def cli(paths, mode, name_regex, pixel_size, dry_run, strict, name, mmap, lazy, no_show): """ PeepingTom command line interface. Opens files in napari and lands in an interactive ipython shell with peepingtom imported as `pt` and the initialised Peeper available as `p`. PATHS: any number of files or globs [default='./*'] \b MODE choices: - lone: each datablock in a separate volume - zip_by_type: one of each datablock type per volume - bunch: all datablocks in a single volume \b EXAMPLES: Open a .star file as particles: peep particles.star Open particles and images from a directory: peep /dir/with/star_and_mrc_files/ Match files such as MyProtein_10.star and MyProtein_001.mrc, and name the respective DataBlocks Protein_10 and Protein_001: peep /path/to/dir/MyProtein* -n 'Protein_\d+' """ # noqa: W605 if not paths: paths = ['./*'] if dry_run: files = pt.io_.find_files(paths) print('Files found:') print(*(str(file) for file in files), sep='\n') sys.exit() peeper = pt.read( *paths, # noqa: F841 name=name, mode=mode, name_regex=name_regex, pixel_size=pixel_size, strict=strict, mmap=mmap, lazy=lazy, ) # set up ipython shell nicely banner = '''=== PeepingTom === initialised variables: - peeper - viewer ''' sh = InteractiveShellEmbed(banner2=banner) sh.enable_gui('qt') sh.push('peeper') if not no_show: sh.run_cell('peeper.show()', silent=True) viewer = peeper.napari_viewer # noqa: F841 sh.push('viewer') sh()
def main(args): red = RedFlyingBaron.from_paths(args, verbose=True) shell = InteractiveShellEmbed(banner1="", banner2="") shell.push(["red", "RedFlyingBaron"]) print "\nRedFlyingBaron instance is available under the name 'red':" print red shell.set_next_input("red") shell()
def cli(paths, mode, name_regex, pixel_size, dry_run, strict, name, lazy, no_show): """ Blik command line interface. Opens files in napari and lands in an interactive ipython shell with blik imported and the initialised DataSet available as `dataset`. PATHS: any number of files or globs [default='./*'] \b MODE choices: - lone: each datablock in a separate volume - zip_by_type: one of each datablock type per volume - bunch: all datablocks in a single volume \b EXAMPLES: Open a .star file as particles: blik particles.star Open particles and images from a directory: blik /dir/with/star_and_mrc_files/ Match files such as MyProtein_10.star and MyProtein_001.mrc, and name the respective DataBlocks Protein_10 and Protein_001: blik /path/to/dir/MyProtein* -n 'Protein_\d+' """ # noqa: W605 if not paths: paths = ['./*'] if dry_run: from blik.io_.reading.main import find_files files = [str(file) for file in find_files(paths)] if files: click.echo('Files found:\n' + '\n'.join(files)) else: click.echo('No files found.') click.get_current_context().exit() import blik from IPython.terminal.embed import InteractiveShellEmbed dataset = blik.read( *paths, # noqa: F841 name=name, mode=mode, name_regex=name_regex, pixel_size=pixel_size, strict=strict, lazy=lazy, ) # set up ipython shell nicely banner = '''=== Blik === initialised variables: - dataset - viewer ''' sh = InteractiveShellEmbed(banner2=banner) sh.enable_gui('qt') sh.push('dataset') if not no_show: sh.run_cell('dataset.show()', silent=True) viewer = dataset.napari_viewer # noqa: F841 sh.push('viewer') sh()