Esempio n. 1
0
 protected boolean split(Object3DGui og) {
   if (!(this instanceof NucleusManager) && og.getChannel() instanceof Nucleus) {
     if (Core.GUIMode) ij.IJ.log("Cannont split nucleus!");
     return false;
   }
   Object3DGui[] newObjects = og.split(splitRad.getFloatValue(2), splitDist.getFloatValue(5));
   if (newObjects.length == 0) {
     if (Core.GUIMode) ij.IJ.log("Object couldn't be split");
     return false;
   }
   Object3D[] objs = og.getChannel().getObjects();
   int nextLabel = objs[objs.length - 1].getValue() + 1;
   for (Object3DGui o : newObjects) {
     o.changeLabel(nextLabel);
     this.listModel.addElement(o); // TODO le mettre a la fin des objets du channel..
     nextLabel++;
   }
   og.getChannel().getSegmented().updateDisplay();
   return true;
 }
Esempio n. 2
0
  public void manualSegmentation() {
    msChannel = null;
    if (currentChannels != null) {
      if (!(currentChannels[0] instanceof Nucleus)) {
        msChannel = (Structure) currentChannels[0];
      } else if (currentChannels.length > 1) {
        msChannel = (Structure) currentChannels[1];
      }
    }
    if (msChannel instanceof VirtualStructure) {
      return;
    }
    if (msChannel != null) {
      ImageInt seg = msChannel.getSegmented();
      ImageHandler raw = msChannel.getFiltered();
      if (raw == null) {
        if (Core.GUIMode) ij.IJ.log("ERROR: no raw images!");
        return;
      }
      if (seg == null) {
        seg =
            new ImageShort(
                msChannel.getChannelName() + "::Segmented", raw.sizeX, raw.sizeY, raw.sizeZ);
        msChannel.setSegmented(seg);
      }
      seg.show();
      raw.show();
      manualSpot =
          new ManualSpot(raw.getImagePlus(), seg.getImagePlus(), (int) seg.getMax(null) + 1);
      manualSpot.setVisible(true);

      JButton msClose = manualSpot.jButtonClose;
      msClose.addActionListener(
          new java.awt.event.ActionListener() {
            @Override
            public void actionPerformed(java.awt.event.ActionEvent evt) {
              if (msChannel != null) {
                msChannel.saveOutput();
                msChannel.createObjects();
                populateObjects();
              }
            }
          });
    }
  }
Esempio n. 3
0
 private void sort(String key, Object3DGui[] objectsGui, int structureIdx) {
   Object3DGui.setAscendingOrger(((ObjectManagerLayout) layout).getAscendingOrder());
   HashMap<Integer, BasicDBObject> objects =
       Core.getExperiment().getConnector().getObjects(currentNucId, structureIdx);
   boolean notFound = false;
   for (Object3DGui o : objectsGui) {
     BasicDBObject dbo = objects.get(o.getLabel());
     if (dbo != null) {
       if (dbo.containsField(key)) o.setValue(dbo.getDouble(key));
       else {
         o.setValue(-1);
         notFound = true;
       }
     }
   }
   if (notFound)
     ij.IJ.log("Warning measurement: " + key + " not found for one or several objects");
   Arrays.sort(objectsGui);
 }
Esempio n. 4
0
  private Object tryOpen(String directory, String name, String path) {
    // set up a stream to read in 132 bytes from the file header
    // These can be checked for "magic" values which are diagnostic
    // of some image types
    InputStream is;
    byte[] buf = new byte[132];
    try {
      if (0 == path.indexOf("http://")) is = new java.net.URL(path).openStream();
      else is = new FileInputStream(path);
      is.read(buf, 0, 132);
      is.close();
    } catch (IOException e) {
      // couldn't open the file for reading
      return null;
    }
    name = name.toLowerCase();
    width = PLUGIN_NOT_FOUND;

    // Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
    if (Menus.getCommands().get("Bio-Formats Importer") != null
        && IJ.getVersion().compareTo("1.37u") >= 0) IJ.suppressPluginNotFoundError();

    // OK now we get to the interesting bit

    // GJ: added Biorad PIC confocal file handler
    // ------------------------------------------
    // These make 12345 if you read them as the right kind of short
    // and should have this value in every Biorad PIC file
    if (buf[54] == 57 && buf[55] == 48) {
      return tryPlugIn("Biorad_Reader", path);
    }
    // GJ: added Gatan Digital Micrograph DM3 handler
    // ----------------------------------------------
    // check if the file ends in .DM3 or .dm3,
    // and bytes make an int value of 3 which is the DM3 version number
    if (name.endsWith(".dm3") && buf[0] == 0 && buf[1] == 0 && buf[2] == 0 && buf[3] == 3) {
      return tryPlugIn("DM3_Reader", path);
    }

    // IPLab file handler
    // Little-endian IPLab files start with "iiii" or "mmmm".
    if (name.endsWith(".ipl")
        || (buf[0] == 105 && buf[1] == 105 && buf[2] == 105 && buf[3] == 105)
        || (buf[0] == 109 && buf[1] == 109 && buf[2] == 109 && buf[3] == 109)) {
      return tryPlugIn("IPLab_Reader", path);
    }

    // Packard InstantImager format (.img) handler -> check HERE
    // before Analyze check below!
    // Check extension and signature bytes KAJ_
    if (name.endsWith(".img") && buf[0] == 75 && buf[1] == 65 && buf[2] == 74 && buf[3] == 0) {
      return tryPlugIn("InstantImager_Reader", path);
    }

    // Analyze format (.img/.hdr) handler
    // Opens the file using the Nifti_Reader if it is installed,
    // otherwise the Analyze_Reader is used. Note that
    // the Analyze_Reader plugin opens and displays the
    // image and does not implement the ImagePlus class.
    if (name.endsWith(".img") || name.endsWith(".hdr")) {
      if (Menus.getCommands().get("NIfTI-Analyze") != null) return tryPlugIn("Nifti_Reader", path);
      else return tryPlugIn("Analyze_Reader", path);
    }

    // NIFTI format (.nii) handler
    if (name.endsWith(".nii") || name.endsWith(".nii.gz") || name.endsWith(".nii.z")) {
      return tryPlugIn("Nifti_Reader", path);
    }

    // Image Cytometry Standard (.ics) handler
    // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
    if (name.endsWith(".ics")) {
      return tryPlugIn("Ics_Opener", path);
    }

    // Princeton Instruments SPE image file (.spe) handler
    // http://rsb.info.nih.gov/ij/plugins/spe.html
    if (name.endsWith(".spe")) {
      return tryPlugIn("OpenSPE_", path);
    }

    // Zeiss Confocal LSM 510 image file (.lsm) handler
    // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
    if (name.endsWith(".lsm")) {
      Object obj = tryPlugIn("LSM_Reader", path);
      if (obj == null && Menus.getCommands().get("Show LSMToolbox") != null)
        obj = tryPlugIn("LSM_Toolbox", "file=" + path);
      return obj;
    }

    // BM: added Bruker file handler 29.07.04
    if (name.equals("ser")
        || name.equals("fid")
        || name.equals("2rr")
        || name.equals("2ii")
        || name.equals("3rrr")
        || name.equals("3iii")
        || name.equals("2dseq")) {
      ij.IJ.showStatus("Opening Bruker " + name + " File");
      return tryPlugIn("BrukerOpener", name + "|" + path);
    }

    // AVI: open AVI files using AVI_Reader plugin
    if (name.endsWith(".avi")) {
      return tryPlugIn("AVI_Reader", path);
    }

    // QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
    if (name.endsWith(".mov") || name.endsWith(".pict")) {
      return tryPlugIn("QT_Movie_Opener", path);
    }

    // ZVI file handler
    // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
    // so we can only look at the extension.
    if (name.endsWith(".zvi")) {
      return tryPlugIn("ZVI_Reader", path);
    }

    // University of North Carolina (UNC) file format handler
    // 'magic' numbers are (int) offsets to data structures and
    // may change in future releases.
    if (name.endsWith(".unc")
        || (buf[3] == 117 && buf[7] == -127 && buf[11] == 36 && buf[14] == 32 && buf[15] == -127)) {
      return tryPlugIn("UNC_Reader", path);
    }

    // Amira file handler
    // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
    if (buf[0] == 0x23
        && buf[1] == 0x20
        && buf[2] == 0x41
        && buf[3] == 0x6d
        && buf[4] == 0x69
        && buf[5] == 0x72
        && buf[6] == 0x61
        && buf[7] == 0x4d
        && buf[8] == 0x65
        && buf[9] == 0x73
        && buf[10] == 0x68
        && buf[11] == 0x20) {
      return tryPlugIn("AmiraMeshReader_", path);
    }

    // Deltavision file handler
    // Open DV files generated on Applied Precision DeltaVision systems
    if (name.endsWith(".dv") || name.endsWith(".r3d")) {
      return tryPlugIn("Deltavision_Opener", path);
    }

    // Albert Cardona: read .mrc files (little endian).
    // Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
    // The parsing of the header is a bare minimum of what could be done.
    if (name.endsWith(".mrc")) {
      return tryPlugIn("Open_MRC_Leginon", path);
    }

    // Albert Cardona: read .dat files from the EMMENU software
    if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
      return tryPlugIn("Open_DAT_EMMENU", path);
    }

    // Timo Rantalainen and Michael Doube: read Stratec pQCT files.
    // File name is IDDDDDDD.MHH, where D is decimal and H is hex.
    if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
      return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
    }

    // Michael Doube: read Scanco ISQ files
    // File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
    try {
      String isqMagic = new String(buf, 0, 16, "UTF-8");
      if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
        return tryPlugIn("org.bonej.io.ISQReader", path);
    } catch (Exception e) {
    }

    // David Mills: read Queen Mary MCD files
    if (name.endsWith(".mcd")) {
      return tryPlugIn("mcdReader", path);
    }
    // David Mills: read Queen Mary TOM files
    if (name.endsWith(".tom")) {
      return tryPlugIn("tomReader", path);
    }

    // ****************** MODIFY HERE ******************
    // do what ever you have to do to recognise your own file type
    // and then call appropriate plugin using the above as models
    // e.g.:

    /*
    // A. Dent: Added XYZ handler
    // ----------------------------------------------
    // check if the file ends in .xyz, and bytes 0 and 1 equal 42
    if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
    // Ok we've identified the file type - now load it
    	return tryPlugIn("XYZ_Reader", path);
    }
    */

    return null;
  }