Changeset 6998


Ignore:
Timestamp:
09/28/10 11:06:35 (9 years ago)
Author:
melissa
Message:

Merged base reader changes into 4.2: r6688, r6756, r6757, r6764, r6853, and r6854.

Location:
branches/4.2/components/bio-formats
Files:
9 edited

Legend:

Unmodified
Added
Removed
  • branches/4.2/components/bio-formats/src/loci/formats/AxisGuesser.java

    r6026 r6998  
    314314      new Location(System.getProperty("user.dir")).listFiles()[0] : 
    315315      new Location(args[0]); 
    316     LOGGER.debug("File = {}", file.getAbsoluteFile()); 
     316    LOGGER.info("File = {}", file.getAbsoluteFile()); 
    317317    String pat = FilePattern.findPattern(file); 
    318     if (pat == null) LOGGER.debug("No pattern found."); 
     318    if (pat == null) LOGGER.info("No pattern found."); 
    319319    else { 
    320       LOGGER.debug("Pattern = {}", pat); 
     320      LOGGER.info("Pattern = {}", pat); 
    321321      FilePattern fp = new FilePattern(pat); 
    322322      if (fp.isValid()) { 
    323         LOGGER.debug("Pattern is valid."); 
     323        LOGGER.info("Pattern is valid."); 
    324324        String id = fp.getFiles()[0]; 
    325325        if (!new Location(id).exists()) { 
    326           LOGGER.debug("File '{}' does not exist.", id); 
     326          LOGGER.info("File '{}' does not exist.", id); 
    327327        } 
    328328        else { 
    329329          // read dimensional information from first file 
    330           LOGGER.debug("Reading first file "); 
     330          LOGGER.info("Reading first file "); 
    331331          ImageReader reader = new ImageReader(); 
    332332          reader.setId(id); 
     
    337337          boolean certain = reader.isOrderCertain(); 
    338338          reader.close(); 
    339           LOGGER.debug("[done]"); 
    340           LOGGER.debug("\tdimOrder = {} ({})", 
     339          LOGGER.info("[done]"); 
     340          LOGGER.info("\tdimOrder = {} ({})", 
    341341            dimOrder, certain ? "certain" : "uncertain"); 
    342           LOGGER.debug("\tsizeZ = {}", sizeZ); 
    343           LOGGER.debug("\tsizeT = {}", sizeT); 
    344           LOGGER.debug("\tsizeC = {}", sizeC); 
     342          LOGGER.info("\tsizeZ = {}", sizeZ); 
     343          LOGGER.info("\tsizeT = {}", sizeT); 
     344          LOGGER.info("\tsizeC = {}", sizeC); 
    345345 
    346346          // guess axes 
     
    354354          String newOrder = ag.getAdjustedOrder(); 
    355355          boolean isCertain = ag.isCertain(); 
    356           LOGGER.debug("Axis types:"); 
     356          LOGGER.info("Axis types:"); 
    357357          for (int i=0; i<blocks.length; i++) { 
    358358            String axis; 
     
    370370                axis = "?"; 
    371371            } 
    372             LOGGER.debug("\t{}\t{} (prefix = {})", 
     372            LOGGER.info("\t{}\t{} (prefix = {})", 
    373373              new Object[] {blocks[i], axis, prefixes[i]}); 
    374374          } 
    375375          if (!dimOrder.equals(newOrder)) { 
    376             LOGGER.debug("Adjusted dimension order = {} ({})", 
     376            LOGGER.info("Adjusted dimension order = {} ({})", 
    377377              newOrder, isCertain ? "certain" : "uncertain"); 
    378378          } 
    379379        } 
    380380      } 
    381       else LOGGER.debug("Pattern is invalid: {}", fp.getErrorMessage()); 
     381      else LOGGER.info("Pattern is invalid: {}", fp.getErrorMessage()); 
    382382    } 
    383383  } 
  • branches/4.2/components/bio-formats/src/loci/formats/FilePattern.java

    r6263 r6998  
    588588      // test file pattern detection based on the given file on disk 
    589589      Location file = new Location(args[0]); 
    590       LOGGER.debug("File = {}", file.getAbsoluteFile()); 
     590      LOGGER.info("File = {}", file.getAbsoluteFile()); 
    591591      pat = findPattern(file); 
    592592    } 
     
    609609      pat = findPattern(nameList[1], null, nameList); 
    610610    } 
    611     if (pat == null) LOGGER.debug("No pattern found."); 
     611    if (pat == null) LOGGER.info("No pattern found."); 
    612612    else { 
    613       LOGGER.debug("Pattern = {}", pat); 
     613      LOGGER.info("Pattern = {}", pat); 
    614614      FilePattern fp = new FilePattern(pat); 
    615615      if (fp.isValid()) { 
    616         LOGGER.debug("Pattern is valid."); 
    617         LOGGER.debug("Files:"); 
     616        LOGGER.info("Pattern is valid."); 
     617        LOGGER.info("Files:"); 
    618618        String[] ids = fp.getFiles(); 
    619619        for (int i=0; i<ids.length; i++) { 
    620           LOGGER.debug("  #{}: {}", i, ids[i]); 
    621         } 
    622       } 
    623       else LOGGER.debug("Pattern is invalid: {}", fp.getErrorMessage()); 
     620          LOGGER.info("  #{}: {}", i, ids[i]); 
     621        } 
     622      } 
     623      else LOGGER.info("Pattern is invalid: {}", fp.getErrorMessage()); 
    624624    } 
    625625  } 
  • branches/4.2/components/bio-formats/src/loci/formats/FormatHandler.java

    r6663 r6998  
    2929// HACK: for scan-deps.pl: The following packages are not actually "optional": 
    3030// optional org.apache.log4j, optional org.slf4j.impl, 
    31 // optional org.apache.xalan, optional org.apache.xml.serializer  
     31// optional org.apache.xalan, optional org.apache.xml.serializer 
    3232 
    3333/** 
  • branches/4.2/components/bio-formats/src/loci/formats/ImageReader.java

    r6993 r6998  
    555555  /* @see IFormatReader#getCurrentFile() */ 
    556556  public String getCurrentFile() { 
    557     return currentId; 
     557    return getReader().getCurrentFile(); 
    558558  } 
    559559 
  • branches/4.2/components/bio-formats/src/loci/formats/in

  • branches/4.2/components/bio-formats/src/loci/formats/meta

  • branches/4.2/components/bio-formats/src/loci/formats/ome

  • branches/4.2/components/bio-formats/src/loci/formats/tiff

  • branches/4.2/components/bio-formats/test/loci/formats/utests

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