/**
* If the file containing the data information does exist, open the data from the {@link
* #imageDataFile XML file}, otherwise, generate the data: first open the color information
* ({@link StainMaker Mahalanobis Cubes}), then retrieve the list of project images ({@link
* GemIdentTools.Thumbnails#GetImageList(String)}), then initialize data and the thread pool, then
* thread a {@link ImageSetHeuristics.ImageInfoGatherer ImageInfoGatherer} to collect data for all
* project images, and finally, it saves the data by serializing itself to the {@link
* #imageDataFile XML file}. For discussion on the usefulness of this phenotype training helper,
* consult section 3.2.3 of the manual.
*
* @see <a href="http://www.gemident.com/manual.html">the GemIdent manual</a>
*/
public void run() {
if (!IOTools.FileExists(imageDataFile)) {
// System.out.println("\nbegin image set heuristics");
if (Run.it.imageset
instanceof
ImageSetInterfaceWithUserColors) { // this is ugly but conceptually it's the only way to
// go I believe
((ImageSetInterfaceWithUserColors) Run.it.imageset).OpenMahalanobisCubes(null);
}
// System.out.println("after Mahalanobis Cubes opened:"+Run.TimeElapsed(time_o)+"s");
// PrintFileHeader();
String[] filenames = Thumbnails.GetImageList(Run.it.imageset.getHomedir());
data = new HashMap<String, double[]>(filenames.length);
postprocessPool = Executors.newFixedThreadPool(Run.it.num_threads);
update = 100 / ((double) filenames.length);
for (String filename : filenames) postprocessPool.execute(new ImageInfoGatherer(filename));
postprocessPool.shutdown();
try {
postprocessPool.awaitTermination(Long.MAX_VALUE, TimeUnit.SECONDS); // effectively infinity
} catch (InterruptedException ignored) {
}
postprocessPool = null;
IOTools.saveToXML(this, Run.it.imageset.getFilenameWithHomePath(imageDataFile));
// System.out.println("\nfinished image set heuristics\n\n\n\n");
} else {
progress.setVisible(false);
ImageSetHeuristics open =
(ImageSetHeuristics)
IOTools.openFromXML(Run.it.imageset.getFilenameWithHomePath(imageDataFile));
data = open.data;
}
}
/**
* Creates the portion of the html file that displays thumbnails for a given cluster
*
* @param out writes the html file to the hard disk
* @param images the images in this cluster
* @param c the cluster number
* @param numThumbPerRow the maximum number of thumbnails to put on a row
* @param tWidth the width of the thumbnails
* @param tHeight the height of the thumbnails
*/
private void CreateHTMLCluster(
PrintWriter out, Set<String> images, int c, int numThumbPerRow, int tWidth, int tHeight) {
out.print("<br>");
out.print("\n");
out.print("<br>");
out.print("\n");
out.print("<H3 align=center>Subset #" + c + "</H3>");
out.print("\n");
out.print("<table width=" + TableWidth + " align=center>");
out.print("\n");
Object[] imageArray = images.toArray();
int numImages = imageArray.length;
// System.out.println("cluster:"+i+" "+images.size()+" images");
for (int i = 0; i < numImages; ) {
// System.out.println("image:"+images.get(i));
out.print("<tr>");
out.print("\n");
for (int w = 0; w < numThumbPerRow; w++) {
if (i + w < numImages) {
out.print("<td width=" + tWidth + " height=" + tHeight + " align=center>");
out.print("\n");
out.print(
"<a href=\""
+ imageArray[i + w]
+ "\"><img src="
+ Thumbnails.getThumbnailFilename((String) imageArray[i + w])
+ " alt="
+ imageArray[i + w]
+ " width="
+ tWidth
+ " height="
+ tHeight
+ " hspace=0 vspace=0 border=0></a>");
out.print("\n");
out.print("</td>");
out.print("\n");
}
}
out.print("</tr>");
out.print("\n");
out.print("<tr>");
out.print("\n");
for (int w = 0; w < numThumbPerRow; w++) {
if (i + w < numImages) {
out.print("<td width=" + tWidth + " align=center>");
out.print("\n");
out.print("<a href=\"" + imageArray[i + w] + "\">" + imageArray[i + w] + "</a>");
out.print("\n");
out.print("</td>");
out.print("\n");
}
}
out.print("</tr>");
out.print("\n");
i += numThumbPerRow;
}
out.print("</table>");
out.print("\n");
}
/**
* Creates the global image composed of the thumbnails of the subimages, not valid for all image
* sets
*
* @param out writes the html file to the hard disk
* @param factor the {@link GemIdentImageSets.ImageSetInterface.Size Size} factor
* @param clusters a list of the cluster sets
* @param tWidth the width of the thumbnails
* @param tHeight the height of the thumbnails
*/
private void CreateHTMLForGlobal(
PrintWriter out, int factor, ArrayList<Set<String>> clusters, int tWidth, int tHeight) {
StringMatrix picFilenameTable = (StringMatrix) Run.it.imageset.getPicFilenameTable();
int borderSize = Math.max(1, (int) Math.round(borderSizeXL / ((double) factor)));
out.print("<br>");
out.print("\n");
out.print("<br>");
out.print("\n");
out.print("<table cellspacing=0 cellpadding=0 border=1 bordercolor=BLACK>");
out.print("\n");
for (int i = 0; i < picFilenameTable.getWidth(); i++) {
out.print("<tr>");
out.print("\n");
for (int j = 0; j < picFilenameTable.getHeight(); j++) {
String filename = picFilenameTable.get(i, j);
if (filename != ImageSetInterface.PIC_NOT_PRESENT) {
String rgbColorString = GetClusterColor(filename, clusters);
out.print(
"<td height="
+ ((tHeight / factor) + 2 * borderSize)
+ " width="
+ ((tWidth / factor) + 2 * borderSize)
+ " bgcolor=rgb("
+ rgbColorString
+ ") border=5 bordercolor=white>");
if (Run.it.imageset.PicWasClassified(filename))
out.print(
"<a href=\""
+ PostProcess.GetBothName(filename)
+ ".jpg\"><img src="
+ Thumbnails.getThumbnailFilename(filename)
+ " alt="
+ filename
+ " width="
+ (tWidth / factor)
+ " height="
+ (tHeight / factor)
+ " border=0 hspace="
+ borderSize
+ " align=center valign=center)></a>");
else
out.print(
"<a href=\""
+ filename
+ "\"><img src="
+ Thumbnails.getThumbnailFilename(filename)
+ " alt="
+ filename
+ " width="
+ (tWidth / factor)
+ " height="
+ (tHeight / factor)
+ " border=0 hspace="
+ borderSize
+ " align=center valign=center)></a>");
} else out.print("<td>");
out.print("</td>");
out.print("\n");
}
out.print("</tr>");
out.print("\n");
}
out.print("</table>");
out.print("\n");
}