// Pressing the mouse stops and starts the sound
public void mousePressed() {
if (tone.isPlaying()) {
tone.stop(); // The sound can be stopped with the function stop().
} else {
tone.repeat();
}
}
public static byte[] convertManyToBytes(
Sample[][] samplesToConvert, SamplingInfo samplingInfo) {
byte[] returnBytes = null;
int numberOfChannels = samplingInfo.numberOfChannels;
int samplesPerChannel = samplesToConvert[0].length;
int bitsPerSample = samplingInfo.bitsPerSample;
int bytesPerSample = bitsPerSample / WavFile.BitsPerByte;
int numberOfBytes = numberOfChannels * samplesPerChannel * bytesPerSample;
returnBytes = new byte[numberOfBytes];
Trivium tri = new Trivium(key, IV);
double halfMaxValueForEachSample = Math.pow(2, WavFile.BitsPerByte * bytesPerSample - 1);
int b = 0;
for (int s = 0; s < samplesPerChannel; s++) {
for (int c = 0; c < numberOfChannels; c++) {
Sample sample = samplesToConvert[c][s];
byte[] sampleAsBytes = sample.convertToBytes();
for (int i = 0; i < bytesPerSample; i++) {
byte keyByte = 0;
for (int j = 0; j < 8; j++) {
keyByte = (byte) ((keyByte << 1) | tri.getBit());
}
returnBytes[b] = (byte) (sampleAsBytes[i] ^ keyByte);
b++;
}
}
}
return returnBytes;
}
public void draw() {
if (tone.isPlaying()) {
background(255);
} else {
background(100);
}
// Set the volume to a range between 0 and 1.0
float ratio = (float) mouseX / width;
tone.setVolume(ratio);
// Set the rate to a range between 0 and 88,200
// Changing the rate alters the pitch
ratio = (float) mouseY / height;
// The rate is set according to the mouseY position.
tone.setRate(ratio * 88200);
// Draw some rectangles to show what is going on
stroke(0);
fill(175);
rect(0, 160, mouseX, 20);
stroke(0);
fill(175);
rect(160, 0, 20, mouseY);
}
public static Sample[][] buildManyFromBytes(SamplingInfo samplingInfo, byte[] bytesToConvert) {
int numberOfBytes = bytesToConvert.length;
int numberOfChannels = samplingInfo.numberOfChannels;
Sample[][] returnSamples = new Sample[numberOfChannels][];
int bytesPerSample = samplingInfo.bitsPerSample / WavFile.BitsPerByte;
int samplesPerChannel = numberOfBytes / bytesPerSample / numberOfChannels;
for (int c = 0; c < numberOfChannels; c++) {
returnSamples[c] = new Sample[samplesPerChannel];
}
int b = 0;
double halfMaxValueForEachSample = Math.pow(2, WavFile.BitsPerByte * bytesPerSample - 1);
Sample samplePrototype = samplingInfo.samplePrototype();
byte[] sampleValueAsBytes = new byte[bytesPerSample];
for (int s = 0; s < samplesPerChannel; s++) {
for (int c = 0; c < numberOfChannels; c++) {
for (int i = 0; i < bytesPerSample; i++) {
sampleValueAsBytes[i] = bytesToConvert[b];
b++;
}
returnSamples[c][s] = samplePrototype.buildFromBytes(sampleValueAsBytes);
}
}
return returnSamples;
}
private void loadSampleData(BufferedInputStream in, Sample sample) throws IOException {
int sampleLength = sample.getLength();
int loopEnd = sample.getLoopEnd();
int loopStart = sample.getLoopStart();
short[] sampleData;
if (sample.getQuality() == 16) {
sampleLength >>= 1;
loopEnd >>= 1;
loopStart >>= 1;
byte[] temp = read(in, 2 * sampleLength);
sampleData = new short[sampleLength + 4];
int tmpPos = 0;
int samp = 0;
for (int i = 0; i < sampleLength; i++, tmpPos += 2) {
samp += make16Bit(temp, tmpPos);
sampleData[i] = (short) (samp);
}
} else {
sampleData = new short[sampleLength + 4];
byte[] temp = read(in, sampleLength);
int samp = 0;
for (int i = 0; i < sampleLength; i++) {
samp += temp[i] & 0xff;
sampleData[i] = (short) (samp << 8);
}
}
if (sampleLength > 0) {
int pos2 = 0;
int loopType = sample.getLoopType();
if ((loopType & Sample.PINGPONG_LOOP) == 0) {
if ((loopType & Sample.FORWARD_LOOP) != 0) pos2 = loopStart;
for (int i = 0; i < 3; i++) sampleData[sampleLength + 1 + i] = sampleData[pos2 + i];
} else if ((loopType & Sample.PINGPONG_LOOP) != 0) {
pos2 = loopStart + loopEnd;
for (int i = 0; i < 3; i++) sampleData[sampleLength + 1 + i] = sampleData[pos2 - 1 - i];
}
System.arraycopy(sampleData, 0, sampleData, 1, sampleLength);
if ((loopType & Sample.FORWARD_LOOP) != 0) sampleData[0] = sampleData[loopStart + loopEnd];
else if ((loopType & Sample.PINGPONG_LOOP) != 0) sampleData[0] = sampleData[loopStart + 2];
}
loopStart <<= 10;
loopEnd <<= 10;
sample.setLoopStart(loopStart);
sample.setLoopEnd(loopEnd);
sample.setLength(sampleLength);
sample.setData(sampleData);
}
private void loadSample(BufferedInputStream in, Sample sample) throws IOException {
// Sample length
int sampleLength = make32Bit(read(in, 4));
// Sample loop start
int loopStart = make32Bit(read(in, 4));
// Sample loop length
int loopEnd = make32Bit(read(in, 4));
if (loopStart + loopEnd > sampleLength) loopEnd = (sampleLength) - loopStart;
// Volume
sample.setVolume(in.read());
// Finetune (signend byte -128...+127)
sample.setFineTune((byte) in.read());
// Type: Bit 0-1: 0 = No loop,
// 1 = Forward loop,
// 2 = Ping-pong loop;
// 4: 16-bit sampledata
int loopType = in.read();
int sampleQuality = ((int) loopType & 0x10) != 0 ? 16 : 8;
if ((loopType & 0x3) == 0 || loopEnd == 0) {
// no looping
loopStart = 0;
loopEnd = sampleLength;
loopType &= 0x10;
}
// Panning (0-255)
sample.setPanning(in.read() & 0xff);
// Relative note number (signed byte)
sample.setRelativeNote((byte) in.read());
// Reserved
in.read();
// Sample name
read(in, 22);
sample.setLength(sampleLength);
sample.setLoopType(loopType);
sample.setQuality(sampleQuality);
sample.setLoopStart(loopStart);
sample.setLoopEnd(loopEnd);
}
private void readFromFilePath_ReadChunks_Data(DataInputStreamLittleEndian reader)
throws IOException {
byte[] data = new byte[4];
reader.read(data);
int subchunk2Size = reader.readInt();
byte[] samplesForChannelsMixedAsBytes = new byte[subchunk2Size];
reader.read(samplesForChannelsMixedAsBytes);
Sample[][] samplesForChannels =
Sample.buildManyFromBytes(samplingInfo, samplesForChannelsMixedAsBytes);
this.samplesForChannels = samplesForChannels;
}
public void setup() {
size(200, 200);
// Start Sonia engine.
Sonia.start(this);
// Create a new sample object.
tone = new Sample("tone.wav");
// Loop the sound forever
// (well, at least until stop() is called)
tone.repeat();
smooth();
}
private void writeToFilePath_WriteChunks_Data(DataOutputStreamLittleEndian writer)
throws IOException {
writer.writeString("data");
int numberOfBytesInSamples =
(int)
(this.samplesForChannels[0].length
* this.samplingInfo.numberOfChannels
* this.samplingInfo.bitsPerSample
/ WavFile.BitsPerByte);
writer.writeInt(numberOfBytesInSamples);
byte[] samplesAsBytes = Sample.convertManyToBytes(this.samplesForChannels, this.samplingInfo);
writer.writeBytes(samplesAsBytes);
}
public static Sample[] superimposeSets(Sample[][] setsToSuperimpose) {
int maxSamplesSoFar = 0;
for (int i = 0; i < setsToSuperimpose.length; i++) {
Sample[] setToSuperimpose = setsToSuperimpose[i];
if (setToSuperimpose.length > maxSamplesSoFar) {
maxSamplesSoFar = setToSuperimpose.length;
}
}
Sample[] returnValues = new Sample[maxSamplesSoFar];
for (int i = 0; i < setsToSuperimpose.length; i++) {
Sample[] setToSuperimpose = setsToSuperimpose[i];
for (int j = 0; j < setToSuperimpose.length; j++) {
Sample sampleToSuperimpose = setToSuperimpose[j];
double sampleValueAsDouble = sampleToSuperimpose.convertToDouble();
if (i > 0) {
sampleValueAsDouble += returnValues[i].convertToDouble();
}
returnValues[i] = sampleToSuperimpose.buildFromDouble(sampleValueAsDouble);
}
}
return returnValues;
}
public void run() {
String line;
String id = null;
config.refgenes = new ArrayList<RefGene>();
config.dbsnp = new ArrayList<dbSNP>();
try {
// System.err.println("quality read start"); // debug
boolean need_ruler_rebuild = false;
boolean need_title = false;
SAMRegion sr = null;
while (true) {
line = br.readLine();
if (line == null) break;
// EOF
String[] stuff = line.split("\t");
if (stuff[0].equals("sample2id")) {
Sample sample = Sample.get_sample(stuff[1]);
for (int i = 2; i < stuff.length; i++) {
config.read2sample.put(new String(stuff[i]), sample);
}
} else if (stuff[0].equals("consensus_label")) {
config.CONSENSUS_TAG = new String(stuff[1]);
} else if (stuff[0].equals("ruler_start")) {
config.ruler_start = Integer.parseInt(stuff[1]);
need_ruler_rebuild = true;
} else if (stuff[0].equals("title")) {
config.title = stuff[1];
need_title = true;
} else if (stuff[0].equals("refGene")) {
config.refgenes.add(new RefGene(stuff));
} else if (stuff[0].equals("dbsnp")) {
config.dbsnp.add(new dbSNP(stuff));
} else if (stuff[0].toUpperCase().indexOf("SAM_") == 0) {
// FUGLY
SAMResourceTags v = SAMResourceTags.valueOf(stuff[0].toUpperCase());
if (v.equals(SAMResourceTags.SAM_URL)) config.sams.add(new SAMResource());
config.sams.get(config.sams.size() - 1).import_data(v, stuff[1]);
} else if (stuff[0].equals("reference_sequence")) {
StringBuffer target_sequence = new StringBuffer();
while (true) {
line = br.readLine();
if (line.equals(">")) {
// config.target_sequence = target_sequence.toString().toCharArray();
config.target_sequence = target_sequence.toString().getBytes();
break;
} else {
target_sequence.append(line);
}
}
} else if (stuff[0].equals("target_region")) {
sr = new SAMRegion();
sr.tname = new String(stuff[1]);
sr.range = new Range(Integer.parseInt(stuff[2]), Integer.parseInt(stuff[3]));
// System.err.println("range " + sr.tname + " " + sr.range.start + " " + sr.range.end);
// // debug
} else {
System.err.println("error, don't recognize tag " + stuff[0]); // debug
}
}
if (config.ruler_start > 0) {
for (dbSNP snp : config.dbsnp) {
snp.consensus_adjust(config.ruler_start);
}
for (RefGene rg : config.refgenes) {
rg.consensus_adjust(config.ruler_start);
}
}
if (config.dbsnp != null) {
for (dbSNP snp : config.dbsnp) {
// System.err.println("adding snp at " + snp.start + " = " + (snp.start +
// config.ruler_start)); // debug
}
config.snp_config.snp_query = new dbSNPSet(config.dbsnp);
}
for (SAMResource sre : config.sams) {
sre.set_region(sr);
}
if (av != null) {
while (av.get_acepanel().is_built() == false) {
// spin until dependency built
try {
System.err.println("MarkupReader spin..."); // debug
Thread.sleep(50);
} catch (Exception e) {
}
}
PadMap pm = av.get_acepanel().get_assembly().get_padmap();
for (RefGene rg : config.refgenes) {
rg.consensus_setup(pm);
}
Runnable later;
if (need_title) {
// System.err.println("title="+config.title); // debug
later =
new Runnable() {
public void run() {
av.setTitle(config.title);
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (need_ruler_rebuild) {
//
// ruler labeling has changed.
//
later =
new Runnable() {
public void run() {
// av.get_acepanel().get_canvas().build_ruler();
if (config.start_unpadded_offset != 0) {
AcePanel ap = av.get_acepanel();
PadMap pm = ap.get_assembly().get_padmap();
int upo = (config.start_unpadded_offset - config.ruler_start) + 1;
// +1: convert to 1-based offset
int po = pm.get_unpadded_to_padded(upo);
System.err.println("upo=" + upo + " po=" + po); // debug
SNPList sl = new SNPList();
sl.addElement(new SNP(po, 0.0));
ap.ace.set_snps(sl);
ap.get_canvas().center_on(po);
ap.get_canvas().repaint();
}
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (config.enable_exon_navigation) {
if (false) {
System.err.println("DEBUG: exon nav disabled");
} else {
av.get_acepanel().init_exon_navigation();
}
}
av.get_acepanel().get_assembly().build_summary_info();
// group samples by tumor/normal, if applicable
// av.repaint();
later =
new Runnable() {
public void run() {
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
// System.err.println("quality read end"); // debug
} catch (Exception e) {
e.printStackTrace(); // debug
}
}
public final List<Sample> parse(
Reader reader, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) {
final List<String> lines = new XReadLines(reader).readLines();
// What are the record offsets?
final int familyPos = missingFields.contains(MissingPedField.NO_FAMILY_ID) ? -1 : 0;
final int samplePos = familyPos + 1;
final int paternalPos = missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : samplePos + 1;
final int maternalPos =
missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : paternalPos + 1;
final int sexPos =
missingFields.contains(MissingPedField.NO_SEX) ? -1 : Math.max(maternalPos, samplePos) + 1;
final int phenotypePos =
missingFields.contains(MissingPedField.NO_PHENOTYPE)
? -1
: Math.max(sexPos, Math.max(maternalPos, samplePos)) + 1;
final int nExpectedFields =
MathUtils.arrayMaxInt(
Arrays.asList(samplePos, paternalPos, maternalPos, sexPos, phenotypePos))
+ 1;
// go through once and determine properties
int lineNo = 1;
boolean isQT = false;
final List<String[]> splits = new ArrayList<String[]>(lines.size());
for (final String line : lines) {
if (line.startsWith(commentMarker)) continue;
if (line.trim().equals("")) continue;
final String[] parts = line.split("\\s+");
if (parts.length != nExpectedFields)
throw new UserException.MalformedFile(
reader.toString(), "Bad PED line " + lineNo + ": wrong number of fields");
if (phenotypePos != -1) {
isQT = isQT || !CATAGORICAL_TRAIT_VALUES.contains(parts[phenotypePos]);
}
splits.add(parts);
lineNo++;
}
logger.info("Phenotype is other? " + isQT);
// now go through and parse each record
lineNo = 1;
final List<Sample> samples = new ArrayList<Sample>(splits.size());
for (final String[] parts : splits) {
String familyID = null, individualID, paternalID = null, maternalID = null;
Gender sex = Gender.UNKNOWN;
String quantitativePhenotype = Sample.UNSET_QT;
Affection affection = Affection.UNKNOWN;
if (familyPos != -1) familyID = maybeMissing(parts[familyPos]);
individualID = parts[samplePos];
if (paternalPos != -1) paternalID = maybeMissing(parts[paternalPos]);
if (maternalPos != -1) maternalID = maybeMissing(parts[maternalPos]);
if (sexPos != -1) {
if (parts[sexPos].equals(SEX_MALE)) sex = Gender.MALE;
else if (parts[sexPos].equals(SEX_FEMALE)) sex = Gender.FEMALE;
else sex = Gender.UNKNOWN;
}
if (phenotypePos != -1) {
if (isQT) {
if (parts[phenotypePos].equals(MISSING_VALUE1)) affection = Affection.UNKNOWN;
else {
affection = Affection.OTHER;
quantitativePhenotype = parts[phenotypePos];
}
} else {
if (parts[phenotypePos].equals(MISSING_VALUE1)) affection = Affection.UNKNOWN;
else if (parts[phenotypePos].equals(MISSING_VALUE2)) affection = Affection.UNKNOWN;
else if (parts[phenotypePos].equals(PHENOTYPE_UNAFFECTED))
affection = Affection.UNAFFECTED;
else if (parts[phenotypePos].equals(PHENOTYPE_AFFECTED)) affection = Affection.AFFECTED;
else
throw new ReviewedGATKException(
"Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo);
}
}
final Sample s =
new Sample(
individualID,
sampleDB,
familyID,
paternalID,
maternalID,
sex,
affection,
quantitativePhenotype);
samples.add(s);
sampleDB.addSample(s);
lineNo++;
}
for (final Sample sample : new ArrayList<Sample>(samples)) {
Sample dad =
maybeAddImplicitSample(
sampleDB, sample.getPaternalID(), sample.getFamilyID(), Gender.MALE);
if (dad != null) samples.add(dad);
Sample mom =
maybeAddImplicitSample(
sampleDB, sample.getMaternalID(), sample.getFamilyID(), Gender.FEMALE);
if (mom != null) samples.add(mom);
}
return samples;
}
public static void main(String[] args) {
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
// Mat mat = Mat.eye( 3, 3, CvType.CV_8UC1 );
// System.out.println( "mat = " + mat.dump() );
Sample n = new Sample();
// n.templateMatching();
// put text in image
// Mat data= Highgui.imread("images/erosion.jpg");
// Core.putText(data, "Sample", new Point(50,80), Core.FONT_HERSHEY_SIMPLEX, 1, new
// Scalar(0,0,0),2);
//
// Highgui.imwrite("images/erosion2.jpg", data);
// getting dct of an image
String path = "images/croppedfeature/go (20).jpg";
path = "images/wordseg/img1.png";
Mat image = Highgui.imread(path, Highgui.IMREAD_GRAYSCALE);
ArrayList<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Imgproc.threshold(image, image, 0, 255, Imgproc.THRESH_OTSU);
Imgproc.threshold(image, image, 220, 128, Imgproc.THRESH_BINARY_INV);
Mat newImg = new Mat(45, 100, image.type());
newImg.setTo(new Scalar(0));
n.copyMat(image, newImg);
int vgap = 25;
int hgap = 45 / 3;
Moments m = Imgproc.moments(image, false);
Mat hu = new Mat();
Imgproc.HuMoments(m, hu);
System.out.println(hu.dump());
// //divide the mat into 12 parts then get the features of each part
// int count=1;
// for(int j=0; j<45; j+=hgap){
// for(int i=0;i<100;i+=vgap){
// Mat result = newImg.submat(j, j+hgap, i, i+vgap);
//
//
// Moments m= Imgproc.moments(result, false);
// double m01= m.get_m01();
// double m00= m.get_m00();
// double m10 = m.get_m10();
// int x= m00!=0? (int)(m10/m00):0;
// int y= m00!=0? (int)(m01/m00):0;
// Mat hu= new Mat();
// Imgproc.HuMoments(m, hu);
// System.out.println(hu.dump());
// System.out.println(count+" :"+x+" and "+y);
// Imgproc.threshold(result, result, 0,254, Imgproc.THRESH_BINARY_INV);
// Highgui.imwrite("images/submat/"+count+".jpg", result);
// count++;
//
// }
// }
//
// for(int i=vgap;i<100;i+=vgap){
// Point pt1= new Point(i, 0);
// Point pt2= new Point(i, 99);
// Core.line(newImg, pt1, pt2, new Scalar(0,0,0));
// }
// for(int i=hgap;i<45;i+=hgap){
// Point pt1= new Point(0, i);
// Point pt2= new Point(99, i);
// Core.line(newImg, pt1, pt2, new Scalar(0,0,0));
// }
// Highgui.imwrite("images/submat/copyto.jpg", newImg);
}
