run_gui

2. run_gui#

mbo_utilities.run_gui() is a convenience function for viewing common data formats used in processing MBO datasets, usable from the terminal, jupyter-lab or a callable from a python script.

  • raw scanimage tiffs

  • any ‘[t(z)xy]’ tiff, with or without the z or t dimensions

  • any numpy array

  • suite2p binary file (WIP, less tested)

Please ask a project maintainer to add a filetype or datatype to this list.

This takes advantage of fastplotlib to open a viewer in qt or jupyter, depending on the environment.

2.1. Jupyter / IPython#

Returns a fastplotlib.ImageWidget:

from mbo_utilities.graphics import run_gui

# load directly from a ScanImage folder
iw = run_gui("path/to/scanimage/folder")

# or from preprocessed ScanMultiROIReordered object
from mbo_utilities.file_io import ScanMultiROIReordered
data = ScanMultiROIReordered(...)
iw = run_gui(data)

If no input is given and Qt is available, the widget will attempt to open a file dialog. This is helpful when called from the command line:

(venv) User ~/projects/AABBCC/
$ run_gui
No data provided.
Rendering qt widget

With a a native file dialog, now you can open a folder or filetype described above.

2.2. Python script (non-Jupyter)#

from mbo_utilities.graphics import run_gui

# Will launch native Qt viewer window
run_gui("path/to/data")

If run from a script without data_in, and Qt is installed, a file dialog will prompt for input.

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