Week 3 HW: Lab Automation

from opentrons import types
import math

metadata = {
    'author': 'Jean Colmenares',
    'protocolName': 'Agar Swirl Pattern - 4 Colors',
    'description': 'Swirl pattern with four colors per branch',
    'source': 'HTGAA 2026 Opentrons Lab',
    'apiLevel': '2.20'
}

TIP_RACK_DECK_SLOT = 9
COLORS_DECK_SLOT = 6
AGAR_DECK_SLOT = 5
PIPETTE_STARTING_TIP_WELL = 'A1'

well_colors = {
    'A1': 'Red',
    'B1': 'Green',
    'C1': 'Orange',
    'D1': 'Blue'
}

def run(protocol):

    tips_20ul = protocol.load_labware(
        'opentrons_96_tiprack_20ul',
        TIP_RACK_DECK_SLOT,
        'Opentrons 20uL Tips'
    )

    pipette_20ul = protocol.load_instrument(
        "p20_single_gen2",
        "right",
        [tips_20ul]
    )

    temperature_module = protocol.load_module(
        'temperature module gen2',
        COLORS_DECK_SLOT
    )

    temperature_plate = temperature_module.load_labware(
        'opentrons_96_aluminumblock_generic_pcr_strip_200ul',
        'Cold Plate'
    )

    color_plate = temperature_plate

    agar_plate = protocol.load_labware(
        'htgaa_agar_plate',
        AGAR_DECK_SLOT,
        'Agar Plate'
    )

    center_location = agar_plate['A1'].top()

    pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

    # ------------------------------------------------------------------
    # Helper functions
    # ------------------------------------------------------------------

    def location_of_color(color_string):
        for well, color in well_colors.items():
            if color.lower() == color_string.lower():
                return color_plate[well]
        raise ValueError(f"No well found with color {color_string}")

    def dispense_and_detach(pipette, volume, location):
        above_location = location.move(types.Point(z=location.point.z + 5))
        pipette.move_to(above_location)
        pipette.dispense(volume, location)
        pipette.move_to(above_location)

     # ------------------------------------------------------------------
    # SWIRL PATTERN — BIG + FIXED COLOR PER BRANCH (P20 SAFE)
    # ------------------------------------------------------------------

    DROP_VOLUME = 3

    branches = 4
    points_per_branch = 24

    radius_start = 3
    radius_step = 1.6
    angle_step = math.pi/9

    branch_colors = ['Red', 'Green', 'Orange', 'Blue']

    for branch in range(branches):

        base_angle = branch * (2*math.pi/branches)
        color = branch_colors[branch]
        source = location_of_color(color)

        for i in range(points_per_branch):

            pipette_20ul.pick_up_tip()

            pipette_20ul.aspirate(DROP_VOLUME, source.bottom(1))

            angle = base_angle + i * angle_step
            radius = radius_start + i * radius_step

            x = radius * math.cos(angle)
            y = radius * math.sin(angle)

            loc = center_location.move(types.Point(x=x, y=y, z=0))
            dispense_and_detach(pipette_20ul, DROP_VOLUME, loc)

            pipette_20ul.drop_tip()

for enzyme_concentration in concentrations:
    add_samples()
    incubate()
    measure_absorbance()