Merge pull request #111 from DeepMicroscopy/storage

A couple of small fixes (unfortunatly checked into the storage branch, where they did not belong).

exact/exact/annotations/static/annotations/js/show-annotation-properties.js

@@ -1,4 +1,29 @@
 
+/* Get area of a polygon/surface */
+function polygon_area(vector) {
+    let total = 0;
+
+    let len = Object.keys(vector).length/2
+    for (let i = 1; i <= len; i++) {
+
+        const addX = vector["x" + i];
+        const addY = vector["y" + (i === len ? 1 : i + 1)];
+        const subX = vector["x" + (i === len ? 1 : i + 1)];
+        const subY = vector["y" + i];
+        total += (addX * addY * 0.5) - (subX * subY * 0.5);
+    }
+    return Math.abs(total);
+}
+
+function rect_area(vector)
+{
+    return Math.round((vector["x2"]-vector["x1"])*(vector["y2"]-vector["y1"]))
+}
+
+function line_length(vector) {
+    return Math.round(Math.sqrt(Math.pow(vector["x2"]-vector["x1"],2)+Math.pow(vector["y2"]-vector["y1"],2)))
+}
+
 /// Bind Annotation Properties to UI
 class ShowAnnotationProperties{
     constructor(viewer, exact_sync) {
@@ -27,7 +52,25 @@ class ShowAnnotationProperties{
 
                 $("#annotationLastEditor").text(annotation.last_editor.username);
                 $("#annotationLastEditor").attr("href", include_server_subdir(`/users/user/${annotation.last_editor.id}/`));
-
+
+                if (annotation.annotation_type.vector_type==3) // line
+                    {
+                        $("#annotationSizeLengthLabel").html('Length (px)');
+                        $("#annotationSize").text(line_length(annotation.vector));
+                    }
+                else 
+                {   
+                    $("#annotationSizeLengthLabel").html('Area (px^2)');
+                    if (annotation.annotation_type.vector_type==1) // rect
+                    {
+                        $("#annotationSize").text(rect_area(annotation.vector));
+
+                    }
+                    else
+                    {
+                        $("#annotationSize").text(polygon_area(annotation.vector));
+                    }
+                }
                 $("#annotationRemark").val(annotation.description);
 
                 if (annotation.verified_by_user !== undefined)

exact/exact/annotations/templates/annotations/annotate_v2.html

@@ -330,6 +330,13 @@ <h5 id="active_image_name">{{ selected_image.name }}</h5>
                                             </td>
                                         </tr>
 
+                                        <tr>
+                                            <td> <label id="annotationSizeLengthLabel">Size/Length:</label></td>
+                                            <td>
+                                                <a id="annotationSize"></a>
+                                            </td>
+                                        </tr>
+
                                         <tr>
                                             <td>Unique ID:</td>
                                             <td>

exact/exact/images/migrations/0031_image_defaultframe_framedescription.py

@@ -42,7 +42,7 @@ class Migration(migrations.Migration):
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('frame_type', models.IntegerField(choices=[(0, 'z Stack'), (1, 'time series'), (255, 'undefined')], default=0)),
-                ('descreption', models.CharField()),
+                ('descreption', models.CharField(default='')),
                 ('frame_id', models.IntegerField(default=0)),
                 ('Image', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='FrameDescriptions', to='images.image')),
             ],

exact/exact/images/models.py

@@ -50,8 +50,8 @@ class FrameDescription(models.Model):
     )
 
     frame_type = models.IntegerField(choices=FRAME_TYPES, default=FrameType.ZSTACK)
-    description = models.CharField()
-    file_path = models.CharField(default='')
+    description = models.CharField(max_length=160)
+    file_path = models.CharField(default='', max_length=320)
     frame_id = models.IntegerField(default=0)
     Image = models.ForeignKey('Image',  on_delete=models.CASCADE, related_name='FrameDescriptions')
 
@@ -271,72 +271,6 @@ def save_file(self, path:Path):
                     converter.convert(str(path), 0)
                     self.objectivePower = 40
                     self.filename = path.name
-                # check if possible multi frame tiff
-                elif (len(Path(path).suffixes)>1) and (Path(path).suffixes[-2].lower().endswith('ome') and Path(path).suffixes[-1].lower().startswith('.tif')):
-
-                    reader = AICSImage(str(path))
-                    im = reader.get_stack().squeeze()
-                    shape = im.shape # shape of 1st frame in series
-
-                    image_saved = False
-                    if (len(shape) == 4 and shape[-1] in [1, 3, 4]) or len(shape) == 3 and shape[-1] not in [1, 3, 4]: 
-                        image_saved = True
-                        frames = shape[0]
-                        self.frames = frames
-                        z_positions=[str(x) for x in np.arange(frames)]
-                        z_positions_num=[x for x in np.arange(frames)]
-
-                        if reader.ome_metadata is None:
-                            logger.warning('OME TIFF without metadata: '+str(path))
-                        elif len(reader.ome_metadata.images)==0:
-                            logger.warning('Number of images is zero'+str(path))
-                        else:
-                            z_positions=[]
-                            z_positions_num=[]
-                            for im_meta in reader.ome_metadata.images:
-                                z_positions.append('%.2f %s' % (im_meta.pixels.planes[0].position_z,im_meta.pixels.planes[0].position_z_unit.value))
-                                z_positions_num.append(im_meta.pixels.planes[0].position_z)
-
-                        folder_path = Path(self.image_set.root_path()) / path.stem
-                        os.makedirs(str(folder_path), exist_ok =True)
-                        os.chmod(str(folder_path), 0o777)
-
-                        self.save() # initially save
-
-                        for frame_id in range(shape[0]):
-                            vi = pyvips.Image.new_from_array(im[frame_id])
-                            vi = vi.scaleimage()
-                            height, width, channels = vi.height, vi.width, vi.bands
-                            self.channels = channels
-
-                            target_file = folder_path / "{}_{}_{}".format(1, frame_id + 1, path.name) #z-axis frame image
-                            vi.tiffsave(str(target_file), tile=True, compression='lzw', bigtiff=True, pyramid=True, tile_width=256, tile_height=256)
-
-                            # save FrameDescription object for each frame
-                            FrameDescription.objects.create(
-                                    Image=self,
-                                    frame_id=frame_id,
-                                    file_path=target_file,
-                                    description=z_positions[frame_id],                                    
-                                    frame_type=FrameDescription.FrameType.ZSTACK,
-                            )
-
-                            # z is the default position
-                            if (0 in z_positions_num):
-                                self.defaultFrame=z_positions_num.index(0)
-
-                            # save first frame or default position for thumbnail etc.
-                            if (frame_id == 0) or (z_positions_num[frame_id]==0):
-                                self.filename = target_file.name
-
-                    else:
-                        path = Path(path).with_suffix('.tiff')
-                        if old_path == path:
-                            path = Path(path).with_suffix('.tif')
-
-                        vi = pyvips.Image.new_from_file(str(old_path))
-                        vi.tiffsave(str(path), tile=True, compression='lzw', bigtiff=True, pyramid=True, tile_width=256, tile_height=256)
-                        self.filename = path.name
 
                 elif path.suffix.lower().endswith(".tiff") or path.suffix.lower().endswith(".tif"):
                     im = tifffile.imread(str(path))

exact/util/slide_server.py

@@ -61,6 +61,10 @@ class OpenSlideWrapper(openslide.OpenSlide):
         Wraps an openslide.OpenSlide object. The rationale here is that OpenSlide.read_region does not support z Stacks / frames as arguments, hence we have to encapsulate it
 
     """
+    @property 
+    def nFrames(self):
+        return 1    
+
     def read_region(self, location, level, size, frame=0):
         return openslide.OpenSlide.read_region(self, location, level, size)