aliby.pipeline.Pipeline

class Pipeline(parameters, store=None)

Bases: ProcessABC

A chained set of Pipeline elements connected through pipes. Tiling, Segmentation,Extraction and Postprocessing should use their own default parameters. These can be overriden passing the key:value of parameters to override to a PipelineParameters class

Attributes

parameters

Methods

from_existing_h5(fpath)	Constructor to process an existing hdf5 file.
from_folder(dir_path)	Constructor to re-process all files in a given folder.
legacy_get_last_tp(step)	Get last time-point in different ways depending on which step we are using
run()	Config holds the general information, use in main Steps: all holds general tasks steps: strain_name holds task for a given strain

check_earlystop
create_pipeline
from_yaml
setLogger

Attributes

parameters

Methods

from_existing_h5(fpath)	Constructor to process an existing hdf5 file.
from_folder(dir_path)	Constructor to re-process all files in a given folder.
legacy_get_last_tp(step)	Get last time-point in different ways depending on which step we are using
run()	Config holds the general information, use in main Steps: all holds general tasks steps: strain_name holds task for a given strain

check_earlystop
create_pipeline
from_yaml
setLogger

__init__(parameters, store=None)

Methods

__init__(parameters[, store])
check_earlystop(filename, es_parameters, ...)
create_pipeline(image_id[, index])
from_existing_h5(fpath)	Constructor to process an existing hdf5 file.
from_folder(dir_path)	Constructor to re-process all files in a given folder.
from_yaml(fpath)
legacy_get_last_tp(step)	Get last time-point in different ways depending on which step we are using
run()	Config holds the general information, use in main Steps: all holds general tasks steps: strain_name holds task for a given strain
setLogger(folder[, file_level, stream_level])

Attributes

iterative_steps
parameters
step_sequence
writer_groups
writers

classmethod from_existing_h5(fpath)

Constructor to process an existing hdf5 file. Notice that it forces a single file, not suitable for multiprocessing of certain positions.

It i s also used as a base for a folder-wide reprocessing.

classmethod from_folder(dir_path)

Constructor to re-process all files in a given folder.

Assumes all files share the same parameters (even if they don’t share the same channel set).

Parameters

dir_path : str or Pathlib indicating the folder containing the files to process

static legacy_get_last_tp(step)

Get last time-point in different ways depending on which step we are using

To support segmentation in aliby < v0.24 TODO Deprecate and replace with State method

Return type

Callable

run()

Config holds the general information, use in main Steps: all holds general tasks steps: strain_name holds task for a given strain