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Make sure gripper is open and blue washer working plate is out for sm…
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…all protocols, fixes #2
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@danr
danr committed Feb 29, 2024
1 parent 009abb7 commit fee45cf
Showing 1 changed file with 94 additions and 86 deletions.
180 changes: 94 additions & 86 deletions cellpainter/cellpainter/small_protocols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ def incu_load(args: SmallProtocolArgs):
).add(Metadata(plate_id=p.id, stage=f'plate from A{pos} to {p.incu_loc}'))
]
program = Seq(*[
RobotarmCmd('ur gripper init and check'),
RobotarmCmd(f'B-neu-to-A-neu'),
*cmds,
RobotarmCmd(f'A-neu-to-B-neu'),
Expand Down Expand Up @@ -170,11 +171,13 @@ def test_circuit(args: SmallProtocolArgs):
program = cell_paint_program([1], protocol_config=protocol_config)
cmds = program.command
cmds = Seq(
BlueCmd(action='get_working_plate', protocol_path=None).fork() if protocol_config.use_blue else Idle(),
RobotarmCmd('ur gripper init and check'),
WaitForResource('blue') if protocol_config.use_blue else Idle(),
*[
cmd.add(metadata)
for cmd, metadata in cmds.collect(flatten_sections=True)
if isinstance(cmd, RobotarmCmd)
# if metadata.step not in {'Triton', 'Stains'}
],
*RobotarmCmds(plate.out_get),
*RobotarmCmds('B21-to-incu'),
Expand Down Expand Up @@ -206,9 +209,12 @@ def test_circuit_with_incubator(args: SmallProtocolArgs):
program = cell_paint_program([num_plates], protocol_config=protocol_config)
cmds = program.command
cmds = Seq(
BlueCmd(action='get_working_plate', protocol_path=None).fork() if protocol_config.use_blue else Idle(),
RobotarmCmd('ur gripper init and check'),
WaitForResource('blue') if protocol_config.use_blue else Idle(),
*[
cmd.add(metadata)
for cmd, metadata in cmds.collect()
for cmd, metadata in cmds.collect(flatten_sections=True)
if any([
isinstance(cmd, RobotarmCmd),
isinstance(cmd, Fork) and cmd.resource == 'incu',
Expand Down Expand Up @@ -1139,90 +1145,92 @@ def nikon_acquire_from_fridge(args: SmallProtocolArgs) -> Program:
# )
# )

# # # @pf_protocols.append
# def nikon_from_fridge(args: SmallProtocolArgs) -> Program:
# '''
# Images plates in the fridge. Params are: job names (comma-separated), project, RT_time_secs, plate1_barcode, plate1_name, plate2_barcode, plate2_name,..., plateN_barcode, plateN_name
# '''
# cmds: list[Command] = []
# if len(args.params) < 5:
# return Program(Seq())
# job_names_csv, project, RT_time_secs_str, *barcode_and_plates = args.params
# job_names = job_names_csv.split(',')
# barcodes = barcode_and_plates[0::2]
# plates = barcode_and_plates[1::2]
# contents = args.fridge_contents
# if contents is not None:
# for barcode in barcodes:
# if sum(
# 1
# for _loc, slot in contents.items()
# if slot['project'] == project
# if slot['plate'] == barcode
# ) != 1:
# raise ValueError(f'Could not find {barcode=} from {project=} in fridge!')
# RT_time_secs = float(RT_time_secs_str)
# chunks: dict[tuple[str, int], list[Command]] = {}
# for i, (barcode, plate) in enumerate(zip(barcodes, plates, strict=True), start=1):
# chunks['fridge -> H11', i] = [
# # get from fridge
# Checkpoint(f'Delay eject {i}'),
# WaitForCheckpoint(f'Delay eject {i}', assume='nothing') + f'slack {i}',
# # Duration(f'Delay eject {i}', Min(2)),
# FridgeEject(plate=barcode, project=project, check_barcode=False).fork_and_wait(),
# Checkpoint(f'RT {i}'),
# PFCmd(f'fridge-to-H11'),
# PFCmd(f'H11-to-H11'),
# ]
# chunks['H11 -> nikon', i] = [
# WaitForCheckpoint(f'RT {i}', plus_secs=RT_time_secs, assume='nothing'),
# Duration(f'RT {i}', Min(3)),
# PFCmd(f'H11-to-H11'),
# NikonStageCmd('goto_loading').fork_and_wait(),
# NikonStageCmd('init_laser').fork_and_wait(),
# PFCmd(f'H11-to-nikon'),
# Seq(
# NikonStageCmd('leave_loading'),
# *[
# NikonAcquire(job_name=job_name, project=project, plate=plate).add(Metadata(plate_id=str(i)))
# for job_name in job_names
# ],
# ).fork(),
# ]
# chunks['nikon -> fridge', i] = [
# WaitForResource('nikon'),
# NikonStageCmd('goto_loading').fork_and_wait(),
# PFCmd(f'nikon-to-H11'),
# NikonStageCmd('leave_loading').fork(),
# BarcodeClear(),
# PFCmd(f'H11-to-fridge'),
# FridgeInsert(
# project,
# # expected_barcode=barcode
# assume_barcode=barcode, # for RMS-SPECS
# ).fork_and_wait(),
# WaitForResource('nikon'),
# ]
# ilv = Interleaving.init('''
# fridge -> H11
# H11 -> nikon
# fridge -> H11
# nikon -> fridge
# H11 -> nikon
# fridge -> H11
# nikon -> fridge
# H11 -> nikon
# nikon -> fridge
# ''')
# for i, substep in ilv.inst(list([i for i, _ in enumerate(plates, start=1)])):
# cmds += [Seq(*chunks[substep, i]).add(Metadata(section=f'{1 + (i-1)//10} {0}'))]
# cmds = [
# Checkpoint('start'),
# *cmds,
# Duration('start', Min(2)),
# ]
# cmd = Seq(*cmds)
# return Program(cmd)
# # @pf_protocols.append
"""
def nikon_from_fridge(args: SmallProtocolArgs) -> Program:
'''
Images plates in the fridge. Params are: job names (comma-separated), project, RT_time_secs, plate1_barcode, plate1_name, plate2_barcode, plate2_name,..., plateN_barcode, plateN_name
'''
cmds: list[Command] = []
if len(args.params) < 5:
return Program(Seq())
job_names_csv, project, RT_time_secs_str, *barcode_and_plates = args.params
job_names = job_names_csv.split(',')
barcodes = barcode_and_plates[0::2]
plates = barcode_and_plates[1::2]
contents = args.fridge_contents
if contents is not None:
for barcode in barcodes:
if sum(
1
for _loc, slot in contents.items()
if slot['project'] == project
if slot['plate'] == barcode
) != 1:
raise ValueError(f'Could not find {barcode=} from {project=} in fridge!')
RT_time_secs = float(RT_time_secs_str)
chunks: dict[tuple[str, int], list[Command]] = {}
for i, (barcode, plate) in enumerate(zip(barcodes, plates, strict=True), start=1):
chunks['fridge -> H11', i] = [
# get from fridge
Checkpoint(f'Delay eject {i}'),
WaitForCheckpoint(f'Delay eject {i}', assume='nothing') + f'slack {i}',
# Duration(f'Delay eject {i}', Min(2)),
FridgeEject(plate=barcode, project=project, check_barcode=False).fork_and_wait(),
Checkpoint(f'RT {i}'),
PFCmd(f'fridge-to-H11'),
PFCmd(f'H11-to-H11'),
]
chunks['H11 -> nikon', i] = [
WaitForCheckpoint(f'RT {i}', plus_secs=RT_time_secs, assume='nothing'),
Duration(f'RT {i}', Min(3)),
PFCmd(f'H11-to-H11'),
NikonStageCmd('goto_loading').fork_and_wait(),
NikonStageCmd('init_laser').fork_and_wait(),
PFCmd(f'H11-to-nikon'),
Seq(
NikonStageCmd('leave_loading'),
*[
NikonAcquire(job_name=job_name, project=project, plate=plate).add(Metadata(plate_id=str(i)))
for job_name in job_names
],
).fork(),
]
chunks['nikon -> fridge', i] = [
WaitForResource('nikon'),
NikonStageCmd('goto_loading').fork_and_wait(),
PFCmd(f'nikon-to-H11'),
NikonStageCmd('leave_loading').fork(),
BarcodeClear(),
PFCmd(f'H11-to-fridge'),
FridgeInsert(
project,
# expected_barcode=barcode
assume_barcode=barcode, # for RMS-SPECS
).fork_and_wait(),
WaitForResource('nikon'),
]
ilv = Interleaving.init('''
fridge -> H11
H11 -> nikon
fridge -> H11
nikon -> fridge
H11 -> nikon
fridge -> H11
nikon -> fridge
H11 -> nikon
nikon -> fridge
''')
for i, substep in ilv.inst(list([i for i, _ in enumerate(plates, start=1)])):
cmds += [Seq(*chunks[substep, i]).add(Metadata(section=f'{1 + (i-1)//10} {0}'))]
cmds = [
Checkpoint('start'),
*cmds,
Duration('start', Min(2)),
]
cmd = Seq(*cmds)
return Program(cmd)
"""

def cmds_to_program(cmds: list[Command]) -> Program:
return Program(Seq(*cmds))
Expand Down

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