Ome tiff export

components/blitz/resources/omero/Constants.ice

@@ -160,6 +160,7 @@ module omero {
         const string NSCOMPANIONFILE = "openmicroscopy.org/omero/import/companionFile";
         const string NSEXPERIMENTERPHOTO = "openmicroscopy.org/omero/experimenter/photo";
         const string NSBULKANNOTATIONS = "openmicroscopy.org/omero/bulk_annotations";
+        const string NSOMETIFF = "openmicroscopy.org/omero/ome_tiff";
         //
         // omero.grid.Param.namespaces in Scripts.ice
         //

components/tools/OmeroWeb/omeroweb/webclient/static/webclient/css/dusty.css

@@ -152,6 +152,32 @@ button::-moz-focus-inner {
 	    height:18px;
 	    display:block;
 	}
+
+    #general_tab .btn_download span {
+        width:20px;
+        height:18px;
+        display:block;
+    }
+
+    #general_tab .btn_download {
+        background: url(../../webgateway/img/icon_download2.png) center center no-repeat;
+    }
+
+    #download_dropdown {
+        float:right;
+        margin: 0px 5px;
+    }
+    #download_dropdown .dropdown {
+        right: 0px;
+        left: auto;
+    }
+    #download_dropdown .dropdown:before {
+        left: 68% !important;
+    }
+    #download_dropdown ul a {
+        background: none;
+        font-size: 80%;
+    }
 
 
 

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

@@ -351,6 +351,63 @@
                     return false;
                 });
 
+
+                // -- Download options --
+                $("#download_dropdown ul").css('visibility', 'hidden');
+                // show on click
+                $("#show_download_dropdown").click(function(e) {
+                    $("ul", $(this).parent()).css('visibility', 'visible');
+                    e.preventDefault();
+                    return false;
+                });
+                // on hover-out, hide drop-down menus
+                $("#download_dropdown ul").hover(function(){}, function(){
+                    $(this).css('visibility', 'hidden');
+                });
+
+                // Handle Download actions
+                $("#create-ometiff").click(function(e){
+
+                    var url = $(this).attr('href');
+                    $("#download_dropdown ul").css('visibility', 'hidden');// hide dropdown menu
+                    var dialog_opts = ['Cancel', 'Create'];
+                    $.getJSON("{% url ome_tiff_info manager.obj_id %}", function(data) {
+
+                        var msg = "This will create an OME-TIFF file from this Image.";
+                        if (data.id && data.ago) {
+                            msg += "<br>Or you can Download one that was created "+ data.ago +" ago.";
+                            var download_ometiff = data.download;
+                            dialog_opts[1] = "Create New";
+                            dialog_opts.push("Download");
+                        } else {
+                            msg += "<br>This will be attached to the Image and available to download.";
+                        }
+
+                        var confirm_ometiff = confirm_dialog(msg,
+                            function() {
+                                var btn = confirm_ometiff.data("clicked_button");
+                                switch (btn) {
+                                    case "Create":   // two options for the same button
+                                    case "Create New":
+                                        $.post( url, function() {
+                                            showActivities();
+                                        });
+                                        break;
+                                    case "Download":
+                                        window.location.href = download_ometiff;
+                                        break;
+                                }
+                            },
+                            "Create OME-TIFF?",
+                            dialog_opts,
+                            null, 200
+                        );
+                    });
+
+                    e.preventDefault();
+                    return false;
+                });
+
             });
 
     </script>
@@ -389,40 +446,51 @@ <h1>
 					<button class="btn silver btn_edit" alt="e" title="edit">
 						<span></span>
 					</button>
-
-					{% comment %}
-					<img src="{% static "webclient/image/color_line12.png" %}" /> 
-					{% endcomment %}
 
 				</div>{% else %}
 
 				<h1 style="word-wrap: break-word;">{{ manager.image.name }}</h1>{% endif %}
 
+
+            <div style="position:relative">
+                <h2 class="data_heading_id" id='image_id' style="float:left">
+                    Image ID: <strong>{{ manager.image.id }}</strong>
+                </h2>
+
+                <!-- open-image link -->
+                <button id="show_link_btn" class="btn silver btn_link" title="Link to this Image">
+                    <span></span>
+                </button>
+                <div id="link_info_popup" class="info_popup" style="right:0px; top:30px; padding:4px; display:none">
+                    <input type="text" size="30">
+                    <img title="Close" src="{% static 'webgateway/img/close.gif' %}" />
+                </div>
 
-            	<h2 class="data_heading_id" id='image_id'>
-            	    Image ID: <strong>{{ manager.image.id }}</strong>
-            	    <!-- open-image link -->
-                    <button id="show_link_btn" class="btn silver btn_link" title="Link to this Image">
-    					<span></span>
-    				</button>
-    				<div id="link_info_popup" class="info_popup" style="right:0px; top:30px; padding:4px; display:none">
-    				    <input type="text" size="30">
-    				    <img title="Close" src="{% static 'webgateway/img/close.gif' %}" />
-    				</div>
-            	</h2>
-
-
+                <!-- download options -->
+                <span id="download_dropdown">
+                    <button id="show_download_dropdown" class="btn silver btn_download" title="Download Image as...">
+                        <span></span>
+                    </button>
+                    <ul class="dropdown">
+                        {% if manager.image.countArchivedFiles %}
+                            <li>
+                                <a id="download-origfile" href="{% url archived_files manager.image.id %}"
+    title="Download {{ manager.image.countArchivedFiles }} Archived file{{ manager.image.countArchivedFiles|pluralize:'s (zip)' }}">
+                                    Archived file{{ manager.image.countArchivedFiles|pluralize:'s (zip)' }}</a>
+                            </li>
+                        {% endif %}
+                        <li>
+                            <a id="create-ometiff" href="{% url ome_tiff_script manager.image.id %}" 
+                                title="Create OME-TIFF File for Download">OME-TIFF</a>
+                        </li>
+                        <li id="download-jpeg"><a href="{% url web_render_image_download manager.image.id %}" title="Download as JPEG">JPEG</a></li>
+                    </ul>
+                </span>
+            </div>
+
+            <div style="clear:both"></div>
             <div style="padding-bottom:6px; position:relative">
-
-                {% if manager.image.countArchivedFiles %}
-                    <div style="float:right; top:30px; padding:4px">
-                        <a href="{% url archived_files manager.image.id %}">
-                        <img src="{% static "webclient/image/nuvola_download_manager16.png" %}"
-                            title="Download {{ manager.image.countArchivedFiles }} Archived file{{ manager.image.countArchivedFiles|pluralize:'s (zip)' }}"/>
-                        </a>
-                    </div>
-                {% endif %}
-
+
 				<button class="btn silver btn_text" href="#" onclick="return openPopup('{% url web_image_viewer manager.image.id %}')"
 				        title="Open full image viewer in new window">
 					<span>

components/tools/OmeroWeb/omeroweb/webclient/urls.py

@@ -88,6 +88,8 @@
     url( r'^(?:(?P<share_id>[0-9]+)/)?render_image_region/(?P<iid>[0-9]+)/(?P<z>[0-9]+)/(?P<t>[0-9]+)/$', webgateway.render_image_region, name="web_render_image_region"),
     url( r'^(?:(?P<share_id>[0-9]+)/)?render_birds_eye_view/(?P<iid>[^/]+)/(?:(?P<size>[^/]+)/)?$', webgateway.render_birds_eye_view, name="web_render_birds_eye_view"),
     url( r'^(?:(?P<share_id>[0-9]+)/)?render_image/(?P<iid>[^/]+)/(?:(?P<z>[^/]+)/)?(?:(?P<t>[^/]+)/)?$', webgateway.render_image, name="web_render_image"),
+    url( r'^(?:(?P<share_id>[0-9]+)/)?render_image_download/(?P<iid>[^/]+)/(?:(?P<z>[^/]+)/)?(?:(?P<t>[^/]+)/)?$', 
+        webgateway.render_image, {'download':True}, name="web_render_image_download"),
     url( r'^(?:(?P<share_id>[0-9]+)/)?img_detail/(?P<iid>[0-9]+)/$', views.image_viewer, name="web_image_viewer"),
     url( r'^(?:(?P<share_id>[0-9]+)/)?imgData/(?P<iid>[0-9]+)/$', webgateway.imageData_json, name="web_imageData_json"),
     url(r'^(?:(?P<share_id>[0-9]+)/)?render_row_plot/(?P<iid>[^/]+)/(?P<z>[^/]+)/(?P<t>[^/]+)/(?P<y>[^/]+)/(?:(?P<w>[^/]+)/)?$', webgateway.render_row_plot, name="web_render_row_plot"),
@@ -131,6 +133,10 @@
     url( r'^script_run/(?P<scriptId>[0-9]+)/$', views.script_run, name='script_run' ),  # runs the script - parameters in POST
     url( r'^get_original_file/(?:(?P<fileId>[0-9]+)/)?$', views.get_original_file, name="get_original_file"), # for stderr, stdout etc
 
+    # ome_tiff_script: generate OME-TIFF and attach to image (use script service). Must be POST
+    url( r'^ome_tiff_script/(?P<imageId>[0-9]+)/$', views.ome_tiff_script, name='ome_tiff_script' ),
+    url( r'^ome_tiff_info/(?P<imageId>[0-9]+)/$', views.ome_tiff_info, name='ome_tiff_info' ),
+
     # ping OMERO server to keep session alive
     url( r'^keepalive_ping/$', views.keepalive_ping, name="keepalive_ping"),
 

components/tools/OmeroWeb/omeroweb/webclient/views.py

@@ -2108,7 +2108,7 @@ def activities(request, conn=None, **kwargs):
                                 obj_data['browse_url'] = getObjectUrl(conn, v)
                                 if v.isLoaded() and hasattr(v, "file"):
                                     #try:
-                                    mimetypes = {'image/png':'png', 'image/jpeg':'jpeg', 'image/tiff': 'tiff'}
+                                    mimetypes = {'image/png':'png', 'image/jpeg':'jpeg', 'text/plain': 'text'}
                                     if v.file.mimetype.val in mimetypes:
                                         obj_data['fileType'] = mimetypes[v.file.mimetype.val]
                                         obj_data['fileId'] = v.file.id.val
@@ -2470,15 +2470,47 @@ def script_run(request, scriptId, conn=None, **kwargs):
                     continue
 
     logger.debug("Running script %s with params %s" % (scriptName, inputMap))
+    rsp = run_script(request, conn, sId, inputMap, scriptName)
+    return HttpResponse(simplejson.dumps(rsp), mimetype='json')
+
+
+@login_required(setGroupContext=True)
+def ome_tiff_script(request, imageId, conn=None, **kwargs):
+    """
+    Uses the scripting service (Batch Image Export script) to generate OME-TIFF for an
+    image and attach this as a file annotation to the image.
+    Script will show up in the 'Activities' for users to monitor and download result etc.
+    """
+    #if not request.method == 'POST':
+    #    return HttpResponse("Need to use POST")
+
+    scriptService = conn.getScriptService()
+    sId = scriptService.getScriptID("/omero/export_scripts/Batch_Image_Export.py")
+
+    imageIds = [long(imageId)]
+    inputMap = {'Data_Type': wrap('Image'), 'IDs': wrap(imageIds)}
+    inputMap['Format'] = wrap('OME-TIFF')
+    rsp = run_script(request, conn, sId, inputMap, scriptName='Create OME-TIFF')
+    return HttpResponse(simplejson.dumps(rsp), mimetype='json')
+
+
+def run_script(request, conn, sId, inputMap, scriptName='Script'):
+    """
+    Starts running a script, adding details to the request.session so that it shows up
+    in the webclient Activities panel and results are available there etc.
+    """
+    request.session.modified = True
+    scriptService = conn.getScriptService()
     try:
         handle = scriptService.runScript(sId, inputMap, None, conn.SERVICE_OPTS)
         # E.g. ProcessCallback/4ab13b23-22c9-4b5f-9318-40f9a1acc4e9 -t:tcp -h 10.37.129.2 -p 53154:tcp -h 10.211.55.2 -p 53154:tcp -h 10.12.1.230 -p 53154
         jobId = str(handle)
+        status = 'in progress'
         request.session['callback'][jobId] = {
             'job_type': "script",
             'job_name': scriptName,
             'start_time': datetime.datetime.now(),
-            'status':'in progress'}
+            'status':status}
         request.session.modified = True
     except Exception, x:
         jobId = str(time())      # E.g. 1312803670.6076391
@@ -2500,9 +2532,25 @@ def script_run(request, scriptId, conn=None, **kwargs):
             'status':status,
             'Message': message,
             'error':error}
-        request.session.modified = True
-        # we return this, although it is now ignored (script window closes)
-        return HttpResponse(simplejson.dumps({'status': status, 'error': error}), mimetype='json')
+        return {'status': status, 'error': error}
 
-    return HttpResponse(simplejson.dumps({'jobId': jobId, 'status':'in progress'}), mimetype='json')
+    return {'jobId': jobId, 'status': status}
 
+@login_required()
+@render_response()
+def ome_tiff_info(request, imageId, conn=None, **kwargs):
+    """
+    Query to see if we have an OME-TIFF attached to the image (assume only 1, since Batch Image Export will delete old ones)
+    """
+    # Any existing OME-TIFF will appear in list
+    links = list( conn.getAnnotationLinks("Image", [imageId], ns=omero.constants.namespaces.NSOMETIFF) )
+    rv = {}
+    if len(links) > 0:
+        links.sort(key=lambda x: x.getId(), reverse=True)   # use highest ID === most recent
+        annlink = links[0]
+        created = annlink.creationEventDate()
+        annId = annlink.getChild().getId()
+        from omeroweb.webgateway.templatetags.common_filters import ago
+        download = reverse("download_annotation", args=[annId])
+        rv = {"created": str(created), "ago": ago(created), "id":annId, "download": download}
+    return rv       # will get returned as json by default

components/tools/OmeroWeb/omeroweb/webgateway/static/webgateway/css/ome.header.css

@@ -659,6 +659,7 @@
 
 #activities_panel {
 	width:400px;
+	overflow-y: auto;
 }
 
 	#activities_spinner, #basket_spinner {

components/tools/OmeroWeb/omeroweb/webgateway/templatetags/common_filters.py

@@ -40,6 +40,33 @@
 def hash(value, key):
     return value[key]
 
+@register.filter
+def ago(value):
+    """ Formats a datetime.datetime object as time Ago. E.g. '3 days 2 hours 10 minutes' """
+    try:
+        ago = datetime.datetime.now() - value
+    except TypeError:
+        return str(value)
+    def plurals(val):
+        return val != 1 and "s" or ""
+    hours, remainder = divmod(ago.seconds, 3600)
+    mins, secs = divmod(remainder, 60)
+    if ago.days >= 365:
+        years = ago.days / 365
+        return "%s year%s" % (years, plurals(years))
+    if ago.days > 28:
+        months = ago.days / 30
+        return "%s month%s" % (months, plurals(months))
+    if ago.days > 0:
+        return "%s day%s" % (ago.days, plurals(ago.days))
+    if hours > 0:
+        return "%s hour%s" % (hours, plurals(hours))
+    if mins > 1:
+        return "%s minutes" % (mins)
+    if mins == 1:
+        return "a minute"
+    return "less than a minute"
+
 @register.filter
 def truncateafter(value, arg):
     """

components/tools/OmeroWeb/omeroweb/webgateway/views.py

@@ -747,6 +747,10 @@ def render_image (request, iid, z=None, t=None, conn=None, **kwargs):
         webgateway_cache.setImage(request, server_id, img, z, t, jpeg_data)
 
     rsp = HttpResponse(jpeg_data, mimetype='image/jpeg')
+    if 'download' in kwargs and kwargs['download']:
+        rsp['Content-Type'] = 'application/force-download'
+        rsp['Content-Length'] = len(jpeg_data)
+        rsp['Content-Disposition'] = 'attachment; filename=%s.jpg' % (img.getName().replace(" ","_"))
     return rsp
 
 @login_required()