Changeset 2970 for trunk


Ignore:
Timestamp:
07/13/07 10:01:57 (13 years ago)
Author:
melissa
Message:
  • Added missing setLogicalChannel calls.
  • Added new metadata categories to ICS reader.
Location:
trunk/loci/formats/in
Files:
8 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/in/FitsReader.java

    r2922 r2970  
    154154      new Integer(core.sizeT[0]), new Integer(core.pixelType[0]), 
    155155      new Boolean(!core.littleEndian[0]), core.currentOrder[0], null, null); 
     156   
     157    store.setLogicalChannel(0, null, null, null, null,  
     158      "monochrome", null, null); 
    156159  } 
    157160 
  • trunk/loci/formats/in/ICSReader.java

    r2922 r2970  
    4646  private static final String[] CATEGORIES = new String[] { 
    4747    "ics_version", "filename", "source", "layout", "representation", 
    48     "parameter", "sensor", "history", "end" 
     48    "parameter", "sensor", "history", "document", "view", "end" 
    4949  }; 
    5050 
     
    5454    "significant_bits", "format", "sign", "compression", "byte_order", 
    5555    "origin", "scale", "units", "labels", "SCIL_TYPE", "type", "model", 
    56     "s_params" 
     56    "s_params", "laser", "gain1", "gain2", "gain3", "gain4", "dwell", 
     57    "shutter1", "shutter2", "shutter3", "pinhole", "laser1", "laser2", 
     58    "laser3", "objective", "PassCount", "step1", "step2", "step3", "view", 
     59    "view1", "date", "GMTdate", "label" 
    5760  }; 
    5861 
     
    6063  private static final String[] SUB_SUB_CATEGORIES = new String[] { 
    6164    "Channels", "PinholeRadius", "LambdaEx", "LambdaEm", "ExPhotonCnt", 
    62     "RefInxMedium", "NumAperture", "RefInxLensMedium", "PinholeSpacing" 
     65    "RefInxMedium", "NumAperture", "RefInxLensMedium", "PinholeSpacing", 
     66    "power", "wavelength", "name", "Type", "Magnification", "NA", 
     67    "WorkingDistance", "Immersion", "Pinhole", "Channel 1", "Channel 2", 
     68    "Channel 3", "Channel 4", "Gain 1", "Gain 2", "Gain 3", "Gain 4", 
     69    "Shutter 1", "Shutter 2", "Shutter 3", "Position", "Size", "Port", 
     70    "Cursor", "Color", "BlackLevel", "Saturation", "Gamma", "IntZoom", 
     71    "Live", "Synchronize", "ShowIndex", "AutoResize", "UseUnits", "Zoom", 
     72    "IgnoreAspect", "ShowCursor", "ShowAll", "Axis", "Order", "Tile", "scale", 
     73    "DimViewOption" 
    6374  }; 
    6475 
  • trunk/loci/formats/in/ImprovisionTiffReader.java

    r2937 r2970  
    186186    store.setDimensions(new Float(fx), new Float(fy), new Float(fz), 
    187187      null, new Float(pixelSizeT / 1000000.0), null); 
    188   
    189     for (int i=0; i<core.sizeC[0]; i++) { 
    190       store.setLogicalChannel(i, cNames[i], null, null, null, null, null, null); 
    191     } 
    192188  } 
    193189 
  • trunk/loci/formats/in/KhorosReader.java

    r2922 r2970  
    199199      new Boolean(core.littleEndian[0]), core.currentOrder[0], null, null); 
    200200   
     201    for (int i=0; i<core.sizeC[0]; i++) { 
     202      store.setLogicalChannel(i, null, null, null, null, 
     203        core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null); 
     204    } 
    201205  } 
    202206 
  • trunk/loci/formats/in/NRRDReader.java

    r2922 r2970  
    236236      new Integer(core.sizeT[0]), new Integer(core.pixelType[0]), 
    237237      new Boolean(core.littleEndian[0]), core.currentOrder[0], null, null); 
     238   
     239    for (int i=0; i<core.sizeC[0]; i++) { 
     240      store.setLogicalChannel(i, null, null, null, null, 
     241        core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null); 
     242    } 
    238243  } 
    239244 
  • trunk/loci/formats/in/PGMReader.java

    r2922 r2970  
    157157      new Integer(core.sizeT[0]), new Integer(core.pixelType[0]), 
    158158      new Boolean(!core.littleEndian[0]), core.currentOrder[0], null, null); 
     159     
     160    for (int i=0; i<core.sizeC[0]; i++) { 
     161      store.setLogicalChannel(i, null, null, null, null, 
     162        core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null); 
     163    } 
    159164  } 
    160165 
  • trunk/loci/formats/in/SlidebookReader.java

    r2922 r2970  
    304304      core.imageCount[i] = core.sizeC[i] * core.sizeZ[i] * core.sizeT[i];  
    305305    }  
     306   
     307    MetadataStore store = getMetadataStore();   
     308 
     309    for (int i=0; i<core.sizeX.length; i++) {  
     310      store.setPixels(new Integer(core.sizeX[i]), new Integer(core.sizeY[i]), 
     311        new Integer(core.sizeZ[i]), new Integer(core.sizeC[i]), 
     312        new Integer(core.sizeT[i]), new Integer(core.pixelType[i]), 
     313        new Boolean(!core.littleEndian[i]), core.currentOrder[i], 
     314        new Integer(i), null); 
     315 
     316      for (int j=0; j<core.sizeC[i]; j++) { 
     317        store.setLogicalChannel(j, null, null, null, null, 
     318          core.sizeC[i] == 1 ? "monochrome" : "RGB", null, new Integer(i)); 
     319      } 
     320    }  
    306321  } 
    307322 
  • trunk/loci/formats/in/VisitechReader.java

    r2925 r2970  
    194194   
    195195    files.add(currentId);  
     196   
     197    MetadataStore store = getMetadataStore(); 
     198    store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]), 
     199      new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]), 
     200      new Integer(core.sizeT[0]), new Integer(core.pixelType[0]), 
     201      new Boolean(!core.littleEndian[0]), core.currentOrder[0], null, null); 
     202 
     203    for (int i=0; i<core.sizeC[0]; i++) { 
     204      store.setLogicalChannel(i, null, null, null, null, 
     205        core.sizeC[0] == 1 ? "monochrome" : "RGB", null, null); 
     206    } 
     207   
    196208  } 
    197209 
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