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Commit f634feca authored by Constantin Pape's avatar Constantin Pape
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Add export scripts for cilia segmentation

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scripts/attributes/__init__.py
+ 1
− 1
View file @ f634feca
from .master import make_cell_tables, make_nucleus_tables
from .master import make_cell_tables, make_nucleus_tables, make_cilia_tables
scripts/attributes/master.py
+ 18
− 0
View file @ f634feca
......@@ -96,3 +96,21 @@ def make_nucleus_tables(folder, name, tmp_folder, resolution,
# TODO additional tables:
# ???
def make_cilia_tables(folder, name, tmp_folder, resolution,
target='slurm', max_jobs=100):
# make the table folder
table_folder = os.path.join(folder, 'tables', name)
os.makedirs(table_folder, exist_ok=True)
seg_key = 't00000/s00/0/cells'
seg_path = get_seg_path(folder, name, seg_key)
# make the basic attributes table
base_out = os.path.join(table_folder, 'default.csv')
base_attributes(seg_path, seg_key, base_out, resolution,
tmp_folder, target=target, max_jobs=max_jobs,
correct_anchors=True)
# TODO additional tables:
# ???
update_platy_browser.py
+ 75
− 18
View file @ f634feca
......@@ -5,7 +5,7 @@ import argparse
from subprocess import check_output, call
from shutil import rmtree
from scripts.attributes import make_cell_tables, make_nucleus_tables
from scripts.attributes import make_cell_tables, make_nucleus_tables, make_cilia_tables
from scripts.export import export_segmentation
from scripts.files import copy_image_data, copy_misc_data
from scripts.files import copy_tables, copy_segmentation, make_folder_structure
......@@ -17,41 +17,56 @@ from scripts.files import copy_tables, copy_segmentation, make_folder_structure
PAINTERA_ROOT = '/g/kreshuk/data/arendt/platyneris_v1/data.n5'
PROJECT_CELLS = 'volumes/paintera/proofread_cells'
PROJECT_NUCLEI = 'volumes/paintera/nuclei'
PROJECT_CILIA = 'volumes/paintera/cilia'
# name for cell and nucleus segmentations
NAME_CELLS = 'sbem-6dpf-1-whole-segmented-cells-labels'
NAME_NUCLEI = 'sbem-6dpf-1-whole-segmented-nuclei-labels'
NAME_CILIA = 'sbem-6dpf-1-whole-segmented-cilia-labels'
# resolutions of cell and nucleus segmentation
RES_CELLS = [.025, .02, .02]
RES_NUCLEI = [.1, .08, .08]
RES_CILIA = [.025, .01, .01]
def check_inputs(update_cell_segmentation,
update_nucleus_segmentation,
update_cilia_segmentation,
update_cell_tables,
update_nucleus_tables):
update_nucleus_tables,
update_cilia_tables):
inputs = (update_cell_segmentation, update_nucleus_segmentation,
update_cell_tables, update_nucleus_tables)
update_cell_tables, update_nucleus_tables,
update_cilia_segmentation, update_cilia_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
if update_cilia_segmentation:
update_cilia_tables = True
return {'have_changes': have_changes,
'update_cell_tables': update_cell_tables,
'update_nucleus_tables': update_nucleus_tables,
'update_cilia_tables': update_cilia_tables}
def get_tags():
tag = check_output(['git', 'tag']).decode('utf-8').rstrip('\n')
new_tag = tag.split('.')
new_tag[-1] = str(int(new_tag[-1]) + 1)
new_tag = '.'.join(new_tag)
def get_tags(new_tag):
tag = check_output(['git', 'describe', '--abbrev=0']).decode('utf-8').rstrip('\n')
if new_tag == '':
new_tag = tag.split('.')
new_tag[-1] = str(int(new_tag[-1]) + 1)
new_tag = '.'.join(new_tag)
return tag, new_tag
def export_segmentations(folder, new_folder,
update_cell_segmentation,
update_nucleus_segmentation,
update_cilia_segmentation,
target, max_jobs):
# update or copy cell segmentation
if update_cell_segmentation:
......@@ -75,6 +90,17 @@ def export_segmentations(folder, new_folder,
else:
copy_segmentation(folder, new_folder, NAME_NUCLEI)
# update or copy cilia segmentation
if update_cilia_segmentation:
tmp_cilia_seg = 'tmp_export_cilia'
export_segmentation(PAINTERA_ROOT, PROJECT_CILIA,
folder, new_folder, NAME_CILIA,
resolution=RES_CILIA,
tmp_folder=tmp_cilia_seg,
target=target, max_jobs=max_jobs)
else:
copy_segmentation(folder, new_folder, NAME_CILIA)
# copy static segmentations
static_seg_names = ('sbem-6dpf-1-whole-segmented-muscles',
'sbem-6dpf-1-whole-segmented-tissue-labels')
......@@ -83,7 +109,9 @@ def export_segmentations(folder, new_folder,
def make_attributes(folder, new_folder,
update_cell_tables, update_nucleus_tables,
update_cell_tables,
update_nucleus_tables,
update_cilia_tables,
target, max_jobs):
# update or copy cell tables
if update_cell_tables:
......@@ -99,6 +127,12 @@ def make_attributes(folder, new_folder,
else:
copy_tables(folder, new_folder, NAME_NUCLEI)
if update_cilia_tables:
make_cilia_tables(new_folder, NAME_CILIA, 'tmp_tables_cilia', RES_CILIA,
target=target, max_jobs=max_jobs)
else:
copy_tables(folder, new_folder, NAME_CILIA)
# copy tables associated with static segmentations
static_seg_names = ('sbem-6dpf-1-whole-segmented-tissue-labels',)
for seg_name in static_seg_names:
......@@ -135,33 +169,45 @@ def clean_up():
# TODO catch all exceptions and handle them properly
def update_platy_browser(update_cell_segmentation=False,
update_nucleus_segmentation=False,
update_cilia_segmentation=False,
update_cell_tables=False,
update_nucleus_tables=False,
description=''):
update_cilia_tables=False,
description='',
new_tag=''):
""" 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_cilia_segmentation: Update the cilia 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.
update_cilia_tables: Update the cilia tables. This needs to be specified if the cilia
segmentation is not updated, but the tables should be updated.
description: Optional descrption for release message.
new_tag: Optional tag to override the default new tag.
"""
# 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:
update_dict = check_inputs(update_cell_segmentation,
update_nucleus_segmentation,
update_cilia_segmentation,
update_cell_tables,
update_nucleus_tables,
update_cilia_tables)
if not update_dict['have_changes']:
print("Nothing needs to be update, skipping")
return
update_cell_tables, update_nucleus_tables, update_cilia_tables =\
update_dict['update_cell_tables'], update_dict['update_nucleus_tables'], update_dict['update_cilia_tables']
# we always increase the release tag (in the last digit)
# when making a new version of segmentation or attributes
tag, new_tag = get_tags()
tag, new_tag = get_tags(new_tag)
print("Updating platy browser from", tag, "to", new_tag)
# make new folder structure
......@@ -184,12 +230,14 @@ def update_platy_browser(update_cell_segmentation=False,
export_segmentations(folder, new_folder,
update_cell_segmentation,
update_nucleus_segmentation,
update_cilia_segmentation,
target=target, max_jobs=max_jobs)
# generate new attribute tables
make_attributes(folder, new_folder,
update_cell_tables,
update_nucleus_tables,
update_cilia_tables,
target=target, max_jobs=max_jobs)
# TODO implement make release properly
......@@ -228,16 +276,25 @@ if __name__ == '__main__':
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_cilia_segmentation', type=str2bool,
default=False, help="Update the cilia 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"))
parser.add_argument('--update_cilia_tables', type=str2bool,
default=False, help=table_help_str("cilia"))
parser.add_argument('--description', type=str, default='',
help="Optional description for release message")
parser.add_argument('--new_tag', type=str, default='',
help="Specify a new tag that will override the default new tag")
args = parser.parse_args()
update_platy_browser(args.update_cell_segmentation,
args.update_nucleus_segmentation,
args.update_cilia_segmentation,
args.update_cell_tables,
args.update_nucleus_tables,
args.description)
args.update_cilia_tables,
args.description,
args.new_tag)
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