Changeset 3097


Ignore:
Timestamp:
08/22/07 13:58:39 (13 years ago)
Author:
curtis
Message:

Whitespace.

Location:
trunk/loci/formats
Files:
48 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/AggregateMetadataStore.java

    r3023 r3097  
    203203    Float lightAttenuation, Integer lightWavelength, Integer otf, 
    204204    Integer detector, Float detectorOffset, Float detectorGain, 
    205     String illuminationType, Integer pinholeSize,  
    206     String photometricInterpretation, String mode, String contrastMethod,  
    207     Integer auxLightSource, Float auxLightAttenuation, String auxTechnique,  
    208     Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor,  
     205    String illuminationType, Integer pinholeSize, 
     206    String photometricInterpretation, String mode, String contrastMethod, 
     207    Integer auxLightSource, Float auxLightAttenuation, String auxTechnique, 
     208    Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor, 
    209209    Float ndFilter, Integer i) 
    210210  { 
     
    216216        photometricInterpretation, mode, contrastMethod, auxLightSource, 
    217217        auxLightAttenuation, auxTechnique, auxLightWavelength, emWave, exWave, 
    218         fluor, ndFilter, i);  
     218        fluor, ndFilter, i); 
    219219    } 
    220220  } 
  • trunk/loci/formats/DataTools.java

    r3084 r3097  
    505505    float min = Float.MAX_VALUE; 
    506506    float max = Float.MIN_VALUE; 
    507     
     507 
    508508    for (int i=0; i<data.length; i++) { 
    509509      if (data[i] < min) min = data[i]; 
  • trunk/loci/formats/DummyMetadataStore.java

    r3023 r3097  
    7777  } 
    7878 
    79   public void setLogicalChannel(int channelIdx, String name,  
    80     Integer samplesPerPixel, Integer filter, Integer lightSource,  
    81     Float lightAttenuation, Integer lightWavelength, Integer otf,  
    82     Integer detector, Float detectorOffset, Float detectorGain,  
    83     String illuminationType, Integer pinholeSize,  
    84     String photometricInterpretation, String mode, String contrastMethod,  
    85     Integer auxLightSource, Float auxLightAttenuation, String auxTechnique,  
    86     Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor,  
    87     Float ndFilter, Integer i)  
     79  public void setLogicalChannel(int channelIdx, String name, 
     80    Integer samplesPerPixel, Integer filter, Integer lightSource, 
     81    Float lightAttenuation, Integer lightWavelength, Integer otf, 
     82    Integer detector, Float detectorOffset, Float detectorGain, 
     83    String illuminationType, Integer pinholeSize, 
     84    String photometricInterpretation, String mode, String contrastMethod, 
     85    Integer auxLightSource, Float auxLightAttenuation, String auxTechnique, 
     86    Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor, 
     87    Float ndFilter, Integer i) 
    8888  { 
    8989  } 
  • trunk/loci/formats/FormatTools.java

    r3080 r3097  
    188188    int len0 = iz == 0 ? zSize : (ic == 0 ? cSize : tSize); 
    189189    int len1 = iz == 1 ? zSize : (ic == 1 ? cSize : tSize); 
    190     
     190 
    191191    return v0 + v1 * len0 + v2 * len0 * len1; 
    192192  } 
  • trunk/loci/formats/ImageTools.java

    r3046 r3097  
    961961  { 
    962962    int[] rtn = new int[w * h]; 
    963     
     963 
    964964    byte[] b = null; 
    965965 
  • trunk/loci/formats/MetadataStore.java

    r3023 r3097  
    193193   * @param channelIdx the index of the channel within the pixels set. 
    194194   * @param name the logical channel's name. 
    195    * @param samplesPerPixel   
     195   * @param samplesPerPixel 
    196196   * @param filter index of the filter associated with this channel. 
    197197   * @param lightSource index of the primary light source. 
     
    219219  void setLogicalChannel(int channelIdx, String name, Integer samplesPerPixel, 
    220220    Integer filter, Integer lightSource, Float lightAttenuation, 
    221     Integer lightWavelength, Integer otf, Integer detector,  
    222     Float detectorOffset, Float detectorGain, String illuminationType,  
    223     Integer pinholeSize, String photometricInterpretation, String mode,  
    224     String contrastMethod, Integer auxLightSource, Float auxLightAttenuation,  
    225     String auxTechnique, Integer auxLightWavelength, Integer emWave,  
     221    Integer lightWavelength, Integer otf, Integer detector, 
     222    Float detectorOffset, Float detectorGain, String illuminationType, 
     223    Integer pinholeSize, String photometricInterpretation, String mode, 
     224    String contrastMethod, Integer auxLightSource, Float auxLightAttenuation, 
     225    String auxTechnique, Integer auxLightWavelength, Integer emWave, 
    226226    Integer exWave, String fluor, Float ndFilter, Integer i); 
    227      
     227 
    228228  /** 
    229229   * Sets a channel's global min and global max in the metadata store for a 
  • trunk/loci/formats/TiffTools.java

    r3094 r3097  
    16131613      imageWidth = colorMap[colorMap.length - 2]; 
    16141614    } 
    1615    
     1615 
    16161616    int row = 0, col = 0; 
    16171617 
  • trunk/loci/formats/in/AVIReader.java

    r3046 r3097  
    526526 
    527527    MetadataStore store = getMetadataStore(); 
    528      
    529     store.setImage(currentId, null, null, null);  
    530      
     528 
     529    store.setImage(currentId, null, null, null); 
     530 
    531531    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    532532      new Integer(core.sizeZ[0]), // SizeZ 
     
    541541    for (int i=0; i<core.sizeC[0]; i++) { 
    542542      store.setLogicalChannel(i, null, null, null, null, null, null, null, null, 
    543         null, null, null, null, core.sizeC[0] == 1 ? "monochrome" : "RGB",  
     543        null, null, null, null, core.sizeC[0] == 1 ? "monochrome" : "RGB", 
    544544        null, null, null, null, null, null, null, null, null, null, null); 
    545545    } 
  • trunk/loci/formats/in/AliconaReader.java

    r3046 r3097  
    168168 
    169169    MetadataStore store = getMetadataStore(); 
    170      
    171     store.setImage(currentId, null, null, null);  
    172      
     170 
     171    store.setImage(currentId, null, null, null); 
     172 
    173173    store.setPixels( 
    174174      new Integer(core.sizeX[0]), 
  • trunk/loci/formats/in/BMPReader.java

    r3046 r3097  
    268268    MetadataStore store = getMetadataStore(); 
    269269 
    270     store.setImage(currentId, null, null, null);  
    271      
     270    store.setImage(currentId, null, null, null); 
     271 
    272272    store.setPixels( 
    273273      new Integer(core.sizeX[0]),  // sizeX 
  • trunk/loci/formats/in/BaseTiffReader.java

    r3023 r3097  
    760760  private void setLogicalChannel(int i) throws FormatException, IOException { 
    761761    getMetadataStore().setLogicalChannel(i, getChannelName(i), null, null, null, 
    762       null, null, null, null, null, null, null, null,  
     762      null, null, null, null, null, null, null, null, 
    763763      getPhotometricInterpretation(i), getMode(i), null, null, null, null, null, 
    764764      getEmWave(i), getExWave(i), null, getNdFilter(i), null); 
  • trunk/loci/formats/in/BioRadReader.java

    r3046 r3097  
    763763      String offset = i == 0 ? offset1 : i == 1 ? gain2 : gain3; 
    764764      store.setLogicalChannel(i, null, null, null, null, null, null, null, null, 
    765        offset == null ? null : new Float(offset),  
    766        gain == null ? null : new Float(gain), null, null, null, null, null,  
     765       offset == null ? null : new Float(offset), 
     766       gain == null ? null : new Float(gain), null, null, null, null, null, 
    767767       null, null, null, null, null, null, null, null, null); 
    768768      store.setDisplayChannel(new Integer(i), new Double(ramp1max), 
  • trunk/loci/formats/in/DeltavisionReader.java

    r3023 r3097  
    386386      store.setLogicalChannel(w, null, null, null, null, null, null, null, null, 
    387387        null, null, null, null, "Monochrome", "Wide-field", null, null, null, 
    388         null, null, new Integer(waves[w]),  
    389         new Integer((int) extHdrFields[0][w][0].getExFilter()), null,  
    390         new Float(extHdrFields[0][w][0].getNdFilter()), null);  
     388        null, null, new Integer(waves[w]), 
     389        new Integer((int) extHdrFields[0][w][0].getExFilter()), null, 
     390        new Float(extHdrFields[0][w][0].getNdFilter()), null); 
    391391    } 
    392392 
  • trunk/loci/formats/in/DicomReader.java

    r3060 r3097  
    319319      SimpleDateFormat fmt = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss"); 
    320320      if (d != null) stamp = fmt.format(d); 
    321       else stamp = null;  
     321      else stamp = null; 
    322322    } 
    323323 
  • trunk/loci/formats/in/EPSReader.java

    r3060 r3097  
    133133      long pos = ras.getFilePointer(); 
    134134      ras.seek(pos); 
    135   
     135 
    136136      char[] chars = new char[2]; 
    137137 
  • trunk/loci/formats/in/FitsReader.java

    r3060 r3097  
    154154 
    155155    MetadataStore store = getMetadataStore(); 
    156       
    157     store.setImage(currentId, null, null, null);  
     156 
     157    store.setImage(currentId, null, null, null); 
    158158    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    159159      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
     
    162162 
    163163    store.setLogicalChannel(0, null, null, null, null, null, null, null, null, 
    164       null, null, null, null, "monochrome", null, null, null, null, null, null,  
     164      null, null, null, null, "monochrome", null, null, null, null, null, null, 
    165165      null, null, null, null, null); 
    166166  } 
  • trunk/loci/formats/in/FluoviewReader.java

    r3046 r3097  
    127127    } 
    128128 
    129     byte[] b = new byte[core.sizeX[0] *  
    130       (int) TiffTools.getImageLength(ifds[0]) *  
     129    byte[] b = new byte[core.sizeX[0] * 
     130      (int) TiffTools.getImageLength(ifds[0]) * 
    131131      getRGBChannelCount() * FormatTools.getBytesPerPixel(core.pixelType[0])]; 
    132132    super.openBytes(0, b); 
  • trunk/loci/formats/in/GIFReader.java

    r3060 r3097  
    330330 
    331331    MetadataStore store = getMetadataStore(); 
    332     store.setImage(currentId, null, null, null);  
     332    store.setImage(currentId, null, null, null); 
    333333 
    334334    core.pixelType[0] = FormatTools.UINT8; 
  • trunk/loci/formats/in/GatanReader.java

    r3060 r3097  
    163163    // The metadata store we're working with. 
    164164    MetadataStore store = getMetadataStore(); 
    165     store.setImage(currentId, null, null, null);  
     165    store.setImage(currentId, null, null, null); 
    166166 
    167167    store.setPixels( 
  • trunk/loci/formats/in/ICSReader.java

    r3073 r3097  
    209209    Location l = new Location(id); 
    210210    //String icsId = l.getPath(), idsId = l.getPath(); 
    211     String icsId = id, idsId = id;  
     211    String icsId = id, idsId = id; 
    212212    int dot = id.lastIndexOf("."); 
    213213    String ext = dot < 0 ? "" : id.substring(dot + 1).toLowerCase(); 
     
    503503    for (int i=0; i<core.sizeC[0]; i++) { 
    504504      store.setLogicalChannel(i, null, null, null, null, null, null, null, null, 
    505        null, null, null, null, null, null, null, null, null, null, null,  
     505       null, null, null, null, null, null, null, null, null, null, null, 
    506506       new Integer(emWave[i]), new Integer(exWave[i]), null, null, null); 
    507507    } 
  • trunk/loci/formats/in/ImageIOReader.java

    r3060 r3097  
    125125    // populate the metadata store 
    126126    MetadataStore store = getMetadataStore(); 
    127     store.setImage(currentId, null, null, null);  
     127    store.setImage(currentId, null, null, null); 
    128128    store.setPixels( 
    129129      new Integer(core.sizeX[0]), 
  • trunk/loci/formats/in/ImarisReader.java

    r3060 r3097  
    207207    store.setImage(fname, d, (String) getMeta("Image comment"), null); 
    208208 
    209     store.setDimensions(new Float(dx), new Float(dy), new Float(dz),  
     209    store.setDimensions(new Float(dx), new Float(dy), new Float(dz), 
    210210      new Float(1), new Float(1), null); 
    211211 
  • trunk/loci/formats/in/KhorosReader.java

    r3060 r3097  
    198198 
    199199    MetadataStore store = getMetadataStore(); 
    200     store.setImage(currentId, null, null, null);  
     200    store.setImage(currentId, null, null, null); 
    201201    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    202202      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
  • trunk/loci/formats/in/LIFReader.java

    r3046 r3097  
    493493      store.setDimensions(xf, yf, zf, null, null, ii); 
    494494      for (int j=0; j<core.sizeC[i]; j++) { 
    495         store.setLogicalChannel(j, null, null, null, null, null, null, null,  
    496           null, null, null, null, null, null, null, null, null, null, null,  
     495        store.setLogicalChannel(j, null, null, null, null, null, null, null, 
     496          null, null, null, null, null, null, null, null, null, null, null, 
    497497          null, null, null, null, null, ii); 
    498498      } 
  • trunk/loci/formats/in/LegacyPictReader.java

    r3060 r3097  
    108108 
    109109    MetadataStore store = getMetadataStore(); 
    110     store.setImage(currentId, null, null, null);  
     110    store.setImage(currentId, null, null, null); 
    111111    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    112112      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
  • trunk/loci/formats/in/LegacyQTReader.java

    r3060 r3097  
    223223 
    224224      MetadataStore store = getMetadataStore(); 
    225       store.setImage(currentId, null, null, null);  
     225      store.setImage(currentId, null, null, null); 
    226226      store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    227227        new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
     
    230230 
    231231      for (int i=0; i<core.sizeC[0]; i++) { 
    232         store.setLogicalChannel(i, null, null, null, null, null, null, null,  
    233           null, null, null, null, null, null, null, null, null, null, null,  
     232        store.setLogicalChannel(i, null, null, null, null, null, null, null, 
     233          null, null, null, null, null, null, null, null, null, null, null, 
    234234          null, null, null, null, null, null); 
    235235      } 
  • trunk/loci/formats/in/LegacyZVIReader.java

    r3060 r3097  
    404404 
    405405      MetadataStore store = getMetadataStore(); 
    406       store.setImage(currentId, null, null, null);  
     406      store.setImage(currentId, null, null, null); 
    407407 
    408408      store.setPixels( 
     
    419419 
    420420      for (int i=0; i<core.sizeC[0]; i++) { 
    421         store.setLogicalChannel(i, null, null, null, null, null, null, null,  
    422           null, null, null, null, null, null, null, null, null, null, null,  
     421        store.setLogicalChannel(i, null, null, null, null, null, null, null, 
     422          null, null, null, null, null, null, null, null, null, null, null, 
    423423          null, null, null, null, null, null); 
    424424      } 
  • trunk/loci/formats/in/LeicaReader.java

    r3092 r3097  
    161161    int c = buf.length / (core.sizeX[series] * core.sizeY[series] * 
    162162      FormatTools.getBytesPerPixel(core.pixelType[series])); 
    163      
     163 
    164164    // if a custom LUT is used, we don't want to split channels 
    165165    if (channelIndices[ndx] > -1) { 
     
    186186    if (channelIndices[ndx] > -1) { 
    187187      b = ImageTools.splitChannels(b)[channelIndices[ndx]]; 
    188     }  
     188    } 
    189189    tiff[series][no].close(); 
    190190    return b; 
     
    250250 
    251251      File f = new File(name).getAbsoluteFile(); 
    252       String[] listing = null;  
     252      String[] listing = null; 
    253253      if (f.exists()) listing = f.getParentFile().list(); 
    254254      else { 
    255         listing =  
     255        listing = 
    256256          (String[]) Location.getIdMap().keySet().toArray(new String[0]); 
    257257      } 
     
    454454        int tempImages = DataTools.bytesToInt(tempData, 0, 4, 
    455455          core.littleEndian[0]); 
    456         
     456 
    457457        File dirFile = new File(id).getAbsoluteFile(); 
    458         String[] listing = null;  
    459         String dirPrefix = "";  
     458        String[] listing = null; 
     459        String dirPrefix = ""; 
    460460        if (dirFile.exists()) { 
    461           listing = dirFile.getParentFile().list();  
    462           dirPrefix = dirFile.getParent();  
    463         }  
     461          listing = dirFile.getParentFile().list(); 
     462          dirPrefix = dirFile.getParent(); 
     463        } 
    464464        else { 
    465           listing =  
     465          listing = 
    466466            (String[]) Location.getIdMap().keySet().toArray(new String[0]); 
    467467        } 
    468          
     468 
    469469        Vector list = new Vector(); 
    470470 
     
    10141014          else { 
    10151015            // using a custom LUT 
    1016             channelIndices[j] = -1;  
     1016            channelIndices[j] = -1; 
    10171017          } 
    10181018 
     
    11021102      if (channelIndices[0] == -1) { 
    11031103        core.sizeC[i] *= 3; 
    1104         core.rgb[i] = true;  
    1105       }   
     1104        core.rgb[i] = true; 
     1105      } 
    11061106 
    11071107      store.setPixels( 
     
    11301130 
    11311131      for (int j=0; j<core.sizeC[i]; j++) { 
    1132         store.setLogicalChannel(i, null, null, null, null, null, null, null,  
    1133           null, null, null, null, null, null, null, null, null, null, null,  
     1132        store.setLogicalChannel(i, null, null, null, null, null, null, null, 
     1133          null, null, null, null, null, null, null, null, null, null, null, 
    11341134          null, null, null, null, null, null); 
    11351135        // TODO: get channel min/max from metadata 
  • trunk/loci/formats/in/MNGReader.java

    r3060 r3097  
    175175 
    176176    MetadataStore store = getMetadataStore(); 
    177     store.setImage(currentId, null, null, null);  
     177    store.setImage(currentId, null, null, null); 
    178178 
    179179    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
  • trunk/loci/formats/in/MRCReader.java

    r3060 r3097  
    9393      float[] f = new float[b.length / 4]; 
    9494      for (int i=0; i<f.length; i++) { 
    95         f[i] = Float.intBitsToFloat(DataTools.bytesToInt(b, i*4,  
    96           4, core.littleEndian[0]));               
     95        f[i] = Float.intBitsToFloat(DataTools.bytesToInt(b, i*4, 
     96          4, core.littleEndian[0])); 
    9797      } 
    98       return ImageTools.makeImage(f, core.sizeX[0], core.sizeY[0], 1,  
     98      return ImageTools.makeImage(f, core.sizeX[0], core.sizeY[0], 1, 
    9999        core.interleaved[0]); 
    100100    } 
     
    232232 
    233233    MetadataStore store = getMetadataStore(); 
    234     store.setImage(currentId, null, null, null);  
     234    store.setImage(currentId, null, null, null); 
    235235    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    236236      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
  • trunk/loci/formats/in/MetamorphReader.java

    r3046 r3097  
    215215    if (!id.toLowerCase().endsWith(".nd")) { 
    216216      Location abs = new Location(currentId).getAbsoluteFile(); 
    217      
     217 
    218218      int idx = id.indexOf("_"); 
    219219      if (idx == -1) idx = id.lastIndexOf("."); 
  • trunk/loci/formats/in/MicromanagerReader.java

    r3076 r3097  
    119119  /* @see loci.formats.IFormatHandler#isThisType(String, boolean) */ 
    120120  public boolean isThisType(String name, boolean open) { 
    121     File f = new File(name).getAbsoluteFile();  
    122     String[] list = null;  
     121    File f = new File(name).getAbsoluteFile(); 
     122    String[] list = null; 
    123123    if (f.exists()) list = f.getParentFile().list(); 
    124124    else list = (String[]) Location.getIdMap().keySet().toArray(new String[0]); 
     
    151151 
    152152    File file = new File(currentId).getAbsoluteFile(); 
    153     in = new RandomAccessStream(file.exists() ? new File(file.getParentFile(),  
     153    in = new RandomAccessStream(file.exists() ? new File(file.getParentFile(), 
    154154      METADATA).getAbsolutePath() : METADATA); 
    155155 
     
    245245 
    246246    MetadataStore store = getMetadataStore(); 
    247     store.setImage(currentId, null, null, null);  
     247    store.setImage(currentId, null, null, null); 
    248248 
    249249    store.setPixels( 
  • trunk/loci/formats/in/NRRDReader.java

    r3060 r3097  
    232232 
    233233    MetadataStore store = getMetadataStore(); 
    234     store.setImage(currentId, null, null, null);  
     234    store.setImage(currentId, null, null, null); 
    235235 
    236236    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
  • trunk/loci/formats/in/OIBReader.java

    r3046 r3097  
    466466        String offset = (String) getMeta(prefix + "AnalogPMTOffset"); 
    467467        String voltage = (String) getMeta(prefix + "AnalogPMTVoltage"); 
    468         
     468 
    469469        store.setDetector(null, null, null, null, null, voltage == null ? null : 
    470470          new Float(voltage), null, null, new Integer(j)); 
    471471 
    472         store.setLogicalChannel(j, null, null, null, null, null, null, null,  
    473           null, offset == null ? null : new Float(offset),  
    474           gain == null ? null : new Float(gain), null, null, null, null, null,  
     472        store.setLogicalChannel(j, null, null, null, null, null, null, null, 
     473          null, offset == null ? null : new Float(offset), 
     474          gain == null ? null : new Float(gain), null, null, null, null, null, 
    475475          null, null, null, null, null, null, null, null, new Integer(i)); 
    476476      } 
  • trunk/loci/formats/in/OIFReader.java

    r3060 r3097  
    374374    // The metadata store we're working with. 
    375375    MetadataStore store = getMetadataStore(); 
    376     store.setImage(currentId, null, null, null);  
     376    store.setImage(currentId, null, null, null); 
    377377 
    378378    switch (imageDepth) { 
     
    420420      String emWave = (String) getMeta(prefix + "EmissionWavelength"); 
    421421      String exWave = (String) getMeta(prefix + "ExcitationWavelength"); 
    422        
     422 
    423423      prefix = "[Channel " + (i+1) + " Parameters] - "; 
    424424      String gain = (String) getMeta(prefix + "CountingPMTGain"); 
    425425      String voltage = (String) getMeta(prefix + "CountingPMTVoltage"); 
    426426      String offset = (String) getMeta(prefix + "CountingPMTOffset"); 
    427       
     427 
    428428      if (gain != null) gain.replaceAll("\"", ""); 
    429429      if (voltage != null) voltage.replaceAll("\"", ""); 
     
    435435      } 
    436436 
    437       store.setLogicalChannel(i, name, null, null, null, null, null, null,  
    438         null, offset == null ? null : new Float(offset),  
    439         gain == null ? null : new Float(gain), null, null, null, null, null,  
    440         null, null, null, null, emWave == null ? null : new Integer(emWave),  
     437      store.setLogicalChannel(i, name, null, null, null, null, null, null, 
     438        null, offset == null ? null : new Float(offset), 
     439        gain == null ? null : new Float(gain), null, null, null, null, null, 
     440        null, null, null, null, emWave == null ? null : new Integer(emWave), 
    441441        exWave == null ? null : new Integer(exWave), null, null, null); 
    442442    } 
  • trunk/loci/formats/in/OMETiffReader.java

    r3046 r3097  
    171171          boolean nullFirstT = aFirstT == null || aFirstT.equals(""); 
    172172          boolean nullNumPlanes = aNumPlanes == null || aNumPlanes.equals(""); 
    173        
     173 
    174174          int firstZ = nullFirstZ ? 0 : Integer.parseInt(aFirstZ); 
    175175          int firstC = nullFirstC ? 0 : Integer.parseInt(aFirstC); 
  • trunk/loci/formats/in/OMEXMLReader.java

    r3046 r3097  
    432432 
    433433    MetadataStore store = getMetadataStore(); 
    434    
     434 
    435435    try { 
    436436      if (store.getClass().getName().equals( 
    437         "loci.formats.ome.OMEXMLMetadataStore"))  
     437        "loci.formats.ome.OMEXMLMetadataStore")) 
    438438      { 
    439439        MetadataStore m = (MetadataStore) r.getVar("omexml"); 
    440         store.setRoot(m.getRoot());  
    441       } 
    442       else {  
     440        store.setRoot(m.getRoot()); 
     441      } 
     442      else { 
    443443        FormatTools.convertMetadata((MetadataRetrieve) r.getVar("omexml"), store); 
    444444      } 
  • trunk/loci/formats/in/OpenlabRawReader.java

    r3023 r3097  
    138138    bytesPerPixel = in.read(); 
    139139    in.read(); 
    140     
     140 
    141141    long stamp = in.readLong(); 
    142142    Date timestamp = null; 
    143143    SimpleDateFormat sdf = null; 
    144     if (stamp > 0) {  
     144    if (stamp > 0) { 
    145145      stamp /= 1000000; 
    146146      stamp -= (67 * 365.25 * 24 * 60 * 60); 
    147      
     147 
    148148      timestamp = new Date(stamp); 
    149149      sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss"); 
    150150      addMeta("Timestamp", sdf.format(timestamp)); 
    151     }  
     151    } 
    152152    in.skipBytes(4); 
    153153    byte[] s = new byte[256]; 
     
    189189    } 
    190190 
    191     store.setImage((String) getMeta("Image name"),  
     191    store.setImage((String) getMeta("Image name"), 
    192192      timestamp == null ? null : sdf.format(timestamp), null, null); 
    193193    store.setPixels( 
  • trunk/loci/formats/in/OpenlabReader.java

    r3046 r3097  
    434434        else if (tag == 69) { 
    435435          in.skipBytes(18); 
    436          
     436 
    437437          xCal = in.readFloat(); 
    438438          yCal = in.readFloat(); 
     
    699699      for (int j=0; j<core.sizeC[0]; j++) { 
    700700        store.setLogicalChannel(j, null, null, null, null, null, null, null, 
    701           null, null, null, null, null, null, null, null, null, null, null,  
     701          null, null, null, null, null, null, null, null, null, null, null, 
    702702          null, null, null, null, null, new Integer(i)); 
    703703      } 
  • trunk/loci/formats/in/PGMReader.java

    r3060 r3097  
    157157 
    158158    MetadataStore store = getMetadataStore(); 
    159     store.setImage(currentId, null, null, null);  
     159    store.setImage(currentId, null, null, null); 
    160160    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
    161161      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
     
    165165    for (int i=0; i<core.sizeC[0]; i++) { 
    166166      store.setLogicalChannel(i, null, null, null, null, null, null, null, 
    167         null, null, null, null, null,  
    168         core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null, null, null,  
     167        null, null, null, null, null, 
     168        core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null, null, null, 
    169169        null, null, null, null, null, null, null); 
    170170    } 
  • trunk/loci/formats/in/PrairieReader.java

    r3092 r3097  
    288288              if (prefix.equals("File") && key.equals("filename")) { 
    289289                File current = new File(id).getAbsoluteFile(); 
    290                 String dir = "";  
     290                String dir = ""; 
    291291                if (current.exists()) { 
    292292                  dir = current.getPath(); 
     
    364364          String gain = (String) getMeta("pmtGain_" + i); 
    365365          String offset = (String) getMeta("pmtOffset_" + i); 
    366     
    367           store.setLogicalChannel(i, null, null,  
     366 
     367          store.setLogicalChannel(i, null, null, 
    368368            null, null, null, null, null, 
    369             null, offset == null ? null : new Float(offset),  
    370             gain == null ? null : new Float(gain), null, null, null, null,  
     369            null, offset == null ? null : new Float(offset), 
     370            gain == null ? null : new Float(gain), null, null, null, null, 
    371371            null, null, null, null, null, null, null, null, null, null); 
    372372        } 
     
    396396            null, null, null, null, null, null, null, null, null, null, null); 
    397397        } 
    398         */  
     398        */ 
    399399      } 
    400400 
     
    412412            if (file.exists()) { 
    413413              dir = parent.getPath(); 
    414               if (!dir.endsWith(File.separator)) dir += File.separator;  
    415             }  
     414              if (!dir.endsWith(File.separator)) dir += File.separator; 
     415            } 
    416416            initFile(dir + listing[i]); 
    417417          } 
     
    435435      } 
    436436    } 
    437     if (currentId == null) currentId = id;  
     437    if (currentId == null) currentId = id; 
    438438  } 
    439439 
  • trunk/loci/formats/in/SlidebookReader.java

    r3060 r3097  
    319319 
    320320      for (int j=0; j<core.sizeC[i]; j++) { 
    321         store.setLogicalChannel(j, null, null, null, null, null, null, null,  
    322           null, null, null, null, null, core.sizeC[i] == 1 ? "monochrome" :  
    323           "RGB", null, null, null, null, null, null, null, null, null, null,  
    324           new Integer(i));  
     321        store.setLogicalChannel(j, null, null, null, null, null, null, null, 
     322          null, null, null, null, null, core.sizeC[i] == 1 ? "monochrome" : 
     323          "RGB", null, null, null, null, null, null, null, null, null, null, 
     324          new Integer(i)); 
    325325      } 
    326326    } 
  • trunk/loci/formats/in/VisitechReader.java

    r3076 r3097  
    117117 
    118118      currentId = null; 
    119       initFile(file.exists() ? new Location(file.getParent(),  
     119      initFile(file.exists() ? new Location(file.getParent(), 
    120120        base + " Report.html").getAbsolutePath() : base + " Report.html"); 
    121121      return; 
     
    190190    int ndx = currentId.lastIndexOf(File.separator); 
    191191    String base = currentId.substring(ndx + 1, currentId.indexOf(" ", ndx)); 
    192    
     192 
    193193    File f = new File(currentId).getAbsoluteFile(); 
    194194 
    195195    for (int i=0; i<core.sizeC[0]; i++) { 
    196       files.add((f.exists() ? f.getParent() + File.separator : "") + base +  
     196      files.add((f.exists() ? f.getParent() + File.separator : "") + base + 
    197197        " " + (i + 1) + ".xys"); 
    198198    } 
    199199    files.add(currentId); 
    200      
     200 
    201201    MetadataStore store = getMetadataStore(); 
    202202    store.setImage(currentId, null, null, null); 
     
    207207 
    208208    for (int i=0; i<core.sizeC[0]; i++) { 
    209       store.setLogicalChannel(i, null, null, null, null, null, null, null,  
    210         null, null, null, null, null, core.sizeC[0] == 1 ?  
    211         "monochrome" : "RGB", null, null, null, null, null, null, null, null,  
     209      store.setLogicalChannel(i, null, null, null, null, null, null, null, 
     210        null, null, null, null, null, core.sizeC[0] == 1 ? 
     211        "monochrome" : "RGB", null, null, null, null, null, null, null, null, 
    212212        null, null, null); 
    213213    } 
  • trunk/loci/formats/in/ZeissLSMReader.java

    r3046 r3097  
    306306        null); // Pixels index 
    307307      for (int i=0; i<core.sizeC[0]; i++) { 
    308         store.setLogicalChannel(i, null, null, null, null, null, null, null,  
    309           null, null, null, null, null, null, null, null, null, null, null,  
    310           null, null, null, null, null, null);  
     308        store.setLogicalChannel(i, null, null, null, null, null, null, null, 
     309          null, null, null, null, null, null, null, null, null, null, null, 
     310          null, null, null, null, null, null); 
    311311      } 
    312312 
     
    351351      long bleachRoiOffset = ras.readInt(); 
    352352      ras.skipBytes(4); 
    353      
     353 
    354354      put("DisplayAspectX", ras.readDouble()); 
    355355      put("DisplayAspectY", ras.readDouble()); 
     
    364364      put("ToolbarFlags", ras.readInt()); 
    365365      ras.skipBytes(20); 
    366        
     366 
    367367      // read referenced structures 
    368368 
     
    394394        long namesOffset = in.readInt() + channelColorsOffset; 
    395395        in.skipBytes(4); 
    396   
     396 
    397397        // read in the intensity value for each color 
    398398 
     
    413413          } 
    414414          if (sb.length() <= 128) put("ChannelName" + i, sb.toString()); 
    415           else put("ChannelName" + i, "");  
     415          else put("ChannelName" + i, ""); 
    416416        } 
    417417      } 
  • trunk/loci/formats/in/ZeissZVIReader.java

    r3093 r3097  
    325325      } 
    326326      else { 
    327         if (metadata.get("MultiChannelEnabled") != null ||  
    328           metadata.get("MultiChannelEnabled 0") != null)  
     327        if (metadata.get("MultiChannelEnabled") != null || 
     328          metadata.get("MultiChannelEnabled 0") != null) 
    329329        { 
    330330          core.currentOrder[0] = 
     
    343343    } 
    344344 
    345     // rearrange axis sizes, if necessary  
    346  
    347     int lastZ = zIndices.size() == 0 ? Integer.MAX_VALUE :  
     345    // rearrange axis sizes, if necessary 
     346 
     347    int lastZ = zIndices.size() == 0 ? Integer.MAX_VALUE : 
    348348      ((Integer) zIndices.get(zIndices.size() - 1)).intValue(); 
    349     int lastT = tIndices.size() == 0 ? Integer.MAX_VALUE :  
     349    int lastT = tIndices.size() == 0 ? Integer.MAX_VALUE : 
    350350      ((Integer) tIndices.get(tIndices.size() - 1)).intValue(); 
    351351 
    352352    if ((zIndex > lastZ || tIndex > lastT) && (zIndex == core.sizeC[0] - 1 || 
    353       tIndex == core.sizeC[0] - 1 ||  
     353      tIndex == core.sizeC[0] - 1 || 
    354354      (zIndex != 0 && zIndex % core.sizeC[0] == 0) || 
    355       (tIndex != 0 && tIndex % core.sizeC[0] == 0)) && zIndex != lastT)  
     355      (tIndex != 0 && tIndex % core.sizeC[0] == 0)) && zIndex != lastT) 
    356356    { 
    357357      if (zIndex >= core.sizeZ[0] || tIndex >= core.sizeT[0]) { 
     
    371371      if (debug) trace(exc); 
    372372    } 
    373    
     373 
    374374    // remove extra (invalid) metadata 
    375375 
     
    436436      } 
    437437 
    438       store.setLogicalChannel(i, name, null, null, null, null, null, null,  
     438      store.setLogicalChannel(i, name, null, null, null, null, null, null, 
    439439        null, null, null, null, null, null, null, null, null, null, null, null, 
    440         emWave == null ? null : new Integer(emWave),  
    441         exWave == null ? null : new Integer(exWave), null, null, null);  
     440        emWave == null ? null : new Integer(emWave), 
     441        exWave == null ? null : new Integer(exWave), null, null, null); 
    442442 
    443443      String black = (String) getMeta("BlackValue " + idx); 
     
    465465      try { exp = new Float(exposure); } 
    466466      catch (Exception e) { } 
    467        
     467 
    468468      store.setPlaneInfo(zct[0], zct[1], zct[2], null, exp, null); 
    469469    } 
     
    583583            core.sizeY[0] = th; 
    584584          } 
    585         
     585 
    586586          s.skipBytes(14); 
    587           
     587 
    588588          int numImageContainers = s.readInt(); 
    589589          s.skipBytes(6); 
     
    654654          try { parseTags(s); } 
    655655          catch (IOException e) { } 
    656         }      
     656        } 
    657657        s.close(); 
    658658        data = null; 
     
    684684    bpp = s.readInt(); 
    685685    s.skipBytes(8); 
    686      
     686 
    687687    pixels.put(new Integer(num), directory); 
    688688    names.put(new Integer(num), entry); 
     
    754754      s.skipBytes(2); 
    755755      int tagID = 0; 
    756      
     756 
    757757      try { tagID = s.readInt(); } 
    758758      catch (IOException e) { } 
     
    795795        if (metadata.get(key) != null) { 
    796796          Object v = metadata.remove(key); 
    797           metadata.put(key + " 0", v);  
     797          metadata.put(key + " 0", v); 
    798798        } 
    799799 
  • trunk/loci/formats/ome/OMEReader.java

    r3023 r3097  
    190190      null); 
    191191    for (int i=0; i<core.sizeC[0]; i++) { 
    192       store.setLogicalChannel(i, null, null, null, null, null, null, null,  
     192      store.setLogicalChannel(i, null, null, null, null, null, null, null, 
    193193        null, null, null, null, null, null, null, null, null, null, null, null, 
    194         null, null, null, null, null);  
     194        null, null, null, null, null); 
    195195    } 
    196196  } 
  • trunk/loci/formats/ome/OMEXMLMetadataStore.java

    r3023 r3097  
    11601160  public void setLogicalChannel(int channelIdx, String name, 
    11611161    Integer samplesPerPixel, Integer filter, Integer lightSource, 
    1162     Float lightAttenuation, Integer lightWavelength, Integer otf,  
    1163     Integer detector, Float detectorOffset, Float detectorGain,  
    1164     String illuminationType, Integer pinholeSize,  
    1165     String photometricInterpretation, String mode, String contrastMethod,  
    1166     Integer auxLightSource, Float auxLightAttenuation, String auxTechnique,  
    1167     Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor,  
     1162    Float lightAttenuation, Integer lightWavelength, Integer otf, 
     1163    Integer detector, Float detectorOffset, Float detectorGain, 
     1164    String illuminationType, Integer pinholeSize, 
     1165    String photometricInterpretation, String mode, String contrastMethod, 
     1166    Integer auxLightSource, Float auxLightAttenuation, String auxTechnique, 
     1167    Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor, 
    11681168    Float ndFilter, Integer i) 
    11691169  { 
     
    12001200 
    12011201    endx = lightSource == null ? 0 : lightSource.intValue(); 
    1202     LightSourceNode light =  
     1202    LightSourceNode light = 
    12031203      (LightSourceNode) getChild(root, "LightSource", endx); 
    12041204    logicalChannel.setLightSource(light); 
     
    12131213 
    12141214    endx = auxLightSource == null ? 0 : auxLightSource.intValue(); 
    1215     LightSourceNode auxLight =  
     1215    LightSourceNode auxLight = 
    12161216      (LightSourceNode) getChild(root, "LightSource", endx); 
    1217     logicalChannel.setAuxLightSource(auxLight);  
     1217    logicalChannel.setAuxLightSource(auxLight); 
    12181218    */ 
    12191219 
  • trunk/loci/formats/ome/OmeisImporter.java

    r3074 r3097  
    7575    reader = new FileStitcher(new ChannelSeparator()); 
    7676    store = new OMEXMLMetadataStore(); 
    77     reader.setOriginalMetadataPopulated(true);  
     77    reader.setOriginalMetadataPopulated(true); 
    7878    reader.setMetadataStore(store); 
    7979  } 
     
    108108      reader.setId(ids[i]); 
    109109      String[] files = reader.getUsedFiles(); 
    110       
     110 
    111111      if (files == null) continue; // invalid files list 
    112112      sb.setLength(0); 
    113       
     113 
    114114      for (int j=files.length - 1; j>=0; j--) { 
    115115        for (int ii=i; ii<fileIds.length; ii++) { 
     
    169169        ": used=" + a2s(used) + "; ids=" + a2s(ids)); 
    170170    } 
    171      
     171 
    172172    boolean[] done = new boolean[ids.length]; 
    173173    int numLeft = ids.length; 
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