Merge pull request #560 from will-moore/max_projection_bytes

Max projection bytes

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -26,7 +26,7 @@
 import os
 from os import path
 import zipfile
-from math import atan2, atan, sin, cos, sqrt, radians, floor, ceil
+from math import atan2, atan, sin, cos, sqrt, radians, floor, ceil, log2
 from copy import deepcopy
 import re
 
@@ -1678,11 +1678,29 @@ def get_panel_image(self, image, panel, orig_name=None):
         t = panel['theT']
         size_x = image.getSizeX()
         size_y = image.getSizeY()
+        size_z = image.getSizeZ()
+        size_c = image.getSizeC()
 
         if 'z_projection' in panel and panel['z_projection']:
             if 'z_start' in panel and 'z_end' in panel:
-                image.setProjection('intmax')
-                image.setProjectionRange(panel['z_start'], panel['z_end'])
+                # check max_projection_bytes
+                pixel_range = image.getPixelRange()
+                bytes_per_pixel = ceil(log2(pixel_range[1]) / 8.0)
+                proj_bytes = (size_z * size_x * size_y
+                              * size_c * bytes_per_pixel)
+
+                cfg = self.conn.getConfigService()
+                max_bytes = int(cfg.getConfigValue(
+                    'omero.pixeldata.max_projection_bytes'))
+
+                if proj_bytes <= max_bytes:
+                    image.setProjection('intmax')
+                    image.setProjectionRange(panel['z_start'], panel['z_end'])
+                else:
+                    print(f'projected_bytes {proj_bytes} exceeds '
+                          f'MAX_PROJECTED_BYTES limit: {max_bytes}')
+                    # Turn off all channels to render a black panel
+                    image.setActiveChannels([])
 
         # If big image, we don't want to render the whole plane
         if self.is_big_image(image):

omero_figure/urls.py

@@ -18,7 +18,7 @@
 
 from omeroweb.webgateway import views as webgateway_views
 from . import views
-from django.urls import path
+from django.urls import path, re_path
 
 
 urlpatterns = [
@@ -33,6 +33,11 @@
     path('imgData/<int:image_id>/', views.img_data_json,
          name='figure_imgData'),
 
+    re_path(r'^max_projection_range_exceeded/'
+            r'(?P<iid>[0-9]+)/(?:(?P<z>[0-9]+)/)?(?:(?P<t>[0-9]+)/)?$',
+            views.max_projection_range_exceeded,
+            name='max_projection_range_exceeded'),
+
     # Send json to OMERO to create pdf using scripting service
     path('make_web_figure/', views.make_web_figure,
          name='make_web_figure'),
@@ -74,6 +79,9 @@
     # Use query ?image=1&image=2
     path('timestamps/', views.timestamps, name='figure_timestamps'),
 
+    # Get pixelsType for images. Use query ?image=1&image=2
+    path('pixels_type/', views.pixels_type, name='figure_pixels_type'),
+
     # Get Z scale for images
     # Use query ?image=1&image=2
     path('z_scale/', views.z_scale, name='figure_z_scale'),

omero_figure/views.py

@@ -91,6 +91,8 @@ def index(request, file_id=None, conn=None, **kwargs):
     max_w, max_h = conn.getMaxPlaneSize()
     max_plane_size = max_w * max_h
     length_units = get_length_units()
+    cfg = conn.getConfigService()
+    max_bytes = cfg.getConfigValue('omero.pixeldata.max_projection_bytes')
     is_public_user = "false"
     if (hasattr(settings, 'PUBLIC_USER')
             and settings.PUBLIC_USER == user.getOmeName()):
@@ -117,6 +119,9 @@ def index(request, file_id=None, conn=None, **kwargs):
                         'const MAX_PLANE_SIZE = %s;' % max_plane_size)
     html = html.replace('const LENGTH_UNITS = LENGTHUNITS;',
                         'const LENGTH_UNITS = %s;' % json.dumps(length_units))
+    if max_bytes:
+        html = html.replace('const MAX_PROJECTION_BYTES = 1024 * 1024 * 256;',
+                            'const MAX_PROJECTION_BYTES = %s;' % max_bytes)
     if export_enabled:
         html = html.replace('const EXPORT_ENABLED = false;',
                             'const EXPORT_ENABLED = true;')
@@ -136,6 +141,39 @@ def index(request, file_id=None, conn=None, **kwargs):
     return HttpResponse(html)
 
 
+@login_required()
+def max_projection_range_exceeded(request, iid, z=None, t=None,
+                                  conn=None, **kwargs):
+    """
+    The app will use this URL instead of `render_image/` if the
+    requested Z-projection range exceeds the maximum projected
+    bytes (given the number of active channels)
+
+    This returns a placeholder image with suitable message
+    """
+
+    from PIL import Image, ImageDraw, ImageFont
+
+    font20 = ImageFont.load_default(20)
+    msg = "Max Z projection disabled"
+    msg_size = font20.getbbox(msg)
+    txt_w = msg_size[2]
+    txt_h = msg_size[3]
+
+    image_size = txt_w + 10
+
+    im = Image.new("RGB", (image_size, image_size), (5, 0, 0))
+    draw = ImageDraw.Draw(im)
+    text_y = im.size[1]/2 - txt_h/2
+    draw.text((im.size[0]/2 - txt_w/2, text_y), msg,
+              font=font20,
+              fill=(256, 256, 256))
+
+    rv = BytesIO()
+    im.save(rv, "jpeg", quality=90)
+    return HttpResponse(rv.getvalue(), content_type="image/jpeg")
+
+
 @login_required()
 def img_data_json(request, image_id, conn=None, **kwargs):
 
@@ -191,6 +229,26 @@ def timestamps(request, conn=None, **kwargs):
     return JsonResponse(data)
 
 
+@login_required()
+def pixels_type(request, conn=None, **kwargs):
+
+    iids = request.GET.getlist('image')
+    data = {}
+    for iid in iids:
+        try:
+            iid = int(iid)
+        except ValueError:
+            pass
+        else:
+            image = conn.getObject('Image', iid)
+            if image is not None:
+                data[image.id] = {
+                    "pixelsType": image.getPixelsType(),
+                    "pixel_range": image.getPixelRange()
+                }
+    return JsonResponse(data)
+
+
 @login_required()
 def z_scale(request, conn=None, **kwargs):
 

src/css/figure.css

@@ -646,11 +646,6 @@
     .z-projection {
         padding: 1px 5px 5px;
     }
-    .z-projection span{
-        background-image: url("../images/projection20.png");
-        width: 20px;
-        height: 20px;
-    }
     .crop-btn span{
         background-image: url("../images/crop20.png");
         width: 20px;

src/index.html

@@ -36,6 +36,7 @@
       const IS_PUBLIC_USER = false;
       // Images larger than this are 'big' tiled images
       const MAX_PLANE_SIZE = 10188864;
+      const MAX_PROJECTION_BYTES = 1024 * 1024 * 256;
 
       const LOCAL_STORAGE_RECOVERED_FIGURE = "recoveredFigure" + USER_ID;
 

src/js/models/figure_model.js

@@ -12,7 +12,7 @@
 
     // Version of the json file we're saving.
     // This only needs to increment when we make breaking changes (not linked to release versions.)
-    var VERSION = 7;
+    var VERSION = 8;
 
 
     // ------------------------- Figure Model -----------------------------------
@@ -280,6 +280,31 @@
                     }
                 });
             }
+
+            if (v < 8) {
+                console.log("Transforming to VERSION 8");
+                // need to load pixelsType.
+                var iids = json.panels.map(p => p.imageId);
+                console.log('Load pixelsType for images', iids);
+                if (iids.length > 0) {
+                    var ptUrl = BASE_WEBFIGURE_URL + 'pixels_type/';
+                    ptUrl += '?image=' + iids.join('&image=');
+                    getJson(ptUrl).then(data => {
+                        // Update all panels
+                        // NB: By the time that this callback runs, the panels will have been created
+                        self.panels.forEach(function(p){
+                            var iid = p.get('imageId');
+                            if (data[iid]) {
+                                p.set({
+                                    'pixelsType': data[iid].pixelsType,
+                                    'pixel_range': data[iid].pixel_range
+                                });
+                            }
+                        });
+                    });
+                }
+            }
+
             return json;
         },
 
@@ -573,6 +598,8 @@
                         'pixel_size_x_unit': data.pixel_size.unitX,
                         'pixel_size_z_unit': data.pixel_size.unitZ,
                         'deltaT': data.deltaT,
+                        'pixelsType': data.meta.pixelsType,
+                        'pixel_range': data.pixel_range,
                     };
                     if (baseUrl) {
                         n.baseUrl = baseUrl;

src/js/models/panel_model.js

@@ -93,6 +93,8 @@
             // we replace these attributes...
             var newData = {'imageId': data.imageId,
                 'name': data.name,
+                'pixelsType': data.pixelsType,
+                'pixel_range': data.pixel_range,
                 'sizeZ': data.sizeZ,
                 'sizeT': data.sizeT,
                 'orig_width': data.orig_width,
@@ -558,6 +560,22 @@
             }
         },
 
+        // Does sizeXYZ, pixelType and Channels exceed MAX_PROJECTION_BYTES?
+        isMaxProjectionBytesExceeded: function() {
+            let bytes_per_pixel = 4;
+            if (this.get("pixel_range")) {
+                bytes_per_pixel = Math.ceil(Math.log2(this.get("pixel_range")[1]) / 8.0);
+            }
+            let sizeC = this.get("channels").length;
+            let sizeXYZ = this.get('orig_width') * this.get('orig_height') * this.get('sizeZ');
+            let total_bytes = bytes_per_pixel * sizeC * sizeXYZ;
+            return total_bytes > MAX_PROJECTION_BYTES;
+        },
+
+        isMaxProjectionExceeded: function() {
+            return this.get('z_projection') && this.isMaxProjectionBytesExceeded();
+        },
+
         // When a multi-select rectangle is drawn around several Panels
         // a resize of the rectangle x1, y1, w1, h1 => x2, y2, w2, h2
         // will resize the Panels within it in proportion.
@@ -723,7 +741,11 @@
 
             // If BIG image, render scaled region
             var region = "";
-            if (this.is_big_image()) {
+            if (this.isMaxProjectionExceeded()) {
+                // if we're trying to do Z-projection with too many planes,
+                // this figure URL renders a suitable error message
+                baseUrl = BASE_WEBFIGURE_URL + 'max_projection_range_exceeded/'
+            } else if (this.is_big_image()) {
                 baseUrl = BASE_WEBFIGURE_URL + 'render_scaled_region/';
                 var rect = this.getViewportAsRect();
                 // Render a region that is 1.5 x larger
@@ -768,6 +790,11 @@
         // offset of the img within it's frame
         get_vp_img_css: function(zoom, frame_w, frame_h, x, y) {
 
+            if (this.isMaxProjectionExceeded()) {
+                // We want the warning placeholder image shown full width, mid-height
+                return {'left':0, 'top':(frame_h - frame_w)/2, 'width':frame_w, 'height': frame_w}
+            }
+
             // For non-big images, we have the full plane in hand
             // css just shows the viewport region
             if (!this.is_big_image()) {

src/js/views/info_panel_view.js

@@ -244,7 +244,8 @@ var InfoPanelView = Backbone.View.extend({
             } else {
                 json.name = title;
                 // compare json summary so far with this Panel
-                var attrs = ["imageId", "orig_width", "orig_height", "sizeT", "sizeZ", "x", "y", "width", "height", "dpi", "min_export_dpi", "max_export_dpi"];
+                var attrs = ["imageId", "orig_width", "orig_height", "sizeT", "sizeZ", "x", "y",
+                             "width", "height", "dpi", "min_export_dpi", "max_export_dpi", "pixelsType"];
                 _.each(attrs, function(a){
                     if (json[a] != this_json[a]) {
                         if (a === 'x' || a === 'y' || a === 'width' || a === 'height') {

src/js/views/modal_views.js

@@ -298,6 +298,8 @@ import { hideModal } from "./util";
                 var newImg = {
                     'imageId': data.id,
                     'name': data.meta.imageName,
+                    'pixelsType': data.meta.pixelsType,
+                    'pixel_range': data.pixel_range,
                     // 'width': data.size.width,
                     // 'height': data.size.height,
                     'sizeZ': data.size.z,

src/js/views/panel_view.js

@@ -34,7 +34,7 @@
                 this.render_layout);
             this.listenTo(this.model, 'change:scalebar change:pixel_size_x', this.render_scalebar);
             this.listenTo(this.model,
-                'change:zoom change:dx change:dy change:width change:height change:channels change:theZ change:theT change:z_start change:z_end change:z_projection change:min_export_dpi',
+                'change:zoom change:dx change:dy change:width change:height change:channels change:theZ change:theT change:z_start change:z_end change:z_projection change:min_export_dpi change:pixel_range',
                 this.render_image);
             this.listenTo(this.model,
                 'change:channels change:zoom change:dx change:dy change:width change:height change:rotation change:labels change:theT change:deltaT change:theZ change:deltaZ change:z_projection change:z_start change:z_end',

src/js/views/right_panel_view.js

@@ -1181,9 +1181,11 @@
                 sum_sizeZ = 0,
                 rotation,
                 z_projection,
+                projection_bytes_exceeded = [],
                 zp;
             if (this.models) {
                 this.models.forEach(function(m, i){
+                    projection_bytes_exceeded.push(m.isMaxProjectionBytesExceeded())
                     rotation = m.get('rotation');
                     max_rotation = Math.max(max_rotation, rotation);
                     sum_rotation += rotation;
@@ -1198,6 +1200,7 @@
                         }
                     }
                 });
+                let proj_bytes_exceeded = projection_bytes_exceeded.some(b => b);
                 var avg_rotation = sum_rotation / this.models.length;
                 if (avg_rotation === max_rotation) {
                     rotation = avg_rotation;
@@ -1213,6 +1216,8 @@
                 const z_projection_disabled = ((sum_sizeZ === this.models.length) || anyBig);
 
                 html = this.template({
+                    max_projection_bytes: MAX_PROJECTION_BYTES,
+                    proj_bytes_exceeded: proj_bytes_exceeded,
                     projectionIconUrl,
                     'z_projection_disabled': z_projection_disabled,
                     'rotation': rotation,

src/js/views/scalebar_form_view.js

@@ -156,8 +156,9 @@ var ScalebarFormView = Backbone.View.extend({
             } else {
                 let pix_sze = m.get('pixel_size_x');
                 // account for floating point imprecision when comparing
+                pix_sze = pix_sze ? pix_sze.toFixed(10) : pix_sze;
                 if (json.pixel_size_x != '-' &&
-                    json.pixel_size_x.toFixed(10) != pix_sze.toFixed(10)) {
+                    json.pixel_size_x.toFixed(10) != pix_sze) {
                         json.pixel_size_x = '-';
                 }
                 if (json.pixel_size_symbol != m.get('pixel_size_x_symbol')) {

src/templates/image_display_options.template.html

@@ -11,11 +11,13 @@
 
 
     <div class="btn-group image-display-options"
-         title="Maximum intensity Z-projection (choose range with 2 handles on Z-slider)">
+         title="Maximum intensity Z-projection <% if (proj_bytes_exceeded) { print('exceeds MAX_PROJECTION_BYTES: ' + max_projection_bytes ) }
+         else { %>(choose range with 2 handles on Z-slider)<% } %>">
         <button type="button" class="btn btn-outline-secondary btn-sm z-projection
                 <% if(z_projection) { %>zp-btn-down<% } else if (typeof z_projection == 'boolean') { %><% } else { %>ch-btn-flat<% }%>"
-                <% if (z_projection_disabled) { %>disabled="disabled"<% } %>
+                <% if ((!z_projection && proj_bytes_exceeded) || z_projection_disabled) { %>disabled="disabled"<% } %>
                 >
+
             <img src="<%= projectionIconUrl %>" />
         </button>
     </div>

src/templates/info_panel.template.html

@@ -40,6 +40,8 @@
                         print(_.escape(c)); print((i < channels.length-1) ? ", " : "");
                     }); %>
                 </small></div>
+                <div class="col-sm-5"><small><strong>Pixels Type</strong>:</small></div>
+                <div class="col-sm-7"><small><%= pixelsType %></small></div>
             </td></tr>
         </tbody>
     </table>