[BioCam]

The Problem

A simulated v1 CLARIOstar sets up, moves its drawer, controls its temperature and reads absorbance, but has no fluorescence or luminescence (clariostar.fluorescence and clariostar.luminescence are None): a protocol that reads fluorescence or luminescence cannot be run, tested or demonstrated without the device. And nothing checks such a protocol's reads before hardware: a fluorescence channel, gain or focal height the device would refuse only shows up on the device.

PR Content

• CLARIOstarPlus(simulation=True) reads fluorescence (one or several fluorescence channels, from the top or the bottom optic, in flying mode, with enhanced dynamic range, as a matrix scan) and luminescence. Every read is checked and encoded exactly as on the device (the same argument checks and the same RUN parameters), and nothing is sent.
• Each measured well reads random counts within the detector's range, or the counts of an earlier result given as simulated_data (from the device or from simulation), so a protocol can be replayed with real data.
• A read's checks and RUN parameters are now one method of each feature (_get_run_parameters), which the simulator calls; the device's reads send the same bytes as before.
• Fluorescence spectra, filter detection and z-profiles raise NotImplementedError in simulation for now.

from pylabrobot.bmg_labtech.clariostar import CLARIOstarPlus
from pylabrobot.lib.fluorescence import FluorescenceChannel
from pylabrobot.resources import cor_96_wellplate_360uL_Fb

clariostar = CLARIOstarPlus(simulation=True)
await clariostar.setup()
plate = cor_96_wellplate_360uL_Fb("plate")
await clariostar.drawer.open()
clariostar.plate_holder.assign_child_resource(plate)
await clariostar.drawer.close()

fitc = FluorescenceChannel(
  excitation_wavelength=485,
  excitation_bandwidth=15,
  emission_wavelength=528,
  emission_bandwidth=20,
)
# random counts in column 1, every argument checked as on the device
result = await clariostar.fluorescence.measure(fitc, gain=1000, wells=plate.get_items("A1:H1"))
# the same wells again, replayed from the earlier result
again = await clariostar.fluorescence.measure(
  fitc, gain=1000, wells=plate.get_items("A1:H1"), simulated_data=[result]
)

# luminescence is simulated the same way, here in two wells
glow = await clariostar.luminescence.measure(
  emission_wavelength=580, emission_bandwidth=80, wells=[plate.get_well("A1"), plate.get_well("H12")]
)

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