Exemple #1
0
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
Exemple #5
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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
Exemple #9
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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
Exemple #10
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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
Exemple #19
0
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
Exemple #21
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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))