Changeset 6601


Ignore:
Timestamp:
06/29/10 15:07:47 (9 years ago)
Author:
melissa
Message:

Added 'unknown' domain and updated various readers to use the unknown domain instead of the graphics domain.

Location:
trunk/components/bio-formats/src/loci/formats
Files:
20 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/bio-formats/src/loci/formats/FormatTools.java

    r6514 r6601  
    185185  public static final String GRAPHICS_DOMAIN = "Graphics"; 
    186186 
     187  /** Identifies an unknown domain. */ 
     188  public static final String UNKNOWN_DOMAIN = "Unknown"; 
     189 
     190  /** List of non-graphics domains. */ 
     191  public static final String[] NON_GRAPHICS_DOMAINS = new String[] { 
     192    LM_DOMAIN, EM_DOMAIN, SPM_DOMAIN, SEM_DOMAIN, FLIM_DOMAIN, MEDICAL_DOMAIN, 
     193    HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, HCS_DOMAIN, UNKNOWN_DOMAIN 
     194  }; 
     195 
    187196  /** List of non-HCS domains. */ 
    188197  public static final String[] NON_HCS_DOMAINS = new String[] { 
    189198    LM_DOMAIN, EM_DOMAIN, SPM_DOMAIN, SEM_DOMAIN, FLIM_DOMAIN, MEDICAL_DOMAIN, 
    190     HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, GRAPHICS_DOMAIN 
     199    HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, UNKNOWN_DOMAIN 
     200  }; 
     201 
     202  /** 
     203   * List of domains that do not require special handling.  Domains that 
     204   * require special handling are {@link #GRAPHICS_DOMAIN} and 
     205   * {@link #HCS_DOMAIN}. 
     206   */ 
     207  public static final String[] NON_SPECIAL_DOMAINS = new String[] { 
     208    LM_DOMAIN, EM_DOMAIN, SPM_DOMAIN, SEM_DOMAIN, FLIM_DOMAIN, MEDICAL_DOMAIN, 
     209    HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, UNKNOWN_DOMAIN 
    191210  }; 
    192211 
     
    195214    HCS_DOMAIN, LM_DOMAIN, EM_DOMAIN, SPM_DOMAIN, SEM_DOMAIN, FLIM_DOMAIN, 
    196215    MEDICAL_DOMAIN, HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, 
    197     GRAPHICS_DOMAIN 
     216    GRAPHICS_DOMAIN, UNKNOWN_DOMAIN 
    198217  }; 
    199218 
  • trunk/components/bio-formats/src/loci/formats/in/ARFReader.java

    r6230 r6601  
    5656  public ARFReader() { 
    5757    super("ARF", "arf"); 
    58     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     58    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    5959  } 
    6060 
  • trunk/components/bio-formats/src/loci/formats/in/AmiraReader.java

    r6230 r6601  
    6868  public AmiraReader() { 
    6969    super("Amira", new String[] {"am", "amiramesh", "grey", "hx", "labels"}); 
    70     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     70    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    7171  } 
    7272 
  • trunk/components/bio-formats/src/loci/formats/in/FitsReader.java

    r6230 r6601  
    5959    super("Flexible Image Transport System", new String[] {"fits", "fts"}); 
    6060    domains = 
    61       new String[] {FormatTools.ASTRONOMY_DOMAIN, FormatTools.GRAPHICS_DOMAIN}; 
     61      new String[] {FormatTools.ASTRONOMY_DOMAIN, FormatTools.UNKNOWN_DOMAIN}; 
    6262  } 
    6363 
  • trunk/components/bio-formats/src/loci/formats/in/ICSReader.java

    r6573 r6601  
    149149    super("Image Cytometry Standard", new String[] {"ics", "ids"}); 
    150150    domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.FLIM_DOMAIN, 
    151       FormatTools.GRAPHICS_DOMAIN}; 
     151      FormatTools.UNKNOWN_DOMAIN}; 
    152152    hasCompanionFiles = true; 
    153153  } 
  • trunk/components/bio-formats/src/loci/formats/in/IPLabReader.java

    r6495 r6601  
    5656    suffixNecessary = false; // allow extensionless IPLab files 
    5757    suffixSufficient = false; 
    58     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     58    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    5959  } 
    6060 
  • trunk/components/bio-formats/src/loci/formats/in/IPWReader.java

    r6495 r6601  
    7676  public IPWReader() { 
    7777    super("Image-Pro Workspace", "ipw"); 
    78     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     78    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    7979  } 
    8080 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisHDFReader.java

    r6230 r6601  
    7575    super("Bitplane Imaris 5.5 (HDF)", "ims"); 
    7676    suffixSufficient = false; 
    77     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     77    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    7878  } 
    7979 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisReader.java

    r6495 r6601  
    6565    super("Bitplane Imaris", "ims"); 
    6666    suffixSufficient = false; 
    67     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     67    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    6868  } 
    6969 
  • trunk/components/bio-formats/src/loci/formats/in/ImarisTiffReader.java

    r6495 r6601  
    5656    suffixSufficient = false; 
    5757    suffixNecessary = true; 
    58     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     58    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    5959  } 
    6060 
  • trunk/components/bio-formats/src/loci/formats/in/ImprovisionTiffReader.java

    r6406 r6601  
    5959    super("Improvision TIFF", new String[] {"tif", "tiff"}); 
    6060    suffixSufficient = false; 
    61     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     61    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    6262  } 
    6363 
  • trunk/components/bio-formats/src/loci/formats/in/IvisionReader.java

    r6531 r6601  
    7878    suffixSufficient = false; 
    7979    suffixNecessary = false; 
    80     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     80    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    8181  } 
    8282 
  • trunk/components/bio-formats/src/loci/formats/in/LIMReader.java

    r6230 r6601  
    5555  public LIMReader() { 
    5656    super("Laboratory Imaging", "lim"); 
    57     domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.GRAPHICS_DOMAIN}; 
     57    domains = new String[] {FormatTools.LM_DOMAIN}; 
    5858  } 
    5959 
  • trunk/components/bio-formats/src/loci/formats/in/NRRDReader.java

    r6333 r6601  
    7373  public NRRDReader() { 
    7474    super("NRRD", new String[] {"nrrd", "nhdr"}); 
    75     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     75    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    7676    hasCompanionFiles = true; 
    7777  } 
  • trunk/components/bio-formats/src/loci/formats/in/NiftiReader.java

    r6495 r6601  
    8080    suffixSufficient = false; 
    8181    domains = new String[] {FormatTools.MEDICAL_DOMAIN, 
    82       FormatTools.GRAPHICS_DOMAIN}; 
     82      FormatTools.UNKNOWN_DOMAIN}; 
    8383    hasCompanionFiles = true; 
    8484  } 
     
    123123    String[] domain = new String[1]; 
    124124    domain[0] = nDimensions <= 3 ? 
    125       FormatTools.GRAPHICS_DOMAIN : FormatTools.MEDICAL_DOMAIN; 
     125      FormatTools.UNKNOWN_DOMAIN : FormatTools.MEDICAL_DOMAIN; 
    126126    return domain; 
    127127  } 
  • trunk/components/bio-formats/src/loci/formats/in/OMETiffReader.java

    r6568 r6601  
    8787    suffixNecessary = false; 
    8888    suffixSufficient = false; 
    89     domains = FormatTools.ALL_DOMAINS; 
     89    domains = FormatTools.NON_GRAPHICS_DOMAINS; 
    9090    hasCompanionFiles = true; 
    9191  } 
     
    149149    FormatTools.assertId(currentId, true, 1); 
    150150    return hasSPW ? new String[] {FormatTools.HCS_DOMAIN} : 
    151       FormatTools.NON_HCS_DOMAINS; 
     151      FormatTools.NON_SPECIAL_DOMAINS; 
    152152  } 
    153153 
     
    357357    Hashtable<String, IFormatReader> readers = 
    358358      new Hashtable<String, IFormatReader>(); 
    359     int s = 0; 
    360359    for (int i=0; i<seriesCount; i++) { 
     360      int s = i; 
    361361      LOGGER.debug("Image[{}] {", i); 
    362362      LOGGER.debug("  id = {}", meta.getImageID(i)); 
  • trunk/components/bio-formats/src/loci/formats/in/OMEXMLReader.java

    r6568 r6601  
    100100  public OMEXMLReader() { 
    101101    super("OME-XML", "ome"); 
    102     domains = FormatTools.ALL_DOMAINS; 
     102    domains = FormatTools.NON_GRAPHICS_DOMAINS; 
    103103    suffixNecessary = false; 
    104104  } 
     
    117117    FormatTools.assertId(currentId, true, 1); 
    118118    return hasSPW ? new String[] {FormatTools.HCS_DOMAIN} : 
    119       FormatTools.NON_HCS_DOMAINS; 
     119      FormatTools.NON_SPECIAL_DOMAINS; 
    120120  } 
    121121 
  • trunk/components/bio-formats/src/loci/formats/in/OpenlabRawReader.java

    r6495 r6601  
    6767    super("Openlab RAW", "raw"); 
    6868    suffixSufficient = false; 
    69     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     69    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    7070  } 
    7171 
  • trunk/components/bio-formats/src/loci/formats/in/OpenlabReader.java

    r6495 r6601  
    115115    super("Openlab LIFF", "liff"); 
    116116    suffixNecessary = false; 
    117     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     117    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    118118  } 
    119119 
  • trunk/components/bio-formats/src/loci/formats/in/SEQReader.java

    r6495 r6601  
    5959  public SEQReader() { 
    6060    super("Image-Pro Sequence", "seq"); 
    61     domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; 
     61    domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; 
    6262  } 
    6363 
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