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Re: [chemclipse-dev] Help with Exception
Another exception in making a test ChromatogramMSD. It seem these data model were tied with eclipse platform.
Exception in thread "main" java.lang.NullPointerException
at org.eclipse.chemclipse.chromatogram.xxd.calculator.preferences.PreferenceSupplier.getPreferenceNode(PreferenceSupplier.java:56)
at org.eclipse.chemclipse.chromatogram.xxd.calculator.preferences.PreferenceSupplier.getPreferences(PreferenceSupplier.java:71)
at org.eclipse.chemclipse.chromatogram.xxd.calculator.preferences.PreferenceSupplier.getSelectedNoiseCalculatorId(PreferenceSupplier.java:82)
at org.eclipse.chemclipse.msd.model.core.AbstractChromatogramMSD.<init>(AbstractChromatogramMSD.java:82)
at org.eclipse.chemclipse.msd.model.implementation.ChromatogramMSD.<init>(ChromatogramMSD.java:20)
at cn.edu.xmu.tidems.control.ChromatogramTest.main(ChromatogramTest.java:28)


ChromatogramTest.java:

public class ChromatogramTest {

public static void main(final String[] args) {

final File file = new File("C:\\Temp\\blank1.ocb");
final IChromatogramMSD msd = new ChromatogramMSD();
final ScanMSD scan = new ScanMSD();
scan.setRetentionTime(0);
for(int i = 0; i < 10000; i++) {
try {
final Ion ion = new Ion(i + 1, (float)Math.random() * 10000);
scan.addIon(ion);
} catch(final Exception e) {
e.printStackTrace();
}
}
msd.addScan(scan);
final ChromatogramWriterMSD writer = new ChromatogramWriterMSD();
try {
writer.writeChromatogram(file, msd, new NullProgressMonitor());
} catch(FileIsNotWriteableException | IOException e) {
e.printStackTrace();
}
}
}

Best regards,

Trig

2016-09-06 16:55 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:
Hi Alex,

that's from the peak model.

The peak intensity model stores relative values. A peak consists of the peak intensity values and a peak maximum (e.g. a mass spectrum). The peak maximum has a total intensity, though each intensity along the retention time scale of the peak can be calculated by using the total intensity of the peak maximum multiplied by the relative intensity value at the given retention time.

Normally, the MAX_INTENSITY is 100.0f, see:
org.eclipse.chemclipse.model.core.IPeakIntensityValues

To calculate percentage values, the max values needs to be known. If other max values than 100.0f are used, you can run the normalize() method after putting your values to the model.

void normalize();


Best,
Philip


Am 06.09.2016 um 10:44 schrieb Alexander Kerner:

Hi all,

Anyone can help me out with this one?

Exception in thread "pool-1-thread-3" org.eclipse.chemclipse.model.exceptions.PeakException: There must be at least one intensity value stored with a relative intensity of IPeakIntensityValues.MAX_INTENSITY.
    at org.eclipse.chemclipse.model.core.AbstractPeakModel.checkModelConditions(AbstractPeakModel.java:403)
    at org.eclipse.chemclipse.model.core.AbstractPeakModel.calculatePeakModel(AbstractPeakModel.java:482)
    at org.eclipse.chemclipse.model.core.AbstractPeakModel.<init>(AbstractPeakModel.java:91)
    at org.eclipse.chemclipse.msd.model.core.AbstractPeakModelMSD.<init>(AbstractPeakModelMSD.java:28)
    at org.eclipse.chemclipse.msd.model.implementation.PeakModelMSD.<init>(PeakModelMSD.java:28)


Im tying to build a dummy peak for JUnit and feeding the model like this:

PeakIntensityValues result = new PeakIntensityValues();
    for (int i = 1; i < 10; i++) {
        result.addIntensityValue(i, i);
    }
    return result;

Best,

Alex

~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Alexander Kerner » Software developer » alexander.kerner@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~
On 09/06/2016 05:03 AM, Trig Chen wrote:
HDF5 concurrent read & write test code snippet：

package hdf5;

import java.io.PrintStream;
import java.util.Arrays;
import java.util.Random;

import ch.systemsx.cisd.hdf5.HDF5Factory;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;

public class Hdf5Test {
static final String hdf5FileName = "myfile.h5";
static final String tag = "mydata";

public static void main(final String[] args) {

// write thread
new Thread(new Runnable() {
@Override
public void run() {
final IHDF5SimpleWriter writer = HDF5Factory.open(hdf5FileName);
final Random r = new Random();
for (int i = 0; i < 10; i++) {
pause(500);
final float[] data = "" float[1000];
for (int n = 0; n < data.length; n++) {
data[n] = r.nextFloat() * 10000f;
}
writer.writeFloatArray(tag + i, data);
printData(data, 5, System.out);
}
writer.close();
}
}).start();

pause(1000);
// read thread
new Thread(new Runnable() {
@Override
public void run() {
final IHDF5SimpleReader reader = HDF5Factory.open(hdf5FileName);
for (int i = 0; i < 10; i++) {
pause(600);
float[] mydata = new float[1000];
mydata = reader.readFloatArray(tag + i);
printData(mydata, 5, System.err);
}
reader.close();
}
}).start();

}

private static void pause(final int millisecond) {
try {
Thread.sleep(millisecond);
} catch (final InterruptedException e) {
e.printStackTrace();
}
}

private static void printData(final float[] data, final int size, final PrintStream out) {
if ((data == null) || (data.length < size)) {
return;
}
final float[] temp = new float[size];
System.arraycopy(data, 0, temp, 0, size);
out.println(Arrays.toString(temp));
}
}



Best regards,

Trig


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_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________
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chemclipse-dev@xxxxxxxxxxx
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https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


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