def upload_image_from_file(file,
dataset_name,
project_name='',
attachments=(),
wait=-1):
attachments = list(attachments)
dataset_id = get_or_create_dataset_id(dataset_name, project_name)
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
r = file_import(cli._client, file, wait)
if r:
links = []
# TODO - doing this as iterable fileset for single file is weird
p = r.pixels[0]
image_id = p.image.id.val
logger.debug('Imported Image ID: %d' % image_id)
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(dataset_id, False)
link.child = omero.model.ImageI(image_id, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
if len(attachments) > 0:
# have to have loadedness -> True to link an annotation
image = conn.getObject("Image", image_id)
for attachment in attachments:
# TODO - add guess_mimetype / namespace here
upload_file_annotation(conn,
image,
attachment,
namespace='pyme.localizations')
return image_id
def list_children(name, ignore):
with cli_login() as cli:
conn = BlitzGateway(client_obj=cli.get_client())
screen = conn.getObject(
'Screen',
attributes={'name': "idr0072-schormann-subcellref/" + name})
return [f"Plate:{x.id}" for x in screen.listChildren()]
def localization_files_from_image_url(image_url, out_dir):
"""
Parameters
----------
image_url : str
url from OMERO web client, gotten typically by clicking the link symbol
with an image selected, i.e. `Link to this image`.
out_dir : str
path / name of tempfile.TemporaryDirectory
Returns
-------
localization_files : list
paths to localization files saved to disk
"""
from urllib.parse import urlparse, parse_qs
from omero.util.populate_roi import DownloadingOriginalFileProvider
url = urlparse(image_url)
# for `Link to this image`
image_id = int(parse_qs(url.query)['show'][0].split('-')[-1])
localization_files = []
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
# Would be nice to specify pyme.localizations namespace, but probably
# reliable to check file extentsion since one can manually attach
# localizations with no namespace specified
# localization_links = list(conn.getAnnotationLinks('Image',
# parent_ids=[image_id],
# ns="pyme.localizations"))
localization_links = list(
conn.getAnnotationLinks('Image', parent_ids=[image_id]))
raw_file_store = conn.createRawFileStore()
for link in localization_links:
try: # select for Blitzwrapped omero types with getFile attr
og_file = link.getChild().getFile()._obj
except AttributeError: # not all BlitzWrapped omero types have getFile
continue
filename = og_file.getName().getValue()
if os.path.splitext(filename)[-1] not in ['.hdf', '.h5r']:
continue
path = os.path.join(out_dir, filename)
localization_files.append(path)
raw_file_store.setFileId(og_file.id.val)
with open(path, 'wb') as f:
f.write(raw_file_store.read(0, og_file.size.val))
return localization_files
def connect_and_upload_file_annotation(image_id,
file,
mimetype='application/octet-stream',
namespace='',
description=None):
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
upload_file_annotation(conn, image_id, file, mimetype, namespace,
description)
def execOmeroCommand(args):
logging.info("exec command:" + str(args))
with cli_login("--server", "localhost", "--port", "4064", "--group",
"pharmbio_read_annotate", "--user", "root", "--password",
omero_rootpass) as cli:
logging.info("Before command")
cli.invoke(args)
logging.info("After command")
cli.close()
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument('username2', help='Target server Username')
parser.add_argument('password2', help='Target server Password')
parser.add_argument('server2', help='Target server')
parser.add_argument('source',
help=('Copy ROIs FROM this: Image:ID or Dataset:ID'))
parser.add_argument('target',
help=('Copy ROIs TO this: Image:ID or Dataset:ID'))
args = parser.parse_args(argv)
with cli_login() as cli:
conn = BlitzGateway(client_obj=cli._client)
conn.SERVICE_OPTS.setOmeroGroup(-1)
conn2 = BlitzGateway(args.username2,
args.password2,
port=4064,
host=args.server2)
conn2.connect()
source_images = []
target_image_ids = []
source = args.source
source_id = int(source.split(":")[1])
target = args.target
target_id = int(target.split(":")[1])
if source.startswith('Image:'):
source_images.append(conn.getObject('Image', source_id))
target_image_ids.append(target_id)
elif source.startswith('Dataset:'):
dataset = conn.getObject('Dataset', source_id)
target_dataset = conn2.getObject('Dataset', target_id)
ids_by_name = image_ids_by_name(target_dataset)
for image in dataset.listChildren():
if image.name in ids_by_name:
source_images.append(image)
target_image_ids.append(ids_by_name[image.name])
else:
print("Source needs to be Image:ID or Dataset:ID")
print("Processing", source_images)
print("...to target images:", target_image_ids)
for image, to_target_id in zip(source_images, target_image_ids):
process_image(conn, conn2, image, to_target_id)
conn2.close()
def execOmeroCommand(args):
logging.info("exec command:" + str(args))
stdout_ = sys.stdout
redirected_stdout = cStringIO.StringIO()
sys.stdout = redirected_stdout
retval = ""
with cli_login("--server", "localhost", "--port", "4064", "--user", "root",
"--password", omero_rootpass) as cli:
logging.info("Before command")
cli.invoke(args)
logging.info("After command")
retval = redirected_stdout.getvalue()
cli.close()
# restore stream
sys.stdout = stdout_
logging.info("retval " + retval)
return retval
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument('--verbose',
'-v',
action='count',
default=0,
help='Increase the command verbosity')
parser.add_argument('--quiet',
'-q',
action='count',
default=0,
help='Decrease the command verbosity')
parser.parse_args(argv)
df = pandas.read_csv(PROCESSED_FILE_PATH, delimiter='\t')
with cli_login() as c:
conn = BlitzGateway(client_obj=c.get_client())
images = get_timelapse_images(conn)
for image in images:
df2 = create_points(conn, df, image)
iid = image.getId()
df2.to_csv(f"{iid}.csv", index=False)
def main(argv):
parser = argparse.ArgumentParser()
# parser.addArgument('--session', type=int, help=(
# 'Connect with this session ID, default is to use or create a '
# 'session from the OMERO CLI'))
parser.add_argument(
'--dataset',
type=int,
help=(
'Add imported files to this Dataset ID (not valid when wait=-1)'))
parser.add_argument(
'--wait',
type=int,
default=-1,
help=('Wait for this number of seconds for each import to complete. '
'0: return immediately, -1: wait indefinitely (default)'))
parser.add_argument('path', nargs='+', help='Files or directories')
args = parser.parse_args(argv)
with cli_login() as cli:
conn = BlitzGateway(client_obj=cli._client)
if args.dataset and not conn.getObject('Dataset', args.dataset):
print('Dataset id not found: %s' % args.dataset)
sys.exit(1)
for fs_path in args.path:
print('Importing: %s' % fs_path)
rsp = full_import(cli._client, fs_path, args.wait)
if rsp:
links = []
for p in rsp.pixels:
print('Imported Image ID: %d' % p.image.id.val)
if args.dataset:
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(args.dataset, False)
link.child = omero.model.ImageI(p.image.id.val, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument('--verbose',
'-v',
action='count',
default=0,
help='Increase the command verbosity')
parser.add_argument('--quiet',
'-q',
action='count',
default=0,
help='Decrease the command verbosity')
parser.add_argument('--dry-run',
'-n',
action='store_true',
help='Run command in dry-run mode')
args = parser.parse_args(argv)
default_level = logging.INFO - 10 * args.verbose + 10 * args.quiet
logging.basicConfig(level=default_level)
with cli_login() as c:
conn = BlitzGateway(client_obj=c.get_client())
attach_tables(conn)
def download_image(image_url, out_dir):
"""
Parameters
----------
image_url : str
url from OMERO web client, gotten typically by clicking the link symbol
with an image selected, i.e. `Link to this image`.
out_dir : str
path / name of tempfile.TemporaryDirectory
Returns
-------
path : str
path to file saved to disk
"""
from urllib.parse import urlparse, parse_qs
from omero.util.populate_roi import DownloadingOriginalFileProvider
url = urlparse(image_url)
# for `Link to this image`
image_id = int(parse_qs(url.query)['show'][0].split('-')[-1])
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
image = conn.getObject("Image", image_id)
total_size, buff_generator = image.exportOmeTiff(BUFF_SIZE)
path = os.path.join(out_dir,
os.path.splitext(image.getName())[0] + '.tif')
with open(path, 'wb') as f:
for buff in buff_generator:
f.write(buff)
return path
def get_or_create_dataset_id(dataset_name, project_name=''):
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
# handle linking with project if given
if project_name != '':
# check if the dataset already exists within the project
project_id = get_or_create_project_id(conn, project_name)
# projects = conn.getContainerService().loadContainerHierarchy('Project',
# None, None)
project = conn.getObject("Project", project_id)
dataset_wrapper = project.findChildByName(dataset_name)
if dataset_wrapper != None:
return dataset_wrapper.getId()
# make a new dataset
dataset_id = create_dataset(conn, dataset_name)
# link it to the project
links = []
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(project_id, False)
link.child = omero.model.DatasetI(dataset_id, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
return dataset_id
# no project specified, check if the dataset already exists
datasets = conn.getContainerService().loadContainerHierarchy(
'Dataset', None, None)
for d in datasets:
if d.getName().getValue() == dataset_name:
return d.getId().getValue()
# otherwise create a new dataset
return create_dataset(conn, dataset_name)
def download_image_data(image_ids_or_dataset_id,
dataset=False,
download_original=False,
channel=None,
z_stack=0,
frame=0,
coord=(0, 0),
width=0,
height=0,
region_spec='rectangle',
skip_failed=False,
download_tar=False,
omero_host='idr.openmicroscopy.org',
omero_secured=False,
config_file=None):
if config_file is None: # IDR connection
omero_username = '******'
omero_password = '******'
else: # other omero instance
with open(config_file) as f:
cfg = json.load(f)
omero_username = cfg['username']
omero_password = cfg['password']
if omero_username == "" or omero_password == "":
omero_username = '******'
omero_password = '******'
if not download_original and region_spec not in ['rectangle', 'center']:
raise ValueError(
'Got unknown value "{0}" as region_spec argument'.format(
region_spec))
with ExitStack() as exit_stack:
conn = exit_stack.enter_context(
BlitzGateway(omero_username,
omero_password,
host=omero_host,
secure=omero_secured))
# exit_stack.callback(conn.connect().close)
if download_tar:
# create an archive file to write images to
archive = exit_stack.enter_context(
tarfile.open('images.tar', mode='w'))
tempdir = exit_stack.enter_context(TemporaryDirectory())
if dataset:
dataset_warning_id = 'Dataset-ID: {0}'.format(
image_ids_or_dataset_id[0])
try:
dataset_id = int(image_ids_or_dataset_id[0])
except ValueError:
image_ids = None
else:
try:
dataset = conn.getObject("Dataset", dataset_id)
except Exception as e:
# respect skip_failed on unexpected errors
if skip_failed:
warn(str(e), dataset_warning_id, warn_skip=True)
else:
raise
else:
image_ids = [image.id for image in dataset.listChildren()]
if image_ids is None:
if skip_failed:
warn(
'Unable to find a dataset with this ID in the '
'database.',
dataset_warning_id,
warn_skip=True)
else:
raise ValueError(
'{0}: Unable to find a dataset with this ID in the '
'database. Aborting!'.format(dataset_warning_id))
else:
# basic argument sanity checks and adjustments
prefix = 'image-'
# normalize image ids by stripping off prefix if it exists
image_ids = [
iid[len(prefix):] if iid[:len(prefix)] == prefix else iid
for iid in image_ids_or_dataset_id
]
for image_id in image_ids:
image_warning_id = 'Image-ID: {0}'.format(image_id)
try:
image_id = int(image_id)
except ValueError:
image = None
else:
try:
image = conn.getObject("Image", image_id)
except Exception as e:
# respect skip_failed on unexpected errors
if skip_failed:
warn(str(e), image_warning_id, warn_skip=True)
continue
else:
raise
if image is None:
if skip_failed:
warn(
'Unable to find an image with this ID in the '
'database.',
image_warning_id,
warn_skip=True)
continue
raise ValueError(
'{0}: Unable to find an image with this ID in the '
'database. Aborting!'.format(image_warning_id))
if not download_original:
try:
# try to extract image properties
# if anything goes wrong here skip the image
# or abort.
image_name = os.path.splitext(image.getName())[0]
image_warning_id = '{0} (ID: {1})'.format(
image_name, image_id)
if region_spec == 'rectangle':
tile = get_clipping_region(image, *coord, width,
height)
elif region_spec == 'center':
tile = get_clipping_region(
image, *_center_to_ul(*coord, width, height))
ori_z, z_stack = z_stack, confine_plane(image, z_stack)
ori_frame, frame = frame, confine_frame(image, frame)
num_channels = image.getSizeC()
if channel is None:
channel_index = 0
else:
channel_index = find_channel_index(image, channel)
except Exception as e:
# respect skip_failed on unexpected errors
if skip_failed:
warn(str(e), image_warning_id, warn_skip=True)
continue
else:
raise
# region sanity checks and warnings
if tile[2] < width or tile[3] < height:
# The downloaded image region will have smaller dimensions
# than the specified width x height.
warn(
'Downloaded image dimensions ({0} x {1}) will be smaller '
'than the specified width and height ({2} x {3}).'.
format(tile[2], tile[3], width,
height), image_warning_id)
# z-stack sanity checks and warnings
if z_stack != ori_z:
warn(
'Specified image plane ({0}) is out of bounds. Using {1} '
'instead.'.format(ori_z, z_stack), image_warning_id)
# frame sanity checks and warnings
if frame != ori_frame:
warn(
'Specified image frame ({0}) is out of bounds. Using '
'frame {1} instead.'.format(ori_frame, frame),
image_warning_id)
# channel index sanity checks and warnings
if channel is None:
if num_channels > 1:
warn(
'No specific channel selected for multi-channel '
'image. Using first of {0} channels.'.format(
num_channels), image_warning_id)
else:
if channel_index == -1 or channel_index >= num_channels:
if skip_failed:
warn(
str(channel) +
' is not a known channel name for this image.',
image_warning_id,
warn_skip=True)
continue
else:
raise ValueError(
'"{0}" is not a known channel name for image {1}. '
'Aborting!'.format(channel, image_warning_id))
# download and save the region as TIFF
fname = '__'.join([image_name, str(image_id)] +
[str(x) for x in tile])
try:
if fname[-5:] != '.tiff':
fname += '.tiff'
fname = fname.replace(' ', '_')
im_array = get_image_array(image, tile, z_stack,
channel_index, frame)
if download_tar:
fname = os.path.join(tempdir, fname)
try:
tiff = TIFF.open(fname, mode='w')
tiff.write_image(im_array)
finally:
tiff.close()
# move image into tarball
if download_tar:
archive.add(fname, os.path.basename(fname))
os.remove(fname)
except Exception as e:
if skip_failed:
# respect skip_failed on unexpected errors
warn(str(e), image_warning_id, warn_skip=True)
continue
else:
raise
else:
try:
# try to extract image properties
# if anything goes wrong here skip the image
# or abort.
image_name = os.path.splitext(image.getName())[0]
image_warning_id = '{0} (ID: {1})'.format(
image_name, image_id)
original_image_name = image.getFileset().listFiles(
)[0].getName()
fname = image_name + "__" + str(
image_id) + os.path.splitext(original_image_name)[1]
fname = fname.replace(' ', '_')
fname = fname.replace('/', '_')
download_directory = "./"
if download_tar:
download_directory = tempdir
with cli_login("-u", omero_username, "-s", omero_host,
"-w", omero_password) as cli:
cli.invoke([
"download", f"Image:{image_id}", download_directory
])
if cli.rv != 0:
raise Exception("Download failed.")
# This will download to download_directory/original_image_name
os.rename(
os.path.join(download_directory, original_image_name),
os.path.join(download_directory, fname))
# move image into tarball
if download_tar:
archive.add(os.path.join(download_directory, fname),
os.path.basename(fname))
os.remove(os.path.join(download_directory, fname))
except Exception as e:
# respect skip_failed on unexpected errors
if skip_failed:
warn(str(e), image_warning_id, warn_skip=True)
continue
else:
raise
from omero.cli import cli_login
with cli_login("root@omero", "-womero") as cli:
cli.loadplugins()
cli.invoke(["import", "/data/hcs.fake", "---file=/tmp/import.out"])
with open("/tmp/import.out", "r") as o:
output = o.read().strip()
cli.invoke(["zarr", "export", output])
#!/usr/bin/env python
import omero
from omero.cli import cli_login
from omero.rtypes import unwrap
import pandas as pd
import re
import warnings
with cli_login() as cli:
client = cli.get_client()
bulkcsv = 'taraoceans.BULK_ANNOTATION.csv'
screenid = 1201
ignore_missing = True
ns = omero.constants.namespaces.NSBULKANNOTATIONS
qs = client.getSession().getQueryService() # noqa
us = client.getSession().getUpdateService() # noqa
df = pd.read_csv(bulkcsv)
q = ('SELECT spl.child.id, spl.child.name FROM ScreenPlateLink spl '
'WHERE spl.parent.id=%d' % screenid)
rs = unwrap(qs.projection(q, None))
class PlateInfo: