Package org.imagearchive.lsm.toolbox.info

Examples of org.imagearchive.lsm.toolbox.info.CZ_LSMInfo

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  }

  private void showEventList(LsmFileInfo info) {
    ArrayList imDirs = info.imageDirectories;
    ImageDirectory imDir = (ImageDirectory) imDirs.get(0);
    CZ_LSMInfo cz = imDir.TIF_CZ_LSMINFO;
    EventList events = cz.eventList;
    if (events != null) {
      String header = new String(
          "Time (sec) \tEvent Type \tEvent Description");
      TextWindow tw = new TextWindow("Time Events for " + info.fileName,
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    return offsets;
  }

  private CZ_LSMInfo getCZ_LSMINFO(RandomAccessStream stream, long position,
      boolean thumb) {
    CZ_LSMInfo cz = new CZ_LSMInfo();
    try {
      if (position == 0)
        return cz;
      stream.seek((int) position + 8);
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      if (verbose)
        IJ.error("LSM ImageDir null.");
      return null;
    } // should not be if it is a true LSM file

    CZ_LSMInfo cz = firstImDir.TIF_CZ_LSMINFO;
    if (cz == null) {
      if (verbose)
        IJ.error("LSM ImageDir null.");
      return null;
    } // should not be, first Directory should have a CZ...
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    ImagePlus[] impTab = new Reader(masterModel).open(f.getParent(), f
        .getName(), false, verbose, false);

    if (impTab != null && impTab.length > 0) {
      LsmFileInfo lsm = (LsmFileInfo) impTab[0].getOriginalFileInfo();
      CZ_LSMInfo cz = ((ImageDirectory) lsm.imageDirectories.get(0)).TIF_CZ_LSMINFO;

      for (int i = 0; i < impTab.length; i++) {
        if (sepDir) {
          finalDir = outputDir + System.getProperty("file.separator")
              + f.getName();
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              ImagePlus imp = WindowManager.getImage(((Integer) v
                  .get(j)).intValue());
              LsmFileInfo openLSM = (LsmFileInfo) imp
                  .getOriginalFileInfo();
              CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) openLSM.imageDirectories
                  .get(0)).TIF_CZ_LSMINFO;
              Recording r = (Recording) cz.scanInfo.recordings.get(0);
              double planeSpacing = ((Double) r.records.get("PLANE SPACING")).doubleValue();
              if (choice.equals("Dump to textfile")) {
                String twstr = new String("");
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              ImagePlus imp = WindowManager.getImage(((Integer) v
                  .get(j)).intValue());
              LsmFileInfo openLSM = (LsmFileInfo) imp
                  .getOriginalFileInfo();
              CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) openLSM.imageDirectories
                  .get(0)).TIF_CZ_LSMINFO;
              if (choice.equals("Dump to textfile")) {
                String twstr = new String("");
                for (int k = 0; k < cz.timeStamps.NumberTimeStamps; k++)
                  twstr = twstr
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              ImagePlus imp = WindowManager.getImage(((Integer) v
                  .get(j)).intValue());
              LsmFileInfo openLSM = (LsmFileInfo) imp
                  .getOriginalFileInfo();
              CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) openLSM.imageDirectories
                  .get(0)).TIF_CZ_LSMINFO;

              if (cz.SpectralScan != 1) {
                IJ
                    .error("Image not issued from spectral scan. Lambda stamp obsolete!");
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              try {
                for (int i = 0; i < imageVals.length; i++) {
                  LsmFileInfo openLSM = (LsmFileInfo) ((ImagePlus) WindowManager
                      .getImage(imageVals[i]))
                      .getOriginalFileInfo();
                  CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) openLSM.imageDirectories
                      .get(0)).TIF_CZ_LSMINFO;
                  Reader reader = new Reader(masterModel);
                  ImagePlus[] imp = reader
                      .open(openLSM.directory,
                          openLSM.fileName, true,
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    if (roi.width < ip.getWidth() || roi.height < ip.getHeight()) {
      x = roi.x;
      y = roi.y + roi.height;
    }
    Color c = Toolbar.getForegroundColor();
    CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) lfi.imageDirectories
        .get(0)).TIF_CZ_LSMINFO;
    if (cz.DimensionZ != 1) {
      Recording r = (Recording) cz.scanInfo.recordings
          .get(0);
      double planeSpacing = ((Double) r.records.get("PLANE SPACING"))
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    if (roi.width < ip.getWidth() || roi.height < ip.getHeight()) {
      x = roi.x;
      y = roi.y + roi.height;
    }
    Color c = Toolbar.getForegroundColor();
    CZ_LSMInfo cz = (CZ_LSMInfo) ((ImageDirectory) lfi.imageDirectories
        .get(0)).TIF_CZ_LSMINFO;
    if ((cz.DimensionTime == 1)
        ^ (cz.DimensionZ == 1)) {
      //int size = imp.getStackSize();
      for (int slice = 1; slice <= cz.timeStamps.NumberTimeStamps; slice++) {
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Related Classes of org.imagearchive.lsm.toolbox.info.CZ_LSMInfo

  • org.imagearchive.lsm.LSM_Reader
  • org.imagearchive.lsm.toolbox.BatchConverter
  • org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
  • org.imagearchive.lsm.toolbox.gui.DetailsFrame
  • org.imagearchive.lsm.toolbox.gui.SelectImageDialog
  • org.imagearchive.lsm.toolbox.Reader
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