"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 = {}