Submodule: file_

save_file

flika.process.file_.save_file(filename=None)

Save the image in the currentWindow to a .tif file.

Parameters:filename (str) – The image or movie will be saved as ‘filename’.tif.

save_points

flika.process.file_.save_points(filename=None)

Saves the points in the current window to a text file

Parameters:filename (str) – Address to save the points to, with .txt

save_movie

flika.process.file_.save_movie(rate, filename)

Saves the currentWindow video as a .mp4 movie by joining .jpg frames together

Parameters:
  • rate (int) – framerate
  • filename (str) – Address to save the movie to, with .mp4

Notes

Once you’ve exported all of the frames you wanted, open a command line and run the following: ffmpeg -r 100 -i %03d.jpg output.mp4 -r: framerate -i: input files. %03d: The files have to be numbered 001.jpg, 002.jpg… etc.

open_image_sequence

flika.process.file_.open_image_sequence(filename=None, from_gui=False)

open_image_sequencefilename(filename=None) Opens an image sequence (.tif, .png) into a newWindow.

Parameters:filename (str) – Address of the first of a series of files that will be stitched together into a movie. If no filename is provided, the last opened file is used.
Returns:newWindow

open_file

flika.process.file_.open_file(filename=None)

Opens an image or movie file (.tif, .stk, .nd2) into a newWindow.

Parameters:filename (str) – Address of file to open. If no filename is provided, the last opened file is used.
Returns:newWindow

open_points

flika.process.file_.open_points(filename=None)

Opens a specified text file and displays the points from that file into the currentWindow

Parameters:filename (str) – Address of file to open. If no filename is provided, the last opened file is used.

Note

Any existing points on a currentWindow will persist when another points file is opened and displayed

get_permutation_tuple

flika.process.file_.get_permutation_tuple(src, dst)

get_permtation_tuple(src, dst)

Parameters:
  • src (list) – The original ordering of the axes in the tiff.
  • dst (list) – The desired ordering of the axes in the tiff.
Returns:

The required permutation so the axes are ordered as desired.
Return type:

result (tuple)

close

flika.process.file_.close(window=None)

Will close a window or a set of windows.

Parameters:
  • 'all' (str) – closes all windows
  • windows (list) – closes each window in the list
  • Window – closes individual window
  • (None) – closes current window