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()
