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