histomicsui 1.7.1.dev16__tar.gz → 1.7.2__tar.gz

{histomicsui-1.7.1.dev16/histomicsui.egg-info → histomicsui-1.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: histomicsui
-Version: 1.7.1.dev16
+Version: 1.7.2
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -21,7 +21,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: NOTICE
-Requires-Dist: girder-large-image-annotation>=1.31.0
+Requires-Dist: girder-large-image-annotation>=1.32.8
 Requires-Dist: girder-slicer-cli-web[girder]>=1.4.0
 Requires-Dist: cachetools
 Requires-Dist: orjson

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/docs/config_options.rst

@@ -50,6 +50,7 @@ _________________
           fillColor: rgba(255, 0, 0, 0.25)
           lineColor: rgb(255, 0, 0)
           lineWidth: 2
+          hotkey: r
         -
           id: Green
           fillColor: rgba(0, 128, 0, 0.25)
@@ -61,6 +62,19 @@ _________________
           lineColor: rgb(0, 0, 255)
           lineWidth: 2
 
+If a hotkey is specified for a group, it will only be active if the group was loaded from the config file.  That is, moving to another folder where the config file does not apply will disable the hotkey.  If you want hotkeys to have modifiers (e.g., require that alt, ctrl, or meta be pressed or explicitly NOT pressed), you can add a hotkey section:
+
+::
+
+    ---
+    hotkeys:
+      -
+        key: r
+        ctrl: true
+        alt: false
+        action: group
+        param: Red
+
 UI Settings
 ___________
 

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/dialogs/saveAnnotation.js

@@ -467,26 +467,26 @@ var SaveAnnotation = View.extend({
 
         // all valid
         if (setFillColor || setLineColor || setLineWidth) {
-            this.annotation.elements().each((element, idx) => { /* eslint-disable backbone/no-silent */
+            this.annotation.elements().each((element, idx) => {
                 if (setFillColor) {
                     if (setFillColor === 'func') {
                         fillColor = colorFromFunc(element, idx, fillColorParam, this._styleableFuncs[fillColorParam.key]);
                     }
-                    element.set('fillColor', fillColor, {silent: true});
+                    element.set('fillColor', fillColor, {delaySave: true});
                 }
                 if (setLineColor) {
                     if (setLineColor === 'func') {
                         lineColor = colorFromFunc(element, idx, lineColorParam, this._styleableFuncs[lineColorParam.key]);
                     }
-                    element.set('lineColor', lineColor, {silent: true});
+                    element.set('lineColor', lineColor, {delaySave: true});
                 }
                 if (setLineWidth) {
-                    element.set('lineWidth', lineWidth, {silent: true});
+                    element.set('lineWidth', lineWidth, {delaySave: true});
                 }
             });
             const annotationData = _.extend({}, this.annotation.get('annotation'));
             annotationData.elements = this.annotation.elements().toJSON();
-            this.annotation.set('annotation', annotationData, {silent: true});
+            this.annotation.set('annotation', annotationData, {delaySave: true});
         }
 
         const visible = this.$('#h-annotation-visible').prop('checked');

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/panels/AnnotationSelector.js

@@ -15,11 +15,6 @@ import showSaveAnnotationDialog from '../dialogs/saveAnnotation';
 import annotationSelectorWidget from '../templates/panels/annotationSelector.pug';
 import '../stylesheets/panels/annotationSelector.styl';
 
-// Too many elements in the draw panel will crash the browser,
-// so we only allow editing of annotations with less than this
-// many elements.
-const MAX_ELEMENTS_LIST_LENGTH = 5000;
-
 /**
  * Create a panel controlling the visibility of annotations
  * on the image view.
@@ -401,24 +396,12 @@ var AnnotationSelector = Panel.extend({
     },
 
     _setActiveAnnotationWithoutLoad(model) {
-        const numElements = ((model.get('annotation') || {}).elements || []).length;
         if (this._activeAnnotation && this._activeAnnotation.id !== model.id) {
             return;
         }
         model.set('displayed', true);
 
-        if (numElements > MAX_ELEMENTS_LIST_LENGTH || model._pageElements) {
-            events.trigger('g:alert', {
-                text: 'This annotation has too many elements to be edited.',
-                type: 'warning',
-                timeout: 5000,
-                icon: 'info'
-            });
-            this._activeAnnotation = null;
-            this.trigger('h:editAnnotation', null);
-        } else {
-            this.trigger('h:editAnnotation', model);
-        }
+        this.trigger('h:editAnnotation', model);
     },
 
     createAnnotation(evt) {
@@ -441,7 +424,10 @@ var AnnotationSelector = Panel.extend({
         );
     },
 
-    _saveAnnotation(annotation) {
+    _saveAnnotation(annotation, options) {
+        if (options && options.delaySave) {
+            return;
+        }
         if (this.viewer && !this.viewer._saving) {
             this.viewer._saving = {};
         }

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/panels/DrawWidget.js

@@ -118,7 +118,8 @@ var DrawWidget = Panel.extend({
                 drawingType: this._drawingType,
                 collapsed: this.$('.s-panel-content.collapse').length && !this.$('.s-panel-content').hasClass('in'),
                 firstRender: true,
-                displayIdStart: 0
+                displayIdStart: 0,
+                partialCount: this.annotation && this.annotation._pageElements
             }));
             this.$('.h-dropdown-content').collapse({toggle: false});
         }
@@ -435,7 +436,7 @@ var DrawWidget = Panel.extend({
             }
             return result;
         }).filter((annot) => !annot.points || annot.points.length);
-        Object.keys(oldids).forEach((id) => this.deleteElement(undefined, id, {silent: elements.length}));
+        Object.keys(oldids).forEach((id) => this.deleteElement(undefined, id, {delaySave: elements.length}));
         this.addElements(
             _.map(elements, (el) => {
                 el = _.extend(el, _.omit(this._style.toJSON(), 'id'));
@@ -997,20 +998,35 @@ var DrawWidget = Panel.extend({
         this._setStyleGroup(this._groups.get(prevGroup).toJSON());
     },
 
+    setStyleGroupById(groupId) {
+        const group = this._groups.get(groupId);
+        if (!group) {
+            return;
+        }
+        this._setStyleGroup(group.toJSON());
+    },
+
     getStyleGroup() {
         return this._style;
     },
 
+    _debounceRender() {
+        if (this._debounceTimer) {
+            window.clearTimeout(this._debounceTimer);
+        }
+        this._debounceTimer = window.setTimeout(() => this.render(), 1);
+    },
+
     _styleGroupEditor() {
         var dlg = editStyleGroups(this._style, this._groups, this.parentView._defaultGroup);
         dlg.$el.on('hidden.bs.modal', () => {
-            this.render();
+            this._debounceRender();
             this.parentView.trigger('h:styleGroupsEdited', this._groups);
         });
     },
 
     _handleStyleGroupsUpdate() {
-        this.render();
+        this._debounceRender();
         this.trigger('h:styleGroupsUpdated', this._groups);
     },
 

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/templates/panels/drawWidget.pug

@@ -104,7 +104,10 @@ block content
             input.h-brush-screen(type="checkbox", checked=opts.brush_screen ? 'checked' : undefined)
             | Screen
   .h-group-count
-    b.h-group-count-label Count:
+    if partialCount
+      b.h-group-count-label(title='* These counts only apply to loaded elements') Count*:
+    else
+      b.h-group-count-label Count:
     span.h-group-count-options
   .h-elements-container
     include drawWidgetElement.pug

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/views/body/ImageView.js

@@ -1168,6 +1168,38 @@ var ImageView = View.extend({
             l: 'line',
             b: 'brush'
         };
+        if (this._hotkeys && this._hotkeys[evt.key.toLowerCase()]) {
+            let used = false;
+            this._hotkeys[evt.key.toLowerCase()].forEach((keyset) => {
+                if (keyset.ctrl !== undefined && evt.originalEvent.ctrlKey !== keyset.ctrl) {
+                    return;
+                }
+                if (keyset.alt !== undefined && evt.originalEvent.altKey !== keyset.alt) {
+                    return;
+                }
+                if (keyset.meta !== undefined && evt.originalEvent.metaKey !== keyset.meta) {
+                    return;
+                }
+                if (keyset.shift !== undefined && evt.originalEvent.shiftKey !== keyset.shift) {
+                    return;
+                }
+                if (keyset.shift === undefined && evt.originalEvent.shiftKey && evt.key.toLowerCase() === keyset.key) {
+                    return;
+                }
+                switch (keyset.action) {
+                    case 'group':
+                        if (this.drawWidget) {
+                            this.drawWidget.setStyleGroupById(keyset.param);
+                            used = true;
+                        }
+                        break;
+                }
+            });
+            if (used) {
+                evt.preventDefault();
+                return;
+            }
+        }
         switch (evt.key) {
             case 'a':
                 this._showOrHideAnnotations();
@@ -1254,6 +1286,11 @@ var ImageView = View.extend({
                     }
                 }
                 break;
+            case 'D':
+                if (evt.shiftKey && (evt.altKey || evt.metaKey)) {
+                    console.log(this);
+                }
+                break;
             default:
                 if (this.drawWidget && drawModes[evt.key] && this.activeAnnotation) {
                     const mode = drawModes[evt.key];
@@ -1343,6 +1380,9 @@ var ImageView = View.extend({
     getElementsInPolygon(poly) {
         const results = [];
         this.viewerWidget.featureLayer.features().forEach((feature) => {
+            if (feature._centroidFeature) {
+                return;
+            }
             const r = feature.polygonSearch(poly, {partial: false});
             r.found.forEach((feature) => {
                 const annotationId = feature.properties ? feature.properties.annotation : null;
@@ -1560,12 +1600,11 @@ var ImageView = View.extend({
         const groupedAnnotations = this.selectedElements.groupBy((element) => element.originalAnnotation.id);
         _.each(groupedAnnotations, (elements, annotationId) => {
             const annotation = this.annotations.get(annotationId);
-            _.each(elements, (element) => { /* eslint-disable backbone/no-silent */
+            _.each(elements, (element) => {
                 const annotationElement = annotation.elements().get(element.id);
-                // silence the event because we want to make one save call for each annotation.
-                annotationElement.set(element.toJSON(), {silent: true});
+                annotationElement.set(element.toJSON(), {delaySave: true});
                 if (!element.get('group')) {
-                    annotationElement.unset('group', {silent: true});
+                    annotationElement.unset('group', {delaySave: true});
                 }
             });
             if (!elements.length) {
@@ -1581,7 +1620,7 @@ var ImageView = View.extend({
         _.each(groupedAnnotations, (elements, annotationId) => { /* eslint-disable backbone/no-silent */
             // silence the event because we want to make one save call for each annotation.
             const elementsCollection = this.annotations.get(annotationId).elements();
-            elementsCollection.remove(elements, {silent: true});
+            elementsCollection.remove(elements, {delaySave: true});
             elementsCollection.trigger('reset', elementsCollection);
         });
     },
@@ -1663,10 +1702,33 @@ var ImageView = View.extend({
             return null;
         });
     },
+    _addHotKey(keyset) {
+        if (keyset.key === undefined || keyset.action === undefined || !keyset.key.length) {
+            return;
+        }
+        keyset = Object.assign({}, keyset);
+        let key = keyset.key;
+        const parts = key.replace(/([+-])(?!$)/g, '\n').split('\n');
+        const modifiers = ['ctrl', 'alt', 'meta', 'shift'];
+        for (let i = 0; i < parts.length - 1; i++) {
+            const mod = parts[i].toLowerCase();
+            if (modifiers.includes(mod)) {
+                keyset[mod] = true;
+            }
+        }
+        key = parts[parts.length - 1];
+        keyset.key = key;
+        key = key.toLowerCase();
+        if (!this._hotkeys[key]) {
+            this._hotkeys[key] = [];
+        }
+        this._hotkeys[key].push(keyset);
+    },
     _getConfig(modelId) {
         if (modelId !== this._folderConfigId) {
             this._folderConfigId = modelId;
             this._folderConfig = {};
+            this._hotkeys = {};
         }
         restRequest({
             url: `folder/${this.model.get('folderId')}/yaml_config/.histomicsui_config.yaml`
@@ -1676,7 +1738,18 @@ var ImageView = View.extend({
                 return;
             }
             this._folderConfig = val;
+            this._hotkeys = {};
+            if (val.hotkeys) {
+                (val.hotkeys || []).forEach((keyset) => {
+                    this._addHotKey(keyset);
+                });
+            }
             if (val.annotationGroups) {
+                (val.annotationGroups.groups || []).forEach((group) => {
+                    if (group.hotkey) {
+                        this._addHotKey({key: group.hotkey, action: 'group', param: group.id});
+                    }
+                });
                 const groups = new StyleCollection();
                 groups.fetch().done(() => {
                     if (!val || this.model.id !== modelId) {

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui/web_client/views/popover/AnnotationContextMenu.js

@@ -68,7 +68,7 @@ const AnnotationContextMenu = View.extend({
             }
         });
         let refresh = false;
-        this.collection.each((element) => { /* eslint-disable backbone/no-silent */
+        this.collection.each((element) => {
             if (this.parentView.drawWidget && this.parentView.activeAnnotation.id === element.originalAnnotation.id &&
                     element.attributes.group !== group && ['point', 'polyline', 'rectangle', 'ellipse', 'circle'].includes(element.attributes.type)) {
                 this.parentView.drawWidget.updateCount(element.attributes.group || this.parentView._defaultGroup, -1);
@@ -78,9 +78,9 @@ const AnnotationContextMenu = View.extend({
             if (group) {
                 styleAttrs.group = group;
             } else {
-                element.unset('group', {silent: true});
+                element.unset('group', {delaySave: true});
             }
-            element.set(styleAttrs, {silent: true});
+            element.set(styleAttrs, {delaySave: true});
         });
         this.collection.trigger('h:save');
         this.trigger('h:close');

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2/histomicsui.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: histomicsui
-Version: 1.7.1.dev16
+Version: 1.7.2
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -21,7 +21,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: NOTICE
-Requires-Dist: girder-large-image-annotation>=1.31.0
+Requires-Dist: girder-large-image-annotation>=1.32.8
 Requires-Dist: girder-slicer-cli-web[girder]>=1.4.0
 Requires-Dist: cachetools
 Requires-Dist: orjson

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/histomicsui.egg-info/requires.txt

@@ -1,4 +1,4 @@
-girder-large-image-annotation>=1.31.0
+girder-large-image-annotation>=1.32.8
 girder-slicer-cli-web[girder]>=1.4.0
 cachetools
 orjson

{histomicsui-1.7.1.dev16 → histomicsui-1.7.2}/setup.py

@@ -43,7 +43,7 @@ setup(
         'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
-        'girder-large-image-annotation>=1.31.0',
+        'girder-large-image-annotation>=1.32.8',
         'girder-slicer-cli-web[girder]>=1.4.0',
         'cachetools',
         'orjson',