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
owner = tag.getDetails().owner.id.val
#print tag.textValue, owner
tags.append([tag.textValue, str(tag.id), str(owner)])
#sort the tags in descending order to allow to see duplicates
tags.sort(key=lambda tag: tag[0].lower())
print "sorted tags", tags
prev_tag = ""
prev_id = 0
for t in tags:
tag_id = str(t[1])
if t[0] == prev_tag:
# move all tagged objects to previous tags and delete
for link in conn.getAnnotationLinks('Image', ann_ids=[tag_id]):
link._obj.child = omero.model.TagAnnotationI(prev_id, False)
link.save()
conn.deleteObjects('TagAnnotation', [tag_id])
prev_tag = t[0]
prev_id = tag_id
# Return some value(s).
# Here, we return anything useful the script has produced.
# NB: The Insight and web clients will display the "Message" output.
msg = "Script ran OK"
client.setOutput("Message", rstring(msg))
client.closeSession()
owner = tag.getDetails().owner.id.val
#print tag.textValue, owner
tags.append([tag.textValue, str(tag.id), str(owner)])
#sort the tags in descending order to allow to see duplicates
tags.sort(key=lambda tag: tag[0].lower())
print "sorted tags", tags
prev_tag = ""
prev_id = 0
for t in tags:
tag_id = str(t[1])
if t[0] == prev_tag:
# move all tagged objects to previous tags and delete
for link in conn.getAnnotationLinks('Image', ann_ids=[tag_id]):
link._obj.child = omero.model.TagAnnotationI(prev_id, False)
link.save()
for link in conn.getAnnotationLinks('Dataset', ann_ids=[tag_id]):
link._obj.child = omero.model.TagAnnotationI(prev_id, False)
link.save()
for link in conn.getAnnotationLinks('Project', ann_ids=[tag_id]):
link._obj.child = omero.model.TagAnnotationI(prev_id, False)
link.save()
conn.deleteObjects('TagAnnotation', [tag_id])
prev_tag = t[0]
prev_id = tag_id
# Return some value(s).
# Here, we return anything useful the script has produced.
ann_ids = []
for ann in image.listAnnotations():
print(ann.getId(), ann.OMERO_TYPE)
ann_ids.append(ann.id)
print(" added by ", ann.link.getDetails().getOwner().getOmeName())
if ann.OMERO_TYPE == omero.model.TagAnnotationI:
print("Tag value:", ann.getTextValue())
# Get Links between Objects and Annotations
# Find links to Images, unlink Images from these annotations
# and link them to a new Tag Annotation
tag_ann = omero.gateway.TagAnnotationWrapper(conn)
tag_ann.setValue("Replacement Tag")
tag_ann.save()
ann_ids = ann_ids[:1] # Just use first annotation
for link in conn.getAnnotationLinks('Image', ann_ids=ann_ids):
print("Image ID:", link.getParent().id)
print("Annotation ID:", link.getChild().id)
# Update the child of the underlying omero.model.ImageAnnotationLinkI
link._obj.child = omero.model.TagAnnotationI(tag_ann.id, False)
link.save()
# Find Annotations linked to Object(s), filter by namespace (optional)
for link in conn.getAnnotationLinks('Image',
parent_ids=[imageId],
ns="test.namespace"):
print("Annotation ID:", link.getChild().id)
# Close connection
# ================
# When you are done, close the session to free up server resources.
