Experiment¶

This module implements the first core class: Experiment, and functions to parse containers, retrieve and build data.

Each experiment consists of multiple containers where data is stored under container folders. A container may correspond to a single field of view, to a subset thereof (e.g. a single channel in microfluidic experiments).

Such containers must meet two requirements:

Cell identifiers are unique within a container;
Lineage reconstruction is defined and performed within a single container.

This module stores classes and functions that allow to:

explore data structure (and metadata if provided)
keep track of every container where to look for data
extract data in a Container instance from text containers
build cells filiation, store time-lapse microscopy data, build trees

class tunacell.base.experiment.Experiment(path='.', filetype=None, filter_set=None, count_items=False)¶

General class that stores experiment details.

Creates an Experiment instance from reading a file, records path, filetype, reads metadata, stores the list of containers.

Parameters:	path (str) – path to experiment root file -- str {None, 'text', 'supersegger'} (filetype) – leave to None for automatic detection.

abspath¶

absolute path on disk of main directory for text containers

Type:	str

label¶

experiment label

Type:	str

filetype¶

one of the available file type (‘simu’ is not a filetype per se…)

Type:	str {‘text’, ‘supersegger’}

fset¶

filterset to be applied when parsing data

Type:	`FilterSet` instance

datatype¶

provides the datatype of raw data stored in each Cell instance .data This attribute is defined only for text filetype, when a descriptor file is associated to the experiment.

Type:	Numpy.dtype instance

metadata¶

experiment metadata

Type:	Metadata instance

containers¶

list of absolute paths to containers

Type:	list of pathlib.Path

period¶

time interval between two successive aquisitions (this should be defined in the experiment metadata)

Type:	float

iter_containers(self, read=True, build=True, prefilt=None,: extend_observables=False, report_NaNs=True, size=None, shuffle=False)

browse containers

analysis_path¶: Get analysis path (with appropriate filterset path)

count_items(independent=True, seed=None, read=True)¶

Parse data to count items: cells, colonies, lineages, containers

Parameters:	independent (bool {True, False}) – lineage decomposition parameter seed (int, or None) – lineage decomposition parameter read (bool {True, False}) – try to read it in analysis folder

fset: Get current FilterSet

get_container(label, read=True, build=True, prefilt=None, extend_observables=False, report_NaNs=True)¶

Open specified container from this experiment.

Parameters:	label (str) – name of the container file to be opened read (bool (default True)) – whether to read data and extract Cell instances list build (bool (default True)) – when read option is active, whether to build Colony instances extend_observables (bool (default False)) – whether to compute secondary observables from raw data report_NaNs (bool (default True)) – whether to report for NaNs found in data
Returns:	container
Return type:	Container instance
Raises:	ParsingExperimentError : when no container corresponds in this exp ParsingContainerError: when despite of existing container filename, – parsing of container failed and nothing is loaded

info()¶: Show informations about experiment

iter_cells(size=None, shuffle=False)¶

Iterate through valid cells.

Applies all filters defined in fset.

Parameters:	size (int (default None)) – limit the number of lineages to size. Works only in mode=’all’ shuffle (bool (default False)) – whether to shuffle the ordering of lineages when mode=’all’
Yields:	cell (`Cell` instance) – filtering removed outlier cells, containers, colonies, and lineages

iter_colonies(filter_for_colonies='from_fset', size=None, shuffle=False)¶

Iterate through valid colonies.

Parameters:	filter_for_colonies (FilterTree instance or str {'from_fset', 'none'}) – size (int (default None)) – limit the number of colonies to size. Works only in mode=’all’ shuffle (bool (default False)) – whether to shuffle the ordering of colonies when mode=’all’
Yields:	colony (`Colony` instance) – filtering removed outlier cells, containers, and colonies

iter_containers(read=True, build=True, filter_for_cells='from_fset', filter_for_containers='from_fset', apply_container_filter=True, extend_observables=False, report_NaNs=True, size=None, shuffle=False)¶

Iterator over containers.

Parameters:	size (int (default None)) – number of containers to be parsed read (bool (default True)) – whether to read data and extract Cell instances build (bool (default True), called only if read is True) – whether to build colonies filter_for_cells (FilterCell instance, or str {'from_fset', 'none'}) – filter applied to cells when data files are parsed filter_for_containers (FilterContainer instance or str {'from_fset', 'none'}) – filter applied to containers when data files are parsed extend_observables (bool (default False)) – whether to construct secondary observables from raw data report_NaNs (bool (default True)) – whether to report for NaNs found in data shuffle (bool (default False)) – when size is set to a number, whether to randomize ordering of upcoming containers
Returns:
Return type:	iterator iver Container instances of current Experiment instance.

iter_lineages(filter_for_lineages='from_fset', size=None, shuffle=False)¶

Iterate through valid lineages.

Parameters:	filter_for_lineages (FilterLineage instance or str {'from_fset', 'none'}) – filter lineages size (int (default None)) – limit the number of lineages to size. Works only in mode=’all’ shuffle (bool (default False)) – whether to shuffle the ordering of lineages when mode=’all’
Yields:	lineage (`Lineage` instance) – filtering removed outlier cells, containers, colonies, and lineages

period

Return the experimental level period

The experimental level period is defined as the smallest acquisition period over all containers.

raw_text_export(path='.', metadata_extension='.yml')¶

Export raw data as text containers in correct directory structure.

Parameters:	path (str) – path to experiment root directory metadata_extension (str (default '.yml')) – type of metadata file (now only yaml file works)

exception tunacell.base.experiment.FiletypeError¶

exception tunacell.base.experiment.ParsingExperimentError¶

tunacell.base.experiment.count_items(exp, independent_decomposition=True, seed=None)¶: Parse the experiment, with associated FilterSet, and count items