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import os
import argparse
from subprocess import check_output, call
from scripts.attributes import make_cell_tables, make_nucleus_tables
from scripts.export import export_segmentation
from scripts.files import copy_tables, copy_segmentation, copy_static_files
# paths for paintera projects
# in order to get the new segmentation, changes need to be committed,
# s.t. they are stored in these files!
PAINTERA_ROOT = '/g/kreshuk/data/arendt/platyneris_v1/data.n5'
# TODO do we need the data postfix ???
PROJECT_CELLS = 'volumes/paintera/proofread_cells/data'
PROJECT_NUCLEI = 'volumes/paintera/nuclei/data'
# name for cell and nucleus segmentations
NAME_CELLS = 'em-segmented-cells-labels'
NAME_NUCLEI = 'em-segmented-nuclei-labels'
def check_inputs(update_cell_segmentation,
update_nucleus_segmentation,
update_cell_tables,
update_nucleus_tables):
inputs = (update_cell_segmentation, update_nucleus_segmentation,
update_cell_tables, update_nucleus_tables)
have_changes = any(inputs)
if update_cell_segmentation:
update_cell_tables = True
if update_nucleus_segmentation:
update_nucleus_tables = True
return have_changes, update_cell_tables, update_nucleus_tables
def get_tags():
tag = check_output(['git', 'describe', '--tags']).decode('utf-8').rstrip('\n')
new_tag = tag.split('.')
new_tag[-1] = str(int(new_tag[-1]) + 1)
new_tag = '.'.join(new_tag)
return tag, new_tag
def make_folder_structure(tag):
new_folder = os.makedirs('data', tag)
# make all sub-folders
os.makedirs(os.path.join(new_folder, 'tables'))
os.makedirs(os.path.join(new_folder, 'images'))
os.makedirs(os.path.join(new_folder, 'segmentations'))
os.makedirs(os.path.join(new_folder, 'misc'))
return new_folder
# TODO
# need lut from new to old segmentation ids
# to auto translate custom attributes
# also support extraction from paintera commit
def export_segmentations(folder, new_folder,
update_cell_segmentation,
update_nucleus_segmentation):
# update or copy cell segmentation
if update_cell_segmentation:
export_segmentation(PAINTERA_ROOT, PROJECT_CELLS,
folder, new_folder, NAME_CELLS,
resolution=[.025, .02, .02])
else:
copy_segmentation(folder, new_folder, NAME_CELLS)
# update or copy nucleus segmentation
if update_nucleus_segmentation:
export_segmentation(PAINTERA_ROOT, PROJECT_NUCLEI,
folder, new_folder, NAME_NUCLEI,
resolution=[.1, .08, .08])
else:
copy_segmentation(folder, new_folder, NAME_NUCLEI)
def make_attributes(folder, new_folder,
update_cell_tables, update_nucleus_tables):
# update or copy cell tables
if update_cell_tables:
make_cell_tables(new_folder, NAME_CELLS)
else:
copy_tables(folder, new_folder, NAME_CELLS)
# update or copy nucleus tables
if update_nucleus_tables:
make_nucleus_tables(new_folder, NAME_NUCLEI)
else:
copy_tables(folder, new_folder, NAME_NUCLEI)
# TODO check for errors
def make_release(tag):
call(['git', 'commit', '-m', 'Automatic platybrowser update'])
call(['git', 'tag', tag])
# TODO autopush ???
# call(['git', 'push', 'origin', 'master', '--tags'])
# TODO catch all exceptions and re-roll if exception was caught
def update_platy_browser(update_cell_segmentation=False,
update_nucleus_segmentation=False,
update_cell_tables=False,
update_nucleus_tables=False):
""" Generate new version of platy-browser derived data.
Arguments:
update_cell_segmentation: Update the cell segmentation volume.
update_nucleus_segmentation: Update the nucleus segmentation volume.
update_cell_tables: Update the cell tables. This needs to be specified if the cell
segmentation is not update, but the tables should be updated.
update_nucleus_tables: Update the nucleus tables. This needs to be specified if the nucleus
segmentation is not updated, but the tables should be updated.
"""
# check inputs
have_changes, update_cell_tables, update_nucleus_tables = check_inputs(update_cell_segmentation,
update_nucleus_segmentation,
update_cell_tables,
update_nucleus_tables)
if not have_changes:
print("Nothing needs to be update, skipping ")
return
# we always increase the release tag (in the last digit)
# when making a new version of segmentation or attributes
tag, new_tag = get_tags()
# make new folder structure
folder = os.path.join('data', tag)
new_folder = make_folder_structure(new_tag)
# export new segmentation(s)
export_segmentations(folder, new_folder,
update_cell_segmentation,
update_nucleus_segmentation)
# generate new attribute tables (if necessary)
make_attributes(folder, new_folder,
update_cell_tables,
update_nucleus_tables)
# copy files that were not touched
copy_static_files(folder, new_folder)
# make new release
make_release(new_tag)
def str2bool(v):
if isinstance(v, bool):
return v
if v.lower() in ('yes', 'true', 't', 'y', '1'):
return True
elif v.lower() in ('no', 'false', 'f', 'n', '0'):
return False
else:
raise argparse.ArgumentTypeError('Boolean value expected.')
def table_help_str(name):
help_str = """Update the %s tables.
Only needs to be specified if the %s segmentation is not updated,
but the tables should be updated."""
return help_str % (name, name)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Update derived data for the platy browser')
parser.add_argument('--update_cell_segmentation', type=str2bool,
default=False, help="Update the cell segmentation.")
parser.add_argument('--update_nucleus_segmentation', type=str2bool,
default=False, help="Update the nucleus segmentation.")
parser.add_argument('--update_cell_tables', type=str2bool,
default=False, help=table_help_str("cell"))
parser.add_argument('--update_nucleus_tables', type=str2bool,
default=False, help=table_help_str("nucleus"))
args = parser.parse_args()
update_platy_browser(args.update_cell_segmentation,
args.update_nucleus_segmentation,
args.update_cell_tables,
args.update_nucleus_tables)