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Re: [chemclipse-dev] Help with Exception
Trig,

that happens when you use the ScanProxy in the following situations: The overview stores another TIC value than the scan really has.

The TIC for each scan stored in the overview needs to be the same as the real TIC value of your scan.

Before click: The TIC from the overview is shown
After click: The real TIC from the scan is shown


Best,
Philip

Am 06.09.2016 um 11:58 schrieb Trig Chen:
I acquired a faked data save it to disk, then opened it. It's strange with mouse's operations.
Please find the test data file and screencast in attachments.

Best regards,

Trig

2016-09-06 17:46 GMT+08:00 Alexander Kerner <alexander.kerner@xxxxxxxxxxxxx>:

Hi Philip,

thanks, that seems to work. Now I need an instance of IChromatogram to build the peak.

Im trying to use ChromatogramMSD, which relies on an available PreferenceSupplier.

Im refactoring the constructor to not fail if the PreferenceSupplier is not available.

What would be a reasonable default value for

PreferenceSupplier.getSelectedSegmentWidth()
?

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 10:55 AM, Philip Wenig wrote:
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
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~
_______________________________________________
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
_______________________________________________ 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 
_______________________________________________
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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