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bookmarks_patch
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bookmarks_patch
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diff --git a/src/main/webapp/index.jsp b/src/main/webapp/index.jsp
index 5ce4a72..b0ee794 100755
--- a/src/main/webapp/index.jsp
+++ b/src/main/webapp/index.jsp
@@ -297,7 +297,7 @@ limitations under the License.
for (var k in queryParams) {
if (queryParams.hasOwnProperty(k)) {
- if (k.startsWith('w')) {
+ if (k.startsWith('w')) {
bookmarkData['wt'][k.substring(1)] = queryParams[k];
} else if (k.startsWith('m')) {
bookmarkData['mut'][k.substring(1)] = queryParams[k];
diff --git a/src/main/webapp/js/main.js b/src/main/webapp/js/main.js
index 04c0466..921f7bc 100755
--- a/src/main/webapp/js/main.js
+++ b/src/main/webapp/js/main.js
@@ -29,7 +29,7 @@
var spinner; // Progress spinner
var currentZoom = 0;
var currentOrientation = 'horizontal';
- var currentViewHeight;
+ var currentViewHeight = 500;
var bookmarkReady = false;
var mgi;
var gene_symbol;
@@ -82,8 +82,8 @@
var volorder = ["203", "204", "202"]; //At startup, search in this order for modality data to display first
- if ('mod' in bookmarkData) {
- volorder.unshift(bookmarkData['mod']);
+ if ('pid' in bookmarkData) {
+ volorder.unshift(bookmarkData['pid']);
}
@@ -364,6 +364,11 @@
$viewHeight.slider('value', bookmarkData['h']);
$viewHeight.slider("option", "slide").call($viewHeight, null, { value: bookmarkData['h']});
}
+
+ // Set scale bar
+ if (bookmarkData['sb']) {
+ scales.currentBarSize = bookmarkData['sb'];
+ }
// Set ready
bookmarkReady = true;
@@ -383,7 +388,7 @@
var bookmark = hostname
+ '?' + bookmarkData['mode'] + '=' + bookmarkData['gene']
- + '&mod=' + currentModality
+ + '&pid=' + currentModality
+ '&h=' + currentViewHeight
+ '&s=' + s
+ '&c=' + c
@@ -391,13 +396,13 @@
+ '&o=' + currentOrientation
+ '&zoom=' + currentZoom
+ '&sb=' + scales.currentBarSize
- + '&w=' + wtView.getCurrentVolume()['animalName']
+ + '&wn=' + wtView.getCurrentVolume()['animalName']
+ '&wx=' + wtView.getIndex('X')
+ '&wy=' + wtView.getIndex('Y')
+ '&wz=' + wtView.getIndex('Z')
+ '&wl=' + wtView.getBrightnessLower()
+ '&wu=' + wtView.getBrightnessUpper()
- + '&m=' + mutView.getCurrentVolume()['animalName']
+ + '&mn=' + mutView.getCurrentVolume()['animalName']
+ '&mx=' + mutView.getIndex('X')
+ '&my=' + mutView.getIndex('Y')
+ '&mz=' + mutView.getIndex('Z')
@@ -451,7 +456,8 @@
views[i].rescale(scales.currentBarSize);
}
- window.dispatchEvent(new Event('resize'));
+ window.dispatchEvent(new Event('resize'));
+ currentZoom = 0;
}
@@ -544,14 +550,14 @@
// only load if baseline data available
if (objSize(wildtypeData) > 0){
- var wtConfig = {specimen: bookmarkData['wt'] };
+ var wtConfig = bookmarkData['wt'];
wtView = new iev.specimenview(wildtypeData, 'wt', container,
WILDTYPE_COLONYID, sliceChange, wtConfig, loadedCb, localStorage);
views.push(wtView);
}
// Set mutant specimen based on bookmark
- var mutConfig = {specimen: bookmarkData['mut']};
+ var mutConfig = bookmarkData['mut'];
mutView = new iev.specimenview(mutantData, 'mut', container,
queryId, sliceChange, mutConfig, loadedCb, localStorage);
views.push(mutView);
@@ -848,8 +854,7 @@
for (var i = 0; i < views.length; i++) {
views[i].setVisibleViews(ortho, count, horizontalView);
}
- window.dispatchEvent(new Event('resize'));
-
+ window.dispatchEvent(new Event('resize'));
currentZoom = 0; // necessary as the zoom resets on change
});
@@ -912,7 +917,7 @@
.slider({
min: 200,
max: 1920,
- value: 500,
+ value: currentViewHeight,
slide: $.proxy(function (event, ui) {
currentViewHeight = ui.value;
$('.sliceWrap').css('height', ui.value);
@@ -1101,6 +1106,7 @@
/* add a new stylesheet fort the specimen view wrapper height as it's not been created yet */
//If we are on a laptop we may not want to set the minimum size too small
var viewHeight = availableViewHeight < 200 ? 200 : availableViewHeight;
+ currentViewHeight = viewHeight;
$("<style type='text/css'> .sliceWrap{height:" + viewHeight + "px;}</style>").appendTo("head");
@@ -1116,13 +1122,14 @@
width: '50%',
clear: 'none'
- });
- $('.sliceWrap').css({
- width: '100%'
- });
- window.dispatchEvent(new Event('resize'));
+ });
+ $('.sliceWrap').css({
+ width: '100%'
+ });
+ window.dispatchEvent(new Event('resize'));
}
+
if (orientation === 'horizontal'){
horizontalView = false;
@@ -1142,8 +1149,11 @@
});
- window.dispatchEvent(new Event('resize'));
+ window.dispatchEvent(new Event('resize'));
+
}
+
+ currentZoom = 0; //reset zoom
}
diff --git a/src/main/webapp/js/specimenview.js b/src/main/webapp/js/specimenview.js
index bf80951..53f5dc8 100755
--- a/src/main/webapp/js/specimenview.js
+++ b/src/main/webapp/js/specimenview.js
@@ -67,7 +67,7 @@ if (typeof dcc === 'undefined')
this.zOffset = 0;
this.ready = false;
this.progressSpinner;
- this.contrast = config['specimen']['brightness'];
+
/** @const */
this.WILDTYPE_COLONYID = 'baseline';
@@ -76,19 +76,18 @@ if (typeof dcc === 'undefined')
this.bookmarkHasVolume = false;
// If the config has a specimen, select that instead
- if (config['specimen']) {
+ if (config.hasOwnProperty('n')) {
for (var key in volumeData) {
if (volumeData.hasOwnProperty(key)) {
var vol = volumeData[key];
- if (vol['animalName'] === config['specimen']['name']) {
+ if (vol['animalName'] === config['n']) {
this.currentVolume = vol;
this.bookmarkHasVolume = true;
break;
}
}
- }
- }
-
+ }
+ }
/*
*
@@ -359,14 +358,14 @@ iev.specimenview.prototype.setBookmarkContrast = function() {
// Set lower contrast level
var lower = parseInt(this.volume.windowLow);
- if (this.contrast['lower'] !== null) {
- lower = Math.max(this.contrast['lower'], parseInt(this.volume.windowLow));
+ if ('l' in this.config) {
+ lower = Math.max(parseInt(this.config['l']), parseInt(this.volume.windowLow));
}
- // Set upper this.contrast level
+ // Set upper contrast level
var upper = parseInt(this.volume.windowHigh);
- if (this.contrast['upper'] !== null) {
- upper = Math.min(this.contrast['upper'], parseInt(this.volume.windowHigh));
+ if ('u' in this.config) {
+ upper = Math.min(parseInt(this.config['u']), parseInt(this.volume.windowHigh));
}
// Set this.volume modifed
@@ -988,12 +987,10 @@ iev.specimenview.prototype.xtk_showtime = function() {
var dims = this.volume.dimensions;
// Let main know of the new dimensions of the orthogonal views
-
// It appears that dimensins are in yxz order. At least with nii loading
- var pos = this.config['specimen']['pos'];
- this.volume.indexX = !isNaN(pos['x']) ? pos['x'] : pos['x']; //Math.floor((dims[0] - 1) / 2);
- this.volume.indexY = !isNaN(pos['y']) ? pos['y'] : pos['y']; //Math.floor((dims[1] - 1) / 2);
- this.volume.indexZ = !isNaN(pos['z']) ? pos['z'] : pos['z']; //Math.floor((dims[2] - 1) / 2);
+ this.volume.indexX = 'x' in this.config ? parseInt(this.config['x']) : Math.floor((dims[0] - 1) / 2);
+ this.volume.indexY = 'y' in this.config ? parseInt(this.config['y']) : Math.floor((dims[1] - 1) / 2);
+ this.volume.indexZ = 'z' in this.config ? parseInt(this.config['z']) : Math.floor((dims[2] - 1) / 2);
this.makeIndexSlider(this.$xSlider, 'X', dims[0] - 1);
this.makeIndexSlider(this.$ySlider, 'Y', dims[1] - 1);