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])
`_handle_cropping`(item)	Crop the stack based on tuple of slices
`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.
`shape`
`start`	Starting time stamp of the stack.
`stop`	Final time stamp of the stack.
`timestamps`	Deprecated since version 0.11.1.