agora.io.reader.StateReader

class agora.io.reader.StateReader(file: str)

Bases: DynamicReader

Analogous to StateWriter:

Possible cases (and data shapes): - max_lbl (ntraps, 1) -> One int per trap. - tp_back, trap, cell_label -> One int per cell_label-timepoint - prev_feats -> A fixed number of floats per cell_label-timepoint (default is 9) - lifetime, p_was_bud, p_is_mother -> (nTotalCells, 2) A (Ncells, 2) matrix where the first column is the trap,

and its index for such trap (+1) is its cell label.

• ba_cum ->. (2^n, 2^n, None) 3d array where the lineage score is contained for all traps - traps in the 3rd dimension 3d array where the lineage score is contained for all traps - traps in the 3rd dimension.

  2^n >= ncells, it is kept in powers of two for efficiency.

Methods

format_bacum
format_tps
format_traps
get_formatted_states
read_all
read_raw
reconstruct_states

__init__(file: str)

Methods

__init__(file)
format_bacum()
format_tps()
format_traps()
get_formatted_states()
read_all()
read_raw(key, dtype)
reconstruct_states(data)

Attributes

data_types
datatypes
group