lumicks.pylake.correlated_stack.CorrelatedStack

class CorrelatedStack(image_name, align=True)

CorrelatedStack acquired with Bluelake. Bluelake can export stacks of images to various formats. These can be opened and correlated to timeline data using CorrelatedStack.

Parameters

image_namestr

Filename for the image stack. Typically a TIFF file recorded from a camera in Bluelake.

alignbool

If enabled, multi-channel images will be reconstructed from the image alignment metadata from Bluelake. The default value is True.

Examples

from lumicks import pylake

# Loading a stack.
stack = pylake.CorrelatedStack("example.tiff")

# Making a plot where force is correlated to images in the stack.
file = pylake.File("example.h5")
stack.plot_correlated(file.force1x)

# Determine the force trace averaged over frame 2...9.
file.force1x.downsampled_over(stack[2:10].frame_timestamp_ranges)

__init__(image_name, align=True)

Methods

__getitem__(item)	All indexing is in frames
_get_frame([frame])
crop_and_rotate([frame, channel, show_title])	Open a widget to interactively edit the image stack.
crop_by_pixels(x_min, x_max, y_min, y_max)	Crop the image stack by pixel values.
define_tether(point1, point2)	Returns a copy of the stack rotated such that the tether defined by point_1 and point_2 is horizontal.
export_tiff(file_name[, roi])	Export a video of a particular scan plot
from_data(data[, name, start_idx, stop_idx])	Deprecated since version 0.10.1.
from_dataset(data[, name, start_idx, stop_idx])	Construct CorrelatedStack from image stack object
get_image([channel])	Get image data for the full stack as an np.ndarray.
plot([frame, channel, show_title, axes, ...])	Plot image from image stack
plot_correlated(channel_slice[, frame, ...])	Downsample channel on a frame by frame basis and plot the results.
plot_tether([axes])	Plot a line at the tether position.

Attributes

frame_timestamp_ranges	List of time stamps.
num_frames	Number of frames in the stack.
raw	Raw frame data.
start	Starting time stamp of the stack.
stop	Final time stamp of the stack.
timestamps	Deprecated since version 0.11.1.