navigate.model.features.restful_features.IlastikSegmentation

class navigate.model.features.restful_features.IlastikSegmentation(model, microscope_name='Nanoscale', zoom_value='N/A')

Bases: object

Ilastik segmentation class.

Uses Ilastik REST API to perform segmentation in a separate process.

__init__(model, microscope_name='Nanoscale', zoom_value='N/A')

Initialize Ilastik segmentation class.

Parameters:

model (Model) – Model object

Methods

__init__(model[, microscope_name, zoom_value])	Initialize Ilastik segmentation class.
data_func(frame_ids)	Perform Ilastik segmentation.
init_func(*args)	Initialize Ilastik segmentation.
mark_position(mask)	Mark position based on the segmentation mask.
update_setting()	Update Ilastik segmentation settings.

Attributes

model	Model object
service_url	url of the service
project_file	project file for Ilastik segmentation
resolution	resolution of the current microscope
zoom	zoom of the current microscope
pieces_num	number of pieces
pieces_size	size of pieces
high_res_microscope_name	high resolution microscope name
high_res_zoom_value	zoom value
config_table	configuration table

data_func(frame_ids)

Perform Ilastik segmentation.

Parameters:

frame_ids (list) – list of frame ids

init_func(*args)

Initialize Ilastik segmentation.

Parameters:

args (list) – list of arguments

mark_position(mask)

Mark position based on the segmentation mask.

Parameters:

mask (numpy.ndarray) – segmentation mask

update_setting()

Update Ilastik segmentation settings.

config_table

configuration table

Type:

dict

high_res_microscope_name

high resolution microscope name

Type:

str

high_res_zoom_value

zoom value

Type:

str

model

Model object

Type:

navigate.model.Model

pieces_num

number of pieces

Type:

int

pieces_size

size of pieces

Type:

int

project_file

project file for Ilastik segmentation

Type:

str

resolution

resolution of the current microscope

Type:

str

service_url

url of the service

Type:

str

zoom

zoom of the current microscope

Type:

str