Changeset 6458


Ignore:
Timestamp:
06/03/10 12:11:21 (9 years ago)
Author:
melissa
Message:

Moved ome.xml.r201004.* to ome.xml.model.* in trunk.

Location:
trunk/components
Files:
146 added
1 deleted
52 edited
8 copied

Legend:

Unmodified
Added
Removed
  • trunk/components/autogen/src/entities.txt

    r6266 r6458  
    10021002 
    10031003[PixelsBinData] 
     1004countable = true 
    10041005path = Image+/Pixels/BinData+ 
    10051006 
     
    15181519type = String 
    15191520 
     1521[UUID Value] 
     1522type = String 
     1523 
    15201524[Well] 
    15211525countable = true 
  • trunk/components/autogen/src/meta/AggregateMetadata.vm

    r6230 r6458  
    3535import java.util.List; 
    3636 
    37 import ome.xml.r201004.enums.*; 
    38 import ome.xml.r201004.primitives.*; 
     37import ome.xml.model.enums.*; 
     38import ome.xml.model.primitives.*; 
    3939 
    4040/** 
  • trunk/components/autogen/src/meta/DummyMetadata.vm

    r6230 r6458  
    3232package loci.formats.meta; 
    3333 
    34 import ome.xml.r201004.enums.*; 
    35 import ome.xml.r201004.primitives.*; 
     34import ome.xml.model.enums.*; 
     35import ome.xml.model.primitives.*; 
    3636 
    3737/** 
  • trunk/components/autogen/src/meta/FilterMetadata.vm

    r6266 r6458  
    3434import loci.common.DataTools; 
    3535 
    36 import ome.xml.r201004.enums.*; 
    37 import ome.xml.r201004.primitives.*; 
     36import ome.xml.model.enums.*; 
     37import ome.xml.model.primitives.*; 
    3838 
    3939/** 
  • trunk/components/autogen/src/meta/MetadataConverter.vm

    r6230 r6458  
    3232package loci.formats.meta; 
    3333 
    34 import ome.xml.r201004.enums.*; 
    35 import ome.xml.r201004.primitives.*; 
     34import ome.xml.model.enums.*; 
     35import ome.xml.model.primitives.*; 
    3636 
    3737/** 
  • trunk/components/bio-formats/src/loci/formats/FormatReader.java

    r6371 r6458  
    4545import loci.formats.services.OMEXMLService; 
    4646 
    47 import ome.xml.r201004.enums.AcquisitionMode; 
    48 import ome.xml.r201004.enums.ArcType; 
    49 import ome.xml.r201004.enums.Binning; 
    50 import ome.xml.r201004.enums.Compression; 
    51 import ome.xml.r201004.enums.ContrastMethod; 
    52 import ome.xml.r201004.enums.Correction; 
    53 import ome.xml.r201004.enums.DetectorType; 
    54 import ome.xml.r201004.enums.DimensionOrder; 
    55 import ome.xml.r201004.enums.EnumerationException; 
    56 import ome.xml.r201004.enums.ExperimentType; 
    57 import ome.xml.r201004.enums.FilamentType; 
    58 import ome.xml.r201004.enums.FillRule; 
    59 import ome.xml.r201004.enums.FilterType; 
    60 import ome.xml.r201004.enums.FontFamily; 
    61 import ome.xml.r201004.enums.FontStyle; 
    62 import ome.xml.r201004.enums.IlluminationType; 
    63 import ome.xml.r201004.enums.Immersion; 
    64 import ome.xml.r201004.enums.LaserMedium; 
    65 import ome.xml.r201004.enums.LaserType; 
    66 import ome.xml.r201004.enums.LineCap; 
    67 import ome.xml.r201004.enums.Marker; 
    68 import ome.xml.r201004.enums.Medium; 
    69 import ome.xml.r201004.enums.MicrobeamManipulationType; 
    70 import ome.xml.r201004.enums.MicroscopeType; 
    71 import ome.xml.r201004.enums.NamingConvention; 
    72 import ome.xml.r201004.enums.PixelType; 
    73 import ome.xml.r201004.enums.Pulse; 
    74 import ome.xml.r201004.enums.handlers.AcquisitionModeEnumHandler; 
    75 import ome.xml.r201004.enums.handlers.ArcTypeEnumHandler; 
    76 import ome.xml.r201004.enums.handlers.BinningEnumHandler; 
    77 import ome.xml.r201004.enums.handlers.CompressionEnumHandler; 
    78 import ome.xml.r201004.enums.handlers.ContrastMethodEnumHandler; 
    79 import ome.xml.r201004.enums.handlers.CorrectionEnumHandler; 
    80 import ome.xml.r201004.enums.handlers.DetectorTypeEnumHandler; 
    81 import ome.xml.r201004.enums.handlers.DimensionOrderEnumHandler; 
    82 import ome.xml.r201004.enums.handlers.ExperimentTypeEnumHandler; 
    83 import ome.xml.r201004.enums.handlers.FilamentTypeEnumHandler; 
    84 import ome.xml.r201004.enums.handlers.FillRuleEnumHandler; 
    85 import ome.xml.r201004.enums.handlers.FilterTypeEnumHandler; 
    86 import ome.xml.r201004.enums.handlers.FontFamilyEnumHandler; 
    87 import ome.xml.r201004.enums.handlers.FontStyleEnumHandler; 
    88 import ome.xml.r201004.enums.handlers.IlluminationTypeEnumHandler; 
    89 import ome.xml.r201004.enums.handlers.ImmersionEnumHandler; 
    90 import ome.xml.r201004.enums.handlers.LaserMediumEnumHandler; 
    91 import ome.xml.r201004.enums.handlers.LaserTypeEnumHandler; 
    92 import ome.xml.r201004.enums.handlers.LineCapEnumHandler; 
    93 import ome.xml.r201004.enums.handlers.MarkerEnumHandler; 
    94 import ome.xml.r201004.enums.handlers.MediumEnumHandler; 
    95 import ome.xml.r201004.enums.handlers.MicrobeamManipulationTypeEnumHandler; 
    96 import ome.xml.r201004.enums.handlers.MicroscopeTypeEnumHandler; 
    97 import ome.xml.r201004.enums.handlers.NamingConventionEnumHandler; 
    98 import ome.xml.r201004.enums.handlers.PixelTypeEnumHandler; 
    99 import ome.xml.r201004.enums.handlers.PulseEnumHandler; 
     47import ome.xml.model.enums.AcquisitionMode; 
     48import ome.xml.model.enums.ArcType; 
     49import ome.xml.model.enums.Binning; 
     50import ome.xml.model.enums.Compression; 
     51import ome.xml.model.enums.ContrastMethod; 
     52import ome.xml.model.enums.Correction; 
     53import ome.xml.model.enums.DetectorType; 
     54import ome.xml.model.enums.DimensionOrder; 
     55import ome.xml.model.enums.EnumerationException; 
     56import ome.xml.model.enums.ExperimentType; 
     57import ome.xml.model.enums.FilamentType; 
     58import ome.xml.model.enums.FillRule; 
     59import ome.xml.model.enums.FilterType; 
     60import ome.xml.model.enums.FontFamily; 
     61import ome.xml.model.enums.FontStyle; 
     62import ome.xml.model.enums.IlluminationType; 
     63import ome.xml.model.enums.Immersion; 
     64import ome.xml.model.enums.LaserMedium; 
     65import ome.xml.model.enums.LaserType; 
     66import ome.xml.model.enums.LineCap; 
     67import ome.xml.model.enums.Marker; 
     68import ome.xml.model.enums.Medium; 
     69import ome.xml.model.enums.MicrobeamManipulationType; 
     70import ome.xml.model.enums.MicroscopeType; 
     71import ome.xml.model.enums.NamingConvention; 
     72import ome.xml.model.enums.PixelType; 
     73import ome.xml.model.enums.Pulse; 
     74import ome.xml.model.enums.handlers.AcquisitionModeEnumHandler; 
     75import ome.xml.model.enums.handlers.ArcTypeEnumHandler; 
     76import ome.xml.model.enums.handlers.BinningEnumHandler; 
     77import ome.xml.model.enums.handlers.CompressionEnumHandler; 
     78import ome.xml.model.enums.handlers.ContrastMethodEnumHandler; 
     79import ome.xml.model.enums.handlers.CorrectionEnumHandler; 
     80import ome.xml.model.enums.handlers.DetectorTypeEnumHandler; 
     81import ome.xml.model.enums.handlers.DimensionOrderEnumHandler; 
     82import ome.xml.model.enums.handlers.ExperimentTypeEnumHandler; 
     83import ome.xml.model.enums.handlers.FilamentTypeEnumHandler; 
     84import ome.xml.model.enums.handlers.FillRuleEnumHandler; 
     85import ome.xml.model.enums.handlers.FilterTypeEnumHandler; 
     86import ome.xml.model.enums.handlers.FontFamilyEnumHandler; 
     87import ome.xml.model.enums.handlers.FontStyleEnumHandler; 
     88import ome.xml.model.enums.handlers.IlluminationTypeEnumHandler; 
     89import ome.xml.model.enums.handlers.ImmersionEnumHandler; 
     90import ome.xml.model.enums.handlers.LaserMediumEnumHandler; 
     91import ome.xml.model.enums.handlers.LaserTypeEnumHandler; 
     92import ome.xml.model.enums.handlers.LineCapEnumHandler; 
     93import ome.xml.model.enums.handlers.MarkerEnumHandler; 
     94import ome.xml.model.enums.handlers.MediumEnumHandler; 
     95import ome.xml.model.enums.handlers.MicrobeamManipulationTypeEnumHandler; 
     96import ome.xml.model.enums.handlers.MicroscopeTypeEnumHandler; 
     97import ome.xml.model.enums.handlers.NamingConventionEnumHandler; 
     98import ome.xml.model.enums.handlers.PixelTypeEnumHandler; 
     99import ome.xml.model.enums.handlers.PulseEnumHandler; 
    100100 
    101101/** 
     
    10751075 
    10761076  /** 
    1077    * Retrieves an {@link ome.xml.r201004.enums.AcquisitionMode} enumeration 
    1078    * value for the given String. 
    1079    * 
    1080    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1077   * Retrieves an {@link ome.xml.model.enums.AcquisitionMode} enumeration 
     1078   * value for the given String. 
     1079   * 
     1080   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    10811081   *  enumeration value is not found. 
    10821082   */ 
     
    10941094 
    10951095  /** 
    1096    * Retrieves an {@link ome.xml.r201004.enums.ArcType} enumeration 
    1097    * value for the given String. 
    1098    * 
    1099    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1096   * Retrieves an {@link ome.xml.model.enums.ArcType} enumeration 
     1097   * value for the given String. 
     1098   * 
     1099   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11001100   *  enumeration value is not found. 
    11011101   */ 
     
    11111111 
    11121112  /** 
    1113    * Retrieves an {@link ome.xml.r201004.enums.Binning} enumeration 
    1114    * value for the given String. 
    1115    * 
    1116    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1113   * Retrieves an {@link ome.xml.model.enums.Binning} enumeration 
     1114   * value for the given String. 
     1115   * 
     1116   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11171117   *  enumeration value is not found. 
    11181118   */ 
     
    11271127  } 
    11281128  /** 
    1129    * Retrieves an {@link ome.xml.r201004.enums.Compression} enumeration 
    1130    * value for the given String. 
    1131    * 
    1132    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1129   * Retrieves an {@link ome.xml.model.enums.Compression} enumeration 
     1130   * value for the given String. 
     1131   * 
     1132   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11331133   *  enumeration value is not found. 
    11341134   */ 
     
    11431143  } 
    11441144  /** 
    1145    * Retrieves an {@link ome.xml.r201004.enums.ContrastMethod} enumeration 
    1146    * value for the given String. 
    1147    * 
    1148    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1145   * Retrieves an {@link ome.xml.model.enums.ContrastMethod} enumeration 
     1146   * value for the given String. 
     1147   * 
     1148   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11491149   *  enumeration value is not found. 
    11501150   */ 
     
    11611161  } 
    11621162  /** 
    1163    * Retrieves an {@link ome.xml.r201004.enums.Correction} enumeration 
    1164    * value for the given String. 
    1165    * 
    1166    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1163   * Retrieves an {@link ome.xml.model.enums.Correction} enumeration 
     1164   * value for the given String. 
     1165   * 
     1166   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11671167   *  enumeration value is not found. 
    11681168   */ 
     
    11771177  } 
    11781178  /** 
    1179    * Retrieves an {@link ome.xml.r201004.enums.DetectorType} enumeration 
    1180    * value for the given String. 
    1181    * 
    1182    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1179   * Retrieves an {@link ome.xml.model.enums.DetectorType} enumeration 
     1180   * value for the given String. 
     1181   * 
     1182   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11831183   *  enumeration value is not found. 
    11841184   */ 
     
    11931193  } 
    11941194  /** 
    1195    * Retrieves an {@link ome.xml.r201004.enums.DimensionOrder} enumeration 
    1196    * value for the given String. 
    1197    * 
    1198    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1195   * Retrieves an {@link ome.xml.model.enums.DimensionOrder} enumeration 
     1196   * value for the given String. 
     1197   * 
     1198   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    11991199   *  enumeration value is not found. 
    12001200   */ 
     
    12111211  } 
    12121212  /** 
    1213    * Retrieves an {@link ome.xml.r201004.enums.ExperimentType} enumeration 
    1214    * value for the given String. 
    1215    * 
    1216    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1213   * Retrieves an {@link ome.xml.model.enums.ExperimentType} enumeration 
     1214   * value for the given String. 
     1215   * 
     1216   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12171217   *  enumeration value is not found. 
    12181218   */ 
     
    12291229  } 
    12301230  /** 
    1231    * Retrieves an {@link ome.xml.r201004.enums.FilamentType} enumeration 
    1232    * value for the given String. 
    1233    * 
    1234    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1231   * Retrieves an {@link ome.xml.model.enums.FilamentType} enumeration 
     1232   * value for the given String. 
     1233   * 
     1234   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12351235   *  enumeration value is not found. 
    12361236   */ 
     
    12451245  } 
    12461246  /** 
    1247    * Retrieves an {@link ome.xml.r201004.enums.FillRule} enumeration 
    1248    * value for the given String. 
    1249    * 
    1250    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1247   * Retrieves an {@link ome.xml.model.enums.FillRule} enumeration 
     1248   * value for the given String. 
     1249   * 
     1250   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12511251   *  enumeration value is not found. 
    12521252   */ 
     
    12611261  } 
    12621262  /** 
    1263    * Retrieves an {@link ome.xml.r201004.enums.FilterType} enumeration 
    1264    * value for the given String. 
    1265    * 
    1266    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1263   * Retrieves an {@link ome.xml.model.enums.FilterType} enumeration 
     1264   * value for the given String. 
     1265   * 
     1266   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12671267   *  enumeration value is not found. 
    12681268   */ 
     
    12771277  } 
    12781278  /** 
    1279    * Retrieves an {@link ome.xml.r201004.enums.FontFamily} enumeration 
    1280    * value for the given String. 
    1281    * 
    1282    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1279   * Retrieves an {@link ome.xml.model.enums.FontFamily} enumeration 
     1280   * value for the given String. 
     1281   * 
     1282   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12831283   *  enumeration value is not found. 
    12841284   */ 
     
    12931293  } 
    12941294  /** 
    1295    * Retrieves an {@link ome.xml.r201004.enums.FontStyle} enumeration 
    1296    * value for the given String. 
    1297    * 
    1298    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1295   * Retrieves an {@link ome.xml.model.enums.FontStyle} enumeration 
     1296   * value for the given String. 
     1297   * 
     1298   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    12991299   *  enumeration value is not found. 
    13001300   */ 
     
    13091309  } 
    13101310  /** 
    1311    * Retrieves an {@link ome.xml.r201004.enums.IlluminationType} enumeration 
    1312    * value for the given String. 
    1313    * 
    1314    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1311   * Retrieves an {@link ome.xml.model.enums.IlluminationType} enumeration 
     1312   * value for the given String. 
     1313   * 
     1314   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13151315   *  enumeration value is not found. 
    13161316   */ 
     
    13271327  } 
    13281328  /** 
    1329    * Retrieves an {@link ome.xml.r201004.enums.Immersion} enumeration 
    1330    * value for the given String. 
    1331    * 
    1332    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1329   * Retrieves an {@link ome.xml.model.enums.Immersion} enumeration 
     1330   * value for the given String. 
     1331   * 
     1332   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13331333   *  enumeration value is not found. 
    13341334   */ 
     
    13431343  } 
    13441344  /** 
    1345    * Retrieves an {@link ome.xml.r201004.enums.LaserMedium} enumeration 
    1346    * value for the given String. 
    1347    * 
    1348    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1345   * Retrieves an {@link ome.xml.model.enums.LaserMedium} enumeration 
     1346   * value for the given String. 
     1347   * 
     1348   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13491349   *  enumeration value is not found. 
    13501350   */ 
     
    13591359  } 
    13601360  /** 
    1361    * Retrieves an {@link ome.xml.r201004.enums.LaserType} enumeration 
    1362    * value for the given String. 
    1363    * 
    1364    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1361   * Retrieves an {@link ome.xml.model.enums.LaserType} enumeration 
     1362   * value for the given String. 
     1363   * 
     1364   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13651365   *  enumeration value is not found. 
    13661366   */ 
     
    13751375  } 
    13761376  /** 
    1377    * Retrieves an {@link ome.xml.r201004.enums.LineCap} enumeration 
    1378    * value for the given String. 
    1379    * 
    1380    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1377   * Retrieves an {@link ome.xml.model.enums.LineCap} enumeration 
     1378   * value for the given String. 
     1379   * 
     1380   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13811381   *  enumeration value is not found. 
    13821382   */ 
     
    13911391  } 
    13921392  /** 
    1393    * Retrieves an {@link ome.xml.r201004.enums.Marker} enumeration 
    1394    * value for the given String. 
    1395    * 
    1396    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1393   * Retrieves an {@link ome.xml.model.enums.Marker} enumeration 
     1394   * value for the given String. 
     1395   * 
     1396   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    13971397   *  enumeration value is not found. 
    13981398   */ 
     
    14071407  } 
    14081408  /** 
    1409    * Retrieves an {@link ome.xml.r201004.enums.Medium} enumeration 
    1410    * value for the given String. 
    1411    * 
    1412    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1409   * Retrieves an {@link ome.xml.model.enums.Medium} enumeration 
     1410   * value for the given String. 
     1411   * 
     1412   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    14131413   *  enumeration value is not found. 
    14141414   */ 
     
    14231423  } 
    14241424  /** 
    1425    * Retrieves an {@link ome.xml.r201004.enums.MicrobeamManipulationType} 
     1425   * Retrieves an {@link ome.xml.model.enums.MicrobeamManipulationType} 
    14261426   * enumeration value for the given String. 
    14271427   * 
    1428    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1428   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    14291429   *  enumeration value is not found. 
    14301430   */ 
     
    14421442  } 
    14431443  /** 
    1444    * Retrieves an {@link ome.xml.r201004.enums.MicroscopeType} enumeration 
    1445    * value for the given String. 
    1446    * 
    1447    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1444   * Retrieves an {@link ome.xml.model.enums.MicroscopeType} enumeration 
     1445   * value for the given String. 
     1446   * 
     1447   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    14481448   *  enumeration value is not found. 
    14491449   */ 
     
    14601460  } 
    14611461  /** 
    1462    * Retrieves an {@link ome.xml.r201004.enums.NamingConvention} enumeration 
    1463    * value for the given String. 
    1464    * 
    1465    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1462   * Retrieves an {@link ome.xml.model.enums.NamingConvention} enumeration 
     1463   * value for the given String. 
     1464   * 
     1465   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    14661466   *  enumeration value is not found. 
    14671467   */ 
     
    14781478  } 
    14791479  /** 
    1480    * Retrieves an {@link ome.xml.r201004.enums.PixelType} enumeration 
    1481    * value for the given String. 
    1482    * 
    1483    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1480   * Retrieves an {@link ome.xml.model.enums.PixelType} enumeration 
     1481   * value for the given String. 
     1482   * 
     1483   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    14841484   *  enumeration value is not found. 
    14851485   */ 
     
    14941494  } 
    14951495  /** 
    1496    * Retrieves an {@link ome.xml.r201004.enums.Pulse} enumeration 
    1497    * value for the given String. 
    1498    * 
    1499    * @throws ome.xml.r201004.enums.EnumerationException if an appropriate 
     1496   * Retrieves an {@link ome.xml.model.enums.Pulse} enumeration 
     1497   * value for the given String. 
     1498   * 
     1499   * @throws ome.xml.model.enums.EnumerationException if an appropriate 
    15001500   *  enumeration value is not found. 
    15011501   */ 
  • trunk/components/bio-formats/src/loci/formats/MetadataTools.java

    r6452 r6458  
    3838import loci.formats.services.OMEXMLService; 
    3939 
    40 import ome.xml.r201004.enums.DimensionOrder; 
    41 import ome.xml.r201004.enums.EnumerationException; 
    42 import ome.xml.r201004.enums.PixelType; 
    43 import ome.xml.r201004.primitives.PositiveInteger; 
     40import ome.xml.model.enums.DimensionOrder; 
     41import ome.xml.model.enums.EnumerationException; 
     42import ome.xml.model.enums.PixelType; 
     43import ome.xml.model.primitives.PositiveInteger; 
    4444 
    4545import org.slf4j.Logger; 
  • trunk/components/bio-formats/src/loci/formats/in/BDReader.java

    r6430 r6458  
    4747import loci.formats.tiff.TiffParser; 
    4848 
    49 import ome.xml.r201004.primitives.NonNegativeInteger; 
    50 import ome.xml.r201004.primitives.PositiveInteger; 
     49import ome.xml.model.primitives.NonNegativeInteger; 
     50import ome.xml.model.primitives.PositiveInteger; 
    5151 
    5252/** 
  • trunk/components/bio-formats/src/loci/formats/in/DeltavisionReader.java

    r6371 r6458  
    3838import loci.formats.meta.MetadataStore; 
    3939 
    40 import ome.xml.r201004.primitives.PositiveInteger; 
     40import ome.xml.model.primitives.PositiveInteger; 
    4141 
    4242/** 
  • trunk/components/bio-formats/src/loci/formats/in/FV1000Reader.java

    r6426 r6458  
    5353import loci.formats.tiff.TiffParser; 
    5454 
    55 import ome.xml.r201004.primitives.PositiveInteger; 
     55import ome.xml.model.primitives.PositiveInteger; 
    5656 
    5757/** 
  • trunk/components/bio-formats/src/loci/formats/in/FlexReader.java

    r6371 r6458  
    4747import loci.formats.tiff.TiffParser; 
    4848 
    49 import ome.xml.r201004.primitives.NonNegativeInteger; 
    50 import ome.xml.r201004.primitives.PositiveInteger; 
     49import ome.xml.model.primitives.NonNegativeInteger; 
     50import ome.xml.model.primitives.PositiveInteger; 
    5151 
    5252import org.xml.sax.Attributes; 
  • trunk/components/bio-formats/src/loci/formats/in/ICSReader.java

    r6430 r6458  
    4141import loci.formats.meta.MetadataStore; 
    4242 
    43 import ome.xml.r201004.primitives.PositiveInteger; 
     43import ome.xml.model.primitives.PositiveInteger; 
    4444 
    4545/** 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisTiffReader.java

    r6230 r6458  
    3535import loci.formats.tiff.IFDList; 
    3636 
    37 import ome.xml.r201004.primitives.PositiveInteger; 
     37import ome.xml.model.primitives.PositiveInteger; 
    3838 
    3939/** 
  • trunk/components/bio-formats/src/loci/formats/in/InCellReader.java

    r6377 r6458  
    3838import loci.formats.meta.MetadataStore; 
    3939 
    40 import ome.xml.r201004.primitives.NonNegativeInteger; 
    41 import ome.xml.r201004.primitives.PositiveInteger; 
     40import ome.xml.model.primitives.NonNegativeInteger; 
     41import ome.xml.model.primitives.PositiveInteger; 
    4242 
    4343import org.xml.sax.Attributes; 
  • trunk/components/bio-formats/src/loci/formats/in/L2DReader.java

    r6377 r6458  
    3838import loci.formats.meta.MetadataStore; 
    3939 
    40 import ome.xml.r201004.primitives.PositiveInteger; 
     40import ome.xml.model.primitives.PositiveInteger; 
    4141 
    4242/** 
  • trunk/components/bio-formats/src/loci/formats/in/LeicaHandler.java

    r6388 r6458  
    3636import loci.formats.meta.MetadataStore; 
    3737 
    38 import ome.xml.r201004.enums.Correction; 
    39 import ome.xml.r201004.enums.DetectorType; 
    40 import ome.xml.r201004.enums.EnumerationException; 
    41 import ome.xml.r201004.enums.Immersion; 
    42 import ome.xml.r201004.enums.LaserMedium; 
    43 import ome.xml.r201004.enums.LaserType; 
    44 import ome.xml.r201004.enums.MicroscopeType; 
    45 import ome.xml.r201004.enums.handlers.CorrectionEnumHandler; 
    46 import ome.xml.r201004.enums.handlers.DetectorTypeEnumHandler; 
    47 import ome.xml.r201004.enums.handlers.ImmersionEnumHandler; 
    48 import ome.xml.r201004.enums.handlers.LaserMediumEnumHandler; 
    49 import ome.xml.r201004.enums.handlers.LaserTypeEnumHandler; 
    50 import ome.xml.r201004.enums.handlers.MicroscopeTypeEnumHandler; 
    51 import ome.xml.r201004.primitives.PercentFraction; 
    52 import ome.xml.r201004.primitives.PositiveInteger; 
     38import ome.xml.model.enums.Correction; 
     39import ome.xml.model.enums.DetectorType; 
     40import ome.xml.model.enums.EnumerationException; 
     41import ome.xml.model.enums.Immersion; 
     42import ome.xml.model.enums.LaserMedium; 
     43import ome.xml.model.enums.LaserType; 
     44import ome.xml.model.enums.MicroscopeType; 
     45import ome.xml.model.enums.handlers.CorrectionEnumHandler; 
     46import ome.xml.model.enums.handlers.DetectorTypeEnumHandler; 
     47import ome.xml.model.enums.handlers.ImmersionEnumHandler; 
     48import ome.xml.model.enums.handlers.LaserMediumEnumHandler; 
     49import ome.xml.model.enums.handlers.LaserTypeEnumHandler; 
     50import ome.xml.model.enums.handlers.MicroscopeTypeEnumHandler; 
     51import ome.xml.model.primitives.PercentFraction; 
     52import ome.xml.model.primitives.PositiveInteger; 
    5353 
    5454import org.xml.sax.Attributes; 
  • trunk/components/bio-formats/src/loci/formats/in/LeicaReader.java

    r6451 r6458  
    4848import loci.formats.tiff.TiffParser; 
    4949 
    50 import ome.xml.r201004.primitives.PositiveInteger; 
     50import ome.xml.model.primitives.PositiveInteger; 
    5151 
    5252import org.slf4j.Logger; 
  • trunk/components/bio-formats/src/loci/formats/in/MIASReader.java

    r6377 r6458  
    4949import loci.formats.tiff.TiffParser; 
    5050 
    51 import ome.xml.r201004.primitives.NonNegativeInteger; 
     51import ome.xml.model.primitives.NonNegativeInteger; 
    5252 
    5353/** 
     
    681681 
    682682      String imageID = MetadataTools.createLSID("Image", well); 
    683       store.setWellSampleImageRef(imageID, 0, well, 0); 
    684683      store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0); 
    685684 
    686685      store.setImageID(imageID, well); 
    687686      store.setImageName("Well " + wellRow + wellCol, well); 
     687      store.setWellSampleImageRef(imageID, 0, well, 0); 
    688688 
    689689      MetadataTools.setDefaultCreationDate(store, id, well); 
  • trunk/components/bio-formats/src/loci/formats/in/MetamorphReader.java

    r6430 r6458  
    4848import loci.formats.tiff.TiffRational; 
    4949 
    50 import ome.xml.r201004.primitives.PositiveInteger; 
     50import ome.xml.model.primitives.PositiveInteger; 
    5151 
    5252/** 
  • trunk/components/bio-formats/src/loci/formats/in/NativeND2Reader.java

    r6409 r6458  
    4545import loci.formats.meta.MetadataStore; 
    4646 
    47 import ome.xml.r201004.primitives.PositiveInteger; 
     47import ome.xml.model.primitives.PositiveInteger; 
    4848 
    4949import org.xml.sax.Attributes; 
  • trunk/components/bio-formats/src/loci/formats/in/NikonReader.java

    r6221 r6458  
    242242    } 
    243243 
    244     return ImageTools.interpolate(pix, buf, colorMap, getSizeX(), getSizeY(), 
     244    byte[] b = new byte[FormatTools.getPlaneSize(this)]; 
     245    ImageTools.interpolate(pix, b, colorMap, getSizeX(), getSizeY(), 
    245246      isLittleEndian()); 
     247    int bpp = FormatTools.getBytesPerPixel(getPixelType()) * 3; 
     248    int rowLen = w * bpp; 
     249    int width = getSizeX() * bpp; 
     250    for (int row=0; row<h; row++) { 
     251      System.arraycopy( 
     252        b, (row + y) * width + x * bpp, buf, row * rowLen, rowLen); 
     253    } 
     254 
     255    return buf; 
    246256  } 
    247257 
  • trunk/components/bio-formats/src/loci/formats/in/NikonTiffReader.java

    r6377 r6458  
    3535import loci.formats.tiff.TiffParser; 
    3636 
    37 import ome.xml.r201004.primitives.PositiveInteger; 
     37import ome.xml.model.primitives.PositiveInteger; 
    3838 
    3939/** 
  • trunk/components/bio-formats/src/loci/formats/in/PerkinElmerReader.java

    r6409 r6458  
    4141import loci.formats.meta.MetadataStore; 
    4242 
    43 import ome.xml.r201004.primitives.PositiveInteger; 
     43import ome.xml.model.primitives.PositiveInteger; 
    4444 
    4545/** 
  • trunk/components/bio-formats/src/loci/formats/in/ScanrReader.java

    r6377 r6458  
    4141import loci.formats.tiff.TiffParser; 
    4242 
    43 import ome.xml.r201004.primitives.NonNegativeInteger; 
     43import ome.xml.model.primitives.NonNegativeInteger; 
    4444 
    4545import org.xml.sax.Attributes; 
  • trunk/components/bio-formats/src/loci/formats/in/ZeissZVIReader.java

    r6377 r6458  
    5151import loci.formats.services.POIService; 
    5252 
    53 import ome.xml.r201004.primitives.PositiveInteger; 
     53import ome.xml.model.primitives.PositiveInteger; 
    5454 
    5555/** 
  • trunk/components/bio-formats/src/loci/formats/meta/AggregateMetadata.java

    r6440 r6458  
    3737import loci.common.DataTools; 
    3838 
    39 import ome.xml.r201004.enums.*; 
    40 import ome.xml.r201004.primitives.*; 
     39import ome.xml.model.enums.*; 
     40import ome.xml.model.primitives.*; 
    4141 
    4242/** 
  • trunk/components/bio-formats/src/loci/formats/meta/DummyMetadata.java

    r6440 r6458  
    3434import java.util.Iterator; 
    3535 
    36 import ome.xml.r201004.Image; 
    37 import ome.xml.r201004.OME; 
    38 import ome.xml.r201004.Pixels; 
    39 import ome.xml.r201004.TiffData; 
    40 import ome.xml.r201004.UUID; 
    41 import ome.xml.r201004.enums.*; 
    42 import ome.xml.r201004.primitives.*; 
     36import ome.xml.model.Image; 
     37import ome.xml.model.OME; 
     38import ome.xml.model.Pixels; 
     39import ome.xml.model.TiffData; 
     40import ome.xml.model.UUID; 
     41import ome.xml.model.enums.*; 
     42import ome.xml.model.primitives.*; 
    4343 
    4444/** 
  • trunk/components/bio-formats/src/loci/formats/meta/FilterMetadata.java

    r6413 r6458  
    3434import loci.common.DataTools; 
    3535 
    36 import ome.xml.r201004.Image; 
    37 import ome.xml.r201004.OME; 
    38 import ome.xml.r201004.Pixels; 
    39 import ome.xml.r201004.TiffData; 
    40 import ome.xml.r201004.UUID; 
    41 import ome.xml.r201004.enums.*; 
    42 import ome.xml.r201004.primitives.*; 
     36import ome.xml.model.Image; 
     37import ome.xml.model.OME; 
     38import ome.xml.model.Pixels; 
     39import ome.xml.model.TiffData; 
     40import ome.xml.model.UUID; 
     41import ome.xml.model.enums.*; 
     42import ome.xml.model.primitives.*; 
    4343 
    4444/** 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataConverter.java

    r6230 r6458  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on May 4, 2010 5:36:22 PM CDT 
     27 * Created by melissa via MetadataAutogen on Jun 2, 2010 7:57:49 PM CDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    3232package loci.formats.meta; 
    3333 
    34 import ome.xml.r201004.enums.*; 
    35 import ome.xml.r201004.primitives.*; 
     34import ome.xml.model.enums.*; 
     35import ome.xml.model.primitives.*; 
    3636 
    3737/** 
     
    6464   */ 
    6565  public static void convertMetadata(MetadataRetrieve src, MetadataStore dest) { 
    66     // TODO 
     66    int booleanAnnotationCount = src.getBooleanAnnotationCount(); 
     67    for (int booleanAnnotationIndex=0; booleanAnnotationIndex<booleanAnnotationCount; booleanAnnotationIndex++) { 
     68      String booleanAnnotationIDValue = src.getBooleanAnnotationID(booleanAnnotationIndex); 
     69      if (booleanAnnotationIDValue != null) dest.setBooleanAnnotationID(booleanAnnotationIDValue, booleanAnnotationIndex); 
     70      String booleanAnnotationNamespaceValue = src.getBooleanAnnotationNamespace(booleanAnnotationIndex); 
     71      if (booleanAnnotationNamespaceValue != null) dest.setBooleanAnnotationNamespace(booleanAnnotationNamespaceValue, booleanAnnotationIndex); 
     72      Boolean booleanAnnotationValueValue = src.getBooleanAnnotationValue(booleanAnnotationIndex); 
     73      if (booleanAnnotationValueValue != null) dest.setBooleanAnnotationValue(booleanAnnotationValueValue, booleanAnnotationIndex); 
     74    } 
     75    int datasetCount = src.getDatasetCount(); 
     76    for (int datasetIndex=0; datasetIndex<datasetCount; datasetIndex++) { 
     77      //String datasetAnnotationRefValue = src.getDatasetAnnotationRef(datasetIndex, annotationRefIndex); 
     78      //if (datasetAnnotationRefValue != null) dest.setDatasetAnnotationRef(datasetAnnotationRefValue, datasetIndex, annotationRefIndex); 
     79      String datasetDescriptionValue = src.getDatasetDescription(datasetIndex); 
     80      if (datasetDescriptionValue != null) dest.setDatasetDescription(datasetDescriptionValue, datasetIndex); 
     81      String datasetExperimenterRefValue = src.getDatasetExperimenterRef(datasetIndex); 
     82      if (datasetExperimenterRefValue != null) dest.setDatasetExperimenterRef(datasetExperimenterRefValue, datasetIndex); 
     83      String datasetGroupRefValue = src.getDatasetGroupRef(datasetIndex); 
     84      if (datasetGroupRefValue != null) dest.setDatasetGroupRef(datasetGroupRefValue, datasetIndex); 
     85      String datasetIDValue = src.getDatasetID(datasetIndex); 
     86      if (datasetIDValue != null) dest.setDatasetID(datasetIDValue, datasetIndex); 
     87      String datasetNameValue = src.getDatasetName(datasetIndex); 
     88      if (datasetNameValue != null) dest.setDatasetName(datasetNameValue, datasetIndex); 
     89      //String datasetProjectRefValue = src.getDatasetProjectRef(datasetIndex, projectRefIndex); 
     90      //if (datasetProjectRefValue != null) dest.setDatasetProjectRef(datasetProjectRefValue, datasetIndex, projectRefIndex); 
     91      //int annotationRefCount = src.getAnnotationRefCount(datasetIndex); 
     92      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     93      //} 
     94      int projectRefCount = src.getProjectRefCount(datasetIndex); 
     95      for (int projectRefIndex=0; projectRefIndex<projectRefCount; projectRefIndex++) { 
     96      } 
     97    } 
     98    int doubleAnnotationCount = src.getDoubleAnnotationCount(); 
     99    for (int doubleAnnotationIndex=0; doubleAnnotationIndex<doubleAnnotationCount; doubleAnnotationIndex++) { 
     100      String doubleAnnotationIDValue = src.getDoubleAnnotationID(doubleAnnotationIndex); 
     101      if (doubleAnnotationIDValue != null) dest.setDoubleAnnotationID(doubleAnnotationIDValue, doubleAnnotationIndex); 
     102      String doubleAnnotationNamespaceValue = src.getDoubleAnnotationNamespace(doubleAnnotationIndex); 
     103      if (doubleAnnotationNamespaceValue != null) dest.setDoubleAnnotationNamespace(doubleAnnotationNamespaceValue, doubleAnnotationIndex); 
     104      Double doubleAnnotationValueValue = src.getDoubleAnnotationValue(doubleAnnotationIndex); 
     105      if (doubleAnnotationValueValue != null) dest.setDoubleAnnotationValue(doubleAnnotationValueValue, doubleAnnotationIndex); 
     106    } 
     107    int experimentCount = src.getExperimentCount(); 
     108    for (int experimentIndex=0; experimentIndex<experimentCount; experimentIndex++) { 
     109      String experimentDescriptionValue = src.getExperimentDescription(experimentIndex); 
     110      if (experimentDescriptionValue != null) dest.setExperimentDescription(experimentDescriptionValue, experimentIndex); 
     111      String experimentExperimenterRefValue = src.getExperimentExperimenterRef(experimentIndex); 
     112      if (experimentExperimenterRefValue != null) dest.setExperimentExperimenterRef(experimentExperimenterRefValue, experimentIndex); 
     113      String experimentIDValue = src.getExperimentID(experimentIndex); 
     114      if (experimentIDValue != null) dest.setExperimentID(experimentIDValue, experimentIndex); 
     115      ExperimentType experimentTypeValue = src.getExperimentType(experimentIndex); 
     116      if (experimentTypeValue != null) dest.setExperimentType(experimentTypeValue, experimentIndex); 
     117      int microbeamManipulationCount = src.getMicrobeamManipulationCount(experimentIndex); 
     118      for (int microbeamManipulationIndex=0; microbeamManipulationIndex<microbeamManipulationCount; microbeamManipulationIndex++) { 
     119        String microbeamManipulationExperimenterRefValue = src.getMicrobeamManipulationExperimenterRef(experimentIndex, microbeamManipulationIndex); 
     120        if (microbeamManipulationExperimenterRefValue != null) dest.setMicrobeamManipulationExperimenterRef(microbeamManipulationExperimenterRefValue, experimentIndex, microbeamManipulationIndex); 
     121        String microbeamManipulationIDValue = src.getMicrobeamManipulationID(experimentIndex, microbeamManipulationIndex); 
     122        if (microbeamManipulationIDValue != null) dest.setMicrobeamManipulationID(microbeamManipulationIDValue, experimentIndex, microbeamManipulationIndex); 
     123        //String microbeamManipulationROIRefValue = src.getMicrobeamManipulationROIRef(experimentIndex, microbeamManipulationIndex, roiRefIndex); 
     124        //if (microbeamManipulationROIRefValue != null) dest.setMicrobeamManipulationROIRef(microbeamManipulationROIRefValue, experimentIndex, microbeamManipulationIndex, roiRefIndex); 
     125        MicrobeamManipulationType microbeamManipulationTypeValue = src.getMicrobeamManipulationType(experimentIndex, microbeamManipulationIndex); 
     126        if (microbeamManipulationTypeValue != null) dest.setMicrobeamManipulationType(microbeamManipulationTypeValue, experimentIndex, microbeamManipulationIndex); 
     127        /* 
     128        int lightSourceSettingsCount = src.getLightSourceSettingsCount(experimentIndex, microbeamManipulationIndex); 
     129        for (int lightSourceSettingsIndex=0; lightSourceSettingsIndex<lightSourceSettingsCount; lightSourceSettingsIndex++) { 
     130          PercentFraction microbeamManipulationLightSourceSettingsAttenuationValue = src.getMicrobeamManipulationLightSourceSettingsAttenuation(experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     131          if (microbeamManipulationLightSourceSettingsAttenuationValue != null) dest.setMicrobeamManipulationLightSourceSettingsAttenuation(microbeamManipulationLightSourceSettingsAttenuationValue, experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     132          String microbeamManipulationLightSourceSettingsIDValue = src.getMicrobeamManipulationLightSourceSettingsID(experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     133          if (microbeamManipulationLightSourceSettingsIDValue != null) dest.setMicrobeamManipulationLightSourceSettingsID(microbeamManipulationLightSourceSettingsIDValue, experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     134          PositiveInteger microbeamManipulationLightSourceSettingsWavelengthValue = src.getMicrobeamManipulationLightSourceSettingsWavelength(experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     135          if (microbeamManipulationLightSourceSettingsWavelengthValue != null) dest.setMicrobeamManipulationLightSourceSettingsWavelength(microbeamManipulationLightSourceSettingsWavelengthValue, experimentIndex, microbeamManipulationIndex, lightSourceSettingsIndex); 
     136        } 
     137        */ 
     138        //int roiRefCount = src.getROIRefCount(experimentIndex, microbeamManipulationIndex); 
     139        //for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
     140        //} 
     141      } 
     142    } 
     143    int experimenterCount = src.getExperimenterCount(); 
     144    for (int experimenterIndex=0; experimenterIndex<experimenterCount; experimenterIndex++) { 
     145      //String experimenterAnnotationRefValue = src.getExperimenterAnnotationRef(experimenterIndex, annotationRefIndex); 
     146      //if (experimenterAnnotationRefValue != null) dest.setExperimenterAnnotationRef(experimenterAnnotationRefValue, experimenterIndex, annotationRefIndex); 
     147      String experimenterDisplayNameValue = src.getExperimenterDisplayName(experimenterIndex); 
     148      if (experimenterDisplayNameValue != null) dest.setExperimenterDisplayName(experimenterDisplayNameValue, experimenterIndex); 
     149      String experimenterEmailValue = src.getExperimenterEmail(experimenterIndex); 
     150      if (experimenterEmailValue != null) dest.setExperimenterEmail(experimenterEmailValue, experimenterIndex); 
     151      String experimenterFirstNameValue = src.getExperimenterFirstName(experimenterIndex); 
     152      if (experimenterFirstNameValue != null) dest.setExperimenterFirstName(experimenterFirstNameValue, experimenterIndex); 
     153      //String experimenterGroupRefValue = src.getExperimenterGroupRef(experimenterIndex, groupRefIndex); 
     154      //if (experimenterGroupRefValue != null) dest.setExperimenterGroupRef(experimenterGroupRefValue, experimenterIndex, groupRefIndex); 
     155      String experimenterIDValue = src.getExperimenterID(experimenterIndex); 
     156      if (experimenterIDValue != null) dest.setExperimenterID(experimenterIDValue, experimenterIndex); 
     157      String experimenterInstitutionValue = src.getExperimenterInstitution(experimenterIndex); 
     158      if (experimenterInstitutionValue != null) dest.setExperimenterInstitution(experimenterInstitutionValue, experimenterIndex); 
     159      String experimenterLastNameValue = src.getExperimenterLastName(experimenterIndex); 
     160      if (experimenterLastNameValue != null) dest.setExperimenterLastName(experimenterLastNameValue, experimenterIndex); 
     161      String experimenterMiddleNameValue = src.getExperimenterMiddleName(experimenterIndex); 
     162      if (experimenterMiddleNameValue != null) dest.setExperimenterMiddleName(experimenterMiddleNameValue, experimenterIndex); 
     163      String experimenterUserNameValue = src.getExperimenterUserName(experimenterIndex); 
     164      if (experimenterUserNameValue != null) dest.setExperimenterUserName(experimenterUserNameValue, experimenterIndex); 
     165      //int annotationRefCount = src.getAnnotationRefCount(experimenterIndex); 
     166      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     167      //} 
     168      //int groupRefCount = src.getGroupRefCount(experimenterIndex); 
     169      //for (int groupRefIndex=0; groupRefIndex<groupRefCount; groupRefIndex++) { 
     170      //} 
     171    } 
     172    int fileAnnotationCount = src.getFileAnnotationCount(); 
     173    for (int fileAnnotationIndex=0; fileAnnotationIndex<fileAnnotationCount; fileAnnotationIndex++) { 
     174      String fileAnnotationBinaryFileFileNameValue = src.getFileAnnotationBinaryFileFileName(fileAnnotationIndex); 
     175      if (fileAnnotationBinaryFileFileNameValue != null) dest.setFileAnnotationBinaryFileFileName(fileAnnotationBinaryFileFileNameValue, fileAnnotationIndex); 
     176      String fileAnnotationBinaryFileMIMETypeValue = src.getFileAnnotationBinaryFileMIMEType(fileAnnotationIndex); 
     177      if (fileAnnotationBinaryFileMIMETypeValue != null) dest.setFileAnnotationBinaryFileMIMEType(fileAnnotationBinaryFileMIMETypeValue, fileAnnotationIndex); 
     178      Integer fileAnnotationBinaryFileSizeValue = src.getFileAnnotationBinaryFileSize(fileAnnotationIndex); 
     179      if (fileAnnotationBinaryFileSizeValue != null) dest.setFileAnnotationBinaryFileSize(fileAnnotationBinaryFileSizeValue, fileAnnotationIndex); 
     180      String fileAnnotationIDValue = src.getFileAnnotationID(fileAnnotationIndex); 
     181      if (fileAnnotationIDValue != null) dest.setFileAnnotationID(fileAnnotationIDValue, fileAnnotationIndex); 
     182      String fileAnnotationNamespaceValue = src.getFileAnnotationNamespace(fileAnnotationIndex); 
     183      if (fileAnnotationNamespaceValue != null) dest.setFileAnnotationNamespace(fileAnnotationNamespaceValue, fileAnnotationIndex); 
     184    } 
     185    int groupCount = src.getGroupCount(); 
     186    for (int groupIndex=0; groupIndex<groupCount; groupIndex++) { 
     187      String groupContactValue = src.getGroupContact(groupIndex); 
     188      if (groupContactValue != null) dest.setGroupContact(groupContactValue, groupIndex); 
     189      String groupDescriptionValue = src.getGroupDescription(groupIndex); 
     190      if (groupDescriptionValue != null) dest.setGroupDescription(groupDescriptionValue, groupIndex); 
     191      String groupIDValue = src.getGroupID(groupIndex); 
     192      if (groupIDValue != null) dest.setGroupID(groupIDValue, groupIndex); 
     193      String groupLeaderValue = src.getGroupLeader(groupIndex); 
     194      if (groupLeaderValue != null) dest.setGroupLeader(groupLeaderValue, groupIndex); 
     195      String groupNameValue = src.getGroupName(groupIndex); 
     196      if (groupNameValue != null) dest.setGroupName(groupNameValue, groupIndex); 
     197    } 
     198    int imageCount = src.getImageCount(); 
     199    for (int imageIndex=0; imageIndex<imageCount; imageIndex++) { 
     200      String imageAcquiredDateValue = src.getImageAcquiredDate(imageIndex); 
     201      if (imageAcquiredDateValue != null) dest.setImageAcquiredDate(imageAcquiredDateValue, imageIndex); 
     202      //String imageAnnotationRefValue = src.getImageAnnotationRef(imageIndex, annotationRefIndex); 
     203      //if (imageAnnotationRefValue != null) dest.setImageAnnotationRef(imageAnnotationRefValue, imageIndex, annotationRefIndex); 
     204      //String imageDatasetRefValue = src.getImageDatasetRef(imageIndex, datasetRefIndex); 
     205      //if (imageDatasetRefValue != null) dest.setImageDatasetRef(imageDatasetRefValue, imageIndex, datasetRefIndex); 
     206      String imageDescriptionValue = src.getImageDescription(imageIndex); 
     207      if (imageDescriptionValue != null) dest.setImageDescription(imageDescriptionValue, imageIndex); 
     208      String imageExperimentRefValue = src.getImageExperimentRef(imageIndex); 
     209      if (imageExperimentRefValue != null) dest.setImageExperimentRef(imageExperimentRefValue, imageIndex); 
     210      String imageExperimenterRefValue = src.getImageExperimenterRef(imageIndex); 
     211      if (imageExperimenterRefValue != null) dest.setImageExperimenterRef(imageExperimenterRefValue, imageIndex); 
     212      String imageGroupRefValue = src.getImageGroupRef(imageIndex); 
     213      if (imageGroupRefValue != null) dest.setImageGroupRef(imageGroupRefValue, imageIndex); 
     214      String imageIDValue = src.getImageID(imageIndex); 
     215      if (imageIDValue != null) dest.setImageID(imageIDValue, imageIndex); 
     216      String imageInstrumentRefValue = src.getImageInstrumentRef(imageIndex); 
     217      if (imageInstrumentRefValue != null) dest.setImageInstrumentRef(imageInstrumentRefValue, imageIndex); 
     218      //String imageMicrobeamManipulationRefValue = src.getImageMicrobeamManipulationRef(imageIndex, microbeamManipulationRefIndex); 
     219      //if (imageMicrobeamManipulationRefValue != null) dest.setImageMicrobeamManipulationRef(imageMicrobeamManipulationRefValue, imageIndex, microbeamManipulationRefIndex); 
     220      String imageNameValue = src.getImageName(imageIndex); 
     221      if (imageNameValue != null) dest.setImageName(imageNameValue, imageIndex); 
     222      Double imageObjectiveSettingsCorrectionCollarValue = src.getImageObjectiveSettingsCorrectionCollar(imageIndex); 
     223      if (imageObjectiveSettingsCorrectionCollarValue != null) dest.setImageObjectiveSettingsCorrectionCollar(imageObjectiveSettingsCorrectionCollarValue, imageIndex); 
     224      String imageObjectiveSettingsIDValue = src.getImageObjectiveSettingsID(imageIndex); 
     225      if (imageObjectiveSettingsIDValue != null) dest.setImageObjectiveSettingsID(imageObjectiveSettingsIDValue, imageIndex); 
     226      Medium imageObjectiveSettingsMediumValue = src.getImageObjectiveSettingsMedium(imageIndex); 
     227      if (imageObjectiveSettingsMediumValue != null) dest.setImageObjectiveSettingsMedium(imageObjectiveSettingsMediumValue, imageIndex); 
     228      Double imageObjectiveSettingsRefractiveIndexValue = src.getImageObjectiveSettingsRefractiveIndex(imageIndex); 
     229      if (imageObjectiveSettingsRefractiveIndexValue != null) dest.setImageObjectiveSettingsRefractiveIndex(imageObjectiveSettingsRefractiveIndexValue, imageIndex); 
     230      //String imageROIRefValue = src.getImageROIRef(imageIndex, roiRefIndex); 
     231      //if (imageROIRefValue != null) dest.setImageROIRef(imageROIRefValue, imageIndex, roiRefIndex); 
     232      //int annotationRefCount = src.getAnnotationRefCount(imageIndex); 
     233      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     234      //} 
     235      int channelCount = src.getChannelCount(imageIndex); 
     236      for (int channelIndex=0; channelIndex<channelCount; channelIndex++) { 
     237        AcquisitionMode channelAcquisitionModeValue = src.getChannelAcquisitionMode(imageIndex, channelIndex); 
     238        if (channelAcquisitionModeValue != null) dest.setChannelAcquisitionMode(channelAcquisitionModeValue, imageIndex, channelIndex); 
     239        //String channelAnnotationRefValue = src.getChannelAnnotationRef(imageIndex, channelIndex, annotationRefIndex); 
     240        //if (channelAnnotationRefValue != null) dest.setChannelAnnotationRef(channelAnnotationRefValue, imageIndex, channelIndex, annotationRefIndex); 
     241        Integer channelColorValue = src.getChannelColor(imageIndex, channelIndex); 
     242        if (channelColorValue != null) dest.setChannelColor(channelColorValue, imageIndex, channelIndex); 
     243        ContrastMethod channelContrastMethodValue = src.getChannelContrastMethod(imageIndex, channelIndex); 
     244        if (channelContrastMethodValue != null) dest.setChannelContrastMethod(channelContrastMethodValue, imageIndex, channelIndex); 
     245        PositiveInteger channelEmissionWavelengthValue = src.getChannelEmissionWavelength(imageIndex, channelIndex); 
     246        if (channelEmissionWavelengthValue != null) dest.setChannelEmissionWavelength(channelEmissionWavelengthValue, imageIndex, channelIndex); 
     247        PositiveInteger channelExcitationWavelengthValue = src.getChannelExcitationWavelength(imageIndex, channelIndex); 
     248        if (channelExcitationWavelengthValue != null) dest.setChannelExcitationWavelength(channelExcitationWavelengthValue, imageIndex, channelIndex); 
     249        String channelFilterSetRefValue = src.getChannelFilterSetRef(imageIndex, channelIndex); 
     250        if (channelFilterSetRefValue != null) dest.setChannelFilterSetRef(channelFilterSetRefValue, imageIndex, channelIndex); 
     251        String channelFluorValue = src.getChannelFluor(imageIndex, channelIndex); 
     252        if (channelFluorValue != null) dest.setChannelFluor(channelFluorValue, imageIndex, channelIndex); 
     253        String channelIDValue = src.getChannelID(imageIndex, channelIndex); 
     254        if (channelIDValue != null) dest.setChannelID(channelIDValue, imageIndex, channelIndex); 
     255        IlluminationType channelIlluminationTypeValue = src.getChannelIlluminationType(imageIndex, channelIndex); 
     256        if (channelIlluminationTypeValue != null) dest.setChannelIlluminationType(channelIlluminationTypeValue, imageIndex, channelIndex); 
     257        PercentFraction channelLightSourceSettingsAttenuationValue = src.getChannelLightSourceSettingsAttenuation(imageIndex, channelIndex); 
     258        if (channelLightSourceSettingsAttenuationValue != null) dest.setChannelLightSourceSettingsAttenuation(channelLightSourceSettingsAttenuationValue, imageIndex, channelIndex); 
     259        String channelLightSourceSettingsIDValue = src.getChannelLightSourceSettingsID(imageIndex, channelIndex); 
     260        if (channelLightSourceSettingsIDValue != null) dest.setChannelLightSourceSettingsID(channelLightSourceSettingsIDValue, imageIndex, channelIndex); 
     261        PositiveInteger channelLightSourceSettingsWavelengthValue = src.getChannelLightSourceSettingsWavelength(imageIndex, channelIndex); 
     262        if (channelLightSourceSettingsWavelengthValue != null) dest.setChannelLightSourceSettingsWavelength(channelLightSourceSettingsWavelengthValue, imageIndex, channelIndex); 
     263        Double channelNDFilterValue = src.getChannelNDFilter(imageIndex, channelIndex); 
     264        if (channelNDFilterValue != null) dest.setChannelNDFilter(channelNDFilterValue, imageIndex, channelIndex); 
     265        String channelNameValue = src.getChannelName(imageIndex, channelIndex); 
     266        if (channelNameValue != null) dest.setChannelName(channelNameValue, imageIndex, channelIndex); 
     267        String channelOTFRefValue = src.getChannelOTFRef(imageIndex, channelIndex); 
     268        if (channelOTFRefValue != null) dest.setChannelOTFRef(channelOTFRefValue, imageIndex, channelIndex); 
     269        Double channelPinholeSizeValue = src.getChannelPinholeSize(imageIndex, channelIndex); 
     270        if (channelPinholeSizeValue != null) dest.setChannelPinholeSize(channelPinholeSizeValue, imageIndex, channelIndex); 
     271        Integer channelPockelCellSettingValue = src.getChannelPockelCellSetting(imageIndex, channelIndex); 
     272        if (channelPockelCellSettingValue != null) dest.setChannelPockelCellSetting(channelPockelCellSettingValue, imageIndex, channelIndex); 
     273        Integer channelSamplesPerPixelValue = src.getChannelSamplesPerPixel(imageIndex, channelIndex); 
     274        if (channelSamplesPerPixelValue != null) dest.setChannelSamplesPerPixel(channelSamplesPerPixelValue, imageIndex, channelIndex); 
     275        //int annotationRefCount = src.getAnnotationRefCount(imageIndex, channelIndex); 
     276        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     277        //} 
     278          Binning detectorSettingsBinningValue = src.getDetectorSettingsBinning(imageIndex, channelIndex); 
     279          if (detectorSettingsBinningValue != null) dest.setDetectorSettingsBinning(detectorSettingsBinningValue, imageIndex, channelIndex); 
     280          Double detectorSettingsGainValue = src.getDetectorSettingsGain(imageIndex, channelIndex); 
     281          if (detectorSettingsGainValue != null) dest.setDetectorSettingsGain(detectorSettingsGainValue, imageIndex, channelIndex); 
     282          String detectorSettingsIDValue = src.getDetectorSettingsID(imageIndex, channelIndex); 
     283          if (detectorSettingsIDValue != null) dest.setDetectorSettingsID(detectorSettingsIDValue, imageIndex, channelIndex); 
     284          Double detectorSettingsOffsetValue = src.getDetectorSettingsOffset(imageIndex, channelIndex); 
     285          if (detectorSettingsOffsetValue != null) dest.setDetectorSettingsOffset(detectorSettingsOffsetValue, imageIndex, channelIndex); 
     286          Double detectorSettingsReadOutRateValue = src.getDetectorSettingsReadOutRate(imageIndex, channelIndex); 
     287          if (detectorSettingsReadOutRateValue != null) dest.setDetectorSettingsReadOutRate(detectorSettingsReadOutRateValue, imageIndex, channelIndex); 
     288          Double detectorSettingsVoltageValue = src.getDetectorSettingsVoltage(imageIndex, channelIndex); 
     289          if (detectorSettingsVoltageValue != null) dest.setDetectorSettingsVoltage(detectorSettingsVoltageValue, imageIndex, channelIndex); 
     290          String lightPathDichroicRefValue = src.getLightPathDichroicRef(imageIndex, channelIndex); 
     291          if (lightPathDichroicRefValue != null) dest.setLightPathDichroicRef(lightPathDichroicRefValue, imageIndex, channelIndex); 
     292          for (int emissionFilterRefIndex=0; emissionFilterRefIndex<src.getLightPathEmissionFilterRefCount(imageIndex, channelIndex); emissionFilterRefIndex++) {  
     293            String lightPathEmissionFilterRefValue = src.getLightPathEmissionFilterRef(imageIndex, channelIndex, emissionFilterRefIndex); 
     294            if (lightPathEmissionFilterRefValue != null) dest.setLightPathEmissionFilterRef(lightPathEmissionFilterRefValue, imageIndex, channelIndex, emissionFilterRefIndex); 
     295          } 
     296          for (int excitationFilterRefIndex=0; excitationFilterRefIndex<src.getLightPathExcitationFilterRefCount(imageIndex, channelIndex); excitationFilterRefIndex++) { 
     297            String lightPathExcitationFilterRefValue = src.getLightPathExcitationFilterRef(imageIndex, channelIndex, excitationFilterRefIndex); 
     298            if (lightPathExcitationFilterRefValue != null) dest.setLightPathExcitationFilterRef(lightPathExcitationFilterRefValue, imageIndex, channelIndex, excitationFilterRefIndex); 
     299          } 
     300          /* 
     301        int emissionFilterRefCount = src.getEmissionFilterRefCount(imageIndex, channelIndex); 
     302        for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) { 
     303        } 
     304        int excitationFilterRefCount = src.getExcitationFilterRefCount(imageIndex, channelIndex); 
     305        for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) { 
     306        } 
     307        */ 
     308      } 
     309      int datasetRefCount = src.getDatasetRefCount(imageIndex); 
     310      for (int datasetRefIndex=0; datasetRefIndex<datasetRefCount; datasetRefIndex++) { 
     311      } 
     312        Double imagingEnvironmentAirPressureValue = src.getImagingEnvironmentAirPressure(imageIndex); 
     313        if (imagingEnvironmentAirPressureValue != null) dest.setImagingEnvironmentAirPressure(imagingEnvironmentAirPressureValue, imageIndex); 
     314        PercentFraction imagingEnvironmentCO2PercentValue = src.getImagingEnvironmentCO2Percent(imageIndex); 
     315        if (imagingEnvironmentCO2PercentValue != null) dest.setImagingEnvironmentCO2Percent(imagingEnvironmentCO2PercentValue, imageIndex); 
     316        PercentFraction imagingEnvironmentHumidityValue = src.getImagingEnvironmentHumidity(imageIndex); 
     317        if (imagingEnvironmentHumidityValue != null) dest.setImagingEnvironmentHumidity(imagingEnvironmentHumidityValue, imageIndex); 
     318        Double imagingEnvironmentTemperatureValue = src.getImagingEnvironmentTemperature(imageIndex); 
     319        if (imagingEnvironmentTemperatureValue != null) dest.setImagingEnvironmentTemperature(imagingEnvironmentTemperatureValue, imageIndex); 
     320      int microbeamManipulationRefCount = src.getMicrobeamManipulationRefCount(imageIndex); 
     321      for (int microbeamManipulationRefIndex=0; microbeamManipulationRefIndex<microbeamManipulationRefCount; microbeamManipulationRefIndex++) { 
     322      } 
     323        //String pixelsAnnotationRefValue = src.getPixelsAnnotationRef(imageIndex, annotationRefIndex); 
     324        //if (pixelsAnnotationRefValue != null) dest.setPixelsAnnotationRef(pixelsAnnotationRefValue, imageIndex, annotationRefIndex); 
     325        DimensionOrder pixelsDimensionOrderValue = src.getPixelsDimensionOrder(imageIndex); 
     326        if (pixelsDimensionOrderValue != null) dest.setPixelsDimensionOrder(pixelsDimensionOrderValue, imageIndex); 
     327        String pixelsIDValue = src.getPixelsID(imageIndex); 
     328        if (pixelsIDValue != null) dest.setPixelsID(pixelsIDValue, imageIndex); 
     329        Double pixelsPhysicalSizeXValue = src.getPixelsPhysicalSizeX(imageIndex); 
     330        if (pixelsPhysicalSizeXValue != null) dest.setPixelsPhysicalSizeX(pixelsPhysicalSizeXValue, imageIndex); 
     331        Double pixelsPhysicalSizeYValue = src.getPixelsPhysicalSizeY(imageIndex); 
     332        if (pixelsPhysicalSizeYValue != null) dest.setPixelsPhysicalSizeY(pixelsPhysicalSizeYValue, imageIndex); 
     333        Double pixelsPhysicalSizeZValue = src.getPixelsPhysicalSizeZ(imageIndex); 
     334        if (pixelsPhysicalSizeZValue != null) dest.setPixelsPhysicalSizeZ(pixelsPhysicalSizeZValue, imageIndex); 
     335        PositiveInteger pixelsSizeCValue = src.getPixelsSizeC(imageIndex); 
     336        if (pixelsSizeCValue != null) dest.setPixelsSizeC(pixelsSizeCValue, imageIndex); 
     337        PositiveInteger pixelsSizeTValue = src.getPixelsSizeT(imageIndex); 
     338        if (pixelsSizeTValue != null) dest.setPixelsSizeT(pixelsSizeTValue, imageIndex); 
     339        PositiveInteger pixelsSizeXValue = src.getPixelsSizeX(imageIndex); 
     340        if (pixelsSizeXValue != null) dest.setPixelsSizeX(pixelsSizeXValue, imageIndex); 
     341        PositiveInteger pixelsSizeYValue = src.getPixelsSizeY(imageIndex); 
     342        if (pixelsSizeYValue != null) dest.setPixelsSizeY(pixelsSizeYValue, imageIndex); 
     343        PositiveInteger pixelsSizeZValue = src.getPixelsSizeZ(imageIndex); 
     344        if (pixelsSizeZValue != null) dest.setPixelsSizeZ(pixelsSizeZValue, imageIndex); 
     345        Double pixelsTimeIncrementValue = src.getPixelsTimeIncrement(imageIndex); 
     346        if (pixelsTimeIncrementValue != null) dest.setPixelsTimeIncrement(pixelsTimeIncrementValue, imageIndex); 
     347        PixelType pixelsTypeValue = src.getPixelsType(imageIndex); 
     348        if (pixelsTypeValue != null) dest.setPixelsType(pixelsTypeValue, imageIndex); 
     349      //int annotationRefCount = src.getAnnotationRefCount(imageIndex); 
     350      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     351      //} 
     352      int binDataCount = src.getPixelsBinDataCount(imageIndex); 
     353      for (int binDataIndex=0; binDataIndex<binDataCount; binDataIndex++) { 
     354        Boolean pixelsBinDataBigEndianValue = src.getPixelsBinDataBigEndian(imageIndex, binDataIndex); 
     355        if (pixelsBinDataBigEndianValue != null) dest.setPixelsBinDataBigEndian(pixelsBinDataBigEndianValue, imageIndex, binDataIndex); 
     356      } 
     357      int planeCount = src.getPlaneCount(imageIndex); 
     358      for (int planeIndex=0; planeIndex<planeCount; planeIndex++) { 
     359        //String planeAnnotationRefValue = src.getPlaneAnnotationRef(imageIndex, planeIndex, annotationRefIndex); 
     360        //if (planeAnnotationRefValue != null) dest.setPlaneAnnotationRef(planeAnnotationRefValue, imageIndex, planeIndex, annotationRefIndex); 
     361        Double planeDeltaTValue = src.getPlaneDeltaT(imageIndex, planeIndex); 
     362        if (planeDeltaTValue != null) dest.setPlaneDeltaT(planeDeltaTValue, imageIndex, planeIndex); 
     363        Double planeExposureTimeValue = src.getPlaneExposureTime(imageIndex, planeIndex); 
     364        if (planeExposureTimeValue != null) dest.setPlaneExposureTime(planeExposureTimeValue, imageIndex, planeIndex); 
     365        String planeHashSHA1Value = src.getPlaneHashSHA1(imageIndex, planeIndex); 
     366        if (planeHashSHA1Value != null) dest.setPlaneHashSHA1(planeHashSHA1Value, imageIndex, planeIndex); 
     367        Double planePositionXValue = src.getPlanePositionX(imageIndex, planeIndex); 
     368        if (planePositionXValue != null) dest.setPlanePositionX(planePositionXValue, imageIndex, planeIndex); 
     369        Double planePositionYValue = src.getPlanePositionY(imageIndex, planeIndex); 
     370        if (planePositionYValue != null) dest.setPlanePositionY(planePositionYValue, imageIndex, planeIndex); 
     371        Double planePositionZValue = src.getPlanePositionZ(imageIndex, planeIndex); 
     372        if (planePositionZValue != null) dest.setPlanePositionZ(planePositionZValue, imageIndex, planeIndex); 
     373        Integer planeTheCValue = src.getPlaneTheC(imageIndex, planeIndex); 
     374        if (planeTheCValue != null) dest.setPlaneTheC(planeTheCValue, imageIndex, planeIndex); 
     375        Integer planeTheTValue = src.getPlaneTheT(imageIndex, planeIndex); 
     376        if (planeTheTValue != null) dest.setPlaneTheT(planeTheTValue, imageIndex, planeIndex); 
     377        Integer planeTheZValue = src.getPlaneTheZ(imageIndex, planeIndex); 
     378        if (planeTheZValue != null) dest.setPlaneTheZ(planeTheZValue, imageIndex, planeIndex); 
     379        //int annotationRefCount = src.getAnnotationRefCount(imageIndex, planeIndex); 
     380        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     381        //} 
     382      } 
     383      int roiRefCount = src.getImageROIRefCount(imageIndex); 
     384      for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
     385      } 
     386        String stageLabelNameValue = src.getStageLabelName(imageIndex); 
     387        if (stageLabelNameValue != null) dest.setStageLabelName(stageLabelNameValue, imageIndex); 
     388        Double stageLabelXValue = src.getStageLabelX(imageIndex); 
     389        if (stageLabelXValue != null) dest.setStageLabelX(stageLabelXValue, imageIndex); 
     390        Double stageLabelYValue = src.getStageLabelY(imageIndex); 
     391        if (stageLabelYValue != null) dest.setStageLabelY(stageLabelYValue, imageIndex); 
     392        Double stageLabelZValue = src.getStageLabelZ(imageIndex); 
     393        if (stageLabelZValue != null) dest.setStageLabelZ(stageLabelZValue, imageIndex); 
     394      int tiffDataCount = src.getTiffDataCount(imageIndex); 
     395      for (int tiffDataIndex=0; tiffDataIndex<tiffDataCount; tiffDataIndex++) { 
     396        Integer tiffDataFirstCValue = src.getTiffDataFirstC(imageIndex, tiffDataIndex); 
     397        if (tiffDataFirstCValue != null) dest.setTiffDataFirstC(tiffDataFirstCValue, imageIndex, tiffDataIndex); 
     398        Integer tiffDataFirstTValue = src.getTiffDataFirstT(imageIndex, tiffDataIndex); 
     399        if (tiffDataFirstTValue != null) dest.setTiffDataFirstT(tiffDataFirstTValue, imageIndex, tiffDataIndex); 
     400        Integer tiffDataFirstZValue = src.getTiffDataFirstZ(imageIndex, tiffDataIndex); 
     401        if (tiffDataFirstZValue != null) dest.setTiffDataFirstZ(tiffDataFirstZValue, imageIndex, tiffDataIndex); 
     402        Integer tiffDataIFDValue = src.getTiffDataIFD(imageIndex, tiffDataIndex); 
     403        if (tiffDataIFDValue != null) dest.setTiffDataIFD(tiffDataIFDValue, imageIndex, tiffDataIndex); 
     404        Integer tiffDataPlaneCountValue = src.getTiffDataPlaneCount(imageIndex, tiffDataIndex); 
     405        if (tiffDataPlaneCountValue != null) dest.setTiffDataPlaneCount(tiffDataPlaneCountValue, imageIndex, tiffDataIndex); 
     406        String uuidFileNameValue = src.getUUIDFileName(imageIndex, tiffDataIndex); 
     407        if (uuidFileNameValue != null) dest.setUUIDFileName(uuidFileNameValue, imageIndex, tiffDataIndex); 
     408      } 
     409    } 
     410    int instrumentCount = src.getInstrumentCount(); 
     411    for (int instrumentIndex=0; instrumentIndex<instrumentCount; instrumentIndex++) { 
     412      String instrumentIDValue = src.getInstrumentID(instrumentIndex); 
     413      if (instrumentIDValue != null) dest.setInstrumentID(instrumentIDValue, instrumentIndex); 
     414      /* 
     415      int arcCount = src.getArcCount(instrumentIndex); 
     416      for (int arcIndex=0; arcIndex<arcCount; arcIndex++) { 
     417        String arcIDValue = src.getArcID(instrumentIndex, arcIndex); 
     418        if (arcIDValue != null) dest.setArcID(arcIDValue, instrumentIndex, arcIndex); 
     419        String arcLotNumberValue = src.getArcLotNumber(instrumentIndex, arcIndex); 
     420        if (arcLotNumberValue != null) dest.setArcLotNumber(arcLotNumberValue, instrumentIndex, arcIndex); 
     421        String arcManufacturerValue = src.getArcManufacturer(instrumentIndex, arcIndex); 
     422        if (arcManufacturerValue != null) dest.setArcManufacturer(arcManufacturerValue, instrumentIndex, arcIndex); 
     423        String arcModelValue = src.getArcModel(instrumentIndex, arcIndex); 
     424        if (arcModelValue != null) dest.setArcModel(arcModelValue, instrumentIndex, arcIndex); 
     425        Double arcPowerValue = src.getArcPower(instrumentIndex, arcIndex); 
     426        if (arcPowerValue != null) dest.setArcPower(arcPowerValue, instrumentIndex, arcIndex); 
     427        String arcSerialNumberValue = src.getArcSerialNumber(instrumentIndex, arcIndex); 
     428        if (arcSerialNumberValue != null) dest.setArcSerialNumber(arcSerialNumberValue, instrumentIndex, arcIndex); 
     429        ArcType arcTypeValue = src.getArcType(instrumentIndex, arcIndex); 
     430        if (arcTypeValue != null) dest.setArcType(arcTypeValue, instrumentIndex, arcIndex); 
     431      } 
     432      */ 
     433      int detectorCount = src.getDetectorCount(instrumentIndex); 
     434      for (int detectorIndex=0; detectorIndex<detectorCount; detectorIndex++) { 
     435        Double detectorAmplificationGainValue = src.getDetectorAmplificationGain(instrumentIndex, detectorIndex); 
     436        if (detectorAmplificationGainValue != null) dest.setDetectorAmplificationGain(detectorAmplificationGainValue, instrumentIndex, detectorIndex); 
     437        Double detectorGainValue = src.getDetectorGain(instrumentIndex, detectorIndex); 
     438        if (detectorGainValue != null) dest.setDetectorGain(detectorGainValue, instrumentIndex, detectorIndex); 
     439        String detectorIDValue = src.getDetectorID(instrumentIndex, detectorIndex); 
     440        if (detectorIDValue != null) dest.setDetectorID(detectorIDValue, instrumentIndex, detectorIndex); 
     441        String detectorLotNumberValue = src.getDetectorLotNumber(instrumentIndex, detectorIndex); 
     442        if (detectorLotNumberValue != null) dest.setDetectorLotNumber(detectorLotNumberValue, instrumentIndex, detectorIndex); 
     443        String detectorManufacturerValue = src.getDetectorManufacturer(instrumentIndex, detectorIndex); 
     444        if (detectorManufacturerValue != null) dest.setDetectorManufacturer(detectorManufacturerValue, instrumentIndex, detectorIndex); 
     445        String detectorModelValue = src.getDetectorModel(instrumentIndex, detectorIndex); 
     446        if (detectorModelValue != null) dest.setDetectorModel(detectorModelValue, instrumentIndex, detectorIndex); 
     447        Double detectorOffsetValue = src.getDetectorOffset(instrumentIndex, detectorIndex); 
     448        if (detectorOffsetValue != null) dest.setDetectorOffset(detectorOffsetValue, instrumentIndex, detectorIndex); 
     449        String detectorSerialNumberValue = src.getDetectorSerialNumber(instrumentIndex, detectorIndex); 
     450        if (detectorSerialNumberValue != null) dest.setDetectorSerialNumber(detectorSerialNumberValue, instrumentIndex, detectorIndex); 
     451        DetectorType detectorTypeValue = src.getDetectorType(instrumentIndex, detectorIndex); 
     452        if (detectorTypeValue != null) dest.setDetectorType(detectorTypeValue, instrumentIndex, detectorIndex); 
     453        Double detectorVoltageValue = src.getDetectorVoltage(instrumentIndex, detectorIndex); 
     454        if (detectorVoltageValue != null) dest.setDetectorVoltage(detectorVoltageValue, instrumentIndex, detectorIndex); 
     455        Double detectorZoomValue = src.getDetectorZoom(instrumentIndex, detectorIndex); 
     456        if (detectorZoomValue != null) dest.setDetectorZoom(detectorZoomValue, instrumentIndex, detectorIndex); 
     457      } 
     458      int dichroicCount = src.getDichroicCount(instrumentIndex); 
     459      for (int dichroicIndex=0; dichroicIndex<dichroicCount; dichroicIndex++) { 
     460        String dichroicIDValue = src.getDichroicID(instrumentIndex, dichroicIndex); 
     461        if (dichroicIDValue != null) dest.setDichroicID(dichroicIDValue, instrumentIndex, dichroicIndex); 
     462        String dichroicLotNumberValue = src.getDichroicLotNumber(instrumentIndex, dichroicIndex); 
     463        if (dichroicLotNumberValue != null) dest.setDichroicLotNumber(dichroicLotNumberValue, instrumentIndex, dichroicIndex); 
     464        String dichroicManufacturerValue = src.getDichroicManufacturer(instrumentIndex, dichroicIndex); 
     465        if (dichroicManufacturerValue != null) dest.setDichroicManufacturer(dichroicManufacturerValue, instrumentIndex, dichroicIndex); 
     466        String dichroicModelValue = src.getDichroicModel(instrumentIndex, dichroicIndex); 
     467        if (dichroicModelValue != null) dest.setDichroicModel(dichroicModelValue, instrumentIndex, dichroicIndex); 
     468        String dichroicSerialNumberValue = src.getDichroicSerialNumber(instrumentIndex, dichroicIndex); 
     469        if (dichroicSerialNumberValue != null) dest.setDichroicSerialNumber(dichroicSerialNumberValue, instrumentIndex, dichroicIndex); 
     470      } 
     471      /* 
     472      int filamentCount = src.getFilamentCount(instrumentIndex); 
     473      for (int filamentIndex=0; filamentIndex<filamentCount; filamentIndex++) { 
     474        String filamentIDValue = src.getFilamentID(instrumentIndex, filamentIndex); 
     475        if (filamentIDValue != null) dest.setFilamentID(filamentIDValue, instrumentIndex, filamentIndex); 
     476        String filamentLotNumberValue = src.getFilamentLotNumber(instrumentIndex, filamentIndex); 
     477        if (filamentLotNumberValue != null) dest.setFilamentLotNumber(filamentLotNumberValue, instrumentIndex, filamentIndex); 
     478        String filamentManufacturerValue = src.getFilamentManufacturer(instrumentIndex, filamentIndex); 
     479        if (filamentManufacturerValue != null) dest.setFilamentManufacturer(filamentManufacturerValue, instrumentIndex, filamentIndex); 
     480        String filamentModelValue = src.getFilamentModel(instrumentIndex, filamentIndex); 
     481        if (filamentModelValue != null) dest.setFilamentModel(filamentModelValue, instrumentIndex, filamentIndex); 
     482        Double filamentPowerValue = src.getFilamentPower(instrumentIndex, filamentIndex); 
     483        if (filamentPowerValue != null) dest.setFilamentPower(filamentPowerValue, instrumentIndex, filamentIndex); 
     484        String filamentSerialNumberValue = src.getFilamentSerialNumber(instrumentIndex, filamentIndex); 
     485        if (filamentSerialNumberValue != null) dest.setFilamentSerialNumber(filamentSerialNumberValue, instrumentIndex, filamentIndex); 
     486        FilamentType filamentTypeValue = src.getFilamentType(instrumentIndex, filamentIndex); 
     487        if (filamentTypeValue != null) dest.setFilamentType(filamentTypeValue, instrumentIndex, filamentIndex); 
     488      } 
     489      */ 
     490      int filterCount = src.getFilterCount(instrumentIndex); 
     491      for (int filterIndex=0; filterIndex<filterCount; filterIndex++) { 
     492        String filterFilterWheelValue = src.getFilterFilterWheel(instrumentIndex, filterIndex); 
     493        if (filterFilterWheelValue != null) dest.setFilterFilterWheel(filterFilterWheelValue, instrumentIndex, filterIndex); 
     494        String filterIDValue = src.getFilterID(instrumentIndex, filterIndex); 
     495        if (filterIDValue != null) dest.setFilterID(filterIDValue, instrumentIndex, filterIndex); 
     496        String filterLotNumberValue = src.getFilterLotNumber(instrumentIndex, filterIndex); 
     497        if (filterLotNumberValue != null) dest.setFilterLotNumber(filterLotNumberValue, instrumentIndex, filterIndex); 
     498        String filterManufacturerValue = src.getFilterManufacturer(instrumentIndex, filterIndex); 
     499        if (filterManufacturerValue != null) dest.setFilterManufacturer(filterManufacturerValue, instrumentIndex, filterIndex); 
     500        String filterModelValue = src.getFilterModel(instrumentIndex, filterIndex); 
     501        if (filterModelValue != null) dest.setFilterModel(filterModelValue, instrumentIndex, filterIndex); 
     502        String filterSerialNumberValue = src.getFilterSerialNumber(instrumentIndex, filterIndex); 
     503        if (filterSerialNumberValue != null) dest.setFilterSerialNumber(filterSerialNumberValue, instrumentIndex, filterIndex); 
     504        FilterType filterTypeValue = src.getFilterType(instrumentIndex, filterIndex); 
     505        if (filterTypeValue != null) dest.setFilterType(filterTypeValue, instrumentIndex, filterIndex); 
     506        Integer transmittanceRangeCutInValue = src.getTransmittanceRangeCutIn(instrumentIndex, filterIndex); 
     507        if (transmittanceRangeCutInValue != null) dest.setTransmittanceRangeCutIn(transmittanceRangeCutInValue, instrumentIndex, filterIndex); 
     508        Integer transmittanceRangeCutInToleranceValue = src.getTransmittanceRangeCutInTolerance(instrumentIndex, filterIndex); 
     509        if (transmittanceRangeCutInToleranceValue != null) dest.setTransmittanceRangeCutInTolerance(transmittanceRangeCutInToleranceValue, instrumentIndex, filterIndex); 
     510        Integer transmittanceRangeCutOutValue = src.getTransmittanceRangeCutOut(instrumentIndex, filterIndex); 
     511        if (transmittanceRangeCutOutValue != null) dest.setTransmittanceRangeCutOut(transmittanceRangeCutOutValue, instrumentIndex, filterIndex); 
     512        Integer transmittanceRangeCutOutToleranceValue = src.getTransmittanceRangeCutOutTolerance(instrumentIndex, filterIndex); 
     513        if (transmittanceRangeCutOutToleranceValue != null) dest.setTransmittanceRangeCutOutTolerance(transmittanceRangeCutOutToleranceValue, instrumentIndex, filterIndex); 
     514        PercentFraction transmittanceRangeTransmittanceValue = src.getTransmittanceRangeTransmittance(instrumentIndex, filterIndex); 
     515        if (transmittanceRangeTransmittanceValue != null) dest.setTransmittanceRangeTransmittance(transmittanceRangeTransmittanceValue, instrumentIndex, filterIndex); 
     516      } 
     517      int filterSetCount = src.getFilterSetCount(instrumentIndex); 
     518      for (int filterSetIndex=0; filterSetIndex<filterSetCount; filterSetIndex++) { 
     519        String filterSetDichroicRefValue = src.getFilterSetDichroicRef(instrumentIndex, filterSetIndex); 
     520        if (filterSetDichroicRefValue != null) dest.setFilterSetDichroicRef(filterSetDichroicRefValue, instrumentIndex, filterSetIndex); 
     521        //String filterSetEmissionFilterRefValue = src.getFilterSetEmissionFilterRef(instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
     522        //if (filterSetEmissionFilterRefValue != null) dest.setFilterSetEmissionFilterRef(filterSetEmissionFilterRefValue, instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
     523        //String filterSetExcitationFilterRefValue = src.getFilterSetExcitationFilterRef(instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
     524        //if (filterSetExcitationFilterRefValue != null) dest.setFilterSetExcitationFilterRef(filterSetExcitationFilterRefValue, instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
     525        String filterSetIDValue = src.getFilterSetID(instrumentIndex, filterSetIndex); 
     526        if (filterSetIDValue != null) dest.setFilterSetID(filterSetIDValue, instrumentIndex, filterSetIndex); 
     527        String filterSetLotNumberValue = src.getFilterSetLotNumber(instrumentIndex, filterSetIndex); 
     528        if (filterSetLotNumberValue != null) dest.setFilterSetLotNumber(filterSetLotNumberValue, instrumentIndex, filterSetIndex); 
     529        String filterSetManufacturerValue = src.getFilterSetManufacturer(instrumentIndex, filterSetIndex); 
     530        if (filterSetManufacturerValue != null) dest.setFilterSetManufacturer(filterSetManufacturerValue, instrumentIndex, filterSetIndex); 
     531        String filterSetModelValue = src.getFilterSetModel(instrumentIndex, filterSetIndex); 
     532        if (filterSetModelValue != null) dest.setFilterSetModel(filterSetModelValue, instrumentIndex, filterSetIndex); 
     533        String filterSetSerialNumberValue = src.getFilterSetSerialNumber(instrumentIndex, filterSetIndex); 
     534        if (filterSetSerialNumberValue != null) dest.setFilterSetSerialNumber(filterSetSerialNumberValue, instrumentIndex, filterSetIndex); 
     535        /* 
     536        int emissionFilterRefCount = src.getEmissionFilterRefCount(instrumentIndex, filterSetIndex); 
     537        for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) { 
     538        } 
     539        int excitationFilterRefCount = src.getExcitationFilterRefCount(instrumentIndex, filterSetIndex); 
     540        for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) { 
     541        } 
     542        */ 
     543      } 
     544      /* 
     545      int laserCount = src.getLaserCount(instrumentIndex); 
     546      for (int laserIndex=0; laserIndex<laserCount; laserIndex++) { 
     547        PositiveInteger laserFrequencyMultiplicationValue = src.getLaserFrequencyMultiplication(instrumentIndex, laserIndex); 
     548        if (laserFrequencyMultiplicationValue != null) dest.setLaserFrequencyMultiplication(laserFrequencyMultiplicationValue, instrumentIndex, laserIndex); 
     549        String laserIDValue = src.getLaserID(instrumentIndex, laserIndex); 
     550        if (laserIDValue != null) dest.setLaserID(laserIDValue, instrumentIndex, laserIndex); 
     551        LaserMedium laserLaserMediumValue = src.getLaserLaserMedium(instrumentIndex, laserIndex); 
     552        if (laserLaserMediumValue != null) dest.setLaserLaserMedium(laserLaserMediumValue, instrumentIndex, laserIndex); 
     553        String laserLotNumberValue = src.getLaserLotNumber(instrumentIndex, laserIndex); 
     554        if (laserLotNumberValue != null) dest.setLaserLotNumber(laserLotNumberValue, instrumentIndex, laserIndex); 
     555        String laserManufacturerValue = src.getLaserManufacturer(instrumentIndex, laserIndex); 
     556        if (laserManufacturerValue != null) dest.setLaserManufacturer(laserManufacturerValue, instrumentIndex, laserIndex); 
     557        String laserModelValue = src.getLaserModel(instrumentIndex, laserIndex); 
     558        if (laserModelValue != null) dest.setLaserModel(laserModelValue, instrumentIndex, laserIndex); 
     559        Boolean laserPockelCellValue = src.getLaserPockelCell(instrumentIndex, laserIndex); 
     560        if (laserPockelCellValue != null) dest.setLaserPockelCell(laserPockelCellValue, instrumentIndex, laserIndex); 
     561        Double laserPowerValue = src.getLaserPower(instrumentIndex, laserIndex); 
     562        if (laserPowerValue != null) dest.setLaserPower(laserPowerValue, instrumentIndex, laserIndex); 
     563        Pulse laserPulseValue = src.getLaserPulse(instrumentIndex, laserIndex); 
     564        if (laserPulseValue != null) dest.setLaserPulse(laserPulseValue, instrumentIndex, laserIndex); 
     565        String laserPumpValue = src.getLaserPump(instrumentIndex, laserIndex); 
     566        if (laserPumpValue != null) dest.setLaserPump(laserPumpValue, instrumentIndex, laserIndex); 
     567        Double laserRepetitionRateValue = src.getLaserRepetitionRate(instrumentIndex, laserIndex); 
     568        if (laserRepetitionRateValue != null) dest.setLaserRepetitionRate(laserRepetitionRateValue, instrumentIndex, laserIndex); 
     569        String laserSerialNumberValue = src.getLaserSerialNumber(instrumentIndex, laserIndex); 
     570        if (laserSerialNumberValue != null) dest.setLaserSerialNumber(laserSerialNumberValue, instrumentIndex, laserIndex); 
     571        Boolean laserTuneableValue = src.getLaserTuneable(instrumentIndex, laserIndex); 
     572        if (laserTuneableValue != null) dest.setLaserTuneable(laserTuneableValue, instrumentIndex, laserIndex); 
     573        LaserType laserTypeValue = src.getLaserType(instrumentIndex, laserIndex); 
     574        if (laserTypeValue != null) dest.setLaserType(laserTypeValue, instrumentIndex, laserIndex); 
     575        PositiveInteger laserWavelengthValue = src.getLaserWavelength(instrumentIndex, laserIndex); 
     576        if (laserWavelengthValue != null) dest.setLaserWavelength(laserWavelengthValue, instrumentIndex, laserIndex); 
     577      } 
     578      */ 
     579      /* 
     580      int lightEmittingDiodeCount = src.getLightEmittingDiodeCount(instrumentIndex); 
     581      for (int lightEmittingDiodeIndex=0; lightEmittingDiodeIndex<lightEmittingDiodeCount; lightEmittingDiodeIndex++) { 
     582        String lightEmittingDiodeIDValue = src.getLightEmittingDiodeID(instrumentIndex, lightEmittingDiodeIndex); 
     583        if (lightEmittingDiodeIDValue != null) dest.setLightEmittingDiodeID(lightEmittingDiodeIDValue, instrumentIndex, lightEmittingDiodeIndex); 
     584        String lightEmittingDiodeLotNumberValue = src.getLightEmittingDiodeLotNumber(instrumentIndex, lightEmittingDiodeIndex); 
     585        if (lightEmittingDiodeLotNumberValue != null) dest.setLightEmittingDiodeLotNumber(lightEmittingDiodeLotNumberValue, instrumentIndex, lightEmittingDiodeIndex); 
     586        String lightEmittingDiodeManufacturerValue = src.getLightEmittingDiodeManufacturer(instrumentIndex, lightEmittingDiodeIndex); 
     587        if (lightEmittingDiodeManufacturerValue != null) dest.setLightEmittingDiodeManufacturer(lightEmittingDiodeManufacturerValue, instrumentIndex, lightEmittingDiodeIndex); 
     588        String lightEmittingDiodeModelValue = src.getLightEmittingDiodeModel(instrumentIndex, lightEmittingDiodeIndex); 
     589        if (lightEmittingDiodeModelValue != null) dest.setLightEmittingDiodeModel(lightEmittingDiodeModelValue, instrumentIndex, lightEmittingDiodeIndex); 
     590        Double lightEmittingDiodePowerValue = src.getLightEmittingDiodePower(instrumentIndex, lightEmittingDiodeIndex); 
     591        if (lightEmittingDiodePowerValue != null) dest.setLightEmittingDiodePower(lightEmittingDiodePowerValue, instrumentIndex, lightEmittingDiodeIndex); 
     592        String lightEmittingDiodeSerialNumberValue = src.getLightEmittingDiodeSerialNumber(instrumentIndex, lightEmittingDiodeIndex); 
     593        if (lightEmittingDiodeSerialNumberValue != null) dest.setLightEmittingDiodeSerialNumber(lightEmittingDiodeSerialNumberValue, instrumentIndex, lightEmittingDiodeIndex); 
     594      } 
     595      */ 
     596        String microscopeLotNumberValue = src.getMicroscopeLotNumber(instrumentIndex); 
     597        if (microscopeLotNumberValue != null) dest.setMicroscopeLotNumber(microscopeLotNumberValue, instrumentIndex); 
     598        String microscopeManufacturerValue = src.getMicroscopeManufacturer(instrumentIndex); 
     599        if (microscopeManufacturerValue != null) dest.setMicroscopeManufacturer(microscopeManufacturerValue, instrumentIndex); 
     600        String microscopeModelValue = src.getMicroscopeModel(instrumentIndex); 
     601        if (microscopeModelValue != null) dest.setMicroscopeModel(microscopeModelValue, instrumentIndex); 
     602        String microscopeSerialNumberValue = src.getMicroscopeSerialNumber(instrumentIndex); 
     603        if (microscopeSerialNumberValue != null) dest.setMicroscopeSerialNumber(microscopeSerialNumberValue, instrumentIndex); 
     604        MicroscopeType microscopeTypeValue = src.getMicroscopeType(instrumentIndex); 
     605        if (microscopeTypeValue != null) dest.setMicroscopeType(microscopeTypeValue, instrumentIndex); 
     606      int otfCount = src.getOTFCount(instrumentIndex); 
     607      for (int otfIndex=0; otfIndex<otfCount; otfIndex++) { 
     608        String otfBinaryFileFileNameValue = src.getOTFBinaryFileFileName(instrumentIndex, otfIndex); 
     609        if (otfBinaryFileFileNameValue != null) dest.setOTFBinaryFileFileName(otfBinaryFileFileNameValue, instrumentIndex, otfIndex); 
     610        String otfBinaryFileMIMETypeValue = src.getOTFBinaryFileMIMEType(instrumentIndex, otfIndex); 
     611        if (otfBinaryFileMIMETypeValue != null) dest.setOTFBinaryFileMIMEType(otfBinaryFileMIMETypeValue, instrumentIndex, otfIndex); 
     612        Integer otfBinaryFileSizeValue = src.getOTFBinaryFileSize(instrumentIndex, otfIndex); 
     613        if (otfBinaryFileSizeValue != null) dest.setOTFBinaryFileSize(otfBinaryFileSizeValue, instrumentIndex, otfIndex); 
     614        String otfFilterSetRefValue = src.getOTFFilterSetRef(instrumentIndex, otfIndex); 
     615        if (otfFilterSetRefValue != null) dest.setOTFFilterSetRef(otfFilterSetRefValue, instrumentIndex, otfIndex); 
     616        String otfidValue = src.getOTFID(instrumentIndex, otfIndex); 
     617        if (otfidValue != null) dest.setOTFID(otfidValue, instrumentIndex, otfIndex); 
     618        Double otfObjectiveSettingsCorrectionCollarValue = src.getOTFObjectiveSettingsCorrectionCollar(instrumentIndex, otfIndex); 
     619        if (otfObjectiveSettingsCorrectionCollarValue != null) dest.setOTFObjectiveSettingsCorrectionCollar(otfObjectiveSettingsCorrectionCollarValue, instrumentIndex, otfIndex); 
     620        String otfObjectiveSettingsIDValue = src.getOTFObjectiveSettingsID(instrumentIndex, otfIndex); 
     621        if (otfObjectiveSettingsIDValue != null) dest.setOTFObjectiveSettingsID(otfObjectiveSettingsIDValue, instrumentIndex, otfIndex); 
     622        Medium otfObjectiveSettingsMediumValue = src.getOTFObjectiveSettingsMedium(instrumentIndex, otfIndex); 
     623        if (otfObjectiveSettingsMediumValue != null) dest.setOTFObjectiveSettingsMedium(otfObjectiveSettingsMediumValue, instrumentIndex, otfIndex); 
     624        Double otfObjectiveSettingsRefractiveIndexValue = src.getOTFObjectiveSettingsRefractiveIndex(instrumentIndex, otfIndex); 
     625        if (otfObjectiveSettingsRefractiveIndexValue != null) dest.setOTFObjectiveSettingsRefractiveIndex(otfObjectiveSettingsRefractiveIndexValue, instrumentIndex, otfIndex); 
     626        Boolean otfOpticalAxisAveragedValue = src.getOTFOpticalAxisAveraged(instrumentIndex, otfIndex); 
     627        if (otfOpticalAxisAveragedValue != null) dest.setOTFOpticalAxisAveraged(otfOpticalAxisAveragedValue, instrumentIndex, otfIndex); 
     628        PositiveInteger otfSizeXValue = src.getOTFSizeX(instrumentIndex, otfIndex); 
     629        if (otfSizeXValue != null) dest.setOTFSizeX(otfSizeXValue, instrumentIndex, otfIndex); 
     630        PositiveInteger otfSizeYValue = src.getOTFSizeY(instrumentIndex, otfIndex); 
     631        if (otfSizeYValue != null) dest.setOTFSizeY(otfSizeYValue, instrumentIndex, otfIndex); 
     632        PixelType otfTypeValue = src.getOTFType(instrumentIndex, otfIndex); 
     633        if (otfTypeValue != null) dest.setOTFType(otfTypeValue, instrumentIndex, otfIndex); 
     634      } 
     635      int objectiveCount = src.getObjectiveCount(instrumentIndex); 
     636      for (int objectiveIndex=0; objectiveIndex<objectiveCount; objectiveIndex++) { 
     637        Double objectiveCalibratedMagnificationValue = src.getObjectiveCalibratedMagnification(instrumentIndex, objectiveIndex); 
     638        if (objectiveCalibratedMagnificationValue != null) dest.setObjectiveCalibratedMagnification(objectiveCalibratedMagnificationValue, instrumentIndex, objectiveIndex); 
     639        Correction objectiveCorrectionValue = src.getObjectiveCorrection(instrumentIndex, objectiveIndex); 
     640        if (objectiveCorrectionValue != null) dest.setObjectiveCorrection(objectiveCorrectionValue, instrumentIndex, objectiveIndex); 
     641        String objectiveIDValue = src.getObjectiveID(instrumentIndex, objectiveIndex); 
     642        if (objectiveIDValue != null) dest.setObjectiveID(objectiveIDValue, instrumentIndex, objectiveIndex); 
     643        Immersion objectiveImmersionValue = src.getObjectiveImmersion(instrumentIndex, objectiveIndex); 
     644        if (objectiveImmersionValue != null) dest.setObjectiveImmersion(objectiveImmersionValue, instrumentIndex, objectiveIndex); 
     645        Boolean objectiveIrisValue = src.getObjectiveIris(instrumentIndex, objectiveIndex); 
     646        if (objectiveIrisValue != null) dest.setObjectiveIris(objectiveIrisValue, instrumentIndex, objectiveIndex); 
     647        Double objectiveLensNAValue = src.getObjectiveLensNA(instrumentIndex, objectiveIndex); 
     648        if (objectiveLensNAValue != null) dest.setObjectiveLensNA(objectiveLensNAValue, instrumentIndex, objectiveIndex); 
     649        String objectiveLotNumberValue = src.getObjectiveLotNumber(instrumentIndex, objectiveIndex); 
     650        if (objectiveLotNumberValue != null) dest.setObjectiveLotNumber(objectiveLotNumberValue, instrumentIndex, objectiveIndex); 
     651        String objectiveManufacturerValue = src.getObjectiveManufacturer(instrumentIndex, objectiveIndex); 
     652        if (objectiveManufacturerValue != null) dest.setObjectiveManufacturer(objectiveManufacturerValue, instrumentIndex, objectiveIndex); 
     653        String objectiveModelValue = src.getObjectiveModel(instrumentIndex, objectiveIndex); 
     654        if (objectiveModelValue != null) dest.setObjectiveModel(objectiveModelValue, instrumentIndex, objectiveIndex); 
     655        Integer objectiveNominalMagnificationValue = src.getObjectiveNominalMagnification(instrumentIndex, objectiveIndex); 
     656        if (objectiveNominalMagnificationValue != null) dest.setObjectiveNominalMagnification(objectiveNominalMagnificationValue, instrumentIndex, objectiveIndex); 
     657        String objectiveSerialNumberValue = src.getObjectiveSerialNumber(instrumentIndex, objectiveIndex); 
     658        if (objectiveSerialNumberValue != null) dest.setObjectiveSerialNumber(objectiveSerialNumberValue, instrumentIndex, objectiveIndex); 
     659        Double objectiveWorkingDistanceValue = src.getObjectiveWorkingDistance(instrumentIndex, objectiveIndex); 
     660        if (objectiveWorkingDistanceValue != null) dest.setObjectiveWorkingDistance(objectiveWorkingDistanceValue, instrumentIndex, objectiveIndex); 
     661      } 
     662    } 
     663    int listAnnotationCount = src.getListAnnotationCount(); 
     664    for (int listAnnotationIndex=0; listAnnotationIndex<listAnnotationCount; listAnnotationIndex++) { 
     665      //String listAnnotationAnnotationRefValue = src.getListAnnotationAnnotationRef(listAnnotationIndex, annotationRefIndex); 
     666      //if (listAnnotationAnnotationRefValue != null) dest.setListAnnotationAnnotationRef(listAnnotationAnnotationRefValue, listAnnotationIndex, annotationRefIndex); 
     667      String listAnnotationIDValue = src.getListAnnotationID(listAnnotationIndex); 
     668      if (listAnnotationIDValue != null) dest.setListAnnotationID(listAnnotationIDValue, listAnnotationIndex); 
     669      String listAnnotationNamespaceValue = src.getListAnnotationNamespace(listAnnotationIndex); 
     670      if (listAnnotationNamespaceValue != null) dest.setListAnnotationNamespace(listAnnotationNamespaceValue, listAnnotationIndex); 
     671      //int annotationRefCount = src.getAnnotationRefCount(listAnnotationIndex); 
     672      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     673      //} 
     674    } 
     675    int longAnnotationCount = src.getLongAnnotationCount(); 
     676    for (int longAnnotationIndex=0; longAnnotationIndex<longAnnotationCount; longAnnotationIndex++) { 
     677      String longAnnotationIDValue = src.getLongAnnotationID(longAnnotationIndex); 
     678      if (longAnnotationIDValue != null) dest.setLongAnnotationID(longAnnotationIDValue, longAnnotationIndex); 
     679      String longAnnotationNamespaceValue = src.getLongAnnotationNamespace(longAnnotationIndex); 
     680      if (longAnnotationNamespaceValue != null) dest.setLongAnnotationNamespace(longAnnotationNamespaceValue, longAnnotationIndex); 
     681      Long longAnnotationValueValue = src.getLongAnnotationValue(longAnnotationIndex); 
     682      if (longAnnotationValueValue != null) dest.setLongAnnotationValue(longAnnotationValueValue, longAnnotationIndex); 
     683    } 
     684    int plateCount = src.getPlateCount(); 
     685    for (int plateIndex=0; plateIndex<plateCount; plateIndex++) { 
     686      //String plateAnnotationRefValue = src.getPlateAnnotationRef(plateIndex, annotationRefIndex); 
     687      //if (plateAnnotationRefValue != null) dest.setPlateAnnotationRef(plateAnnotationRefValue, plateIndex, annotationRefIndex); 
     688      NamingConvention plateColumnNamingConventionValue = src.getPlateColumnNamingConvention(plateIndex); 
     689      if (plateColumnNamingConventionValue != null) dest.setPlateColumnNamingConvention(plateColumnNamingConventionValue, plateIndex); 
     690      Integer plateColumnsValue = src.getPlateColumns(plateIndex); 
     691      if (plateColumnsValue != null) dest.setPlateColumns(plateColumnsValue, plateIndex); 
     692      String plateDescriptionValue = src.getPlateDescription(plateIndex); 
     693      if (plateDescriptionValue != null) dest.setPlateDescription(plateDescriptionValue, plateIndex); 
     694      String plateExternalIdentifierValue = src.getPlateExternalIdentifier(plateIndex); 
     695      if (plateExternalIdentifierValue != null) dest.setPlateExternalIdentifier(plateExternalIdentifierValue, plateIndex); 
     696      String plateIDValue = src.getPlateID(plateIndex); 
     697      if (plateIDValue != null) dest.setPlateID(plateIDValue, plateIndex); 
     698      String plateNameValue = src.getPlateName(plateIndex); 
     699      if (plateNameValue != null) dest.setPlateName(plateNameValue, plateIndex); 
     700      NamingConvention plateRowNamingConventionValue = src.getPlateRowNamingConvention(plateIndex); 
     701      if (plateRowNamingConventionValue != null) dest.setPlateRowNamingConvention(plateRowNamingConventionValue, plateIndex); 
     702      Integer plateRowsValue = src.getPlateRows(plateIndex); 
     703      if (plateRowsValue != null) dest.setPlateRows(plateRowsValue, plateIndex); 
     704      //String plateScreenRefValue = src.getPlateScreenRef(plateIndex, screenRefIndex); 
     705      //if (plateScreenRefValue != null) dest.setPlateScreenRef(plateScreenRefValue, plateIndex, screenRefIndex); 
     706      String plateStatusValue = src.getPlateStatus(plateIndex); 
     707      if (plateStatusValue != null) dest.setPlateStatus(plateStatusValue, plateIndex); 
     708      Double plateWellOriginXValue = src.getPlateWellOriginX(plateIndex); 
     709      if (plateWellOriginXValue != null) dest.setPlateWellOriginX(plateWellOriginXValue, plateIndex); 
     710      Double plateWellOriginYValue = src.getPlateWellOriginY(plateIndex); 
     711      if (plateWellOriginYValue != null) dest.setPlateWellOriginY(plateWellOriginYValue, plateIndex); 
     712      //int annotationRefCount = src.getAnnotationRefCount(plateIndex); 
     713      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     714      //} 
     715      int plateAcquisitionCount = src.getPlateAcquisitionCount(plateIndex); 
     716      for (int plateAcquisitionIndex=0; plateAcquisitionIndex<plateAcquisitionCount; plateAcquisitionIndex++) { 
     717        //String plateAcquisitionAnnotationRefValue = src.getPlateAcquisitionAnnotationRef(plateIndex, plateAcquisitionIndex, annotationRefIndex); 
     718        //if (plateAcquisitionAnnotationRefValue != null) dest.setPlateAcquisitionAnnotationRef(plateAcquisitionAnnotationRefValue, plateIndex, plateAcquisitionIndex, annotationRefIndex); 
     719        String plateAcquisitionDescriptionValue = src.getPlateAcquisitionDescription(plateIndex, plateAcquisitionIndex); 
     720        if (plateAcquisitionDescriptionValue != null) dest.setPlateAcquisitionDescription(plateAcquisitionDescriptionValue, plateIndex, plateAcquisitionIndex); 
     721        String plateAcquisitionEndTimeValue = src.getPlateAcquisitionEndTime(plateIndex, plateAcquisitionIndex); 
     722        if (plateAcquisitionEndTimeValue != null) dest.setPlateAcquisitionEndTime(plateAcquisitionEndTimeValue, plateIndex, plateAcquisitionIndex); 
     723        String plateAcquisitionIDValue = src.getPlateAcquisitionID(plateIndex, plateAcquisitionIndex); 
     724        if (plateAcquisitionIDValue != null) dest.setPlateAcquisitionID(plateAcquisitionIDValue, plateIndex, plateAcquisitionIndex); 
     725        Integer plateAcquisitionMaximumFieldCountValue = src.getPlateAcquisitionMaximumFieldCount(plateIndex, plateAcquisitionIndex); 
     726        if (plateAcquisitionMaximumFieldCountValue != null) dest.setPlateAcquisitionMaximumFieldCount(plateAcquisitionMaximumFieldCountValue, plateIndex, plateAcquisitionIndex); 
     727        String plateAcquisitionNameValue = src.getPlateAcquisitionName(plateIndex, plateAcquisitionIndex); 
     728        if (plateAcquisitionNameValue != null) dest.setPlateAcquisitionName(plateAcquisitionNameValue, plateIndex, plateAcquisitionIndex); 
     729        String plateAcquisitionStartTimeValue = src.getPlateAcquisitionStartTime(plateIndex, plateAcquisitionIndex); 
     730        if (plateAcquisitionStartTimeValue != null) dest.setPlateAcquisitionStartTime(plateAcquisitionStartTimeValue, plateIndex, plateAcquisitionIndex); 
     731        //String plateAcquisitionWellSampleRefValue = src.getPlateAcquisitionWellSampleRef(plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
     732        //if (plateAcquisitionWellSampleRefValue != null) dest.setPlateAcquisitionWellSampleRef(plateAcquisitionWellSampleRefValue, plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
     733        //int annotationRefCount = src.getAnnotationRefCount(plateIndex, plateAcquisitionIndex); 
     734        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     735        //} 
     736        int wellSampleRefCount = src.getWellSampleRefCount(plateIndex, plateAcquisitionIndex); 
     737        for (int wellSampleRefIndex=0; wellSampleRefIndex<wellSampleRefCount; wellSampleRefIndex++) { 
     738        } 
     739      } 
     740      int screenRefCount = src.getScreenRefCount(plateIndex); 
     741      for (int screenRefIndex=0; screenRefIndex<screenRefCount; screenRefIndex++) { 
     742      } 
     743      int wellCount = src.getWellCount(plateIndex); 
     744      for (int wellIndex=0; wellIndex<wellCount; wellIndex++) { 
     745        //String wellAnnotationRefValue = src.getWellAnnotationRef(plateIndex, wellIndex, annotationRefIndex); 
     746        //if (wellAnnotationRefValue != null) dest.setWellAnnotationRef(wellAnnotationRefValue, plateIndex, wellIndex, annotationRefIndex); 
     747        Integer wellColorValue = src.getWellColor(plateIndex, wellIndex); 
     748        if (wellColorValue != null) dest.setWellColor(wellColorValue, plateIndex, wellIndex); 
     749        NonNegativeInteger wellColumnValue = src.getWellColumn(plateIndex, wellIndex); 
     750        if (wellColumnValue != null) dest.setWellColumn(wellColumnValue, plateIndex, wellIndex); 
     751        String wellExternalDescriptionValue = src.getWellExternalDescription(plateIndex, wellIndex); 
     752        if (wellExternalDescriptionValue != null) dest.setWellExternalDescription(wellExternalDescriptionValue, plateIndex, wellIndex); 
     753        String wellExternalIdentifierValue = src.getWellExternalIdentifier(plateIndex, wellIndex); 
     754        if (wellExternalIdentifierValue != null) dest.setWellExternalIdentifier(wellExternalIdentifierValue, plateIndex, wellIndex); 
     755        String wellIDValue = src.getWellID(plateIndex, wellIndex); 
     756        if (wellIDValue != null) dest.setWellID(wellIDValue, plateIndex, wellIndex); 
     757        String wellReagentRefValue = src.getWellReagentRef(plateIndex, wellIndex); 
     758        if (wellReagentRefValue != null) dest.setWellReagentRef(wellReagentRefValue, plateIndex, wellIndex); 
     759        NonNegativeInteger wellRowValue = src.getWellRow(plateIndex, wellIndex); 
     760        if (wellRowValue != null) dest.setWellRow(wellRowValue, plateIndex, wellIndex); 
     761        String wellStatusValue = src.getWellStatus(plateIndex, wellIndex); 
     762        if (wellStatusValue != null) dest.setWellStatus(wellStatusValue, plateIndex, wellIndex); 
     763        //int annotationRefCount = src.getAnnotationRefCount(plateIndex, wellIndex); 
     764        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     765        //} 
     766        int wellSampleCount = src.getWellSampleCount(plateIndex, wellIndex); 
     767        for (int wellSampleIndex=0; wellSampleIndex<wellSampleCount; wellSampleIndex++) { 
     768          //String wellSampleAnnotationRefValue = src.getWellSampleAnnotationRef(plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
     769          //if (wellSampleAnnotationRefValue != null) dest.setWellSampleAnnotationRef(wellSampleAnnotationRefValue, plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
     770          String wellSampleIDValue = src.getWellSampleID(plateIndex, wellIndex, wellSampleIndex); 
     771          if (wellSampleIDValue != null) dest.setWellSampleID(wellSampleIDValue, plateIndex, wellIndex, wellSampleIndex); 
     772          String wellSampleImageRefValue = src.getWellSampleImageRef(plateIndex, wellIndex, wellSampleIndex); 
     773          if (wellSampleImageRefValue != null) dest.setWellSampleImageRef(wellSampleImageRefValue, plateIndex, wellIndex, wellSampleIndex); 
     774          NonNegativeInteger wellSampleIndexValue = src.getWellSampleIndex(plateIndex, wellIndex, wellSampleIndex); 
     775          if (wellSampleIndexValue != null) dest.setWellSampleIndex(wellSampleIndexValue, plateIndex, wellIndex, wellSampleIndex); 
     776          Double wellSamplePositionXValue = src.getWellSamplePositionX(plateIndex, wellIndex, wellSampleIndex); 
     777          if (wellSamplePositionXValue != null) dest.setWellSamplePositionX(wellSamplePositionXValue, plateIndex, wellIndex, wellSampleIndex); 
     778          Double wellSamplePositionYValue = src.getWellSamplePositionY(plateIndex, wellIndex, wellSampleIndex); 
     779          if (wellSamplePositionYValue != null) dest.setWellSamplePositionY(wellSamplePositionYValue, plateIndex, wellIndex, wellSampleIndex); 
     780          Integer wellSampleTimepointValue = src.getWellSampleTimepoint(plateIndex, wellIndex, wellSampleIndex); 
     781          if (wellSampleTimepointValue != null) dest.setWellSampleTimepoint(wellSampleTimepointValue, plateIndex, wellIndex, wellSampleIndex); 
     782          //int annotationRefCount = src.getAnnotationRefCount(plateIndex, wellIndex, wellSampleIndex); 
     783          //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     784          //} 
     785        } 
     786      } 
     787    } 
     788    int projectCount = src.getProjectCount(); 
     789    for (int projectIndex=0; projectIndex<projectCount; projectIndex++) { 
     790      //String projectAnnotationRefValue = src.getProjectAnnotationRef(projectIndex, annotationRefIndex); 
     791      //if (projectAnnotationRefValue != null) dest.setProjectAnnotationRef(projectAnnotationRefValue, projectIndex, annotationRefIndex); 
     792      String projectDescriptionValue = src.getProjectDescription(projectIndex); 
     793      if (projectDescriptionValue != null) dest.setProjectDescription(projectDescriptionValue, projectIndex); 
     794      String projectExperimenterRefValue = src.getProjectExperimenterRef(projectIndex); 
     795      if (projectExperimenterRefValue != null) dest.setProjectExperimenterRef(projectExperimenterRefValue, projectIndex); 
     796      String projectGroupRefValue = src.getProjectGroupRef(projectIndex); 
     797      if (projectGroupRefValue != null) dest.setProjectGroupRef(projectGroupRefValue, projectIndex); 
     798      String projectIDValue = src.getProjectID(projectIndex); 
     799      if (projectIDValue != null) dest.setProjectID(projectIDValue, projectIndex); 
     800      String projectNameValue = src.getProjectName(projectIndex); 
     801      if (projectNameValue != null) dest.setProjectName(projectNameValue, projectIndex); 
     802      //int annotationRefCount = src.getAnnotationRefCount(projectIndex); 
     803      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     804      //} 
     805    } 
     806    int roiCount = src.getROICount(); 
     807    for (int roiIndex=0; roiIndex<roiCount; roiIndex++) { 
     808      //String roiAnnotationRefValue = src.getROIAnnotationRef(roiIndex, annotationRefIndex); 
     809      //if (roiAnnotationRefValue != null) dest.setROIAnnotationRef(roiAnnotationRefValue, roiIndex, annotationRefIndex); 
     810      String roiDescriptionValue = src.getROIDescription(roiIndex); 
     811      if (roiDescriptionValue != null) dest.setROIDescription(roiDescriptionValue, roiIndex); 
     812      String roiidValue = src.getROIID(roiIndex); 
     813      if (roiidValue != null) dest.setROIID(roiidValue, roiIndex); 
     814      String roiNameValue = src.getROIName(roiIndex); 
     815      if (roiNameValue != null) dest.setROIName(roiNameValue, roiIndex); 
     816      String roiNamespaceValue = src.getROINamespace(roiIndex); 
     817      if (roiNamespaceValue != null) dest.setROINamespace(roiNamespaceValue, roiIndex); 
     818      //int annotationRefCount = src.getAnnotationRefCount(roiIndex); 
     819      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     820      //} 
     821      //int shapeCount = src.getShapeCount(roiIndex, shapeIndex); 
     822      /* 
     823      for (int shapeIndex=0; shapeIndex<shapeCount; shapeIndex++) { 
     824        //int annotationRefCount = src.getAnnotationRefCount(roiIndex, shapeIndex); 
     825        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     826        //} 
     827          String ellipseDescriptionValue = src.getEllipseDescription(roiIndex, shapeIndex); 
     828          if (ellipseDescriptionValue != null) dest.setEllipseDescription(ellipseDescriptionValue, roiIndex, shapeIndex); 
     829          Integer ellipseFillValue = src.getEllipseFill(roiIndex, shapeIndex); 
     830          if (ellipseFillValue != null) dest.setEllipseFill(ellipseFillValue, roiIndex, shapeIndex); 
     831          Integer ellipseFontSizeValue = src.getEllipseFontSize(roiIndex, shapeIndex); 
     832          if (ellipseFontSizeValue != null) dest.setEllipseFontSize(ellipseFontSizeValue, roiIndex, shapeIndex); 
     833          String ellipseIDValue = src.getEllipseID(roiIndex, shapeIndex); 
     834          if (ellipseIDValue != null) dest.setEllipseID(ellipseIDValue, roiIndex, shapeIndex); 
     835          String ellipseLabelValue = src.getEllipseLabel(roiIndex, shapeIndex); 
     836          if (ellipseLabelValue != null) dest.setEllipseLabel(ellipseLabelValue, roiIndex, shapeIndex); 
     837          String ellipseNameValue = src.getEllipseName(roiIndex, shapeIndex); 
     838          if (ellipseNameValue != null) dest.setEllipseName(ellipseNameValue, roiIndex, shapeIndex); 
     839          Double ellipseRadiusXValue = src.getEllipseRadiusX(roiIndex, shapeIndex); 
     840          if (ellipseRadiusXValue != null) dest.setEllipseRadiusX(ellipseRadiusXValue, roiIndex, shapeIndex); 
     841          Double ellipseRadiusYValue = src.getEllipseRadiusY(roiIndex, shapeIndex); 
     842          if (ellipseRadiusYValue != null) dest.setEllipseRadiusY(ellipseRadiusYValue, roiIndex, shapeIndex); 
     843          Integer ellipseStrokeValue = src.getEllipseStroke(roiIndex, shapeIndex); 
     844          if (ellipseStrokeValue != null) dest.setEllipseStroke(ellipseStrokeValue, roiIndex, shapeIndex); 
     845          String ellipseStrokeDashArrayValue = src.getEllipseStrokeDashArray(roiIndex, shapeIndex); 
     846          if (ellipseStrokeDashArrayValue != null) dest.setEllipseStrokeDashArray(ellipseStrokeDashArrayValue, roiIndex, shapeIndex); 
     847          Double ellipseStrokeWidthValue = src.getEllipseStrokeWidth(roiIndex, shapeIndex); 
     848          if (ellipseStrokeWidthValue != null) dest.setEllipseStrokeWidth(ellipseStrokeWidthValue, roiIndex, shapeIndex); 
     849          Integer ellipseTheCValue = src.getEllipseTheC(roiIndex, shapeIndex); 
     850          if (ellipseTheCValue != null) dest.setEllipseTheC(ellipseTheCValue, roiIndex, shapeIndex); 
     851          Integer ellipseTheTValue = src.getEllipseTheT(roiIndex, shapeIndex); 
     852          if (ellipseTheTValue != null) dest.setEllipseTheT(ellipseTheTValue, roiIndex, shapeIndex); 
     853          Integer ellipseTheZValue = src.getEllipseTheZ(roiIndex, shapeIndex); 
     854          if (ellipseTheZValue != null) dest.setEllipseTheZ(ellipseTheZValue, roiIndex, shapeIndex); 
     855          String ellipseTransformValue = src.getEllipseTransform(roiIndex, shapeIndex); 
     856          if (ellipseTransformValue != null) dest.setEllipseTransform(ellipseTransformValue, roiIndex, shapeIndex); 
     857          Double ellipseXValue = src.getEllipseX(roiIndex, shapeIndex); 
     858          if (ellipseXValue != null) dest.setEllipseX(ellipseXValue, roiIndex, shapeIndex); 
     859          Double ellipseYValue = src.getEllipseY(roiIndex, shapeIndex); 
     860          if (ellipseYValue != null) dest.setEllipseY(ellipseYValue, roiIndex, shapeIndex); 
     861          String lineDescriptionValue = src.getLineDescription(roiIndex, shapeIndex); 
     862          if (lineDescriptionValue != null) dest.setLineDescription(lineDescriptionValue, roiIndex, shapeIndex); 
     863          Integer lineFillValue = src.getLineFill(roiIndex, shapeIndex); 
     864          if (lineFillValue != null) dest.setLineFill(lineFillValue, roiIndex, shapeIndex); 
     865          Integer lineFontSizeValue = src.getLineFontSize(roiIndex, shapeIndex); 
     866          if (lineFontSizeValue != null) dest.setLineFontSize(lineFontSizeValue, roiIndex, shapeIndex); 
     867          String lineIDValue = src.getLineID(roiIndex, shapeIndex); 
     868          if (lineIDValue != null) dest.setLineID(lineIDValue, roiIndex, shapeIndex); 
     869          String lineLabelValue = src.getLineLabel(roiIndex, shapeIndex); 
     870          if (lineLabelValue != null) dest.setLineLabel(lineLabelValue, roiIndex, shapeIndex); 
     871          String lineNameValue = src.getLineName(roiIndex, shapeIndex); 
     872          if (lineNameValue != null) dest.setLineName(lineNameValue, roiIndex, shapeIndex); 
     873          Integer lineStrokeValue = src.getLineStroke(roiIndex, shapeIndex); 
     874          if (lineStrokeValue != null) dest.setLineStroke(lineStrokeValue, roiIndex, shapeIndex); 
     875          String lineStrokeDashArrayValue = src.getLineStrokeDashArray(roiIndex, shapeIndex); 
     876          if (lineStrokeDashArrayValue != null) dest.setLineStrokeDashArray(lineStrokeDashArrayValue, roiIndex, shapeIndex); 
     877          Double lineStrokeWidthValue = src.getLineStrokeWidth(roiIndex, shapeIndex); 
     878          if (lineStrokeWidthValue != null) dest.setLineStrokeWidth(lineStrokeWidthValue, roiIndex, shapeIndex); 
     879          Integer lineTheCValue = src.getLineTheC(roiIndex, shapeIndex); 
     880          if (lineTheCValue != null) dest.setLineTheC(lineTheCValue, roiIndex, shapeIndex); 
     881          Integer lineTheTValue = src.getLineTheT(roiIndex, shapeIndex); 
     882          if (lineTheTValue != null) dest.setLineTheT(lineTheTValue, roiIndex, shapeIndex); 
     883          Integer lineTheZValue = src.getLineTheZ(roiIndex, shapeIndex); 
     884          if (lineTheZValue != null) dest.setLineTheZ(lineTheZValue, roiIndex, shapeIndex); 
     885          String lineTransformValue = src.getLineTransform(roiIndex, shapeIndex); 
     886          if (lineTransformValue != null) dest.setLineTransform(lineTransformValue, roiIndex, shapeIndex); 
     887          Double lineX1Value = src.getLineX1(roiIndex, shapeIndex); 
     888          if (lineX1Value != null) dest.setLineX1(lineX1Value, roiIndex, shapeIndex); 
     889          Double lineX2Value = src.getLineX2(roiIndex, shapeIndex); 
     890          if (lineX2Value != null) dest.setLineX2(lineX2Value, roiIndex, shapeIndex); 
     891          Double lineY1Value = src.getLineY1(roiIndex, shapeIndex); 
     892          if (lineY1Value != null) dest.setLineY1(lineY1Value, roiIndex, shapeIndex); 
     893          Double lineY2Value = src.getLineY2(roiIndex, shapeIndex); 
     894          if (lineY2Value != null) dest.setLineY2(lineY2Value, roiIndex, shapeIndex); 
     895          String maskDescriptionValue = src.getMaskDescription(roiIndex, shapeIndex); 
     896          if (maskDescriptionValue != null) dest.setMaskDescription(maskDescriptionValue, roiIndex, shapeIndex); 
     897          Integer maskFillValue = src.getMaskFill(roiIndex, shapeIndex); 
     898          if (maskFillValue != null) dest.setMaskFill(maskFillValue, roiIndex, shapeIndex); 
     899          Integer maskFontSizeValue = src.getMaskFontSize(roiIndex, shapeIndex); 
     900          if (maskFontSizeValue != null) dest.setMaskFontSize(maskFontSizeValue, roiIndex, shapeIndex); 
     901          String maskIDValue = src.getMaskID(roiIndex, shapeIndex); 
     902          if (maskIDValue != null) dest.setMaskID(maskIDValue, roiIndex, shapeIndex); 
     903          String maskLabelValue = src.getMaskLabel(roiIndex, shapeIndex); 
     904          if (maskLabelValue != null) dest.setMaskLabel(maskLabelValue, roiIndex, shapeIndex); 
     905          String maskNameValue = src.getMaskName(roiIndex, shapeIndex); 
     906          if (maskNameValue != null) dest.setMaskName(maskNameValue, roiIndex, shapeIndex); 
     907          Integer maskStrokeValue = src.getMaskStroke(roiIndex, shapeIndex); 
     908          if (maskStrokeValue != null) dest.setMaskStroke(maskStrokeValue, roiIndex, shapeIndex); 
     909          String maskStrokeDashArrayValue = src.getMaskStrokeDashArray(roiIndex, shapeIndex); 
     910          if (maskStrokeDashArrayValue != null) dest.setMaskStrokeDashArray(maskStrokeDashArrayValue, roiIndex, shapeIndex); 
     911          Double maskStrokeWidthValue = src.getMaskStrokeWidth(roiIndex, shapeIndex); 
     912          if (maskStrokeWidthValue != null) dest.setMaskStrokeWidth(maskStrokeWidthValue, roiIndex, shapeIndex); 
     913          Integer maskTheCValue = src.getMaskTheC(roiIndex, shapeIndex); 
     914          if (maskTheCValue != null) dest.setMaskTheC(maskTheCValue, roiIndex, shapeIndex); 
     915          Integer maskTheTValue = src.getMaskTheT(roiIndex, shapeIndex); 
     916          if (maskTheTValue != null) dest.setMaskTheT(maskTheTValue, roiIndex, shapeIndex); 
     917          Integer maskTheZValue = src.getMaskTheZ(roiIndex, shapeIndex); 
     918          if (maskTheZValue != null) dest.setMaskTheZ(maskTheZValue, roiIndex, shapeIndex); 
     919          String maskTransformValue = src.getMaskTransform(roiIndex, shapeIndex); 
     920          if (maskTransformValue != null) dest.setMaskTransform(maskTransformValue, roiIndex, shapeIndex); 
     921          Double maskXValue = src.getMaskX(roiIndex, shapeIndex); 
     922          if (maskXValue != null) dest.setMaskX(maskXValue, roiIndex, shapeIndex); 
     923          Double maskYValue = src.getMaskY(roiIndex, shapeIndex); 
     924          if (maskYValue != null) dest.setMaskY(maskYValue, roiIndex, shapeIndex); 
     925          String pathDefinitionValue = src.getPathDefinition(roiIndex, shapeIndex); 
     926          if (pathDefinitionValue != null) dest.setPathDefinition(pathDefinitionValue, roiIndex, shapeIndex); 
     927          String pathDescriptionValue = src.getPathDescription(roiIndex, shapeIndex); 
     928          if (pathDescriptionValue != null) dest.setPathDescription(pathDescriptionValue, roiIndex, shapeIndex); 
     929          Integer pathFillValue = src.getPathFill(roiIndex, shapeIndex); 
     930          if (pathFillValue != null) dest.setPathFill(pathFillValue, roiIndex, shapeIndex); 
     931          Integer pathFontSizeValue = src.getPathFontSize(roiIndex, shapeIndex); 
     932          if (pathFontSizeValue != null) dest.setPathFontSize(pathFontSizeValue, roiIndex, shapeIndex); 
     933          String pathIDValue = src.getPathID(roiIndex, shapeIndex); 
     934          if (pathIDValue != null) dest.setPathID(pathIDValue, roiIndex, shapeIndex); 
     935          String pathLabelValue = src.getPathLabel(roiIndex, shapeIndex); 
     936          if (pathLabelValue != null) dest.setPathLabel(pathLabelValue, roiIndex, shapeIndex); 
     937          String pathNameValue = src.getPathName(roiIndex, shapeIndex); 
     938          if (pathNameValue != null) dest.setPathName(pathNameValue, roiIndex, shapeIndex); 
     939          Integer pathStrokeValue = src.getPathStroke(roiIndex, shapeIndex); 
     940          if (pathStrokeValue != null) dest.setPathStroke(pathStrokeValue, roiIndex, shapeIndex); 
     941          String pathStrokeDashArrayValue = src.getPathStrokeDashArray(roiIndex, shapeIndex); 
     942          if (pathStrokeDashArrayValue != null) dest.setPathStrokeDashArray(pathStrokeDashArrayValue, roiIndex, shapeIndex); 
     943          Double pathStrokeWidthValue = src.getPathStrokeWidth(roiIndex, shapeIndex); 
     944          if (pathStrokeWidthValue != null) dest.setPathStrokeWidth(pathStrokeWidthValue, roiIndex, shapeIndex); 
     945          Integer pathTheCValue = src.getPathTheC(roiIndex, shapeIndex); 
     946          if (pathTheCValue != null) dest.setPathTheC(pathTheCValue, roiIndex, shapeIndex); 
     947          Integer pathTheTValue = src.getPathTheT(roiIndex, shapeIndex); 
     948          if (pathTheTValue != null) dest.setPathTheT(pathTheTValue, roiIndex, shapeIndex); 
     949          Integer pathTheZValue = src.getPathTheZ(roiIndex, shapeIndex); 
     950          if (pathTheZValue != null) dest.setPathTheZ(pathTheZValue, roiIndex, shapeIndex); 
     951          String pathTransformValue = src.getPathTransform(roiIndex, shapeIndex); 
     952          if (pathTransformValue != null) dest.setPathTransform(pathTransformValue, roiIndex, shapeIndex); 
     953          String pointDescriptionValue = src.getPointDescription(roiIndex, shapeIndex); 
     954          if (pointDescriptionValue != null) dest.setPointDescription(pointDescriptionValue, roiIndex, shapeIndex); 
     955          Integer pointFillValue = src.getPointFill(roiIndex, shapeIndex); 
     956          if (pointFillValue != null) dest.setPointFill(pointFillValue, roiIndex, shapeIndex); 
     957          Integer pointFontSizeValue = src.getPointFontSize(roiIndex, shapeIndex); 
     958          if (pointFontSizeValue != null) dest.setPointFontSize(pointFontSizeValue, roiIndex, shapeIndex); 
     959          String pointIDValue = src.getPointID(roiIndex, shapeIndex); 
     960          if (pointIDValue != null) dest.setPointID(pointIDValue, roiIndex, shapeIndex); 
     961          String pointLabelValue = src.getPointLabel(roiIndex, shapeIndex); 
     962          if (pointLabelValue != null) dest.setPointLabel(pointLabelValue, roiIndex, shapeIndex); 
     963          String pointNameValue = src.getPointName(roiIndex, shapeIndex); 
     964          if (pointNameValue != null) dest.setPointName(pointNameValue, roiIndex, shapeIndex); 
     965          Integer pointStrokeValue = src.getPointStroke(roiIndex, shapeIndex); 
     966          if (pointStrokeValue != null) dest.setPointStroke(pointStrokeValue, roiIndex, shapeIndex); 
     967          String pointStrokeDashArrayValue = src.getPointStrokeDashArray(roiIndex, shapeIndex); 
     968          if (pointStrokeDashArrayValue != null) dest.setPointStrokeDashArray(pointStrokeDashArrayValue, roiIndex, shapeIndex); 
     969          Double pointStrokeWidthValue = src.getPointStrokeWidth(roiIndex, shapeIndex); 
     970          if (pointStrokeWidthValue != null) dest.setPointStrokeWidth(pointStrokeWidthValue, roiIndex, shapeIndex); 
     971          Integer pointTheCValue = src.getPointTheC(roiIndex, shapeIndex); 
     972          if (pointTheCValue != null) dest.setPointTheC(pointTheCValue, roiIndex, shapeIndex); 
     973          Integer pointTheTValue = src.getPointTheT(roiIndex, shapeIndex); 
     974          if (pointTheTValue != null) dest.setPointTheT(pointTheTValue, roiIndex, shapeIndex); 
     975          Integer pointTheZValue = src.getPointTheZ(roiIndex, shapeIndex); 
     976          if (pointTheZValue != null) dest.setPointTheZ(pointTheZValue, roiIndex, shapeIndex); 
     977          String pointTransformValue = src.getPointTransform(roiIndex, shapeIndex); 
     978          if (pointTransformValue != null) dest.setPointTransform(pointTransformValue, roiIndex, shapeIndex); 
     979          Double pointXValue = src.getPointX(roiIndex, shapeIndex); 
     980          if (pointXValue != null) dest.setPointX(pointXValue, roiIndex, shapeIndex); 
     981          Double pointYValue = src.getPointY(roiIndex, shapeIndex); 
     982          if (pointYValue != null) dest.setPointY(pointYValue, roiIndex, shapeIndex); 
     983          Boolean polylineClosedValue = src.getPolylineClosed(roiIndex, shapeIndex); 
     984          if (polylineClosedValue != null) dest.setPolylineClosed(polylineClosedValue, roiIndex, shapeIndex); 
     985          String polylineDescriptionValue = src.getPolylineDescription(roiIndex, shapeIndex); 
     986          if (polylineDescriptionValue != null) dest.setPolylineDescription(polylineDescriptionValue, roiIndex, shapeIndex); 
     987          Integer polylineFillValue = src.getPolylineFill(roiIndex, shapeIndex); 
     988          if (polylineFillValue != null) dest.setPolylineFill(polylineFillValue, roiIndex, shapeIndex); 
     989          Integer polylineFontSizeValue = src.getPolylineFontSize(roiIndex, shapeIndex); 
     990          if (polylineFontSizeValue != null) dest.setPolylineFontSize(polylineFontSizeValue, roiIndex, shapeIndex); 
     991          String polylineIDValue = src.getPolylineID(roiIndex, shapeIndex); 
     992          if (polylineIDValue != null) dest.setPolylineID(polylineIDValue, roiIndex, shapeIndex); 
     993          String polylineLabelValue = src.getPolylineLabel(roiIndex, shapeIndex); 
     994          if (polylineLabelValue != null) dest.setPolylineLabel(polylineLabelValue, roiIndex, shapeIndex); 
     995          String polylineNameValue = src.getPolylineName(roiIndex, shapeIndex); 
     996          if (polylineNameValue != null) dest.setPolylineName(polylineNameValue, roiIndex, shapeIndex); 
     997          String polylinePointsValue = src.getPolylinePoints(roiIndex, shapeIndex); 
     998          if (polylinePointsValue != null) dest.setPolylinePoints(polylinePointsValue, roiIndex, shapeIndex); 
     999          Integer polylineStrokeValue = src.getPolylineStroke(roiIndex, shapeIndex); 
     1000          if (polylineStrokeValue != null) dest.setPolylineStroke(polylineStrokeValue, roiIndex, shapeIndex); 
     1001          String polylineStrokeDashArrayValue = src.getPolylineStrokeDashArray(roiIndex, shapeIndex); 
     1002          if (polylineStrokeDashArrayValue != null) dest.setPolylineStrokeDashArray(polylineStrokeDashArrayValue, roiIndex, shapeIndex); 
     1003          Double polylineStrokeWidthValue = src.getPolylineStrokeWidth(roiIndex, shapeIndex); 
     1004          if (polylineStrokeWidthValue != null) dest.setPolylineStrokeWidth(polylineStrokeWidthValue, roiIndex, shapeIndex); 
     1005          Integer polylineTheCValue = src.getPolylineTheC(roiIndex, shapeIndex); 
     1006          if (polylineTheCValue != null) dest.setPolylineTheC(polylineTheCValue, roiIndex, shapeIndex); 
     1007          Integer polylineTheTValue = src.getPolylineTheT(roiIndex, shapeIndex); 
     1008          if (polylineTheTValue != null) dest.setPolylineTheT(polylineTheTValue, roiIndex, shapeIndex); 
     1009          Integer polylineTheZValue = src.getPolylineTheZ(roiIndex, shapeIndex); 
     1010          if (polylineTheZValue != null) dest.setPolylineTheZ(polylineTheZValue, roiIndex, shapeIndex); 
     1011          String polylineTransformValue = src.getPolylineTransform(roiIndex, shapeIndex); 
     1012          if (polylineTransformValue != null) dest.setPolylineTransform(polylineTransformValue, roiIndex, shapeIndex); 
     1013          String rectangleDescriptionValue = src.getRectangleDescription(roiIndex, shapeIndex); 
     1014          if (rectangleDescriptionValue != null) dest.setRectangleDescription(rectangleDescriptionValue, roiIndex, shapeIndex); 
     1015          Integer rectangleFillValue = src.getRectangleFill(roiIndex, shapeIndex); 
     1016          if (rectangleFillValue != null) dest.setRectangleFill(rectangleFillValue, roiIndex, shapeIndex); 
     1017          Integer rectangleFontSizeValue = src.getRectangleFontSize(roiIndex, shapeIndex); 
     1018          if (rectangleFontSizeValue != null) dest.setRectangleFontSize(rectangleFontSizeValue, roiIndex, shapeIndex); 
     1019          Double rectangleHeightValue = src.getRectangleHeight(roiIndex, shapeIndex); 
     1020          if (rectangleHeightValue != null) dest.setRectangleHeight(rectangleHeightValue, roiIndex, shapeIndex); 
     1021          String rectangleIDValue = src.getRectangleID(roiIndex, shapeIndex); 
     1022          if (rectangleIDValue != null) dest.setRectangleID(rectangleIDValue, roiIndex, shapeIndex); 
     1023          String rectangleLabelValue = src.getRectangleLabel(roiIndex, shapeIndex); 
     1024          if (rectangleLabelValue != null) dest.setRectangleLabel(rectangleLabelValue, roiIndex, shapeIndex); 
     1025          String rectangleNameValue = src.getRectangleName(roiIndex, shapeIndex); 
     1026          if (rectangleNameValue != null) dest.setRectangleName(rectangleNameValue, roiIndex, shapeIndex); 
     1027          Integer rectangleStrokeValue = src.getRectangleStroke(roiIndex, shapeIndex); 
     1028          if (rectangleStrokeValue != null) dest.setRectangleStroke(rectangleStrokeValue, roiIndex, shapeIndex); 
     1029          String rectangleStrokeDashArrayValue = src.getRectangleStrokeDashArray(roiIndex, shapeIndex); 
     1030          if (rectangleStrokeDashArrayValue != null) dest.setRectangleStrokeDashArray(rectangleStrokeDashArrayValue, roiIndex, shapeIndex); 
     1031          Double rectangleStrokeWidthValue = src.getRectangleStrokeWidth(roiIndex, shapeIndex); 
     1032          if (rectangleStrokeWidthValue != null) dest.setRectangleStrokeWidth(rectangleStrokeWidthValue, roiIndex, shapeIndex); 
     1033          Integer rectangleTheCValue = src.getRectangleTheC(roiIndex, shapeIndex); 
     1034          if (rectangleTheCValue != null) dest.setRectangleTheC(rectangleTheCValue, roiIndex, shapeIndex); 
     1035          Integer rectangleTheTValue = src.getRectangleTheT(roiIndex, shapeIndex); 
     1036          if (rectangleTheTValue != null) dest.setRectangleTheT(rectangleTheTValue, roiIndex, shapeIndex); 
     1037          Integer rectangleTheZValue = src.getRectangleTheZ(roiIndex, shapeIndex); 
     1038          if (rectangleTheZValue != null) dest.setRectangleTheZ(rectangleTheZValue, roiIndex, shapeIndex); 
     1039          String rectangleTransformValue = src.getRectangleTransform(roiIndex, shapeIndex); 
     1040          if (rectangleTransformValue != null) dest.setRectangleTransform(rectangleTransformValue, roiIndex, shapeIndex); 
     1041          Double rectangleWidthValue = src.getRectangleWidth(roiIndex, shapeIndex); 
     1042          if (rectangleWidthValue != null) dest.setRectangleWidth(rectangleWidthValue, roiIndex, shapeIndex); 
     1043          Double rectangleXValue = src.getRectangleX(roiIndex, shapeIndex); 
     1044          if (rectangleXValue != null) dest.setRectangleX(rectangleXValue, roiIndex, shapeIndex); 
     1045          Double rectangleYValue = src.getRectangleY(roiIndex, shapeIndex); 
     1046          if (rectangleYValue != null) dest.setRectangleY(rectangleYValue, roiIndex, shapeIndex); 
     1047          String textDescriptionValue = src.getTextDescription(roiIndex, shapeIndex); 
     1048          if (textDescriptionValue != null) dest.setTextDescription(textDescriptionValue, roiIndex, shapeIndex); 
     1049          Integer textFillValue = src.getTextFill(roiIndex, shapeIndex); 
     1050          if (textFillValue != null) dest.setTextFill(textFillValue, roiIndex, shapeIndex); 
     1051          Integer textFontSizeValue = src.getTextFontSize(roiIndex, shapeIndex); 
     1052          if (textFontSizeValue != null) dest.setTextFontSize(textFontSizeValue, roiIndex, shapeIndex); 
     1053          String textIDValue = src.getTextID(roiIndex, shapeIndex); 
     1054          if (textIDValue != null) dest.setTextID(textIDValue, roiIndex, shapeIndex); 
     1055          String textLabelValue = src.getTextLabel(roiIndex, shapeIndex); 
     1056          if (textLabelValue != null) dest.setTextLabel(textLabelValue, roiIndex, shapeIndex); 
     1057          String textNameValue = src.getTextName(roiIndex, shapeIndex); 
     1058          if (textNameValue != null) dest.setTextName(textNameValue, roiIndex, shapeIndex); 
     1059          Integer textStrokeValue = src.getTextStroke(roiIndex, shapeIndex); 
     1060          if (textStrokeValue != null) dest.setTextStroke(textStrokeValue, roiIndex, shapeIndex); 
     1061          String textStrokeDashArrayValue = src.getTextStrokeDashArray(roiIndex, shapeIndex); 
     1062          if (textStrokeDashArrayValue != null) dest.setTextStrokeDashArray(textStrokeDashArrayValue, roiIndex, shapeIndex); 
     1063          Double textStrokeWidthValue = src.getTextStrokeWidth(roiIndex, shapeIndex); 
     1064          if (textStrokeWidthValue != null) dest.setTextStrokeWidth(textStrokeWidthValue, roiIndex, shapeIndex); 
     1065          Integer textTheCValue = src.getTextTheC(roiIndex, shapeIndex); 
     1066          if (textTheCValue != null) dest.setTextTheC(textTheCValue, roiIndex, shapeIndex); 
     1067          Integer textTheTValue = src.getTextTheT(roiIndex, shapeIndex); 
     1068          if (textTheTValue != null) dest.setTextTheT(textTheTValue, roiIndex, shapeIndex); 
     1069          Integer textTheZValue = src.getTextTheZ(roiIndex, shapeIndex); 
     1070          if (textTheZValue != null) dest.setTextTheZ(textTheZValue, roiIndex, shapeIndex); 
     1071          String textTransformValue = src.getTextTransform(roiIndex, shapeIndex); 
     1072          if (textTransformValue != null) dest.setTextTransform(textTransformValue, roiIndex, shapeIndex); 
     1073          String textValueValue = src.getTextValue(roiIndex, shapeIndex); 
     1074          if (textValueValue != null) dest.setTextValue(textValueValue, roiIndex, shapeIndex); 
     1075          Double textXValue = src.getTextX(roiIndex, shapeIndex); 
     1076          if (textXValue != null) dest.setTextX(textXValue, roiIndex, shapeIndex); 
     1077          Double textYValue = src.getTextY(roiIndex, shapeIndex); 
     1078          if (textYValue != null) dest.setTextY(textYValue, roiIndex, shapeIndex); 
     1079      } 
     1080      */ 
     1081    } 
     1082    int screenCount = src.getScreenCount(); 
     1083    for (int screenIndex=0; screenIndex<screenCount; screenIndex++) { 
     1084      //String screenAnnotationRefValue = src.getScreenAnnotationRef(screenIndex, annotationRefIndex); 
     1085      //if (screenAnnotationRefValue != null) dest.setScreenAnnotationRef(screenAnnotationRefValue, screenIndex, annotationRefIndex); 
     1086      String screenDescriptionValue = src.getScreenDescription(screenIndex); 
     1087      if (screenDescriptionValue != null) dest.setScreenDescription(screenDescriptionValue, screenIndex); 
     1088      String screenIDValue = src.getScreenID(screenIndex); 
     1089      if (screenIDValue != null) dest.setScreenID(screenIDValue, screenIndex); 
     1090      String screenNameValue = src.getScreenName(screenIndex); 
     1091      if (screenNameValue != null) dest.setScreenName(screenNameValue, screenIndex); 
     1092      //String screenPlateRefValue = src.getScreenPlateRef(screenIndex, plateRefIndex); 
     1093      //if (screenPlateRefValue != null) dest.setScreenPlateRef(screenPlateRefValue, screenIndex, plateRefIndex); 
     1094      String screenProtocolDescriptionValue = src.getScreenProtocolDescription(screenIndex); 
     1095      if (screenProtocolDescriptionValue != null) dest.setScreenProtocolDescription(screenProtocolDescriptionValue, screenIndex); 
     1096      String screenProtocolIdentifierValue = src.getScreenProtocolIdentifier(screenIndex); 
     1097      if (screenProtocolIdentifierValue != null) dest.setScreenProtocolIdentifier(screenProtocolIdentifierValue, screenIndex); 
     1098      String screenReagentSetDescriptionValue = src.getScreenReagentSetDescription(screenIndex); 
     1099      if (screenReagentSetDescriptionValue != null) dest.setScreenReagentSetDescription(screenReagentSetDescriptionValue, screenIndex); 
     1100      String screenReagentSetIdentifierValue = src.getScreenReagentSetIdentifier(screenIndex); 
     1101      if (screenReagentSetIdentifierValue != null) dest.setScreenReagentSetIdentifier(screenReagentSetIdentifierValue, screenIndex); 
     1102      String screenTypeValue = src.getScreenType(screenIndex); 
     1103      if (screenTypeValue != null) dest.setScreenType(screenTypeValue, screenIndex); 
     1104      //int annotationRefCount = src.getAnnotationRefCount(screenIndex); 
     1105      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     1106      //} 
     1107      int plateRefCount = src.getPlateRefCount(screenIndex); 
     1108      for (int plateRefIndex=0; plateRefIndex<plateRefCount; plateRefIndex++) { 
     1109      } 
     1110      int reagentCount = src.getReagentCount(screenIndex); 
     1111      for (int reagentIndex=0; reagentIndex<reagentCount; reagentIndex++) { 
     1112        //String reagentAnnotationRefValue = src.getReagentAnnotationRef(screenIndex, reagentIndex, annotationRefIndex); 
     1113        //if (reagentAnnotationRefValue != null) dest.setReagentAnnotationRef(reagentAnnotationRefValue, screenIndex, reagentIndex, annotationRefIndex); 
     1114        String reagentDescriptionValue = src.getReagentDescription(screenIndex, reagentIndex); 
     1115        if (reagentDescriptionValue != null) dest.setReagentDescription(reagentDescriptionValue, screenIndex, reagentIndex); 
     1116        String reagentIDValue = src.getReagentID(screenIndex, reagentIndex); 
     1117        if (reagentIDValue != null) dest.setReagentID(reagentIDValue, screenIndex, reagentIndex); 
     1118        String reagentNameValue = src.getReagentName(screenIndex, reagentIndex); 
     1119        if (reagentNameValue != null) dest.setReagentName(reagentNameValue, screenIndex, reagentIndex); 
     1120        String reagentReagentIdentifierValue = src.getReagentReagentIdentifier(screenIndex, reagentIndex); 
     1121        if (reagentReagentIdentifierValue != null) dest.setReagentReagentIdentifier(reagentReagentIdentifierValue, screenIndex, reagentIndex); 
     1122        //int annotationRefCount = src.getAnnotationRefCount(screenIndex, reagentIndex); 
     1123        //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     1124        //} 
     1125      } 
     1126    } 
     1127    int stringAnnotationCount = src.getStringAnnotationCount(); 
     1128    for (int stringAnnotationIndex=0; stringAnnotationIndex<stringAnnotationCount; stringAnnotationIndex++) { 
     1129      String stringAnnotationIDValue = src.getStringAnnotationID(stringAnnotationIndex); 
     1130      if (stringAnnotationIDValue != null) dest.setStringAnnotationID(stringAnnotationIDValue, stringAnnotationIndex); 
     1131      String stringAnnotationNamespaceValue = src.getStringAnnotationNamespace(stringAnnotationIndex); 
     1132      if (stringAnnotationNamespaceValue != null) dest.setStringAnnotationNamespace(stringAnnotationNamespaceValue, stringAnnotationIndex); 
     1133      String stringAnnotationValueValue = src.getStringAnnotationValue(stringAnnotationIndex); 
     1134      if (stringAnnotationValueValue != null) dest.setStringAnnotationValue(stringAnnotationValueValue, stringAnnotationIndex); 
     1135    } 
     1136    int timestampAnnotationCount = src.getTimestampAnnotationCount(); 
     1137    for (int timestampAnnotationIndex=0; timestampAnnotationIndex<timestampAnnotationCount; timestampAnnotationIndex++) { 
     1138      String timestampAnnotationIDValue = src.getTimestampAnnotationID(timestampAnnotationIndex); 
     1139      if (timestampAnnotationIDValue != null) dest.setTimestampAnnotationID(timestampAnnotationIDValue, timestampAnnotationIndex); 
     1140      String timestampAnnotationNamespaceValue = src.getTimestampAnnotationNamespace(timestampAnnotationIndex); 
     1141      if (timestampAnnotationNamespaceValue != null) dest.setTimestampAnnotationNamespace(timestampAnnotationNamespaceValue, timestampAnnotationIndex); 
     1142      String timestampAnnotationValueValue = src.getTimestampAnnotationValue(timestampAnnotationIndex); 
     1143      if (timestampAnnotationValueValue != null) dest.setTimestampAnnotationValue(timestampAnnotationValueValue, timestampAnnotationIndex); 
     1144    } 
     1145    int xmlAnnotationCount = src.getXMLAnnotationCount(); 
     1146    for (int xmlAnnotationIndex=0; xmlAnnotationIndex<xmlAnnotationCount; xmlAnnotationIndex++) { 
     1147      String xmlAnnotationIDValue = src.getXMLAnnotationID(xmlAnnotationIndex); 
     1148      if (xmlAnnotationIDValue != null) dest.setXMLAnnotationID(xmlAnnotationIDValue, xmlAnnotationIndex); 
     1149      String xmlAnnotationNamespaceValue = src.getXMLAnnotationNamespace(xmlAnnotationIndex); 
     1150      if (xmlAnnotationNamespaceValue != null) dest.setXMLAnnotationNamespace(xmlAnnotationNamespaceValue, xmlAnnotationIndex); 
     1151      String xmlAnnotationValueValue = src.getXMLAnnotationValue(xmlAnnotationIndex); 
     1152      if (xmlAnnotationValueValue != null) dest.setXMLAnnotationValue(xmlAnnotationValueValue, xmlAnnotationIndex); 
     1153    } 
    671154  } 
     1155 
    681156} 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataRetrieve.java

    r6440 r6458  
    3333 * 
    3434 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    35  * Created by callan via xsd-fu on 2010-06-02 14:15:02.248588 
     35 * Created by melissa via xsd-fu on 2010-06-03 11:40:17.511048 
    3636 * 
    3737 *----------------------------------------------------------------------------- 
     
    4040package loci.formats.meta; 
    4141 
    42 import ome.xml.r201004.enums.*; 
    43 import ome.xml.r201004.primitives.*; 
     42import ome.xml.model.enums.*; 
     43import ome.xml.model.primitives.*; 
    4444 
    4545/** 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataStore.java

    r6428 r6458  
    3333 * 
    3434 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    35  * Created by callan via xsd-fu on 2010-06-01 11:45:36.959537 
     35 * Created by melissa via xsd-fu on 2010-06-03 11:40:16.267317 
    3636 * 
    3737 *----------------------------------------------------------------------------- 
     
    4040package loci.formats.meta; 
    4141 
    42 import ome.xml.r201004.enums.*; 
    43 import ome.xml.r201004.primitives.*; 
     42import ome.xml.model.enums.*; 
     43import ome.xml.model.primitives.*; 
    4444 
    4545/** 
  • trunk/components/bio-formats/src/loci/formats/ome/AbstractOMEXMLMetadata.java

    r6233 r6458  
    3333 
    3434import ome.xml.DOMUtil; 
    35 import ome.xml.r201004.OME; 
    36 import ome.xml.r201004.OMEModelObject; 
     35import ome.xml.model.OME; 
     36import ome.xml.model.OMEModelObject; 
    3737 
    3838import org.w3c.dom.Document; 
  • trunk/components/bio-formats/src/loci/formats/ome/OMEXMLMetadataImpl.java

    r6440 r6458  
    3333 * 
    3434 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    35  * Created by callan via xsd-fu on 2010-06-02 14:15:07.135315 
     35 * Created by melissa via xsd-fu on 2010-06-03 11:40:18.758353 
    3636 * 
    3737 *----------------------------------------------------------------------------- 
     
    4040package loci.formats.ome; 
    4141 
    42 import ome.xml.r201004.*; 
    43 import ome.xml.r201004.enums.*; 
    44 import ome.xml.r201004.primitives.*; 
     42import ome.xml.model.*; 
     43import ome.xml.model.enums.*; 
     44import ome.xml.model.primitives.*; 
    4545 
    4646/** 
    4747 * A metadata store implementation for constructing and manipulating OME-XML 
    4848 * DOMs for the 2010-04 version of OME-XML. It requires the 
    49  * ome.xml.r201004 package to compile (part of ome-xml.jar). 
     49 * ome.xml.model package to compile (part of ome-xml.jar). 
    5050 * 
    5151 * <dl><dt><b>Source code:</b></dt> 
     
    16151615        // ExperimenterRef property storage 
    16161616        // 
    1617         // Indexes: {u'Project': [u'int projectIndex'], u'Image': [u'int imageIndex'], u'Experiment': [u'int experimentIndex'], u'MicrobeamManipulation': [u'int experimentIndex', u'int microbeamManipulationIndex'], u'Dataset': [u'int datasetIndex']} 
     1617        // Indexes: {u'Project': [u'int projectIndex'], u'MicrobeamManipulation': [u'int experimentIndex', u'int microbeamManipulationIndex'], u'Image': [u'int imageIndex'], u'Experiment': [u'int experimentIndex'], u'Dataset': [u'int datasetIndex']} 
    16181618        // {u'Project': {u'OME': None}, u'Image': {u'OME': None}, u'Dataset': {u'OME': None}, u'Experiment': {u'OME': None}, u'MicrobeamManipulation': {u'Experiment': {u'OME': None}}} 
    16191619        // Is multi path? True 
  • trunk/components/bio-formats/src/loci/formats/services/OMEXMLServiceImpl.java

    r6428 r6458  
    4242import loci.formats.ome.OMEXMLMetadataImpl; 
    4343import ome.xml.OMEXMLFactory; 
    44 import ome.xml.r201004.OME; 
    45 import ome.xml.r201004.OMEModel; 
    46 import ome.xml.r201004.OMEModelImpl; 
    47 import ome.xml.r201004.OMEModelObject; 
    48 import ome.xml.r201004.StructuredAnnotations; 
     44import ome.xml.model.OME; 
     45import ome.xml.model.OMEModel; 
     46import ome.xml.model.OMEModelImpl; 
     47import ome.xml.model.OMEModelObject; 
     48import ome.xml.model.StructuredAnnotations; 
    4949 
    5050import org.slf4j.Logger; 
     
    100100   */ 
    101101  public OMEXMLServiceImpl() { 
    102     checkClassDependency(ome.xml.r201004.OMEModelObject.class); 
     102    checkClassDependency(ome.xml.model.OMEModelObject.class); 
    103103  } 
    104104 
     
    202202   * classes should not leak out of the interface. 
    203203   * @param xml String of XML to create the root node from. 
    204    * @return An ome.xml.r201004.OMEModelObject subclass root node. 
     204   * @return An ome.xml.model.OMEModelObject subclass root node. 
    205205   * @throws IOException If there is an error reading from the string. 
    206206   * @throws SAXException If there is an error parsing the XML. 
  • trunk/components/bio-formats/src/loci/formats/tiff/TiffParser.java

    r6430 r6458  
    762762 
    763763    long imageWidth = ifd.getImageWidth(); 
     764    long imageHeight = ifd.getImageLength(); 
    764765 
    765766    int bps0 = bitsPerSample[0]; 
     
    794795 
    795796    int skipBits = (int) (8 - ((imageWidth * bps0 * nChannels) % 8)); 
    796     if (skipBits == 8) skipBits = 0; 
     797    if (skipBits == 8 || 
     798      (bytes.length * 8 < bps0 * (nChannels * imageWidth + imageHeight))) 
     799    { 
     800      skipBits = 0; 
     801    } 
    797802 
    798803    // set up YCbCr-specific values 
     
    824829      for (int channel=0; channel<nChannels; channel++) { 
    825830        int index = numBytes * (sample * nChannels + channel); 
    826         int outputIndex = channel * nSamples + ndx * numBytes; 
     831        int outputIndex = (channel * nSamples + ndx) * numBytes; 
    827832 
    828833        // unpack non-YCbCr samples 
     
    838843            { 
    839844              value = bb.getBits(bps0) & 0xffff; 
    840               //if (littleEndian && bps0 > 8) { 
    841               //  value = DataTools.swap(value) >> (64 - bps0); 
    842               //} 
    843               if ((ndx % imageWidth) == imageWidth - 1/* && bps0 < 8*/) { 
     845              if ((ndx % imageWidth) == imageWidth - 1) { 
    844846                bb.skipBits(skipBits); 
    845847              } 
  • trunk/components/bio-formats/test/loci/formats/utests/IMetadataBasedOMEModelMock.java

    r6413 r6458  
    3636 
    3737import loci.formats.ome.OMEXMLMetadataImpl; 
    38 import ome.xml.r201004.Arc; 
    39 import ome.xml.r201004.BinaryFile; 
    40 import ome.xml.r201004.BooleanAnnotation; 
    41 import ome.xml.r201004.Channel; 
    42 import ome.xml.r201004.Detector; 
    43 import ome.xml.r201004.Dichroic; 
    44 import ome.xml.r201004.DoubleAnnotation; 
    45 import ome.xml.r201004.External; 
    46 import ome.xml.r201004.Filament; 
    47 import ome.xml.r201004.Filter; 
    48 import ome.xml.r201004.FilterSet; 
    49 import ome.xml.r201004.Image; 
    50 import ome.xml.r201004.Instrument; 
    51 import ome.xml.r201004.Laser; 
    52 import ome.xml.r201004.LightEmittingDiode; 
    53 import ome.xml.r201004.LongAnnotation; 
    54 import ome.xml.r201004.MetadataOnly; 
    55 import ome.xml.r201004.OME; 
    56 import ome.xml.r201004.OMEModel; 
    57 import ome.xml.r201004.OTF; 
    58 import ome.xml.r201004.Objective; 
    59 import ome.xml.r201004.ObjectiveSettings; 
    60 import ome.xml.r201004.Pixels; 
    61 import ome.xml.r201004.Plate; 
    62 import ome.xml.r201004.ROI; 
    63 import ome.xml.r201004.Rectangle; 
    64 import ome.xml.r201004.StringAnnotation; 
    65 import ome.xml.r201004.StructuredAnnotations; 
    66 import ome.xml.r201004.TimestampAnnotation; 
    67 import ome.xml.r201004.Union; 
    68 import ome.xml.r201004.Well; 
    69 import ome.xml.r201004.WellSample; 
    70 import ome.xml.r201004.XMLAnnotation; 
    71 import ome.xml.r201004.primitives.NonNegativeInteger; 
    72 import ome.xml.r201004.primitives.PositiveInteger; 
     38import ome.xml.model.Arc; 
     39import ome.xml.model.BinaryFile; 
     40import ome.xml.model.BooleanAnnotation; 
     41import ome.xml.model.Channel; 
     42import ome.xml.model.Detector; 
     43import ome.xml.model.Dichroic; 
     44import ome.xml.model.DoubleAnnotation; 
     45import ome.xml.model.External; 
     46import ome.xml.model.Filament; 
     47import ome.xml.model.Filter; 
     48import ome.xml.model.FilterSet; 
     49import ome.xml.model.Image; 
     50import ome.xml.model.Instrument; 
     51import ome.xml.model.Laser; 
     52import ome.xml.model.LightEmittingDiode; 
     53import ome.xml.model.LongAnnotation; 
     54import ome.xml.model.MetadataOnly; 
     55import ome.xml.model.OME; 
     56import ome.xml.model.OMEModel; 
     57import ome.xml.model.OTF; 
     58import ome.xml.model.Objective; 
     59import ome.xml.model.ObjectiveSettings; 
     60import ome.xml.model.Pixels; 
     61import ome.xml.model.Plate; 
     62import ome.xml.model.ROI; 
     63import ome.xml.model.Rectangle; 
     64import ome.xml.model.StringAnnotation; 
     65import ome.xml.model.StructuredAnnotations; 
     66import ome.xml.model.TimestampAnnotation; 
     67import ome.xml.model.Union; 
     68import ome.xml.model.Well; 
     69import ome.xml.model.WellSample; 
     70import ome.xml.model.XMLAnnotation; 
     71import ome.xml.model.primitives.NonNegativeInteger; 
     72import ome.xml.model.primitives.PositiveInteger; 
    7373 
    7474/** 
  • trunk/components/bio-formats/test/loci/formats/utests/InOut201004Test.java

    r6413 r6458  
    6060import static org.testng.AssertJUnit.*; 
    6161 
    62 import ome.xml.r201004.Annotation; 
    63 import ome.xml.r201004.Arc; 
    64 import ome.xml.r201004.BinaryFile; 
    65 import ome.xml.r201004.BooleanAnnotation; 
    66 import ome.xml.r201004.DoubleAnnotation; 
    67 import ome.xml.r201004.External; 
    68 import ome.xml.r201004.Filament; 
    69 import ome.xml.r201004.LightEmittingDiode; 
    70 import ome.xml.r201004.LongAnnotation; 
    71 import ome.xml.r201004.OMEModel; 
    72 import ome.xml.r201004.OMEModelImpl; 
    73 import ome.xml.r201004.OMEModelObject; 
    74 import ome.xml.r201004.Objective; 
    75 import ome.xml.r201004.ObjectiveSettings; 
    76 import ome.xml.r201004.Reference; 
    77 import ome.xml.r201004.StringAnnotation; 
    78 import ome.xml.r201004.StructuredAnnotations; 
    79 import ome.xml.r201004.TiffData; 
    80 import ome.xml.r201004.TimestampAnnotation; 
    81 import ome.xml.r201004.UUID; 
    82 import ome.xml.r201004.XMLAnnotation; 
    83 import ome.xml.r201004.Channel; 
    84 import ome.xml.r201004.Dichroic; 
    85 import ome.xml.r201004.Detector; 
    86 import ome.xml.r201004.Filter; 
    87 import ome.xml.r201004.FilterSet; 
    88 import ome.xml.r201004.Image; 
    89 import ome.xml.r201004.Instrument; 
    90 import ome.xml.r201004.Laser; 
    91 import ome.xml.r201004.MetadataOnly; 
    92 import ome.xml.r201004.OME; 
    93 import ome.xml.r201004.OTF; 
    94 import ome.xml.r201004.Pixels; 
    95 import ome.xml.r201004.Plate; 
    96 import ome.xml.r201004.Rectangle; 
    97 import ome.xml.r201004.ROI; 
    98 import ome.xml.r201004.Shape; 
    99 import ome.xml.r201004.Union; 
    100 import ome.xml.r201004.Well; 
    101 import ome.xml.r201004.WellSample; 
    102 import ome.xml.r201004.enums.ArcType; 
    103 import ome.xml.r201004.enums.DimensionOrder; 
    104 import ome.xml.r201004.enums.EnumerationException; 
    105 import ome.xml.r201004.enums.FilamentType; 
    106 import ome.xml.r201004.enums.FilterType; 
    107 import ome.xml.r201004.enums.LaserType; 
    108 import ome.xml.r201004.enums.NamingConvention; 
    109 import ome.xml.r201004.enums.PixelType; 
    110 import ome.xml.r201004.primitives.NonNegativeInteger; 
    111 import ome.xml.r201004.primitives.PositiveInteger; 
     62import ome.xml.model.Annotation; 
     63import ome.xml.model.Arc; 
     64import ome.xml.model.BinaryFile; 
     65import ome.xml.model.BooleanAnnotation; 
     66import ome.xml.model.DoubleAnnotation; 
     67import ome.xml.model.External; 
     68import ome.xml.model.Filament; 
     69import ome.xml.model.LightEmittingDiode; 
     70import ome.xml.model.LongAnnotation; 
     71import ome.xml.model.OMEModel; 
     72import ome.xml.model.OMEModelImpl; 
     73import ome.xml.model.OMEModelObject; 
     74import ome.xml.model.Objective; 
     75import ome.xml.model.ObjectiveSettings; 
     76import ome.xml.model.Reference; 
     77import ome.xml.model.StringAnnotation; 
     78import ome.xml.model.StructuredAnnotations; 
     79import ome.xml.model.TiffData; 
     80import ome.xml.model.TimestampAnnotation; 
     81import ome.xml.model.UUID; 
     82import ome.xml.model.XMLAnnotation; 
     83import ome.xml.model.Channel; 
     84import ome.xml.model.Dichroic; 
     85import ome.xml.model.Detector; 
     86import ome.xml.model.Filter; 
     87import ome.xml.model.FilterSet; 
     88import ome.xml.model.Image; 
     89import ome.xml.model.Instrument; 
     90import ome.xml.model.Laser; 
     91import ome.xml.model.MetadataOnly; 
     92import ome.xml.model.OME; 
     93import ome.xml.model.OTF; 
     94import ome.xml.model.Pixels; 
     95import ome.xml.model.Plate; 
     96import ome.xml.model.Rectangle; 
     97import ome.xml.model.ROI; 
     98import ome.xml.model.Shape; 
     99import ome.xml.model.Union; 
     100import ome.xml.model.Well; 
     101import ome.xml.model.WellSample; 
     102import ome.xml.model.enums.ArcType; 
     103import ome.xml.model.enums.DimensionOrder; 
     104import ome.xml.model.enums.EnumerationException; 
     105import ome.xml.model.enums.FilamentType; 
     106import ome.xml.model.enums.FilterType; 
     107import ome.xml.model.enums.LaserType; 
     108import ome.xml.model.enums.NamingConvention; 
     109import ome.xml.model.enums.PixelType; 
     110import ome.xml.model.primitives.NonNegativeInteger; 
     111import ome.xml.model.primitives.PositiveInteger; 
    112112 
    113113import org.testng.annotations.BeforeClass; 
  • trunk/components/bio-formats/test/loci/formats/utests/OMEModelMock.java

    r6413 r6458  
    3535package loci.formats.utests; 
    3636 
    37 import ome.xml.r201004.OME; 
     37import ome.xml.model.OME; 
    3838 
    3939/** 
  • trunk/components/bio-formats/test/loci/formats/utests/ObjectBasedOMEModelMock.java

    r6413 r6458  
    3535package loci.formats.utests; 
    3636 
    37 import ome.xml.r201004.Arc; 
    38 import ome.xml.r201004.BinaryFile; 
    39 import ome.xml.r201004.BooleanAnnotation; 
    40 import ome.xml.r201004.Channel; 
    41 import ome.xml.r201004.Detector; 
    42 import ome.xml.r201004.Dichroic; 
    43 import ome.xml.r201004.DoubleAnnotation; 
    44 import ome.xml.r201004.External; 
    45 import ome.xml.r201004.Filament; 
    46 import ome.xml.r201004.Filter; 
    47 import ome.xml.r201004.FilterSet; 
    48 import ome.xml.r201004.Image; 
    49 import ome.xml.r201004.Instrument; 
    50 import ome.xml.r201004.Laser; 
    51 import ome.xml.r201004.LightEmittingDiode; 
    52 import ome.xml.r201004.LongAnnotation; 
    53 import ome.xml.r201004.MetadataOnly; 
    54 import ome.xml.r201004.OME; 
    55 import ome.xml.r201004.OMEModel; 
    56 import ome.xml.r201004.OTF; 
    57 import ome.xml.r201004.Objective; 
    58 import ome.xml.r201004.ObjectiveSettings; 
    59 import ome.xml.r201004.Pixels; 
    60 import ome.xml.r201004.Plate; 
    61 import ome.xml.r201004.ROI; 
    62 import ome.xml.r201004.Rectangle; 
    63 import ome.xml.r201004.StringAnnotation; 
    64 import ome.xml.r201004.StructuredAnnotations; 
    65 import ome.xml.r201004.TiffData; 
    66 import ome.xml.r201004.TimestampAnnotation; 
    67 import ome.xml.r201004.UUID; 
    68 import ome.xml.r201004.Union; 
    69 import ome.xml.r201004.Well; 
    70 import ome.xml.r201004.WellSample; 
    71 import ome.xml.r201004.XMLAnnotation; 
    72 import ome.xml.r201004.primitives.NonNegativeInteger; 
    73 import ome.xml.r201004.primitives.PositiveInteger; 
     37import ome.xml.model.Arc; 
     38import ome.xml.model.BinaryFile; 
     39import ome.xml.model.BooleanAnnotation; 
     40import ome.xml.model.Channel; 
     41import ome.xml.model.Detector; 
     42import ome.xml.model.Dichroic; 
     43import ome.xml.model.DoubleAnnotation; 
     44import ome.xml.model.External; 
     45import ome.xml.model.Filament; 
     46import ome.xml.model.Filter; 
     47import ome.xml.model.FilterSet; 
     48import ome.xml.model.Image; 
     49import ome.xml.model.Instrument; 
     50import ome.xml.model.Laser; 
     51import ome.xml.model.LightEmittingDiode; 
     52import ome.xml.model.LongAnnotation; 
     53import ome.xml.model.MetadataOnly; 
     54import ome.xml.model.OME; 
     55import ome.xml.model.OMEModel; 
     56import ome.xml.model.OTF; 
     57import ome.xml.model.Objective; 
     58import ome.xml.model.ObjectiveSettings; 
     59import ome.xml.model.Pixels; 
     60import ome.xml.model.Plate; 
     61import ome.xml.model.ROI; 
     62import ome.xml.model.Rectangle; 
     63import ome.xml.model.StringAnnotation; 
     64import ome.xml.model.StructuredAnnotations; 
     65import ome.xml.model.TiffData; 
     66import ome.xml.model.TimestampAnnotation; 
     67import ome.xml.model.UUID; 
     68import ome.xml.model.Union; 
     69import ome.xml.model.Well; 
     70import ome.xml.model.WellSample; 
     71import ome.xml.model.XMLAnnotation; 
     72import ome.xml.model.primitives.NonNegativeInteger; 
     73import ome.xml.model.primitives.PositiveInteger; 
    7474 
    7575/** 
  • trunk/components/bio-formats/utils/MinimumWriter.java

    r6386 r6458  
    88import loci.formats.services.OMEXMLService; 
    99 
    10 import ome.xml.r201004.enums.DimensionOrder; 
    11 import ome.xml.r201004.enums.PixelType; 
    12 import ome.xml.r201004.primitives.PositiveInteger; 
     10import ome.xml.model.enums.DimensionOrder; 
     11import ome.xml.model.enums.PixelType; 
     12import ome.xml.model.primitives.PositiveInteger; 
    1313 
    1414/** 
  • trunk/components/bio-formats/utils/WriteRGBMovie.java

    r6294 r6458  
    88import loci.formats.services.OMEXMLService; 
    99 
    10 import ome.xml.r201004.enums.DimensionOrder; 
    11 import ome.xml.r201004.enums.EnumerationException; 
    12 import ome.xml.r201004.enums.PixelType; 
    13 import ome.xml.r201004.primitives.PositiveInteger; 
     10import ome.xml.model.enums.DimensionOrder; 
     11import ome.xml.model.enums.EnumerationException; 
     12import ome.xml.model.enums.PixelType; 
     13import ome.xml.model.primitives.PositiveInteger; 
    1414 
    1515/** 
  • trunk/components/flow-cytometry/src/loci/apps/flow/FlowCytometry.java

    r6230 r6458  
    7575import loci.formats.services.OMEXMLService; 
    7676 
    77 import ome.xml.r201004.enums.*; 
    78 import ome.xml.r201004.primitives.*; 
     77import ome.xml.model.enums.*; 
     78import ome.xml.model.primitives.*; 
    7979 
    8080import visad.DataReferenceImpl; 
  • trunk/components/legacy/ome-editor/src/loci/ome/editor/MetadataPane.java

    r6294 r6458  
    9191import ome.xml.DOMUtil; 
    9292import ome.xml.OMEXMLNode; 
    93 import ome.xml.r201004.enums.DimensionOrder; 
    94 import ome.xml.r201004.enums.EnumerationException; 
    95 import ome.xml.r201004.primitives.PositiveInteger; 
     93import ome.xml.model.enums.DimensionOrder; 
     94import ome.xml.model.enums.EnumerationException; 
     95import ome.xml.model.primitives.PositiveInteger; 
    9696 
    9797import org.openmicroscopy.xml.AttributeNode; 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java

    r6450 r6458  
    5757import loci.plugins.util.WindowTools; 
    5858 
    59 import ome.xml.r201004.enums.DimensionOrder; 
    60 import ome.xml.r201004.enums.EnumerationException; 
     59import ome.xml.model.enums.DimensionOrder; 
     60import ome.xml.model.enums.EnumerationException; 
    6161 
    6262import org.apache.log4j.Level; 
  • trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java

    r6279 r6458  
    5858import loci.formats.IFormatWriter; 
    5959import loci.formats.ImageWriter; 
     60import loci.formats.MetadataTools; 
    6061import loci.formats.gui.AWTImageTools; 
    6162import loci.formats.gui.ExtensionFileFilter; 
     
    6869import loci.plugins.util.WindowTools; 
    6970 
    70 import ome.xml.r201004.enums.DimensionOrder; 
    71 import ome.xml.r201004.enums.EnumerationException; 
    72 import ome.xml.r201004.enums.PixelType; 
    73 import ome.xml.r201004.primitives.PositiveInteger; 
     71import ome.xml.model.enums.DimensionOrder; 
     72import ome.xml.model.enums.EnumerationException; 
     73import ome.xml.model.enums.PixelType; 
     74import ome.xml.model.primitives.PositiveInteger; 
    7475 
    7576/** 
     
    278279      store.setPixelsSizeT(new PositiveInteger(imp.getNFrames()), 0); 
    279280 
     281      if (store.getImageID(0) == null) { 
     282        store.setImageID(MetadataTools.createLSID("Image", 0), 0); 
     283      } 
     284      if (store.getPixelsID(0) == null) { 
     285        store.setPixelsID(MetadataTools.createLSID("Pixels", 0), 0); 
     286      } 
     287 
    280288      if (store.getPixelsType(0) == null) { 
    281289        try { 
     
    285293        catch (EnumerationException e) { } 
    286294      } 
    287       if (store.getPixelsBinDataBigEndian(0, 0) == null) { 
     295      if (store.getPixelsBinDataCount(0) == 0 || 
     296        store.getPixelsBinDataBigEndian(0, 0) == null) 
     297      { 
    288298        store.setPixelsBinDataBigEndian(Boolean.FALSE, 0, 0); 
    289299      } 
     
    294304        catch (EnumerationException e) { } 
    295305      } 
    296       if (store.getChannelSamplesPerPixel(0, 0) == null) { 
     306      if (store.getChannelCount(0) == 0 || 
     307        store.getChannelSamplesPerPixel(0, 0) == null) 
     308      { 
    297309        store.setChannelSamplesPerPixel(new Integer(channels), 0, 0); 
     310      } 
     311      for (int channel=0; channel<store.getChannelCount(0); channel++) { 
     312        if (store.getChannelID(0, channel) == null) { 
     313          String lsid = MetadataTools.createLSID("Channel", 0, channel); 
     314          store.setChannelID(lsid, 0, channel); 
     315        } 
    298316      } 
    299317 
  • trunk/components/native/bf-cpp/source/minimum_writer.cpp

    r6386 r6458  
    5555using jace::proxy::loci::formats::meta::IMetadata; 
    5656#include "ome-xml.h" 
    57 using jace::proxy::ome::xml::r201004::enums::DimensionOrder; 
    58 using jace::proxy::ome::xml::r201004::enums::PixelType; 
    59 using jace::proxy::ome::xml::r201004::primitives::PositiveInteger; 
     57using jace::proxy::ome::xml::model::enums::DimensionOrder; 
     58using jace::proxy::ome::xml::model::enums::PixelType; 
     59using jace::proxy::ome::xml::model::primitives::PositiveInteger; 
    6060 
    6161#include <iostream> 
  • trunk/components/native/bf-cpp/src/conflicts.txt

    r6412 r6458  
    5151loci.formats.out.TiffWriter.COMPRESSION_LZW 
    5252loci.formats.out.TiffWriter.COMPRESSION_JPEG 
    53 ome.xml.r201004.enums.Compression.NONE 
    54 ome.xml.r201004.enums.LineCap.LINE 
     53ome.xml.model.enums.Compression.NONE 
     54ome.xml.model.enums.LineCap.LINE 
  • trunk/components/ome-plugins/src/loci/plugins/ome/LociUploader.java

    r6294 r6458  
    5151import loci.plugins.util.LibraryChecker; 
    5252 
    53 import ome.xml.r201004.enums.DimensionOrder; 
    54 import ome.xml.r201004.enums.EnumerationException; 
    55 import ome.xml.r201004.enums.PixelType; 
    56 import ome.xml.r201004.primitives.PositiveInteger; 
     53import ome.xml.model.enums.DimensionOrder; 
     54import ome.xml.model.enums.EnumerationException; 
     55import ome.xml.model.enums.PixelType; 
     56import ome.xml.model.primitives.PositiveInteger; 
    5757 
    5858/** 
  • trunk/components/ome-xml/src/ome/xml/model/AbstractOMEModelObject.java

    r6195 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004; 
     24package ome.xml.model; 
    2525 
    2626import java.util.ArrayList; 
    2727import java.util.List; 
    2828 
    29 import ome.xml.r201004.enums.EnumerationException; 
     29import ome.xml.model.enums.EnumerationException; 
    3030 
    3131import org.w3c.dom.Document; 
  • trunk/components/ome-xml/src/ome/xml/model/OMEModel.java

    r6196 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004; 
     24package ome.xml.model; 
    2525 
    2626import java.util.List; 
  • trunk/components/ome-xml/src/ome/xml/model/OMEModelImpl.java

    r6429 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004; 
     24package ome.xml.model; 
    2525 
    2626import java.util.ArrayList; 
     
    5454 
    5555  /* (non-Javadoc) 
    56    * @see ome.xml.r201004.OMEModel#removeModelObject(java.lang.String) 
     56   * @see ome.xml.model.OMEModel#removeModelObject(java.lang.String) 
    5757   */ 
    5858  public OMEModelObject removeModelObject(String id) { 
     
    6161   
    6262  /* (non-Javadoc) 
    63    * @see ome.xml.r201004.OMEModel#addModelObject(java.lang.String, ome.xml.r201004.OMEModelObject) 
     63   * @see ome.xml.model.OMEModel#addModelObject(java.lang.String, ome.xml.model.OMEModelObject) 
    6464   */ 
    6565  public OMEModelObject addModelObject(String id, OMEModelObject object) { 
     
    6868 
    6969  /* (non-Javadoc) 
    70    * @see ome.xml.r201004.OMEModel#getModelObject(java.lang.String) 
     70   * @see ome.xml.model.OMEModel#getModelObject(java.lang.String) 
    7171   */ 
    7272  public OMEModelObject getModelObject(String id) { 
     
    7575 
    7676  /* (non-Javadoc) 
    77    * @see ome.xml.r201004.OMEModel#getModelObjects() 
     77   * @see ome.xml.model.OMEModel#getModelObjects() 
    7878   */ 
    7979  public Map<String, OMEModelObject> getModelObjects() { 
     
    8282 
    8383  /* (non-Javadoc) 
    84    * @see ome.xml.r201004.OMEModel#addReference(java.lang.String, ome.xml.r201004.Reference) 
     84   * @see ome.xml.model.OMEModel#addReference(java.lang.String, ome.xml.model.Reference) 
    8585   */ 
    8686  public boolean addReference(OMEModelObject a, Reference b) { 
     
    9494 
    9595  /* (non-Javadoc) 
    96    * @see ome.xml.r201004.OMEModel#getReferences() 
     96   * @see ome.xml.model.OMEModel#getReferences() 
    9797   */ 
    9898  public Map<OMEModelObject, List<Reference>> getReferences() { 
     
    101101 
    102102  /* (non-Javadoc) 
    103    * @see ome.xml.r201004.OMEModel#resolveReferences() 
     103   * @see ome.xml.model.OMEModel#resolveReferences() 
    104104   */ 
    105105  public int resolveReferences() { 
  • trunk/components/ome-xml/src/ome/xml/model/OMEModelObject.java

    r6178 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004; 
     24package ome.xml.model; 
    2525 
    26 import ome.xml.r201004.enums.EnumerationException; 
     26import ome.xml.model.enums.EnumerationException; 
    2727 
    2828import org.w3c.dom.Document; 
  • trunk/components/ome-xml/src/ome/xml/model/enums/Enumeration.java

    r6137 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.enums; 
     24package ome.xml.model.enums; 
    2525 
    2626/** 
  • trunk/components/ome-xml/src/ome/xml/model/enums/EnumerationException.java

    r6137 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.enums; 
     24package ome.xml.model.enums; 
    2525 
    2626/** 
  • trunk/components/ome-xml/src/ome/xml/model/enums/handlers/IEnumerationHandler.java

    r6362 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.enums.handlers; 
     24package ome.xml.model.enums.handlers; 
    2525 
    26 import ome.xml.r201004.enums.Enumeration; 
    27 import ome.xml.r201004.enums.EnumerationException; 
     26import ome.xml.model.enums.Enumeration; 
     27import ome.xml.model.enums.EnumerationException; 
    2828 
    2929/** 
  • trunk/components/ome-xml/src/ome/xml/model/primitives/NonNegativeInteger.java

    r6196 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.primitives; 
     24package ome.xml.model.primitives; 
    2525 
    2626/** 
  • trunk/components/ome-xml/src/ome/xml/model/primitives/PercentFraction.java

    r6196 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.primitives; 
     24package ome.xml.model.primitives; 
    2525 
    2626/** 
  • trunk/components/ome-xml/src/ome/xml/model/primitives/PositiveInteger.java

    r6196 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.primitives; 
     24package ome.xml.model.primitives; 
    2525 
    2626/** 
  • trunk/components/ome-xml/src/ome/xml/model/primitives/PrimitiveType.java

    r6196 r6458  
    2222*/ 
    2323 
    24 package ome.xml.r201004.primitives; 
     24package ome.xml.model.primitives; 
    2525 
    2626/** 
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