Changeset 6266


Ignore:
Timestamp:
05/10/10 21:41:22 (10 years ago)
Author:
melissa
Message:

Re-added AggregateMetadata, DummyMetadata, and FilterMetadata.

Location:
trunk/components
Files:
3 added
7 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/autogen/src/MetadataAutogen.java

    r5523 r6266  
    132132        "meta/MetadataConverter.vm", "meta/MetadataConverter.java"); 
    133133 
     134      // NB : these IMetadata implementations are no longer necessary 
     135      /* 
    134136      // generate version-specific OME-XML metadata implementations 
    135137      for (String versionKey : entityList.versions()) { 
     
    138140          "ome/OMEXML" + versionKey + "Metadata.java"); 
    139141      } 
     142      */ 
    140143    } 
    141144  } 
  • trunk/components/autogen/src/entities.txt

    r6230 r6266  
    2626# index parameter to allow differentiation between them. 
    2727 
    28 # Root/UUID 
     28# TODO add descriptions as appropriate 
    2929 
    3030[Arc] 
    31 countable = true 
    3231path = Instrument+/Arc+ 
    3332 
     
    5352type = ArcType 
    5453 
    55 [FileAnnotationBinaryFile] 
    56 countable = true 
    57 path = FileAnnotationBinaryFile+ 
    58  
    59 [FileAnnotationBinaryFile FileName] 
    60 type = String 
    61  
    62 [FileAnnotationBinaryFile MIMEType] 
    63 type = String 
    64  
    65 [FileAnnotationBinaryFile FileSize] 
    66 type = Integer 
    67  
    68 [OTFBinaryFile] 
    69 countable = true 
    70 path = OTFBinaryFile+ 
    71  
    72 [OTFBinaryFile FileName] 
    73 type = String 
    74  
    75 [OTFBinaryFile MIMEType] 
    76 type = String 
    77  
    78 [OTFBinaryFile FileSize] 
    79 type = Integer 
    80  
    8154[BooleanAnnotation] 
    8255countable = true 
     
    10073 
    10174[Channel AnnotationRef] 
    102 type = String 
    10375countable = true 
    10476path = Image+/Channel+/AnnotationRef+ 
     77type = String 
    10578 
    10679[Channel Color] 
     
    146119type = Integer 
    147120 
     121[Channel LightSourceSettingsAttenuation] 
     122type = PercentFraction 
     123 
     124[Channel LightSourceSettingsID] 
     125type = String 
     126 
     127[Channel LightSourceSettingsWavelength] 
     128type = PositiveInteger 
     129 
    148130[Dataset] 
    149131countable = true 
     
    152134[Dataset AnnotationRef] 
    153135countable = true 
    154 type = String 
    155136path = Dataset+/AnnotationRef+ 
     137type = String 
    156138 
    157139[Dataset Description] 
     
    357339[Experimenter GroupRef] 
    358340countable = true 
    359 type = String 
    360341path = Experimenter+/GroupRef+ 
     342type = String 
    361343 
    362344[Experimenter ID] 
     
    376358 
    377359[Filament] 
    378 countable = true 
    379360path = Instrument+/Filament+ 
    380361 
     
    404385path = FileAnnotation+ 
    405386 
     387[FileAnnotation BinaryFileFileName] 
     388type = String 
     389 
     390[FileAnnotation BinaryFileMIMEType] 
     391type = String 
     392 
     393[FileAnnotation BinaryFileSize] 
     394type = Integer 
     395 
    406396[FileAnnotation ID] 
    407397type = String 
     
    436426 
    437427[FilterSet] 
    438 countable= true 
     428countable = true 
    439429path = Instrument+/FilterSet+ 
    440430 
     
    533523path = Image+/ROIRef+ 
    534524type = String 
     525 
     526[Image ObjectiveSettingsCorrectionCollar] 
     527type = Double 
     528 
     529[Image ObjectiveSettingsID] 
     530type = String 
     531 
     532[Image ObjectiveSettingsMedium] 
     533type = Medium 
     534 
     535[Image ObjectiveSettingsRefractiveIndex] 
     536type = Double 
    535537 
    536538[ImagingEnvironment] 
     
    558560 
    559561[Laser] 
    560 countable = true 
    561562path = Instrument+/Laser+ 
    562563 
     
    607608 
    608609[LightEmittingDiode] 
    609 countable = true 
    610610path = Instrument+/LightEmittingDiode+ 
    611611 
     
    636636 
    637637[LightPath EmissionFilterRef] 
    638 type = String 
    639638countable = true 
    640639path = Image+/Channel+/LightPath/EmissionFilterRef+ 
     640type = String 
    641641 
    642642[LightPath ExcitationFilterRef] 
    643 type = String 
    644643countable = true 
    645644path = Image+/Channel+/LightPath/ExcitationFilterRef+ 
    646  
    647 [ChannelLightSourceSettings] 
    648 countable = false 
    649 path = Image+/Channel+/LightSourceSettings 
    650  
    651 [ChannelLightSourceSettings ID] 
    652 type = String 
    653  
    654 [ChannelLightSourceSettings Wavelength] 
    655 type = PositiveInteger 
    656  
    657 [MicrobeamManipulationLightSourceSettings] 
    658 countable = true 
    659 path = Experiment+/MicrobeamManipulation+/LightSourceSettings+ 
    660  
    661 [MicrobeamManipulationLightSourceSettings ID] 
    662 type = String 
    663  
    664 [MicrobeamManipulationLightSourceSettings Wavelength] 
    665 type = PositiveInteger 
     645type = String 
    666646 
    667647[Line] 
     
    815795type = MicrobeamManipulationType 
    816796 
     797[MicrobeamManipulationLightSourceSettings] 
     798countable = true 
     799path = Experiment+/MicrobeamManipulation+/LightSourceSettings+ 
     800 
     801[MicrobeamManipulationLightSourceSettings Attenuation] 
     802type = PercentFraction 
     803 
     804[MicrobeamManipulationLightSourceSettings ID] 
     805type = String 
     806 
     807[MicrobeamManipulationLightSourceSettings Wavelength] 
     808type = PositiveInteger 
     809 
    817810[Microscope] 
    818811countable = false 
     
    838831path = Instrument+/OTF+ 
    839832 
     833[OTF BinaryFileFileName] 
     834type = String 
     835 
     836[OTF BinaryFileMIMEType] 
     837type = String 
     838 
     839[OTF BinaryFileSize] 
     840type = Integer 
     841 
    840842[OTF FilterSetRef] 
    841843type = String 
     
    856858type = PixelType 
    857859 
     860[OTF ObjectiveSettingsCorrectionCollar] 
     861type = Double 
     862 
     863[OTF ObjectiveSettingsID] 
     864type = String 
     865 
     866[OTF ObjectiveSettingsMedium] 
     867type = Medium 
     868 
     869[OTF ObjectiveSettingsRefractiveIndex] 
     870type = Double 
     871 
    858872[Objective] 
    859873countable = true 
     
    894908 
    895909[Objective WorkingDistance] 
    896 type = Double 
    897  
    898 [ImageObjectiveSettings] 
    899 countable = false 
    900 path = Image+/ObjectiveSettings 
    901  
    902 [ImageObjectiveSettings CorrectionCollar] 
    903 type = Double 
    904  
    905 [ImageObjectiveSettings ID] 
    906 type = String 
    907  
    908 [ImageObjectiveSettings Medium] 
    909 type = Medium 
    910  
    911 [ImageObjectiveSettings RefractiveIndex] 
    912 type = Double 
    913  
    914 [OTFObjectiveSettings] 
    915 countable = false 
    916 path = Instrument+/OTF+/ObjectiveSettings 
    917  
    918 [OTFObjectiveSettings CorrectionCollar] 
    919 type = Double 
    920  
    921 [OTFObjectiveSettings ID] 
    922 type = String 
    923  
    924 [OTFObjectiveSettings Medium] 
    925 type = Medium 
    926  
    927 [OTFObjectiveSettings RefractiveIndex] 
    928910type = Double 
    929911 
     
    969951 
    970952[Path Transform] 
    971 type = Strin 
     953type = String 
    972954 
    973955[Path Definition] 
    974956type = String 
    975  
    976 [PixelsBinData] 
    977 countable = true 
    978 path = Image+/Pixels/BinData+ 
    979  
    980 [PixelsBinData BigEndian] 
    981 type = Boolean 
    982957 
    983958[Pixels] 
     
    10261001type = PixelType 
    10271002 
     1003[PixelsBinData] 
     1004path = Image+/Pixels/BinData+ 
     1005 
     1006[PixelsBinData BigEndian] 
     1007type = Boolean 
     1008 
    10281009[Plane] 
    10291010countable = true 
    1030 path = Image+/Plane+ 
     1011path = Image+/Pixels/Plane+ 
    10311012 
    10321013[Plane AnnotationRef] 
    10331014countable = true 
    1034 path = Image+/Plane+/AnnotationRef+ 
     1015path = Image+/Pixels/Plane+/AnnotationRef+ 
    10351016type = String 
    10361017 
     
    11151096[PlateAcquisition AnnotationRef] 
    11161097countable = true 
    1117 path = Plate+/PlateAcquistion+/AnnotationRef+ 
     1098path = Plate+/PlateAcquisition+/AnnotationRef+ 
    11181099type = String 
    11191100 
     
    11371118 
    11381119[PlateAcquisition WellSampleRef] 
     1120countable = true 
     1121path = Plate+/PlateAcquisition+/WellSampleRef+ 
    11391122type = String 
    11401123 
     
    15921575type = Double 
    15931576 
    1594 [WellSample PositionZ] 
    1595 type = Double 
     1577[WellSample Timepoint] 
     1578type = Integer 
     1579 
     1580[WellSampleRef] 
     1581countable = true 
     1582path = Plate+/PlateAcquisition+/WellSampleRef+ 
    15961583 
    15971584[XMLAnnotation] 
     
    16071594[XMLAnnotation Value] 
    16081595type = String 
     1596 
     1597[ScreenRef] 
     1598countable = true 
     1599path = Plate+/ScreenRef+ 
     1600type = String 
     1601 
     1602[MicrobeamManipulationROIRef] 
     1603countable = true 
     1604path = Experiment+/MicrobeamManipulation+/ROIRef+ 
     1605 
     1606[ImageROIRef] 
     1607countable = true 
     1608path = Image+/ROIRef+ 
     1609 
     1610[ProjectRef] 
     1611countable = true 
     1612path = Dataset+/ProjectRef+ 
     1613 
     1614[PlateRef] 
     1615countable = true 
     1616path = Screen+/PlateRef+ 
     1617 
     1618[MicrobeamManipulationRef] 
     1619countable = true 
     1620path = Image+/MicrobeamManipulationRef+ 
     1621 
     1622[ExperimenterGroupRef] 
     1623countable = true 
     1624path = Experimenter+/GroupRef+ 
     1625 
     1626[FilterSetExcitationFilterRef] 
     1627countable = true 
     1628path = Instrument+/FilterSet+/ExcitationFilterRef+ 
     1629 
     1630[FilterSetEmissionFilterRef] 
     1631countable = true 
     1632path = Instrument+/FilterSet+/EmissionFilterRef+ 
     1633 
     1634[LightPathExcitationFilterRef] 
     1635countable = true 
     1636path = Image+/Channel+/LightPath/ExcitationFilterRef+ 
     1637 
     1638[LightPathEmissionFilterRef] 
     1639countable = true 
     1640path = Image+/Channel+/LightPath/EmissionFilterRef+ 
     1641 
     1642[DatasetRef] 
     1643countable = true 
     1644path = Image+/DatasetRef+ 
     1645 
     1646[ChannelAnnotationRef] 
     1647countable = true 
     1648path = Image+/Channel+/AnnotationRef+ 
     1649 
     1650[DatasetAnnotationRef] 
     1651countable = true 
     1652path = Dataset+/AnnotationRef+ 
     1653 
     1654[ExperimenterAnnotationRef] 
     1655countable = true 
     1656path = Experimenter+/AnnotationRef+ 
     1657 
     1658[ImageAnnotationRef] 
     1659countable = true 
     1660path = Image+/AnnotationRef+ 
     1661 
     1662[ListAnnotationAnnotationRef] 
     1663countable = true 
     1664path = ListAnnotation+/AnnotationRef+ 
     1665 
     1666[PixelsAnnotationRef] 
     1667countable = true 
     1668path = Image+/Pixels/AnnotationRef+ 
     1669 
     1670[PlaneAnnotationRef] 
     1671countable = true 
     1672path = Image+/Pixels/Plane+/AnnotationRef+ 
     1673 
     1674[PlateAnnotationRef] 
     1675countable = true 
     1676path = Plate+/AnnotationRef+ 
     1677 
     1678[PlateAcquisitionAnnotationRef] 
     1679countable = true 
     1680path = Plate+/PlateAcquisition+/AnnotationRef+ 
     1681 
     1682[ProjectAnnotationRef] 
     1683countable = true 
     1684path = Project+/AnnotationRef+ 
     1685 
     1686[ROIAnnotationRef] 
     1687countable = true 
     1688path = ROI+/AnnotationRef+ 
     1689 
     1690[ReagentAnnotationRef] 
     1691countable = true 
     1692path = Screen+/Reagent+/AnnotationRef+ 
     1693 
     1694[ScreenAnnotationRef] 
     1695countable = true 
     1696path = Screen+/AnnotationRef+ 
     1697 
     1698[WellAnnotationRef] 
     1699countable = true 
     1700path = Plate+/Well+/AnnotationRef+ 
     1701 
     1702[WellSampleAnnotationRef] 
     1703countable = true 
     1704path = Plate+/Well+/WellSample+/AnnotationRef+ 
     1705 
     1706[ShapeAnnotationRef] 
     1707countable = true 
     1708path = ROI+/Shape+/AnnotationRef+ 
  • trunk/components/autogen/src/meta/FilterMetadata.vm

    r6230 r6266  
    9494  public void set$entity$prop($q.type() $q.var($prop), $q.argsList()) { 
    9595#if ($q.type() == "String") 
    96     String value = filter ? DataTools.sanitize($q.var($prop)) : $q.var($prop); 
    97     store.set$entity$prop(value, $q.varsList()); 
     96    String filteredValue = filter ? DataTools.sanitize($q.var($prop)) : $q.var($prop); 
     97    store.set$entity$prop(filteredValue, $q.varsList()); 
    9898#else 
    9999    store.set$entity$prop($q.var($prop), $q.varsList()); 
  • trunk/components/bio-formats/src/loci/formats/FormatReader.java

    r6262 r6266  
    3838import loci.formats.in.MetadataLevel; 
    3939import loci.formats.in.MetadataOptions; 
    40 //import loci.formats.meta.DummyMetadata; 
     40import loci.formats.meta.DummyMetadata; 
     41import loci.formats.meta.FilterMetadata; 
    4142import loci.formats.meta.IMetadata; 
    4243import loci.formats.meta.MetadataStore; 
     
    108109   * semantics of {@link #getMetadataStore()} prevent "null" access. 
    109110   */ 
    110   protected MetadataStore metadataStore = /*new DummyMetadata()*/null; 
     111  protected MetadataStore metadataStore = new DummyMetadata(); 
    111112 
    112113  /** Metadata parsing options. */ 
     
    411412  /** Return a properly configured loci.formats.meta.FilterMetadata. */ 
    412413  protected MetadataStore makeFilterMetadata() { 
    413     // TODO : uncomment once FilterMetadata is updated 
    414     //return new FilterMetadata(getMetadataStore(), isMetadataFiltered()); 
    415     return getMetadataStore(); 
     414    return new FilterMetadata(getMetadataStore(), isMetadataFiltered()); 
    416415  } 
    417416 
  • trunk/components/bio-formats/src/loci/formats/FormatTools.java

    r6230 r6266  
    3030import loci.common.ReflectException; 
    3131import loci.common.ReflectedUniverse; 
    32 //import loci.formats.meta.DummyMetadata; 
     32import loci.formats.meta.DummyMetadata; 
    3333import loci.formats.meta.MetadataRetrieve; 
    3434import loci.formats.meta.MetadataStore; 
     
    743743    MetadataStore store = r.getMetadataStore(); 
    744744    MetadataRetrieve retrieve = store instanceof MetadataRetrieve ? 
    745       (MetadataRetrieve) store : /*new DummyMetadata()*/ null; 
     745      (MetadataRetrieve) store : new DummyMetadata(); 
    746746 
    747747    String filename = pattern.replaceAll(SERIES_NUM, String.valueOf(series)); 
  • trunk/components/bio-formats/src/loci/formats/FormatWriter.java

    r6230 r6266  
    2727import java.io.IOException; 
    2828 
    29 //import loci.formats.meta.DummyMetadata; 
     29import loci.formats.meta.DummyMetadata; 
    3030import loci.formats.meta.MetadataRetrieve; 
    3131 
     
    6666   * prevent "null" access. 
    6767   */ 
    68   protected MetadataRetrieve metadataRetrieve = /*new DummyMetadata()*/ null; 
     68  protected MetadataRetrieve metadataRetrieve = new DummyMetadata(); 
    6969 
    7070  // -- Constructors -- 
  • trunk/components/bio-formats/src/loci/formats/in/ZeissZVIReader.java

    r6230 r6266  
    4747import loci.formats.codec.JPEGCodec; 
    4848import loci.formats.codec.ZlibCodec; 
    49 //import loci.formats.meta.DummyMetadata; 
     49import loci.formats.meta.DummyMetadata; 
    5050import loci.formats.meta.MetadataStore; 
    5151import loci.formats.services.POIService; 
     
    494494        int imageNum = getImageNumber(name, -1); 
    495495        if (imageNum == -1) { 
    496           // TODO 
    497           parseTags(imageNum, name, /*new DummyMetadata()*/null); 
     496          parseTags(imageNum, name, new DummyMetadata()); 
    498497        } 
    499498        else tagsToParse.add(name); 
     
    846845        addGlobalMeta(key, value); 
    847846 
    848         // TODO 
    849         if (key.startsWith("ImageTile")/* && !(store instanceof DummyMetadata)*/ ) { 
     847        if (key.startsWith("ImageTile") && !(store instanceof DummyMetadata)) { 
    850848          if (!tiles.containsKey(new Integer(value))) { 
    851849            tiles.put(new Integer(value), new Integer(1)); 
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