Codomain web

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

@@ -7621,7 +7621,8 @@ 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
@@ -7645,12 +7646,17 @@ 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):
@@ -7894,6 +7900,40 @@ 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()
+    def isReverseIntensity(self, channelIndex):
+        """
+        Returns True if the specified channel has ReverseIntensityContext
+        set on it.
+
+        :return:    True if ReverseIntensityContext found
+        :rtype:     Boolean
+        """
+        ctx = self._re.getCodomainMapContext(channelIndex)
+        reverse = False
+        for c in ctx:
+            if isinstance(c, omero.model.ReverseIntensityContext):
+                reverse = True
+        return reverse
+
     @assert_re(ignoreExceptions=(omero.ConcurrencyException))
     def getRenderingDefId(self):
         """

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

@@ -206,19 +206,35 @@ 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/disable 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:
@@ -227,10 +243,11 @@ 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):
@@ -754,8 +771,8 @@ 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':
@@ -1858,9 +1875,9 @@ def getRenderingSettings(image):
         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: