navigate.model.features.volume_search.VolumeSearch

class navigate.model.features.volume_search.VolumeSearch(model, target_resolution='Nanoscale', target_zoom='N/A', flipx=False, flipy=False, overlap=0.1, debug=False)

Bases: object

VolumeSearch.

Find the outer boundary of a tissue, moving the stage through z. Assumes there is no tissue out-of-frame in the x,y-directions.

Construct a list of stage positions that will tile the entire tissue boundary in x,y,z at target_resolution, target_zoom. Current resolution and zoom is self.model.active_microscope_name and self.model.configuration[“experiment”][“MicroscopeState”][“zoom”].

__init__(model, target_resolution='Nanoscale', target_zoom='N/A', flipx=False, flipy=False, overlap=0.1, debug=False)

Initialize VolumeSearch

Parameters:

• model (navigate.model.model.Model) – Navigate Model

• target_resolution (str) – Name of microscope to use for tiled imaging of tissue

• target_zoom (str) – Resolution of microscope (target_resolution) to use for tiled imaging of tissue

• flipx (bool) – Flip the direction in which new tiles are added.

• flipy (bool) – Flip the direction in which new tiles are added.

• overlap (float) – Value between 0 and 1 indicating percent overlap of tiles.

• debug (bool) – If True, save debug images to disk.

Methods

__init__(model[, target_resolution, ...])	Initialize VolumeSearch
cleanup()	Cleanup function
data_func(frame_ids)	Data function.
end_data_func()	End data function.
init_data_func()	Initialize data function
pre_signal_func()	Initialize signal function
signal_end()	Signal end function.
signal_func()	Signal function.
signal_response_func(*args)	Signal response function.

Attributes

model	Navigate Model
target_resolution	Name of microscope to use for tiled imaging of tissue
target_zoom	Resolution of microscope (target_resolution) to use for tiled imaging
z_steps	Number of z-steps to take
z_step_size	Size of z-step
z_pos	Current z-position
f_step_size	Size of focus step
f_pos	Current focus position
f_offset	Current z-index
curr_z_index	Current z-index
sinx	1 if flipx is False, -1 if flipx is True
siny	1 if flipy is False, -1 if flipy is True
overlap	Percent overlap of tiles
has_tissue_queue	Queue for communicating whether tissue was found
direction	1 if moving up, -1 if moving down
has_tissue	True if tissue was found
first_boundary	Boundary of tissue
pre_boundary	Boundary of tissue
end_flag	True if the search is complete
config_table	Feature configuration
debug	True if debug mode is enabled
volumes_selected	Debug image

cleanup()

Cleanup function

data_func(frame_ids)

Data function.

Find the tissue boundary in the current frame.

Parameters:

frame_ids (list) – List of frame ids to process.

Returns:

True if the data function should be called again.

Return type:

bool

end_data_func()

End data function.

Map the tissue boundary to stage positions.

Returns:

True if the search is complete.

Return type:

bool

init_data_func()

Initialize data function

pre_signal_func()

Initialize signal function

signal_end()

Signal end function.

Check if the search is complete.

Returns:

True if the search is complete.

Return type:

bool

signal_func()

Signal function.

Move the stage to the next z-position.

Returns:

True if the signal function should be called again.

Return type:

bool

signal_response_func(*args)

Signal response function.

Check if tissue was found. If not, move the stage to the next z-position.

Returns:

True if the signal function should be called again.

Return type:

bool

config_table

Feature configuration

Type:

dict

curr_z_index

Current z-index

Type:

int

debug

True if debug mode is enabled

Type:

bool

direction

1 if moving up, -1 if moving down

Type:

int

end_flag

True if the search is complete

Type:

bool

f_offset

Current z-index

Type:

int

f_pos

Current focus position

Type:

float

f_step_size

Size of focus step

Type:

float

first_boundary

Boundary of tissue

Type:

dict

has_tissue

True if tissue was found

Type:

bool

has_tissue_queue

Queue for communicating whether tissue was found

Type:

Queue

model

Navigate Model

Type:

navigate.model.model.Model

overlap

Percent overlap of tiles

Type:

float

pre_boundary

Boundary of tissue

Type:

dict

sinx

1 if flipx is False, -1 if flipx is True

Type:

int

siny

1 if flipy is False, -1 if flipy is True

Type:

int

target_resolution

Name of microscope to use for tiled imaging of tissue

Type:

str

target_zoom

Resolution of microscope (target_resolution) to use for tiled imaging

Type:

str

volumes_selected

Debug image

Type:

np.ndarray

z_pos

Current z-position

Type:

float

z_step_size

Size of z-step

Type:

float

z_steps

Number of z-steps to take

Type:

int