Codomain web

components/tools/OmeroPy/src/omero/gateway/__init__.py

@@ -6812,6 +6812,23 @@ def getWindowMax(self):
                 return None
         return si.getGlobalMax().val
 
+    def isReverseIntensity(self):
+        """
+        Returns True if this channel has ReverseIntensityContext
+        set on it.
+
+        :return:    True if ReverseIntensityContext found
+        :rtype:     Boolean
+        """
+        if self._re is None:
+            return None
+        ctx = self._re.getCodomainMapContext(self._idx)
+        reverse = False
+        for c in ctx:
+            if isinstance(c, omero.model.ReverseIntensityContext):
+                reverse = True
+        return reverse
+
 ChannelWrapper = _ChannelWrapper
 
 
@@ -7656,7 +7673,8 @@ def getZoomLevelScaling(self):
             rv[i] = float(level)/sizeXList[0]
         return rv
 
-    def setActiveChannels(self, channels, windows=None, colors=None):
+    def setActiveChannels(self, channels, windows=None, colors=None,
+                          reverseMaps=None):
         """
         Sets the active channels on the rendering engine.
         Also sets rendering windows and channel colors
@@ -7680,12 +7698,17 @@ def setActiveChannels(self, channels, windows=None, colors=None):
                             Must be list for each channel
         :param colors:      List of colors. ['F00', None, '00FF00'].
                             Must be item for each channel
+        :param reverseMaps: List of boolean (or None). If True/False then
+                            set/remove reverseIntensityMap on channel
         """
         abs_channels = [abs(c) for c in channels]
         idx = 0     # index of windows/colors args above
         for c in range(len(self.getChannels())):
             self._re.setActive(c, (c+1) in channels, self._conn.SERVICE_OPTS)
             if (c+1) in channels:
+                if (reverseMaps is not None and
+                        reverseMaps[idx] is not None):
+                    self.setReverseIntensity(c, reverseMaps[idx])
                 if (windows is not None
                         and windows[idx][0] is not None
                         and windows[idx][1] is not None):
@@ -7932,6 +7955,24 @@ def isGreyscaleRenderingModel(self):
         """
         return self.getRenderingModel().value.lower() == 'greyscale'
 
+    @assert_re()
+    def setReverseIntensity(self, channelIndex, reverse=True):
+        """
+        Sets or removes a ReverseIntensityMapContext from the
+        specified channel. If set, the intensity of the channel
+        is mapped in reverse: brightest -> darkest.
+
+        :param channelIndex:    The index of channel (int)
+        :param reverse:         If True, set reverse intensity (boolean)
+        """
+        r = omero.romio.ReverseIntensityMapContext()
+        # Always remove map from channel
+        # (doesn't throw exception, even if not on channel)
+        self._re.removeCodomainMapFromChannel(r, channelIndex)
+        # If we want to reverse, add it to the channel (again)
+        if reverse:
+            self._re.addCodomainMapToChannel(r, channelIndex)
+
     @assert_re(ignoreExceptions=(omero.ConcurrencyException))
     def getRenderingDefId(self):
         """
@@ -7976,13 +8017,18 @@ def getAllRenderingDefs(self, eid=-1):
             waves = rdef.iterateWaveRendering()
             d['c'] = []
             for w in waves:
+                reverse = False
+                for c in w.copySpatialDomainEnhancement():
+                    if isinstance(c, omero.model.ReverseIntensityContext):
+                        reverse = True
                 color = ColorHolder.fromRGBA(
                     w.getRed().val, w.getGreen().val, w.getBlue().val, 255)
                 r = {
                     'active': w.getActive().val,
                     'start': w.getInputStart().val,
                     'end': w.getInputEnd().val,
                     'color': color.getHtml(),
+                    'reverseIntensity': reverse,
                     'rgb': {'red': w.getRed().val,
                             'green': w.getGreen().val,
                             'blue': w.getBlue().val}

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

@@ -1600,8 +1600,9 @@ def load_metadata_preview(request, c_type, c_id, conn=None, share_id=None,
             if c['active']:
                 act = ""
             color = c['lut'] if 'lut' in c else c['color']
-            chs.append('%s%s|%d:%d$%s'
-                       % (act, i+1, c['start'], c['end'], color))
+            reverse = 'r' if c['reverseIntensity'] else '-r'
+            chs.append('%s%s|%d:%d%s$%s'
+                       % (act, i+1, c['start'], c['end'], reverse, color))
         rdefQueries.append({
             'id': r['id'],
             'owner': r['owner'],

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

@@ -46,6 +46,7 @@ def channelMarshal(channel):
     chan = {'emissionWave': channel.getEmissionWave(),
             'label': channel.getLabel(),
             'color': channel.getColor().getHtml(),
+            'reverseIntensity': channel.isReverseIntensity(),
             'window': {'min': channel.getWindowMin(),
                        'max': channel.getWindowMax(),
                        'start': channel.getWindowStart(),

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

@@ -52,4 +52,8 @@
 }
 .lutpicker input {
 	width: 10px;
+}
+#reverseIntensity {
+	display: block;
+	float: left;
 }

components/tools/OmeroWeb/omeroweb/webgateway/static/webgateway/js/ome.colorbtn.js

@@ -24,8 +24,8 @@ $.fn.colorbtn = function(cfg) {
     };
     var that = this;
 
-    var colors = ["FF0000", "00FF00", "0000FF", "FFFFFF", "FFFF00", "EE82EE"];
-    var colorNames = ["red", "green", "blue", "white", "yellow", "magenta"];
+    var colors = ["FF0000", "00FF00", "0000FF", "FFFFFF", "FFFF00", "EE00EE", "00FFFF"];
+    var colorNames = ["red", "green", "blue", "white", "yellow", "magenta", "cyan"];
     var picker = null;
 
     /* The basic setup */
@@ -39,10 +39,14 @@ $.fn.colorbtn = function(cfg) {
     var ok_callback = function () {
       // On 'OK' we get the color saved by 'callback' above and apply it to the color-btn, then trigger
       var data_color = self.attr('data-picked-color');
+      var reverse_intensity = self.data('data-reverse-intensity');
       // data_color could be 'FF0000' or 'cool.lut'
       if (data_color) {
         self.attr('data-color', data_color);
         self.trigger('changed');
+      } else if (reverse_intensity !== undefined) {
+        self.data('data-reverse-intensity', reverse_intensity);
+        self.trigger('changed');
       }
     };
 
@@ -53,6 +57,11 @@ $.fn.colorbtn = function(cfg) {
       var box = jQuery("#"+this.cfg.prefix+"-box").append('<h1>Choose color</h1>');
       box.postit();
 
+      var reverseIntensityHtml = '<div><input id="reverseIntensity" type="checkbox" style="width:20px"></input>';
+          reverseIntensityHtml += '<label for="reverseIntensity" style="font-size:15px; font-weight: normal;">Reverse Intensity</label></div>';
+          reverseIntensityHtml += '<div style="clear:both"></div>';
+      $(reverseIntensityHtml).appendTo(box);
+
       // Add Lookup Table list - gets populated in show_picker() below.
       var $luts = $('<div id="' + this.cfg.prefix + '-luts" class="lutpicker"></div>').appendTo(box);
 
@@ -99,6 +108,8 @@ $.fn.colorbtn = function(cfg) {
     }
 
     this.show_picker = function () {
+      // 'data-reverse-intensity' is a string in template, not boolean.
+      var reverse_intensity = self.data('data-reverse-intensity');
       if (!picker) {
         if (jQuery('#'+this.cfg.prefix+'-box').length === 0) {
           this._prepare_picker();
@@ -108,7 +119,7 @@ $.fn.colorbtn = function(cfg) {
       }
       var currColor = self.attr('data-color');
 
-      // lookup LUTs
+      // lookup LUTs & build list with other colors
       var $luts = $("#" + this.cfg.prefix + "-luts");
       if ($luts.is(':empty')) {
         $.getJSON(cfg.server + '/luts/', function(data){
@@ -141,11 +152,12 @@ $.fn.colorbtn = function(cfg) {
       $('.cpickerPane').hide();
       $luts.show();
       $('.showColorPicker a').html('Show Color Picker');
+      $('#reverseIntensity').prop('checked', reverse_intensity);
       // Highlight current color/lut
       $("label", $luts).css('background', 'none');
       $("label[for='" + currColor + "']", $luts).css('background', '#cddcfc')
 
-      // bind appropriate handler (wraps ref to button)
+      // unbind and re-bind appropriate handler (wraps ref to button)
       $("#cbpicker-OK-btn").unbind('click').bind('click', ok_callback)
         .bind('click',function(){
           jQuery("#"+that.cfg.prefix+"-box").hide();
@@ -154,6 +166,10 @@ $.fn.colorbtn = function(cfg) {
         self.attr('data-picked-color', this.value);
         ok_callback();
       });
+      $("#reverseIntensity").off('click').click(function(){
+        self.data('data-reverse-intensity', this.checked);
+        ok_callback();
+      });
       self.removeAttr('data-picked-color');
 
       var oldColor = self.attr("data-color"),

components/tools/OmeroWeb/omeroweb/webgateway/static/webgateway/js/ome.viewport.js

@@ -631,6 +631,16 @@ jQuery._WeblitzViewport = function (container, server, options) {
     this.setChannelActive(idx, !_this.loadedImg.channels[idx].active);
   };
 
+  this.setChannelReverseIntensity = function (idx, reverse, noreload) {
+    if (_this.loadedImg.channels[idx].reverseIntensity !== reverse) {
+      _this.loadedImg.channels[idx].reverseIntensity = reverse;
+      _this.self.trigger('channelChange', [_this, idx, _this.loadedImg.channels[idx]]);
+      if (!noreload) {
+        _load();
+      }
+    }
+  };
+
   this.getCCount = function () {
     return _this.loadedImg.size.c;
   };
@@ -950,6 +960,7 @@ jQuery._WeblitzViewport = function (container, server, options) {
             e1.channels[i].color == e2.channels[i].color &&
             e1.channels[i].windowStart == e2.channels[i].windowStart &&
             e1.channels[i].windowEnd == e2.channels[i].windowEnd &&
+            e1.channels[i].reverseIntensity == e2.channels[i].reverseIntensity &&
             e1.channels[i].metalabel == e2.channels[i].metalabel)) {
         return false;
       }
@@ -966,6 +977,7 @@ jQuery._WeblitzViewport = function (container, server, options) {
                      color: channels[i].color,
                      windowStart: channels[i].window.start,
                      windowEnd: channels[i].window.end,
+                     reverseIntensity: channels[i].reverseIntensity,
                      metalabel: channels[i].metalabel};
       entry.channels.push(channel);
     }
@@ -991,6 +1003,7 @@ jQuery._WeblitzViewport = function (container, server, options) {
         this.setChannelColor(i, entry.channels[i].color, true);
         this.setChannelActive(i, entry.channels[i].active, true);
         this.setChannelLabel(i, entry.channels[i].metalabel, true);
+        this.setChannelReverseIntensity(i, entry.channels[i].reverseIntensity, true);
       }
       _load();
     }
@@ -1067,6 +1080,7 @@ jQuery._WeblitzViewport = function (container, server, options) {
       var ch = channels[i].active ? '' : '-';
       ch += parseInt(i, 10)+1;
       ch += '|' + channels[i].window.start + ':' + channels[i].window.end;
+      ch += channels[i].reverseIntensity ? 'r' : '-r';
       ch += '$' + OME.rgbToHex(channels[i].color);
       chs.push(ch);
     }
@@ -1136,6 +1150,12 @@ jQuery._WeblitzViewport = function (container, server, options) {
         }
         if (t.length > 1) {
           t = t[1].split('$');
+          if (t[0].endsWith('-r')) {
+            this.setChannelReverseIntensity(idx, false, true);
+          } else if (t[0].endsWith('r')) {
+            this.setChannelReverseIntensity(idx, true, true);
+          }
+          t[0] = t[0].replace('-r', '').replace('r', '');  // remove 'r' if present
           var range = t[0].split(':');
           if (range.length == 2) {
             this.setChannelWindow(idx, parseFloat(range[0], 10), parseFloat(range[1], 10), true);

components/tools/OmeroWeb/omeroweb/webgateway/static/webgateway/js/omero_image.js

@@ -211,6 +211,10 @@
                 $('#wblitz-ch'+i+'-cw-start').val(channels[i].window.start).change();
                 $('#wblitz-ch'+i+'-cw-end').val(channels[i].window.end).change();
         }
+        // Colorpicker buttons store 'reverse-intensity' with .data() to populate colorbtn dialog
+        $(".picker").each(function(i, pickerBtn) {
+            $(pickerBtn).data('data-reverse-intensity', channels[i].reverseIntensity);
+        });
         hidePicker();
 
         updateUndoRedo(viewport);
@@ -244,9 +248,12 @@
         if (on_batchCopyRDefs) {
             return batchCopyRDefs_action('ok');
         }
+        var revInt;
         for (var i=0; i<viewport.getCCount(); i++) {
             viewport.setChannelActive(i, $('#rd-wblitz-ch'+i).get(0).checked, true);
             viewport.setChannelColor(i, $('#wblitz-ch'+i+'-color').attr('data-color'), true);
+            revInt = $('#wblitz-ch'+i+'-color').data('data-reverse-intensity');
+            if (revInt !== undefined) {viewport.setChannelReverseIntensity(i, revInt, true);}
             var noreload = ((i+1) < viewport.getCCount());    // prevent reload, except on the last loop
             viewport.setChannelWindow(i, $('#wblitz-ch'+i+'-cw-start').get(0).value, $('#wblitz-ch'+i+'-cw-end').get(0).value, noreload);
         }
@@ -515,6 +522,10 @@
 
 
         /* Prepare color picker buttons */
+        $(".picker").each(function(i, pickerBtn) {
+            console.log(this, channels[i].reverseIntensity);
+            $(pickerBtn).data('data-reverse-intensity', channels[i].reverseIntensity);
+        });
         $(".picker")
             .colorbtn({'server': viewport.viewport_server})
             .bind('showing', function () {

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

@@ -207,19 +207,35 @@ def _split_channel_info(rchannels):
     channels = []
     windows = []
     colors = []
+    reverses = []
     for chan in rchannels.split(','):
+        # chan  1|12:1386r$0000FF
         chan = chan.split('|', 1)
+        # chan ['1', '12:1386r$0000FF']
         t = chan[0].strip()
+        # t = '1'
         color = None
+        rev = None
+        # Not normally used...
         if t.find('$') >= 0:
             t, color = t.split('$')
         try:
             channels.append(int(t))
             ch_window = (None, None)
             if len(chan) > 1:
                 t = chan[1].strip()
+                # t = '12:1386r$0000FF'
                 if t.find('$') >= 0:
                     t, color = t.split('$', 1)
+                    # color = '0000FF'
+                    # t = 12:1386r
+                # Optional flag to enable reverse codomain
+                if t.endswith('-r'):
+                    rev = False
+                    t = t[:-2]
+                elif t.endswith('r'):
+                    rev = True
+                    t = t[:-1]
                 t = t.split(':')
                 if len(t) == 2:
                     try:
@@ -228,10 +244,11 @@ def _split_channel_info(rchannels):
                         pass
             windows.append(ch_window)
             colors.append(color)
+            reverses.append(rev)
         except ValueError:
             pass
     logger.debug(str(channels)+","+str(windows)+","+str(colors))
-    return channels, windows, colors
+    return channels, windows, colors, reverses
 
 
 def getImgDetailsFromReq(request, as_string=False):
@@ -755,8 +772,8 @@ def _get_prepared_image(request, iid, server_id=None, conn=None,
         return
     if 'c' in r:
         logger.debug("c="+r['c'])
-        channels, windows, colors = _split_channel_info(r['c'])
-        if not img.setActiveChannels(channels, windows, colors):
+        channels, windows, colors, reverses = _split_channel_info(r['c'])
+        if not img.setActiveChannels(channels, windows, colors, reverses):
             logger.debug(
                 "Something bad happened while setting the active channels...")
     if r.get('m', None) == 'g':
@@ -1854,19 +1871,20 @@ def getRenderingSettings(image):
             start = ch.getWindowStart()
             end = ch.getWindowEnd()
             color = ch.getLut()
+            rev = 'r' if ch.isReverseIntensity() else ''
             if not color or len(color) == 0:
                 color = ch.getColor().getHtml()
-            chs.append("%s%s|%s:%s$%s" % (act, i+1, start, end, color))
+            chs.append("%s%s|%s:%s%s$%s" % (act, i+1, start, end, rev, color))
         rv['c'] = ",".join(chs)
         rv['m'] = "g" if image.isGreyscaleRenderingModel() else "c"
         rv['z'] = image.getDefaultZ() + 1
         rv['t'] = image.getDefaultT() + 1
         return rv
 
     def applyRenderingSettings(image, rdef):
-        channels, windows, colors = _split_channel_info(rdef['c'])
+        channels, windows, colors, reverse = _split_channel_info(rdef['c'])
         # also prepares _re
-        image.setActiveChannels(channels, windows, colors)
+        image.setActiveChannels(channels, windows, colors, reverse)
         if rdef['m'] == 'g':
             image.setGreyscaleRenderingModel()
         else:

components/tools/OmeroWeb/test/integration/test_marshal.py

@@ -69,6 +69,7 @@ def test_image_detail(self):
                 'start': 88,
                 'min': 88
             },
+            'reverseIntensity': False,
             'emissionWave': 500,
             'label': "500"
         }