agora.io.reader.StateReader¶
- class StateReader(file)[source]¶
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
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