def marshal_images(conn,
parent,
parent_id,
mapann_value,
query=False,
mapann_ns=[],
mapann_names=[],
load_pixels=False,
group_id=-1,
experimenter_id=-1,
page=1,
date=False,
thumb_version=False,
limit=settings.PAGE):
''' Marshals images
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param plate_id The Plate ID to filter by.
@type plate_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param load_pixels Whether to load the X,Y,Z dimensions
@type load_pixels Boolean
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
images = []
# early exit
if (parent_id is None or not isinstance(parent_id, long)) or not parent:
return images
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
query=query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
from_join_clauses = []
qs = conn.getQueryService()
extra_values = []
if load_pixels:
extra_values.append("""
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
""")
if date:
extra_values.append(""",
image.details.creationEvent.time as date,
image.acquisitionDate as acqDate
""")
q = """
select new map(image.id as id,
image.name as name,
image.details.owner.id as ownerId,
image as image_details_permissions,
image.fileset.id as filesetId %s)
from Image image
""" % "".join(extra_values)
if load_pixels:
# We use 'left outer join', since we still want images if no pixels
q += ' left outer join image.pixels pix '
q += """
where image.id in (
"""
if parent == 'plate':
from_join_clauses.append("""
ImageAnnotationLink ial
join ial.child a
join a.mapValue mv
join ial.parent image
join image.wellSamples ws join ws.well well
join well.plate plate
""")
params.addLong("pid", parent_id)
where_clause.append('plate.id = :pid')
if parent == 'dataset':
from_join_clauses.append("""
ImageAnnotationLink ial
join ial.child a
join a.mapValue mv
join ial.parent image
join image.datasetLinks dil join dil.parent dataset
""")
params.addLong("did", parent_id)
where_clause.append('dataset.id = :did')
q += """
%s %s
order by lower(image.name))
""" % (' select image.id from ' + ' '.join(from_join_clauses),
build_clause(where_clause, 'where', 'and'))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)[0]
d = [
e["id"], e["name"], e["ownerId"], e["image_details_permissions"],
e["filesetId"]
]
kwargs = {'conn': conn, 'row': d[0:5]}
if load_pixels:
d = [e["sizeX"], e["sizeY"], e["sizeZ"]]
kwargs['row_pixels'] = d
if date:
kwargs['acqDate'] = e['acqDate']
kwargs['date'] = e['date']
im = _marshal_image(**kwargs)
images.append(im)
# Load thumbnails separately
# We want version of most recent thumbnail (max thumbId) owned by user
if thumb_version and len(images) > 0:
user_id = conn.getUserId()
iids = [i['id'] for i in images]
params = omero.sys.ParametersI()
params.addIds(iids)
params.add('thumbOwner', wrap(user_id))
q = """select image.id, thumbs.version from Image image
join image.pixels pix join pix.thumbnails thumbs
where image.id in (:ids)
and thumbs.id = (
select max(t.id)
from Thumbnail t
where t.pixels = pix.id
and t.details.owner.id = :thumbOwner
)
"""
thumb_versions = {}
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for t in qs.projection(q, params, service_opts):
iid, tv = unwrap(t)
thumb_versions[iid] = tv
# For all images, set thumb version if we have it...
for i in images:
if i['id'] in thumb_versions:
i['thumbVersion'] = thumb_versions[i['id']]
return images
def _marshal_image(conn, row, tags_on_images):
image = tree._marshal_image(conn, row[0:5])
image['clientPath'] = unwrap(row[5])
image['tags'] = tags_on_images.get(image['id']) or []
return image
def marshal_images(conn, parent, parent_id,
mapann_value, query=False,
mapann_ns=[], mapann_names=[],
load_pixels=False,
group_id=-1, experimenter_id=-1,
page=1, date=False, thumb_version=False,
limit=settings.PAGE):
''' Marshals images
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param plate_id The Plate ID to filter by.
@type plate_id L{long}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param load_pixels Whether to load the X,Y,Z dimensions
@type load_pixels Boolean
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
images = []
# early exit
if (parent_id is None or not isinstance(parent_id, long)) or not parent:
return images
params, where_clause = _set_parameters(
mapann_ns=mapann_ns, mapann_names=mapann_names,
query=query, mapann_value=mapann_value,
params=None, experimenter_id=experimenter_id,
page=page, limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
from_join_clauses = []
qs = conn.getQueryService()
extra_values = []
if load_pixels:
extra_values.append("""
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
""")
if date:
extra_values.append(""",
image.details.creationEvent.time as date,
image.acquisitionDate as acqDate
""")
q = """
select new map(image.id as id,
image.name as name,
image.details.owner.id as ownerId,
image as image_details_permissions,
image.fileset.id as filesetId %s)
from Image image
""" % "".join(extra_values)
if load_pixels:
# We use 'left outer join', since we still want images if no pixels
q += ' left outer join image.pixels pix '
q += """
where image.id in (
"""
if parent == 'plate':
from_join_clauses.append("""
ImageAnnotationLink ial
join ial.child a
join a.mapValue mv
join ial.parent image
join image.wellSamples ws join ws.well well
join well.plate plate
""")
params.addLong("pid", parent_id)
where_clause.append('plate.id = :pid')
if parent == 'dataset':
from_join_clauses.append("""
ImageAnnotationLink ial
join ial.child a
join a.mapValue mv
join ial.parent image
join image.datasetLinks dil join dil.parent dataset
""")
params.addLong("did", parent_id)
where_clause.append('dataset.id = :did')
q += """
%s %s
order by lower(image.name))
""" % (' select image.id from ' + ' '.join(from_join_clauses),
build_clause(where_clause, 'where', 'and'))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)[0]
d = [e["id"],
e["name"],
e["ownerId"],
e["image_details_permissions"],
e["filesetId"]]
kwargs = {'conn': conn, 'row': d[0:5]}
if load_pixels:
d = [e["sizeX"], e["sizeY"], e["sizeZ"]]
kwargs['row_pixels'] = d
if date:
kwargs['acqDate'] = e['acqDate']
kwargs['date'] = e['date']
im = _marshal_image(**kwargs)
images.append(im)
# Load thumbnails separately
# We want version of most recent thumbnail (max thumbId) owned by user
if thumb_version and len(images) > 0:
user_id = conn.getUserId()
iids = [i['id'] for i in images]
params = omero.sys.ParametersI()
params.addIds(iids)
params.add('thumbOwner', wrap(user_id))
q = """select image.id, thumbs.version from Image image
join image.pixels pix join pix.thumbnails thumbs
where image.id in (:ids)
and thumbs.id = (
select max(t.id)
from Thumbnail t
where t.pixels = pix.id
and t.details.owner.id = :thumbOwner
)
"""
thumb_versions = {}
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for t in qs.projection(q, params, service_opts):
iid, tv = unwrap(t)
thumb_versions[iid] = tv
# For all images, set thumb version if we have it...
for i in images:
if i['id'] in thumb_versions:
i['thumbVersion'] = thumb_versions[i['id']]
return images
def _marshal_image(conn, row, tags_on_images):
image = tree._marshal_image(conn, row[0:5])
image['clientPath'] = unwrap(row[5])
image['tags'] = tags_on_images.get(image['id']) or []
return image