Changeset 6457
- Timestamp:
- 06/03/10 11:40:39 (10 years ago)
- Location:
- branches/4.2/components
- Files:
-
- 147 added
- 1 deleted
- 54 edited
- 7 copied
Legend:
- Unmodified
- Added
- Removed
-
branches/4.2/components/autogen/src/entities.txt
r6266 r6457 1002 1002 1003 1003 [PixelsBinData] 1004 countable = true 1004 1005 path = Image+/Pixels/BinData+ 1005 1006 … … 1518 1519 type = String 1519 1520 1521 [UUID Value] 1522 type = String 1523 1520 1524 [Well] 1521 1525 countable = true -
branches/4.2/components/autogen/src/meta/AggregateMetadata.vm
r6230 r6457 35 35 import java.util.List; 36 36 37 import ome.xml. r201004.enums.*;38 import ome.xml. r201004.primitives.*;37 import ome.xml.model.enums.*; 38 import ome.xml.model.primitives.*; 39 39 40 40 /** -
branches/4.2/components/autogen/src/meta/DummyMetadata.vm
r6230 r6457 32 32 package loci.formats.meta; 33 33 34 import ome.xml. r201004.enums.*;35 import ome.xml. r201004.primitives.*;34 import ome.xml.model.enums.*; 35 import ome.xml.model.primitives.*; 36 36 37 37 /** -
branches/4.2/components/autogen/src/meta/FilterMetadata.vm
r6266 r6457 34 34 import loci.common.DataTools; 35 35 36 import ome.xml. r201004.enums.*;37 import ome.xml. r201004.primitives.*;36 import ome.xml.model.enums.*; 37 import ome.xml.model.primitives.*; 38 38 39 39 /** -
branches/4.2/components/autogen/src/meta/MetadataConverter.vm
r6230 r6457 32 32 package loci.formats.meta; 33 33 34 import ome.xml. r201004.enums.*;35 import ome.xml. r201004.primitives.*;34 import ome.xml.model.enums.*; 35 import ome.xml.model.primitives.*; 36 36 37 37 /** -
branches/4.2/components/bio-formats/src/loci/formats/FormatReader.java
r6370 r6457 45 45 import loci.formats.services.OMEXMLService; 46 46 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;47 import ome.xml.model.enums.AcquisitionMode; 48 import ome.xml.model.enums.ArcType; 49 import ome.xml.model.enums.Binning; 50 import ome.xml.model.enums.Compression; 51 import ome.xml.model.enums.ContrastMethod; 52 import ome.xml.model.enums.Correction; 53 import ome.xml.model.enums.DetectorType; 54 import ome.xml.model.enums.DimensionOrder; 55 import ome.xml.model.enums.EnumerationException; 56 import ome.xml.model.enums.ExperimentType; 57 import ome.xml.model.enums.FilamentType; 58 import ome.xml.model.enums.FillRule; 59 import ome.xml.model.enums.FilterType; 60 import ome.xml.model.enums.FontFamily; 61 import ome.xml.model.enums.FontStyle; 62 import ome.xml.model.enums.IlluminationType; 63 import ome.xml.model.enums.Immersion; 64 import ome.xml.model.enums.LaserMedium; 65 import ome.xml.model.enums.LaserType; 66 import ome.xml.model.enums.LineCap; 67 import ome.xml.model.enums.Marker; 68 import ome.xml.model.enums.Medium; 69 import ome.xml.model.enums.MicrobeamManipulationType; 70 import ome.xml.model.enums.MicroscopeType; 71 import ome.xml.model.enums.NamingConvention; 72 import ome.xml.model.enums.PixelType; 73 import ome.xml.model.enums.Pulse; 74 import ome.xml.model.enums.handlers.AcquisitionModeEnumHandler; 75 import ome.xml.model.enums.handlers.ArcTypeEnumHandler; 76 import ome.xml.model.enums.handlers.BinningEnumHandler; 77 import ome.xml.model.enums.handlers.CompressionEnumHandler; 78 import ome.xml.model.enums.handlers.ContrastMethodEnumHandler; 79 import ome.xml.model.enums.handlers.CorrectionEnumHandler; 80 import ome.xml.model.enums.handlers.DetectorTypeEnumHandler; 81 import ome.xml.model.enums.handlers.DimensionOrderEnumHandler; 82 import ome.xml.model.enums.handlers.ExperimentTypeEnumHandler; 83 import ome.xml.model.enums.handlers.FilamentTypeEnumHandler; 84 import ome.xml.model.enums.handlers.FillRuleEnumHandler; 85 import ome.xml.model.enums.handlers.FilterTypeEnumHandler; 86 import ome.xml.model.enums.handlers.FontFamilyEnumHandler; 87 import ome.xml.model.enums.handlers.FontStyleEnumHandler; 88 import ome.xml.model.enums.handlers.IlluminationTypeEnumHandler; 89 import ome.xml.model.enums.handlers.ImmersionEnumHandler; 90 import ome.xml.model.enums.handlers.LaserMediumEnumHandler; 91 import ome.xml.model.enums.handlers.LaserTypeEnumHandler; 92 import ome.xml.model.enums.handlers.LineCapEnumHandler; 93 import ome.xml.model.enums.handlers.MarkerEnumHandler; 94 import ome.xml.model.enums.handlers.MediumEnumHandler; 95 import ome.xml.model.enums.handlers.MicrobeamManipulationTypeEnumHandler; 96 import ome.xml.model.enums.handlers.MicroscopeTypeEnumHandler; 97 import ome.xml.model.enums.handlers.NamingConventionEnumHandler; 98 import ome.xml.model.enums.handlers.PixelTypeEnumHandler; 99 import ome.xml.model.enums.handlers.PulseEnumHandler; 100 100 101 101 /** … … 1075 1075 1076 1076 /** 1077 * Retrieves an {@link ome.xml. r201004.enums.AcquisitionMode} enumeration1078 * value for the given String. 1079 * 1080 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1077 * 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 1081 1081 * enumeration value is not found. 1082 1082 */ … … 1094 1094 1095 1095 /** 1096 * Retrieves an {@link ome.xml. r201004.enums.ArcType} enumeration1097 * value for the given String. 1098 * 1099 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1096 * 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 1100 1100 * enumeration value is not found. 1101 1101 */ … … 1111 1111 1112 1112 /** 1113 * Retrieves an {@link ome.xml. r201004.enums.Binning} enumeration1114 * value for the given String. 1115 * 1116 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1113 * 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 1117 1117 * enumeration value is not found. 1118 1118 */ … … 1127 1127 } 1128 1128 /** 1129 * Retrieves an {@link ome.xml. r201004.enums.Compression} enumeration1130 * value for the given String. 1131 * 1132 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1129 * 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 1133 1133 * enumeration value is not found. 1134 1134 */ … … 1143 1143 } 1144 1144 /** 1145 * Retrieves an {@link ome.xml. r201004.enums.ContrastMethod} enumeration1146 * value for the given String. 1147 * 1148 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1145 * 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 1149 1149 * enumeration value is not found. 1150 1150 */ … … 1161 1161 } 1162 1162 /** 1163 * Retrieves an {@link ome.xml. r201004.enums.Correction} enumeration1164 * value for the given String. 1165 * 1166 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1163 * 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 1167 1167 * enumeration value is not found. 1168 1168 */ … … 1177 1177 } 1178 1178 /** 1179 * Retrieves an {@link ome.xml. r201004.enums.DetectorType} enumeration1180 * value for the given String. 1181 * 1182 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1179 * 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 1183 1183 * enumeration value is not found. 1184 1184 */ … … 1193 1193 } 1194 1194 /** 1195 * Retrieves an {@link ome.xml. r201004.enums.DimensionOrder} enumeration1196 * value for the given String. 1197 * 1198 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1195 * 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 1199 1199 * enumeration value is not found. 1200 1200 */ … … 1211 1211 } 1212 1212 /** 1213 * Retrieves an {@link ome.xml. r201004.enums.ExperimentType} enumeration1214 * value for the given String. 1215 * 1216 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1213 * 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 1217 1217 * enumeration value is not found. 1218 1218 */ … … 1229 1229 } 1230 1230 /** 1231 * Retrieves an {@link ome.xml. r201004.enums.FilamentType} enumeration1232 * value for the given String. 1233 * 1234 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1231 * 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 1235 1235 * enumeration value is not found. 1236 1236 */ … … 1245 1245 } 1246 1246 /** 1247 * Retrieves an {@link ome.xml. r201004.enums.FillRule} enumeration1248 * value for the given String. 1249 * 1250 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1247 * 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 1251 1251 * enumeration value is not found. 1252 1252 */ … … 1261 1261 } 1262 1262 /** 1263 * Retrieves an {@link ome.xml. r201004.enums.FilterType} enumeration1264 * value for the given String. 1265 * 1266 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1263 * 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 1267 1267 * enumeration value is not found. 1268 1268 */ … … 1277 1277 } 1278 1278 /** 1279 * Retrieves an {@link ome.xml. r201004.enums.FontFamily} enumeration1280 * value for the given String. 1281 * 1282 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1279 * 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 1283 1283 * enumeration value is not found. 1284 1284 */ … … 1293 1293 } 1294 1294 /** 1295 * Retrieves an {@link ome.xml. r201004.enums.FontStyle} enumeration1296 * value for the given String. 1297 * 1298 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1295 * 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 1299 1299 * enumeration value is not found. 1300 1300 */ … … 1309 1309 } 1310 1310 /** 1311 * Retrieves an {@link ome.xml. r201004.enums.IlluminationType} enumeration1312 * value for the given String. 1313 * 1314 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1311 * 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 1315 1315 * enumeration value is not found. 1316 1316 */ … … 1327 1327 } 1328 1328 /** 1329 * Retrieves an {@link ome.xml. r201004.enums.Immersion} enumeration1330 * value for the given String. 1331 * 1332 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1329 * 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 1333 1333 * enumeration value is not found. 1334 1334 */ … … 1343 1343 } 1344 1344 /** 1345 * Retrieves an {@link ome.xml. r201004.enums.LaserMedium} enumeration1346 * value for the given String. 1347 * 1348 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1345 * 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 1349 1349 * enumeration value is not found. 1350 1350 */ … … 1359 1359 } 1360 1360 /** 1361 * Retrieves an {@link ome.xml. r201004.enums.LaserType} enumeration1362 * value for the given String. 1363 * 1364 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1361 * 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 1365 1365 * enumeration value is not found. 1366 1366 */ … … 1375 1375 } 1376 1376 /** 1377 * Retrieves an {@link ome.xml. r201004.enums.LineCap} enumeration1378 * value for the given String. 1379 * 1380 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1377 * 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 1381 1381 * enumeration value is not found. 1382 1382 */ … … 1391 1391 } 1392 1392 /** 1393 * Retrieves an {@link ome.xml. r201004.enums.Marker} enumeration1394 * value for the given String. 1395 * 1396 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1393 * 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 1397 1397 * enumeration value is not found. 1398 1398 */ … … 1407 1407 } 1408 1408 /** 1409 * Retrieves an {@link ome.xml. r201004.enums.Medium} enumeration1410 * value for the given String. 1411 * 1412 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1409 * 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 1413 1413 * enumeration value is not found. 1414 1414 */ … … 1423 1423 } 1424 1424 /** 1425 * Retrieves an {@link ome.xml. r201004.enums.MicrobeamManipulationType}1425 * Retrieves an {@link ome.xml.model.enums.MicrobeamManipulationType} 1426 1426 * enumeration value for the given String. 1427 1427 * 1428 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1428 * @throws ome.xml.model.enums.EnumerationException if an appropriate 1429 1429 * enumeration value is not found. 1430 1430 */ … … 1442 1442 } 1443 1443 /** 1444 * Retrieves an {@link ome.xml. r201004.enums.MicroscopeType} enumeration1445 * value for the given String. 1446 * 1447 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1444 * 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 1448 1448 * enumeration value is not found. 1449 1449 */ … … 1460 1460 } 1461 1461 /** 1462 * Retrieves an {@link ome.xml. r201004.enums.NamingConvention} enumeration1463 * value for the given String. 1464 * 1465 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1462 * 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 1466 1466 * enumeration value is not found. 1467 1467 */ … … 1478 1478 } 1479 1479 /** 1480 * Retrieves an {@link ome.xml. r201004.enums.PixelType} enumeration1481 * value for the given String. 1482 * 1483 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1480 * 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 1484 1484 * enumeration value is not found. 1485 1485 */ … … 1494 1494 } 1495 1495 /** 1496 * Retrieves an {@link ome.xml. r201004.enums.Pulse} enumeration1497 * value for the given String. 1498 * 1499 * @throws ome.xml. r201004.enums.EnumerationException if an appropriate1496 * 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 1500 1500 * enumeration value is not found. 1501 1501 */ -
branches/4.2/components/bio-formats/src/loci/formats/MetadataTools.java
r6233 r6457 38 38 import loci.formats.services.OMEXMLService; 39 39 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;40 import ome.xml.model.enums.DimensionOrder; 41 import ome.xml.model.enums.EnumerationException; 42 import ome.xml.model.enums.PixelType; 43 import ome.xml.model.primitives.PositiveInteger; 44 44 45 45 import org.slf4j.Logger; -
branches/4.2/components/bio-formats/src/loci/formats/in/BDReader.java
r6430 r6457 47 47 import loci.formats.tiff.TiffParser; 48 48 49 import ome.xml. r201004.primitives.NonNegativeInteger;50 import ome.xml. r201004.primitives.PositiveInteger;49 import ome.xml.model.primitives.NonNegativeInteger; 50 import ome.xml.model.primitives.PositiveInteger; 51 51 52 52 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/DeltavisionReader.java
r6370 r6457 38 38 import loci.formats.meta.MetadataStore; 39 39 40 import ome.xml. r201004.primitives.PositiveInteger;40 import ome.xml.model.primitives.PositiveInteger; 41 41 42 42 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/FV1000Reader.java
r6426 r6457 53 53 import loci.formats.tiff.TiffParser; 54 54 55 import ome.xml. r201004.primitives.PositiveInteger;55 import ome.xml.model.primitives.PositiveInteger; 56 56 57 57 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/FlexReader.java
r6370 r6457 47 47 import loci.formats.tiff.TiffParser; 48 48 49 import ome.xml. r201004.primitives.NonNegativeInteger;50 import ome.xml. r201004.primitives.PositiveInteger;49 import ome.xml.model.primitives.NonNegativeInteger; 50 import ome.xml.model.primitives.PositiveInteger; 51 51 52 52 import org.xml.sax.Attributes; -
branches/4.2/components/bio-formats/src/loci/formats/in/ICSReader.java
r6430 r6457 41 41 import loci.formats.meta.MetadataStore; 42 42 43 import ome.xml. r201004.primitives.PositiveInteger;43 import ome.xml.model.primitives.PositiveInteger; 44 44 45 45 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/ImarisTiffReader.java
r6230 r6457 35 35 import loci.formats.tiff.IFDList; 36 36 37 import ome.xml. r201004.primitives.PositiveInteger;37 import ome.xml.model.primitives.PositiveInteger; 38 38 39 39 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/InCellReader.java
r6376 r6457 38 38 import loci.formats.meta.MetadataStore; 39 39 40 import ome.xml. r201004.primitives.NonNegativeInteger;41 import ome.xml. r201004.primitives.PositiveInteger;40 import ome.xml.model.primitives.NonNegativeInteger; 41 import ome.xml.model.primitives.PositiveInteger; 42 42 43 43 import org.xml.sax.Attributes; -
branches/4.2/components/bio-formats/src/loci/formats/in/L2DReader.java
r6376 r6457 38 38 import loci.formats.meta.MetadataStore; 39 39 40 import ome.xml. r201004.primitives.PositiveInteger;40 import ome.xml.model.primitives.PositiveInteger; 41 41 42 42 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/LeicaHandler.java
r6388 r6457 36 36 import loci.formats.meta.MetadataStore; 37 37 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;38 import ome.xml.model.enums.Correction; 39 import ome.xml.model.enums.DetectorType; 40 import ome.xml.model.enums.EnumerationException; 41 import ome.xml.model.enums.Immersion; 42 import ome.xml.model.enums.LaserMedium; 43 import ome.xml.model.enums.LaserType; 44 import ome.xml.model.enums.MicroscopeType; 45 import ome.xml.model.enums.handlers.CorrectionEnumHandler; 46 import ome.xml.model.enums.handlers.DetectorTypeEnumHandler; 47 import ome.xml.model.enums.handlers.ImmersionEnumHandler; 48 import ome.xml.model.enums.handlers.LaserMediumEnumHandler; 49 import ome.xml.model.enums.handlers.LaserTypeEnumHandler; 50 import ome.xml.model.enums.handlers.MicroscopeTypeEnumHandler; 51 import ome.xml.model.primitives.PercentFraction; 52 import ome.xml.model.primitives.PositiveInteger; 53 53 54 54 import org.xml.sax.Attributes; -
branches/4.2/components/bio-formats/src/loci/formats/in/LeicaReader.java
r6416 r6457 48 48 import loci.formats.tiff.TiffParser; 49 49 50 import ome.xml. r201004.primitives.PositiveInteger;50 import ome.xml.model.primitives.PositiveInteger; 51 51 52 52 import org.slf4j.Logger; -
branches/4.2/components/bio-formats/src/loci/formats/in/MIASReader.java
r6376 r6457 49 49 import loci.formats.tiff.TiffParser; 50 50 51 import ome.xml. r201004.primitives.NonNegativeInteger;51 import ome.xml.model.primitives.NonNegativeInteger; 52 52 53 53 /** … … 681 681 682 682 String imageID = MetadataTools.createLSID("Image", well); 683 store.setWellSampleImageRef(imageID, 0, well, 0);684 683 store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0); 685 684 686 685 store.setImageID(imageID, well); 687 686 store.setImageName("Well " + wellRow + wellCol, well); 687 store.setWellSampleImageRef(imageID, 0, well, 0); 688 688 689 689 MetadataTools.setDefaultCreationDate(store, id, well); -
branches/4.2/components/bio-formats/src/loci/formats/in/MetamorphReader.java
r6430 r6457 48 48 import loci.formats.tiff.TiffRational; 49 49 50 import ome.xml. r201004.primitives.PositiveInteger;50 import ome.xml.model.primitives.PositiveInteger; 51 51 52 52 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/NativeND2Reader.java
r6409 r6457 45 45 import loci.formats.meta.MetadataStore; 46 46 47 import ome.xml. r201004.primitives.PositiveInteger;47 import ome.xml.model.primitives.PositiveInteger; 48 48 49 49 import org.xml.sax.Attributes; -
branches/4.2/components/bio-formats/src/loci/formats/in/NikonReader.java
r6221 r6457 242 242 } 243 243 244 return ImageTools.interpolate(pix, buf, colorMap, getSizeX(), getSizeY(), 244 if (x == 0 && y == 0 && getSizeX() == w && getSizeY() == h) { 245 return ImageTools.interpolate(pix, buf, colorMap, getSizeX(), getSizeY(), 246 isLittleEndian()); 247 } 248 249 byte[] b = new byte[FormatTools.getPlaneSize(this)]; 250 ImageTools.interpolate(pix, b, colorMap, getSizeX(), getSizeY(), 245 251 isLittleEndian()); 252 int bpp = FormatTools.getBytesPerPixel(getPixelType()) * 3; 253 int rowLen = w * bpp; 254 int width = getSizeX() * bpp; 255 for (int row=0; row<h; row++) { 256 System.arraycopy( 257 b, (row + y) * width + x * bpp, buf, row * rowLen, rowLen); 258 } 259 260 return buf; 246 261 } 247 262 -
branches/4.2/components/bio-formats/src/loci/formats/in/NikonTiffReader.java
r6376 r6457 35 35 import loci.formats.tiff.TiffParser; 36 36 37 import ome.xml. r201004.primitives.PositiveInteger;37 import ome.xml.model.primitives.PositiveInteger; 38 38 39 39 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/PerkinElmerReader.java
r6409 r6457 41 41 import loci.formats.meta.MetadataStore; 42 42 43 import ome.xml. r201004.primitives.PositiveInteger;43 import ome.xml.model.primitives.PositiveInteger; 44 44 45 45 /** -
branches/4.2/components/bio-formats/src/loci/formats/in/ScanrReader.java
r6376 r6457 41 41 import loci.formats.tiff.TiffParser; 42 42 43 import ome.xml. r201004.primitives.NonNegativeInteger;43 import ome.xml.model.primitives.NonNegativeInteger; 44 44 45 45 import org.xml.sax.Attributes; -
branches/4.2/components/bio-formats/src/loci/formats/in/ZeissZVIReader.java
r6376 r6457 51 51 import loci.formats.services.POIService; 52 52 53 import ome.xml. r201004.primitives.PositiveInteger;53 import ome.xml.model.primitives.PositiveInteger; 54 54 55 55 /** -
branches/4.2/components/bio-formats/src/loci/formats/meta/AggregateMetadata.java
r6415 r6457 25 25 * 26 26 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 27 * Created by melissa via MetadataAutogen on May 10, 2010 9:27:03 PM CDT27 * Created by melissa via MetadataAutogen on Jun 3, 2010 10:53:27 AM CDT 28 28 * 29 29 *----------------------------------------------------------------------------- … … 35 35 import java.util.List; 36 36 37 import loci.common.DataTools; 38 39 import ome.xml.r201004.enums.*; 40 import ome.xml.r201004.primitives.*; 37 import ome.xml.model.enums.*; 38 import ome.xml.model.primitives.*; 41 39 42 40 /** … … 554 552 } 555 553 554 /* @see MetadataRetrieve#getPixelsBinDataCount(int) */ 555 public int getPixelsBinDataCount(int imageIndex) { 556 for (Iterator iter = delegates.iterator(); iter.hasNext();) { 557 Object o = iter.next(); 558 if (o instanceof MetadataRetrieve) { 559 MetadataRetrieve retrieve = (MetadataRetrieve) o; 560 int result = retrieve.getPixelsBinDataCount(imageIndex); 561 if (result >= 0) return result; 562 } 563 } 564 return -1; 565 } 566 556 567 /* @see MetadataRetrieve#getPlaneCount(int) */ 557 568 public int getPlaneCount(int imageIndex) { … … 6430 6441 // - UUID property retrieval - 6431 6442 6432 public String getUUIDValue(int imageIndex, int tiffDataIndex) {6433 for (Iterator iter = delegates.iterator(); iter.hasNext();) {6434 Object o = iter.next();6435 if (o instanceof MetadataRetrieve) {6436 MetadataRetrieve retrieve = (MetadataRetrieve) o;6437 String result = retrieve.getUUIDValue(imageIndex, tiffDataIndex);6438 if (result != null) return result;6439 }6440 }6441 return null;6442 }6443 6444 6443 /* @see MetadataRetrieve#getUUIDFileName(int, int) */ 6445 6444 public String getUUIDFileName(int imageIndex, int tiffDataIndex) { … … 6449 6448 MetadataRetrieve retrieve = (MetadataRetrieve) o; 6450 6449 String result = retrieve.getUUIDFileName(imageIndex, tiffDataIndex); 6450 if (result != null) return result; 6451 } 6452 } 6453 return null; 6454 } 6455 6456 /* @see MetadataRetrieve#getUUIDValue(int, int) */ 6457 public String getUUIDValue(int imageIndex, int tiffDataIndex) { 6458 for (Iterator iter = delegates.iterator(); iter.hasNext();) { 6459 Object o = iter.next(); 6460 if (o instanceof MetadataRetrieve) { 6461 MetadataRetrieve retrieve = (MetadataRetrieve) o; 6462 String result = retrieve.getUUIDValue(imageIndex, tiffDataIndex); 6451 6463 if (result != null) return result; 6452 6464 } … … 11439 11451 11440 11452 // - UUID property storage - 11441 11442 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex) {11443 for (Iterator iter = delegates.iterator(); iter.hasNext();) {11444 Object o = iter.next();11445 if (o instanceof MetadataStore) {11446 MetadataStore store = (MetadataStore) o;11447 store.setUUIDValue(value, imageIndex, tiffDataIndex);11448 }11449 }11450 }11451 11453 11452 11454 /* @see MetadataStore#setUUIDFileName(String, int, int) */ … … 11461 11463 } 11462 11464 11465 /* @see MetadataStore#setUUIDValue(String, int, int) */ 11466 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex) { 11467 for (Iterator iter = delegates.iterator(); iter.hasNext();) { 11468 Object o = iter.next(); 11469 if (o instanceof MetadataStore) { 11470 MetadataStore store = (MetadataStore) o; 11471 store.setUUIDValue(value, imageIndex, tiffDataIndex); 11472 } 11473 } 11474 } 11475 11463 11476 // - Well property storage - 11464 11477 -
branches/4.2/components/bio-formats/src/loci/formats/meta/DummyMetadata.java
r6415 r6457 25 25 * 26 26 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 27 * Created by melissa via MetadataAutogen on May 10, 2010 9:27:03 PM CDT27 * Created by melissa via MetadataAutogen on Jun 3, 2010 10:53:27 AM CDT 28 28 * 29 29 *----------------------------------------------------------------------------- … … 32 32 package loci.formats.meta; 33 33 34 import ome.xml.r201004.Image; 35 import ome.xml.r201004.OME; 36 import ome.xml.r201004.Pixels; 37 import ome.xml.r201004.TiffData; 38 import ome.xml.r201004.UUID; 39 import ome.xml.r201004.enums.*; 40 import ome.xml.r201004.primitives.*; 34 import ome.xml.model.enums.*; 35 import ome.xml.model.primitives.*; 41 36 42 37 /** … … 233 228 } 234 229 230 /* @see MetadataRetrieve#getPixelsBinDataCount(int) */ 231 public int getPixelsBinDataCount(int imageIndex) { 232 return -1; 233 } 234 235 235 /* @see MetadataRetrieve#getPlaneCount(int) */ 236 236 public int getPlaneCount(int imageIndex) { … … 2253 2253 // - UUID property retrieval - 2254 2254 2255 public String getUUIDValue(int imageIndex, int tiffDataIndex) {2256 return null;2257 }2258 2259 2255 /* @see MetadataRetrieve#getUUIDFileName(int, int) */ 2260 2256 public String getUUIDFileName(int imageIndex, int tiffDataIndex) { 2261 2257 return null; 2262 2258 } 2259 /* @see MetadataRetrieve#getUUIDValue(int, int) */ 2260 public String getUUIDValue(int imageIndex, int tiffDataIndex) { 2261 return null; 2262 } 2263 2263 2264 2264 // - Well property retrieval - … … 4177 4177 // - UUID property storage - 4178 4178 4179 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex) {4180 }4181 4182 4179 /* @see MetadataStore#setUUIDFileName(String, int, int) */ 4183 4180 public void setUUIDFileName(String fileName, int imageIndex, int tiffDataIndex) { 4184 4181 } 4185 4182 4183 /* @see MetadataStore#setUUIDValue(String, int, int) */ 4184 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex) { 4185 } 4186 4186 4187 // - Well property storage - 4187 4188 -
branches/4.2/components/bio-formats/src/loci/formats/meta/FilterMetadata.java
r6415 r6457 25 25 * 26 26 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 27 * Created by melissa via MetadataAutogen on May 10, 2010 9:27:03 PM CDT27 * Created by melissa via MetadataAutogen on Jun 3, 2010 10:53:27 AM CDT 28 28 * 29 29 *----------------------------------------------------------------------------- … … 34 34 import loci.common.DataTools; 35 35 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.*; 36 import ome.xml.model.enums.*; 37 import ome.xml.model.primitives.*; 43 38 44 39 /** … … 2532 2527 // -- UUID property storage - 2533 2528 2534 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex)2535 {2536 String filteredValue = filter ? DataTools.sanitize(value) : value;2537 store.setUUIDValue(filteredValue, imageIndex, tiffDataIndex);2538 }2539 2540 2529 /* @see MetadataStore#setUUIDFileName(String, int, int) */ 2541 2530 public void setUUIDFileName(String fileName, int imageIndex, int tiffDataIndex) { … … 2544 2533 } 2545 2534 2535 /* @see MetadataStore#setUUIDValue(String, int, int) */ 2536 public void setUUIDValue(String value, int imageIndex, int tiffDataIndex) { 2537 String filteredValue = filter ? DataTools.sanitize(value) : value; 2538 store.setUUIDValue(filteredValue, imageIndex, tiffDataIndex); 2539 } 2540 2546 2541 // -- Well property storage - 2547 2542 -
branches/4.2/components/bio-formats/src/loci/formats/meta/MetadataConverter.java
r6230 r6457 32 32 package loci.formats.meta; 33 33 34 import ome.xml. r201004.enums.*;35 import ome.xml. r201004.primitives.*;34 import ome.xml.model.enums.*; 35 import ome.xml.model.primitives.*; 36 36 37 37 /** -
branches/4.2/components/bio-formats/src/loci/formats/meta/MetadataRetrieve.java
r6415 r6457 33 33 * 34 34 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 35 * Created by callan via xsd-fu on 2010-05-28 12:37:01.22286235 * Created by melissa via xsd-fu on 2010-06-03 10:29:38.469040 36 36 * 37 37 *----------------------------------------------------------------------------- … … 40 40 package loci.formats.meta; 41 41 42 import ome.xml. r201004.enums.*;43 import ome.xml. r201004.primitives.*;42 import ome.xml.model.enums.*; 43 import ome.xml.model.primitives.*; 44 44 45 45 /** … … 73 73 public interface MetadataRetrieve { 74 74 75 // -- Entity counting -- 75 // -- Entity counting (manual definitions) -- 76 77 int getPixelsBinDataCount(int imageIndex); 78 79 // -- Entity counting (code generated definitions) -- 76 80 77 81 // AnnotationRef entity counting … … 635 639 // 636 640 // EmissionFilterRef property storage 637 //638 // {u'LightPath': {u'Channel': {u'Pixels': {u'Image': {u'OME': None}}}}, u'FilterSet': {u'Instrument': {u'OME': None}}}639 // Is multi path? True640 641 //642 // EmissionFilterRef property storage643 //644 // {u'LightPath': {u'Channel': {u'Pixels': {u'Image': {u'OME': None}}}}, u'FilterSet': {u'Instrument': {u'OME': None}}}645 // Is multi path? True646 647 //648 // ExcitationFilterRef property storage649 641 // 650 642 // {u'LightPath': {u'Channel': {u'Pixels': {u'Image': {u'OME': None}}}}, u'FilterSet': {u'Instrument': {u'OME': None}}} -
branches/4.2/components/bio-formats/src/loci/formats/meta/MetadataStore.java
r6415 r6457 33 33 * 34 34 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 35 * Created by callan via xsd-fu on 2010-05-28 12:36:56.00758235 * Created by melissa via xsd-fu on 2010-06-03 10:29:37.250861 36 36 * 37 37 *----------------------------------------------------------------------------- … … 40 40 package loci.formats.meta; 41 41 42 import ome.xml. r201004.enums.*;43 import ome.xml. r201004.primitives.*;42 import ome.xml.model.enums.*; 43 import ome.xml.model.primitives.*; 44 44 45 45 /** … … 447 447 448 448 // 449 // EmissionFilterRef property storage450 //451 // {u'LightPath': {u'Channel': {u'Pixels': {u'Image': {u'OME': None}}}}, u'FilterSet': {u'Instrument': {u'OME': None}}}452 // Is multi path? True453 454 //455 // ExcitationFilterRef property storage456 //457 // {u'LightPath': {u'Channel': {u'Pixels': {u'Image': {u'OME': None}}}}, u'FilterSet': {u'Instrument': {u'OME': None}}}458 // Is multi path? True459 460 //461 449 // ExcitationFilterRef property storage 462 450 // -
branches/4.2/components/bio-formats/src/loci/formats/ome/AbstractOMEXMLMetadata.java
r6233 r6457 33 33 34 34 import ome.xml.DOMUtil; 35 import ome.xml. r201004.OME;36 import ome.xml. r201004.OMEModelObject;35 import ome.xml.model.OME; 36 import ome.xml.model.OMEModelObject; 37 37 38 38 import org.w3c.dom.Document; -
branches/4.2/components/bio-formats/src/loci/formats/ome/OMEXMLMetadataImpl.java
r6430 r6457 33 33 * 34 34 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY. 35 * Created by melissa via xsd-fu on 2010-06-0 1 11:06:50.71867235 * Created by melissa via xsd-fu on 2010-06-03 10:29:39.713258 36 36 * 37 37 *----------------------------------------------------------------------------- … … 40 40 package loci.formats.ome; 41 41 42 import ome.xml. r201004.*;43 import ome.xml. r201004.enums.*;44 import ome.xml. r201004.primitives.*;42 import ome.xml.model.*; 43 import ome.xml.model.enums.*; 44 import ome.xml.model.primitives.*; 45 45 46 46 /** … … 97 97 } 98 98 99 // -- Entity counting -- 99 // -- Entity counting (manual definitions) -- 100 101 public int getPixelsBinDataCount(int imageIndex) 102 { 103 return root.getImage(imageIndex).getPixels().sizeOfBinDataList(); 104 } 105 106 // -- Entity counting (code generated definitions) -- 100 107 101 108 // AnnotationRef entity counting -
branches/4.2/components/bio-formats/src/loci/formats/services/OMEXMLServiceImpl.java
r6272 r6457 42 42 import loci.formats.ome.OMEXMLMetadataImpl; 43 43 import 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;44 import ome.xml.model.OME; 45 import ome.xml.model.OMEModel; 46 import ome.xml.model.OMEModelImpl; 47 import ome.xml.model.OMEModelObject; 48 import ome.xml.model.StructuredAnnotations; 49 49 50 50 import org.slf4j.Logger; … … 100 100 */ 101 101 public OMEXMLServiceImpl() { 102 checkClassDependency(ome.xml. r201004.OMEModelObject.class);102 checkClassDependency(ome.xml.model.OMEModelObject.class); 103 103 } 104 104 … … 202 202 * classes should not leak out of the interface. 203 203 * @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. 205 205 * @throws IOException If there is an error reading from the string. 206 206 * @throws SAXException If there is an error parsing the XML. -
branches/4.2/components/bio-formats/src/loci/formats/tiff/TiffParser.java
r6430 r6457 762 762 763 763 long imageWidth = ifd.getImageWidth(); 764 long imageHeight = ifd.getImageLength(); 764 765 765 766 int bps0 = bitsPerSample[0]; … … 794 795 795 796 int skipBits = (int) (8 - ((imageWidth * bps0 * nChannels) % 8)); 796 if (skipBits == 8) skipBits = 0; 797 798 if (skipBits == 8 || 799 (bytes.length * 8 < bps0 * (nChannels * imageWidth + imageHeight))) 800 { 801 skipBits = 0; 802 } 797 803 798 804 // set up YCbCr-specific values … … 824 830 for (int channel=0; channel<nChannels; channel++) { 825 831 int index = numBytes * (sample * nChannels + channel); 826 int outputIndex = channel * nSamples + ndx* numBytes;832 int outputIndex = (channel * nSamples + ndx) * numBytes; 827 833 828 834 // unpack non-YCbCr samples … … 838 844 { 839 845 value = bb.getBits(bps0) & 0xffff; 840 //if (littleEndian && bps0 > 8) { 841 // value = DataTools.swap(value) >> (32 - bps0); 842 //} 843 if ((ndx % imageWidth) == imageWidth - 1/* && bps0 < 8*/) { 846 if ((ndx % imageWidth) == imageWidth - 1) { 844 847 bb.skipBits(skipBits); 845 848 } -
branches/4.2/components/bio-formats/test/loci/formats/utests/IMetadataBasedOMEModelMock.java
r6415 r6457 36 36 37 37 import 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;38 import ome.xml.model.Arc; 39 import ome.xml.model.BinaryFile; 40 import ome.xml.model.BooleanAnnotation; 41 import ome.xml.model.Channel; 42 import ome.xml.model.Detector; 43 import ome.xml.model.Dichroic; 44 import ome.xml.model.DoubleAnnotation; 45 import ome.xml.model.External; 46 import ome.xml.model.Filament; 47 import ome.xml.model.Filter; 48 import ome.xml.model.FilterSet; 49 import ome.xml.model.Image; 50 import ome.xml.model.Instrument; 51 import ome.xml.model.Laser; 52 import ome.xml.model.LightEmittingDiode; 53 import ome.xml.model.LongAnnotation; 54 import ome.xml.model.MetadataOnly; 55 import ome.xml.model.OME; 56 import ome.xml.model.OMEModel; 57 import ome.xml.model.OTF; 58 import ome.xml.model.Objective; 59 import ome.xml.model.ObjectiveSettings; 60 import ome.xml.model.Pixels; 61 import ome.xml.model.Plate; 62 import ome.xml.model.ROI; 63 import ome.xml.model.Rectangle; 64 import ome.xml.model.StringAnnotation; 65 import ome.xml.model.StructuredAnnotations; 66 import ome.xml.model.TimestampAnnotation; 67 import ome.xml.model.Union; 68 import ome.xml.model.Well; 69 import ome.xml.model.WellSample; 70 import ome.xml.model.XMLAnnotation; 71 import ome.xml.model.primitives.NonNegativeInteger; 72 import ome.xml.model.primitives.PositiveInteger; 73 73 74 74 /** -
branches/4.2/components/bio-formats/test/loci/formats/utests/InOut201004Test.java
r6415 r6457 60 60 import static org.testng.AssertJUnit.*; 61 61 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;62 import ome.xml.model.Annotation; 63 import ome.xml.model.Arc; 64 import ome.xml.model.BinaryFile; 65 import ome.xml.model.BooleanAnnotation; 66 import ome.xml.model.DoubleAnnotation; 67 import ome.xml.model.External; 68 import ome.xml.model.Filament; 69 import ome.xml.model.LightEmittingDiode; 70 import ome.xml.model.LongAnnotation; 71 import ome.xml.model.OMEModel; 72 import ome.xml.model.OMEModelImpl; 73 import ome.xml.model.OMEModelObject; 74 import ome.xml.model.Objective; 75 import ome.xml.model.ObjectiveSettings; 76 import ome.xml.model.Reference; 77 import ome.xml.model.StringAnnotation; 78 import ome.xml.model.StructuredAnnotations; 79 import ome.xml.model.TiffData; 80 import ome.xml.model.TimestampAnnotation; 81 import ome.xml.model.UUID; 82 import ome.xml.model.XMLAnnotation; 83 import ome.xml.model.Channel; 84 import ome.xml.model.Dichroic; 85 import ome.xml.model.Detector; 86 import ome.xml.model.Filter; 87 import ome.xml.model.FilterSet; 88 import ome.xml.model.Image; 89 import ome.xml.model.Instrument; 90 import ome.xml.model.Laser; 91 import ome.xml.model.MetadataOnly; 92 import ome.xml.model.OME; 93 import ome.xml.model.OTF; 94 import ome.xml.model.Pixels; 95 import ome.xml.model.Plate; 96 import ome.xml.model.Rectangle; 97 import ome.xml.model.ROI; 98 import ome.xml.model.Shape; 99 import ome.xml.model.Union; 100 import ome.xml.model.Well; 101 import ome.xml.model.WellSample; 102 import ome.xml.model.enums.ArcType; 103 import ome.xml.model.enums.DimensionOrder; 104 import ome.xml.model.enums.EnumerationException; 105 import ome.xml.model.enums.FilamentType; 106 import ome.xml.model.enums.FilterType; 107 import ome.xml.model.enums.LaserType; 108 import ome.xml.model.enums.NamingConvention; 109 import ome.xml.model.enums.PixelType; 110 import ome.xml.model.primitives.NonNegativeInteger; 111 import ome.xml.model.primitives.PositiveInteger; 112 112 113 113 import org.testng.annotations.BeforeClass; -
branches/4.2/components/bio-formats/test/loci/formats/utests/OMEModelMock.java
r6415 r6457 35 35 package loci.formats.utests; 36 36 37 import ome.xml. r201004.OME;37 import ome.xml.model.OME; 38 38 39 39 /** -
branches/4.2/components/bio-formats/test/loci/formats/utests/ObjectBasedOMEModelMock.java
r6415 r6457 35 35 package loci.formats.utests; 36 36 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;37 import ome.xml.model.Arc; 38 import ome.xml.model.BinaryFile; 39 import ome.xml.model.BooleanAnnotation; 40 import ome.xml.model.Channel; 41 import ome.xml.model.Detector; 42 import ome.xml.model.Dichroic; 43 import ome.xml.model.DoubleAnnotation; 44 import ome.xml.model.External; 45 import ome.xml.model.Filament; 46 import ome.xml.model.Filter; 47 import ome.xml.model.FilterSet; 48 import ome.xml.model.Image; 49 import ome.xml.model.Instrument; 50 import ome.xml.model.Laser; 51 import ome.xml.model.LightEmittingDiode; 52 import ome.xml.model.LongAnnotation; 53 import ome.xml.model.MetadataOnly; 54 import ome.xml.model.OME; 55 import ome.xml.model.OMEModel; 56 import ome.xml.model.OTF; 57 import ome.xml.model.Objective; 58 import ome.xml.model.ObjectiveSettings; 59 import ome.xml.model.Pixels; 60 import ome.xml.model.Plate; 61 import ome.xml.model.ROI; 62 import ome.xml.model.Rectangle; 63 import ome.xml.model.StringAnnotation; 64 import ome.xml.model.StructuredAnnotations; 65 import ome.xml.model.TiffData; 66 import ome.xml.model.TimestampAnnotation; 67 import ome.xml.model.UUID; 68 import ome.xml.model.Union; 69 import ome.xml.model.Well; 70 import ome.xml.model.WellSample; 71 import ome.xml.model.XMLAnnotation; 72 import ome.xml.model.primitives.NonNegativeInteger; 73 import ome.xml.model.primitives.PositiveInteger; 74 74 75 75 /** -
branches/4.2/components/bio-formats/test/loci/formats/utests/tiff/TiffParserTest.java
r6128 r6457 177 177 } 178 178 179 @Test (expectedExceptions={ FormatException.class })179 @Test 180 180 public void testBitsPerSampleMismatch() throws IOException, FormatException { 181 181 mock = new BitsPerSampleSamplesPerPixelMismatchMock(); 182 182 tiffParser = mock.getTiffParser(); 183 183 assertTrue(tiffParser.checkHeader()); 184 tiffParser.getFirstIFD().getBitsPerSample(); 184 int[] samples = tiffParser.getFirstIFD().getBitsPerSample(); 185 assertEquals(samples.length, mock.getSamplesPerPixel()); 185 186 } 186 187 -
branches/4.2/components/bio-formats/utils/MinimumWriter.java
r6294 r6457 8 8 import loci.formats.services.OMEXMLService; 9 9 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;10 import ome.xml.model.enums.DimensionOrder; 11 import ome.xml.model.enums.EnumerationException; 12 import ome.xml.model.enums.PixelType; 13 import ome.xml.model.primitives.PositiveInteger; 14 14 15 15 /** -
branches/4.2/components/bio-formats/utils/WriteRGBMovie.java
r6294 r6457 8 8 import loci.formats.services.OMEXMLService; 9 9 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;10 import ome.xml.model.enums.DimensionOrder; 11 import ome.xml.model.enums.EnumerationException; 12 import ome.xml.model.enums.PixelType; 13 import ome.xml.model.primitives.PositiveInteger; 14 14 15 15 /** -
branches/4.2/components/flow-cytometry/src/loci/apps/flow/FlowCytometry.java
r6230 r6457 75 75 import loci.formats.services.OMEXMLService; 76 76 77 import ome.xml. r201004.enums.*;78 import ome.xml. r201004.primitives.*;77 import ome.xml.model.enums.*; 78 import ome.xml.model.primitives.*; 79 79 80 80 import visad.DataReferenceImpl; -
branches/4.2/components/legacy/ome-editor/src/loci/ome/editor/MetadataPane.java
r6294 r6457 91 91 import ome.xml.DOMUtil; 92 92 import ome.xml.OMEXMLNode; 93 import ome.xml. r201004.enums.DimensionOrder;94 import ome.xml. r201004.enums.EnumerationException;95 import ome.xml. r201004.primitives.PositiveInteger;93 import ome.xml.model.enums.DimensionOrder; 94 import ome.xml.model.enums.EnumerationException; 95 import ome.xml.model.primitives.PositiveInteger; 96 96 97 97 import org.openmicroscopy.xml.AttributeNode; -
branches/4.2/components/loci-plugins/src/loci/plugins/in/ImportProcess.java
r6324 r6457 57 57 import loci.plugins.util.WindowTools; 58 58 59 import ome.xml. r201004.enums.DimensionOrder;60 import ome.xml. r201004.enums.EnumerationException;59 import ome.xml.model.enums.DimensionOrder; 60 import ome.xml.model.enums.EnumerationException; 61 61 62 62 import org.apache.log4j.Level; -
branches/4.2/components/loci-plugins/src/loci/plugins/out/Exporter.java
r6341 r6457 68 68 import loci.plugins.util.WindowTools; 69 69 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;70 import ome.xml.model.enums.DimensionOrder; 71 import ome.xml.model.enums.EnumerationException; 72 import ome.xml.model.enums.PixelType; 73 import ome.xml.model.primitives.PositiveInteger; 74 74 75 75 /** … … 285 285 catch (EnumerationException e) { } 286 286 } 287 if (store.getPixelsBinDataBigEndian(0, 0) == null) { 287 if (store.getPixelsBinDataCount(0) == 0 || 288 store.getPixelsBinDataBigEndian(0, 0) == null) 289 { 288 290 store.setPixelsBinDataBigEndian(Boolean.FALSE, 0, 0); 289 291 } -
branches/4.2/components/ome-plugins/src/loci/plugins/ome/LociUploader.java
r6294 r6457 51 51 import loci.plugins.util.LibraryChecker; 52 52 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;53 import ome.xml.model.enums.DimensionOrder; 54 import ome.xml.model.enums.EnumerationException; 55 import ome.xml.model.enums.PixelType; 56 import ome.xml.model.primitives.PositiveInteger; 57 57 58 58 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/AbstractOMEModelObject.java
r6195 r6457 22 22 */ 23 23 24 package ome.xml. r201004;24 package ome.xml.model; 25 25 26 26 import java.util.ArrayList; 27 27 import java.util.List; 28 28 29 import ome.xml. r201004.enums.EnumerationException;29 import ome.xml.model.enums.EnumerationException; 30 30 31 31 import org.w3c.dom.Document; … … 53 53 54 54 /* (non-Javadoc) 55 * @see ome.xml. r201004.OMEModelObject#update(org.w3c.dom.Element)55 * @see ome.xml.model.OMEModelObject#update(org.w3c.dom.Element) 56 56 */ 57 57 public void update(Element element) throws EnumerationException { … … 60 60 61 61 /* (non-Javadoc) 62 * @see ome.xml. r201004.OMEModelObject#update(org.w3c.dom.Element, ome.xml.r201004.OMEModel)62 * @see ome.xml.model.OMEModelObject#update(org.w3c.dom.Element, ome.xml.model.OMEModel) 63 63 */ 64 64 public void update(Element element, OMEModel model) … … 68 68 69 69 /* (non-Javadoc) 70 * @see ome.xml. r201004.OMEModelObject#asXMLElement(org.w3c.dom.Document)70 * @see ome.xml.model.OMEModelObject#asXMLElement(org.w3c.dom.Document) 71 71 */ 72 72 public abstract Element asXMLElement(Document document); … … 85 85 86 86 /* (non-Javadoc) 87 * @see ome.xml. r201004.OMEModelObject#link(ome.xml.r201004.Reference, ome.xml.r201004.OMEModelObject)87 * @see ome.xml.model.OMEModelObject#link(ome.xml.model.Reference, ome.xml.model.OMEModelObject) 88 88 */ 89 89 public abstract void link(Reference reference, OMEModelObject o); -
branches/4.2/components/ome-xml/src/ome/xml/model/OMEModel.java
r6196 r6457 22 22 */ 23 23 24 package ome.xml. r201004;24 package ome.xml.model; 25 25 26 26 import java.util.List; -
branches/4.2/components/ome-xml/src/ome/xml/model/OMEModelObject.java
r6178 r6457 22 22 */ 23 23 24 package ome.xml. r201004;24 package ome.xml.model; 25 25 26 import ome.xml. r201004.enums.EnumerationException;26 import ome.xml.model.enums.EnumerationException; 27 27 28 28 import org.w3c.dom.Document; -
branches/4.2/components/ome-xml/src/ome/xml/model/enums/Enumeration.java
r6137 r6457 22 22 */ 23 23 24 package ome.xml. r201004.enums;24 package ome.xml.model.enums; 25 25 26 26 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/enums/EnumerationException.java
r6137 r6457 22 22 */ 23 23 24 package ome.xml. r201004.enums;24 package ome.xml.model.enums; 25 25 26 26 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/enums/handlers/IEnumerationHandler.java
r6362 r6457 22 22 */ 23 23 24 package ome.xml. r201004.enums.handlers;24 package ome.xml.model.enums.handlers; 25 25 26 import ome.xml. r201004.enums.Enumeration;27 import ome.xml. r201004.enums.EnumerationException;26 import ome.xml.model.enums.Enumeration; 27 import ome.xml.model.enums.EnumerationException; 28 28 29 29 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/primitives/NonNegativeInteger.java
r6196 r6457 22 22 */ 23 23 24 package ome.xml. r201004.primitives;24 package ome.xml.model.primitives; 25 25 26 26 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/primitives/PercentFraction.java
r6196 r6457 22 22 */ 23 23 24 package ome.xml. r201004.primitives;24 package ome.xml.model.primitives; 25 25 26 26 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/primitives/PositiveInteger.java
r6196 r6457 22 22 */ 23 23 24 package ome.xml. r201004.primitives;24 package ome.xml.model.primitives; 25 25 26 26 /** -
branches/4.2/components/ome-xml/src/ome/xml/model/primitives/PrimitiveType.java
r6196 r6457 22 22 */ 23 23 24 package ome.xml. r201004.primitives;24 package ome.xml.model.primitives; 25 25 26 26 /** -
branches/4.2/components/ome-xml/test/ome/xml/utests/NonNegativeIntegerTest.java
r6196 r6457 37 37 import static org.testng.AssertJUnit.*; 38 38 39 import ome.xml. r201004.primitives.NonNegativeInteger;39 import ome.xml.model.primitives.NonNegativeInteger; 40 40 41 41 import org.testng.annotations.Test; -
branches/4.2/components/ome-xml/test/ome/xml/utests/PercentFractionTest.java
r6196 r6457 37 37 import static org.testng.AssertJUnit.*; 38 38 39 import ome.xml. r201004.primitives.PercentFraction;39 import ome.xml.model.primitives.PercentFraction; 40 40 41 41 import org.testng.annotations.Test; -
branches/4.2/components/ome-xml/test/ome/xml/utests/PositiveIntegerTest.java
r6196 r6457 37 37 import static org.testng.AssertJUnit.*; 38 38 39 import ome.xml. r201004.primitives.PositiveInteger;39 import ome.xml.model.primitives.PositiveInteger; 40 40 41 41 import org.testng.annotations.Test;
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