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Load & Save Projects

In cylindra, a project is managed by a CylindraProject instance.

Save the Current Session as a Project

API: save_project

GUI: File > Save Project or Ctrl+K → Ctrl+S

If you want to save the current session as a project, you can use this method to save the current state.

  • project.json ... The main project file, which has the description of this project.
  • default_spline_config.json ... The default SplineConfig. See here for the details.
  • globalprops.csv ... The global properties of the splines.
  • localprops.csv ... The local properties of the splines.
  • CSV or parquet files ... Coordinates and features of molecules.
  • script.py ... An executable Python script to reproduce the session.
  • spline-*.json ... The spline objects in JSON format (not human readable, should always be read by from_json) method.

The project can be a directory, a zip file or a tar file.

Load Project

API: load_project

GUI: File > Load Project or Ctrl+K → Ctrl+P

Saved projects can be loaded to the GUI. Loading a project does not rerun the script. It uses the saved files to reproduce the session.

Load Project

Stash the Session

GUI: File > Stash

You may want to temporarily save the session for later use. In cylindra, some "stash" operations are available. Stashed sessions are cached in the user directory, and can be readily loaded from the GUI.

Note

If you already know the git stash command, you should be familiar with this.

Reuse the Existing Projects

API: load_project_for_reanalysis

GUI: Analysis > Load Project for Reanalysis

Drawing splines is a most time-consuming step. cylindra is implemented with a method that automatically filter the script in a project file and only run until it reaches any non-manual line. For example, if you have a project file that contains a script.py file with a main function like this:

def main(ui):
    ui.open_image(path='path/to/image.tif', ...)
    ui.register_path(coords=[[19, 190, 29], [19, 100, 50]], ...)
    ui.register_path(coords=[[20, 100, 32], [20, 190.0, 63]], ...)
    ui.fit_splines(splines='all', ...)
    ui.refine_splines(splines='all', ...)

then, the filtered script will be:

def main(ui):
    ui.open_image(path='path/to/image.tif', ...)
    ui.register_path(coords=[[19, 190, 29], [19, 100, 50]], ...)
    ui.register_path(coords=[[20, 100, 32], [20, 190.0, 63]], ...)