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Merge pull request #342 from will-moore/initial_shape_id_set_undefined
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Unset initial_shape_id once selected
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@jburel
jburel authored Sep 8, 2020
2 parents eb9749d + 8711915 commit c411712
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Showing 3 changed files with 115 additions and 34 deletions.
130 changes: 96 additions & 34 deletions plugin/omero_iviewer/views.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,43 @@ def persist_rois(request, conn=None, **kwargs):
return JsonResponse(ret)


def get_query_for_rois_by_plane(the_z=None, the_t=None, z_end=None,
t_end=None, load_shapes=False):

clauses = ['roi.image.id = :id']
if the_z is not None:
where_z = "(shapes.theZ = %s or shapes.theZ is null)" % the_z
if z_end is not None:
where_z = """((shapes.theZ >= %s and shapes.theZ <= %s)
or shapes.theZ is null)""" % (the_z, z_end)
clauses.append(where_z)
if the_t is not None:
where_t = "(shapes.theT = %s or shapes.theT is null)" % the_t
if t_end is not None:
where_t = """((shapes.theT >= %s and shapes.theT <= %s)
or shapes.theT is null)""" % (the_t, t_end)
clauses.append(where_t)

query = """
select distinct(roi.id) from Roi roi
join roi.shapes as shapes
where %s
""" % ' and '.join(clauses)

if load_shapes:
# If we want to load ALL shapes for the ROIs (omero-marshal fails if
# any shapes are None) we use the query above to get ROI IDs, then
# load all ROIs with Shapes
query = """
select roi from Roi roi
join fetch roi.details.owner join fetch roi.details.creationEvent
left outer join fetch roi.shapes
where roi.id in (%s) order by roi.id
""" % (query)

return query


@login_required()
def rois_by_plane(request, image_id, the_z, the_t, z_end=None, t_end=None,
conn=None, **kwargs):
Expand All @@ -239,32 +276,8 @@ def rois_by_plane(request, image_id, the_z, the_t, z_end=None, t_end=None,
filter.limit = rint(limit)
params.theFilter = filter

where_z = "shapes.theZ = %s or shapes.theZ is null" % the_z
where_t = "shapes.theT = %s or shapes.theT is null" % the_t
if z_end is not None:
where_z = """(shapes.theZ >= %s and shapes.theZ <= %s)
or shapes.theZ is null""" % (the_z, z_end)
if t_end is not None:
where_t = """(shapes.theT >= %s and shapes.theT <= %s)
or shapes.theT is null""" % (the_t, t_end)

filter_query = """
select distinct(roi) from Roi roi
join roi.shapes as shapes
where (%s) and (%s)
and roi.image.id = :id
""" % (where_z, where_t)

# We want to load ALL shapes for the ROIs (omero-marshal fails if
# any shapes are None) but we want to filter by Shape so we use an inner
# query to get the ROI IDs filtered by Shape.
query = """
select roi from Roi roi
join fetch roi.details.owner join fetch roi.details.creationEvent
left outer join fetch roi.shapes
where roi.id in (%s) order by roi.id
""" % (filter_query)

query = get_query_for_rois_by_plane(the_z, the_t, z_end, t_end,
load_shapes=True)
rois = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
marshalled = []
for r in rois:
Expand All @@ -273,7 +286,8 @@ def rois_by_plane(request, image_id, the_z, the_t, z_end=None, t_end=None,
marshalled.append(encoder.encode(r))

# Modify query to only select count() and NOT paginate
query = filter_query.replace("distinct(roi)", "count(distinct roi)")
query = get_query_for_rois_by_plane(the_z, the_t, z_end, t_end)
query = query.replace("distinct(roi.id)", "count(distinct roi.id)")
params = omero.sys.ParametersI()
params.addId(image_id)
result = query_service.projection(query, params, conn.SERVICE_OPTS)
Expand Down Expand Up @@ -348,28 +362,73 @@ def plane_shape_counts(request, image_id, conn=None, **kwargs):
return JsonResponse({'data': counts})


def get_shape_info(conn, shape_id):
"""Returns dict of roi_id, image_id, theZ, theT from a shape ID."""
params = omero.sys.ParametersI()
params.addId(shape_id)

query = """
select roi.id,
image.id,
shape.theZ,
shape.theT
from Shape shape
join shape.roi roi
join roi.image image
where shape.id=:id"""

shapes = conn.getQueryService().projection(query, params,
conn.SERVICE_OPTS)
rsp = None
if len(shapes) > 0:
s = unwrap(shapes[0])
rsp = {
'roi_id': s[0],
'image_id': s[1],
'theZ': s[2],
'theT': s[3],
}
return rsp


@login_required()
def roi_page_data(request, obj_type, obj_id, conn=None, **kwargs):
"""
Get info for loading the correct 'page' of ROIs
Returns {image: {'id': 1}, roi_index: 123, roi_count: 3456}
"""
qs = conn.getQueryService()
image_id = None
roi_id = None
shape_info = None
ids = []
if obj_type == 'roi':
roi_id = int(obj_id)
roi = conn.getQueryService().get('Roi', roi_id)
roi = qs.get('Roi', roi_id)
image_id = roi.image.id.val
params = omero.sys.ParametersI()

params.addId(image_id)
query = "select roi.id from Roi roi where roi.image.id = :id"
ids = [i[0].val for i in qs.projection(query, params,
conn.SERVICE_OPTS)]
elif obj_type == 'shape':
image_id, roi_id = get_image_roi_id_for_shape(conn, obj_id)
shape_info = get_shape_info(conn, obj_id)
if shape_info is not None:
image_id = shape_info.get('image_id')
roi_id = shape_info.get('roi_id')
the_z = shape_info.get('theZ')
the_t = shape_info.get('theT')
query = get_query_for_rois_by_plane(the_z, the_t)
params = omero.sys.ParametersI()
params.addId(image_id)
result = qs.projection(query, params, conn.SERVICE_OPTS)
for roi in result:
ids.append(unwrap(roi[0]))
if image_id is None:
raise Http404(f'Could not find {obj_type}: {obj_id}')
qs = conn.getQueryService()
params = omero.sys.ParametersI()

params.addId(image_id)
query = "select roi.id from Roi roi where roi.image.id = :id"
ids = [i[0].val for i in qs.projection(query, params, conn.SERVICE_OPTS)]
ids.sort()
index = ids.index(roi_id)
rsp = {
Expand All @@ -378,6 +437,9 @@ def roi_page_data(request, obj_type, obj_id, conn=None, **kwargs):
'roi_index': index,
'roi_count': len(ids)
}
if shape_info is not None:
rsp['theT'] = shape_info.get('theT')
rsp['theZ'] = shape_info.get('theZ')
return JsonResponse(rsp)


Expand Down
7 changes: 7 additions & 0 deletions src/model/regions_info.js
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Original file line number Diff line number Diff line change
Expand Up @@ -366,6 +366,13 @@ export default class RegionsInfo {
success : (response) => {
const page = parseInt(response.roi_index / this.roi_page_size);
this.roi_page_number = page;
// This will update the viewer (change listeners)
if (response.theZ != undefined) {
this.image_info.dimensions.z = response.theZ;
}
if (response.theT != undefined) {
this.image_info.dimensions.t = response.theT;
}
this.requestData(true);
}, error : (error) => {
this.is_pending = false;
Expand Down
12 changes: 12 additions & 0 deletions src/viewers/ol3-viewer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -851,18 +851,30 @@ export default class Ol3Viewer extends EventSubscriber {
let viewerT = this.viewer.getDimensionIndex('t');
let viewerZ = this.viewer.getDimensionIndex('z');
let viewerC = this.viewer.getDimensionIndex('c');
// Update this.image_config.image_info to load a new Z/T plane...
let shape =
this.image_config.regions_info.getShape(shapeSelection);
let correctPlane = true;
let shapeT = typeof shape.TheT === 'number' ? shape.TheT : -1;
if (shapeT !== -1 && shapeT !== viewerT) {
this.image_config.image_info.dimensions.t = shapeT;
correctPlane = false;
delay += 25;
}
let shapeZ = typeof shape.TheZ === 'number' ? shape.TheZ : -1;
if (shapeZ !== -1 && shapeZ !== viewerZ) {
this.image_config.image_info.dimensions.z = shapeZ;
correctPlane = false;
delay += 25;
}
if (correctPlane) {
// remove initial_shape_id, so we don't get directed to shape again when browsing
// a new plane, (when ROIs are loaded and initRegions() is called again)
this.image_config.image_info.initial_shape_id = undefined;
} else {
// browsing to new plane - this will select Shape when ROIs load
this.image_config.image_info.initial_shape_id = shape['@id'];
}
let shapeC = typeof shape.TheC === 'number' ? shape.TheC : -1;
if (shapeC !== -1 && viewerC.indexOf(shapeC) === -1) {
this.image_config.image_info.channels[shapeC].active = true;
Expand Down

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