histomicsui 1.5.1.dev6__tar.gz → 1.5.1.dev12__tar.gz

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: histomicsui
-Version: 1.5.1.dev6
+Version: 1.5.1.dev12
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/histomicsui/web_client/dialogs/metadataPlot.js

@@ -26,7 +26,8 @@ const MetadataPlotDialog = View.extend({
     _submit(evt) {
         evt.preventDefault();
         const configOptions = {
-            folder: this.$('#h-plot-folder').is(':checked')
+            folder: this.$('#h-plot-folder').is(':checked'),
+            format: this.$('#h-plot-format').val()
         };
         ['x', 'y', 'r', 'c', 's'].forEach((series) => {
             const val = this.$('#h-plot-series-' + series).val();

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/histomicsui/web_client/panels/MetadataPlot.js

@@ -125,14 +125,24 @@ var MetadataPlot = Panel.extend({
             for (const [root, entry] of Object.entries(meta)) {
                 if (_.isArray(entry) && entry.length >= 1 && _.isObject(entry[0])) {
                     for (const [key, value] of Object.entries(entry[0])) {
-                        let type;
+                        let type, distinct;
                         if (_.isFinite(value)) {
                             type = 'number';
                         } else if (_.isString(value)) {
                             type = 'string';
                         }
+                        if (Number.isInteger(value) || _.isString(value)) {
+                            distinct = {};
+                            const maxDistinct = 20;
+                            for (let eidx = 0; eidx < entry.length && Object.keys(distinct).length <= maxDistinct; eidx += 1) {
+                                distinct[entry[eidx][key]] = true;
+                            }
+                            if (Object.keys(distinct).length > maxDistinct) {
+                                distinct = null;
+                            }
+                        }
                         if (type) {
-                            results.push({root, key, type, sort: `${root}.${key}`.toLowerCase()});
+                            results.push({root, key, type, distinct, sort: `${root}.${key}`.toLowerCase()});
                         }
                     }
                 }
@@ -152,7 +162,7 @@ var MetadataPlot = Panel.extend({
         const plotOptions = this.getPlotOptions();
         const optDict = {};
         plotOptions.forEach((opt) => { optDict[opt.sort] = opt; });
-        const plotData = {data: [], fieldToPlot: {}, plotToOpt: {}, ranges: {}};
+        const plotData = {data: [], fieldToPlot: {}, plotToOpt: {}, ranges: {}, format: plotConfig.format};
         const usedFields = ['x', 'y', 'r', 'c', 's'].filter((series) => plotConfig[series] && optDict[plotConfig[series]]).map((series) => {
             if (!plotData.fieldToPlot[plotConfig[series]]) {
                 plotData.fieldToPlot[plotConfig[series]] = [];
@@ -188,10 +198,14 @@ var MetadataPlot = Panel.extend({
                             entry._roots[opt.root] = entry._roots[opt.root] || meta[opt.root][idx];
                         }
                         if (value === undefined || (opt.type === 'number' && !_.isFinite(value))) {
-                            end = true;
+                            if (plotData.format !== 'violin' || key !== 'x') {
+                                end = true;
+                            }
                         }
-                        if (opt.type === 'string') {
+                        if (opt.type === 'string' || (['s', 'c'].includes(key) && opt.distinct)) {
                             value = '' + value;
+                        } else {
+                            value = +value;
                         }
                         entry[key] = value;
                     });
@@ -207,13 +221,13 @@ var MetadataPlot = Panel.extend({
                     return;
                 }
                 if (!plotData.ranges[key]) {
-                    if (_.isFinite(value)) {
+                    if (!_.isString(value)) {
                         plotData.ranges[key] = {min: value, max: value};
                     } else {
                         plotData.ranges[key] = {distinct: {}};
                     }
                 }
-                if (_.isFinite(value)) {
+                if (plotData.ranges[key].min !== undefined) {
                     if (value < plotData.ranges[key].min) {
                         plotData.ranges[key].min = value;
                     }
@@ -222,11 +236,17 @@ var MetadataPlot = Panel.extend({
                     }
                 } else {
                     plotData.ranges[key].distinct[value] = true;
+                }
+            });
+        });
+        if (plotData.data.length) {
+            Object.entries(plotData.data[0]).forEach(([key, value]) => {
+                if (plotData.ranges[key] && plotData.ranges[key].distinct) {
                     plotData.ranges[key].list = Object.keys(plotData.ranges[key].distinct).sort();
                     plotData.ranges[key].count = plotData.ranges[key].list.length;
                 }
             });
-        });
+        }
         return plotData;
     },
 
@@ -279,6 +299,24 @@ var MetadataPlot = Panel.extend({
             type: plotData.data.length > 100 ? 'scattergl' : 'scatter',
             mode: 'markers'
         };
+        if (plotData.format === 'violin') {
+            plotlyData.type = 'violin';
+            plotlyData.x = plotlyData.marker.symbol;
+            // plotlyData.points = none;
+            plotlyData.box = {visible: true};
+            plotlyData.meanline = {visible: true};
+            plotlyData.yaxis = {zeroline: false};
+            plotlyData.scalemode = 'width';
+            plotlyData.width = 0.9;
+            if (plotData.ranges.c && plotData.ranges.c.distinct) {
+                plotlyData.transforms = [{
+                    type: 'groupby',
+                    groups: plotlyData.x,
+                    styles: Object.keys(plotData.ranges.c.distinct).map((k, kidx) => ({target: kidx, value: {line: {color: colorBrewerPaired12[kidx]}}}))
+                }];
+            }
+        }
+        console.log(plotlyData);
         return [plotlyData];
     },
 
@@ -315,7 +353,7 @@ var MetadataPlot = Panel.extend({
                 if (maximized) {
                     plotOptions.margin.l += 20;
                     plotOptions.margin.b += 40;
-                    plotOptions.xaxis = {title: {text: `${plotData.plotToOpt.x.root} - ${plotData.plotToOpt.x.key}`}};
+                    plotOptions.xaxis = {title: {text: plotData.format !== 'violin' ? `${plotData.plotToOpt.x.root} - ${plotData.plotToOpt.x.key}` : `${plotData.plotToOpt.s.root} - ${plotData.plotToOpt.s.key}`}};
                     plotOptions.yaxis = {title: {text: `${plotData.plotToOpt.y.root} - ${plotData.plotToOpt.y.key}`}};
                 }
                 window.Plotly.newPlot(elem[0], this.plotDataToPlotly(plotData), plotOptions);

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/histomicsui/web_client/templates/dialogs/metadataPlot.pug

@@ -6,21 +6,32 @@
           span(aria-hidden='true') ×
         h4.modal-title Metadata Plot
       .modal-body
+        .form-group
+          label(for='h-plot-format') Format
+          -
+            var plotFormats = [
+              {key: 'scatter', label: 'Scatter'},
+              {key: 'violin', label: 'Violin'}]
+          select#h-plot-format.form-control
+            each opt in plotFormats
+              option(value=opt.key, selected=plotConfig.format === opt.key) #{opt.label}
         -
           var seriesList = [
-            {key: 'x', label: 'x-axis', number: true},
+            {key: 'x', label: 'x-axis', number: true, comment: 'Not used in violin plots'},
             {key: 'y', label: 'y-axis', number: true},
             {key: 'r', label: 'Radius'},
             {key: 'c', label: 'Color'},
-            {key: 's', label: 'Symbol', string: true}]
+            {key: 's', label: 'Symbol', string: true, comment: 'Grouping for violin plots'}]
         for series in seriesList
           .form-group
             label(for='h-plot-series-' + series.key) #{series.label}
+            if series.comment
+              p.g-hui-description #{series.comment}
             select.form-control(id='h-plot-series-' + series.key)
               if !series.number
                 option(value='_none_', selected=plotConfig[series.key] === undefined) None
               each opt in plotOptions
-                if (!series.number || opt.type === 'number') && (!series.string || opt.type === 'string')
+                if (!series.number || opt.type === 'number') && (!series.string || opt.type === 'string' || opt.distinct)
                   - var selected = plotConfig[series.key] === opt.sort
                   option(value=opt.sort, selected=selected) #{opt.root + ' - ' + opt.key}
         .form-group

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/histomicsui/webroot.mako

@@ -16,7 +16,7 @@
     <script src="${staticPublicPath}/built/girder_app.min.js"></script>
     <script>
     $(function () {
-      $('body').addClass('hui-body')
+      $('body').addClass('hui-body');
       girder.router.enabled(false);
       girder.events.trigger('g:appload.before');
       var app = new girder.plugins.histomicsui.App({

{histomicsui-1.5.1.dev6 → histomicsui-1.5.1.dev12}/histomicsui.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: histomicsui
-Version: 1.5.1.dev6
+Version: 1.5.1.dev12
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.