Re: [chemclipse-dev] Help: display chromatogram during acquisition

[Philip Wenig <philip.wenig@xxxxxxxxxxxxx>]

Trig

another question:

Have you implemented and registered an appropriate converter for your *.tms files?

When you use the MSD Chromatogram navigator, are your *.tms files labeled with the red chromatogram logo?

Best,
Philip

Am 31.08.2016 8:53 vorm. schrieb Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:

When recording the chromatogram, you could use your chromatogram object to display the data and fire the updates, see how the chromatogram editor is created. It requires a file or an IChromatogramMSD instance:

org.eclipse.chemclipse.ux.extension.msd.ui.editors.ChromatogramEditorMSD

    private void loadChromatogram() {

        try {
            /*
             * Import the chromatogram without showing it on the gui. The GUI
             * will take care itself of this action.
             */
            Object object = part.getObject();
            if(object instanceof String) {
                /*
                 * Try to load the chromatogram from file.
                 */
                File file = new File((String)object);
                importChromatogram(file);
            } else if(object instanceof IChromatogramMSD) {
                IChromatogramMSD chromatogram = (IChromatogramMSD)object;
                chromatogramSelection = new ChromatogramSelectionMSD(chromatogram);
                chromatogramFile = null;
            }
        } catch(Exception e) {
            logger.warn(e);
        }
    }

Have a look at the convenient class that helps to open a chromatogram from file or from instance:

org.eclipse.chemclipse.ux.extension.msd.ui.support.ChromatogramEditorSupport

public void openEditor(IChromatogram chromatogram, EModelService modelService, MApplication application, EPartService partService) {
...

Please also check, that the retention time (in milliseconds) is set in each scan of your chromatogram.


Best,
Philip

Am 30.08.2016 um 17:52 schrieb Trig Chen:

Hi all,

I'm developing a plugin in OpenChrom to control our home-made in situ TOF mass spectrometer.

In the device control view, I wrote the following code for the "Acquire data" button:

new Job("Acquisition") {

@Override

protected IStatus run(final IProgressMonitor monitor) {

               final File saveFile = new File("20160830112233.tms");

               // new a empty AbstractChromatogramMSD to hold the acquiring data

               final XmTideTofChromatogram tideMSChromatogram = new XmTideTofChromatogram();

tideMSChromatogram.setFile(saveFile);

final ZipBufferWriter writer = new ZipBufferWriter(saveFile);  // a zip writer to save data to disk

               

               // create ChromatogramEditorMSD part and setObject(tideMSChromatogram)  in UIJob

openMSDEditor(tideMSChromatogram); 

               //acquires scans and adds to tideMSChromatogram

for(int i = 0; i < usbDevice.getSpectraNumber(); i++) {

                        //acquires one scan and adds it to tideMSChromatogram: tideMSChromatogram.addScan(scan), also writes scan data to disk

                       // How to fire update of the ChromatogramEditorMSD ??? 

usbDevice.acquireMassSpectrum(tideMSChromatogram, writer, i);

}

      

               // writes tic and close file in end

writer.writeOverviewFolder(tideMSChromatogram);

}

}.schedule();

When the button clicked, a ChromatogramEditorMSD  part created, but nothing display, just empty figure.

What's wrong with my codes?

Best regards,

Trig

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