\n", + "\n", + "Edit the lists below for the selected examples, then run this cell. For example, set `\"partial\": [\"C4\", \"C5\", \"D4\"]` only if those wells contain suitable samples or blanks. Leave unselected examples as `[]`. Full-plate endpoint absorbance reads every well and does not use these lists.\n", + "\n", + "There is no text-entry prompt for wells. An empty or invalid list for a selected example stops that cell before a read starts. Correct the relevant list here, rerun this configuration cell, then rerun the measurement cell. Lowercase names are accepted and duplicate wells are read once.\n", + "\n", + "To change samples between examples, update the relevant list and rerun this cell. If an earlier input prompt is still waiting, use the notebook toolbar's **Interrupt/Stop** control before continuing." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-wells-command", + "metadata": {}, + "outputs": [], + "source": [ + "measurement_wells = {\n", + " \"partial\": [], # Example: [\"C4\", \"C5\", \"D4\"] — replace with your populated wells.\n", + " \"reference\": [],\n", + " \"kinetic\": [],\n", + " \"scan\": [],\n", + " \"luminescence\": [],\n", + " \"cancel\": [],\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "measurement-prompts", + "metadata": {}, + "source": [ + "### Readiness confirmations and well validation\n", + "\n", + "Each selected example asks you to confirm that the correct plate is seated, its geometry and filters match, and your hands are clear. Enter skips that example. Reads eject the tray when finished, so you can replace the plate before the next example; the next read closes the tray after your confirmation.\n", + "\n", + "The helpers below confirm readiness and validate the configured well lists. Defining them does not request input or operate the reader. Well validation uses the current plate geometry and never prompts for input." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "measurement-prompts-command", + "metadata": {}, + "outputs": [], + "source": [ + "def confirm_measurement(example: str, requirements: str) -> bool:\n", + " \"\"\"Confirm readiness for a selected example with a previously loaded plate.\"\"\"\n", + " label = measurement_examples[example]\n", + " if example not in selected_examples or not plate_loaded:\n", + " print(f\"Skipping {label}: not selected or plate loading not confirmed.\")\n", + " return False\n", + " print(requirements)\n", + " ready = input(\n", + " f\"Run {label}? Confirm plate seated, matching geometry/filters, and hands clear [y/N]: \"\n", + " ).strip().lower() in (\"y\", \"yes\")\n", + " if not ready:\n", + " print(f\"Skipping {label}: readiness not confirmed.\")\n", + " return ready\n", + "\n", + "\n", + "def validate_wells(geometry: PlateGeometry, entries: list[str]) -> list[str]:\n", + " \"\"\"Validate configured populated wells without requesting interactive input.\"\"\"\n", + " valid_wells = {\n", + " f\"{chr(ord('A') + row)}{column + 1}\"\n", + " for row in range(geometry.rows)\n", + " for column in range(geometry.columns)\n", + " }\n", + " wells = [well.strip().upper() for well in entries]\n", + " if not wells or any(well not in valid_wells for well in wells):\n", + " raise ValueError(\n", + " f\"Set measurement_wells for this example to a nonempty list of populated wells \"\n", + " f'within the {geometry.rows}x{geometry.columns} plate, e.g. [\"C4\", \"C5\"]. '\n", + " \"Rerun the configuration cell, then this measurement cell. No read was started.\"\n", + " )\n", + " return list(dict.fromkeys(wells))" ] }, { @@ -390,7 +546,7 @@ "source": [ "## Absorbance\n", "\n", - "Run an endpoint read at 450 nm. Results are plate-shaped optical-density values; unselected wells are `None`. The tray ejects when the read finishes." + "Optionally run a full-plate endpoint read at 450 nm: **every well is measured**, including empty wells. Choose the selected-well example instead if you only want to measure populated wells. Results are plate-shaped optical-density values. The tray ejects when the read finishes." ] }, { @@ -400,7 +556,11 @@ "metadata": {}, "outputs": [], "source": [ - "absorbance = await reader.read_absorbance(plate, wavelength=450)" + "if confirm_measurement(\n", + " \"endpoint\",\n", + " \"This reads EVERY well at 450 nm. Confirm a suitable absorbance plate and a matching 450 nm excitation filter.\",\n", + "):\n", + " absorbance = await reader.read_absorbance(plate, wavelength=450)" ] }, { @@ -408,7 +568,7 @@ "id": "partial", "metadata": {}, "source": [ - "Select individual wells for a partial-plate read." + "Select populated wells for an optional partial-plate read at 450 nm. Unselected wells are `None` in the result." ] }, { @@ -418,11 +578,12 @@ "metadata": {}, "outputs": [], "source": [ - "partial = await reader.read_absorbance(\n", - " plate,\n", - " wavelength=450,\n", - " wells=[\"C4\", \"C5\", \"C6\", \"D4\", \"D5\", \"D6\"],\n", - ")" + "if confirm_measurement(\n", + " \"partial\",\n", + " \"Use samples or blanks suitable for absorbance at 450 nm and a matching excitation filter.\",\n", + "):\n", + " wells = validate_wells(plate, measurement_wells[\"partial\"])\n", + " partial = await reader.read_absorbance(plate, wavelength=450, wells=wells)" ] }, { @@ -430,7 +591,7 @@ "id": "reference", "metadata": {}, "source": [ - "Use a supported reference filter when reference-subtracted absorbance is required." + "For optional reference-subtracted absorbance, use supported 450 nm and 620 nm excitation filters matching the catalog and installed slide. Configure only the populated wells you want to read." ] }, { @@ -440,12 +601,17 @@ "metadata": {}, "outputs": [], "source": [ - "reference_subtracted = await reader.read_absorbance(\n", + "if confirm_measurement(\n", + " \"reference\",\n", + " \"Use absorbance samples or blanks and supported 450 nm and 620 nm excitation filters matching the catalog.\",\n", + "):\n", + " wells = validate_wells(plate, measurement_wells[\"reference\"])\n", + " reference_subtracted = await reader.read_absorbance(\n", " plate,\n", " wavelength=450,\n", " reference_wavelength=620,\n", - " wells=[\"C4\", \"C5\", \"C6\", \"D4\", \"D5\", \"D6\"],\n", - ")" + " wells=wells,\n", + " )" ] }, { @@ -465,14 +631,19 @@ "metadata": {}, "outputs": [], "source": [ - "from pylabrobot.molecular_devices.filtermax import KineticTiming\n", + "if confirm_measurement(\n", + " \"kinetic\",\n", + " \"Use absorbance samples or blanks and a matching 450 nm excitation filter. This collects 3 reads at 15-second intervals.\",\n", + "):\n", + " from pylabrobot.molecular_devices.filtermax import KineticTiming\n", "\n", - "kinetic = await reader.read_absorbance(\n", + " wells = validate_wells(plate, measurement_wells[\"kinetic\"])\n", + " kinetic = await reader.read_absorbance(\n", " plate,\n", " wavelength=450,\n", - " wells=[\"C4\"],\n", + " wells=wells,\n", " kinetic=KineticTiming(interval=15, reads=3),\n", - ")" + " )" ] }, { @@ -492,14 +663,19 @@ "metadata": {}, "outputs": [], "source": [ - "from pylabrobot.molecular_devices.filtermax import WellScanSettings\n", + "if confirm_measurement(\n", + " \"scan\",\n", + " \"Use absorbance samples or blanks and a matching 450 nm excitation filter for a circular fill scan.\",\n", + "):\n", + " from pylabrobot.molecular_devices.filtermax import WellScanSettings\n", "\n", - "scan = await reader.read_absorbance(\n", + " wells = validate_wells(plate, measurement_wells[\"scan\"])\n", + " scan = await reader.read_absorbance(\n", " plate,\n", " wavelength=450,\n", - " wells=[\"C4\"],\n", + " wells=wells,\n", " well_scan=WellScanSettings(pattern=\"fill\", density=5),\n", - ")" + " )" ] }, { @@ -519,12 +695,17 @@ "metadata": {}, "outputs": [], "source": [ - "luminescence = await reader.read_luminescence(\n", + "if confirm_measurement(\n", + " \"luminescence\",\n", + " \"Use a plate and samples suitable for luminescence, with the catalog-matched open position on the installed emission slide.\",\n", + "):\n", + " wells = validate_wells(plate, measurement_wells[\"luminescence\"])\n", + " luminescence = await reader.read_luminescence(\n", " plate,\n", - " wells=[\"C4\"],\n", + " wells=wells,\n", " integration=0.4,\n", " read_height=1.0,\n", - ")" + " )" ] }, { @@ -544,23 +725,28 @@ "metadata": {}, "outputs": [], "source": [ - "import asyncio\n", + "if confirm_measurement(\n", + " \"cancel\",\n", + " \"This starts and then cancels a kinetic absorbance measurement. Use absorbance samples or blanks and a matching 450 nm excitation filter.\",\n", + "):\n", + " import asyncio\n", "\n", - "from pylabrobot.molecular_devices.filtermax import FilterMaxReadCancelled\n", + " from pylabrobot.molecular_devices.filtermax import FilterMaxReadCancelled, KineticTiming\n", "\n", - "read_task = asyncio.create_task(\n", + " wells = validate_wells(plate, measurement_wells[\"cancel\"])\n", + " read_task = asyncio.create_task(\n", " reader.read_absorbance(\n", - " plate,\n", - " wavelength=450,\n", - " wells=[\"C4\"],\n", - " kinetic=KineticTiming(interval=30, reads=10),\n", + " plate,\n", + " wavelength=450,\n", + " wells=wells,\n", + " kinetic=KineticTiming(interval=30, reads=10),\n", " )\n", - ")\n", - "await asyncio.sleep(2)\n", - "await reader.cancel_read()\n", - "try:\n", + " )\n", + " await asyncio.sleep(2)\n", + " await reader.cancel_read()\n", + " try:\n", " await read_task\n", - "except FilterMaxReadCancelled:\n", + " except FilterMaxReadCancelled:\n", " pass" ] }, diff --git a/pylabrobot/molecular_devices/filtermax/tests/hello_world_tests.py b/pylabrobot/molecular_devices/filtermax/tests/hello_world_tests.py new file mode 100644 index 00000000000..8441575659e --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/hello_world_tests.py @@ -0,0 +1,180 @@ +"""Exercise the hello-world prompts with a fake reader, without opening a serial port.""" + +import ast +import asyncio +import inspect +import json +import unittest +from pathlib import Path +from typing import Any, Optional +from unittest.mock import AsyncMock, patch + +from pylabrobot.molecular_devices.filtermax import ( + FilterMaxF5, + FilterMaxReadCancelled, + PlateGeometry, +) + +NOTEBOOK = ( + Path(__file__).resolve().parents[4] + / "docs/user_guide/molecular_devices/filtermax/hello-world.ipynb" +) + + +class HelloWorldTests(unittest.IsolatedAsyncioTestCase): + """Check measurement opt-in and loading gates in the runnable notebook cells.""" + + async def run_notebook( + self, + answers: list[str], + well_selections: Optional[dict[str, list[str]]] = None, + reader: Optional[AsyncMock] = None, + ) -> AsyncMock: + """Execute the connected walkthrough with scripted input and mocked hardware.""" + if reader is None: + reader = AsyncMock(spec=FilterMaxF5) + cancelled = asyncio.Event() + real_sleep = asyncio.sleep + + async def read_absorbance(plate: PlateGeometry, **kwargs: Any) -> list: + """Keep the cancellation example active until it receives a cancel request.""" + kinetic = kwargs.get("kinetic") + if kinetic is not None and kinetic.reads == 10: + await cancelled.wait() + raise FilterMaxReadCancelled(140, "Cancelled", "read") + return [] + + async def skip_sleep(seconds: float) -> None: + """Yield to the read task without the demonstration's two-second delay.""" + await real_sleep(0) + + reader.read_absorbance.side_effect = read_absorbance + reader.cancel_read.side_effect = cancelled.set + namespace = {"reader": reader} + notebook = json.loads(NOTEBOOK.read_text()) + connected = False + with ( + patch("builtins.input", side_effect=answers) as prompt, + patch("builtins.print"), + patch("asyncio.sleep", side_effect=skip_sleep), + ): + for cell in notebook["cells"]: + if cell["cell_type"] != "code": + continue + source = "".join(cell["source"]) + compiled = compile( + source, f"{NOTEBOOK}:{cell['id']}", "exec", ast.PyCF_ALLOW_TOP_LEVEL_AWAIT + ) + connected = connected or cell["id"] == "connect" + if connected: + result = eval(compiled, namespace) + if inspect.isawaitable(result): + await result + if cell["id"] == "measurement-wells-command" and well_selections is not None: + namespace["measurement_wells"].update(well_selections) + self.assertEqual(prompt.call_count, len(answers)) + + reader.setup.assert_awaited_once() + reader.get_instrument_info.assert_awaited_once() + reader.get_status.assert_awaited_once() + reader.get_filter_slides.assert_awaited_once() + reader.set_temperature.assert_awaited_once_with(25.0) + reader.deactivate_temperature_control.assert_awaited_once() + reader.start_shaking.assert_awaited_once_with(pattern="linear", speed="medium", duration=5) + reader.get_error_log.assert_awaited_once() + reader.clear_error_log.assert_awaited_once() + reader.stop.assert_awaited_once() + return reader + + async def test_default_skips_measurements(self) -> None: + """Empty opt-in runs the default controls without extra tray motions or reads.""" + reader = await self.run_notebook(["yes", ""]) + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_not_awaited() + reader.cancel_read.assert_not_awaited() + reader.move_plate_tray_out.assert_awaited_once() + reader.move_plate_tray_in.assert_awaited_once() + + async def test_each_example_runs_independently(self) -> None: + """Each example works even when all earlier measurement examples were skipped.""" + for index in range(7): + with self.subTest(example=index): + selections = ["yes" if choice == index else "" for choice in range(7)] + examples = ["endpoint", "partial", "reference", "kinetic", "scan", "luminescence", "cancel"] + reader = await self.run_notebook( + ["yes", "yes", *selections, "yes", "yes"], + {examples[index]: [" c4 ", "C5", "c4"]}, + ) + if index == 5: + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_awaited_once() + measurement = reader.read_luminescence + else: + reader.read_absorbance.assert_awaited_once() + reader.read_luminescence.assert_not_awaited() + measurement = reader.read_absorbance + if index == 0: + self.assertNotIn("wells", measurement.call_args.kwargs) + else: + self.assertEqual(measurement.call_args.kwargs["wells"], ["C4", "C5"]) + if index == 6: + reader.cancel_read.assert_awaited_once() + else: + reader.cancel_read.assert_not_awaited() + self.assertEqual(reader.move_plate_tray_out.await_count, 2) + self.assertEqual(reader.move_plate_tray_in.await_count, 2) + operations = [entry[0] for entry in reader.mock_calls] + openings = [i for i, name in enumerate(operations) if name == "move_plate_tray_out"] + closings = [i for i, name in enumerate(operations) if name == "move_plate_tray_in"] + read_name = "read_luminescence" if index == 5 else "read_absorbance" + self.assertLess(openings[1], closings[1]) + self.assertLess(closings[1], operations.index(read_name)) + + async def test_no_examples_selected(self) -> None: + """Opt-in alone does not open the loading tray or start measurements.""" + reader = await self.run_notebook(["yes", "yes", *([""] * 7)]) + reader.move_plate_tray_out.assert_awaited_once() + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_not_awaited() + + async def test_declining_plate_loading_skips_all_reads(self) -> None: + """No selected example can run or close the loading tray without confirmation.""" + reader = await self.run_notebook(["yes", "yes", *(["yes"] * 7), ""]) + self.assertEqual(reader.move_plate_tray_out.await_count, 2) + reader.move_plate_tray_in.assert_awaited_once() + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_not_awaited() + reader.cancel_read.assert_not_awaited() + + async def test_declining_example_readiness_skips_all_reads(self) -> None: + """A loaded plate alone does not authorize any of the selected examples.""" + reader = await self.run_notebook(["yes", "yes", *(["yes"] * 7), "yes", *([""] * 7)]) + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_not_awaited() + reader.cancel_read.assert_not_awaited() + + async def test_multiple_examples_use_configured_wells(self) -> None: + """Use separate edited well lists without asking for well input.""" + reader = await self.run_notebook( + ["yes", "yes", "", "yes", "", "", "", "yes", "", "yes", "yes", "yes"], + {"partial": ["c4", "c5", "C4"], "luminescence": ["d6"]}, + ) + reader.read_absorbance.assert_awaited_once() + reader.read_luminescence.assert_awaited_once() + self.assertEqual(reader.read_absorbance.call_args.kwargs["wells"], ["C4", "C5"]) + self.assertEqual(reader.read_luminescence.call_args.kwargs["wells"], ["D6"]) + + async def test_invalid_wells_stop_without_reading_or_reprompting(self) -> None: + """Empty and invalid settings fail before a read instead of looping on stdin.""" + for wells in ([], [""], ["A0"], ["A13"], ["I1"], ["C4", ""], ["C4, C5"]): + with self.subTest(wells=wells): + reader = AsyncMock(spec=FilterMaxF5) + with self.assertRaisesRegex(ValueError, "measurement_wells"): + await self.run_notebook( + ["yes", "yes", "", "yes", "", "", "", "", "", "yes", "yes"], + {"partial": wells}, + reader, + ) + reader.read_absorbance.assert_not_awaited() + reader.read_luminescence.assert_not_awaited() + reader.cancel_read.assert_not_awaited() From d271e03f9cd26631d375effadd3fe2d877709ed1 Mon Sep 17 00:00:00 2001 From: Harley King Date: Thu, 1 Oct 2026 10:40:47 -0400 Subject: [PATCH 7/8] stop tracking uv.lock --- .gitignore | 1 + uv.lock 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46 +- .../filtermax/tests/operation_tests.py | 353 +++++++ .../filtermax/tests/protocol_tests.py | 45 + .../filtermax/tests/setup_tests.py | 5 +- 14 files changed, 1415 insertions(+), 555 deletions(-) delete mode 100644 pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py create mode 100644 pylabrobot/molecular_devices/filtermax/tests/operation_tests.py diff --git a/docs/api/pylabrobot.molecular_devices.rst b/docs/api/pylabrobot.molecular_devices.rst index 2bb6d20e290..90b138096b0 100644 --- a/docs/api/pylabrobot.molecular_devices.rst +++ b/docs/api/pylabrobot.molecular_devices.rst @@ -22,6 +22,7 @@ FilterMax F5 KineticTiming ShakingSettings WellScanSettings + WellScanPoint AbsorbanceResult LuminescenceResult FluorescenceResult diff --git a/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml b/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml index 11f3ddc2c74..846bca664af 100644 --- a/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml +++ b/docs/user_guide/molecular_devices/filtermax/filtermax_example_slides.xml @@ -1,200 +1,200 @@ - - - - 0 - 1 - 1 - 1 - false - - - 1 - 2 - 2 - 1 - false - - - 2 - 1 - 1 - 0 - false - - - 1 - 2 - 535 - 535 - 25 - 0 - false - false - 6590-0044 - - - 2 - 2 - 485 - 485 - 20 - 0 - false - false - 6590-0043 - - - 3 - 4 - 485 - 485 - 20 - 0 - false - false - 6590-0043 - - - 5 - 8 - 370 - 370 - 80 - 0 - false - false - 6590-0073 - - - 1 - 1 - 260 - 260 - 12 - 1 - false - false - 6590-0001 - - - 2 - 1 - 340 - 340 - 10 - 1 - false - false - 6590-0032 - - - 3 - 1 - 405 - 405 - 10 - 1 - false - false - 6590-0037 - - - 4 - 1 - 450 - 450 - 8 - 1 - false - false - 6590-0005 - - - 5 - 1 - 595 - 595 - 8 - 1 - false - false - 6590-0024 - - - 6 - 1 - 620 - 620 - 8 - 1 - false - false - 6590-0027 - - - 1 - 2 - 595 - 595 - 35 - 2 - false - false - 6590-0058 - - - 2 - 2 - 535 - 535 - 25 - 2 - false - false - 6590-0057 - - - 3 - 4 - 535 - 535 - 25 - 2 - false - false - 6590-0057 - - - 4 - 4 - 535 - 535 - 25 - 2 - false - false - 6590-0057 - - - 5 - 10 - 625 - 625 - 35 - 2 - false - false - 6590-0059 - - - 6 - 16 - 0 - 0 - 0 - 2 - false - false - - + + + + 0 + 1 + 1 + 1 + false + + + 1 + 2 + 2 + 1 + false + + + 2 + 1 + 1 + 0 + false + + + 1 + 2 + 535 + 535 + 25 + 0 + false + false + 6590-0044 + + + 2 + 2 + 485 + 485 + 20 + 0 + false + false + 6590-0043 + + + 3 + 4 + 485 + 485 + 20 + 0 + false + false + 6590-0043 + + + 5 + 8 + 370 + 370 + 80 + 0 + false + false + 6590-0073 + + + 1 + 1 + 260 + 260 + 12 + 1 + false + false + 6590-0001 + + + 2 + 1 + 340 + 340 + 10 + 1 + false + false + 6590-0032 + + + 3 + 1 + 405 + 405 + 10 + 1 + false + false + 6590-0037 + + + 4 + 1 + 450 + 450 + 8 + 1 + false + false + 6590-0005 + + + 5 + 1 + 595 + 595 + 8 + 1 + false + false + 6590-0024 + + + 6 + 1 + 620 + 620 + 8 + 1 + false + false + 6590-0027 + + + 1 + 2 + 595 + 595 + 35 + 2 + false + false + 6590-0058 + + + 2 + 2 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 3 + 4 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 4 + 4 + 535 + 535 + 25 + 2 + false + false + 6590-0057 + + + 5 + 10 + 625 + 625 + 35 + 2 + false + false + 6590-0059 + + + 6 + 16 + 0 + 0 + 0 + 2 + false + false + + \ No newline at end of file diff --git a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb index b21ea69718b..6575b1a7dba 100644 --- a/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb +++ b/docs/user_guide/molecular_devices/filtermax/hello-world.ipynb @@ -27,7 +27,9 @@ "source": [ "## How it communicates\n", "\n", - "The F5 uses an ASTM-like framed serial protocol, not the SpectraMax `!COMMAND` protocol. PLR handles framing, checksums, acknowledgements, response chunking, device errors, and cancellation internally. Raw commands are intentionally not public." + "The F5 uses an ASTM-like framed serial protocol, not the SpectraMax `!COMMAND` protocol. PLR handles framing, checksums, acknowledgements, response chunking, device errors, and cancellation internally. Raw commands are intentionally not public.\n", + "\n", + "Ordinary operations queue while another operation owns the reader. A measurement keeps ownership through preparation, kinetic intervals, and tray recovery, so a concurrent status or temperature query waits until it finishes." ] }, { @@ -302,7 +304,9 @@ "source": [ "## Shaking\n", "\n", - "Shaking is a finite-duration operation. Patterns are `\"linear\"` or `\"orbital\"`; speeds are `\"low\"`, `\"medium\"`, or `\"high\"`." + "Shaking is a finite-duration operation. Patterns are `\"linear\"` or `\"orbital\"`; speeds are `\"low\"`, `\"medium\"`, or `\"high\"`.\n", + "\n", + "`stop_shaking()` signals an active shake or its enclosing read and waits for recovery. The operation task raises `FilterMaxReadCancelled`; stopping while idle does nothing." ] }, { @@ -438,7 +442,9 @@ "source": [ "## Plate geometry\n", "\n", - "The captured Costar 96-well clear plate geometry is available as a convenience. It must match the loaded plate, including orientation. For another plate, replace the assignment below with `PlateGeometry` using its measured dimensions in millimetres before proceeding. If you replace the plate between examples, update this geometry to match." + "The captured Costar 96-well clear plate geometry is available as a convenience. It must match the loaded plate, including orientation. For another plate, replace the assignment below with `PlateGeometry` using its measured dimensions in millimetres before proceeding. If you replace the plate between examples, update this geometry to match.\n", + "\n", + "`PlateGeometry.well_depth` is the physical well depth in millimetres. All geometry dimensions and offsets use millimetres." ] }, { @@ -653,7 +659,7 @@ "source": [ "## Well scans\n", "\n", - "The captured F5 software exposes horizontal and circular fill scans. Scan results preserve every `(x, y, value)` point for each selected well." + "The captured F5 software exposes horizontal and circular fill scans. Scan results preserve each sample's `(grid_column, grid_row, value)`. Columns and rows are zero-based indices in the requested scan grid, not physical distances. Horizontal scans use row zero; fill scans retain positions in the full square grid, with points outside the circular mask omitted. Physical point spacing has not been verified and is not configurable." ] }, { @@ -715,7 +721,9 @@ "source": [ "## Cancel a read\n", "\n", - "`cancel_read()` is state-aware: it does nothing while idle and cooperatively stops an active read. A cancelled read raises `FilterMaxReadCancelled` in the read task and returns the reader to an idle, tray-ejected state." + "`cancel_read()` does nothing while idle and signals the owner of an active read immediately. Cancellation finishes any device message already underway before sending STOP, then attempts tray ejection. The read task raises `FilterMaxReadCancelled`; `cancel_read()` waits for recovery to finish. Recovery failures are logged, so check them before relying on tray position.\n", + "\n", + "Cancellation is also checked between preparation commands, result messages, and kinetic cycles. Cancelling the Python read task keeps the connection owned until recovery finishes, then propagates `asyncio.CancelledError`. Repeated cancellation requests do not send duplicate STOP commands." ] }, { @@ -778,7 +786,9 @@ "source": [ "## Disconnect\n", "\n", - "Always release the serial port when finished." + "Always release the serial port when finished.\n", + "\n", + "`stop()` cancels an active read or shake, waits for recovery, and queues closure of the port behind remaining operations." ] }, { diff --git a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md index ff7be6818fc..5dc64acafc9 100644 --- a/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md +++ b/docs/user_guide/molecular_devices/filtermax/protocol-coverage.md @@ -34,6 +34,18 @@ maps to the host serial device, save the results and shut the guest down normall PLR. Confirm the VM is powered off: closing SoftMax or an empty unprivileged `fuser` result does not establish that VirtualBox released the host device. +The driver serializes complete request/response exchanges. Ordinary calls queue behind an active +operation; a measurement retains ownership through its preparation, kinetic intervals, STOP +recovery, and tray ejection. Cancellation signals the operation owner and is checked between +complete device messages. An ENQ already received commits the receiver to consuming all +continuation frames through ETX and EOT before STOP can be sent. An empty transaction or EOT +after ETB is a protocol error, not a successful partial response. + +Only pending firmware work receives STOP; cancellation and recovery share that accounting so +STOP is not sent twice. Cancelling the Python task also waits for its owner's cleanup before +propagating `asyncio.CancelledError`. Recovery errors are logged without replacing the original +failure, and a successful read whose tray ejection fails reports that failure. + The instrument does not emit a separate busy token in the captured operations. A command owns the half-duplex transaction until its response arrives. Long reads return one or more framed result messages. Kinetic timing is scheduled client-side, matching SoftMax's observed behavior. Result @@ -100,6 +112,11 @@ SF B 1 595 35 2 535 25 2 535 25 4 535 25 4 625 35 10 0 0 16 | Dual luminescence C4, 400 ms | `LUM 1 2 0 0 3 3 1 1 0 0 0 400000 0 3 1 1 0 O INFO` | Two raw channel messages, then `INFO` | | Luminescence, three-read kinetic | `LUM 3 1 0 3 3 1 1 0 0 0 400000 0 3 1 3 0 O INFO` | Repeated row messages; countdown field is 3, 2, 1 | +Scan results expose zero-based `grid_column` and `grid_row` indices, not physical coordinates. +Horizontal scans use grid row zero. Fill scans preserve the full square-grid indices after +applying the circular mask. Physical point spacing has not been verified and is not configurable. +Plate geometry uses millimetres, including the `well_depth` field. + Absorbance values are returned in milli-OD and converted to OD. Luminescence values remain raw RLU. SoftMax exposed only row-order reads, only horizontal/fill well scans, and one absorbance wavelength optionally paired with one reference wavelength. diff --git a/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py b/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py deleted file mode 100644 index 4604aa24999..00000000000 --- a/pylabrobot/legacy/plate_reading/molecular_devices/filtermax_f5.py +++ /dev/null @@ -1,14 +0,0 @@ -"""Deprecated import location for the current FilterMax F5 v1 driver.""" - -import warnings - -from pylabrobot.molecular_devices.filtermax import FilterMaxF5, FilterSlideCatalog - -warnings.warn( - "pylabrobot.legacy.plate_reading.molecular_devices.filtermax_f5 is deprecated; " - "use pylabrobot.molecular_devices.filtermax instead.", - DeprecationWarning, - stacklevel=2, -) - -__all__ = ["FilterMaxF5", "FilterSlideCatalog"] diff --git a/pylabrobot/molecular_devices/filtermax/catalog.py b/pylabrobot/molecular_devices/filtermax/catalog.py index 3bf2b331cb8..1b4c4e5e289 100644 --- a/pylabrobot/molecular_devices/filtermax/catalog.py +++ b/pylabrobot/molecular_devices/filtermax/catalog.py @@ -24,19 +24,24 @@ def _local_name(tag: str) -> str: + """Remove an XML namespace from an element name.""" return tag.rsplit("}", 1)[-1] def _children(element: ET.Element) -> Dict[str, str]: + """Read trimmed text fields from one catalog record.""" return {_local_name(child.tag): (child.text or "").strip() for child in element} @dataclass(frozen=True) class FilterSlideCatalog: + """Filter definitions indexed by slide, position, wavelength, and technique.""" + filters: Tuple[FilterDefinition, ...] @classmethod def from_softmax_xml(cls, path: Union[str, Path]) -> "FilterSlideCatalog": + """Load a SoftMax XML export locally, without communicating with the reader.""" root = ET.parse(path).getroot() slides: Dict[int, Tuple[int, str, FilterKind]] = {} for element in root: @@ -92,6 +97,7 @@ def from_softmax_xml(cls, path: Union[str, Path]) -> "FilterSlideCatalog": return cls(tuple(parsed)) def filters_for_slide(self, kind: FilterKind, slide_id: int) -> Tuple[FilterDefinition, ...]: + """Return the selected slide's definitions in one-based slot order.""" return tuple( sorted( (item for item in self.filters if item.kind == kind and item.slide_id == slide_id), @@ -108,6 +114,11 @@ def resolve( slide_id: Optional[int] = None, position: Optional[int] = None, ) -> FilterSelection: + """Resolve a wavelength in nm to one compatible slide and one-based slot. + + Ambiguous matches require a slide ID or position; absent matches raise + FilterMaxFilterNotFoundError. Resolution does not query installed hardware. + """ matches = [ item for item in self.filters diff --git a/pylabrobot/molecular_devices/filtermax/errors.py b/pylabrobot/molecular_devices/filtermax/errors.py index 0e5bdd645a3..e6077a004d2 100644 --- a/pylabrobot/molecular_devices/filtermax/errors.py +++ b/pylabrobot/molecular_devices/filtermax/errors.py @@ -47,6 +47,7 @@ class FilterMaxDeviceError(FilterMaxError): """An error reported by the FilterMax firmware.""" def __init__(self, code: int, detail: str, command: str): + """Preserve the firmware code, detail text, and failed request.""" self.code = code self.detail = detail self.command = command diff --git a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py index 767daf2e7e0..cd0e5c6261f 100644 --- a/pylabrobot/molecular_devices/filtermax/filtermax_f5.py +++ b/pylabrobot/molecular_devices/filtermax/filtermax_f5.py @@ -3,11 +3,10 @@ from __future__ import annotations import asyncio -import contextlib import logging import re import time -from typing import Dict, List, Optional, Sequence, Tuple +from typing import Any, Callable, Coroutine, Dict, List, Literal, Optional, Sequence, Tuple, TypeVar from pylabrobot.io.serial import Serial @@ -45,6 +44,8 @@ logger = logging.getLogger(__name__) +_Result = TypeVar("_Result") + _F5_DEVICE_CODE = 57855 _STARTUP_BAUDRATES = (38400, 9600) _ERROR_RE = re.compile(r"^- E(?P\d+):\s*(?P.*)$", re.DOTALL) @@ -57,6 +58,7 @@ def _hundredths(value: float) -> int: + """Convert millimetres to the device geometry units.""" return int(round(value * 100)) @@ -76,6 +78,7 @@ def __init__( port: str, filter_slide_catalog: Optional[FilterSlideCatalog] = None, ) -> None: + """Configure a serial reader without opening its port.""" self.name = name self.port = port self.filter_slide_catalog = filter_slide_catalog @@ -95,14 +98,62 @@ def __init__( self._transport = FilterMaxTransport(self.io) self._operation_lock = asyncio.Lock() self._cancel_event = asyncio.Event() - self._read_done = asyncio.Event() - self._read_done.set() - self._read_active = False + self._operation_done = asyncio.Event() + self._operation_done.set() + self._active_operation: Optional[Literal["command", "read", "shake"]] = None + self._pending_read = False + self._pending_shake = False self._setup_complete = False self._instrument_info: Optional[InstrumentInfo] = None self._errors: List[FilterMaxDeviceError] = [] - async def setup(self) -> None: + async def _command(self, payload: str, timeout: float = 60.0) -> str: + """Exchange one command and record firmware errors for this session.""" + try: + return (await self._transport.exchange(payload, timeout)).payload + except FilterMaxDeviceError as error: + self._errors.append(error) + logger.error("[%s] FilterMax command failed: %s", self.name, error) + raise + + @staticmethod + def _parse_instrument_info(payload: str) -> InstrumentInfo: + """Parse the captured identity fields into an instrument record.""" + lines = payload.lstrip("+\r").split("\r") + if len(lines) < 12: + raise FilterMaxProtocolError(f"Malformed FilterMax identity response: {payload!r}") + values: Dict[str, str] = {} + for line in lines[4:]: + if ":" in line: + key, value = line.split(":", 1) + values[key.strip()] = value.strip() + try: + return InstrumentInfo( + model=lines[0], + firmware=lines[1], + device_number=int(lines[2]), + serial_number=lines[3], + excitation_slide_id=int(values["Excitation Filter Slider Nr"]), + emission_slide_id=int(values["Emission Filter Slider Nr"]), + device_code=int(values["Device Code"]), + plate_control=values["Plate Control"].upper() == "TRUE", + pic_firmware=values["PIC Firmware"].lstrip("+ "), + cpld_version=int(values["CPLD Version"]), + raw=payload, + ) + except (KeyError, ValueError) as exc: + raise FilterMaxProtocolError(f"Malformed FilterMax identity fields: {payload!r}") from exc + + async def _get_instrument_info(self) -> InstrumentInfo: + """Query instrument identity while holding operation ownership.""" + return self._parse_instrument_info(await self._command("?", timeout=10)) + + def _check_cancelled(self) -> None: + """Prevent another hardware step after cooperative cancellation.""" + if self._cancel_event.is_set(): + raise FilterMaxReadCancelled(140, "cancelled by caller", "STOP") + + async def _setup(self) -> None: """Connect at 38,400 or 9,600 baud and verify the instrument identity. Only a silent initial ENQ permits trying the next rate. Once a byte is received, @@ -116,7 +167,9 @@ async def setup(self) -> None: logger.info("[%s] connecting to %s at %d baud", self.name, self.port, baudrate) await self.io.setup() try: - info = await self.get_instrument_info() + self._check_cancelled() + info = await self._get_instrument_info() + self._check_cancelled() if info.device_code != _F5_DEVICE_CODE or info.model != "Anthos Fluoro": raise FilterMaxIdentityError( f"Expected FilterMax F5 device code {_F5_DEVICE_CODE}, received " @@ -146,52 +199,14 @@ async def setup(self) -> None: ) return - async def stop(self) -> None: - if self._read_active: - await self.cancel_read() + async def _stop(self) -> None: + """Close the serial connection while holding operation ownership.""" await self.io.stop() self._setup_complete = False logger.info("[%s] disconnected", self.name) - async def _command(self, payload: str, timeout: float = 60.0) -> str: - try: - return (await self._transport.exchange(payload, timeout)).payload - except FilterMaxDeviceError as error: - self._errors.append(error) - logger.error("[%s] FilterMax command failed: %s", self.name, error) - raise - - @staticmethod - def _parse_instrument_info(payload: str) -> InstrumentInfo: - lines = payload.lstrip("+\r").split("\r") - if len(lines) < 12: - raise FilterMaxProtocolError(f"Malformed FilterMax identity response: {payload!r}") - values: Dict[str, str] = {} - for line in lines[4:]: - if ":" in line: - key, value = line.split(":", 1) - values[key.strip()] = value.strip() - try: - return InstrumentInfo( - model=lines[0], - firmware=lines[1], - device_number=int(lines[2]), - serial_number=lines[3], - excitation_slide_id=int(values["Excitation Filter Slider Nr"]), - emission_slide_id=int(values["Emission Filter Slider Nr"]), - device_code=int(values["Device Code"]), - plate_control=values["Plate Control"].upper() == "TRUE", - pic_firmware=values["PIC Firmware"].lstrip("+ "), - cpld_version=int(values["CPLD Version"]), - raw=payload, - ) - except (KeyError, ValueError) as exc: - raise FilterMaxProtocolError(f"Malformed FilterMax identity fields: {payload!r}") from exc - - async def get_instrument_info(self) -> InstrumentInfo: - return self._parse_instrument_info(await self._command("?", timeout=10)) - - async def get_status(self) -> FilterMaxStatus: + async def _get_status(self) -> FilterMaxStatus: + """Query readiness and firmware state bits under one operation owner.""" text = (await self._command("STAT", timeout=5)).lstrip("+ ") state_payload = (await self._command("SGS", timeout=5)).lstrip("+ ") try: @@ -210,15 +225,19 @@ async def get_error_log(self) -> Tuple[FilterMaxDeviceError, ...]: return tuple(self._errors) async def clear_error_log(self) -> None: + """Clear only the device errors observed by this driver session.""" self._errors.clear() - async def move_plate_tray_out(self) -> None: + async def _move_plate_tray_out(self) -> None: + """Eject the tray while holding operation ownership.""" await self._command("E P", timeout=30) - async def move_plate_tray_in(self) -> None: + async def _move_plate_tray_in(self) -> None: + """Load the tray while holding operation ownership.""" await self._command("L P", timeout=30) - async def get_filter_slides(self) -> InstalledFilterSlides: + async def _get_filter_slides(self) -> InstalledFilterSlides: + """Query installed slide IDs while holding operation ownership.""" payload = (await self._command("CS", timeout=5)).lstrip("+ ") try: excitation, emission = (int(value) for value in payload.split()) @@ -226,44 +245,125 @@ async def get_filter_slides(self) -> InstalledFilterSlides: raise FilterMaxProtocolError(f"Malformed CS response: {payload!r}") from exc return InstalledFilterSlides(excitation_slide_id=excitation, emission_slide_id=emission) - async def move_filter_slide_out(self, kind: FilterKind) -> None: + async def _move_filter_slide_out(self, kind: FilterKind) -> None: + """Eject the selected slide while holding operation ownership.""" await self._command(f"E {'A' if kind == 'excitation' else 'B'}", timeout=30) - async def move_filter_slide_in(self, kind: FilterKind) -> None: + async def _move_filter_slide_in(self, kind: FilterKind) -> None: + """Load the selected slide while holding operation ownership.""" await self._command(f"L {'A' if kind == 'excitation' else 'B'}", timeout=30) - async def get_temperature(self) -> float: + async def _get_temperature(self) -> float: + """Read chamber temperature in degrees Celsius under operation ownership.""" payload = (await self._command("TG", timeout=5)).lstrip("+ ") try: return float(payload) except ValueError as exc: raise FilterMaxProtocolError(f"Malformed TG response: {payload!r}") from exc - async def set_temperature(self, temperature: float) -> None: + async def _set_temperature(self, temperature: float) -> None: + """Set chamber temperature in degrees Celsius under operation ownership.""" if not 20 <= temperature <= 45: raise ValueError("FilterMax temperature setpoint must be between 20 and 45 °C") value = f"{temperature:g}" await self._command(f"TS {value}", timeout=10) logger.info("[%s] temperature setpoint set to %.1f °C", self.name, temperature) - async def deactivate_temperature_control(self) -> None: + async def _deactivate_temperature_control(self) -> None: + """Disable chamber heating under operation ownership.""" await self._command("TS 0", timeout=10) logger.info("[%s] temperature control deactivated", self.name) - async def start_shaking( + async def _stop_pending_unlocked(self) -> None: + """Send at most one STOP while the caller owns the transport transaction.""" + if not (self._pending_read or self._pending_shake): + return + self._pending_read = False + self._pending_shake = False + await self._transport.send_request("STOP") + try: + await self._transport.receive_message(15, command="STOP") + except FilterMaxReadCancelled as error: + self._errors.append(error) + logger.info("[%s] stopped pending FilterMax operation", self.name) + return + except FilterMaxDeviceError as error: + self._errors.append(error) + raise + raise FilterMaxProtocolError("STOP did not return the captured E140 cancellation response") + + async def _recover_failed_read(self) -> None: + """Stop pending firmware work without competing with another transaction.""" + async with self._transport._transaction(): + await self._stop_pending_unlocked() + + async def _receive_measurement_messages( + self, + command: str, + count: int, + timeout: float, + *, + final_cycle: bool = True, + shaking: bool = False, + ) -> List[FilterMaxMessage]: + """Own a result stream and service cancellation between complete device messages.""" + self._check_cancelled() + async with self._transport._transaction(): + if shaking: + self._pending_shake = True + else: + self._pending_read = True + try: + await self._transport.send_request(command) + messages: List[FilterMaxMessage] = [] + for _ in range(count): + messages.append( + await self._transport.receive_message( + timeout, command=command, cancel_event=self._cancel_event + ) + ) + except _CancelRequested: + try: + await self._stop_pending_unlocked() + except Exception: + logger.warning("[%s] FilterMax cancellation recovery failed", self.name, exc_info=True) + raise FilterMaxReadCancelled(140, "cancelled by caller", command) from None + except FilterMaxDeviceError as error: + self._pending_read = False + self._pending_shake = False + self._errors.append(error) + raise + if shaking: + self._pending_shake = False + elif final_cycle: + self._pending_read = False + self._check_cancelled() + return messages + + async def _start_shaking( self, pattern: ShakePattern, speed: ShakeSpeed, duration: int = 5, ) -> None: + """Perform finite shaking under operation ownership, with cooperative cancellation.""" if duration < 1: raise ValueError("duration must be at least 1") pattern_code, pattern_parameter = _SHAKE_WIRE[pattern] speed_parameter = _SHAKE_SPEED_WIRE[speed] - await self._command( - f"SHAKE {pattern_code} {pattern_parameter} 3 {speed_parameter} {duration}", - timeout=duration + 30, - ) + try: + await self._receive_measurement_messages( + f"SHAKE {pattern_code} {pattern_parameter} 3 {speed_parameter} {duration}", + count=1, + timeout=duration + 30, + shaking=True, + ) + except BaseException: + try: + await self._recover_failed_read() + except Exception: + logger.warning("[%s] FilterMax shaking recovery failed", self.name, exc_info=True) + raise logger.info( "[%s] completed %s/%s shaking for %d seconds", self.name, @@ -272,22 +372,8 @@ async def start_shaking( duration, ) - async def stop_shaking(self) -> None: - if self._read_active: - await self.cancel_read() - return - try: - await self._command("STOP", timeout=10) - except FilterMaxReadCancelled: - return - - async def cancel_read(self) -> None: - if not self._read_active: - return - self._cancel_event.set() - await self._read_done.wait() - def _require_catalog(self) -> FilterSlideCatalog: + """Return the configured catalog or explain why measurement cannot start.""" if self.filter_slide_catalog is None: raise FilterMaxCatalogError( "Measurement methods require FilterSlideCatalog.from_softmax_xml(...)" @@ -296,6 +382,7 @@ def _require_catalog(self) -> FilterSlideCatalog: @staticmethod def _plate_command(plate: PlateGeometry, read_height: float) -> str: + """Encode physical geometry and read height in hundredths of a millimetre.""" values = ( _hundredths(plate.length), _hundredths(plate.width), @@ -319,6 +406,7 @@ def _plate_command(plate: PlateGeometry, read_height: float) -> str: return "PLATE Temp " + " ".join(str(value) for value in values) async def _send_filter_catalog(self, kind: FilterKind, slide_id: int) -> None: + """Send the installed slide definitions under operation ownership.""" catalog = self._require_catalog() filters = catalog.filters_for_slide(kind, slide_id) if not filters: @@ -331,6 +419,7 @@ async def _send_filter_catalog(self, kind: FilterKind, slide_id: int) -> None: @staticmethod def _row_name(index: int) -> str: + """Return the supported one-letter plate row name.""" if not 0 <= index < 26: raise ValueError("FilterMax driver currently supports plate rows A-Z") return chr(ord("A") + index) @@ -341,6 +430,7 @@ def _normalize_wells( wells: Optional[Sequence[str]], plate: PlateGeometry, ) -> Tuple[Tuple[str, ...], int, int]: + """Validate well names and return the inclusive hardware row span.""" if wells is None: normalized = tuple( f"{cls._row_name(row)}{column + 1}" @@ -365,6 +455,7 @@ def _normalize_wells( @staticmethod def _parse_values(payload: str) -> List[float]: + """Parse a row of numeric measurement values.""" if not payload.startswith("+ "): raise FilterMaxProtocolError(f"Expected measurement data, received {payload!r}") try: @@ -372,56 +463,31 @@ def _parse_values(payload: str) -> List[float]: except ValueError as exc: raise FilterMaxProtocolError(f"Malformed measurement values: {payload!r}") from exc - async def _receive_measurement_messages( - self, - command: str, - count: int, - timeout: float, - ) -> List[FilterMaxMessage]: - await self._transport.send_request(command) - messages: List[FilterMaxMessage] = [] - try: - for index in range(count): - messages.append( - await self._transport.receive_message( - timeout, - command=command, - cancel_event=self._cancel_event if index == 0 else None, - ) - ) - except _CancelRequested: - await self._transport.send_request("STOP") + async def _finish_read(self, *, failed: bool) -> None: + """Recover and eject, preserving an original read failure if cleanup also fails.""" + if failed: try: - await self._transport.receive_message(15, command="STOP") - except FilterMaxReadCancelled as error: - self._errors.append(error) + await self._recover_failed_read() + except Exception: + logger.warning("[%s] FilterMax STOP recovery failed", self.name, exc_info=True) + try: + await self._move_plate_tray_out() + except Exception: + logger.warning("[%s] FilterMax tray recovery failed", self.name, exc_info=True) + if not failed: raise - raise FilterMaxProtocolError("STOP did not return the captured E140 cancellation response") - except FilterMaxDeviceError as error: - self._errors.append(error) - raise - return messages async def _wait_until(self, target: float) -> None: + """Wait for a nominal kinetic timepoint, including cancellation of overdue cycles.""" + self._check_cancelled() delay = target - time.monotonic() if delay <= 0: return try: await asyncio.wait_for(self._cancel_event.wait(), timeout=delay) except asyncio.TimeoutError: - return - raise FilterMaxReadCancelled(140, "cancelled between kinetic cycles", "STOP") - - async def _recover_failed_read(self) -> None: - """Stop an incomplete firmware read before attempting tray recovery.""" - - try: - await self._transport.exchange("STOP", timeout=15) - except FilterMaxReadCancelled: - logger.info("[%s] stopped incomplete FilterMax read", self.name) - except FilterMaxDeviceError as error: - self._errors.append(error) - logger.warning("[%s] FilterMax read recovery returned: %s", self.name, error) + pass + self._check_cancelled() async def _prepare_measurement( self, @@ -432,32 +498,41 @@ async def _prepare_measurement( read_height: float, shaking: Optional[ShakingSettings], ) -> None: - slides = await self.get_filter_slides() + """Configure a measurement with cancellation checks between complete commands.""" + self._check_cancelled() + slides = await self._get_filter_slides() + self._check_cancelled() installed = slides.excitation_slide_id if kind == "excitation" else slides.emission_slide_id if installed != slide_id: raise FilterMaxSlideNotInstalledError( f"Required {kind} slide ID {slide_id}, but installed ID is {installed}" ) if shaking is not None: - await self.move_plate_tray_in() - await self.start_shaking( + await self._move_plate_tray_in() + self._check_cancelled() + await self._start_shaking( shaking.pattern, shaking.speed, duration=shaking.duration, ) + self._check_cancelled() await self._command(self._plate_command(plate, read_height), timeout=10) + self._check_cancelled() if plate.orientation == "portrait": await self._command("SHIFT", timeout=10) + self._check_cancelled() await self._send_filter_catalog(kind, slide_id) - await self.move_plate_tray_in() + self._check_cancelled() + await self._move_plate_tray_in() + self._check_cancelled() @staticmethod - def _scan_layout(settings: WellScanSettings) -> Tuple[Tuple[int, float, float], ...]: + def _scan_layout(settings: WellScanSettings) -> Tuple[Tuple[int, int, int], ...]: + """Return raw indices and integer grid positions for retained scan points.""" density = settings.density - spacing = settings.point_spacing center = (density - 1) / 2 if settings.pattern == "horizontal": - return tuple((index, (index - center) * spacing, 0.0) for index in range(density)) + return tuple((index, index, 0) for index in range(density)) radius = density / 2 points = [] for y_index in range(density): @@ -466,10 +541,10 @@ def _scan_layout(settings: WellScanSettings) -> Tuple[Tuple[int, float, float], y = y_index - center if x * x + y * y <= radius * radius: raw_index = y_index * density + x_index - points.append((raw_index, x * spacing, y * spacing)) + points.append((raw_index, x_index, y_index)) return tuple(points) - async def read_absorbance( + async def _read_absorbance( self, plate: PlateGeometry, wavelength: int, @@ -483,6 +558,7 @@ async def read_absorbance( shaking: Optional[ShakingSettings] = None, well_scan: Optional[WellScanSettings] = None, ) -> List[AbsorbanceResult]: + """Measure and parse absorbance under exclusive operation ownership.""" catalog = self._require_catalog() primary = catalog.resolve( kind="excitation", @@ -505,119 +581,113 @@ async def read_absorbance( selected = set(selected_wells) row_count = last_row - first_row + 1 grid_x, grid_y = well_scan.grid_shape if well_scan is not None else (1, 1) - scan_layout = self._scan_layout(well_scan) if well_scan is not None else ((0, 0.0, 0.0),) + scan_layout = self._scan_layout(well_scan) if well_scan is not None else ((0, 0, 0),) raw_point_count = grid_x * grid_y scan_code = 4 if well_scan is not None else 0 timing = kinetic or KineticTiming(interval=1, reads=1) results: List[AbsorbanceResult] = [] - async with self._operation_lock: - self._cancel_event.clear() - self._read_done.clear() - self._read_active = True - completed = False - try: - await self._prepare_measurement( - plate, - kind="excitation", - slide_id=primary.slide_id, - read_height=plate.absorbance_z, - shaking=shaking, + completed = False + try: + await self._prepare_measurement( + plate, + kind="excitation", + slide_id=primary.slide_id, + read_height=plate.absorbance_z, + shaking=shaking, + ) + kinetic_started = time.monotonic() + for cycle in range(timing.reads): + self._check_cancelled() + if cycle: + if shaking is not None and shaking.between_reads: + await self._start_shaking(shaking.pattern, shaking.speed, shaking.duration) + await self._wait_until(kinetic_started + cycle * timing.interval) + # SoftMax reports kinetic timepoints on the requested schedule, even when a read + # overruns its interval. Preserve that protocol-level meaning instead of exposing + # transport and calibration latency as kinetic elapsed time. + elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 + remaining = timing.reads - cycle + if kinetic is not None: + mode = 3 + kinetic_flag = 2 + elif reference is not None: + mode = 1 + kinetic_flag = 0 + else: + mode = 0 + kinetic_flag = 0 + wavelengths = ( + f"2 {primary.wavelength} {reference.wavelength}" + if reference is not None + else f"1 {primary.wavelength}" ) - kinetic_started = time.monotonic() - for cycle in range(timing.reads): - if cycle: - if shaking is not None and shaking.between_reads: - await self.start_shaking(shaking.pattern, shaking.speed, shaking.duration) - await self._wait_until(kinetic_started + cycle * timing.interval) - # SoftMax reports kinetic timepoints on the requested schedule, even when a read - # overruns its interval. Preserve that protocol-level meaning instead of exposing - # transport and calibration latency as kinetic elapsed time. - elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 - remaining = timing.reads - cycle - if kinetic is not None: - mode = 3 - kinetic_flag = 2 - elif reference is not None: - mode = 1 - kinetic_flag = 0 - else: - mode = 0 - kinetic_flag = 0 - wavelengths = ( - f"2 {primary.wavelength} {reference.wavelength}" - if reference is not None - else f"1 {primary.wavelength}" - ) - orientation_code = 4 if plate.orientation == "portrait" else 3 - command = ( - f"ABS {mode} {wavelengths} {first_row + 1} {last_row + 1} " - f"{grid_x} {grid_y} {scan_code} 0 0 0 0 {orientation_code} 1 " - f"{remaining} {kinetic_flag} O e INFO" - ) - timestamp = time.time() - final_cycle = cycle == timing.reads - 1 - messages = await self._receive_measurement_messages( - command, - row_count * grid_y + int(final_cycle), - timeout=max(60, raw_point_count * 3), - ) - data_messages = messages[:-1] if final_cycle else messages - data = empty_plate_data(plate.rows, plate.columns) - scan_points: Dict[str, Tuple[WellScanPoint, ...]] = {} - for row_offset in range(row_count): - row = first_row + row_offset - raw_values_by_column: List[List[float]] = [[] for _ in range(plate.columns)] - for scan_y in range(grid_y): - message = data_messages[row_offset * grid_y + scan_y] - values = self._parse_values(message.payload) - expected = plate.columns * grid_x - if len(values) != expected: - raise FilterMaxProtocolError( - f"Expected {expected} absorbance values for row {row + 1}, got {len(values)}" - ) - for column in range(plate.columns): - raw_values_by_column[column].extend(values[column * grid_x : (column + 1) * grid_x]) + orientation_code = 4 if plate.orientation == "portrait" else 3 + command = ( + f"ABS {mode} {wavelengths} {first_row + 1} {last_row + 1} " + f"{grid_x} {grid_y} {scan_code} 0 0 0 0 {orientation_code} 1 " + f"{remaining} {kinetic_flag} O e INFO" + ) + timestamp = time.time() + final_cycle = cycle == timing.reads - 1 + messages = await self._receive_measurement_messages( + command, + row_count * grid_y + int(final_cycle), + timeout=max(60, raw_point_count * 3), + final_cycle=final_cycle, + ) + data_messages = messages[:-1] if final_cycle else messages + data = empty_plate_data(plate.rows, plate.columns) + scan_points: Dict[str, Tuple[WellScanPoint, ...]] = {} + for row_offset in range(row_count): + row = first_row + row_offset + raw_values_by_column: List[List[float]] = [[] for _ in range(plate.columns)] + for scan_y in range(grid_y): + message = data_messages[row_offset * grid_y + scan_y] + values = self._parse_values(message.payload) + expected = plate.columns * grid_x + if len(values) != expected: + raise FilterMaxProtocolError( + f"Expected {expected} absorbance values for row {row + 1}, got {len(values)}" + ) for column in range(plate.columns): - well = f"{self._row_name(row)}{column + 1}" - raw_points = raw_values_by_column[column] - converted = [raw_points[index] / 1000 for index, _, _ in scan_layout] - if well not in selected: - continue - data[row][column] = sum(converted) / len(converted) - if well_scan is not None: - scan_points[well] = tuple( - WellScanPoint(x=x, y=y, value=value) - for (_, x, y), value in zip(scan_layout, converted) - ) - temperature = await self.get_temperature() - results.append( - AbsorbanceResult( - data=data, - wavelengths=( - (primary.wavelength, reference.wavelength) - if reference is not None - else (primary.wavelength,) - ), - reference_subtracted=reference is not None, - temperature=temperature, - timestamp=timestamp, - elapsed_time=elapsed_time, - scan_points=scan_points, - ) + raw_values_by_column[column].extend(values[column * grid_x : (column + 1) * grid_x]) + for column in range(plate.columns): + well = f"{self._row_name(row)}{column + 1}" + raw_points = raw_values_by_column[column] + converted = [raw_points[index] / 1000 for index, _, _ in scan_layout] + if well not in selected: + continue + data[row][column] = sum(converted) / len(converted) + if well_scan is not None: + scan_points[well] = tuple( + WellScanPoint(grid_column=column_index, grid_row=row_index, value=value) + for (_, column_index, row_index), value in zip(scan_layout, converted) + ) + temperature = await self._get_temperature() + self._check_cancelled() + results.append( + AbsorbanceResult( + data=data, + wavelengths=( + (primary.wavelength, reference.wavelength) + if reference is not None + else (primary.wavelength,) + ), + reference_subtracted=reference is not None, + temperature=temperature, + timestamp=timestamp, + elapsed_time=elapsed_time, + scan_points=scan_points, ) - completed = True - finally: - if not completed: - with contextlib.suppress(Exception): - await self._recover_failed_read() - with contextlib.suppress(Exception): - await self.move_plate_tray_out() - self._read_active = False - self._read_done.set() + ) + self._check_cancelled() + completed = True + finally: + await self._finish_read(failed=not completed) return results - async def read_luminescence( + async def _read_luminescence( self, plate: PlateGeometry, *, @@ -630,6 +700,7 @@ async def read_luminescence( kinetic: Optional[KineticTiming] = None, shaking: Optional[ShakingSettings] = None, ) -> List[LuminescenceResult]: + """Measure and parse luminescence under exclusive operation ownership.""" if plate.orientation != "landscape": raise FilterMaxUnsupportedOperationError( "Portrait orientation has been captured only for absorbance measurements" @@ -653,75 +724,70 @@ async def read_luminescence( integration_microseconds = int(round(integration * 1_000_000)) results: List[LuminescenceResult] = [] - async with self._operation_lock: - self._cancel_event.clear() - self._read_done.clear() - self._read_active = True - completed = False - try: - await self._prepare_measurement( - plate, - kind="emission", - slide_id=lum_filter.slide_id, - read_height=read_height, - shaking=shaking, + completed = False + try: + await self._prepare_measurement( + plate, + kind="emission", + slide_id=lum_filter.slide_id, + read_height=read_height, + shaking=shaking, + ) + kinetic_started = time.monotonic() + for cycle in range(timing.reads): + self._check_cancelled() + if cycle: + if shaking is not None and shaking.between_reads: + await self._start_shaking(shaking.pattern, shaking.speed, shaking.duration) + await self._wait_until(kinetic_started + cycle * timing.interval) + # The instrument starts an overdue cycle immediately, but its result still belongs + # to the nominal kinetic timepoint (the behavior observed in SoftMax captures). + elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 + remaining = timing.reads - cycle + mode = 3 if kinetic is not None else (1 if channels == 2 else 0) + wavelengths = "2 0 0" if channels == 2 else "1 0" + command = ( + f"LUM {mode} {wavelengths} {first_row + 1} {last_row + 1} 1 1 0 0 0 " + f"{integration_microseconds} 0 3 1 {remaining} 0 O INFO" ) - kinetic_started = time.monotonic() - for cycle in range(timing.reads): - if cycle: - if shaking is not None and shaking.between_reads: - await self.start_shaking(shaking.pattern, shaking.speed, shaking.duration) - await self._wait_until(kinetic_started + cycle * timing.interval) - # The instrument starts an overdue cycle immediately, but its result still belongs - # to the nominal kinetic timepoint (the behavior observed in SoftMax captures). - elapsed_time = cycle * timing.interval if kinetic is not None else 0.0 - remaining = timing.reads - cycle - mode = 3 if kinetic is not None else (1 if channels == 2 else 0) - wavelengths = "2 0 0" if channels == 2 else "1 0" - command = ( - f"LUM {mode} {wavelengths} {first_row + 1} {last_row + 1} 1 1 0 0 0 " - f"{integration_microseconds} 0 3 1 {remaining} 0 O INFO" - ) - timestamp = time.time() - final_cycle = cycle == timing.reads - 1 - messages = await self._receive_measurement_messages( - command, - row_count * channels + int(final_cycle), - timeout=90, - ) - data_messages = messages[:-1] if final_cycle else messages - for channel in range(channels): - data = empty_plate_data(plate.rows, plate.columns) - for row_offset in range(row_count): - message = data_messages[channel * row_count + row_offset] - values = self._parse_values(message.payload) - if len(values) != plate.columns: - raise FilterMaxProtocolError( - f"Expected {plate.columns} luminescence values, got {len(values)}" - ) - row = first_row + row_offset - for column, value in enumerate(values): - well = f"{self._row_name(row)}{column + 1}" - if well in selected: - data[row][column] = value - results.append( - LuminescenceResult( - data=data, - channel=channel + 1, - temperature=await self.get_temperature(), - timestamp=timestamp, - elapsed_time=elapsed_time, + timestamp = time.time() + final_cycle = cycle == timing.reads - 1 + messages = await self._receive_measurement_messages( + command, + row_count * channels + int(final_cycle), + timeout=90, + final_cycle=final_cycle, + ) + data_messages = messages[:-1] if final_cycle else messages + for channel in range(channels): + data = empty_plate_data(plate.rows, plate.columns) + for row_offset in range(row_count): + message = data_messages[channel * row_count + row_offset] + values = self._parse_values(message.payload) + if len(values) != plate.columns: + raise FilterMaxProtocolError( + f"Expected {plate.columns} luminescence values, got {len(values)}" ) + row = first_row + row_offset + for column, value in enumerate(values): + well = f"{self._row_name(row)}{column + 1}" + if well in selected: + data[row][column] = value + temperature = await self._get_temperature() + self._check_cancelled() + results.append( + LuminescenceResult( + data=data, + channel=channel + 1, + temperature=temperature, + timestamp=timestamp, + elapsed_time=elapsed_time, ) - completed = True - finally: - if not completed: - with contextlib.suppress(Exception): - await self._recover_failed_read() - with contextlib.suppress(Exception): - await self.move_plate_tray_out() - self._read_active = False - self._read_done.set() + ) + self._check_cancelled() + completed = True + finally: + await self._finish_read(failed=not completed) return results async def _validate_unavailable_fluorescence_filters( @@ -732,6 +798,7 @@ async def _validate_unavailable_fluorescence_filters( excitation_slide_id: Optional[int], emission_slide_id: Optional[int], ) -> None: + """Validate selected filters, then reject unverified fluorescence commands.""" catalog = self._require_catalog() excitation = catalog.resolve( kind="excitation", @@ -745,7 +812,7 @@ async def _validate_unavailable_fluorescence_filters( wavelength=emission_wavelength, slide_id=emission_slide_id, ) - installed = await self.get_filter_slides() + installed = await self._get_filter_slides() if installed.excitation_slide_id != excitation.slide_id: raise FilterMaxSlideNotInstalledError( f"Required excitation slide ID {excitation.slide_id}, but installed ID is " @@ -761,7 +828,7 @@ async def _validate_unavailable_fluorescence_filters( f"ID {excitation.slide_id}; no command was inferred" ) - async def read_fluorescence( + async def _read_fluorescence( self, plate: PlateGeometry, excitation_wavelength: int, @@ -770,6 +837,7 @@ async def read_fluorescence( excitation_slide_id: Optional[int] = None, emission_slide_id: Optional[int] = None, ) -> List[FluorescenceResult]: + """Validate an unsupported fluorescence request under operation ownership.""" del plate await self._validate_unavailable_fluorescence_filters( "fluorescence", @@ -780,7 +848,7 @@ async def read_fluorescence( ) raise AssertionError("unreachable") - async def read_time_resolved_fluorescence( + async def _read_time_resolved_fluorescence( self, plate: PlateGeometry, excitation_wavelength: int, @@ -789,6 +857,7 @@ async def read_time_resolved_fluorescence( excitation_slide_id: Optional[int] = None, emission_slide_id: Optional[int] = None, ) -> List[TimeResolvedFluorescenceResult]: + """Validate an unsupported time-resolved request under operation ownership.""" del plate await self._validate_unavailable_fluorescence_filters( "time_resolved_fluorescence", @@ -799,7 +868,7 @@ async def read_time_resolved_fluorescence( ) raise AssertionError("unreachable") - async def read_fluorescence_polarization( + async def _read_fluorescence_polarization( self, plate: PlateGeometry, excitation_wavelength: int, @@ -808,6 +877,7 @@ async def read_fluorescence_polarization( excitation_slide_id: Optional[int] = None, emission_slide_id: Optional[int] = None, ) -> List[FluorescencePolarizationResult]: + """Validate an unsupported polarization request under operation ownership.""" del plate await self._validate_unavailable_fluorescence_filters( "fluorescence_polarization", @@ -817,3 +887,263 @@ async def read_fluorescence_polarization( emission_slide_id, ) raise AssertionError("unreachable") + + async def _run_operation( + self, + operation: Callable[[], Coroutine[Any, Any, _Result]], + kind: Literal["command", "read", "shake"] = "command", + ) -> _Result: + """Queue an operation and shield its wire ownership until cleanup completes.""" + async with self._operation_lock: + self._cancel_event = asyncio.Event() + done = self._operation_done = asyncio.Event() + self._active_operation = kind + task = asyncio.create_task(operation()) + try: + return await asyncio.shield(task) + except asyncio.CancelledError: + self._cancel_event.set() + # Repeated cancellation of the caller must not release a live serial transaction. + while not task.done(): + try: + await asyncio.shield(task) + except asyncio.CancelledError: + continue + except Exception: + break + if not task.cancelled(): + try: + task.result() + except FilterMaxReadCancelled: + pass + except Exception: + logger.warning( + "[%s] operation failed during task cancellation", self.name, exc_info=True + ) + raise + finally: + self._active_operation = None + done.set() + + async def _cancel_active(self) -> None: + """Signal the current owner and wait on that operation's own completion event.""" + done = self._operation_done + self._cancel_event.set() + await done.wait() + + async def cancel_read(self) -> None: + """Cancel the active read and wait for its recovery; do nothing while idle. + + The read task raises FilterMaxReadCancelled. Cancellation waits for a device + message already in progress to finish before STOP and tray ejection. + """ + if self._active_operation == "read": + await self._cancel_active() + + async def stop_shaking(self) -> None: + """Cancel active shaking or its enclosing read, waiting for recovery. + + The operation task raises FilterMaxReadCancelled. This is a no-op while idle. + """ + if self._active_operation in ("read", "shake"): + await self._cancel_active() + + async def stop(self) -> None: + """Cancel active measurement or shaking, then queue closure of the serial port.""" + if self._active_operation in ("read", "shake"): + await self._cancel_active() + await self._run_operation(self._stop) + + async def setup(self) -> None: + """Connect and verify the F5 identity, queuing behind any active operation. + + Try 38,400 baud, then 9,600 only if the initial handshake is silent. + Repeated setup keeps the current connection; failed setup releases the port.""" + return await self._run_operation(self._setup) + + async def get_instrument_info(self) -> InstrumentInfo: + """Queue an identity query and return firmware, serial number, and installed options.""" + return await self._run_operation(self._get_instrument_info) + + async def get_status(self) -> FilterMaxStatus: + """Queue readiness and state-bit queries as one operation.""" + return await self._run_operation(self._get_status) + + async def move_plate_tray_out(self) -> None: + """Queue tray ejection and wait for its completion.""" + return await self._run_operation(self._move_plate_tray_out) + + async def move_plate_tray_in(self) -> None: + """Queue tray loading and wait for its completion.""" + return await self._run_operation(self._move_plate_tray_in) + + async def get_filter_slides(self) -> InstalledFilterSlides: + """Queue a query for the installed excitation and emission slide IDs.""" + return await self._run_operation(self._get_filter_slides) + + async def move_filter_slide_out(self, kind: FilterKind) -> None: + """Queue ejection of the selected excitation or emission slide.""" + return await self._run_operation(lambda: self._move_filter_slide_out(kind)) + + async def move_filter_slide_in(self, kind: FilterKind) -> None: + """Queue loading of the selected excitation or emission slide.""" + return await self._run_operation(lambda: self._move_filter_slide_in(kind)) + + async def get_temperature(self) -> float: + """Queue a chamber-temperature query and return degrees Celsius.""" + return await self._run_operation(self._get_temperature) + + async def set_temperature(self, temperature: float) -> None: + """Queue a temperature setpoint in degrees Celsius, from 20 through 45.""" + return await self._run_operation(lambda: self._set_temperature(temperature)) + + async def deactivate_temperature_control(self) -> None: + """Queue deactivation of chamber heating.""" + return await self._run_operation(self._deactivate_temperature_control) + + async def start_shaking( + self, + pattern: ShakePattern, + speed: ShakeSpeed, + duration: int = 5, + ) -> None: + """Queue finite shaking for duration seconds. + + Patterns are linear or orbital; speeds are low, medium, or high. + stop_shaking() requests cancellation; this task then raises FilterMaxReadCancelled.""" + return await self._run_operation( + lambda: self._start_shaking(pattern, speed, duration), kind="shake" + ) + + async def read_absorbance( + self, + plate: PlateGeometry, + wavelength: int, + *, + wells: Optional[Sequence[str]] = None, + reference_wavelength: Optional[int] = None, + slide_id: Optional[int] = None, + filter_position: Optional[int] = None, + reference_filter_position: Optional[int] = None, + kinetic: Optional[KineticTiming] = None, + shaking: Optional[ShakingSettings] = None, + well_scan: Optional[WellScanSettings] = None, + ) -> List[AbsorbanceResult]: + """Queue absorbance measurements and eject the tray when finished. + + Wavelengths are in nm, plate dimensions in mm, and kinetic intervals in seconds. + Each result contains row-major optical densities, with unselected wells set to None. + Hardware reads complete rows; wells only masks the returned data. A reference + wavelength requests firmware subtraction. Scan values retain integer grid indices. + Kinetic elapsed_time follows the nominal schedule even when cycles overrun. + Cancellation raises FilterMaxReadCancelled after STOP and tray recovery are attempted.""" + return await self._run_operation( + lambda: self._read_absorbance( + plate, + wavelength, + wells=wells, + reference_wavelength=reference_wavelength, + slide_id=slide_id, + filter_position=filter_position, + reference_filter_position=reference_filter_position, + kinetic=kinetic, + shaking=shaking, + well_scan=well_scan, + ), + kind="read", + ) + + async def read_luminescence( + self, + plate: PlateGeometry, + *, + wells: Optional[Sequence[str]] = None, + channels: int = 1, + slide_id: Optional[int] = None, + filter_position: Optional[int] = None, + integration: float = 0.4, + read_height: float = 1.0, + kinetic: Optional[KineticTiming] = None, + shaking: Optional[ShakingSettings] = None, + ) -> List[LuminescenceResult]: + """Queue luminescence measurements and eject the tray when finished. + + integration and kinetic intervals are seconds; read_height is in mm. Results + contain row-major raw RLU and one-based channels, ordered by cycle then channel. + Hardware reads complete rows; unselected wells are None in the returned data. + Kinetic elapsed_time follows the nominal schedule even when cycles overrun. + Cancellation raises FilterMaxReadCancelled after STOP and tray recovery are attempted.""" + return await self._run_operation( + lambda: self._read_luminescence( + plate, + wells=wells, + channels=channels, + slide_id=slide_id, + filter_position=filter_position, + integration=integration, + read_height=read_height, + kinetic=kinetic, + shaking=shaking, + ), + kind="read", + ) + + async def read_fluorescence( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[FluorescenceResult]: + """Validate filters with wavelengths in nm, then report this unsupported mode.""" + return await self._run_operation( + lambda: self._read_fluorescence( + plate, + excitation_wavelength, + emission_wavelength, + excitation_slide_id=excitation_slide_id, + emission_slide_id=emission_slide_id, + ) + ) + + async def read_time_resolved_fluorescence( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[TimeResolvedFluorescenceResult]: + """Validate filters with wavelengths in nm, then report this unsupported mode.""" + return await self._run_operation( + lambda: self._read_time_resolved_fluorescence( + plate, + excitation_wavelength, + emission_wavelength, + excitation_slide_id=excitation_slide_id, + emission_slide_id=emission_slide_id, + ) + ) + + async def read_fluorescence_polarization( + self, + plate: PlateGeometry, + excitation_wavelength: int, + emission_wavelength: int, + *, + excitation_slide_id: Optional[int] = None, + emission_slide_id: Optional[int] = None, + ) -> List[FluorescencePolarizationResult]: + """Validate filters with wavelengths in nm, then report this unsupported mode.""" + return await self._run_operation( + lambda: self._read_fluorescence_polarization( + plate, + excitation_wavelength, + emission_wavelength, + excitation_slide_id=excitation_slide_id, + emission_slide_id=emission_slide_id, + ) + ) diff --git a/pylabrobot/molecular_devices/filtermax/models.py b/pylabrobot/molecular_devices/filtermax/models.py index f8b2e790b57..832eeb2b70d 100644 --- a/pylabrobot/molecular_devices/filtermax/models.py +++ b/pylabrobot/molecular_devices/filtermax/models.py @@ -21,6 +21,8 @@ @dataclass(frozen=True) class InstrumentInfo: + """Instrument identity, firmware, installed slide IDs, and reported options.""" + model: str firmware: str device_number: int @@ -36,6 +38,8 @@ class InstrumentInfo: @dataclass(frozen=True) class FilterMaxStatus: + """Readiness text and the raw SGS firmware state bits.""" + ready: bool text: str state_bits: Tuple[int, ...] @@ -43,12 +47,16 @@ class FilterMaxStatus: @dataclass(frozen=True) class InstalledFilterSlides: + """Installed excitation and emission slide identifiers.""" + excitation_slide_id: int emission_slide_id: int @dataclass(frozen=True) class FilterDefinition: + """One catalog filter; wavelengths and bandwidths are in nm and positions are one-based.""" + kind: FilterKind slide_id: int slide_name: str @@ -62,6 +70,8 @@ class FilterDefinition: @dataclass(frozen=True) class FilterSelection: + """Resolved slide and one-based slot, with wavelength and bandwidth in nm.""" + kind: FilterKind slide_id: int position: int @@ -71,10 +81,13 @@ class FilterSelection: @dataclass(frozen=True) class KineticTiming: + """Number of cycles and their nominal start-to-start interval in seconds.""" + interval: float reads: int def __post_init__(self) -> None: + """Validate the supported settings.""" if self.interval <= 0: raise ValueError("interval must be positive") if self.reads < 1: @@ -83,30 +96,38 @@ def __post_init__(self) -> None: @dataclass(frozen=True) class ShakingSettings: + """Finite shaking for duration seconds, optionally repeated between kinetic reads.""" + pattern: ShakePattern speed: ShakeSpeed duration: int between_reads: bool = False def __post_init__(self) -> None: + """Validate the supported settings.""" if self.duration < 1: raise ValueError("duration must be at least 1") @dataclass(frozen=True) class WellScanSettings: + """Horizontal or circular-fill sampling on a grid with density points per axis. + + Grid positions do not imply a physical distance. Horizontal scans have one row; + fill scans sample a square grid and retain its circular mask. + """ + pattern: WellScanPattern density: int - point_spacing: float = 0.23 def __post_init__(self) -> None: + """Validate the supported settings.""" if self.density < 1: raise ValueError("density must be at least 1") - if self.point_spacing <= 0: - raise ValueError("point_spacing must be positive") @property def grid_shape(self) -> Tuple[int, int]: + """Return the number of grid columns and rows requested from the reader.""" return (self.density, 1) if self.pattern == "horizontal" else (self.density, self.density) @@ -119,7 +140,7 @@ class PlateGeometry: length: float width: float height: float - bottom_row_offset: float + well_depth: float left_column_offset: float top_row_offset: float column_spacing: float @@ -131,15 +152,10 @@ class PlateGeometry: orientation: PlateOrientation = "landscape" def __post_init__(self) -> None: + """Validate the supported settings.""" if self.orientation not in ("landscape", "portrait"): raise ValueError(f"Unsupported FilterMax plate orientation {self.orientation!r}") - @property - def well_depth(self) -> float: - """Return the well depth stored under the legacy ``bottom_row_offset`` name.""" - - return self.bottom_row_offset - @classmethod def costar_96_clear_landscape(cls) -> "PlateGeometry": """Return the live-optimized geometry captured from the validation plate.""" @@ -150,7 +166,7 @@ def costar_96_clear_landscape(cls) -> "PlateGeometry": length=127.70, width=85.70, height=14.27, - bottom_row_offset=10.69, + well_depth=10.69, left_column_offset=14.05, top_row_offset=11.18, column_spacing=9.02, @@ -171,7 +187,7 @@ def costar_96_clear_portrait(cls) -> "PlateGeometry": length=127.70, width=85.70, height=14.27, - bottom_row_offset=10.69, + well_depth=10.69, left_column_offset=14.05, top_row_offset=11.18, column_spacing=9.02, @@ -186,8 +202,14 @@ def costar_96_clear_portrait(cls) -> "PlateGeometry": @dataclass(frozen=True) class WellScanPoint: - x: float - y: float + """One optical-density measurement at zero-based positions in the scan grid. + + grid_column and grid_row are integer indices, not millimetres. Fill-scan indices + refer to the full square grid; horizontal scans use grid_row=0. + """ + + grid_column: int + grid_row: int value: float @@ -196,6 +218,13 @@ class WellScanPoint: @dataclass(frozen=True) class AbsorbanceResult: + """Row-major optical densities, with unselected wells represented by None. + + wavelengths are in nm; temperature is in degrees Celsius; timestamp is Unix + seconds at command submission. elapsed_time is the nominal kinetic timepoint + in seconds, not measured latency. scan_points preserves the retained grid samples. + """ + data: PlateData wavelengths: Tuple[int, ...] reference_subtracted: bool @@ -207,6 +236,12 @@ class AbsorbanceResult: @dataclass(frozen=True) class LuminescenceResult: + """Row-major raw RLU for a one-based channel; unselected wells are None. + + temperature is in degrees Celsius; timestamp is Unix seconds at command + submission; elapsed_time is the nominal kinetic timepoint in seconds. + """ + data: PlateData channel: int temperature: Optional[float] @@ -216,6 +251,12 @@ class LuminescenceResult: @dataclass(frozen=True) class FluorescenceResult: + """Reserved fluorescence result with wavelengths in nm; acquisition is unsupported. + + data is row-major with None for unselected wells. temperature is in degrees + Celsius, timestamp in Unix seconds, and elapsed_time in nominal kinetic seconds. + """ + data: PlateData excitation_wavelength: int emission_wavelength: int @@ -226,12 +267,20 @@ class FluorescenceResult: @dataclass(frozen=True) class TimeResolvedFluorescenceResult(FluorescenceResult): + """Reserved time-resolved result; delay and integration are seconds.""" + delay: float = 0.0 integration: float = 0.0 @dataclass(frozen=True) class FluorescencePolarizationResult: + """Reserved parallel/perpendicular plate data; acquisition is unsupported. + + Wavelengths are in nm, temperature in degrees Celsius, timestamp in Unix + seconds, and elapsed_time in nominal kinetic seconds. Unselected wells are None. + """ + parallel_data: PlateData perpendicular_data: PlateData excitation_wavelength: int @@ -242,4 +291,5 @@ class FluorescencePolarizationResult: def empty_plate_data(rows: int, columns: int) -> PlateData: + """Allocate independent plate rows with no measured values.""" return [[None for _ in range(columns)] for _ in range(rows)] diff --git a/pylabrobot/molecular_devices/filtermax/protocol.py b/pylabrobot/molecular_devices/filtermax/protocol.py index 204f6e4f044..361bb9e2652 100644 --- a/pylabrobot/molecular_devices/filtermax/protocol.py +++ b/pylabrobot/molecular_devices/filtermax/protocol.py @@ -5,8 +5,9 @@ import asyncio import re import time +from contextlib import asynccontextmanager from dataclasses import dataclass -from typing import List, Optional +from typing import AsyncIterator, List, Optional from pylabrobot.io.serial import Serial @@ -31,7 +32,7 @@ class _CancelRequested(Exception): - pass + """Cancellation was observed before the next device message began.""" class _HandshakeTimeout(FilterMaxTimeoutError): @@ -45,6 +46,7 @@ def checksum(data: bytes) -> int: def build_frame(payload: str, frame_number: int = 1, final: bool = True) -> bytes: + """Encode a numbered ASCII payload with its terminator and checksum.""" if not 0 <= frame_number <= 7: raise ValueError("frame_number must be between 0 and 7") terminator = ETX if final else ETB @@ -54,6 +56,8 @@ def build_frame(payload: str, frame_number: int = 1, final: bool = True) -> byte @dataclass(frozen=True) class FilterMaxMessage: + """A complete, checksum-validated device message.""" + payload: str frame_count: int @@ -62,8 +66,15 @@ class FilterMaxTransport: """Private command transport. Public raw-command access is intentionally not exposed.""" def __init__(self, io: Serial): + """Use one lock for each complete exchange or measurement stream.""" self.io = io - self._send_lock = asyncio.Lock() + self._transaction_lock = asyncio.Lock() + + @asynccontextmanager + async def _transaction(self) -> AsyncIterator[None]: + """Own the wire until all replies, including a possible STOP reply, are consumed.""" + async with self._transaction_lock: + yield async def _read_byte( self, @@ -71,6 +82,7 @@ async def _read_byte( *, cancel_event: Optional[asyncio.Event] = None, ) -> int: + """Read before the deadline, checking cancellation only at a message boundary.""" while True: if cancel_event is not None and cancel_event.is_set(): raise _CancelRequested @@ -82,6 +94,7 @@ async def _read_byte( await asyncio.sleep(0) async def _expect(self, expected: int, deadline: float) -> None: + """Read and validate one control byte.""" actual = await self._read_byte(deadline) if actual != expected: raise FilterMaxProtocolError( @@ -89,20 +102,20 @@ async def _expect(self, expected: int, deadline: float) -> None: ) async def send_request(self, payload: str, timeout: float = 5.0) -> None: - """Send one captured host transaction without waiting for the device message.""" + """Send a request while the caller holds transaction ownership.""" deadline = time.monotonic() + timeout - async with self._send_lock: - await self.io.write(bytes((ENQ,))) - try: - await self._expect(ACK, deadline) - except FilterMaxTimeoutError as exc: - raise _HandshakeTimeout("Timed out waiting for ACK to the initial FilterMax ENQ") from exc - await self.io.write(build_frame(payload)) + await self.io.write(bytes((ENQ,))) + try: await self._expect(ACK, deadline) - await self.io.write(bytes((EOT,))) + except FilterMaxTimeoutError as exc: + raise _HandshakeTimeout("Timed out waiting for ACK to the initial FilterMax ENQ") from exc + await self.io.write(build_frame(payload)) + await self._expect(ACK, deadline) + await self.io.write(bytes((EOT,))) async def _read_frame_after_stx(self, deadline: float) -> bytes: + """Read a whole frame and validate its terminator and checksum.""" frame = bytearray((STX,)) while not frame.endswith(b"\r\n"): if len(frame) > 4096: @@ -131,7 +144,11 @@ async def receive_message( command: str = "", cancel_event: Optional[asyncio.Event] = None, ) -> FilterMaxMessage: - """Receive and acknowledge one device message, including all continuation frames.""" + """Receive a whole message under transaction ownership. + + Cancellation is checked before ENQ. Once ENQ is received, all continuation + frames and the final EOT are consumed before control returns to the owner. + """ deadline = time.monotonic() + timeout first = await self._read_byte(deadline, cancel_event=cancel_event) @@ -144,7 +161,7 @@ async def receive_message( while True: control = await self._read_byte(deadline) if control == EOT: - break + raise FilterMaxProtocolError("FilterMax EOT arrived before a final ETX frame") if control != STX: raise FilterMaxProtocolError(f"Expected device STX or EOT, received 0x{control:02X}") frame = await self._read_frame_after_stx(deadline) @@ -177,5 +194,7 @@ async def exchange( *, cancel_event: Optional[asyncio.Event] = None, ) -> FilterMaxMessage: - await self.send_request(payload) - return await self.receive_message(timeout, command=payload, cancel_event=cancel_event) + """Serialize a complete request and its response.""" + async with self._transaction(): + await self.send_request(payload) + return await self.receive_message(timeout, command=payload, cancel_event=cancel_event) diff --git a/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py index 7f8e2b7e231..67fdc34fd00 100644 --- a/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py +++ b/pylabrobot/molecular_devices/filtermax/tests/filtermax_f5_tests.py @@ -209,8 +209,7 @@ async def test_absorbance_portrait_uses_captured_shift_and_orientation_code(self self.assertEqual((len(result.data), len(result.data[0])), (8, 12)) self.assertAlmostEqual(result.data[7][11], 0.081) # type: ignore[arg-type] self.assertIn( - "PLATE Temp 12770 8570 1427 1069 1405 1118 12 8 " - "902 900 640 640 0 300 0 1027 1 1", + "PLATE Temp 12770 8570 1427 1069 1405 1118 12 8 902 900 640 640 0 300 0 1027 1 1", host_payloads(io), ) self.assertIn("SHIFT", host_payloads(io)) @@ -247,9 +246,44 @@ async def test_absorbance_fill_preserves_points(self) -> None: self.assertEqual(len(result.scan_points["C4"]), 21) self.assertAlmostEqual(result.scan_points["C4"][0].value, 16 / 1000) self.assertEqual( - len({(point.x, point.y) for point in result.scan_points["C4"]}), + len({(point.grid_column, point.grid_row) for point in result.scan_points["C4"]}), 21, ) + positions = [(point.grid_column, point.grid_row) for point in result.scan_points["C4"]] + self.assertEqual(positions[:3], [(1, 0), (2, 0), (3, 0)]) + self.assertEqual(positions[-3:], [(1, 4), (2, 4), (3, 4)]) + self.assertIn((2, 2), positions) + self.assertAlmostEqual(result.data[2][3], 0.137) # type: ignore[arg-type] + + async def test_horizontal_scan_preserves_grid_indices_and_mean(self) -> None: + """Scan positions are integer sample indices, with unchanged optical densities.""" + row = "+ " + " ".join(str(value) for value in range(36)) + incoming = b"".join( + ( + exchange_response("+ 2 1"), + exchange_response("+"), + exchange_response("+"), + exchange_response("+ -67"), + measurement_response(row, "+ INFO"), + exchange_response("+ 25.0"), + exchange_response("+ 6512"), + ) + ) + driver, _ = self.make_driver(incoming) + result = ( + await driver.read_absorbance( + PlateGeometry.costar_96_clear_landscape(), + 450, + wells=["A2"], + well_scan=WellScanSettings(pattern="horizontal", density=3), + ) + )[0] + self.assertEqual( + [(point.grid_column, point.grid_row) for point in result.scan_points["A2"]], + [(0, 0), (1, 0), (2, 0)], + ) + self.assertEqual([point.value for point in result.scan_points["A2"]], [0.003, 0.004, 0.005]) + self.assertAlmostEqual(result.data[0][1], 0.004) # type: ignore[arg-type] def test_fill_density_28_matches_softmax_616_point_mask(self) -> None: layout = FilterMaxF5._scan_layout(WellScanSettings(pattern="fill", density=28)) @@ -311,7 +345,7 @@ async def test_luminescence_kinetic_info_arrives_only_after_final_cycle(self) -> commands = [payload for payload in host_payloads(io) if payload.startswith("LUM ")] self.assertEqual([command.split()[-4] for command in commands], ["3", "2", "1"]) - async def test_malformed_read_is_stopped_before_tray_recovery(self) -> None: + async def test_malformed_values_after_final_info_still_eject_tray(self) -> None: incoming = b"".join( ( exchange_response("+ 2 1"), @@ -319,7 +353,6 @@ async def test_malformed_read_is_stopped_before_tray_recovery(self) -> None: exchange_response("+"), exchange_response("+ -67"), measurement_response("+ 1 2", "+ INFO"), - exchange_response("- E140: "), exchange_response("+ 6512"), ) ) @@ -330,7 +363,8 @@ async def test_malformed_read_is_stopped_before_tray_recovery(self) -> None: 450, wells=["C4"], ) - self.assertEqual(host_payloads(io)[-2:], ["STOP", "E P"]) + self.assertEqual(host_payloads(io)[-1], "E P") + self.assertNotIn("STOP", host_payloads(io)) async def test_captured_e62_is_preserved_in_session_error_log(self) -> None: error = "- E62: ABS Led 7 ADCValue: 16277 Gain 255 LedHighPoti 44 LedLowPoti 255" diff --git a/pylabrobot/molecular_devices/filtermax/tests/operation_tests.py b/pylabrobot/molecular_devices/filtermax/tests/operation_tests.py new file mode 100644 index 00000000000..3b9c634d56e --- /dev/null +++ b/pylabrobot/molecular_devices/filtermax/tests/operation_tests.py @@ -0,0 +1,353 @@ +"""Exercise operation ownership and cooperative cancellation over a yielding serial stream.""" + +import asyncio +import unittest +from pathlib import Path +from typing import Optional + +from pylabrobot.molecular_devices.filtermax import ( + FilterMaxF5, + FilterMaxReadCancelled, + FilterMaxTimeoutError, + FilterSlideCatalog, + KineticTiming, + PlateGeometry, +) +from pylabrobot.molecular_devices.filtermax.protocol import ( + ACK, + ENQ, + EOT, + FilterMaxTransport, + build_frame, +) +from pylabrobot.molecular_devices.filtermax.tests.filtermax_f5_tests import ( + FakeSerial, + device_message, + exchange_response, + host_payloads, + measurement_response, +) + +ROW = "+ " + " ".join("100" for _ in range(12)) +PREPARATION = b"".join(exchange_response(reply) for reply in ("+ 2 1", "+", "+", "+ -67")) +RECOVERY = exchange_response("- E140: ") + exchange_response("+ 6512") + + +class PausingSerial(FakeSerial): + """Yield at every byte and optionally pause immediately before a specified read.""" + + def __init__(self, incoming: bytes, pause_at: Optional[int] = None, empty_on_resume=False): + """Configure a deterministic boundary at which another task may request cancellation.""" + super().__init__(incoming) + self.pause_at = pause_at + self.empty_on_resume = empty_on_resume + self.bytes_read = 0 + self.paused = asyncio.Event() + self.resume = asyncio.Event() + self.stop_read_positions: list[int] = [] + + async def write(self, data: bytes) -> None: + """Record exactly how much of a device response preceded STOP.""" + await asyncio.sleep(0) + if data == build_frame("STOP"): + self.stop_read_positions.append(self.bytes_read) + await super().write(data) + + async def read(self, num_bytes: int = 1) -> bytes: + """Pause once, then deliver bytes while retaining real serial scheduling points.""" + await asyncio.sleep(0) + if self.bytes_read == self.pause_at: + self.pause_at = None + self.paused.set() + await self.resume.wait() + if self.empty_on_resume: + return b"" + if not self.incoming: + raise FilterMaxTimeoutError("Scripted serial response exhausted") + data = await super().read(num_bytes) + self.bytes_read += len(data) + return data + + +class TestFilterMaxOperations(unittest.IsolatedAsyncioTestCase): + """Test public APIs without creating a hardware connection.""" + + def make_driver(self, io: PausingSerial) -> FilterMaxF5: + """Attach the byte-level serial double to the production transport.""" + catalog = FilterSlideCatalog.from_softmax_xml(Path(__file__).with_name("filtermax_slides.xml")) + reader = FilterMaxF5("test", "COM1", catalog) + reader.io = io # type: ignore[assignment] + reader._transport = FilterMaxTransport(io) # type: ignore[arg-type] + return reader + + async def test_query_waits_for_measurement_and_tray_recovery(self) -> None: + """Temperature polling cannot consume measurement rows or run before ejection.""" + first = PREPARATION + measurement_response(ROW, "+ INFO") + io = PausingSerial( + first + exchange_response("+ 25") + exchange_response("+ 6512") + exchange_response("+ 26"), + pause_at=len(PREPARATION) + 2, + ) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450, wells=["A1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + query = asyncio.create_task(reader.get_temperature()) + await asyncio.sleep(0) + self.assertFalse(query.done()) + io.resume.set() + result, temperature = await asyncio.wait_for(asyncio.gather(read, query), 2) + self.assertEqual(result[0].data[0][0], 0.1) + self.assertEqual(temperature, 26) + self.assertEqual(host_payloads(io)[-3:], ["TG", "E P", "TG"]) + + async def test_cancel_at_result_boundaries(self) -> None: + """Cancellation before results, after a row, or within a frame drains safely.""" + continuation = ( + bytes((ENQ,)) + + build_frame(ROW[:15], final=False) + + build_frame(ROW[15:], frame_number=2) + + bytes((EOT,)) + ) + cases = ( + ("before_first", b"", 0, True), + ("after_row", device_message(ROW), len(device_message(ROW)) - 1, False), + ("within_continuation", continuation, 12, False), + ) + for mode in ("absorbance", "luminescence"): + for label, message, offset, empty in cases: + with self.subTest(mode=mode, boundary=label): + prefix = PREPARATION + bytes((ACK, ACK)) + io = PausingSerial( + prefix + message + RECOVERY, pause_at=len(prefix) + offset, empty_on_resume=empty + ) + reader = self.make_driver(io) + plate = PlateGeometry.costar_96_clear_landscape() + read = asyncio.create_task( + reader.read_absorbance(plate, 450, wells=["A1", "B1"]) + if mode == "absorbance" + else reader.read_luminescence(plate, wells=["A1", "B1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + cancellations = [asyncio.create_task(reader.cancel_read()) for _ in range(2)] + await asyncio.sleep(0) + io.resume.set() + outcomes = await asyncio.wait_for( + asyncio.gather(read, *cancellations, return_exceptions=True), 2 + ) + self.assertIsInstance(outcomes[0], FilterMaxReadCancelled) + self.assertEqual(outcomes[1:], [None, None]) + self.assertEqual(host_payloads(io)[-2:], ["STOP", "E P"]) + self.assertEqual(host_payloads(io).count("STOP"), 1) + self.assertGreaterEqual(io.stop_read_positions[0], len(prefix) + len(message)) + self.assertFalse(reader._operation_lock.locked()) + + async def test_cancel_during_preparation_sends_no_measurement_or_stop(self) -> None: + """A preparation response is drained before cancellation prevents the next step.""" + slides = exchange_response("+ 2 1") + io = PausingSerial(slides + exchange_response("+ 6512"), pause_at=len(slides) - 1) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450, wells=["A1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + cancel = asyncio.create_task(reader.cancel_read()) + await asyncio.sleep(0) + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(read, cancel, return_exceptions=True), 2) + self.assertIsInstance(results[0], FilterMaxReadCancelled) + self.assertEqual(host_payloads(io), ["CS", "E P"]) + + async def test_kinetic_cancellation_never_starts_another_cycle(self) -> None: + """Cancellation works during an interval and before an overdue cycle.""" + from unittest.mock import patch + + for interval in (60, 1e-9): + for mode in ("absorbance", "luminescence"): + with self.subTest(interval=interval, mode=mode): + io = PausingSerial( + PREPARATION + measurement_response(ROW) + exchange_response("+ 25") + RECOVERY + ) + reader = self.make_driver(io) + waiting = asyncio.Event() + release = asyncio.Event() + original_wait = reader._wait_until + + async def wait_at_cycle(target: float) -> None: + """Expose the interval boundary without relying on a wall-clock sleep.""" + waiting.set() + if interval < 1: + await release.wait() + await original_wait(target) + + with patch.object(reader, "_wait_until", side_effect=wait_at_cycle): + plate = PlateGeometry.costar_96_clear_landscape() + timing = KineticTiming(interval=interval, reads=3) + read = asyncio.create_task( + reader.read_absorbance(plate, 450, wells=["A1"], kinetic=timing) + if mode == "absorbance" + else reader.read_luminescence(plate, wells=["A1"], kinetic=timing) + ) + await asyncio.wait_for(waiting.wait(), 1) + cancel = asyncio.create_task(reader.cancel_read()) + await asyncio.sleep(0) + release.set() + results = await asyncio.wait_for( + asyncio.gather(read, cancel, return_exceptions=True), 2 + ) + self.assertIsInstance(results[0], FilterMaxReadCancelled) + self.assertEqual(sum(p.startswith(("ABS ", "LUM ")) for p in host_payloads(io)), 1) + self.assertEqual(host_payloads(io)[-2:], ["STOP", "E P"]) + + async def test_repeated_task_cancellation_keeps_ownership_through_cleanup(self) -> None: + """Interrupting the caller cannot leave a half-read frame for a queued query.""" + message = device_message(ROW) + prefix = PREPARATION + bytes((ACK, ACK)) + io = PausingSerial( + prefix + message + RECOVERY + exchange_response("+ 26"), pause_at=len(prefix) + 12 + ) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450, wells=["A1", "B1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + query = asyncio.create_task(reader.get_temperature()) + for _ in range(3): + read.cancel() + await asyncio.sleep(0) + self.assertTrue(reader._operation_lock.locked()) + self.assertFalse(query.done()) + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(read, query, return_exceptions=True), 2) + self.assertIsInstance(results[0], asyncio.CancelledError) + self.assertEqual(results[1], 26) + self.assertEqual(host_payloads(io)[-3:], ["STOP", "E P", "TG"]) + self.assertFalse(reader._operation_lock.locked()) + + async def test_shutdown_cancels_read_before_closing_serial(self) -> None: + """Shutdown waits for the active owner to stop and eject before releasing the port.""" + message = device_message(ROW) + prefix = PREPARATION + bytes((ACK, ACK)) + io = PausingSerial(prefix + message + RECOVERY, pause_at=len(prefix) + 10) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_luminescence(PlateGeometry.costar_96_clear_landscape(), wells=["A1", "B1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + stop = asyncio.create_task(reader.stop()) + await asyncio.sleep(0) + self.assertFalse(io.stop_called) + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(read, stop, return_exceptions=True), 2) + self.assertIsInstance(results[0], FilterMaxReadCancelled) + self.assertIsNone(results[1]) + self.assertEqual(host_payloads(io)[-2:], ["STOP", "E P"]) + self.assertTrue(io.stop_called) + + async def test_shaking_is_cancelled_by_its_owner(self) -> None: + """Stopping a standalone shake uses its owner instead of a competing exchange.""" + io = PausingSerial( + bytes((ACK, ACK)) + exchange_response("- E140: "), pause_at=2, empty_on_resume=True + ) + reader = self.make_driver(io) + shake = asyncio.create_task(reader.start_shaking("linear", "medium", 30)) + await asyncio.wait_for(io.paused.wait(), 1) + stop = asyncio.create_task(reader.stop_shaking()) + await asyncio.sleep(0) + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(shake, stop, return_exceptions=True), 2) + self.assertIsInstance(results[0], FilterMaxReadCancelled) + self.assertEqual(host_payloads(io), ["SHAKE X 0 3 40 30", "STOP"]) + + async def test_recovery_errors_preserve_original_failure_and_release_waiters(self) -> None: + """STOP and tray faults are logged without replacing the malformed-response error.""" + from pylabrobot.molecular_devices.filtermax import FilterMaxProtocolError + + malformed = bytes((ACK, ACK, ENQ, EOT)) + io = PausingSerial( + PREPARATION + + malformed + + exchange_response("- E62: stop failed") + + exchange_response("- E21: tray failed") + + exchange_response("+ 26"), + pause_at=len(PREPARATION) + 3, + ) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450, wells=["A1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + cancel = asyncio.create_task(reader.cancel_read()) + await asyncio.sleep(0) + with self.assertLogs( + "pylabrobot.molecular_devices.filtermax.filtermax_f5", level="WARNING" + ) as log: + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(read, cancel, return_exceptions=True), 2) + self.assertIsInstance(results[0], FilterMaxProtocolError) + self.assertIn("before a final ETX", str(results[0])) + self.assertIsNone(results[1]) + self.assertIn("STOP recovery failed", "\n".join(log.output)) + self.assertIn("tray recovery failed", "\n".join(log.output)) + self.assertEqual(host_payloads(io).count("STOP"), 1) + self.assertEqual(await reader.get_temperature(), 26) + + async def test_idle_cancellation_does_not_transmit(self) -> None: + """Repeated cancellation is idempotent when no operation is active.""" + io = PausingSerial(b"") + reader = self.make_driver(io) + await reader.cancel_read() + await reader.cancel_read() + await reader.stop_shaking() + self.assertEqual(io.writes, []) + + async def test_cancelled_setup_drains_identity_and_closes_port(self) -> None: + """Cancelling the caller cannot leave an opened port or partial identity response.""" + from pylabrobot.molecular_devices.filtermax.tests.setup_tests import IDENTITY + + io = PausingSerial(exchange_response(IDENTITY), pause_at=12) + reader = self.make_driver(io) + setup = asyncio.create_task(reader.setup()) + await asyncio.wait_for(io.paused.wait(), 1) + setup.cancel() + await asyncio.sleep(0) + self.assertFalse(io.stop_called) + io.resume.set() + with self.assertRaises(asyncio.CancelledError): + await asyncio.wait_for(setup, 2) + self.assertEqual(io.incoming, b"") + self.assertTrue(io.stop_called) + self.assertFalse(reader._setup_complete) + self.assertFalse(reader._operation_lock.locked()) + + async def test_cancelled_queued_call_never_sends_a_command(self) -> None: + """Cancelling a waiting operation cannot leak a coroutine or change the wire.""" + io = PausingSerial(exchange_response("+ 25"), pause_at=12) + reader = self.make_driver(io) + first = asyncio.create_task(reader.get_temperature()) + await asyncio.wait_for(io.paused.wait(), 1) + queued = asyncio.create_task(reader.move_plate_tray_out()) + await asyncio.sleep(0) + queued.cancel() + with self.assertRaises(asyncio.CancelledError): + await queued + io.resume.set() + self.assertEqual(await asyncio.wait_for(first, 2), 25) + self.assertEqual(host_payloads(io), ["TG"]) + + async def test_cancellation_after_final_info_needs_no_stop(self) -> None: + """A completed firmware operation is not stopped again during cancellation cleanup.""" + read_response = PREPARATION + measurement_response(ROW, "+ INFO") + io = PausingSerial(read_response + exchange_response("+ 6512"), pause_at=len(read_response) - 1) + reader = self.make_driver(io) + read = asyncio.create_task( + reader.read_absorbance(PlateGeometry.costar_96_clear_landscape(), 450, wells=["A1"]) + ) + await asyncio.wait_for(io.paused.wait(), 1) + cancel = asyncio.create_task(reader.cancel_read()) + await asyncio.sleep(0) + io.resume.set() + results = await asyncio.wait_for(asyncio.gather(read, cancel, return_exceptions=True), 2) + self.assertIsInstance(results[0], FilterMaxReadCancelled) + self.assertNotIn("STOP", host_payloads(io)) + self.assertEqual(host_payloads(io)[-1], "E P") diff --git a/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py index ad63263cc63..87c89974fcd 100644 --- a/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py +++ b/pylabrobot/molecular_devices/filtermax/tests/protocol_tests.py @@ -1,3 +1,4 @@ +import asyncio import unittest from pylabrobot.molecular_devices.filtermax.errors import ( @@ -34,11 +35,55 @@ async def read(self, num_bytes: int = 1) -> bytes: return data +class YieldingSerial(FakeSerial): + """Expose interleaving that a serial executor permits between every byte.""" + + async def write(self, data: bytes) -> None: + """Yield before writing to the simulated port.""" + await asyncio.sleep(0) + await super().write(data) + + async def read(self, num_bytes: int = 1) -> bytes: + """Yield before returning the next bytes.""" + await asyncio.sleep(0) + return await super().read(num_bytes) + + def device_message(payload: str) -> bytes: return bytes((ENQ,)) + build_frame(payload) + bytes((EOT,)) class TestFilterMaxProtocol(unittest.IsolatedAsyncioTestCase): + async def test_concurrent_exchanges_keep_their_own_responses(self) -> None: + """Another request cannot consume an outstanding response's control bytes.""" + incoming = b"".join( + bytes((ACK, ACK)) + device_message(payload) for payload in ("+ 24.6", "+ 24.7") + ) + transport = FilterMaxTransport(YieldingSerial(incoming)) # type: ignore[arg-type] + first, second = await asyncio.wait_for( + asyncio.gather(transport.exchange("TG"), transport.exchange("TG")), timeout=1 + ) + self.assertEqual((first.payload, second.payload), ("+ 24.6", "+ 24.7")) + + async def test_eot_requires_a_final_frame(self) -> None: + """Empty transactions and truncated continuation chains cannot return data.""" + for frames in (b"", build_frame("+ 24.6", final=False)): + with self.subTest(frames=frames): + incoming = bytes((ACK, ACK, ENQ)) + frames + bytes((EOT,)) + transport = FilterMaxTransport(FakeSerial(incoming)) # type: ignore[arg-type] + with self.assertRaises(FilterMaxProtocolError): + await transport.exchange("TG") + + async def test_frame_numbers_wrap_through_zero(self) -> None: + """A valid continuation sequence can span more than seven frames.""" + frames = b"".join( + build_frame(str(index), frame_number=(index + 1) % 8, final=index == 8) for index in range(9) + ) + incoming = bytes((ACK, ACK, ENQ)) + frames + bytes((EOT,)) + transport = FilterMaxTransport(FakeSerial(incoming)) # type: ignore[arg-type] + message = await transport.exchange("?") + self.assertEqual((message.payload, message.frame_count), ("012345678", 9)) + def test_captured_checksum(self) -> None: self.assertEqual(build_frame("TG"), b"\x021TG\x03CF\r\n") self.assertEqual(build_frame("CS"), b"\x021CS\x03CA\r\n") diff --git a/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py b/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py index bd76817a9d5..cbc19064b73 100644 --- a/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py +++ b/pylabrobot/molecular_devices/filtermax/tests/setup_tests.py @@ -151,7 +151,10 @@ async def test_wrong_identity_at_either_rate_is_not_retried(self) -> None: """Receiving an identity establishes a rate even when the device is wrong.""" for baudrate in (38400, 9600): with self.subTest(baudrate=baudrate): - responses = {38400: b"", baudrate: exchange_response(IDENTITY.replace("57855", "1"))} + responses: dict[int, bytes | BaseException] = { + 38400: b"", + baudrate: exchange_response(IDENTITY.replace("57855", "1")), + } driver, io = self.make_driver(responses) with self.assertRaises(FilterMaxIdentityError): await driver.setup()