/**
* Creates a set of HTML files (one for each size in {@link
* GemIdentImageSets.ImageSetInterface.Size Size} with a global view (if the image set is a large
* global image) where the thumbnails have colored borders where each cluster shares a common
* color. After, each cluster's thumbnails are displayed without the global context. All
* thumbnails link to the raw image.
*/
private void CreateHTMLOutputAndOpen() {
int tWidth = Thumbnails.tWidth / 2;
int tHeight = Thumbnails.tHeight / 2;
int numThumbPerRow = (int) Math.round(TableWidth / (double) tWidth);
ArrayList<Set<String>> clusters = GetImageListsFromClusters();
for (ImageSetInterface.Size size : ImageSetInterface.Size.values()) {
int factor = 0;
switch (size) {
case XL:
factor = 1;
break;
case L:
factor = 2;
break;
case M:
factor = 4;
break;
case S:
factor = 8;
break;
case XS:
factor = 16;
break;
case XXS:
factor = 32;
break;
}
PrintWriter out = null;
try {
out =
new PrintWriter(
new BufferedWriter(
new FileWriter(
Run.it.imageset.getFilenameWithHomePath(
Subsets + NumClusters + size + ".html"))));
} catch (IOException e) {
System.out.println(Subsets + NumClusters + ".html" + " cannot be created");
}
out.print("<HTML>");
CreateHTMLHeader(out);
if (!(Run.it.imageset instanceof NonGlobalImageSet))
CreateHTMLForGlobal(out, factor, clusters, tWidth, tHeight);
for (int c = 1; c <= NumClusters; c++)
CreateHTMLCluster(out, clusters.get(c - 1), c, numThumbPerRow, tWidth, tHeight);
out.print("</HTML>");
out.close();
}
IOTools.RunProgramInOS(Subsets + NumClusters + "M.html");
}
/**
* 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;
}
}