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
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')
dtype = "Image"
js_object_attr = "id"
if dataset_id:
objects = conn.getObjects('Image', opts={'dataset': dataset_id})
obj_ids = [i.id for i in objects]
elif plate_id:
dtype = "Well"
js_object_attr = "wellId"
obj_ids = get_well_ids(conn, plate_id)
query_service = conn.getQueryService()
if script_name == "Rating":
params = ParametersI()
params.addIds(obj_ids)
query = """select oal from %sAnnotationLink 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.class=LongAnnotation
and ch.ns='openmicroscopy.org/omero/insight/rating'""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
ratings = {}
for l in links:
ratings[l.parent.id.val] = l.child.longValue.val
# 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 ratings = %s;
index = ratings[data.%s] == params.rating
return (params.rating === '-' || index);
})
""" % (json.dumps(ratings), js_object_attr)
filter_params = [{
'name': 'rating',
'type': 'text',
'values': ['-', '1', '2', '3', '4', '5'],
'default': '-',
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
if script_name == "Comment":
params = ParametersI()
params.addIds(obj_ids)
query = """select oal from %sAnnotationLink as oal
left outer join fetch oal.child as ch
left outer join oal.parent as pa
where pa.id in (:ids) and ch.class=CommentAnnotation""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
comments = {}
for l in links:
iid = l.parent.id.val
if iid not in comments:
comments[iid] = ""
comments[iid] = " ".join([comments[iid], l.child.textValue.val])
# Return a JS function that will be passed a data object
# e.g. {'type': 'Image', 'id': 1}
# and a params object of {'paramName': value}
# and should return true or false
f = """(function filter(data, params) {
var comments = %s;
index = comments[data.%s] &&
comments[data.%s].indexOf(params.comment) > -1
return (params.comment === '' || index);
})
""" % (json.dumps(comments), js_object_attr, js_object_attr)
filter_params = [{
'name': 'comment',
'type': 'text',
'default': '',
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
if script_name == "Tag":
params = ParametersI()
params.addIds(obj_ids)
query = """select oal from %sAnnotationLink as oal
left outer join fetch oal.child as ch
left outer join oal.parent as pa
where pa.id in (:ids) and ch.class=TagAnnotation""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
tags = {}
all_tags = []
for l in links:
iid = l.parent.id.val
text = l.child.textValue.val
all_tags.append(text)
if iid not in tags:
tags[iid] = []
tags[iid].append(text)
# remove duplicates
all_tags = list(set(all_tags))
# Return a JS function that will be passed a data object
# e.g. {'type': 'Image', 'id': 1}
# and a params object of {'paramName': value}
# and should return true or false
f = """(function filter(data, params) {
var tags = %s;
index = tags[data.%s] && tags[data.%s].indexOf(params.tag) > -1
return (params.tag === 'Choose_Tag' || index);
})
""" % (json.dumps(tags), js_object_attr, js_object_attr)
all_tags.insert(0, "Choose_Tag")
filter_params = [{
'name': 'tag',
'type': 'text',
'default': "Choose_Tag",
'values': all_tags,
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
def get_script(request, script_name, conn):
"""Return a JS function to filter images by various params."""
project_id = request.GET.get('project')
dataset_id = request.GET.get('dataset')
plate_id = request.GET.get('plate')
image_ids = request.GET.getlist('image')
dtype = "Image"
js_object_attr = "id"
if project_id:
obj_ids = get_project_image_ids(conn, project_id)
elif dataset_id:
objects = conn.getObjects('Image', opts={'dataset': dataset_id})
obj_ids = [i.id for i in objects]
elif plate_id:
dtype = "Well"
js_object_attr = "wellId"
obj_ids = get_well_ids(conn, plate_id)
else:
obj_ids = [int(i) for i in image_ids]
query_service = conn.getQueryService()
params = ParametersI()
# Include "-1" so that if we have no object IDs that the query does
# not fail. It will not match anything.
params.addIds([-1] + obj_ids)
if script_name == "Rating":
query = """select oal from %sAnnotationLink 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.class=LongAnnotation
and ch.ns='openmicroscopy.org/omero/insight/rating'""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
ratings = {}
for l in links:
ratings[l.parent.id.val] = l.child.longValue.val
# 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 ratings = %s;
var index = ratings[data.%s] == params.rating
return (params.rating === '-' || index);
})
""" % (json.dumps(ratings), js_object_attr)
filter_params = [{
'name': 'rating',
'type': 'text',
'values': ['-', '1', '2', '3', '4', '5'],
'default': '-',
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
if script_name == "Comment":
query = """select oal from %sAnnotationLink as oal
left outer join fetch oal.child as ch
left outer join oal.parent as pa
where pa.id in (:ids) and ch.class=CommentAnnotation""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
comments = {}
for l in links:
iid = l.parent.id.val
if iid not in comments:
comments[iid] = ""
comments[iid] = " ".join([comments[iid], l.child.textValue.val])
# Return a JS function that will be passed a data object
# e.g. {'type': 'Image', 'id': 1}
# and a params object of {'paramName': value}
# and should return true or false
f = """(function filter(data, params) {
var comments = %s;
var index = comments[data.%s] &&
comments[data.%s].indexOf(params.comment) > -1
return (params.comment === '' || index);
})
""" % (json.dumps(comments), js_object_attr, js_object_attr)
filter_params = [{
'name': 'comment',
'type': 'text',
'default': '',
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
if script_name == "Tag":
query = """select oal from %sAnnotationLink as oal
left outer join fetch oal.child as ch
left outer join oal.parent as pa
where pa.id in (:ids) and ch.class=TagAnnotation""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
tags = {}
all_tags = []
for l in links:
iid = l.parent.id.val
text = l.child.textValue.val
all_tags.append(text)
if iid not in tags:
tags[iid] = []
tags[iid].append(text)
# remove duplicates
all_tags = list(set(all_tags))
# Return a JS function that will be passed a data object
# e.g. {'type': 'Image', 'id': 1}
# and a params object of {'paramName': value}
# and should return true or false
f = """(function filter(data, params) {
var tags = %s;
var index = tags[data.%s] && tags[data.%s].indexOf(params.tag) > -1
return (params.tag === 'Choose_Tag' || index);
})
""" % (json.dumps(tags), js_object_attr, js_object_attr)
all_tags.insert(0, "Choose_Tag")
filter_params = [{
'name': 'tag',
'type': 'text',
'default': "Choose_Tag",
'values': all_tags,
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
if script_name == "Key_Value":
query = """select oal from %sAnnotationLink as oal
left outer join fetch oal.child as ch
left outer join oal.parent as pa
where pa.id in (:ids) and ch.class=MapAnnotation""" % dtype
links = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
# Dict of {'key': {iid: 'value', iid: 'value'}}
map_values = defaultdict(dict)
for l in links:
iid = l.parent.id.val
for kv in l.child.getMapValue():
map_values[kv.name][iid] = kv.value
key_placeholder = "Pick key..."
# Return a JS function that will be passed a data object
# e.g. {'type': 'Image', 'id': 1}
# and a params object of {'paramName': value}
# and should return true or false
f = """
(function filter(data, params) {
var map_values = %s;
var key_placeholder = "%s";
if (params.key === key_placeholder) return true;
if (map_values[params.key] && map_values[params.key][data.%s]) {
var match = map_values[params.key][data.%s].indexOf(params.query) > -1;
return (params.query === '' || match);
}
return false;
})
""" % (json.dumps(map_values), key_placeholder, js_object_attr,
js_object_attr)
keys = list(map_values.keys())
keys.sort(key=lambda x: x.lower())
filter_params = [{
'name': 'key',
'type': 'text',
'values': [key_placeholder] + keys,
'default': key_placeholder
}, {
'name': 'query',
'type': 'text',
'default': ''
}]
return JsonResponse({
'f': f,
'params': filter_params,
})
rows = query_service.projection(query, params)
plate_ids = [row[0].val for row in rows]
assert plate_ids
# Loop through each field of those plates.
query = """
SELECT id, image.name, image.fileset.id, well.row, well.column, well.plate.name
FROM WellSample
WHERE well.plate.id IN (:ids)
"""
params = ParametersI()
params.addIds(plate_ids)
rows = query_service.projection(query, params)
for row in rows:
field_id = row[0].val
image_name = row[1].val
fileset_id = row[2].val
well_row = row[3].val
well_column = row[4].val
plate_name = row[5].val
# Figure the expected image name for this field.
image_name_expected = '{} [Well {}{}, Field 1]' \
.format(plate_name, chr(65 + well_row), 1 + well_column)
rows = query_service.projection(query, params)
plate_ids = [row[0].val for row in rows]
assert plate_ids
# Loop through each field of those plates.
query = """
SELECT id, image.name, image.fileset.id, well.row, well.column, well.plate.name
FROM WellSample
WHERE well.plate.id IN (:ids)
"""
params = ParametersI()
params.addIds(plate_ids)
rows = query_service.projection(query, params)
for row in rows:
field_id = row[0].val
image_name = row[1].val
fileset_id = row[2].val
well_row = row[3].val
well_column = row[4].val
plate_name = row[5].val
# Figure the expected image name for this field.
image_name_expected = '{} [Well {}{}, Field 1]' \
.format(plate_name, chr(65 + well_row), 1 + well_column)
