Changeset 4671


Ignore:
Timestamp:
12/03/08 17:36:13 (12 years ago)
Author:
melissa
Message:

Added the Iris property of Objective to the MetadataStore and MetadataRetrieve interfaces. Note that this property is not supported by existing OME-XML schemas, but will be present in the next release. It is being added now to support OMERO's needs.

Location:
trunk/components
Files:
11 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/bio-formats-auto/src/entities.txt

    r4638 r4671  
    10681068path = - 
    10691069 
     1070# NB: This will be added in the next OME-XML release. 
     1071[Objective Iris] 
     1072type = Boolean 
     1073description = TODO 
     1074 
     1075[Objective Iris 200809] 
     1076path = - 
     1077 
     1078[Objective Iris 200802] 
     1079path = - 
     1080 
     1081[Objective Iris 200706] 
     1082path = - 
     1083 
     1084[Objective Iris 2003FC] 
     1085path = - 
     1086 
    10701087#TODO figure out how to reconcile the two filter models 
    10711088 
  • trunk/components/bio-formats/src/loci/formats/meta/AggregateMetadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    15961596  } 
    15971597 
     1598  /* @see MetadataRetrieve#getObjectiveIris(int, int) */ 
     1599  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     1600    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     1601      Object o = iter.next(); 
     1602      if (o instanceof MetadataRetrieve) { 
     1603        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     1604        Boolean result = retrieve.getObjectiveIris(instrumentIndex, objectiveIndex); 
     1605        if (result != null) return result; 
     1606      } 
     1607    } 
     1608    return null; 
     1609  } 
     1610 
    15981611  /* @see MetadataRetrieve#getObjectiveLensNA(int, int) */ 
    15991612  public Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex) { 
     
    36793692  } 
    36803693 
     3694  /* @see MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     3695  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     3696    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     3697      Object o = iter.next(); 
     3698      if (o instanceof MetadataStore) { 
     3699        MetadataStore store = (MetadataStore) o; 
     3700        store.setObjectiveIris(iris, instrumentIndex, objectiveIndex); 
     3701      } 
     3702    } 
     3703  } 
     3704 
    36813705  /* @see MetadataStore#setObjectiveLensNA(Float, int, int) */ 
    36823706  public void setObjectiveLensNA(Float lensNA, int instrumentIndex, int objectiveIndex) { 
  • trunk/components/bio-formats/src/loci/formats/meta/DummyMetadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    589589    return null; 
    590590  } 
     591  /* @see MetadataRetrieve#getObjectiveIris(int, int) */ 
     592  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     593    return null; 
     594  } 
    591595  /* @see MetadataRetrieve#getObjectiveLensNA(int, int) */ 
    592596  public Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex) { 
     
    13581362  } 
    13591363 
     1364  /* @see MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     1365  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     1366  } 
     1367 
    13601368  /* @see MetadataStore#setObjectiveLensNA(Float, int, int) */ 
    13611369  public void setObjectiveLensNA(Float lensNA, int instrumentIndex, int objectiveIndex) { 
  • trunk/components/bio-formats/src/loci/formats/meta/FilterMetadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    615615  } 
    616616 
     617  /* @see MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     618  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     619    store.setObjectiveIris(iris, instrumentIndex, objectiveIndex); 
     620  } 
     621 
    617622  /* @see MetadataStore#setObjectiveLensNA(Float, int, int) */ 
    618623  public void setObjectiveLensNA(Float lensNA, int instrumentIndex, int objectiveIndex) { 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataConverter.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    362362        String objectiveImmersionValue = src.getObjectiveImmersion(instrumentIndex, objectiveIndex); 
    363363        if (objectiveImmersionValue != null) dest.setObjectiveImmersion(objectiveImmersionValue, instrumentIndex, objectiveIndex); 
     364        Boolean objectiveIrisValue = src.getObjectiveIris(instrumentIndex, objectiveIndex); 
     365        if (objectiveIrisValue != null) dest.setObjectiveIris(objectiveIrisValue, instrumentIndex, objectiveIndex); 
    364366        Float objectiveLensNAValue = src.getObjectiveLensNA(instrumentIndex, objectiveIndex); 
    365367        if (objectiveLensNAValue != null) dest.setObjectiveLensNA(objectiveLensNAValue, instrumentIndex, objectiveIndex); 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataRetrieve.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    757757   * @param objectiveIndex index of the Objective 
    758758   */ 
     759  Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex); 
     760 
     761  /** 
     762   * For a particular Objective, gets TODO. 
     763   * @param instrumentIndex index of the Instrument 
     764   * @param objectiveIndex index of the Objective 
     765   */ 
    759766  Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex); 
    760767 
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataStore.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    812812  /** 
    813813   * For a particular Objective, sets TODO. 
     814   * @param iris TODO 
     815   * @param instrumentIndex index of the Instrument 
     816   * @param objectiveIndex index of the Objective 
     817   */ 
     818  void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex); 
     819 
     820  /** 
     821   * For a particular Objective, sets TODO. 
    814822   * @param lensNA TODO 
    815823   * @param instrumentIndex index of the Instrument 
  • trunk/components/bio-formats/src/loci/formats/ome/OMEXML2003FCMetadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    796796  public String getObjectiveImmersion(int instrumentIndex, int objectiveIndex) { 
    797797    // NB: Immersion unsupported for schema version 2003-FC 
     798    return null; 
     799  } 
     800 
     801  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveIris(int, int) */ 
     802  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     803    // NB: Iris unsupported for schema version 2003-FC 
    798804    return null; 
    799805  } 
     
    19731979  public void setObjectiveImmersion(String immersion, int instrumentIndex, int objectiveIndex) { 
    19741980    // NB: Immersion unsupported for schema version 2003-FC 
     1981  } 
     1982 
     1983  /* @see loci.formats.meta.MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     1984  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     1985    // NB: Iris unsupported for schema version 2003-FC 
    19751986  } 
    19761987 
  • trunk/components/bio-formats/src/loci/formats/ome/OMEXML200706Metadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    816816  } 
    817817 
     818  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveIris(int, int) */ 
     819  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     820    // NB: Iris unsupported for schema version 2007-06 
     821    return null; 
     822  } 
     823 
    818824  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveLensNA(int, int) */ 
    819825  public Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex) { 
     
    20022008    ObjectiveNode objectiveNode = getObjectiveNode(instrumentIndex, objectiveIndex, true); 
    20032009    objectiveNode.setImmersion(immersion); 
     2010  } 
     2011 
     2012  /* @see loci.formats.meta.MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     2013  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     2014    // NB: Iris unsupported for schema version 2007-06 
    20042015  } 
    20052016 
  • trunk/components/bio-formats/src/loci/formats/ome/OMEXML200802Metadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    816816  } 
    817817 
     818  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveIris(int, int) */ 
     819  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     820    // NB: Iris unsupported for schema version 2008-02 
     821    return null; 
     822  } 
     823 
    818824  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveLensNA(int, int) */ 
    819825  public Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex) { 
     
    20042010    ObjectiveNode objectiveNode = getObjectiveNode(instrumentIndex, objectiveIndex, true); 
    20052011    objectiveNode.setImmersion(immersion); 
     2012  } 
     2013 
     2014  /* @see loci.formats.meta.MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     2015  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     2016    // NB: Iris unsupported for schema version 2008-02 
    20062017  } 
    20072018 
  • trunk/components/bio-formats/src/loci/formats/ome/OMEXML200809Metadata.java

    r4638 r4671  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Nov 19, 2008 11:18:16 AM PST 
     27 * Created by melissa via MetadataAutogen on Dec 3, 2008 5:11:46 PM PST 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    814814  } 
    815815 
     816  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveIris(int, int) */ 
     817  public Boolean getObjectiveIris(int instrumentIndex, int objectiveIndex) { 
     818    // NB: Iris unsupported for schema version 2008-09 
     819    return null; 
     820  } 
     821 
    816822  /* @see loci.formats.meta.MetadataRetrieve#getObjectiveLensNA(int, int) */ 
    817823  public Float getObjectiveLensNA(int instrumentIndex, int objectiveIndex) { 
     
    20022008    ObjectiveNode objectiveNode = getObjectiveNode(instrumentIndex, objectiveIndex, true); 
    20032009    objectiveNode.setImmersion(immersion); 
     2010  } 
     2011 
     2012  /* @see loci.formats.meta.MetadataStore#setObjectiveIris(Boolean, int, int) */ 
     2013  public void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex) { 
     2014    // NB: Iris unsupported for schema version 2008-09 
    20042015  } 
    20052016 
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