/**
* Performs an XPATH lookup in an xml document whose filename is specified by the first parameter
* (assumed to be in the auxiliary subdirectory) The XPATH expression is supplied as the second
* string parameter The return value is of type string e.g. this is currently used primarily for
* looking up the Company Prefix Index for encoding a GS1 Company Prefix into a 64-bit EPC tag
*/
private String xpathlookup(String xml, String expression) {
try {
// Parse the XML as a W3C document.
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document document =
builder.parse(new File(xmldir + File.separator + "auxiliary" + File.separator + xml));
XPath xpath = XPathFactory.newInstance().newXPath();
String rv = (String) xpath.evaluate(expression, document, XPathConstants.STRING);
return rv;
} catch (ParserConfigurationException e) {
System.err.println("ParserConfigurationException caught...");
e.printStackTrace();
return null;
} catch (XPathExpressionException e) {
System.err.println("XPathExpressionException caught...");
e.printStackTrace();
return null;
} catch (SAXException e) {
System.err.println("SAXException caught...");
e.printStackTrace();
return null;
} catch (IOException e) {
System.err.println("IOException caught...");
e.printStackTrace();
return null;
}
}
/**
* Create an Archival Unit
*
* @return true If successful
*/
private boolean createAu() {
Configuration config = getAuConfigFromForm();
AuProxy au;
Element element;
try {
au = getRemoteApi().createAndSaveAuConfiguration(getPlugin(), config);
} catch (ArchivalUnit.ConfigurationException exception) {
return error("Configuration failed: " + exception.getMessage());
} catch (IOException exception) {
return error("Unable to save configuration: " + exception.getMessage());
}
/*
* Successful creation - add the AU name and ID to the response document
*/
element = getXmlUtils().createElement(getResponseRoot(), AP_E_AU);
XmlUtils.addText(element, au.getName());
element = getXmlUtils().createElement(getResponseRoot(), AP_E_AUID);
XmlUtils.addText(element, au.getAuId());
return true;
}
public void write(SecureItemTable tbl, char[] password) throws IOException {
OutputStream os = new FileOutputStream(file);
OutputStream xmlout;
if (password.length == 0) {
xmlout = os;
os = null;
} else {
PBEKeySpec keyspec = new PBEKeySpec(password);
Cipher c;
try {
SecretKeyFactory fac = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
SecretKey key = fac.generateSecret(keyspec);
c = Cipher.getInstance("PBEWithMD5AndDES");
c.init(Cipher.ENCRYPT_MODE, key, pbeSpec);
} catch (java.security.GeneralSecurityException exc) {
os.close();
IOException ioe = new IOException("Security exception during write");
ioe.initCause(exc);
throw ioe;
}
CipherOutputStream out = new CipherOutputStream(os, c);
xmlout = out;
}
try {
TransformerFactory tf = TransformerFactory.newInstance();
Transformer t = tf.newTransformer();
DOMSource src = new DOMSource(tbl.getDocument());
StringWriter writer = new StringWriter();
StreamResult sr = new StreamResult(writer);
t.transform(src, sr);
OutputStreamWriter osw = new OutputStreamWriter(xmlout, StandardCharsets.UTF_8);
osw.write(writer.toString());
osw.close();
} catch (Exception exc) {
IOException ioe = new IOException("Unable to serialize XML");
ioe.initCause(exc);
throw ioe;
} finally {
xmlout.close();
if (os != null) os.close();
}
tbl.setDirty(false);
return;
}
public void save() throws IOException {
synchronized (this) {
FileWriter fw = null;
try {
fw = new FileWriter(file);
fw.write(toString());
} finally {
if (fw != null)
try {
fw.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
public static void loadDict(String strDict) {
try {
BufferedReader br = new BufferedReader(new FileReader(strDict));
String line = null;
while ((line = br.readLine()) != null) {
int idx = line.indexOf(',');
if (idx > 0) {
htDict.put(line.substring(0, idx), line.substring(idx + 1));
}
}
} catch (FileNotFoundException fnfe) {
fnfe.printStackTrace(System.out);
} catch (IOException ioe) {
ioe.printStackTrace(System.out);
}
}
public void toSave() {
try {
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
DOMSource source = new DOMSource(document);
transformer.setOutputProperty(OutputKeys.ENCODING, "GB2312");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
PrintWriter pw = new PrintWriter(new FileOutputStream(filename));
StreamResult result = new StreamResult(pw);
transformer.transform(source, result);
} catch (TransformerException mye) {
mye.printStackTrace();
} catch (IOException exp) {
exp.printStackTrace();
}
}
/**
* EPML2PNML
*
* @param args String[]
*/
private static void EPML2PNML(String[] args) {
if (args.length != 2) {
System.out.println("���ṩEPML�ļ�·����PNML���Ŀ¼!");
System.exit(-1);
}
epmlImport epml = new epmlImport();
// load the single epml file
String filename = args[0];
try {
EPCResult epcRes = (EPCResult) epml.importFile(new FileInputStream(filename));
// convert all epc models to pnml files
ArrayList<ConfigurableEPC> alEPCs = epcRes.getAllEPCs();
PnmlExport export = new PnmlExport();
for (ConfigurableEPC epc : alEPCs) {
String id = epc.getIdentifier();
if (id.equals("1An_klol")
|| id.equals("1An_l1y8")
|| id.equals("1Ex_dzq9")
|| id.equals("1Ex_e6dx")
|| id.equals("1Ku_9soy")
|| id.equals("1Ku_a4cg")
|| id.equals("1Or_lojl")
|| id.equals("1Pr_d1ur")
|| id.equals("1Pr_djki")
|| id.equals("1Pr_dkfa")
|| id.equals("1Pr_dl73")
|| id.equals("1Ve_musj")
|| id.equals("1Ve_mvwz")) continue;
// save pnml files to the same folder
File outFile = new File(args[1] + "/" + id + ".pnml");
if (outFile.exists()) continue;
FileOutputStream fos = new FileOutputStream(outFile);
PetriNet petri = AMLtoPNML.convert(epc);
try {
export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
} catch (Exception ex1) {
ex1.printStackTrace(System.out);
}
}
} catch (IOException ex) {
ex.printStackTrace(System.out);
}
System.out.println("EPML Conversion Done");
}
private void copyFiles(String string, String string2) {
File src = new File(string);
File dest = new File(string2);
FileInputStream fin;
try {
fin = new FileInputStream(src);
FileOutputStream fout = new FileOutputStream(dest);
int c;
while ((c = fin.read()) >= 0) fout.write(c);
fin.close();
fout.close();
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Carica un file XML e ne restituisce un riferimento per DOM
*
* @param path - path to xml file
* @return reference to xml document
*/
private static Document loadDocument(String path) {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setNamespaceAware(false);
try {
DocumentBuilder db = dbf.newDocumentBuilder();
Document d = db.parse(new File(path));
return d;
} catch (ParserConfigurationException ex) {
ex.printStackTrace();
System.exit(10);
} catch (SAXException sxe) {
sxe.printStackTrace();
} catch (IOException ioe) {
ioe.printStackTrace();
}
return null;
}
void reloadJTree(String url) {
System.out.println("reload " + url);
Document dom;
try {
URL uurl = new URL(url);
HTMLWrapper hw = new HTMLWrapper(url);
dom = hw.getDOM();
} catch (IOException e) {
e.printStackTrace();
try {
dom = HTML2DOM.getDOM(new FileInputStream(url));
} catch (IOException ie) {
JOptionPane.showMessageDialog(this, "can't get document of the url: " + url);
ie.printStackTrace();
return;
}
}
document = dom;
jtree.setRootNode(dom);
}
private static void AML2PNML(String[] args) {
if (args.length != 3) {
System.out.println("���ṩAML����Ŀ¼��PNML���Ŀ¼�Լ��ֵ��ļ�!");
System.exit(-1);
}
System.out.println("����Ŀ¼��" + args[0]);
System.out.println("���Ŀ¼��" + args[1]);
System.out.println("�ֵ��ļ���" + args[2]);
// load the dict
AMLtoPNML.loadDict(args[2]);
File srcDir = new File(args[0]);
File[] lstAML = srcDir.listFiles();
PnmlExport export = new PnmlExport();
for (int i = 0; i < lstAML.length; i++) {
if (lstAML[i].isDirectory()) {
continue;
}
System.out.print(lstAML[i].getName() + "==>");
try {
FileInputStream fis = new FileInputStream(lstAML[i]);
int idx = lstAML[i].getName().indexOf(".xml");
File outFile = new File(args[1] + "/" + lstAML[i].getName().substring(0, idx) + ".pnml");
FileOutputStream fos = new FileOutputStream(outFile);
EPCResult epcRes = (EPCResult) AMLtoPNML.importFile(fis);
ConfigurableEPC epc = epcRes.getMainEPC();
PetriNet petri = AMLtoPNML.convert(epc);
export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
System.out.println(outFile.getName());
} catch (FileNotFoundException ex) {
ex.printStackTrace(System.out);
} catch (IOException ioe) {
ioe.printStackTrace(System.out);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
System.out.println("Conversion Done");
}
public static void main(String[] args) throws InvalidConfigurationException {
// Reading data from xml
try {
new InputData().readFromFile(XML_TEST_FILENAME);
} catch (SAXException e) {
System.out.println(e.getMessage());
} catch (IOException e) {
System.out.println(e.getMessage());
} catch (ParserConfigurationException e) {
System.out.println(e.getMessage());
}
// Configuration conf = new DefaultConfiguration();
Configuration conf = new Configuration("myconf");
TimetableFitnessFunction fitnessFunction = new TimetableFitnessFunction();
InitialConstraintChecker timetableConstraintChecker = new InitialConstraintChecker();
// Creating genes
Gene[] testGenes = new Gene[CHROMOSOME_SIZE];
for (int i = 0; i < CHROMOSOME_SIZE; i++) {
testGenes[i] =
new GroupClassTeacherLessonTimeSG(
conf,
new Gene[] {
new GroupGene(conf, 1),
new ClassGene(conf, 1),
new TeacherGene(conf, 1),
new LessonGene(conf, 1),
new TimeGene(conf, 1)
});
}
System.out.println("==================================");
// Creating chromosome
Chromosome testChromosome;
testChromosome = new Chromosome(conf, testGenes);
testChromosome.setConstraintChecker(timetableConstraintChecker);
// Setup configuration
conf.setSampleChromosome(testChromosome);
conf.setPopulationSize(POPULATION_SIZE);
conf.setFitnessFunction(fitnessFunction); // add fitness function
BestChromosomesSelector myBestChromosomesSelector = new BestChromosomesSelector(conf);
conf.addNaturalSelector(myBestChromosomesSelector, false);
conf.setRandomGenerator(new StockRandomGenerator());
conf.setEventManager(new EventManager());
conf.setFitnessEvaluator(new DefaultFitnessEvaluator());
CrossoverOperator myCrossoverOperator = new CrossoverOperator(conf);
conf.addGeneticOperator(myCrossoverOperator);
TimetableMutationOperator myMutationOperator = new TimetableMutationOperator(conf);
conf.addGeneticOperator(myMutationOperator);
conf.setKeepPopulationSizeConstant(false);
// Creating genotype
// Population pop = new Population(conf, testChromosome);
// Genotype population = new Genotype(conf, pop);
Genotype population = Genotype.randomInitialGenotype(conf);
System.out.println("Our Chromosome: \n " + testChromosome.getConfiguration().toString());
System.out.println("------------evolution-----------------------------");
// Begin evolution
Calendar cal = Calendar.getInstance();
start_t = cal.getTimeInMillis();
for (int i = 0; i < MAX_EVOLUTIONS; i++) {
System.out.println(
"generation#: " + i + " population size:" + (Integer) population.getPopulation().size());
if (population.getFittestChromosome().getFitnessValue() >= THRESHOLD) break;
population.evolve();
}
cal = Calendar.getInstance();
finish_t = cal.getTimeInMillis();
System.out.println("--------------end of evolution--------------------");
Chromosome fittestChromosome = (Chromosome) population.getFittestChromosome();
System.out.println(
"-------------The best chromosome---fitness="
+ fittestChromosome.getFitnessValue()
+ "---");
System.out.println(" Group Class Time");
for (int i = 0; i < CHROMOSOME_SIZE; i++) {
GroupClassTeacherLessonTimeSG s =
(GroupClassTeacherLessonTimeSG) fittestChromosome.getGene(i);
System.out.println(
"Gene "
+ i
+ " contains: "
+ (Integer) s.geneAt(GROUP).getAllele()
+ " "
+ (Integer) s.geneAt(CLASS).getAllele()
+ " "
+ (Integer) s.geneAt(TEACHER).getAllele()
+ " "
+ (Integer) s.geneAt(LESSON).getAllele()
+ " "
+ (Integer) s.geneAt(TIME).getAllele());
// GroupGene gg = (GroupGene)s.geneAt(GROUP);
// System.out.println("gg's idGroup"+gg.getAllele()+" gg.getGroupSize()"+ gg.getGroupSize() );
}
System.out.println("Elapsed time:" + (double) (finish_t - start_t) / 1000 + "s");
// Display the best solution
OutputData od = new OutputData();
od.printToConsole(fittestChromosome);
// Write population to the disk
try {
od.printToFile(population, GENOTYPE_FILENAME, BEST_CHROMOSOME_FILENAME);
} catch (IOException e) {
System.out.println("IOException raised! " + e.getMessage());
}
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}
// -----------------------------------------------------
// Description: Determine if a template exists for the
// given file and return true on success.
// -----------------------------------------------------
boolean templateExistFor(String fileName, String destinationDirectory) {
templateIdentified = false;
// from template
int intOriginX = 0;
int intOriginY = 0;
// from template
int intX = 0;
int intY = 0;
int intWidth = 0;
int intHeight = 0;
// calculated
int viaTemplateX = 0;
int viaTemplateY = 0;
int viaTemplatePlusWidth = 0;
int viaTemplatePlusHeight = 0;
String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
String pathPlusFileName_woext =
destinationDirectory + File.separator + fileName_woext + File.separator + fileName_woext;
try {
File folder = new File(templateLocation);
File[] listOfFiles = folder.listFiles();
long startTime = System.currentTimeMillis();
for (File file : listOfFiles) {
if (file.isFile()) {
templateName = "";
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(file);
doc.getDocumentElement().normalize();
System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
NodeList nList = doc.getElementsByTagName("condition");
for (int temp = 0; temp < nList.getLength(); temp++) {
Node nNode = nList.item(temp);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
String myX = getTagValue("x", eElement);
String myY = getTagValue("y", eElement);
String myWidth = getTagValue("width", eElement);
String myHeight = getTagValue("height", eElement);
String mySuffix = getTagValue("suffix", eElement);
String myRequirements = getTagValue("required", eElement);
intX = Integer.parseInt(myX);
intY = Integer.parseInt(myY);
intWidth = Integer.parseInt(myWidth);
intHeight = Integer.parseInt(myHeight);
viaTemplateX = intX - (intOriginX - pageX);
viaTemplateY = intY - (intOriginY - pageY);
viaTemplatePlusWidth = viaTemplateX + intWidth;
viaTemplatePlusHeight = viaTemplateY + intHeight;
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-crop",
String.format("%dx%d+%d+%d", intWidth, intHeight, viaTemplateX, viaTemplateY),
"+repage",
pathPlusFileName_woext + "_" + mySuffix + ".png");
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-fill",
"none",
"-stroke",
"red",
"-strokewidth",
"3",
"-draw",
String.format(
"rectangle %d,%d %d,%d",
viaTemplateX, viaTemplateY, viaTemplatePlusWidth, viaTemplatePlusHeight),
"+repage",
pathPlusFileName_woext + "_draw.png");
Spawn.execute(
Settings.Programs.TESSERACT.path(),
pathPlusFileName_woext + "_" + mySuffix + ".png",
pathPlusFileName_woext + "_" + mySuffix);
String line = ""; // String that holds current file line
String accumulate = "";
try {
FileReader input = new FileReader(pathPlusFileName_woext + "_" + mySuffix + ".txt");
BufferedReader bufRead = new BufferedReader(input);
line = bufRead.readLine();
while (line != null) {
accumulate += line;
line = bufRead.readLine();
}
bufRead.close();
input.close();
} catch (IOException e) {
e.printStackTrace();
}
String[] requirements = myRequirements.split("#");
for (String requirement : requirements) {
if (requirement.equals(accumulate.trim())) {
templateName = file.getName();
templateIdentified = true;
return templateIdentified;
}
}
}
}
}
}
// record end time
long endTime = System.currentTimeMillis();
System.out.println(
"Template Search [" + fileName + "] " + (endTime - startTime) / 1000 + " seconds");
} catch (Exception e) {
e.printStackTrace();
}
return templateIdentified;
}
// -----------------------------------------------------
// Description: Read the text from the file.
// AHHGAYUU!
// -----------------------------------------------------
String interpretText(String destinationDirectory, String fileName_woext, String suffix) {
String line = "";
String accumulate = "";
Scanner reader = null;
int dataType = 1; // For current testing
try {
File file =
new File(
destinationDirectory
+ File.separator
+ fileName_woext
+ File.separator
+ fileName_woext
+ "_"
+ suffix
+ ".txt");
reader = new Scanner(new FileReader(file));
if (dataType == 1) { // multiline
while (reader.hasNextLine()) {
accumulate += reader.nextLine().trim() + " ";
}
accumulate = accumulate.trim();
} else if (dataType == 2) { // address
if (reader.hasNextLine()) {
accumulate = reader.nextLine().trim();
}
if (reader.hasNextLine()) {
accumulate += "," + reader.nextLine().trim();
}
if (reader.hasNextLine()) {
line = reader.nextLine().trim();
int index = line.indexOf(",");
String line31 = line.substring(0, index);
int i = 0;
int hi = line.length() - index;
for (i = hi; i > 0; i--) {
if (Character.isDigit(line.charAt(i))) break;
}
String line32 = line.substring(index + 1, i);
String line33 = line.substring(i + 1, line.length() - 1);
accumulate += "," + line31 + "," + line32 + "," + line33;
}
} else if (dataType == 3) { // single text
accumulate = reader.nextLine();
} else if (dataType == 4) { // numeric
// coming soon
}
reader.close();
return accumulate;
} catch (IOException e) {
e.printStackTrace();
}
return "";
}