Week 3 HW: Lab Automation

import subprocess, sys
subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy", "pandas"])
import numpy as np
import pandas as pd

from opentrons import types

metadata = {    # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata
    'author': 'Dominik Einfalt',
    'protocolName': 'HTGAA Opentrons Lab',
    'description': 'PetriPlant - Image on petri dish',
    'source': 'HTGAA 2026 Opentrons Lab',
    'apiLevel': '2.20'
}

##############################################################################
###   Robot deck setup constants - don't change these
##############################################################################

TIP_RACK_DECK_SLOT = 9
COLORS_DECK_SLOT = 6
AGAR_DECK_SLOT = 5
PIPETTE_STARTING_TIP_WELL = 'B1'

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


def run(protocol):
  ##############################################################################
  ###   Load labware, modules and pipettes
  ##############################################################################

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

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

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

  # Temperature Module Plate
  temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul',
                                                      'Cold Plate')
  # Choose where to take the colors from
  color_plate = temperature_plate

  # Agar Plate
  agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')  ## TA MUST CALIBRATE EACH PLATE!
  # Get the top-center of the plate, make sure the plate was calibrated before running this
  center_location = agar_plate['A1'].top()

  pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

  ##############################################################################
  ###   Patterning
  ##############################################################################

  ###
  ### Helper functions for this lab
  ###

  # pass this e.g. 'Red' and get back a Location which can be passed to aspirate()
  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}")

  # For this lab, instead of calling pipette.dispense(1, loc) use this: dispense_and_detach(pipette, 1, loc)
  def dispense_and_detach(pipette, volume, location):
      """
      Move laterally 5mm above the plate (to avoid smearing a drop); then drop down to the plate,
      dispense, move back up 5mm to detach drop, and stay high to be ready for next lateral move.
      5mm because a 4uL drop is 2mm diameter; and a 2deg tilt in the agar pour is >3mm difference across a plate.
      """
      assert(isinstance(volume, (int, float)))
      above_location = location.move(types.Point(z=location.point.z + 5))  # 5mm above
      pipette.move_to(above_location)       # Go to 5mm above the dispensing location
      pipette.dispense(volume, location)    # Go straight downwards and dispense
      pipette.move_to(above_location)       # Go straight up to detach drop and stay high

  ###
  ### YOUR CODE HERE to create your design
  ###

   #Coordinates of my Design
  url = 'https://edit.htgaa.org/2026a-dominik-einfalt/webpages/raw/branch/main/content/homework/IMG/points_Petriplant.csv'
  world_coord = pd.read_csv(url)
  data = world_coord
  data.columns = ["x", "y"]


  x_value = data['x']
  y_value = data['y']

  #Change to location of green
  cell_well = color_plate['B1']


  # Aspirate
  pipette_20ul.pick_up_tip()

  for i in range(len(x_value)):
    if i%20 == 0:
      # pick up more every 20 uL, but only as much as we're going to need!
      pipette_20ul.aspirate(min(20, len(x_value)-i), cell_well)

    adjusted_location = center_location.move(types.Point(x_value[i], y_value[i]))
    pipette_20ul.dispense(1, adjusted_location)
    hover_location = adjusted_location.move(types.Point(z = 2))
    pipette_20ul.move_to(hover_location)

  pipette_20ul.drop_tip()

  # Don't forget to end with a drop_tip()

from opentrons import types
import math

metadata = {    # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata
    'author': '',
    'protocolName': '',
    'description': '',
    'source': 'HTGAA 2026 Opentrons Lab',
    'apiLevel': '2.20'
}

##############################################################################
###   Robot deck setup constants - don't change these
##############################################################################

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'
}


def run(protocol):
  ##############################################################################
  ###   Load labware, modules and pipettes
  ##############################################################################

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

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

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

  # Temperature Module Plate
  temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul',
                                                      'Cold Plate')
  # Choose where to take the colors from
  color_plate = temperature_plate

  # Agar Plate
  agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')  ## TA MUST CALIBRATE EACH PLATE!
  # Get the top-center of the plate, make sure the plate was calibrated before running this
  center_location = agar_plate['A1'].top()

  pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

  ##############################################################################
  ###   Patterning
  ##############################################################################

  ###
  ### Helper functions for this lab
  ###

  # pass this e.g. 'Red' and get back a Location which can be passed to aspirate()
  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}")

  # For this lab, instead of calling pipette.dispense(1, loc) use this: dispense_and_detach(pipette, 1, loc)
  def dispense_and_detach(pipette, volume, location):
      """
      Move laterally 5mm above the plate (to avoid smearing a drop); then drop down to the plate,
      dispense, move back up 5mm to detach drop, and stay high to be ready for next lateral move.
      5mm because a 4uL drop is 2mm diameter; and a 2deg tilt in the agar pour is >3mm difference across a plate.
      """
      assert(isinstance(volume, (int, float)))
      above_location = location.move(types.Point(z=location.point.z + 5))  # 5mm above
      pipette.move_to(above_location)       # Go to 5mm above the dispensing location
      pipette.dispense(volume, location)    # Go straight downwards and dispense
      pipette.move_to(above_location)       # Go straight up to detach drop and stay high

  ###
  ### YOUR CODE HERE to create your design
  ###


  startY = 34
  # halfStartY = int(startY/2)
  halfStartY = 17

  cursor = center_location.move(types.Point(x=-halfStartY, y = startY))

  triangle_radius = 15  # mm from center to each corner

# Equilateral triangle centered at (0,0)
  corners = [
    (0, triangle_radius),  # top corner
    (-triangle_radius * math.sin(math.pi/3),
     -triangle_radius / 2),  # bottom left
    (triangle_radius * math.sin(math.pi/3),
     -triangle_radius / 2)   # bottom right
    ]

  rows = 10
  spacing = 3.5

  points = []

  # Calculate offset to center the y-coordinates of the generated points
  total_height = (rows - 1) * spacing
  y_offset = total_height / 2

  for row in range(rows):
    for col in range(row + 1):
        x = (col - row/2) * spacing
        y = row * spacing - y_offset  # Adjust y to center the triangle vertically

        points.append((x, y))

  def barycentric_weights(px, py, c1, c2, c3):
    x1,y1 = c1
    x2,y2 = c2
    x3,y3 = c3

    det = (y2 - y3)*(x1 - x3) + (x3 - x2)*(y1 - y3)

    w1 = ((y2 - y3)*(px - x3) + (x3 - x2)*(py - y3)) / det
    w2 = ((y3 - y1)*(px - x3) + (x1 - x3)*(py - y3)) / det
    w3 = 1 - w1 - w2

    return w1, w2, w3

  total_volume = 3  # µL per dot

  red_well = color_plate['A1']
  green_well = color_plate['B1']
  orange_well = color_plate['C1']

  # Max volume the pipette can hold in one go
  pipette_max_vol = pipette_20ul.max_volume # This is 20uL for p20_single_gen2

  # Helper function to perform aspirate/multi-dispense/refill
  def perform_multi_dispense_for_color(pipette, color_source_well, all_dispense_tasks):
    if not all_dispense_tasks:
        return # Nothing to dispense

    pipette.pick_up_tip()
    current_volume_in_pipette = 0

    for i, (vol_to_dispense, loc_to_dispense) in enumerate(all_dispense_tasks):
      if current_volume_in_pipette < vol_to_dispense:
        # Calculate how much volume is still needed for the *remaining* dispenses
        remaining_needed = sum(task[0] for task in all_dispense_tasks[i:])

        # Calculate space available in pipette
        space_in_pipette = pipette_max_vol - current_volume_in_pipette

        # Aspirate the minimum of space available, and what is actually needed for remaining tasks
        amount_to_aspirate = min(space_in_pipette, remaining_needed)

        # Make sure we don't try to aspirate 0 or negative volume
        if amount_to_aspirate > 0:
          pipette.aspirate(amount_to_aspirate, color_source_well)
          current_volume_in_pipette += amount_to_aspirate

      dispense_and_detach(pipette, vol_to_dispense, loc_to_dispense)
      current_volume_in_pipette -= vol_to_dispense

    pipette.drop_tip()


  # =========================
  # RED PASS
  # =========================
  red_dispense_tasks = []
  for (x, y) in points:
    w1, w2, w3 = barycentric_weights(x, y, corners[0], corners[1], corners[2])
    red_vol = total_volume * w1
    if red_vol > 0:
      dispense_location = center_location.move(
          types.Point(x=x, y=y)
      )
      red_dispense_tasks.append((red_vol, dispense_location))

  perform_multi_dispense_for_color(pipette_20ul, red_well, red_dispense_tasks)


  # =========================
  # GREEN PASS
  # =========================
  green_dispense_tasks = []
  for (x, y) in points:
    w1, w2, w3 = barycentric_weights(x, y, corners[0], corners[1], corners[2])
    green_vol = total_volume * w2
    if green_vol > 0:
      dispense_location = center_location.move(
          types.Point(x=x, y=y)
      )
      green_dispense_tasks.append((green_vol, dispense_location))

  perform_multi_dispense_for_color(pipette_20ul, green_well, green_dispense_tasks)


  # =========================
  # ORANGE PASS
  # =========================
  orange_dispense_tasks = []
  for (x, y) in points:
    w1, w2, w3 = barycentric_weights(x, y, corners[0], corners[1], corners[2])
    orange_vol = total_volume * w3
    if orange_vol > 0:
      dispense_location = center_location.move(
          types.Point(x=x, y=y)
      )
      orange_dispense_tasks.append((orange_vol, dispense_location))

  perform_multi_dispense_for_color(pipette_20ul, orange_well, orange_dispense_tasks)