def get_script(request, script_name, conn): """Return a JS function to filter images by various params.""" dataset_id = request.GET.get('dataset') plate_id = request.GET.get('plate') field_id = request.GET.get('field') image_ids = request.GET.getlist('image') if plate_id and field_id: img_ids = get_image_ids(conn, plate_id, field_id) elif dataset_id: objects = conn.getObjects('Image', opts={'dataset': dataset_id}) img_ids = [i.id for i in objects] else: img_ids = [long(i) for i in image_ids] query_service = conn.getQueryService() if script_name == "ROI_count": # Want to get ROI count for images in plate # Get ROI counts params = ParametersI() params.addIds(img_ids) query = "select roi.image.id, count(roi.id) from Roi roi "\ "where roi.image.id in (:ids) group by roi.image" p = query_service.projection(query, params, conn.SERVICE_OPTS) roi_counts = {} for i in p: roi_counts[i[0].val] = i[1].val min_count = min(roi_counts.values()) max_count = max(roi_counts.values()) # Return a JS function that will be passed an object # e.g. {'type': 'Image', 'id': 1} # and should return true or false f = """(function filter(data, params) { var roi_counts = %s; if (isNaN(params.count) || params.count == '') return true; if (params.operator === '=') return roi_counts[data.id] == params.count; if (params.operator === '<') return roi_counts[data.id] < params.count; if (params.operator === '>') return roi_counts[data.id] > params.count; }) """ % json.dumps(roi_counts) filter_params = [ {'name': 'operator', 'type': 'text', 'values': ['>', '=', '<'], 'default': '>'}, {'name': 'count', 'type': 'number', 'default': '', 'title': '%s-%s' % (min_count, max_count)} ] return JsonResponse( { 'f': f, 'params': filter_params, })
def get_data(request, data_name, conn): """Return data for images in a Project, Dataset or Plate.""" project_id = request.GET.get('project') dataset_id = request.GET.get('dataset') plate_id = request.GET.get('plate') field_id = request.GET.get('field') if project_id: img_ids = get_project_image_ids(conn, project_id) elif dataset_id: objects = conn.getObjects('Image', opts={'dataset': dataset_id}) img_ids = [i.id for i in objects] elif plate_id and field_id: img_ids = get_image_ids(conn, plate_id, field_id) else: img_ids = request.GET.getlist('image') query_service = conn.getQueryService() if data_name == "ROI_stats_max_size": if plate_id: ns = "roi.pixel.intensities.summary" return get_image_map_annotations(conn, plate_id, 0, ns, "Max Points") if data_name == "ROI_count": # Want to get ROI count for images params = ParametersI() # Include "-1" so that if we have no Image IDs that the query does # not fail. It will not match anything. params.addIds([-1] + img_ids) query = "select roi.image.id, count(roi.id) from Roi roi "\ "where roi.image.id in (:ids) group by roi.image" p = query_service.projection(query, params, conn.SERVICE_OPTS) roi_counts = {} for i in img_ids: # Add placeholder 0 for all images roi_counts[i] = 0 for i in p: roi_counts[i[0].val] = i[1].val return roi_counts if data_name == "sizeT": # Want to get sizeT for images params = ParametersI() # Include "-1" so that if we have no Image IDs that the query does # not fail. It will not match anything. params.addIds([-1] + img_ids) query = "select pixels.image.id, pixels.sizeT from Pixels pixels "\ "where pixels.image.id in (:ids)" p = query_service.projection(query, params, conn.SERVICE_OPTS) size_t = {} for i in p: size_t[i[0].val] = i[1].val return size_t
def get_data(request, data_name, conn): """Return data for images in a Dataset or Plate.""" dataset_id = request.GET.get('dataset') plate_id = request.GET.get('plate') field_id = request.GET.get('field') if plate_id and field_id: img_ids = get_image_ids(conn, plate_id, field_id) elif dataset_id: objects = conn.getObjects('Image', opts={'dataset': dataset_id}) img_ids = [i.id for i in objects] query_service = conn.getQueryService() if data_name == "ROI_stats_max_size": if plate_id: ns = "roi.pixel.intensities.summary" return get_image_map_annotations(conn, plate_id, 0, ns, "Max Points") if data_name == "ROI_count": # Want to get ROI count for images params = ParametersI() params.addIds(img_ids) query = "select roi.image.id, count(roi.id) from Roi roi "\ "where roi.image.id in (:ids) group by roi.image" p = query_service.projection(query, params, conn.SERVICE_OPTS) roi_counts = {} for i in p: roi_counts[i[0].val] = i[1].val return roi_counts if data_name == "sizeT": # Want to get sizeT for images params = ParametersI() params.addIds(img_ids) query = "select pixels.image.id, pixels.sizeT from Pixels pixels "\ "where pixels.image.id in (:ids)" p = query_service.projection(query, params, conn.SERVICE_OPTS) size_t = {} for i in p: size_t[i[0].val] = i[1].val return size_t
def get_image_map_annotations(conn, plate_id, field_id, ns, key=None): """Get image IDs for images in Plate""" conn.SERVICE_OPTS.setOmeroGroup('-1') query_service = conn.getQueryService() iids = get_image_ids(conn, plate_id, field_id) params = ParametersI() params.addIds(iids) query = """select oal from ImageAnnotationLink as oal join fetch oal.details.owner left outer join fetch oal.child as ch left outer join fetch oal.parent as pa where pa.id in (:ids) and ch.ns='%s'""" % ns links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS) if key is None: return links map_values = {} for l in links: for kv in l.child.getMapValue(): if key == kv.name: map_values[l.parent.id.val] = long(kv.value) return map_values