GUI

[ChristianNitzsche]

No description provided.

[mcquin]

Hi @ChristianNitzsche ! Can you please update your branch against this master? It look like stitching/__main__.py has merge conflicts.

[mcquin]

Please reformat this file to use 4-spaces for indentation.

[mcquin]

Please refactor this function to reduce the number of nested if/else and try/except blocks. For example,

if self.reader == 0:
    tkMessageBox.showinfo("Error", "Please choose a .cif file.")
    return

if type(self.dirPath) == tuple or not os.path.isdir(self.dirPath):
    tkMessageBox.showinfo("Error", "Please choose an output directory.")
    return

...

[mcquin]

Generally, if not True is discouraged. Try this insead:

if self.reader == 0:
    tkMessageBox.showinfo("Error", "Please choose a .cif file.")
    return

flag = False

...

[mcquin]

@ChristianNitzsche This is super! I'm very excited about your contribution! We should think about restructuring the application, as stitching/__main__.py is functionally overloaded. How do you feel about the following structure:

stitching/stitching.py: does the work of reading CIF files, tiling images, and saving TIFs. Purely functional, no GUI involvement. Also validates parameters and raises exceptions on invalid input.

stitching/gui.py: handles the GUI interactions such as prompting for input/output directories and displaying montages.

stitching/__main__.py: process command line options (if any) and decides whether or not to start the GUI or run headless. This could be implicit (e.g., start the GUI if no CLI options are provided, otherwise run headless) or explicit (e.g., require -h/--headless flag to run without GUI). Would also be responsible for starting/stopping the JVM.

It might look something like:

# stitching/__main__.py
import stitching.gui
import stitching.stitching

@click.command
# click options (headless, input/output/etc), headless defaults to False
def main(headless, image, output, etc):
    try:
        # start javabridge
        if headless:
            # create a montage from CLI parameters
        else:
            # start the GUI
    finally:
        # stop javabridge

if name == '__main__':
    main()

Does that sound reasonable?

@minh-doan Can you please verify installation and functionality of this branch?