def get_annotations_list(connection, fetch_images=False):
switch_to_default_search_group(connection)
tag_sets = list()
tags = list()
for t in connection.getObjects("TagAnnotation"):
if _is_tagset(t):
tag_sets.append(t)
else:
tags.append(t)
annotations = list()
for ts in tag_sets:
tags_map = _get_tags_list(connection, ts, fetch_images, append_raw_object=True)
for tmi in tags_map:
tobj = tmi.pop('obj')
try:
tags.pop(tags.index(tobj))
except ValueError:
pass
tagset_json = _tagset_to_json(ts, tags_map)
annotations.append(tagset_json)
for t in tags:
imgs_list = list()
if fetch_images:
imgs_list = _get_images_by_tag(t.getId(), connection)
annotations.append(_tag_to_json(t, imgs_list))
return annotations
def _get_images_by_tag(tag_id, connection):
switch_to_default_search_group(connection)
imgs_generator = connection.getObjectsByAnnotations('Image', [tag_id])
images = list()
for img in imgs_generator:
images.append(_image_to_json(img, connection))
return images
def get_images_quick_list(connection, expand_imgs_series=False):
switch_to_default_search_group(connection)
images_list = []
# get OMERO images
imgs = connection.getObjects('Image')
if not expand_imgs_series:
imgs = _reduce_images_series(imgs)
for img in imgs:
images_list.append(
{
'omero_id': img.getId(),
'name': img.getName(),
'img_type': 'OMERO_IMG' # right now we only need to separate OMERO imgs from "special" ones like MIRAX
}
)
# get "special" images like MIRAX ones (actually, right now only the MIRAX ones...)
query_filter = {'mimetype': 'mirax/index'}
imgs = connection.getObjects('OriginalFile', attributes=query_filter)
for img in imgs:
images_list.append(
{
'omero_id': img.getId(),
'name': img.getName(),
'img_type': 'MIRAX'
}
)
return images_list
def get_annotations_list(connection, fetch_images=False):
switch_to_default_search_group(connection)
tag_sets = list()
tags = list()
for t in connection.getObjects("TagAnnotation"):
if _is_tagset(t):
tag_sets.append(t)
else:
tags.append(t)
annotations = list()
for ts in tag_sets:
tags_map = _get_tags_list(connection,
ts,
fetch_images,
append_raw_object=True)
for tmi in tags_map:
tobj = tmi.pop('obj')
try:
tags.pop(tags.index(tobj))
except ValueError:
pass
tagset_json = _tagset_to_json(ts, tags_map)
annotations.append(tagset_json)
for t in tags:
imgs_list = list()
if fetch_images:
imgs_list = _get_images_by_tag(t.getId(), connection)
annotations.append(_tag_to_json(t, imgs_list))
return annotations
def _get_images_by_tag(tag_id, connection):
switch_to_default_search_group(connection)
imgs_generator = connection.getObjectsByAnnotations('Image', [tag_id])
images = list()
for img in imgs_generator:
images.append(_image_to_json(img, connection))
return images
def get_dataset(connection, dataset_id, fetch_images=False, expand_img_series=False):
switch_to_default_search_group(connection)
dataset = connection.getObject('Dataset', dataset_id)
if dataset is not None:
if fetch_images:
images = _get_images_for_dataset(dataset, not expand_img_series)
else:
images = []
return _dataset_to_json(dataset, connection=connection, image_objects=images)
return None
def get_tag(connection, tag_id, fetch_images=False):
switch_to_default_search_group(connection)
tag = connection.getObject('TagAnnotation', tag_id)
if tag is not None and not _is_tagset(tag):
images = list()
if fetch_images:
images = _get_images_by_tag(tag_id, connection)
return _tag_to_json(tag, images)
else:
return None
def get_tagset(connection, tagset_id, fetch_tags=False, fetch_images=False):
switch_to_default_search_group(connection)
tagset = connection.getObject('TagAnnotation', tagset_id)
if tagset is not None and _is_tagset(tagset):
tags_map = list()
if fetch_tags:
tags_map = _get_tags_list(connection, tagset, fetch_images)
return _tagset_to_json(tagset, tags_map)
else:
return None
def get_tag(connection, tag_id, fetch_images=False):
switch_to_default_search_group(connection)
tag = connection.getObject('TagAnnotation', tag_id)
if tag is not None and not _is_tagset(tag):
images = list()
if fetch_images:
images = _get_images_by_tag(tag_id, connection)
return _tag_to_json(tag, images)
else:
return None
def get_tagset(connection, tagset_id, fetch_tags=False, fetch_images=False):
switch_to_default_search_group(connection)
tagset = connection.getObject('TagAnnotation', tagset_id)
if tagset is not None and _is_tagset(tagset):
tags_map = list()
if fetch_tags:
tags_map = _get_tags_list(connection, tagset, fetch_images)
return _tagset_to_json(tagset, tags_map)
else:
return None
def get_image(connection, image_id, fetch_rois=False):
switch_to_default_search_group(connection)
img = connection.getObject('Image', image_id)
if img is not None:
if fetch_rois:
roi_service = connection.getRoiService()
results = roi_service.findByImage(int(image_id), None)
rois = list(results.rois)
else:
rois = []
return _image_to_json(img, connection, True, rois)
return None
def get_image(connection, image_id, fetch_rois=False):
switch_to_default_search_group(connection)
img = connection.getObject('Image', image_id)
if img is not None:
if fetch_rois:
roi_service = connection.getRoiService()
results = roi_service.findByImage(int(image_id), None)
rois = list(results.rois)
else:
rois = []
return _image_to_json(img, connection, True, rois)
return None
def get_projects(connection, fetch_datasets=False):
switch_to_default_search_group(connection)
projects = list(connection.listProjects())
projects_json = []
for proj in projects:
if fetch_datasets:
datasets = list(proj.listChildren())
else:
datasets = []
projects_json.append(_project_to_json(proj, connection=connection,
datasets_map=((d, []) for d in datasets)))
return projects_json
def get_projects(connection, fetch_datasets=False):
switch_to_default_search_group(connection)
projects = list(connection.listProjects())
projects_json = []
for proj in projects:
if fetch_datasets:
datasets = list(proj.listChildren())
else:
datasets = []
projects_json.append(
_project_to_json(proj,
connection=connection,
datasets_map=((d, []) for d in datasets)))
return projects_json
def get_dataset(connection,
dataset_id,
fetch_images=False,
expand_img_series=False):
switch_to_default_search_group(connection)
dataset = connection.getObject('Dataset', dataset_id)
if dataset is not None:
if fetch_images:
images = _get_images_for_dataset(dataset, not expand_img_series)
else:
images = []
return _dataset_to_json(dataset,
connection=connection,
image_objects=images)
return None
def get_project(connection, project_id, fetch_datasets=False, fetch_images=False,
expand_img_series=False):
switch_to_default_search_group(connection)
project = connection.getObject('Project', project_id)
if project is not None:
datasets_map = []
if fetch_datasets:
datasets = list(project.listChildren())
for ds in datasets:
if fetch_images:
images = _get_images_for_dataset(ds, not expand_img_series)
else:
images = []
datasets_map.append((ds, images))
return _project_to_json(project, datasets_map=datasets_map,
connection=connection)
return None
def find_annotations(search_pattern, connection, fetch_images=False):
switch_to_default_search_group(connection)
query_service = connection.getQueryService()
query_params = omero.sys.ParametersI()
query_params.addString('search_pattern', '%%%s%%' % search_pattern)
query = '''
SELECT t FROM TagAnnotation t
WHERE lower(t.description) LIKE lower(:search_pattern)
OR lower(t.textValue) LIKE lower(:search_pattern)
'''
annotations = list()
for res in query_service.findAllByQuery(query, query_params):
res = TagAnnotationWrapper(connection, res)
if _is_tagset(res):
annotations.append(_tagset_to_json(res))
else:
imgs_list = list()
if fetch_images:
imgs_list = _get_images_by_tag(res.getId(), connection)
annotations.append(_tag_to_json(res, imgs_list))
return annotations
def get_project(connection,
project_id,
fetch_datasets=False,
fetch_images=False,
expand_img_series=False):
switch_to_default_search_group(connection)
project = connection.getObject('Project', project_id)
if project is not None:
datasets_map = []
if fetch_datasets:
datasets = list(project.listChildren())
for ds in datasets:
if fetch_images:
images = _get_images_for_dataset(ds, not expand_img_series)
else:
images = []
datasets_map.append((ds, images))
return _project_to_json(project,
datasets_map=datasets_map,
connection=connection)
return None
def find_annotations(search_pattern, connection, fetch_images=False):
switch_to_default_search_group(connection)
query_service = connection.getQueryService()
query_params = omero.sys.ParametersI()
query_params.addString('search_pattern', '%%%s%%' % search_pattern)
query = '''
SELECT t FROM TagAnnotation t
WHERE lower(t.description) LIKE lower(:search_pattern)
OR lower(t.textValue) LIKE lower(:search_pattern)
'''
annotations = list()
for res in query_service.findAllByQuery(query, query_params):
res = TagAnnotationWrapper(connection, res)
if _is_tagset(res):
annotations.append(_tagset_to_json(res))
else:
imgs_list = list()
if fetch_images:
imgs_list = _get_images_by_tag(res.getId(), connection)
annotations.append(_tag_to_json(res, imgs_list))
return annotations
def get_images_quick_list(connection, expand_imgs_series=False):
switch_to_default_search_group(connection)
images_list = []
# get OMERO images
imgs = connection.getObjects('Image')
if not expand_imgs_series:
imgs = _reduce_images_series(imgs)
for img in imgs:
images_list.append({
'omero_id': img.getId(),
'name': img.getName(),
'img_type':
'OMERO_IMG' # right now we only need to separate OMERO imgs from "special" ones like MIRAX
})
# get "special" images like MIRAX ones (actually, right now only the MIRAX ones...)
query_filter = {'mimetype': 'mirax/index'}
imgs = connection.getObjects('OriginalFile', attributes=query_filter)
for img in imgs:
images_list.append({
'omero_id': img.getId(),
'name': img.getName(),
'img_type': 'MIRAX'
})
return images_list
def get_original_files(connection, name, mimetype=None):
switch_to_default_search_group(connection)
query_filter = {'name': name}
if mimetype:
query_filter['mimetype'] = mimetype
return list(connection.getObjects('OriginalFile', attributes=query_filter))
def get_original_files(connection, name, mimetype=None):
switch_to_default_search_group(connection)
query_filter = {'name': name}
if mimetype:
query_filter['mimetype'] = mimetype
return list(connection.getObjects('OriginalFile', attributes=query_filter))