4-3-3 fixes.

components/tools/OmeroPy/scripts/omero/util_scripts/Channel_Offsets.py

@@ -230,57 +230,57 @@ def runAsScript():
     scripts.List("IDs", optional=False, grouping="2",
         description="List of Dataset IDs or Image IDs to process.").ofType(rlong(0)),
 
-    scripts.Bool("Channel_1", grouping="3", default=True,
+    scripts.String("New_Dataset_Name", grouping="3",
+        description="If you want the new image(s) in a new Dataset, put name here"),
+
+    scripts.Bool("Channel_1", grouping="4", default=True,
         description="Choose to include this channel in the output image"),
 
-    scripts.Int("Channel1_X_shift", grouping="3.1", default=0,
+    scripts.Int("Channel1_X_shift", grouping="4.1", default=0,
         description="Number of pixels to shift this channel in the X direction. (negative to shift left)"),
 
-    scripts.Int("Channel1_Y_shift", grouping="3.2", default=0,
+    scripts.Int("Channel1_Y_shift", grouping="4.2", default=0,
         description="Number of pixels to shift this channel in the Y direction. (negative to shift up)"),
 
-    scripts.Int("Channel1_Z_shift", grouping="3.3", default=0,
+    scripts.Int("Channel1_Z_shift", grouping="4.3", default=0,
         description="Offset channel by a number of Z-sections"),
 
-    scripts.Bool("Channel_2", grouping="4", default=True,
+    scripts.Bool("Channel_2", grouping="5", default=True,
         description="Choose to include this channel in the output image"),
 
-    scripts.Int("Channel2_X_shift", grouping="4.1", default=0,
+    scripts.Int("Channel2_X_shift", grouping="5.1", default=0,
         description="Number of pixels to shift this channel in the X direction. (negative to shift left)"),
 
-    scripts.Int("Channel2_Y_shift", grouping="4.2", default=0,
+    scripts.Int("Channel2_Y_shift", grouping="5.2", default=0,
         description="Number of pixels to shift this channel in the Y direction. (negative to shift up)"),
 
-    scripts.Int("Channel2_Z_shift", grouping="4.3", default=0,
+    scripts.Int("Channel2_Z_shift", grouping="5.3", default=0,
         description="Offset channel by a number of Z-sections"),
 
-    scripts.Bool("Channel_3", grouping="5", default=False,
+    scripts.Bool("Channel_3", grouping="6", default=False,
         description="Choose to include this channel in the output image"),
 
-    scripts.Int("Channel3_X_shift", grouping="5.1", default=0,
+    scripts.Int("Channel3_X_shift", grouping="6.1", default=0,
         description="Number of pixels to shift this channel in the X direction. (negative to shift left)"),
 
-    scripts.Int("Channel3_Y_shift", grouping="5.2", default=0,
+    scripts.Int("Channel3_Y_shift", grouping="6.2", default=0,
         description="Number of pixels to shift this channel in the Y direction. (negative to shift up)"),
 
-    scripts.Int("Channel3_Z_shift", grouping="5.3", default=0,
+    scripts.Int("Channel3_Z_shift", grouping="6.3", default=0,
         description="Offset channel by a number of Z-sections"),
 
-    scripts.Bool("Channel_4", grouping="6", default=False,
+    scripts.Bool("Channel_4", grouping="7", default=False,
         description="Choose to include this channel in the output image"),
 
-    scripts.Int("Channel4_X_shift", grouping="6.1", default=0,
+    scripts.Int("Channel4_X_shift", grouping="7.1", default=0,
         description="Number of pixels to shift this channel in the X direction. (negative to shift left)"),
 
-    scripts.Int("Channel4_Y_shift", grouping="6.2", default=0,
+    scripts.Int("Channel4_Y_shift", grouping="7.2", default=0,
         description="Number of pixels to shift this channel in the Y direction. (negative to shift up)"),
 
-    scripts.Int("Channel4_Z_shift", grouping="6.3", default=0,
+    scripts.Int("Channel4_Z_shift", grouping="7.3", default=0,
         description="Offset channel by a number of Z-sections"),
 
-    scripts.String("New_Dataset_Name", grouping="7",
-        description="If you want the new image(s) in a new Dataset, put name here"),
-
     version = "4.2.0",
     authors = ["William Moore", "OME Team"],
     institutions = ["University of Dundee"],

components/tools/OmeroWeb/omeroweb/media/omeroweb/javascript/popup.js

@@ -38,19 +38,19 @@ function openPopup(url) {
     return false;
 }
 
-var activitiesWindow = null;
+
 function popupActivites(url) {
     // IE8 doesn't support arbitrary text for 'name' 2nd arg.  #6118
-    activitiesWindow = window.open(url, 'Activities', config='height=600,width=850,left=50,top=50,toolbar=no,menubar=no,scrollbars=yes,resizable=yes,location=no,directories=no,status=no');
+    var w = 650;
+    var h = 400;
+    var left = parseInt((screen.availWidth/2) - (w/2));
+    var top = parseInt((screen.availHeight - h)/3);
+    var activitiesWindow = window.open(url, 'Activities', config='height='+h+',width='+w+',left='+left+',top='+top+',toolbar=no,menubar=no,scrollbars=yes,resizable=yes,location=no,directories=no,status=no');
     if(!activitiesWindow.closed) activitiesWindow.focus();
-    return false;
-}
-function refreshActivitiesWindow(url) {
-    if (activitiesWindow != undefined) {
-        if(!activitiesWindow.closed) activitiesWindow.location.href = url;
-    }
+    return activitiesWindow;
 }
 
+
 function openCenteredWindow(url) {
     var width = 550;
     var height = 600;

components/tools/OmeroWeb/omeroweb/settings.py

@@ -170,6 +170,11 @@ def leave_none_unset(s):
     "omero.web.server_email": ["SERVER_EMAIL", None, identity],
     "omero.web.server_list": ["SERVER_LIST", '[["localhost", 4064, "omero"]]', json.loads],
     "omero.web.use_eman2": ["USE_EMAN2", "false", parse_boolean],
+    # the following parameters configure when to show/hide the 'Volume viewer' icon in the Image metadata panel
+    "omero.web.open_astex_max_side": ["OPEN_ASTEX_MAX_SIDE", 400, int],
+    "omero.web.open_astex_min_side": ["OPEN_ASTEX_MIN_SIDE", 20, int],
+    "omero.web.open_astex_max_voxels": ["OPEN_ASTEX_MAX_VOXELS", 27000000, int],  # 300 x 300 x 300
+
     "omero.web.scripts_to_ignore": ["SCRIPTS_TO_IGNORE", '["/omero/figure_scripts/Movie_Figure.py", "/omero/figure_scripts/Split_View_Figure.py", "/omero/figure_scripts/Thumbnail_Figure.py", "/omero/figure_scripts/ROI_Split_Figure.py", "/omero/export_scripts/Make_Movie.py"]', parse_paths],
 }
 

components/tools/OmeroWeb/omeroweb/webclient/controller/container.py

@@ -143,24 +143,29 @@ def openAstexViewerCompatible(self):
         Is the image suitable to be viewed with the Volume viewer 'Open Astex Viewer' applet?
         Image must be a 'volume' of suitable dimensions and not too big.
         """
-        MIN_Z = 20
+        from django.conf import settings 
+        MAX_SIDE = settings.OPEN_ASTEX_MAX_SIDE     # default is 400
+        MIN_SIDE = settings.OPEN_ASTEX_MIN_SIDE     # default is 20
+        MAX_VOXELS = settings.OPEN_ASTEX_MAX_VOXELS # default is 15625000 (250 * 250 * 250)
 
-        MAX_VOL = (400 * 400 * 400)
+        print "Max side, min side, max voxels", MAX_SIDE, MIN_SIDE, MAX_VOXELS
         if self.image is None:
             return False
         sizeZ = self.image.getSizeZ()
-        if sizeZ < MIN_Z: return False
+        if self.image.getSizeC() > 1: return False
         sizeX = self.image.getSizeX()
         sizeY = self.image.getSizeY()
+        if sizeZ < MIN_SIDE or sizeX < MIN_SIDE or sizeY < MIN_SIDE: return False
+        if sizeX > MAX_SIDE or sizeY > MAX_SIDE or sizeZ > MAX_SIDE: return False
         voxelCount = (sizeX * sizeY * sizeZ)
-        if voxelCount > MAX_VOL: return False
+        if voxelCount > MAX_VOXELS: return False
 
         try:    # if scipy ndimage is not available for interpolation, can only handle smaller images
             import scipy.ndimage
         except ImportError:
             logger.debug("Failed to import scipy.ndimage - Open Astex Viewer limited to display of smaller images.")
-            MAX_VOL = (160 * 160 * 160)
-            if voxelCount > MAX_VOL: return False
+            MAX_VOXELS = (160 * 160 * 160)
+            if voxelCount > MAX_VOXELS: return False
 
         return True
 
@@ -419,7 +424,7 @@ def annotationList(self):
                 else:
                     annTypes[annClass].append(ann)
 
-        self.text_annotations.sort(key=lambda x: x.creationEventDate())
+        self.text_annotations.sort(key=lambda x: x.creationEventDate(), reverse=True)
         self.file_annotations.sort(key=lambda x: x.creationEventDate())
         self.rating_annotations.sort(key=lambda x: x.creationEventDate())
         self.tag_annotations.sort(key=lambda x: x.textValue)

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/annotations/open_astex_viewer.html

@@ -306,8 +306,15 @@ <h3>{{ image.getName|slice:":20" }}</h3>
         <!--    {% if pixelRange %} ({{ pixelRange.0|floatformat:4 }} - {{ pixelRange.1|floatformat:4 }}) {% endif %} -->
             <hr />
         <form onsubmit="return false">
-            Map Size:
-            <div id="data_urls">
+            Map Size: {{ image.getSizeX }} x {{ image.getSizeY }} x {{ image.getSizeZ }}
+            {% if sizeOptions.small %}
+            <div>
+                (scaled to: {{ sizeOptions.small.x|floatformat:0 }} x {{ sizeOptions.small.y|floatformat:0 }} x {{ sizeOptions.small.z|floatformat:0 }})
+            </div>
+
+            {% endif %}
+            <!-- Hiding resize options for now - Not performing as expected -->
+            <div id="data_urls" style="display:none">
                 {% if sizeOptions.small %}
                 <div>
                     <input type="radio" name="sizeMap" checked="true" value="small" />

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/base/header.html

@@ -24,24 +24,43 @@
 
 {% ifnotequal nav.menu "status" %}
 <script>
+
+    var launchActivities = function() {
+        activities_Window = popupActivites('{% url status %}');
+    }
+
+    // this is called by the setInterval loop below
+    var progressAjaxUpdate = function(i) {
+        $.ajaxSetup({ cache: false });      // IE8 etc caches json by default
+        $.getJSON("{% url progress %}", function(data) {
+            if (data.inprogress==0) {
+                if (i != undefined) clearInterval(i);
+                $("#progress").hide();
+                $("#jobstatus").html(data.inprogress + ' job(s) in progress');
+                if(data.failure>0) {
+                    $("#jobstatus").html(data.failure + ' job(s) failed');
+                } else {
+                    $("#jobstatus").html('0 job(s)');
+                } return;
+            }
+            $("#progress").show();
+            $("#jobstatus").html(data.inprogress + ' job(s) in progress');
+            $.ajaxSetup({ cache: true });
+        });
+    }
 
     var refreshProgressBar = function() {
-        refreshActivitiesWindow('{% url status %}');
+        if (window.activities_Window) {
+            if (window.activities_Window.refresh_page) {
+                window.activities_Window.refresh_page();
+            };
+            window.activities_Window.webclient_window = window;
+            //activities_Window.testBrowseParent();
+        }
+        progressAjaxUpdate();
         var i = setInterval(function (){
-            $.getJSON("{% url progress %}", function(data) {
-                if (data.inprogress==0) {
-                    clearInterval(i);
-                    $("#progress").hide();
-                    if(data.failure>0) {
-                        $("#jobstatus").html(data.failure + ' job(s) failed');
-                    } else {
-                        $("#jobstatus").html(data.jobs + ' job(s)');
-                    } return;
-                }
-                $("#progress").show();
-                $("#jobstatus").html(data.inprogress + ' job(s) in progress');
-            });
-        }, 10000);
+                progressAjaxUpdate(i);
+        }, 5000);
     }
     $(document).ready(function() {
         refreshProgressBar();
@@ -54,7 +73,7 @@
         {% endifnotequal %}
         {% ifnotequal nav.menu "status" %}
         <div id="queue">
-            <a href="#" onClick="popupActivites('{% url status %}');" class="align_left">STATUS:</a>
+            <a href="#" onClick="launchActivities();" class="align_left">ACTIVITIES:</a>
             <div id="jobstatus">0 job(s)</div>
             <img src="{% url webstatic "images/spinner.gif" %}" id="progress" style="display: none;"/>
         </div>

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/scripts/script_ui.html

@@ -39,44 +39,55 @@
     <link rel="stylesheet" href="{% url webstatic "css/tooltip.css" %}" type="text/css" media="screen"/>
 
     <script type="text/javascript">
-        jQuery.fn.runScript = function() {
+        jQuery.fn.runScript = function(actWindow) {
             var $form = $(this);
             var postData = $form.serialize();
-            var actionUrl = $form.attr('action');
+            var actionUrl="{% url script_run paramData.id %}";
+            $.ajaxSetup({ cache: false });
             $.ajax({
                 type: "POST",
                 url: actionUrl,
                 data: postData,
                 contentType:'json',
                 success: function(data){
+                    $.ajaxSetup({ cache: true });
                     if(data.status == 'in progress') {
-                        // we don't try to open 'Activities' window here, since it triggers popup blockers
-                        window.opener.refreshProgressBar();
+                        window.opener.refreshProgressBar();     // also refreshes Activities window
                         self.close();
                     }
                     else {
-                        // error is stored in http session - displayed in 'Activities' window.
+                        window.opener.refreshProgressBar();     // also refreshes Activities window
                         self.close();
                     }
                 },
                 error: function(data) {
+                    window.opener.refreshProgressBar();
                     self.close();
                 }
             });
             return false;
         };
 
+
         $(document).ready(function() {
-            $('form').submit(function() {
-                $("#submit").attr("disabled", true); // make sure we don't submit twice.
-                $(this).runScript();
+            $("#submit").click(function(e){
+                window.open('', 'Activities').close();
+
+                var actWindow = popupActivites('{% url status %}');
+                window.opener.activities_Window = actWindow;    // allows webclient window to update Activities window
+                actWindow.webclient_window = window.opener;
+                $('#script_form').runScript(actWindow);
+                e.preventDefault();
+                return false;
+            });
 
-                // if an "existing" window is opened by the window behind this one, we can't focus it...
-                window.open("", 'Activities').close();    // make sure there is no existing 'Activities' window
-                window.opener.popupActivites('{% url status %}');
+            // this simply prevents any attempt to 'submit' the form (default behavior)
+            $('form').submit(function(e){
+                e.preventDefault();
                 return false;
             });
 
+
             // for any 'list' parameters with enum options, controls to add / remove
             $(".addListSelect").click(function(e) {
                 var $lastSelect = $(this).parent().children('select').last();
@@ -177,7 +188,7 @@
 
 <body>
 
-    <form method="post" action="{% url script_run paramData.id %}">
+    <form id='script_form' method="post">
         <div style="padding:10px; margin-bottom:40px">
             <h3 id="scriptName">{{ paramData.name }}</h3>
             <div id='script_desc'>{{ paramData.description|linebreaks }}