"30Green-TX2":"Vph1-mRUBY2",
"30Violet-SAPPHIRE":"Tom70-TSapphire",
"30Violet-DAPI":"Psr1-mTagBFP2"}
##########################################################
### Stage Positions ###
##########################################################
## Provide a MManager .pos file path or a list of
## stage_positions.StagePosition objects
positions_file = r"D:\PoistionLists\20161116_PosList.pos"
log_file_path = r"D:\MMLogs"
positions = stage_positions.positions_list_from_json(positions_file)
afc_override = None
if afc_override is not None:
for position in positions:
position.afc = 10646.9700
##########################################################
### Saving settings ###
##########################################################
## File name prefix
file_name_prefix = "20161116_4ColorYeast"
log_file_name = "20161116_4ColorYeast.log"
## Where to save the data?
## DO NOT set this to the C: drive. IT WILL FILL UP.
def __init__(self,
verbose=False,
positions_path="",
channels={},
z_params={},
save_dir="",
n_timepoints=1,
starting_t=0,
frequency=300,
file_name_prefix="MDA",
backup_save_path="",
experiment_metadata={},
stage_position_list=[],
afc_on_during_move=True,
scope=None,
file_log=True,
delay_after_move = .1,
restarts_allowed = 2,
end_location_settings=[],
scope_name = "",
path_to_config = None,
path_to_micromanager = None,
log_file_path = None,
synchro_devices = [],
state_dump_path = None
):
"""Initilization of Timelapse MDA object.
"""
self.state_dump_path = state_dump_path
self.scope_name = scope_name
self.mm_config = path_to_config
self.mm_path = path_to_micromanager
self.mm_log_path = log_file_path
self.scope = scope
self.verbose = verbose
self.restarts_allowed = restarts_allowed
self.restarts_used = 0
self.force_focus = False
if file_log:
self.file_log = []
if positions_path: ## if a path to a position list file was provided
try:
self.positions = stage_positions.positions_list_from_json(positions_path)
except:
print "Could not load pos list from %s" % positions_path
raise ValueError('Could not load your position list!')
elif stage_position_list:
print "Using stage_positions_provided"
self.positions = {i.LABEL:i for i in stage_position_list}
self.pos_order = sorted(self.positions.keys(), key= lambda x: int(x[3:]))
self.channels = channels
self.z_params = z_params
self.save_dir = save_dir
self.path_set_up = False
self.n_timepoints=n_timepoints
self.starting_t=starting_t
self.frequency=frequency
self.file_name_prefix=file_name_prefix
self.backup_save_path=backup_save_path
self.experiment_metadata=experiment_metadata
self.progress={}
self.errors={}
self.last_attempted_t = 0
self.afc_on_during_move = afc_on_during_move
self.delay_after_move = delay_after_move
self.end_location_settings = end_location_settings
self.synchronized_devices = synchro_devices
self.start_times = {}
