Thumbnail figure

components/tools/OmeroPy/src/omero/util/imageUtil.py

@@ -119,7 +119,7 @@ def getThumbnailSet(thumbnailStore, length, pixelIds):
 		return None
 
 def paintThumbnailGrid(thumbnailStore, length, spacing, pixelIds, colCount, bg=(255,255,255), 
-			leftLabel=None, textColour=(0,0,0), fontsize=None):
+			leftLabel=None, textColour=(0,0,0), fontsize=None, topLabel=None):
 	""" 
 	Retrieves thumbnails for each pixelId, and places them in a grid, with White background. 
 	Option to add a vertical label to the left of the canvas
@@ -144,22 +144,28 @@ def paintThumbnailGrid(thumbnailStore, length, spacing, pixelIds, colCount, bg=(
 	while (colCount * rowCount) < imgCount:	# check that we have enough rows and cols...
 		rowCount += 1
 
-	leftSpace = spacing
+	leftSpace = topSpace = spacing
+	minWidth = 0
 
 	textHeight = 0
-	if leftLabel:
+	if leftLabel or topLabel:
 		# if no images (no rows), need to make at least one row to show label
-		if rowCount == 0: rowCount = 1
+		if leftLabel is not None and rowCount == 0: rowCount = 1
 		if fontsize == None: 
 			fontsize = length/10 + 5
 		font = getFont(fontsize)
-		textHeight = font.getsize("Textq")[1]
-		leftSpace = spacing + textHeight + spacing
-
+		if leftLabel:
+			textWidth, textHeight = font.getsize(leftLabel)
+			leftSpace = spacing + textHeight + spacing
+		if topLabel:
+			textWidth, textHeight = font.getsize(topLabel)
+			topSpace = spacing + textHeight + spacing
+			minWidth = leftSpace + textWidth + spacing
+
 	# work out the canvas size needed, and create a white canvas
 	colsNeeded = min(colCount, imgCount)
-	canvasWidth = leftSpace + colsNeeded * (length+spacing)
-	canvasHeight = rowCount * (length+spacing) + spacing
+	canvasWidth = max(minWidth, (leftSpace + colsNeeded * (length+spacing)))
+	canvasHeight = topSpace + rowCount * (length+spacing) + spacing
 	mode = "RGB"
 	size = (canvasWidth, canvasHeight)
 	canvas = Image.new(mode, size, bg)
@@ -177,6 +183,16 @@ def paintThumbnailGrid(thumbnailStore, length, spacing, pixelIds, colCount, bg=(
 		verticalCanvas = textCanvas.rotate(90)
 		pasteImage(verticalCanvas, canvas, 0, 0)
 		del draw
+
+	if topLabel is not None:
+		labelCanvasWidth = canvasWidth
+		labelCanvasHeight = textHeight + spacing
+		labelSize = (labelCanvasWidth, labelCanvasHeight)
+		textCanvas = Image.new(mode, labelSize, bg)
+		draw = ImageDraw.Draw(textCanvas)
+		draw.text((spacing, spacing), topLabel, font=font, fill=textColour)
+		pasteImage(textCanvas, canvas, leftSpace, 0)
+		del draw
 
 	# loop through the images, getting a thumbnail and placing it on a new row and column
 	r = 0
@@ -189,7 +205,7 @@ def paintThumbnailGrid(thumbnailStore, length, spacing, pixelIds, colCount, bg=(
 				thumbImage = Image.open(StringIO.StringIO(thumbnail))	# make an "Image" from the string-encoded thumbnail
 				# paste the image onto the canvas at the correct coordinates for the current row and column 
 				x = c*(length+spacing) + leftSpace
-				y = r*(length+spacing) + spacing
+				y = r*(length+spacing) + topSpace
 				pasteImage(thumbImage, canvas, x, y)
 
 		# increment the column, and if we're at the last column, start a new row

components/tools/OmeroWeb/omeroweb/webclient/controller/container.py

@@ -197,7 +197,16 @@ def listFigureScripts(self, objDict=None):
                     if i.getSizeC() > 1:
                         splitView['enabled'] = True
                         break
+        thumbnailFig = {'id': 'Thumbnail', 'name': 'Thumbnail Figure', 'enabled': False,
+            'tooltip': "Export a figure of thumbnails, optionally sorted by tag"}
+        # Thumbnail figure is enabled if we have Datasets or Images selected
+        if self.image or self.dataset:
+            thumbnailFig['enabled'] = True
+        elif objDict is not None:
+            if 'image' in objDict or 'dataset' in objDict:
+                thumbnailFig['enabled'] = True
         figureScripts.append(splitView)
+        figureScripts.append(thumbnailFig)
         return figureScripts
 
 

components/tools/OmeroWeb/omeroweb/webclient/static/webclient/javascript/ome.split_view_figure.js

@@ -17,14 +17,6 @@
 //
 
 $(document).ready(function() {
-    OME.setupAjaxError("{% url fsend %}");      // just in case!
-
-    $('#script_form').ajaxForm({
-        success: function(data) {
-            window.opener.OME.showActivities();
-            self.close();
-        }
-    });
 
 
     // Basically what we're doing here is supplementing the form fields
@@ -307,7 +299,4 @@ $(document).ready(function() {
             setImgSize(ui.value);
         }
     });
-
-    // For 'number' fields, only allow numbers input.
-    $(".number").numbersOnly();
 });

components/tools/OmeroWeb/omeroweb/webclient/static/webclient/javascript/ome.thumbnail_figure.js

@@ -0,0 +1,266 @@
+//
+// Copyright (C) 2013 University of Dundee & Open Microscopy Environment.
+// All rights reserved.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+
+$(document).ready(function() {
+
+    // Clear selection (only needed on page 'refresh')
+    $("#tagChooser option").removeAttr('selected');
+
+
+    // Show / Hide un-tagged images after sorting or checkbox click
+    var updateNotTagged = function() {
+        var show_untagged_images = $("input[name=Show_Untagged_Images]").is(":checked");
+        if (show_untagged_images) {
+            $(".notTagged").show();
+        } else {
+            $(".notTagged").hide();
+        }
+    };
+    $("input[name=Show_Untagged_Images]").click(updateNotTagged);
+
+
+    // Add <br> to break up long rows of thumbnails
+    var updateRowCount = function(){
+        var colCount = parseInt($("input[name=Max_Columns]").val(), 10);
+        $(".thumbnail_set td:has(.img_panel)").each(function(){
+            var $td = $(this);
+            $("br", $td).remove();  // remove old <br>
+            // $(":nth-child(" + colCount + "n)", $td).after("<br/>");
+            // <td> may have <div> children that break up child thumbs
+            var i = 1;
+            $td.children().each(function(){
+                var $child = $(this);
+                if (i % colCount === 0) {
+                    $child.after("<br/>")
+                }
+                if (this.nodeName.toLowerCase() == 'div') {
+                    i = 1;      // new row
+                } else {
+                    i++;
+                }
+            });
+        });
+    };
+    $("input[name=Max_Columns]").bind('keyup input', updateRowCount);
+
+    updateRowCount();   // initialise layout
+
+
+    // If no tags are chosen, we need to return to initial state
+    var clearTagSorting = function() {
+        $(".thumbnail_set").each(function() {
+            var $this = $(this),
+                $toRemove = $('tr:has(.img_panel)', $this);
+
+            $tr = $('<tr><td></td></tr>');
+            $tr.appendTo($this);
+            $td = $('<td></td>').appendTo($tr);
+            $(".img_panel", $this).appendTo($td);
+            // now that we've moved the images, we can clean up!
+            $toRemove.remove();
+            updateRowCount();
+        });
+    }
+
+
+    // Initialise the Chosen plugin, handle Adding / Removing of Tags...
+    var $TagIdsInput = $("input[name=Tag_IDs]");
+    var selectedTagIds = [];
+    $("#tagChooser")
+        .chosen({placeholder_text:'Choose Tags'})
+        .change(function(evt, data) {
+            if (data.deselected) {
+                var toRemove = data.deselected;
+                selectedTagIds.splice(selectedTagIds.indexOf(toRemove), 1);
+            } else if (data.selected) {
+                selectedTagIds.push(data.selected);
+            }
+            // update input for form submission
+            $TagIdsInput.val(selectedTagIds.join(","));
+
+            if (selectedTagIds.length == 0) {
+                clearTagSorting();
+                return;
+            }
+
+            var tagValues = {};
+            // Have to look-up the Tag names from the UI
+            $("#tagChooser option:selected").each(function(){
+                var $this = $(this);
+                tagValues[$this.attr('value')] = $this.text();
+            });
+
+            // Now we need to sort images by ids....
+            // Let's assign letters to tags in order, so we can use to sort,
+            // E.g. 'Metaphase' == 'a', 'Anaphase' == 'b', 'Dead' == 'c'
+            // Then we can combine: 'Metaphase'+'Dead' ==> 'ac', 'Anaphase'+'Dead' ==> 'bc'
+            // And sort: 'a', 'ab', 'abc', 'b', 'bc', 'c', '' (untagged)
+            var letters = "abcdefghijklmnopqrstuvwxyz",
+                tagLetters = {},
+                letterTags = {};    // backwards map to decode
+            for (var t=0; t<selectedTagIds.length; t++){
+                tagLetters[selectedTagIds[t]] = letters[t];
+                letterTags[letters[t]] = selectedTagIds[t];
+            }
+
+            // E.g. 'ac' ==> ['Metaphase', 'Dead']
+            var getTagsFromKey = function(key) {
+                var rv = [];
+                for (var k=0; k<key.length; k++) {
+                    var tagId = letterTags[key[k]];
+                    rv.push(tagValues[tagId]);
+                }
+                return rv;
+            }
+
+            // For each 'Dataset' (or set of Images)...
+            $(".thumbnail_set").each(function() {
+                // Make a data structure of image-ids : [tag ids]
+                var $this = $(this),
+                    imageTags = {},
+                    imgIds = [];
+                $(".img_panel", $this).each(function(){
+                    var $img = $(this),
+                        iId = $img.attr('data-iId'),
+                        tagString = $img.attr('data-tags');
+                    imageTags[iId] = tagString.split(",");
+                    imgIds.push(iId);
+                });
+
+                // Prepare for sorting...
+                sortedImgs = []
+                for (var i=0; i<imgIds.length; i++) {
+                    // Build up a string based on the image's Tags, that can be used to sort
+                    var imgId = imgIds[i],
+                        tagIds = imageTags[imgId],
+                        letterKeys = [];
+                    for (var c=0; c<selectedTagIds.length; c++) {
+                        var tid = selectedTagIds[c];
+                        if (tagIds.indexOf(tid) > -1) {
+                            letterKeys.push(tagLetters[tid]);
+                        }
+                    }
+                    var tagKey = letterKeys.join("");    // E.g. 'a' or 'bc'
+                    sortedImgs.push({'id':imgId, 'tagKey':tagKey});
+                }
+                // Do the Sorting!
+                sortedImgs.sort(function(a, b) {
+                    var x = a['tagKey'], y = b['tagKey'];
+                    if (x.length === 0) return 1;
+                    if (y.length === 0) return -1;
+                    return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+                });
+
+                // Group Images with same tags. E.g. all of the with key 'ac'
+                var results = [],        // List of {'tagNames':[], 'imgIds':[]}
+                    rkey = "", rIds = [];
+                for (var s=0; s<sortedImgs.length; s++) {
+                    var sImg = sortedImgs[s];
+                    if (sImg.tagKey == rkey) {
+                        rIds.push(sImg.id);
+                    } else {
+                        if (rIds.length > 0) {
+                            results.push({'rkey':rkey, 'tags': getTagsFromKey(rkey), 'imgIds':rIds});
+                        }
+                        rIds = [sImg.id];
+                        rkey = sImg.tagKey;
+                    }
+                }
+                results.push({'rkey':rkey, 'tags': getTagsFromKey(rkey), 'imgIds':rIds});
+
+
+                // Update the UI
+                var $toRemove = $('tr:has(.img_panel)', $this);
+
+                // For each Tag combination... (E.g. 'Metaphase'+'Dead')
+                var topLevelTag = "";
+                var $td, $tr;
+                for (var r=0; r<results.length; r++) {
+
+                    var tagData = results[r],
+                        tagsText = tagData.tags.join(", ");     // 'Metaphase, Dead'
+                    if (tagsText.length === 0) {
+                        tagsText = "Not Tagged";
+                    }
+                    if (tagsText.length === 0 || tagData.tags[0] !== topLevelTag) {
+                        // start a new container...
+                        topLevelTag = tagData.tags[0] || tagsText;      // Group under 1st tag (unless we have no tags)
+
+                        $tr = $('<tr><th><h2>' + topLevelTag + '</h2></th></tr>');
+                        $tr.appendTo($this);
+                        $td = $('<td></td>').appendTo($tr);
+                    }
+                    $td.append('<div class="subsetLabel">'+ tagsText + '</div>');
+
+                    if (tagsText === "Not Tagged") {
+                        $tr.addClass('notTagged');
+                    }
+
+                    // Add the images (move from previous position)...
+                    for (var i=0; i<tagData.imgIds.length; i++) {
+                        $('#thumbnail-'+tagData.imgIds[i]).appendTo($td);
+                    }
+
+                }
+                // now that we've moved the images, we can clean up!
+                $toRemove.remove();
+
+                // tidy up by hiding subset labels where there is only 1 subset
+                // AND the subset has only 1 Tag
+                $('tr:has(.img_panel)', $this).each(function(){
+                    var $subsetLabels = $(this).find('.subsetLabel');
+                    if (($subsetLabels.length === 1)
+                            && ($subsetLabels.text().split(", ").length === 1)) {
+                        $subsetLabels.hide();
+                    }
+                });
+
+                updateNotTagged();
+                updateRowCount();
+            });
+
+    });
+
+    // Hacks to make the Chosen plugin to wide enough.
+    $(".chzn-container").width('350px');
+    $(".chzn-container input").width('300px');
+
+    // Bonus feature - Zoom the preview thumbs with slider
+    // Make a list of styles (for quick access on zoom)
+    var img_panel_styles = [];
+    $(".img_panel").each(function(){
+        img_panel_styles.push(this.style);
+    });
+    var setImgSize = function(size) {
+        console.log(size);
+        var i, l = img_panel_styles.length;
+        for (i=0; i<l; i++) {
+            img_panel_styles[i].maxWidth = size + "px";
+            img_panel_styles[i].maxHeight = size + "px";
+        }
+    };
+    $("#img_size_slider").slider({
+        max: 96,
+        min: 20,
+        value: 50,
+        slide: function(event, ui) {
+            setImgSize(ui.value);
+        }
+    });
+
+});