Merge pull request #542 from Tom-TBT/plateAcquisition_view

PlateAcquisition filtering with plate display

omeroweb/webclient/templates/webclient/data/includes/center_plugin.thumbs.js.html

@@ -666,7 +666,7 @@
             html = "<option value='0'>Choose Tag</option>" + html;
             $("#filter_by_tag").html(html);
 
-            // hide filtered images 
+            // hide filtered images
             $("#dataIcons li.row").each(function() {
                 var $this = $(this),
                     iid = parseInt($this.attr("data-id"), 10);
@@ -1005,14 +1005,9 @@
 
             switch(nodeType) {
                 case 'plate':
-                    // Only load plates if it has a single 'Run' (or none)
-                    if (node.children.length < 2) {
-                        url += 'load_plate/' + nodeType + '/' + nodeId + '/?index=' + newField;
-                        if (show) {
-                            url += "&show=" + show;
-                        }
-                    } else {
-                        url = undefined;
+                    url += 'load_plate/' + nodeType + '/' + nodeId + '/?index=' + newField;
+                    if (show) {
+                        url += "&show=" + show;
                     }
                     break;
                 case 'acquisition':

omeroweb/webclient/templates/webclient/data/plate.html

@@ -22,11 +22,11 @@
 -->
 {% endcomment %}
 
-    
+
     <link rel="stylesheet" type="text/css" href="{% static "webgateway/css/ome.plateview.css"|add:url_suffix %}" media="all" />
 
     <script type="text/javascript">
-        
+
         $(document).ready(function() {
 
             // Drag to resize #wellImagesContainer bottom panel
@@ -169,7 +169,7 @@
             wpv.self.selectable({
                 filter: 'td.well',
                 distance: 2,
-                stop: function(){  
+                stop: function(){
                     var $selected = $('td.ui-selected', this);
                     syncTreeSelection($selected, {{ index }}, '{{ manager.getPermsCss }}');
                     showImagesInWell();
@@ -218,7 +218,7 @@
             {% endif %}
 
             // Kick-off loading...
-            wpv.load({{ manager.getPlateId }}, {{ index }});
+            wpv.load({{ manager.getPlateId }}, {{ index }}, {{ acquisition }});
 
 
             // Lower panel.....
@@ -297,7 +297,7 @@
 
     </script>
 
-    
+
     <!--content-->
 <!-- We add/remove class .showWellImages to #content_details expose #wellImages panel -->
 <div class='fillSpace' style="top: 0px; height: 29px">

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:

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

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;
     }

omeroweb/webgateway/urls.py

@@ -365,7 +365,7 @@
 """
 
 webgateway_plategrid_json = re_path(
-    r"^plate/(?P<pid>[0-9]+)/(?:(?P<field>[0-9]+)/)?$",
+    r"^plate/(?P<pid>[0-9]+)/(?:(?P<field>[0-9]+)/)?(?:(?P<acquisition>[0-9]+)/)?$",
     views.plateGrid_json,
     name="webgateway_plategrid_json",
 )

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