diff --git a/omeroweb/webclient/views.py b/omeroweb/webclient/views.py
index c9dd82121f..504ce999d3 100755
--- a/omeroweb/webclient/views.py
+++ b/omeroweb/webclient/views.py
@@ -1468,6 +1468,23 @@ def load_plate(request, o1_type=None, o1_id=None, conn=None, **kwargs):
template = None
if "plate" in kw or "acquisition" in kw:
fields = manager.getNumberOfFields()
+ if "acquisition" in kw:
+ # need to offset the index for 0-indexing at acquisition level
+ qs = conn.getQueryService()
+ p = omero.sys.ParametersI()
+ p.add("acqid", rlong(o1_id))
+ query = (
+ "SELECT max(index(ws)) - min(index(ws)) "
+ "FROM Well w "
+ "JOIN w.wellSamples ws "
+ "WHERE ws.plateAcquisition.id = :acqid "
+ "GROUP BY w.id"
+ )
+ res = [r[0].getValue() for r in qs.projection(query, p, conn.SERVICE_OPTS)]
+ if len(res) >= 1:
+ # The range of the fields is set for the current acquisition
+ fields = (0, max(res))
+
if fields is not None:
form_well_index = WellIndexForm(initial={"index": index, "range": fields})
if index == 0:
diff --git a/omeroweb/webgateway/plategrid.py b/omeroweb/webgateway/plategrid.py
index 636eb56d15..9d6e8a966d 100644
--- a/omeroweb/webgateway/plategrid.py
+++ b/omeroweb/webgateway/plategrid.py
@@ -13,7 +13,7 @@
import logging
import omero.sys
-from omero.rtypes import rint
+from omero.rtypes import rint, rlong
logger = logging.getLogger(__name__)
@@ -25,16 +25,26 @@ class PlateGrid(object):
methods useful for displaying the contents of the plate as a grid.
"""
- def __init__(self, conn, pid, fid, thumbprefix="", plate_layout=None):
+ def __init__(self, conn, pid, fid, thumbprefix="", plate_layout=None, acqid=None):
"""
Constructor
param: plate_layout is "expand" to expand plate to multiple of 8 x 12
or "shrink" to ignore all wells before the first row/column
+
+ fid: the field index relative to the lowest "absolute field index"
+ for that well. When filtering the image samples with an
+ acquisition ID (acqid), the lowest field index may be
+ different for each well.
+ In the range [0, max_sample_per_well]
+ (or [0, max_sample_per_well_per_acquisition] with an acqid)
+
+ acqid: the acquisition ID to filter the WellSamples.
"""
self.plate = conn.getObject("plate", int(pid))
self._conn = conn
self.field = fid
+ self.acquisition = acqid
self._thumbprefix = thumbprefix
self._metadata = None
self.plate_layout = plate_layout
@@ -57,8 +67,22 @@ def metadata(self):
"join ws.image img "
"join img.details.owner author "
"where well.plate.id = :id "
- "and index(ws) = :wsidx"
)
+ if self.acquisition is not None:
+ # Offseting field index per well for the plateacquisition
+ query += (
+ "and ws.plateAcquisition.id = :acqid "
+ "and index(ws) - ("
+ " SELECT MIN(index(ws_inner)) "
+ " FROM Well well_inner "
+ " JOIN well_inner.wellSamples ws_inner "
+ " WHERE ws_inner.plateAcquisition.id = :acqid "
+ " AND well_inner.id = well.id "
+ ") = :wsidx "
+ )
+ params.add("acqid", rlong(self.acquisition))
+ else:
+ query += "and index(ws) = :wsidx "
results = q.projection(query, params, self._conn.SERVICE_OPTS)
min_row = 0
diff --git a/omeroweb/webgateway/static/webgateway/js/ome.plateview.js b/omeroweb/webgateway/static/webgateway/js/ome.plateview.js
index 7b8b911dab..ed69bca6d0 100644
--- a/omeroweb/webgateway/static/webgateway/js/ome.plateview.js
+++ b/omeroweb/webgateway/static/webgateway/js/ome.plateview.js
@@ -4,7 +4,7 @@
* Depends on jquery
*
* Copyright (c) 2011 Glencoe Software, Inc. All rights reserved.
- *
+ *
* This software is distributed under the terms described by the LICENCE file
* you can find at the root of the distribution bundle, which states you are
* free to use it only for non commercial purposes.
@@ -39,14 +39,14 @@
* - adds the pv-focus css class to the thumb pointed to by the elm jQuery object
* removing it from any other thumbnail eventually focused on this plate
* - elm is the jQuery object for the thumb to be focused
- *
+ *
* plate.rmFocus(elm)
* - removes the pv-focus css class to the thumb pointed to by the elm jQuery object
* or from any thumbnail in this plate if elm is null or undefined
* - elm is the optional jQuery object for the thumb to loose focused
*
* - Events -
- *
+ *
* thumbClick(ev, welldata, thumb)
* - triggered when there's a mouse click on a thumb.
* - welldata holds a dictionary holding metadata for the clicked well
@@ -65,7 +65,7 @@
* - thumb is the jQuery object for the thumb image
*
* - jQuery obj data attributes -
- *
+ *
* noFocus
* - if true, prevents css pv-focus class to be added on setFocus
*
@@ -205,13 +205,17 @@ jQuery._WeblitzPlateview = function (container, options) {
_this.self.trigger('_resetLoaded');
};
- this.load = function (pid,field) {
+ this.load = function (pid,field,acquisition) {
$('table img', _this.self).remove();
$('table div.placeholder', _this.self).removeClass('placeholder').addClass('loading');
if (field === undefined) {
field = 0;
}
- var url = opts.baseurl+'/plate/'+pid+'/'+field+'/';
+
+ var url = opts.baseurl+'/plate/'+pid+'/'+field+'/'
+ if (acquisition) {
+ url += acquisition+'/';
+ }
if (opts.size) {
url += '?size='+opts.size;
}
diff --git a/omeroweb/webgateway/urls.py b/omeroweb/webgateway/urls.py
index 449360d6f1..3d529ab41a 100644
--- a/omeroweb/webgateway/urls.py
+++ b/omeroweb/webgateway/urls.py
@@ -365,7 +365,7 @@
"""
webgateway_plategrid_json = re_path(
- r"^plate/(?P
[0-9]+)/(?:(?P[0-9]+)/)?$",
+ r"^plate/(?P[0-9]+)/(?:(?P[0-9]+)/)?(?:(?P[0-9]+)/)?$",
views.plateGrid_json,
name="webgateway_plategrid_json",
)
diff --git a/omeroweb/webgateway/views.py b/omeroweb/webgateway/views.py
index 4448d376ab..228d8a124d 100644
--- a/omeroweb/webgateway/views.py
+++ b/omeroweb/webgateway/views.py
@@ -1602,7 +1602,7 @@ def urlprefix(iid):
@login_required()
@jsonp
-def plateGrid_json(request, pid, field=0, conn=None, **kwargs):
+def plateGrid_json(request, pid, field=0, acquisition=None, conn=None, **kwargs):
"""
Layout depends on settings 'omero.web.plate_layout' which
can be overridden with request param e.g. ?layout=shrink.
@@ -1614,6 +1614,13 @@ def plateGrid_json(request, pid, field=0, conn=None, **kwargs):
field = int(field or 0)
except ValueError:
field = 0
+
+ if acquisition is not None:
+ try:
+ acquisition = int(acquisition)
+ except ValueError:
+ acquisition = None
+
prefix = kwargs.get("thumbprefix", "webgateway_render_thumbnail")
thumbsize = getIntOrDefault(request, "size", None)
logger.debug(thumbsize)
@@ -1631,8 +1638,9 @@ def get_thumb_url(iid):
conn,
pid,
field,
- kwargs.get("urlprefix", get_thumb_url),
+ thumbprefix=kwargs.get("urlprefix", get_thumb_url),
plate_layout=layout,
+ acqid=acquisition,
)
plate = plateGrid.plate
@@ -1773,6 +1781,8 @@ def marshal_pos(w):
d[x] = {"value": p.getValue(), "unit": str(p.getUnit())}
return d
+ plate = well.getParent()
+ run_d = {r.getId(): r.getName() for r in plate.listPlateAcquisitions()}
wellImgs = []
for ws in well.listChildren():
# optionally filter by acquisition 'run'
@@ -1788,6 +1798,8 @@ def marshal_pos(w):
pos = marshal_pos(ws)
if len(pos.keys()) > 0:
m["position"] = pos
+ if ws.plateAcquisition is not None:
+ m["name"] += f" [Run: {run_d[ws.plateAcquisition._id._val]}]"
wellImgs.append(m)
return wellImgs