Changeset 6055


Ignore:
Timestamp:
03/20/10 04:46:40 (10 years ago)
Author:
curtis
Message:

Use boxing in a few places.

Location:
trunk/components/bio-formats/src/loci/formats/in
Files:
46 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/bio-formats/src/loci/formats/in/AliconaReader.java

    r6026 r6055  
    245245      double pixelSizeY = Double.parseDouble(pntY) * 1000000; 
    246246 
    247       store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), 0, 0); 
    248       store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), 0, 0); 
     247      store.setDimensionsPhysicalSizeX(pixelSizeX, 0, 0); 
     248      store.setDimensionsPhysicalSizeY(pixelSizeY, 0, 0); 
    249249    } 
    250250  } 
  • trunk/components/bio-formats/src/loci/formats/in/AnalyzeReader.java

    r6026 r6055  
    289289    store.setImageDescription(description, 0); 
    290290 
    291     store.setDimensionsPhysicalSizeX(new Double(voxelWidth * 0.001), 0, 0); 
    292     store.setDimensionsPhysicalSizeY(new Double(voxelHeight * 0.001), 0, 0); 
    293     store.setDimensionsPhysicalSizeZ(new Double(sliceThickness * 0.001), 0, 0); 
     291    store.setDimensionsPhysicalSizeX(voxelWidth * 0.001, 0, 0); 
     292    store.setDimensionsPhysicalSizeY(voxelHeight * 0.001, 0, 0); 
     293    store.setDimensionsPhysicalSizeZ(sliceThickness * 0.001, 0, 0); 
    294294    store.setDimensionsTimeIncrement(new Double(deltaT * 1000), 0, 0); 
    295295  } 
  • trunk/components/bio-formats/src/loci/formats/in/BDReader.java

    r6043 r6055  
    340340      store.setWellRow(row.charAt(0)-'A', 0, i); 
    341341 
    342       store.setWellSampleIndex(new Integer(i), 0, i, 0); 
     342      store.setWellSampleIndex(i, 0, i, 0); 
    343343 
    344344      String imageID = MetadataTools.createLSID("Image", i); 
  • trunk/components/bio-formats/src/loci/formats/in/BMPReader.java

    r6026 r6055  
    301301    double correctedY = pixelSizeY == 0 ? 0.0 : 1000000.0 / pixelSizeY; 
    302302 
    303     store.setDimensionsPhysicalSizeX(new Double(correctedX), 0, 0); 
    304     store.setDimensionsPhysicalSizeY(new Double(correctedY), 0, 0); 
     303    store.setDimensionsPhysicalSizeX(correctedX, 0, 0); 
     304    store.setDimensionsPhysicalSizeY(correctedY, 0, 0); 
    305305  } 
    306306 
  • trunk/components/bio-formats/src/loci/formats/in/BaseTiffReader.java

    r6026 r6055  
    439439    TiffRational xResolution = firstIFD.getIFDRationalValue(IFD.X_RESOLUTION); 
    440440    TiffRational yResolution = firstIFD.getIFDRationalValue(IFD.Y_RESOLUTION); 
    441     float pixX = xResolution == null ? 0f : 1 / xResolution.floatValue(); 
    442     float pixY = yResolution == null ? 0f : 1 / yResolution.floatValue(); 
     441    double pixX = xResolution == null ? 0 : 1 / xResolution.doubleValue(); 
     442    double pixY = yResolution == null ? 0 : 1 / yResolution.doubleValue(); 
    443443 
    444444    switch (resolutionUnit) { 
     
    455455    } 
    456456 
    457     store.setDimensionsPhysicalSizeX(new Double(pixX), 0, 0); 
    458     store.setDimensionsPhysicalSizeY(new Double(pixY), 0, 0); 
    459     store.setDimensionsPhysicalSizeZ(new Double(0), 0, 0); 
     457    store.setDimensionsPhysicalSizeX(pixX, 0, 0); 
     458    store.setDimensionsPhysicalSizeY(pixY, 0, 0); 
     459    store.setDimensionsPhysicalSizeZ(0.0, 0, 0); 
    460460  } 
    461461 
  • trunk/components/bio-formats/src/loci/formats/in/BioRadReader.java

    r6026 r6055  
    536536                height /= getSizeY(); 
    537537 
    538                 store.setDimensionsPhysicalSizeX(new Double(width), 0, 0); 
    539                 store.setDimensionsPhysicalSizeY(new Double(height), 0, 0); 
     538                store.setDimensionsPhysicalSizeX(width, 0, 0); 
     539                store.setDimensionsPhysicalSizeY(height, 0, 0); 
    540540 
    541541                break; 
     
    883883 
    884884    store.setObjectiveLensNA(new Double(lens), 0, 0); 
    885     store.setObjectiveNominalMagnification(new Integer((int) magFactor), 0, 0); 
     885    store.setObjectiveNominalMagnification((int) magFactor, 0, 0); 
    886886    store.setObjectiveCorrection("Unknown", 0, 0); 
    887887    store.setObjectiveImmersion("Unknown", 0, 0); 
  • trunk/components/bio-formats/src/loci/formats/in/BurleighReader.java

    r6026 r6055  
    178178    MetadataTools.setDefaultCreationDate(store, id, 0); 
    179179 
    180     store.setDimensionsPhysicalSizeX(new Double(xSize / getSizeX()), 0, 0); 
    181     store.setDimensionsPhysicalSizeY(new Double(ySize / getSizeY()), 0, 0); 
    182     store.setDimensionsPhysicalSizeZ(new Double(zSize / getSizeZ()), 0, 0); 
     180    store.setDimensionsPhysicalSizeX(xSize / getSizeX(), 0, 0); 
     181    store.setDimensionsPhysicalSizeY(ySize / getSizeY(), 0, 0); 
     182    store.setDimensionsPhysicalSizeZ(zSize / getSizeZ(), 0, 0); 
    183183  } 
    184184 
  • trunk/components/bio-formats/src/loci/formats/in/CellomicsReader.java

    • Property svn:executable deleted
    r6026 r6055  
    170170    double height = pixelHeight == 0 ? 0.0 : 1000000.0 / pixelHeight; 
    171171 
    172     store.setDimensionsPhysicalSizeX(new Double(width), 0, 0); 
    173     store.setDimensionsPhysicalSizeY(new Double(height), 0, 0); 
     172    store.setDimensionsPhysicalSizeX(width, 0, 0); 
     173    store.setDimensionsPhysicalSizeY(height, 0, 0); 
    174174  } 
    175175 
  • trunk/components/bio-formats/src/loci/formats/in/DeltavisionReader.java

    r6026 r6055  
    506506      store.setLogicalChannelEmWave(new Integer(waves[w]), 0, w); 
    507507      if ((int) hdrC.exWavelen > 0) { 
    508         store.setLogicalChannelExWave(new Integer((int) hdrC.exWavelen), 0, w); 
     508        store.setLogicalChannelExWave((int) hdrC.exWavelen, 0, w); 
    509509      } 
    510510      if (ndFilters[w] == null) ndFilters[w] = new Double(hdrC.ndFilter); 
     
    696696            double mhz = Double.parseDouble(value) / 1000; 
    697697            for (int c=0; c<getSizeC(); c++) { 
    698               store.setDetectorSettingsReadOutRate(new Double(mhz), 0, c); 
     698              store.setDetectorSettingsReadOutRate(mhz, 0, c); 
    699699            } 
    700700          } 
     
    707707          try { 
    708708            // this is the camera temperature, not the environment temperature 
    709             //store.setImagingEnvironmentTemperature(new Double(value), 0); 
     709            //store.setImagingEnvironmentTemperature(value, 0); 
    710710          } 
    711711          catch (NumberFormatException e) { 
  • trunk/components/bio-formats/src/loci/formats/in/FV1000Reader.java

    r6026 r6055  
    10421042      if (getSizeZ() == 1) pixelSizeZ = 0d; 
    10431043      if (getSizeT() == 1) pixelSizeT = 0d; 
    1044       store.setDimensionsPhysicalSizeZ(new Double(pixelSizeZ), i, 0); 
    1045       store.setDimensionsTimeIncrement(new Double(pixelSizeT), i, 0); 
     1044      store.setDimensionsPhysicalSizeZ(pixelSizeZ, i, 0); 
     1045      store.setDimensionsTimeIncrement(pixelSizeT, i, 0); 
    10461046 
    10471047      // populate LogicalChannel data 
     
    12501250            store.setShapeTheT(tIndex, 0, nextROI, nextShape); 
    12511251 
    1252             store.setShapeFontSize(new Integer(fontSize), 0, nextROI, 
     1252            store.setShapeFontSize(fontSize, 0, nextROI, 
    12531253              nextShape); 
    12541254            store.setShapeFontFamily(fontName, 0, nextROI, nextShape); 
    12551255            store.setShapeText(name, 0, nextROI, nextShape); 
    1256             store.setShapeStrokeWidth(new Integer(lineWidth), 0, nextROI, 
     1256            store.setShapeStrokeWidth(lineWidth, 0, nextROI, 
    12571257              nextShape); 
    12581258            store.setShapeStrokeColor(String.valueOf(color), 0, nextROI, 
  • trunk/components/bio-formats/src/loci/formats/in/FlexReader.java

    r6026 r6055  
    440440    for (int row=0; row<wellRows; row++) { 
    441441      for (int col=0; col<wellColumns; col++) { 
    442         store.setWellRow(new Integer(row), 0, row * wellColumns + col); 
    443         store.setWellColumn(new Integer(col), 0, row * wellColumns + col); 
     442        store.setWellRow(row, 0, row * wellColumns + col); 
     443        store.setWellColumn(col, 0, row * wellColumns + col); 
    444444      } 
    445445    } 
     
    497497      if (wellRows == 0 && wellColumns == 0) { 
    498498        well = pos[1]; 
    499         store.setWellRow(new Integer(wellNumber[pos[1]][0]), pos[2], pos[1]); 
    500         store.setWellColumn(new Integer(wellNumber[pos[1]][1]), pos[2], pos[1]); 
    501       } 
    502  
    503       store.setWellSampleIndex(new Integer(i), pos[2], well, pos[0]); 
     499        store.setWellRow(wellNumber[pos[1]][0], pos[2], pos[1]); 
     500        store.setWellColumn(wellNumber[pos[1]][1], pos[2], pos[1]); 
     501      } 
     502 
     503      store.setWellSampleIndex(i, pos[2], well, pos[0]); 
    504504      store.setWellSampleImageRef(imageID, pos[2], well, pos[0]); 
    505505      if (pos[0] < xPositions.size()) { 
  • trunk/components/bio-formats/src/loci/formats/in/FluoviewReader.java

    r6026 r6055  
    467467 
    468468    // populate Dimensions 
    469     store.setDimensionsPhysicalSizeX(new Double(voxelX), 0, 0); 
    470     store.setDimensionsPhysicalSizeY(new Double(voxelY), 0, 0); 
    471     store.setDimensionsPhysicalSizeZ(new Double(voxelZ), 0, 0); 
    472     store.setDimensionsTimeIncrement(new Double(voxelT), 0, 0); 
     469    store.setDimensionsPhysicalSizeX(voxelX, 0, 0); 
     470    store.setDimensionsPhysicalSizeY(voxelY, 0, 0); 
     471    store.setDimensionsPhysicalSizeZ(voxelZ, 0, 0); 
     472    store.setDimensionsTimeIncrement(voxelT, 0, 0); 
    473473    if ((int) voxelC > 0) { 
    474       store.setDimensionsWaveIncrement(new Integer((int) voxelC), 0, 0); 
     474      store.setDimensionsWaveIncrement((int) voxelC, 0, 0); 
    475475    } 
    476476 
     
    487487    for (int i=0; i<getSizeC(); i++) { 
    488488      // CTR CHECK 
    489 //      store.setDisplayChannel(new Integer(i), null, null, 
    490 //        gamma == null ? null : new Double(gamma.doubleValue()), null); 
     489//      store.setDisplayChannel(i, null, null, gamma, null); 
    491490 
    492491      if (voltages[i] != null) { 
  • trunk/components/bio-formats/src/loci/formats/in/GatanReader.java

    r6026 r6055  
    235235    for (int i=0; i<getSizeC(); i++) { 
    236236      // CTR CHECK 
    237 //      store.setDisplayChannel(new Integer(i), null, null, 
    238 //        new Double(gamma), null); 
     237//      store.setDisplayChannel(i, null, null, gamma, null); 
    239238    } 
    240239 
    241240    // CTR CHECK 
    242     //store.setObjectiveCalibratedMagnification(new Double(mag), 0, 0); 
    243     //store.setDetectorVoltage(new Double(voltage), 0, 0); 
     241    //store.setObjectiveCalibratedMagnification(mag, 0, 0); 
     242    //store.setDetectorVoltage(voltage, 0, 0); 
    244243 
    245244    if (info == null) info = ""; 
  • trunk/components/bio-formats/src/loci/formats/in/HISReader.java

    r6026 r6055  
    238238      store.setImageCreationDate(date[i], i); 
    239239 
    240       store.setPlaneTimingExposureTime(new Double(exposureTime[i]), i, 0, 0); 
     240      store.setPlaneTimingExposureTime(exposureTime[i], i, 0, 0); 
    241241 
    242242      String detectorID = MetadataTools.createLSID("Detector", 0, i); 
    243243      store.setDetectorID(detectorID, 0, i); 
    244       store.setDetectorOffset(new Double(offset[i]), 0, i); 
     244      store.setDetectorOffset(offset[i], 0, i); 
    245245      store.setDetectorType("Unknown", 0, i); 
    246246      store.setDetectorSettingsDetector(detectorID, i, 0); 
  • trunk/components/bio-formats/src/loci/formats/in/ICSReader.java

    r6030 r6055  
    807807        else if (axes[i].equals("ch")) { 
    808808          int c = pixelSizes[i].intValue(); 
    809           if (c > 0) store.setDimensionsWaveIncrement(new Integer(c), 0, 0); 
     809          if (c > 0) store.setDimensionsWaveIncrement(c, 0, 0); 
    810810        } 
    811811      } 
     
    813813    else if (sizes != null) { 
    814814      if (sizes.length > 0) { 
    815         store.setDimensionsPhysicalSizeX(new Double(sizes[0]), 0, 0); 
     815        store.setDimensionsPhysicalSizeX(sizes[0], 0, 0); 
    816816      } 
    817817      if (sizes.length > 1) { 
    818818        sizes[1] /= getSizeY(); 
    819         store.setDimensionsPhysicalSizeY(new Double(sizes[1]), 0, 0); 
     819        store.setDimensionsPhysicalSizeY(sizes[1], 0, 0); 
    820820      } 
    821821    } 
  • trunk/components/bio-formats/src/loci/formats/in/IPLabReader.java

    r6026 r6055  
    259259 
    260260          // CTR CHECK 
    261           //store.setDisplayChannel(new Integer(core[0].sizeC), 
    262           //  new Double(black), new Double(white), new Double(gamma), null); 
     261          //store.setDisplayChannel(core[0].sizeC, black, white, gamma, null); 
    263262        } 
    264263      } 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisHDFReader.java

    r6026 r6055  
    341341      if (py == 1) py = (maxY - minY) / core[i].sizeY; 
    342342      if (pz == 1) pz = (maxZ - minZ) / core[i].sizeZ; 
    343       store.setDimensionsPhysicalSizeX(new Double(px), i, 0); 
    344       store.setDimensionsPhysicalSizeY(new Double(py), i, 0); 
    345       store.setDimensionsPhysicalSizeZ(new Double(pz), i, 0); 
     343      store.setDimensionsPhysicalSizeX(px, i, 0); 
     344      store.setDimensionsPhysicalSizeY(py, i, 0); 
     345      store.setDimensionsPhysicalSizeZ(pz, i, 0); 
    346346    } 
    347347 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisReader.java

    r6026 r6055  
    200200    store.setDimensionsPhysicalSizeY(new Double(dy), 0, 0); 
    201201    store.setDimensionsPhysicalSizeZ(new Double(dz), 0, 0); 
    202     store.setDimensionsTimeIncrement(new Double(1), 0, 0); 
    203     store.setDimensionsWaveIncrement(new Integer(1), 0, 0); 
     202    store.setDimensionsTimeIncrement(1.0, 0, 0); 
     203    store.setDimensionsWaveIncrement(1, 0, 0); 
    204204 
    205205    // populate LogicalChannel data 
  • trunk/components/bio-formats/src/loci/formats/in/ImprovisionTiffReader.java

    r5624 r6055  
    215215    MetadataTools.populatePixels(store, this); 
    216216 
    217     store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), 0, 0); 
    218     store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), 0, 0); 
    219     store.setDimensionsPhysicalSizeZ(new Double(pixelSizeZ), 0, 0); 
    220     store.setDimensionsTimeIncrement(new Double(pixelSizeT / 1000000.0), 0, 0); 
     217    store.setDimensionsPhysicalSizeX(pixelSizeX, 0, 0); 
     218    store.setDimensionsPhysicalSizeY(pixelSizeY, 0, 0); 
     219    store.setDimensionsPhysicalSizeZ(pixelSizeZ, 0, 0); 
     220    store.setDimensionsTimeIncrement(pixelSizeT / 1000000.0, 0, 0); 
    221221  } 
    222222 
  • trunk/components/bio-formats/src/loci/formats/in/InCellReader.java

    r6026 r6055  
    444444    store.setPlateRowNamingConvention(rowName, 0); 
    445445    store.setPlateColumnNamingConvention(colName, 0); 
    446     store.setPlateWellOriginX(new Double(0.5), 0); 
    447     store.setPlateWellOriginY(new Double(0.5), 0); 
     446    store.setPlateWellOriginX(0.5, 0); 
     447    store.setPlateWellOriginY(0.5, 0); 
    448448 
    449449    // populate Well data 
     
    459459 
    460460      String imageID = MetadataTools.createLSID("Image", i); 
    461       store.setWellSampleIndex(new Integer(i), 0, well, sampleIndex); 
     461      store.setWellSampleIndex(i, 0, well, sampleIndex); 
    462462      store.setWellSampleImageRef(imageID, 0, well, sampleIndex); 
    463463      store.setWellSamplePosX(posX.get(field), 0, well, sampleIndex); 
     
    685685      } 
    686686      else if (qName.equals("ObjectiveCalibration")) { 
    687         store.setObjectiveNominalMagnification(new Integer((int) 
    688           Double.parseDouble(attributes.getValue("magnification"))), 0, 0); 
     687        store.setObjectiveNominalMagnification((int) 
     688          Double.parseDouble(attributes.getValue("magnification")), 0, 0); 
    689689        store.setObjectiveLensNA(new Double( 
    690690          attributes.getValue("numerical_aperture")), 0, 0); 
     
    766766        for (int r=0; r<wellRows; r++) { 
    767767          for (int c=0; c<wellCols; c++) { 
    768             store.setWellRow(new Integer(r), nextPlate, r*wellCols + c); 
    769             store.setWellColumn(new Integer(c), nextPlate, r*wellCols + c); 
     768            store.setWellRow(r, nextPlate, r*wellCols + c); 
     769            store.setWellColumn(c, nextPlate, r*wellCols + c); 
    770770          } 
    771771        } 
  • trunk/components/bio-formats/src/loci/formats/in/IvisionReader.java

    • Property svn:executable deleted
  • trunk/components/bio-formats/src/loci/formats/in/JPEG2000Reader.java

    • Property svn:executable deleted
  • trunk/components/bio-formats/src/loci/formats/in/LEOReader.java

    r6026 r6055  
    115115      new FilterMetadata(getMetadataStore(), isMetadataFiltered()); 
    116116 
    117     store.setDimensionsPhysicalSizeX(new Double(xSize), 0, 0); 
    118     store.setDimensionsPhysicalSizeY(new Double(xSize), 0, 0); 
     117    store.setDimensionsPhysicalSizeX(xSize, 0, 0); 
     118    store.setDimensionsPhysicalSizeY(xSize, 0, 0); 
    119119 
    120     store.setObjectiveWorkingDistance(new Double(workingDistance), 0, 0); 
     120    store.setObjectiveWorkingDistance(workingDistance, 0, 0); 
    121121 
    122122    date = DateTools.formatDate(date, "HH:mm dd-MMM-yyyy"); 
  • trunk/components/bio-formats/src/loci/formats/in/LeicaHandler.java

    r6009 r6055  
    449449      else if (id.equals("dblStepSize")) { 
    450450        double zStep = Double.parseDouble(value) * 1000000; 
    451         store.setDimensionsPhysicalSizeZ(new Double(zStep), numDatasets, 0); 
     451        store.setDimensionsPhysicalSizeZ(zStep, numDatasets, 0); 
    452452      } 
    453453      else if (id.equals("nDelayTime_s")) { 
     
    667667            MetadataTools.createLSID("Filter", numDatasets, nextFilter); 
    668668          store.setFilterID(filter, numDatasets, nextFilter); 
    669           store.setTransmittanceRangeCutIn(new Integer(m.cutIn), numDatasets, 
    670             nextFilter); 
    671           store.setTransmittanceRangeCutOut(new Integer(m.cutOut), numDatasets, 
    672             nextFilter); 
     669          store.setTransmittanceRangeCutIn(m.cutIn, numDatasets, nextFilter); 
     670          store.setTransmittanceRangeCutOut(m.cutOut, numDatasets, nextFilter); 
    673671          store.setLogicalChannelSecondaryEmissionFilter(filter, numDatasets, 
    674672            nextChannel); 
     
    742740        } 
    743741        firstStamp = ms; 
    744         store.setPlaneTimingDeltaT(new Double(0), numDatasets, 0, count); 
     742        store.setPlaneTimingDeltaT(0.0, numDatasets, 0, count); 
    745743      } 
    746744      else { 
     
    749747        if (count < nImages) { 
    750748          ms -= firstStamp; 
    751           store.setPlaneTimingDeltaT( 
    752             new Double(ms / 1000.0), numDatasets, 0, count); 
     749          store.setPlaneTimingDeltaT(ms / 1000.0, numDatasets, 0, count); 
    753750        } 
    754751      } 
     
    871868      if (fontName != null) store.setShapeFontFamily(fontName, series, roi, 0); 
    872869      if (fontSize != null) { 
    873         store.setShapeFontSize( 
    874           new Integer((int) Double.parseDouble(fontSize)), series, roi, 0); 
     870        store.setShapeFontSize((int) Double.parseDouble(fontSize), 
     871          series, roi, 0); 
    875872      } 
    876873      store.setShapeStrokeColor(String.valueOf(color), series, roi, 0); 
    877       store.setShapeStrokeWidth(new Integer(linewidth), series, roi, 0); 
     874      store.setShapeStrokeWidth(linewidth, series, roi, 0); 
    878875 
    879876      if (!normalized) normalize(); 
     
    950947        double coordinate = x.get(i).doubleValue() * 1000000; 
    951948        coordinate *= (1 / physicalSizeX); 
    952         x.setElementAt(new Double(coordinate), i); 
     949        x.setElementAt(coordinate, i); 
    953950      } 
    954951 
     
    956953        double coordinate = y.get(i).doubleValue() * 1000000; 
    957954        coordinate *= (1 / physicalSizeY); 
    958         y.setElementAt(new Double(coordinate), i); 
     955        y.setElementAt(coordinate, i); 
    959956      } 
    960957 
  • trunk/components/bio-formats/src/loci/formats/in/LeicaReader.java

    r6036 r6055  
    977977      store.setImageInstrumentRef(instrumentID, i); 
    978978 
    979       store.setDimensionsPhysicalSizeX(new Double(physicalSizes[i][0]), i, 0); 
    980       store.setDimensionsPhysicalSizeY(new Double(physicalSizes[i][1]), i, 0); 
    981       store.setDimensionsPhysicalSizeZ(new Double(physicalSizes[i][2]), i, 0); 
     979      store.setDimensionsPhysicalSizeX(physicalSizes[i][0], i, 0); 
     980      store.setDimensionsPhysicalSizeY(physicalSizes[i][1], i, 0); 
     981      store.setDimensionsPhysicalSizeZ(physicalSizes[i][2], i, 0); 
    982982      if ((int) physicalSizes[i][3] > 0) { 
    983         store.setDimensionsWaveIncrement( 
    984           new Integer((int) physicalSizes[i][3]), i, 0); 
     983        store.setDimensionsWaveIncrement((int) physicalSizes[i][3], i, 0); 
    985984      } 
    986985      if ((int) physicalSizes[i][4] > 0) { 
    987         store.setDimensionsTimeIncrement(new Double(physicalSizes[i][4]), i, 0); 
     986        store.setDimensionsTimeIncrement(physicalSizes[i][4], i, 0); 
    988987      } 
    989988 
     
    992991          long time = DateTools.getTime(timestamps[i][j], DATE_FORMAT); 
    993992          double elapsedTime = (double) (time - firstPlane) / 1000; 
    994           store.setPlaneTimingDeltaT(new Double(elapsedTime), i, 0, j); 
    995           store.setPlaneTimingExposureTime( 
    996             new Double(exposureTime[i]), i, 0, j); 
     993          store.setPlaneTimingDeltaT(elapsedTime, i, 0, j); 
     994          store.setPlaneTimingExposureTime(exposureTime[i], i, 0, j); 
    997995        } 
    998996      } 
     
    11401138          store.setObjectiveModel(model.toString().trim(), series, objective); 
    11411139          store.setObjectiveLensNA(new Double(na), series, objective); 
    1142           store.setObjectiveNominalMagnification( 
    1143             new Integer((int) Double.parseDouble(mag)), series, objective); 
     1140          store.setObjectiveNominalMagnification((int) 
     1141            Double.parseDouble(mag), series, objective); 
    11441142        } 
    11451143        else if (tokens[2].equals("OrderNumber")) { 
     
    12181216        double pos = Double.parseDouble(data) * 1000000; 
    12191217        for (int q=0; q<core[series].imageCount; q++) { 
    1220           store.setStagePositionPositionZ(new Double(pos), series, 0, q); 
     1218          store.setStagePositionPositionZ(pos, series, 0, q); 
    12211219        } 
    12221220      } 
  • trunk/components/bio-formats/src/loci/formats/in/MIASReader.java

    r6026 r6055  
    682682        int wellCol = (wellIndex % wellColumns) + 1; 
    683683 
    684         store.setWellRow(new Integer(row), 0, well); 
    685         store.setWellColumn(new Integer(wellCol - 1), 0, well); 
     684        store.setWellRow(row, 0, well); 
     685        store.setWellColumn(wellCol - 1, 0, well); 
    686686 
    687687        String imageID = MetadataTools.createLSID("Image", well); 
    688688        store.setWellSampleImageRef(imageID, 0, well, 0); 
    689         store.setWellSampleIndex(new Integer(well), 0, well, 0); 
     689        store.setWellSampleIndex(well, 0, well, 0); 
    690690 
    691691        // populate Image/Pixels metadata 
     
    909909        else if (key.equals("Magnification")) { 
    910910          int mag = (int) Double.parseDouble(value); 
    911           store.setObjectiveNominalMagnification(new Integer(mag), 0, 0); 
     911          store.setObjectiveNominalMagnification(mag, 0, 0); 
    912912        } 
    913913        else if (key.startsWith("Mode_")) { 
  • trunk/components/bio-formats/src/loci/formats/in/MRCReader.java

    r6044 r6055  
    234234    double z = (zlen / mz) == Double.POSITIVE_INFINITY ? 1 : (zlen / mz); 
    235235 
    236     store.setDimensionsPhysicalSizeX(new Double(x), 0, 0); 
    237     store.setDimensionsPhysicalSizeY(new Double(y), 0, 0); 
    238     store.setDimensionsPhysicalSizeZ(new Double(z), 0, 0); 
     236    store.setDimensionsPhysicalSizeX(x, 0, 0); 
     237    store.setDimensionsPhysicalSizeY(y, 0, 0); 
     238    store.setDimensionsPhysicalSizeZ(z, 0, 0); 
    239239  } 
    240240 
  • trunk/components/bio-formats/src/loci/formats/in/MetamorphReader.java

    r6026 r6055  
    595595        stepSize = zDistances[0]; 
    596596      } 
    597       store.setDimensionsPhysicalSizeZ(new Double(stepSize), i, 0); 
     597      store.setDimensionsPhysicalSizeZ(stepSize, i, 0); 
    598598 
    599599      int waveIndex = 0; 
     
    716716 
    717717        if (stageX != null && p < stageX.length) { 
    718           store.setStagePositionPositionX(new Double(stageX[p]), i, 0, p); 
     718          store.setStagePositionPositionX(stageX[p], i, 0, p); 
    719719        } 
    720720        if (stageY != null && p < stageY.length) { 
    721           store.setStagePositionPositionY(new Double(stageY[p]), i, 0, p); 
     721          store.setStagePositionPositionY(stageY[p], i, 0, p); 
    722722        } 
    723723        if (p < zDistances.length) { 
    724724          if (zDistances[p] != 0d) distance += zDistances[p]; 
    725725          else distance += zDistances[0]; 
    726           store.setStagePositionPositionZ(new Double(distance), i, 0, p); 
     726          store.setStagePositionPositionZ(distance, i, 0, p); 
    727727        } 
    728728      } 
     
    731731 
    732732    store.setDetectorID(detectorID, 0, 0); 
    733     store.setDetectorZoom(new Double(zoom), 0, 0); 
     733    store.setDetectorZoom(zoom, 0, 0); 
    734734    if (handler != null && handler.getZoom() != 0) { 
    735       store.setDetectorZoom(new Double(handler.getZoom()), 0, 0); 
     735      store.setDetectorZoom(handler.getZoom(), 0, 0); 
    736736    } 
    737737    store.setDetectorType("Unknown", 0, 0); 
  • trunk/components/bio-formats/src/loci/formats/in/MetamorphTiffReader.java

    r6026 r6055  
    139139        String stamp = timestamps.get(coords[2]); 
    140140        long ms = DateTools.getTime(stamp, parse); 
    141         store.setPlaneTimingDeltaT(new Double((ms - startDate) / 1000.0), 
    142           0, 0, i); 
     141        store.setPlaneTimingDeltaT((ms - startDate) / 1000.0, 0, 0, i); 
    143142      } 
    144143      if (i < exposures.size()) { 
     
    152151 
    153152    store.setImagingEnvironmentTemperature( 
    154       new Double(handler.getTemperature()), 0); 
    155     store.setDimensionsPhysicalSizeX(new Double(handler.getPixelSizeX()), 0, 0); 
    156     store.setDimensionsPhysicalSizeY(new Double(handler.getPixelSizeY()), 0, 0); 
     153      handler.getTemperature(), 0); 
     154    store.setDimensionsPhysicalSizeX(handler.getPixelSizeX(), 0, 0); 
     155    store.setDimensionsPhysicalSizeY(handler.getPixelSizeY(), 0, 0); 
    157156  } 
    158157} 
  • trunk/components/bio-formats/src/loci/formats/in/MicromanagerReader.java

    r6026 r6055  
    496496    store.setDetectorType(cameraMode, 0, 0); 
    497497 
    498     store.setImagingEnvironmentTemperature(new Double(temperature), 0); 
     498    store.setImagingEnvironmentTemperature(temperature, 0); 
    499499  } 
    500500 
  • trunk/components/bio-formats/src/loci/formats/in/NativeND2Reader.java

    r6026 r6055  
    929929    // populate Dimensions data 
    930930    for (int i=0; i<getSeriesCount(); i++) { 
    931       store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), i, 0); 
    932       store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), i, 0); 
    933       store.setDimensionsPhysicalSizeZ(new Double(pixelSizeZ), i, 0); 
     931      store.setDimensionsPhysicalSizeX(pixelSizeX, i, 0); 
     932      store.setDimensionsPhysicalSizeY(pixelSizeY, i, 0); 
     933      store.setDimensionsPhysicalSizeZ(pixelSizeZ, i, 0); 
    934934    } 
    935935 
     
    943943          if (tsT.size() == getImageCount()) stampIndex = n; 
    944944          double stamp = tsT.get(stampIndex).doubleValue(); 
    945           store.setPlaneTimingDeltaT(new Double(stamp), i, 0, n); 
     945          store.setPlaneTimingDeltaT(stamp, i, 0, n); 
    946946 
    947947          int index = i * getSizeC() + coords[1]; 
  • trunk/components/bio-formats/src/loci/formats/in/NikonTiffReader.java

    r5668 r6055  
    211211    store.setImageDescription("", 0); 
    212212 
    213     store.setDimensionsPhysicalSizeX(new Double(physicalSizeX), 0, 0); 
    214     store.setDimensionsPhysicalSizeY(new Double(physicalSizeY), 0, 0); 
    215     store.setDimensionsPhysicalSizeZ(new Double(physicalSizeZ), 0, 0); 
     213    store.setDimensionsPhysicalSizeX(physicalSizeX, 0, 0); 
     214    store.setDimensionsPhysicalSizeY(physicalSizeY, 0, 0); 
     215    store.setDimensionsPhysicalSizeZ(physicalSizeZ, 0, 0); 
    216216 
    217217    String instrumentID = MetadataTools.createLSID("Instrument", 0); 
     
    222222    store.setObjectiveID(objectiveID, 0, 0); 
    223223    store.setObjectiveSettingsObjective(objectiveID, 0); 
    224     store.setObjectiveNominalMagnification(new Integer(magnification), 0, 0); 
     224    store.setObjectiveNominalMagnification(magnification, 0, 0); 
    225225 
    226226    if (correction == null) correction = "Unknown"; 
    227227    store.setObjectiveCorrection(correction, 0, 0); 
    228     store.setObjectiveLensNA(new Double(lensNA), 0, 0); 
    229     store.setObjectiveWorkingDistance(new Double(workingDistance), 0, 0); 
     228    store.setObjectiveLensNA(lensNA, 0, 0); 
     229    store.setObjectiveWorkingDistance(workingDistance, 0, 0); 
    230230    if (immersion == null) immersion = "Unknown"; 
    231231    store.setObjectiveImmersion(immersion, 0, 0); 
     
    246246 
    247247    for (int c=0; c<getEffectiveSizeC(); c++) { 
    248       store.setLogicalChannelPinholeSize(new Double(pinholeSize), 0, c); 
     248      store.setLogicalChannelPinholeSize(pinholeSize, 0, c); 
    249249      if (c < exWave.size()) { 
    250250        store.setLogicalChannelExWave(exWave.get(c), 0, c); 
  • trunk/components/bio-formats/src/loci/formats/in/OxfordInstrumentsReader.java

    r6026 r6055  
    183183    store.setImageDescription(comment, 0); 
    184184    store.setImageCreationDate(dateTime.toString(), 0); 
    185     store.setDimensionsPhysicalSizeX(new Double(xSize / getSizeX()), 0, 0); 
    186     store.setDimensionsPhysicalSizeY(new Double(ySize / getSizeY()), 0, 0); 
     185    store.setDimensionsPhysicalSizeX(xSize / getSizeX(), 0, 0); 
     186    store.setDimensionsPhysicalSizeY(ySize / getSizeY(), 0, 0); 
    187187  } 
    188188 
  • trunk/components/bio-formats/src/loci/formats/in/PCIReader.java

    r6026 r6055  
    287287    } 
    288288    else MetadataTools.setDefaultCreationDate(store, id, 0); 
    289     store.setDimensionsPhysicalSizeX(new Double(scaleFactor), 0, 0); 
    290     store.setDimensionsPhysicalSizeY(new Double(scaleFactor), 0, 0); 
     289    store.setDimensionsPhysicalSizeX(scaleFactor, 0, 0); 
     290    store.setDimensionsPhysicalSizeY(scaleFactor, 0, 0); 
    291291 
    292292    for (int i=0; i<timestamps.size(); i++) { 
  • trunk/components/bio-formats/src/loci/formats/in/PerkinElmerReader.java

    r6026 r6055  
    681681 
    682682    // populate Dimensions element 
    683     store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), 0, 0); 
    684     store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), 0, 0); 
     683    store.setDimensionsPhysicalSizeX(pixelSizeX, 0, 0); 
     684    store.setDimensionsPhysicalSizeY(pixelSizeY, 0, 0); 
    685685 
    686686    // populate Image element 
     
    720720    for (int i=0; i<getImageCount(); i++) { 
    721721      int[] zct = getZCTCoords(i); 
    722       store.setPlaneTimingDeltaT(new Double(i * secondsPerPlane), 0, 0, i); 
     722      store.setPlaneTimingDeltaT(i * secondsPerPlane, 0, 0, i); 
    723723      if (zct[1] < exposureTimes.size()) { 
    724724        store.setPlaneTimingExposureTime(exposureTimes.get(zct[1]), 0, 0, i); 
     
    726726 
    727727      if (zct[0] < zPositions.size()) { 
    728         store.setStagePositionPositionX(new Double(0.0), 0, 0, i); 
    729         store.setStagePositionPositionY(new Double(0.0), 0, 0, i); 
     728        store.setStagePositionPositionX(0.0, 0, 0, i); 
     729        store.setStagePositionPositionY(0.0, 0, 0, i); 
    730730        store.setStagePositionPositionZ(zPositions.get(zct[0]), 0, 0, i); 
    731731      } 
  • trunk/components/bio-formats/src/loci/formats/in/PrairieReader.java

    r6026 r6055  
    285285        store.setImageInstrumentRef(instrumentID, 0); 
    286286 
    287         store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), 0, 0); 
    288         store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), 0, 0); 
     287        store.setDimensionsPhysicalSizeX(pixelSizeX, 0, 0); 
     288        store.setDimensionsPhysicalSizeY(pixelSizeY, 0, 0); 
    289289        for (int i=0; i<getSizeC(); i++) { 
    290290          String gain = i < gains.size() ? gains.get(i) : null; 
  • trunk/components/bio-formats/src/loci/formats/in/QuesantReader.java

    r6026 r6055  
    168168    else MetadataTools.setDefaultCreationDate(store, id, 0); 
    169169    store.setImageDescription(comment, 0); 
    170     store.setDimensionsPhysicalSizeX(new Double(xSize / getSizeX()), 0, 0); 
    171     store.setDimensionsPhysicalSizeY(new Double(xSize / getSizeY()), 0, 0); 
     170    store.setDimensionsPhysicalSizeX((double) xSize / getSizeX(), 0, 0); 
     171    store.setDimensionsPhysicalSizeY((double) xSize / getSizeY(), 0, 0); 
    172172  } 
    173173 
  • trunk/components/bio-formats/src/loci/formats/in/ScanrReader.java

    r6026 r6055  
    426426      int wellCol = well % wellColumns; 
    427427 
    428       store.setWellColumn(new Integer(wellCol), 0, well); 
    429       store.setWellRow(new Integer(wellRow), 0, well); 
    430  
    431       store.setWellSampleIndex(new Integer(i), 0, well, field); 
     428      store.setWellColumn(wellCol, 0, well); 
     429      store.setWellRow(wellRow, 0, well); 
     430 
     431      store.setWellSampleIndex(i, 0, well, field); 
    432432      String imageID = MetadataTools.createLSID("Image", i); 
    433433      store.setWellSampleImageRef(imageID, 0, well, field); 
  • trunk/components/bio-formats/src/loci/formats/in/SeikoReader.java

    r6026 r6055  
    109109 
    110110    store.setImageDescription(comment, 0); 
    111     store.setDimensionsPhysicalSizeX(new Double(xSize), 0, 0); 
    112     store.setDimensionsPhysicalSizeY(new Double(ySize), 0, 0); 
     111    store.setDimensionsPhysicalSizeX(xSize, 0, 0); 
     112    store.setDimensionsPhysicalSizeY(ySize, 0, 0); 
    113113  } 
    114114 
  • trunk/components/bio-formats/src/loci/formats/in/TCSReader.java

    r6026 r6055  
    449449    } 
    450450 
    451     store.setDimensionsPhysicalSizeX(new Double(voxelX), 0, 0); 
    452     store.setDimensionsPhysicalSizeY(new Double(voxelY), 0, 0); 
    453     store.setDimensionsPhysicalSizeZ(new Double(voxelZ), 0, 0); 
     451    store.setDimensionsPhysicalSizeX(voxelX, 0, 0); 
     452    store.setDimensionsPhysicalSizeY(voxelY, 0, 0); 
     453    store.setDimensionsPhysicalSizeZ(voxelZ, 0, 0); 
    454454  } 
    455455 
  • trunk/components/bio-formats/src/loci/formats/in/TillVisionReader.java

    r6026 r6055  
    426426        int waveIncrement = Integer.parseInt(waves.get(i)); 
    427427        if (waveIncrement > 0) { 
    428           store.setDimensionsWaveIncrement(new Integer(waveIncrement), i, 0); 
     428          store.setDimensionsWaveIncrement(waveIncrement, i, 0); 
    429429        } 
    430430      } 
  • trunk/components/bio-formats/src/loci/formats/in/TopometrixReader.java

    r6026 r6055  
    176176    MetadataTools.populatePixels(store, this); 
    177177 
    178     store.setDimensionsPhysicalSizeX(new Double(xSize / getSizeX()), 0, 0); 
    179     store.setDimensionsPhysicalSizeY(new Double(ySize / getSizeY()), 0, 0); 
     178    store.setDimensionsPhysicalSizeX((double) xSize / getSizeX(), 0, 0); 
     179    store.setDimensionsPhysicalSizeY((double) ySize / getSizeY(), 0, 0); 
    180180    store.setImageDescription(comment, 0); 
    181181    store.setImageCreationDate(DateTools.formatDate(date, 
  • trunk/components/bio-formats/src/loci/formats/in/UnisokuReader.java

    r6026 r6055  
    203203    store.setImageDescription(remark, 0); 
    204204    store.setImageCreationDate(date, 0); 
    205     store.setDimensionsPhysicalSizeX(new Double(pixelSizeX), 0, 0); 
    206     store.setDimensionsPhysicalSizeY(new Double(pixelSizeY), 0, 0); 
     205    store.setDimensionsPhysicalSizeX(pixelSizeX, 0, 0); 
     206    store.setDimensionsPhysicalSizeY(pixelSizeY, 0, 0); 
    207207  } 
    208208 
  • trunk/components/bio-formats/src/loci/formats/in/WATOPReader.java

    r6026 r6055  
    143143    store.setImageDescription(comment, 0); 
    144144    store.setImageCreationDate(date, 0); 
    145     store.setDimensionsPhysicalSizeX(new Double(xSize / getSizeX()), 0, 0); 
    146     store.setDimensionsPhysicalSizeY(new Double(ySize / getSizeY()), 0, 0); 
     145    store.setDimensionsPhysicalSizeX((double) xSize / getSizeX(), 0, 0); 
     146    store.setDimensionsPhysicalSizeY((double) ySize / getSizeY(), 0, 0); 
    147147  } 
    148148 
  • trunk/components/bio-formats/src/loci/formats/in/ZeissLSMReader.java

    r6026 r6055  
    412412 
    413413      initMetadata(series); 
    414       store.setPixelsBigEndian(new Boolean(!isLittleEndian()), series, 0); 
     414      store.setPixelsBigEndian(!isLittleEndian(), series, 0); 
    415415    } 
    416416    for (int series=0; series<ifdsList.size(); series++) { 
     
    863863      if (zct[2] < timestamps.size()) { 
    864864        double thisStamp = timestamps.get(zct[2]).doubleValue(); 
    865         store.setPlaneTimingDeltaT(new Double(thisStamp - firstStamp), 
    866           series, 0, i); 
     865        store.setPlaneTimingDeltaT(thisStamp - firstStamp, series, 0, i); 
    867866        int index = zct[2] + 1; 
    868867        double nextStamp = index < timestamps.size() ? 
     
    871870          thisStamp = timestamps.get(zct[2] - 1).doubleValue(); 
    872871        } 
    873         store.setPlaneTimingExposureTime(new Double(nextStamp - thisStamp), 
    874           series, 0, i); 
     872        store.setPlaneTimingExposureTime(nextStamp - thisStamp, series, 0, i); 
    875873      } 
    876874    } 
     
    987985      } 
    988986      store.setDetectorType("PMT", series, nextDetector); 
    989       store.setDetectorZoom(new Double(zoom), series, nextDetector); 
     987      store.setDetectorZoom(zoom, series, nextDetector); 
    990988      nextDetectChannel++; 
    991989      nextDetector++; 
     
    12801278 
    12811279      store.setShapeFontFamily(fontName, series, i, 0); 
    1282       store.setShapeFontSize(new Integer(fontHeight), series, i, 0); 
     1280      store.setShapeFontSize(fontHeight, series, i, 0); 
    12831281      store.setShapeFontStyle(fontItalic ? "normal" : "italic", series, i, 0); 
    12841282      store.setShapeFontWeight(String.valueOf(fontWeight), series, i, 0); 
    1285       store.setShapeLocked(new Boolean(moveable), series, i, 0); 
     1283      store.setShapeLocked(moveable, series, i, 0); 
    12861284      store.setShapeStrokeColor(String.valueOf(color), series, i, 0); 
    1287       store.setShapeStrokeWidth(new Integer(lineWidth), series, i, 0); 
     1285      store.setShapeStrokeWidth(lineWidth, series, i, 0); 
    12881286      store.setShapeTextDecoration(fontUnderlined ? "underline" : 
    12891287        fontStrikeout ? "line-through" : "normal", series, i, 0); 
    1290       store.setShapeVisibility(new Boolean(enabled), series, i, 0); 
     1288      store.setShapeVisibility(enabled, series, i, 0); 
    12911289 
    12921290      in.seek(offset + blockLength); 
     
    16521650      } 
    16531651 
    1654       zoom = (Double) getDoubleValue(RECORDING_ZOOM); 
     1652      zoom = getDoubleValue(RECORDING_ZOOM); 
    16551653 
    16561654      String objective = getStringValue(RECORDING_OBJECTIVE); 
  • trunk/components/bio-formats/src/loci/formats/in/ZeissZVIReader.java

    r6037 r6055  
    725725      } 
    726726 
    727       store.setStagePositionPositionX(new Double(stageX), 0, 0, plane); 
    728       store.setStagePositionPositionY(new Double(stageY), 0, 0, plane); 
     727      store.setStagePositionPositionX(stageX, 0, 0, plane); 
     728      store.setStagePositionPositionY(stageY, 0, 0, plane); 
    729729    } 
    730730 
     
    949949        else if (key.startsWith("Objective Magnification")) { 
    950950          double mag = Double.parseDouble(value); 
    951           store.setObjectiveNominalMagnification(new Integer((int) mag), 0, 0); 
     951          store.setObjectiveNominalMagnification((int) mag, 0, 0); 
    952952        } 
    953953        else if (key.startsWith("Objective ID")) { 
     
    967967                Double.parseDouble(tokens[q].substring(0, slash - q)); 
    968968              String na = tokens[q].substring(slash + 1); 
    969               store.setObjectiveNominalMagnification(new Integer(mag), 0, 0); 
     969              store.setObjectiveNominalMagnification(mag, 0, 0); 
    970970              store.setObjectiveLensNA(new Double(na), 0, 0); 
    971971              store.setObjectiveCorrection(tokens[q - 1], 0, 0); 
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