Merge branch 'ome:master' into image-outline

licenses.txt

@@ -10,17 +10,21 @@ Library: backbone.mousetrap
 Site: https://github.com/elasticsales/backbone.mousetrap
 License: MIT
 
-Library: bootstrap3
+Library: bootstrap
 Site: http://getbootstrap.com/
-License: Apache Software License, Version 2
+License: MIT
 
-Library: bootstrap-colorpicker
-Site: http://mjolnic.com/bootstrap-colorpicker/
-License: Apache Software License, Version 2
+Library: bootstrap icons
+Site: https://github.com/twbs/icons
+License: MIT
+
+Library: dompurify
+Site: https://www.npmjs.com/package/dompurify
+License: Apache License Version 2.0, or Mozilla Public License Version 2.0
 
-Library: json2js
-Site: http://www.JSON.org/json2.js
-License: Public Domain
+Library: jquery
+Site: https://jquery.com/
+License: MIT
 
 Library: markdown-browser-0.6.0-beta1
 Site: https://github.com/evilstreak/markdown-js
@@ -34,14 +38,18 @@ Library: mousetrap-1.5.3
 Site: craig.is/killing/mice
 License: Apache Software License, Version 2
 
-Library: shape-editor-3.0.0
-Site: https://github.com/ome/shape-editor
-License: BSD
+Library: @popperjs/core
+Site: https://www.npmjs.com/package/@popperjs/core
+License: MIT
 
 Library: raphael
 Site: https://github.com/fanstatic/js.raphael
 License: BSD
 
+Library: sortablejs
+Site: https://www.npmjs.com/package/sortablejs
+License: MIT
+
 Library: underscore
 Site: https://github.com/jashkenas/underscore
 License: MIT

omero_figure/omeroutils.py

@@ -17,6 +17,8 @@
 
 from omero.sys import ParametersI
 from omero.gateway import PlaneInfoWrapper
+from omero.model.enums import UnitsTime
+from omero.model import TimeI
 
 
 def get_timestamps(conn, image):
@@ -28,13 +30,34 @@ def get_timestamps(conn, image):
     info_list = conn.getQueryService().findAllByQuery(
         query, params, conn.SERVICE_OPTS)
     timemap = {}
-    for info in info_list:
-        t_index = info.theT.getValue()
-        if info.deltaT is not None:
-            # Use wrapper to help unit conversion
-            plane_info = PlaneInfoWrapper(conn, info)
-            delta_t = plane_info.getDeltaT('SECOND')
-            timemap[t_index] = delta_t.getValue()
+    # check if any PlaneInfo was found
+    if len(info_list) > 0:
+        # get time info from the PlaneInfo
+        for info in info_list:
+            t_index = info.theT.getValue()
+            if info.deltaT is not None:
+                # Use wrapper to help unit conversion
+                plane_info = PlaneInfoWrapper(conn, info)
+                delta_t = plane_info.getDeltaT('SECOND')
+                timemap[t_index] = delta_t.getValue()
+    # double check to see if timemap actually got populated
+    if len(info_list) == 0 or len(timemap) == 0:
+        # get time info from the timeIncrement of the Pixels
+        time_increment = 0
+        converted_value = 0
+        try:
+            pixels = image.getPrimaryPixels()._obj
+            time_increment = pixels.getTimeIncrement()
+            secs_unit = getattr(UnitsTime, "SECOND")
+            seconds = TimeI(time_increment, secs_unit)
+            converted_value = seconds.getValue()
+
+        except Exception as error:
+            print(f"An exception occured: {error}\n"
+                  "maybe the image has no 'timeIncrement' set")
+        if converted_value != 0:
+            for i in range(image.getSizeT()):
+                timemap[i] = i*converted_value
     time_list = []
     for t in range(image.getSizeT()):
         if t in timemap:

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -505,7 +505,7 @@ def draw_ellipse(self, shape):
         cy = self.page_height - c['y']
         rx = shape['radiusX'] * self.scale
         ry = shape['radiusY'] * self.scale
-        rotation = (shape['rotation'] + self.panel['rotation']) * -1
+        rotation = (shape.get('rotation', 0) + self.panel['rotation']) * -1
         r, g, b, a = self.get_rgba(shape['strokeColor'])
         self.canvas.setStrokeColorRGB(r, g, b, alpha=a)
 
@@ -809,7 +809,7 @@ def draw_ellipse(self, shape):
         cy = ctr['y']
         rx = self.scale * shape['radiusX']
         ry = self.scale * shape['radiusY']
-        rotation = (shape['rotation'] + self.panel['rotation']) * -1
+        rotation = (shape.get('rotation', 0) + self.panel['rotation']) * -1
 
         width = int((rx * 2) + w)
         height = int((ry * 2) + w)
@@ -820,7 +820,9 @@ def draw_ellipse(self, shape):
         rgba = ShapeToPdfExport.get_rgba_int(shape['strokeColor'])
         ellipse_draw.ellipse((0, 0, width, height), fill=rgba)
         rgba = self.get_rgba_int(shape.get('fillColor', '#00000000'))
-        ellipse_draw.ellipse((w, w, width - w, height - w), fill=rgba)
+        # when rx is ~zero (for a Point, scaled down) don't need inner ellipse
+        if (width - w) >= w:
+            ellipse_draw.ellipse((w, w, width - w, height - w), fill=rgba)
         temp_ellipse = temp_ellipse.rotate(rotation, resample=Image.BICUBIC,
                                            expand=True)
         # Use ellipse as mask, so transparent part is not pasted

setup.py

@@ -90,5 +90,5 @@ def run(self):
         'sdist': require_npm(sdist, True),
         'develop': require_npm(develop),
       },
-      tests_require=['pytest', 'numpy'],
+      tests_require=['pytest'],
       )

src/css/figure.css

@@ -1267,6 +1267,10 @@
     .ellipse-icon{
         background-image: url("../images/ellipse-icon-16.png");
     }
+    .point-icon{
+        background-image: url("../images/point-icon-24.png");
+        background-position: center;
+    }
     .polygon-icon{
         background-image: url("../images/polygon-icon-16.png");
     }

src/js/models/panel_model.js

@@ -282,7 +282,7 @@
                 return true;
             }
             var points;
-            if (shape.type === "Ellipse") {
+            if (shape.type === "Ellipse" || shape.type === "Point") {
                 points = [[shape.cx, shape.cy]];
             } else if (shape.type === "Rectangle") {
                 points = [[shape.x, shape.y],
@@ -569,7 +569,7 @@
         // labels_map is {labelKey: {size:s, text:t, position:p, color:c}} or {labelKey: false} to delete
         // where labelKey specifies the label to edit. "l.text + '_' + l.size + '_' + l.color + '_' + l.position"
         edit_labels: function(labels_map) {
-            
+
             var oldLabs = this.get('labels');
             // Need to clone the list of labels...
             var labs = [],
@@ -595,7 +595,7 @@
             // Extract all the keys (even duplicates)
             var keys = labs.map(lbl => this.get_label_key(lbl));
 
-            // get all unique labels based on filtering keys 
+            // get all unique labels based on filtering keys
             //(i.e removing duplicate keys based on the index of the first occurrence of the value)
             var filtered_lbls = labs.filter((lbl, index) => index == keys.indexOf(this.get_label_key(lbl)));
 
@@ -617,12 +617,29 @@
             this.save('channels', chs);
         },
 
-        toggle_channel: function(cIndex, active ) {
+        save_channels: function(channels) {
+            // channels should be a list of objects [{key:value}, {}..]
+            var oldChs = this.get('channels');
+            // Clone channels, applying changes
+            var chs = this.get('channels').map((oldCh, idx) => {
+                return $.extend(true, {}, oldCh, channels[idx]);
+            });
+            this.save('channels', chs);
+        },
 
+        toggle_channel: function(cIndex, active) {
             if (typeof active == "undefined") {
                 active = !this.get('channels')[cIndex].active;
             }
-            this.save_channel(cIndex, 'active', active);
+
+            if (this.get("hilo_enabled") && active) {
+                let newChs = this.get('channels').map(function(channel, idx) {
+                    return {'active': idx == cIndex};
+                });
+                this.save_channels(newChs);
+            } else {
+                this.save_channel(cIndex, 'active', active);
+            }
         },
 
         save_channel_window: function(cIndex, new_w) {

src/js/models/undo.js

@@ -193,7 +193,8 @@ export const UndoManager = Backbone.Model.extend({
         // into undo / redo operations to go into our Edit below
         var createUndo = function(callList) {
             var undos = [];
-            for (var u=0; u<callList.length; u++) {
+            // add in reverse order
+            for (var u=(callList.length - 1); u>=0; u--) {
                 undos.push(callList[u]);
             }
             // get the currently selected panels

src/js/shapeEditorTest.js

@@ -254,6 +254,11 @@ $(function() {
                           "y": 260.5,
                           "x": 419});
 
+    shapeManager.addShapeJson({"type": "Point",
+                          "strokeWidth": 2,
+                          "y": 30,
+                          "x": 30});
+
     var s = shapeManager.addShapeJson({"type": "Line",
                                "strokeColor": "#00ff00",
                                "strokeWidth": 2,

src/js/shape_editor/ellipse.js

@@ -476,7 +476,7 @@ Ellipse.prototype.createHandles = function createHandles() {
     handle = this.paper.rect(hx - hsize / 2, hy - hsize / 2, hsize, hsize);
     handle.attr({ cursor: "move" });
     handle.h_id = key;
-    handle.line = self;
+    // handle.line = self;
 
     if (this.manager.canEdit) {
       handle.drag(_handle_drag(), _handle_drag_start(), _handle_drag_end());
@@ -511,7 +511,7 @@ Ellipse.prototype.getHandleCoords = function getHandleCoords() {
   };
 };
 
-// Class for creating Lines.
+// Class for creating Ellipse.
 var CreateEllipse = function CreateEllipse(options) {
   this.paper = options.paper;
   this.manager = options.manager;