Merge pull request #4432 from will-moore/masks_in_web_viewer

Masks in web viewer

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

@@ -332,14 +332,26 @@ def stringToSvg(string):
 
 def rgb_int2css(rgbint):
     """
-    converts a bin int number into css colour, E.g. -1006567680 to '#00ff00'
+    converts a bin int number into css colour and alpha fraction.
+    E.g. -1006567680 to '#00ff00', 0.5
     """
     alpha = rgbint // 256 // 256 // 256 % 256
     alpha = float(alpha) / 256
     r, g, b = (rgbint // 256 // 256 % 256, rgbint // 256 % 256, rgbint % 256)
     return "#%02x%02x%02x" % (r, g, b), alpha
 
 
+def rgb_int2rgba(rgbint):
+    """
+    converts a bin int number into (r, g, b, alpha) tuple.
+    E.g. 1694433280 to (255, 0, 0, 0.390625)
+    """
+    alpha = rgbint // 256 // 256 // 256 % 256
+    alpha = float(alpha) / 256
+    r, g, b = (rgbint // 256 // 256 % 256, rgbint // 256 % 256, rgbint % 256)
+    return (r, g, b, alpha)
+
+
 def chgrpMarshal(conn, rsp):
     """
     Helper for marshalling a Chgrp response.

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

@@ -31,6 +31,7 @@ $.fn.roi_display = function(options) {
         if (options != null) {
             var orig_width = options.width;
             var orig_height = options.height;
+            var webgateway_index = options.webgateway_index;    // base url
             var json_url = options.json_url;
         }
 
@@ -102,6 +103,10 @@ $.fn.roi_display = function(options) {
 
         var draw_shape = function(shape) {
             var newShape = null;
+            if (shape['type'] == 'Mask') {
+              var src = webgateway_index + 'render_shape_mask/' + shape['id'] + '/';
+              newShape = paper.image(src, shape['x'], shape['y'], shape['width'], shape['height']);
+            }
             if (shape['type'] == 'Ellipse') {
               newShape = paper.ellipse(shape['cx'], shape['cy'], shape['rx'], shape['ry']);
             }

components/tools/OmeroWeb/omeroweb/webgateway/templates/webgateway/viewport/omero_image.html

@@ -362,6 +362,7 @@
       if (!viewport.viewportimg.get(0).show_rois) {
           var options = {'width':{{ image.getSizeX }},
                      'height':{{ image.getSizeY }},
+                     'webgateway_index':'{% url "webgateway" %}',
                      'json_url':'{% url 'webgateway_get_rois_json' image.id %}'};
           if (viewport.loadedImg.tiles) {
               options['tiles'] = true;
@@ -450,7 +451,8 @@
       $roi_table.append($(roi_html));
 
       get_shape_icon_src = function(type, klass) {
-          var shape_icons = {'Line':'line16.png', 'Ellipse':'ellipse16.png', 'Polygon':'polygon16.png', 'Rectangle':'rectangle16.png',
+          var shape_icons = {'Line':'line16.png', 'Ellipse':'ellipse16.png',
+            'Polygon':'polygon16.png', 'Rectangle':'rectangle16.png', 'Mask': 'mask16.png',
             'Point':'point16.png', 'Label':'text16.png', 'PolyLine':'line16.png'}
           if (type in shape_icons) {
               return "<img class='"+ klass +"' src='{% static 'webgateway/img/' %}" + shape_icons[type] + "' />";

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

@@ -147,6 +147,12 @@
 L{views.render_shape_thumbnail}. Uses current rendering settings.
 """
 
+render_shape_mask = (r'^render_shape_mask/(?P<shapeId>[0-9]+)/$',
+                     'webgateway.views.render_shape_mask')
+"""
+Returns a mask for the specified shape
+"""
+
 render_birds_eye_view = (
     r'^render_birds_eye_view/(?P<iid>[0-9]+)/(?:(?P<size>[0-9]+)/)?$',
     'webgateway.views.render_birds_eye_view')
@@ -410,6 +416,7 @@
     render_col_plot,
     render_roi_thumbnail,
     render_shape_thumbnail,
+    render_shape_mask,
     render_thumbnail,
     render_birds_eye_view,
     render_ome_tiff,

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

@@ -31,7 +31,7 @@
 from omero.util.ROI_utils import pointsStringToXYlist, xyListToBbox
 from plategrid import PlateGrid
 from omero_version import build_year
-from marshal import imageMarshal, shapeMarshal
+from marshal import imageMarshal, shapeMarshal, rgb_int2rgba
 
 try:
     from hashlib import md5
@@ -78,6 +78,13 @@
     except:
         logger.error('No Pillow installed')
 
+try:
+    import numpy
+    numpyInstalled = True
+except ImportError:
+    logger.error('No numpy installed')
+    numpyInstalled = False
+
 
 def index(request):
     """ /webgateway/ index placeholder """
@@ -650,6 +657,64 @@ def resizeXY(xy):
     return HttpResponse(jpeg, content_type='image/jpeg')
 
 
+@login_required()
+def render_shape_mask(request, shapeId, conn=None, **kwargs):
+    """ Returns mask as a png (supports transparency) """
+
+    if not numpyInstalled:
+        raise NotImplementedError("numpy not installed")
+    params = omero.sys.Parameters()
+    params.map = {'id': rlong(shapeId)}
+    shape = conn.getQueryService().findByQuery(
+        "select s from Shape s where s.id = :id", params,
+        conn.SERVICE_OPTS)
+    if shape is None:
+        raise Http404("Shape ID: %s not found" % shapeId)
+    width = int(shape.getWidth().getValue())
+    height = int(shape.getHeight().getValue())
+    color = unwrap(shape.getFillColor())
+    fill = (255, 255, 0, 255)
+    if color is not None:
+        color = rgb_int2rgba(color)
+        fill = (color[0], color[1], color[2], int(color[3] * 255))
+    mask_packed = shape.getBytes()
+    # convert bytearray into something we can use
+    intarray = numpy.fromstring(mask_packed, dtype=numpy.uint8)
+    binarray = numpy.unpackbits(intarray)
+
+    # Couldn't get the 'proper' way of doing this to work,
+    # TODO: look at this again later. Faster than simple way below:
+    # E.g. takes ~2 seconds for 1984 x 1984 mask
+    # pixels = ""
+    # steps = len(binarray) / 8
+    # for i in range(steps):
+    #     b = binarray[i*8: (i+1)*8]
+    #     pixels += struct.pack("8B", b[0], b[1], b[2], b[3], b[4],
+    #                           b[5], b[6], b[7])
+    # for b in binarray:
+    #     pixels += struct.pack("1B", b)
+    # im = Image.frombytes("1", size=(width, height), data=pixels)
+
+    # Simple approach - Just set each pixel in turn
+    # E.g. takes ~12 seconds for 1984 x 1984 mask with most pixels '1'
+    # Or ~5 seconds for same size mask with most pixels "0"
+    img = Image.new("RGBA", size=(width, height), color=(0, 0, 0, 0))
+    x = 0
+    y = 0
+    for pix in binarray:
+        if pix == 1:
+            img.putpixel((x, y), fill)
+        x += 1
+        if x > width - 1:
+            x = 0
+            y += 1
+    rv = StringIO()
+    # return a png (supports transparency)
+    img.save(rv, 'png', quality=int(100))
+    png = rv.getvalue()
+    return HttpResponse(png, content_type='image/png')
+
+
 def _get_signature_from_request(request):
     """
     returns a string that identifies this image, along with the settings