examples: draft instrument

Author: dbirman

examples/isi_instrument.py

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+"""Generates an example JSON file for an ISI (Intrinsic Signal Imaging) instrument
+
+Based on the ISI Full Rig BOM (AIBS part 0113_000-00, Rev A).
+The rig consists of:
+  - ISI Table Assembly (0113_100-00)
+  - ISI System Structure (0113_200-00)
+  - Camera, Stage, and Mount Assembly (0113_300-00)
+  - Headframe Clamp Assembly (0113_400-00)
+  - ISI Eye Tracking Assembly (0123_500-00)
+  - Camera/Lens Assembly (0113_550-00) with tandem Nikon lenses and Andor Zyla sCMOS
+  - LED Light Ring Assembly (0113_530-00)
+"""
+
+import argparse
+from datetime import date
+
+from aind_data_schema_models.coordinates import AnatomicalRelative
+from aind_data_schema_models.devices import (
+    CameraChroma,
+    CameraTarget,
+    DataInterface,
+    DetectorType,
+    FilterType,
+)
+from aind_data_schema_models.modalities import Modality
+from aind_data_schema_models.organizations import Organization
+from aind_data_schema_models.units import FrequencyUnit, SizeUnit
+
+from aind_data_schema.components.coordinates import CoordinateSystemLibrary
+from aind_data_schema.components.devices import (
+    Camera,
+    CameraAssembly,
+    Computer,
+    DAQDevice,
+    Device,
+    Filter,
+    Lens,
+    LightEmittingDiode,
+    Monitor,
+    MotorizedStage,
+)
+from aind_data_schema.core.instrument import Instrument
+
+acquisition_computer = Computer(
+    name="Acquisition Computer",
+    notes="3U custom rackmount, Intel Xeon E5-1620v3 3.5GHz, Nvidia GT 730 2GB, Advantech PCIE-1672PC frame grabber, 240GB SSD + 2x1TB HDD. Pogo Linux quote 90846.",
+)
+
+stim_computer = Computer(
+    name="Stim Computer",
+    notes="Intel Xeon E5-1620v3 3.5GHz, 16GB DDR4 ECC, Western Digital RE4 500GB. Pogo Linux quote 90854.",
+)
+
+ni_daq = DAQDevice(
+    name="NI USB-6008",
+    manufacturer=Organization.NATIONAL_INSTRUMENTS,
+    model="USB-6008",
+    data_interface=DataInterface.USB,
+)
+
+newport_linear_stage = MotorizedStage(
+    name="Newport M-ILS100PP Linear Stage",
+    manufacturer=Organization.MKS_NEWPORT,
+    model="M-ILS100PP",
+    travel=100,
+    travel_unit=SizeUnit.MM,
+    notes="High performance linear stage, 100 mm travel, stepper motor, metric. Controlled by Newport SMC100PP.",
+)
+
+newport_motor_controller = Device(
+    name="Newport SMC100PP Motor Controller",
+    manufacturer=Organization.MKS_NEWPORT,
+    model="SMC100PP",
+    notes="Single-axis stepper motor controller/driver for Newport M-ILS100PP stage. USB interface.",
+)
+
+isi_camera = Camera(
+    name="Andor Zyla 5.5 sCMOS",
+    manufacturer=Organization.OTHER,
+    model="Zyla 5.5 sCMOS",
+    detector_type=DetectorType.CAMERA,
+    data_interface=DataInterface.USB,
+    chroma=CameraChroma.BW,
+    notes="Andor Technology Zyla 5.5 sCMOS scientific camera used for intrinsic signal imaging. "
+    "Vendor part: Zyla 5.5 sCMOS. Manufacturer is Andor (Oxford Instruments).",
+)
+
+isi_lens_35mm = Lens(
+    name="Nikon NIKKOR 35mm f/1.4",
+    manufacturer=Organization.NIKON,
+    model="NIKKOR 35mm f/1.4",
+    notes="Front lens of tandem-lens assembly for ISI. B&H part NI3514.",
+)
+
+isi_lens_105mm = Lens(
+    name="Nikon Micro-NIKKOR 105mm f/2.8",
+    manufacturer=Organization.NIKON,
+    model="Micro-NIKKOR 105mm f/2.8",
+    notes="Rear lens of tandem-lens assembly for ISI, facing the camera. B&H part NI10528M.",
+)
+
+isi_bandpass_filter = Filter(
+    name="Semrock FF01-630/92-50 Bandpass Filter",
+    manufacturer=Organization.SEMROCK,
+    model="FF01-630/92-50",
+    filter_type=FilterType.BANDPASS,
+    center_wavelength=630,
+    wavelength_unit=SizeUnit.NM,
+    notes="630/92 nm BrightLine single-band bandpass filter, 50 mm diameter, housed and mounted.",
+)
+
+isi_camera_assembly = CameraAssembly(
+    name="ISI Brain Camera Assembly",
+    target=CameraTarget.BRAIN,
+    relative_position=[AnatomicalRelative.SUPERIOR],
+    camera=isi_camera,
+    lens=isi_lens_35mm,
+    filter=isi_bandpass_filter,
+)
+
+eye_tracking_camera = Camera(
+    name="Allied Vision MAKO G-125C",
+    manufacturer=Organization.ALLIED,
+    model="MAKO G-125C",
+    detector_type=DetectorType.CAMERA,
+    data_interface=DataInterface.ETH,
+    chroma=CameraChroma.BW,
+    notes="Allied Vision Technologies GigE camera, PoE, 1.2 MP, 30 fps. Used for eye tracking. "
+    "1st Vision part AVT-GK-125C.",
+)
+
+eye_tracking_lens = Lens(
+    name="InfiniStix 130mm W.D. 0.73x",
+    manufacturer=Organization.INFINITY_PHOTO_OPTICAL,
+    model="InfiniStix Proximity Series 130mm W.D./0.73x",
+    notes="Infinity Photo-Optical InfiniStix proximity series lens for eye tracking camera.",
+)
+
+eye_tracking_camera_assembly = CameraAssembly(
+    name="Eye Tracking Camera Assembly",
+    target=CameraTarget.EYE,
+    relative_position=[AnatomicalRelative.ANTERIOR],
+    camera=eye_tracking_camera,
+    lens=eye_tracking_lens,
+)
+
+eye_tracking_dichroic = Filter(
+    name="Semrock FF750-SDi02-25x36 Dichroic",
+    manufacturer=Organization.SEMROCK,
+    model="FF750-SDi02-25x36",
+    filter_type=FilterType.DICHROIC,
+    cut_off_wavelength=750,
+    wavelength_unit=SizeUnit.NM,
+    notes="Dichroic beamsplitter used in eye tracking light path to separate 850 nm IR illumination.",
+)
+
+eye_tracking_ir_led = LightEmittingDiode(
+    name="Eye Tracking IR LED 850nm",
+    manufacturer=Organization.OTHER,
+    model="LZ4-40R608-0000",
+    wavelength=850,
+    wavelength_unit=SizeUnit.NM,
+    notes="LED Engin Inc. (now ams OSRAM) LZ4-40R608-0000 infrared LED for eye tracking illumination. "
+    "Digikey part 1537-1045-ND.",
+)
+
+eye_tracking_collimating_lens = Lens(
+    name="Thorlabs LB1092-B-ML Bi-Convex Lens",
+    manufacturer=Organization.THORLABS,
+    model="LB1092-B-ML",
+    notes="Mounted N-BK7 bi-convex lens, 1/2 inch diameter, f=15.0 mm, ARC 650-1050 nm. "
+    "Used in eye tracking IR illumination path.",
+)
+
+led_ring_green = LightEmittingDiode(
+    name="LED Ring Green 527nm",
+    manufacturer=Organization.OTHER,
+    model="C503B-GCN-CY0C0791",
+    wavelength=527,
+    wavelength_unit=SizeUnit.NM,
+    notes="Cree Inc. 5mm green clear LED, 527 nm, 30 deg. 19 units in LED light ring assembly (0113_530-00). "
+    "Digikey part C503B-GCN-CY0C0791-ND.",
+)
+
+led_ring_red = LightEmittingDiode(
+    name="LED Ring Red 635nm",
+    manufacturer=Organization.OTHER,
+    model="HLMP-EG08-Y2000",
+    wavelength=635,
+    wavelength_unit=SizeUnit.NM,
+    notes="Avago Technologies 5mm red clear LED, 635 nm. 9 units in LED light ring assembly (0113_530-00). "
+    "Digikey part 516-1377-ND.",
+)
+
+stimulus_monitor = Monitor(
+    name="ASUS PA248Q Stimulus Monitor",
+    manufacturer=Organization.ASUS,
+    model="PA248Q",
+    refresh_rate=60,
+    width=1920,
+    height=1200,
+    size_unit=SizeUnit.PX,
+    viewing_distance=15,
+    viewing_distance_unit=SizeUnit.CM,
+    relative_position=[AnatomicalRelative.ANTERIOR],
+    notes="24-inch widescreen LED-backlit LCD monitor used for visual stimulation. "
+    "2 units per rig. Viewing distance must be set at time of use.",
+)
+
+temperature_controller = Device(
+    name="WPI ATC2000 Animal Temperature Controller",
+    manufacturer=Organization.OTHER,
+    model="ATC2000",
+    notes="World Precision Instruments ATC2000 animal temperature controller. "
+    "Regulates heating plate temperature during imaging.",
+)
+
+somnosuite = Device(
+    name="Kent Scientific SomnoSuite",
+    manufacturer=Organization.OTHER,
+    model="SOMNO",
+    notes="Kent Scientific SomnoSuite low-flow digital vaporizer for isoflurane anesthesia delivery. "
+    "Used with low profile facemasks (SOMNO-0801) and induction chamber (SOMNO-0705).",
+)
+
+physiosuite = Device(
+    name="Kent Scientific PhysioSuite",
+    manufacturer=Organization.OTHER,
+    model="PS-MSTAT-RT",
+    notes="Kent Scientific PhysioSuite with MouseSTAT pulse oximeter and heart rate monitor. "
+    "Includes RightTemp module for temperature monitoring.",
+)
+
+inst = Instrument(
+    location="ISI Full Rig",
+    instrument_id="ISI1",
+    modification_date=date(2016, 7, 18),
+    modalities=[Modality.ISI],
+    coordinate_system=CoordinateSystemLibrary.BREGMA_ARI,
+    temperature_control=True,
+    notes="AIBS Intrinsic Signal Imaging full rig (0113_000-00, Rev A). "
+    "Tandem-lens ISI camera assembly uses Nikon 35mm f/1.4 (front) face-to-face with Nikon 105mm f/2.8 (rear). "
+    "Eye tracking arm (0123_500-00) uses 850 nm IR illumination with dichroic beamsplitter. "
+    "LED light ring contains 19x green (527 nm) and 9x red (635 nm) LEDs for cortical illumination.",
+    components=[
+        acquisition_computer,
+        stim_computer,
+        ni_daq,
+        newport_linear_stage,
+        newport_motor_controller,
+        isi_camera_assembly,
+        isi_lens_105mm,
+        eye_tracking_camera_assembly,
+        eye_tracking_dichroic,
+        eye_tracking_ir_led,
+        eye_tracking_collimating_lens,
+        led_ring_green,
+        led_ring_red,
+        stimulus_monitor,
+        temperature_controller,
+        somnosuite,
+        physiosuite,
+    ],
+)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--output-dir", default=None, help="Output directory for generated JSON file")
+    args = parser.parse_args()
+
+    serialized = inst.model_dump_json()
+    deserialized = Instrument.model_validate_json(serialized)
+    deserialized.write_standard_file(prefix="isi", output_directory=args.output_dir)