def omero_url_reader(path):
match = parse_omero_url(path)
gateway = get_gateway(path, match.get("host"))
if match.get("type").lower() == ("image"):
wrapper = _lookup(gateway,
ProxyStringType("Image")(f"Image:{match.get('id')}"))
if wrapper:
return load_omero_wrapper(wrapper)
def _configure(self, parser):
parser.add_login_arguments()
sub = parser.sub()
images = parser.add(sub, self.images)
images.add_style_argument()
images.add_limit_arguments()
images.add_argument("--order",
default="newest",
choices=("newest", "oldest", "largest"),
help="order of the rows returned")
images.add_argument("--archived",
action="store_true",
help="list only images with archived data")
rename = parser.add(sub, self.rename)
rename.add_argument(
"fileset",
type=ProxyStringType("Fileset"),
help="Fileset which should be renamed: ID or Fileset:ID")
rename.add_argument("--no-move",
action="store_true",
help="do not move original files and import log")
repos = parser.add(sub, self.repos)
repos.add_style_argument()
repos.add_argument("--managed",
action="store_true",
help="repos only managed repositories")
sets = parser.add(sub, self.sets)
sets.add_style_argument()
sets.add_limit_arguments()
sets.add_argument("--order",
default="newest",
choices=("newest", "oldest", "prefix"),
help="order of the rows returned")
sets.add_argument("--without-images",
action="store_true",
help="list only sets without images (i.e. corrupt)")
sets.add_argument("--with-transfer",
nargs="+",
action="append",
help="list sets by their in-place import method")
sets.add_argument(
"--check",
action="store_true",
help="checks each fileset for validity (admins only)")
for x in (images, sets):
x.add_argument("--extended",
action="store_true",
help="provide more details for each (slow)")
def omero_url_reader(path: str) -> List[LayerData]:
match = parse_omero_url(path)
if not match:
return []
gateway = get_gateway(path, match.get("host"))
if match.get("type", "").lower() == "image":
wrapper = lookup_obj(
gateway,
ProxyStringType("Image")(f"Image:{match.get('id')}"))
if isinstance(wrapper, ImageWrapper):
return load_image_wrapper(wrapper)
return []
def _configure(self, parser):
parser.add_argument("object",
type=ProxyStringType("OriginalFile"),
help="Object to download of form <object>:<id>. "
"OriginalFile is assumed if <object>: is omitted.")
parser.add_argument(
"filename",
help=
"Local filename (or path for Fileset) to be saved to. '-' for stdout"
)
parser.set_defaults(func=self.__call__)
parser.add_login_arguments()
def _configure(self, parser):
parser.add_login_arguments()
sub = parser.sub()
info = parser.add(sub, self.info, DESC["INFO"])
copy = parser.add(sub, self.copy, DESC["COPY"])
edit = parser.add(sub, self.edit, DESC["EDIT"])
test = parser.add(sub, self.test, DESC["TEST"])
# list = parser.add(sub, self.list, DESC["LIST"])
# jpeg = parser.add(sub, self.jpeg, DESC["JPEG"])
# jpeg.add_argument(
# "--out", default="-",
# help="Local filename to be saved to. '-' for stdout")
render_type = ProxyStringType("Image")
render_help = ("rendering def source of form <object>:<id>. "
"Image is assumed if <object>: is omitted.")
for x in (info, copy, edit, test):
x.add_argument("object", type=render_type, help=render_help)
edit.add_argument(
"--copy",
help="Batch edit images by copying rendering settings",
action="store_true")
for x in (copy, edit):
x.add_argument("--skipthumbs",
help="Don't re-generate thumbnails",
action="store_true")
output_formats = ['plain'] + list(
pydict_text_io.get_supported_formats())
info.add_argument("--style",
choices=output_formats,
default='plain',
help="Output format")
copy.add_argument("target",
type=render_type,
help=render_help,
nargs="+")
edit.add_argument(
"channels",
help="Rendering definition, local file or OriginalFile:ID")
test.add_argument("--force", action="store_true")
test.add_argument("--thumb", action="store_true")
def run(studyfile, targetstr):
try:
# `omero shell --login` automatically creates the client object
session = client.getSession()
cli = None
except NameError:
cli = CLI()
cli.loadplugins()
cli.onecmd('login')
session = cli.get_client().getSession()
try:
us = session.getUpdateService()
target = ProxyStringType()(targetstr)
with open(studyfile) as f:
rowkvs = get_pairs(f)
links = create_map_annotation([target], rowkvs, ns)
ids = us.saveAndReturnIds(links)
print 'Created MapAnnotation links: %s' % ids
finally:
if cli:
cli.close()
def _configure(self, parser):
parser.add_login_arguments()
sub = parser.sub()
images = parser.add(sub, self.images)
images.add_style_argument()
images.add_limit_arguments()
images.add_argument(
"--order", default="newest",
choices=("newest", "oldest", "largest"),
help="order of the rows returned")
images.add_argument(
"--archived", action="store_true",
help="list only images with archived data")
mkdir = parser.add(sub, self.mkdir)
mkdir.add_argument(
"new_dir",
help="directory to create in the repository")
mkdir.add_argument(
"--parents", action="store_true",
help="ensure whole path exists")
rename = parser.add(sub, self.rename)
rename.add_argument(
"fileset",
type=ProxyStringType("Fileset"),
help="Fileset which should be renamed: ID or Fileset:ID")
rename.add_argument(
"--no-move", action="store_true",
help="do not move original files and import log")
repos = parser.add(sub, self.repos)
repos.add_style_argument()
repos.add_argument(
"--managed", action="store_true",
help="repos only managed repositories")
sets = parser.add(sub, self.sets)
sets.add_style_argument()
sets.add_limit_arguments()
sets.add_argument(
"--order", default="newest",
choices=("newest", "oldest", "prefix"),
help="order of the rows returned")
sets.add_argument(
"--without-images", action="store_true",
help="list only sets without images (i.e. corrupt)")
sets.add_argument(
"--with-transfer", nargs="+", action="append",
help="list sets by their in-place import method")
sets.add_argument(
"--check", action="store_true",
help="verify the file checksums for each fileset (admins only)")
ls = parser.add(sub, self.ls)
ls.add_argument(
"fileset",
type=ProxyStringType("Fileset"))
logfile = parser.add(sub, self.logfile)
logfile.add_argument("fileset", type=ProxyStringType("Fileset"))
logfile.add_argument(
"filename", nargs="?", default="-",
help="Local filename to be saved to. '-' for stdout")
logopts = logfile.add_mutually_exclusive_group()
logopts.add_argument(
"--name", action="store_true",
help="return the path of the logfile within the ManagedRepository")
logopts.add_argument(
"--size", action="store_true",
help="return the size of the logfile in bytes")
usage = parser.add(sub, self.usage)
usage.set_args_unsorted()
usage.add_login_arguments()
usage.add_style_argument()
usage.add_argument(
"--wait", type=long,
help="Number of seconds to wait for the processing to complete "
"(Indefinite < 0; No wait=0).", default=-1)
usage.add_argument(
"--size-only", action="store_true",
help="Print total bytes used in bytes")
usage.add_argument(
"--report", action="store_true",
help="Print detailed breakdown of disk usage")
usage.add_argument(
"--sum-by", nargs="+", choices=("user", "group", "component"),
help=("Breakdown of disk usage by a combination of "
"user, group and component"))
usage.add_argument(
"--sort-by", nargs="+",
choices=("user", "group", "component", "size", "files"),
help=("Sort the report table by one or more of "
"user, group, component, size and files"))
usage.add_argument(
"--reverse", action="store_true",
help="Reverse sort order")
unit_group = usage.add_mutually_exclusive_group()
unit_group.add_argument(
"--units", choices="KMGTP",
help="Units to use for disk usage")
unit_group.add_argument(
"--human-readable", action="store_true",
help="Use most appropriate units")
usage.add_argument(
"--groups", action="store_true",
help="Print size for all current user's groups")
usage.add_argument(
"obj", nargs="*",
help=("Objects to be queried in the form "
"'<Class>:<Id>[,<Id> ...]', or '<Class>:*' "
"to query all the objects of the given type "))
for x in (images, sets):
x.add_argument(
"--extended", action="store_true",
help="provide more details for each (slow)")
logger = logging.getLogger(__name__)
PIXEL_TYPES = {
omero_enums.PixelsTypeint8: np.int8,
omero_enums.PixelsTypeuint8: np.uint8,
omero_enums.PixelsTypeint16: np.int16,
omero_enums.PixelsTypeuint16: np.uint16,
omero_enums.PixelsTypeint32: np.int32,
omero_enums.PixelsTypeuint32: np.uint32,
omero_enums.PixelsTypefloat: np.float32,
omero_enums.PixelsTypedouble: np.float64,
}
PROXIES = (
ProxyStringType("Image"),
ProxyStringType("Dataset"),
ProxyStringType("Project"),
)
def timer(func):
"""Print the runtime of the decorated function"""
@functools.wraps(func)
def wrapper_timer(*args, **kwargs):
start_time = time.perf_counter() # 1
value = func(*args, **kwargs)
end_time = time.perf_counter() # 2
run_time = end_time - start_time # 3
logger.debug(f"Finished {func.__name__!r} in {run_time:.4f} secs")
return value
def _configure(self, parser):
parser.add_login_arguments()
sub = parser.sub()
summary = parser.add(sub, self.summary)
original = parser.add(sub, self.original)
measures = parser.add(sub, self.measures)
bulkanns = parser.add(sub, self.bulkanns)
mapanns = parser.add(sub, self.mapanns)
allanns = parser.add(sub, self.allanns)
parser.add(sub, self.testtables)
rois = parser.add(sub, self.rois)
populate = parser.add(sub, self.populate)
populateroi = parser.add(sub, self.populateroi)
pixelsize = parser.add(sub, self.pixelsize)
populate.add_argument("--batch",
type=long,
default=1000,
help="Number of objects to process at once")
self._add_wait(populate)
for x in (summary, original, bulkanns, measures, mapanns, allanns,
rois, populate, populateroi, pixelsize):
x.add_argument("obj",
type=ProxyStringType(),
help="Object in Class:ID format")
for x in (bulkanns, measures, mapanns, allanns, rois, populate,
populateroi):
x.add_argument("--report",
action="store_true",
help=("Show additional information"))
for x in (rois, populate, populateroi):
dry_or_not = x.add_mutually_exclusive_group()
dry_or_not.add_argument("-n", "--dry-run", action="store_true")
dry_or_not.add_argument("-f",
"--force",
action="store_false",
dest="dry_run")
for x in (bulkanns, measures, mapanns, allanns):
x.add_argument("--parents",
action="store_true",
help="Also search parents for annotations")
for x in (mapanns, allanns):
x.add_argument("--ns",
default=None,
help="Restrict to this namespace")
x.add_argument(
"--nsre",
help="Restrict to this namespace (regular expression)")
rois.add_argument("--delete",
action="store_true",
help="Delete all ROIs")
populate.add_argument("--context",
default=self.POPULATE_CONTEXTS[0][0],
choices=[a[0] for a in self.POPULATE_CONTEXTS])
datafile = populate.add_mutually_exclusive_group()
datafile.add_argument("--file", help="Input file")
datafile.add_argument("--fileid",
type=long,
help="Input OriginalFile ID")
cfgfile = populate.add_mutually_exclusive_group()
cfgfile.add_argument("--cfg", help="YAML configuration file")
cfgfile.add_argument("--cfgid",
type=long,
help="YAML configuration OriginalFile ID")
populate.add_argument(
"--attach",
action="store_true",
help=
("Upload input or configuration files and attach to parent object"
))
populate.add_argument(
"--localcfg",
help=("Local configuration file or a JSON object string"))
populateroi.add_argument(
"--measurement",
type=int,
default=None,
help="Index of the measurement to populate. By default, all")
pixelsize.add_argument("--x",
type=float,
default=None,
help="Physical pixel size X")
pixelsize.add_argument("--y",
type=float,
default=None,
help="Physical pixel size Y")
pixelsize.add_argument("--z",
type=float,
default=None,
help="Physical pixel size Z")
pixelsize.add_argument(
"--unit",
default="micrometer",
help="Unit (nanometer, micrometer, etc.) (default: micrometer)")
