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Ticket #12121: 0004-specification-Add-Iris-enum.patch

File 0004-specification-Add-Iris-enum.patch, 5.6 KB (added by rleigh, 10 years ago)

  • components/formats-api/src/loci/formats/meta/MetadataConverter.java 

    From 67b54e0d7fa7ca17a353afa518557f00f0db5ad3 Mon Sep 17 00:00:00 2001
From: Roger Leigh <r.leigh@dundee.ac.uk>
Date: Fri, 18 Apr 2014 15:56:46 +0100
Subject: [PATCH 4/7] specification: Add Iris enum

---
 .../formats-api/src/loci/formats/meta/MetadataConverter.java   |  2 +-
 components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java |  4 +++-
 components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java |  6 +++++-
 components/specification/released-schema/2013-10-dev-2/ome.xsd | 10 ++++++++--
 .../specification/src/ome/specification/XMLMockObjects.java    |  3 ++-
 5 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/components/formats-api/src/loci/formats/meta/MetadataConverter.java b/components/formats-api/src/loci/formats/meta/MetadataConverter.java
index a1f28b8..b3ca4cc 100644
    a b public final class MetadataConverter { 
    15521552        catch (NullPointerException e) { } 
    15531553 
    15541554        try { 
    1555           Boolean iris = src.getObjectiveIris(i, q); 
     1555          Iris iris = src.getObjectiveIris(i, q); 
    15561556          dest.setObjectiveIris(iris, i, q); 
    15571557        } 
    15581558        catch (NullPointerException e) { } 

  • components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java 

    diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
index 3b5afd9..2c5eff3 100644
    a b import loci.formats.meta.MetadataStore; 
    5555import ome.xml.model.enums.AcquisitionMode; 
    5656import ome.xml.model.enums.Binning; 
    5757import ome.xml.model.enums.IlluminationType; 
     58import ome.xml.model.enums.Iris; 
    5859import ome.xml.model.primitives.Color; 
    5960import ome.xml.model.primitives.NonNegativeInteger; 
    6061import ome.xml.model.primitives.PercentFraction; 
    … … public class ZeissCZIReader extends FormatReader { 
    23012302        } 
    23022303        String iris = getFirstNodeValue(objective, "Iris"); 
    23032304        if (iris != null) { 
    2304           store.setObjectiveIris(new Boolean(iris), 0, i); 
     2305          Boolean irisValue = new Boolean(iris); 
     2306          store.setObjectiveIris(irisValue.booleanValue() == true ? Iris.PRESENT : Iris.ABSENT, 0, i); 
    23052307        } 
    23062308      } 
    23072309    } 

  • components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java 

    diff --git a/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java b/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java
index d7ffbec..257062a 100644
    a b import loci.formats.tiff.TiffCompression; 
    5353import loci.formats.tiff.TiffConstants; 
    5454import loci.formats.tiff.TiffParser; 
    5555 
     56import ome.xml.model.enums.Iris; 
    5657import ome.xml.model.primitives.Color; 
    5758import ome.xml.model.primitives.NonNegativeInteger; 
    5859import ome.xml.model.primitives.PositiveFloat; 
    … … public class ZeissLSMReader extends FormatReader { 
    13001301          recording.magnification, instrument, 0); 
    13011302      } 
    13021303      store.setObjectiveLensNA(recording.lensNA, instrument, 0); 
    1303       store.setObjectiveIris(recording.iris, instrument, 0); 
     1304      if (recording.iris != null) { 
     1305          store.setObjectiveIris(recording.iris.booleanValue() == true ? Iris.PRESENT : Iris.ABSENT, 
     1306                                 instrument, 0); 
     1307      } 
    13041308      store.setObjectiveID(objectiveID, instrument, 0); 
    13051309    } 
    13061310    else if (block instanceof Laser) { 

  • components/specification/released-schema/2013-10-dev-2/ome.xsd 

    diff --git a/components/specification/released-schema/2013-10-dev-2/ome.xsd b/components/specification/released-schema/2013-10-dev-2/ome.xsd
index db31ccb..19d8880 100644
    a b  
    15971597                                                        </xsd:documentation> 
    15981598                                                </xsd:annotation> 
    15991599                                        </xsd:attribute> 
    1600                                         <xsd:attribute name="Iris" use="optional" type="xsd:boolean"> 
     1600                                        <xsd:attribute name="Iris" use="optional"> 
    16011601                                                <xsd:annotation> 
    16021602                                                        <xsd:documentation> 
    1603                                                                 Records whether or not the objective was fitted with an Iris. [flag] 
     1603                                                                Records whether or not the objective was fitted with an Iris.  Present if an Iris is present, or else Absent. 
    16041604                                                        </xsd:documentation> 
    16051605                                                </xsd:annotation> 
     1606                                                <xsd:simpleType> 
     1607                                                  <xsd:restriction base="xsd:string"> 
     1608                                                    <xsd:enumeration value="Absent"/> 
     1609                                                    <xsd:enumeration value="Present"/> 
     1610                                                  </xsd:restriction> 
     1611                                                </xsd:simpleType> 
    16061612                                        </xsd:attribute> 
    16071613                                </xsd:extension> 
    16081614                        </xsd:complexContent> 

  • components/specification/src/ome/specification/XMLMockObjects.java 

    diff --git a/components/specification/src/ome/specification/XMLMockObjects.java b/components/specification/src/ome/specification/XMLMockObjects.java
index 9c2afe3..3754eeb 100644
    a b import ome.xml.model.enums.ExperimentType; 
    9999import ome.xml.model.enums.FilamentType; 
    100100import ome.xml.model.enums.FilterType; 
    101101import ome.xml.model.enums.IlluminationType; 
     102import ome.xml.model.enums.Iris; 
    102103import ome.xml.model.enums.Medium; 
    103104import ome.xml.model.enums.Immersion; 
    104105import ome.xml.model.enums.LaserType; 
    … … public class XMLMockObjects 
    369370    objective.setCalibratedMagnification(1.0); 
    370371    objective.setCorrection(CORRECTION); 
    371372    objective.setImmersion(IMMERSION); 
    372     objective.setIris(true); 
     373    objective.setIris(Iris.PRESENT); 
    373374    objective.setLensNA(0.5); 
    374375    objective.setNominalMagnification(1.5); 
    375376    objective.setWorkingDistance(1.0); 

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