Changeset 6470


Ignore:
Timestamp:
06/03/10 16:58:47 (10 years ago)
Author:
curtis
Message:

Fix some Eclipse warnings.

Location:
trunk/components/loci-plugins/src/loci/plugins
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java

    r6229 r6470  
    5858import javax.swing.SwingConstants; 
    5959import javax.swing.SwingUtilities; 
     60import javax.swing.WindowConstants; 
    6061import javax.swing.border.EmptyBorder; 
    6162import javax.swing.event.ListSelectionEvent; 
     
    103104  public ConfigWindow() { 
    104105    setTitle("LOCI Plugins Configuration"); 
    105     setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); 
     106    setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); 
    106107 
    107108    // build UI 
     
    296297    log.println(); 
    297298    log.println("-- Formats --"); 
    298     FormatEntry[] formats = null; 
    299299    try { 
    300300      Class<?> irClass = Class.forName("loci.formats.ImageReader"); 
     
    316316 
    317317    // enumerate list of libraries 
    318     final String libCore = "Core library"; 
    319     final String libNative = "Native library"; 
    320     final String libPlugin = "ImageJ plugin"; 
    321     final String libJava = "Java library"; 
    322318 
    323319    String javaVersion = System.getProperty("java.version") + 
     
    379375 
    380376    HashMap<String, String> versions = new HashMap<String, String>(); 
    381     if (javaVersion != null) versions.put("javaVersion", javaVersion); 
    382     if (bfVersion != null) versions.put("bfVersion", bfVersion); 
     377    versions.put("javaVersion", javaVersion); 
     378    versions.put("bfVersion", bfVersion); 
    383379    if (qtVersion != null) versions.put("qtVersion", qtVersion); 
    384380    if (clibIIOVersion != null) versions.put("clibIIOVersion", clibIIOVersion); 
  • trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java

    r6467 r6470  
    3838import java.awt.GridBagConstraints; 
    3939import java.awt.GridBagLayout; 
    40 import java.awt.GridLayout; 
    4140import java.awt.Insets; 
    4241import java.awt.Panel; 
    4342import java.awt.event.ActionEvent; 
    4443import java.awt.event.ActionListener; 
    45 import java.awt.image.BufferedImage; 
    46 import java.io.IOException; 
    4744import java.util.StringTokenizer; 
    4845 
    4946import javax.swing.Box; 
    50 import javax.swing.ImageIcon; 
    51 import javax.swing.JLabel; 
    5247import javax.swing.JPanel; 
    5348 
    54 import loci.formats.FormatException; 
    55 import loci.formats.FormatTools; 
    56 import loci.formats.gui.AWTImageTools; 
    5749import loci.formats.gui.BufferedImageReader; 
    58 import loci.plugins.BF; 
    5950import loci.plugins.util.WindowTools; 
    6051 
  • trunk/components/loci-plugins/src/loci/plugins/macro/LociFunctions.java

    r6246 r6470  
    190190  } 
    191191 
     192  @SuppressWarnings("deprecation") 
    192193  public void setMetadataCollected(Boolean collect) { 
    193194    r.setMetadataCollected(collect.booleanValue()); 
    194195  } 
    195196 
     197  @SuppressWarnings("deprecation") 
    196198  public void isMetadataCollected(Boolean[] collect) { 
    197199    collect[0] = new Boolean(r.isMetadataCollected()); 
     
    334336        "Instructions on doing so will be printed to the Results window."); 
    335337 
    336       IJ.write("To gain access to more advanced features of Bio-Formats"); 
    337       IJ.write("from within a macro, put the following line at the"); 
    338       IJ.write("beginning of your macro:"); 
    339       IJ.write(""); 
    340       IJ.write("run(\"Bio-Formats Macro Extensions\");"); 
    341       IJ.write(""); 
    342       IJ.write("This will enable the following macro functions:"); 
    343       IJ.write(""); 
    344       IJ.write("-= Usable any time =-"); 
    345       IJ.write(""); 
    346       IJ.write("Ext.getFormat(id, format)"); 
    347       IJ.write("-- Retrieves the file format of the given id (filename)."); 
    348       IJ.write("Ext.setId(id)"); 
    349       IJ.write("-- Initializes the given id (filename)."); 
    350       IJ.write("Ext.isThisType(name, thisType)"); 
    351       IJ.write("-- True if Bio-Formats recognizes the given file as a"); 
    352       IJ.write("-- supported image file format; if necessary, will "); 
    353       IJ.write("-- examine the file contents to decide for sure."); 
    354       IJ.write("Ext.isThisTypeFast(name, thisType)"); 
    355       IJ.write("-- True if Bio-Formats recognizes the given filename as a"); 
    356       IJ.write("-- supported image file format; will decide based on file"); 
    357       IJ.write("-- extension only, without examining file contents."); 
    358       IJ.write("Ext.isMetadataComplete(complete)"); 
    359       IJ.write("-- True if Bio-Formats completely parses the current"); 
    360       IJ.write("-- dataset's file format. If this function returns false,"); 
    361       IJ.write("-- there are known limitations or missing features in how"); 
    362       IJ.write("-- Bio-Formats handles this file format."); 
    363       IJ.write("Ext.fileGroupOption(id, fileGroupOption)"); 
    364       IJ.write("-- Returns a code indicating the file grouping policy for"); 
    365       IJ.write("-- for the current dataset. Possible values are:"); 
    366       IJ.write("--   must, can, cannot, unknown"); 
    367       IJ.write(""); 
    368       IJ.write("-= Usable before initializing a file =-"); 
    369       IJ.write(""); 
    370       IJ.write("Ext.setNormalized(normalize)"); 
    371       IJ.write("-- Sets whether to normalize floating point data to [0-1]."); 
    372       IJ.write("Ext.isNormalized(normalize)"); 
    373       IJ.write("-- Gets whether float data is being normalized to [0-1]."); 
    374       IJ.write("Ext.setMetadataCollected(collect)"); 
    375       IJ.write("-- Sets whether Bio-Formats should extract metadata at all."); 
    376       IJ.write("Ext.isMetadataCollected(collect)"); 
    377       IJ.write("-- Gets whether Bio-Formats is supposed to extract metadata."); 
    378       IJ.write("Ext.setOriginalMetadataPopulated(populate)"); 
    379       IJ.write("-- Sets whether Bio-Formats should save proprietary metadata"); 
    380       IJ.write("-- to the OME metadata store as custom attributes."); 
    381       IJ.write("Ext.isOriginalMetadataPopulated(populate)"); 
    382       IJ.write("-- Sets whether Bio-Formats is saving proprietary metadata"); 
    383       IJ.write("-- to the OME metadata store as custom attributes."); 
    384       IJ.write("Ext.setGroupFiles(group)"); 
    385       IJ.write("-- For multi-file formats, sets whether to force grouping."); 
    386       IJ.write("Ext.isGroupFiles(group)"); 
    387       IJ.write("-- Gets whether grouping is forced for multi-file formats.."); 
    388       IJ.write("Ext.setMetadataFiltered(filter)"); 
    389       IJ.write("-- Sets whether to filter out ugly metadata from the table"); 
    390       IJ.write("-- (i.e., entries with unprintable characters, and extremely"); 
    391       IJ.write("-- long values)."); 
    392       IJ.write("Ext.isMetadataFiltered(filter)"); 
    393       IJ.write("-- Gets whether ugly metadata is being filtered out."); 
    394       IJ.write(""); 
    395       IJ.write("-== Usable after initializing a file ==-"); 
    396       IJ.write(""); 
    397       IJ.write("Ext.getSeriesCount(seriesCount)"); 
    398       IJ.write("-- Gets the number of image series in the active dataset."); 
    399       IJ.write("Ext.setSeries(seriesNum)"); 
    400       IJ.write("-- Sets the current series within the active dataset."); 
    401       IJ.write("Ext.getSeries(seriesNum)"); 
    402       IJ.write("-- Gets the current series within the active dataset."); 
    403       IJ.write("Ext.getUsedFileCount(count)"); 
    404       IJ.write("-- Gets the number of files that are part of this dataset."); 
    405       IJ.write("Ext.getUsedFile(i, used)"); 
    406       IJ.write("-- Gets the i'th filename part of this dataset."); 
    407       IJ.write("Ext.getCurrentFile(file)"); 
    408       IJ.write("-- Gets the base filename used to initialize this dataset."); 
    409       IJ.write("Ext.openImage(title, no)"); 
    410       IJ.write("-- Opens the no'th plane in a new window named 'title'."); 
    411       IJ.write("Ext.openImage(title, no, x, y, width, height)"); 
    412       IJ.write("-- Opens a subset of the no'th plane in a new window"); 
    413       IJ.write("-- named 'title'."); 
    414       IJ.write("Ext.close()"); 
    415       IJ.write("-- Closes the active dataset."); 
    416       IJ.write("Ext.closeFileOnly()"); 
    417       IJ.write("-- Closes open files, leaving the current dataset active."); 
    418       IJ.write(""); 
    419       IJ.write("-== Applying to the current series ==-"); 
    420       IJ.write(""); 
    421       IJ.write("Ext.getImageCount(imageCount)"); 
    422       IJ.write("-- Gets the total number of planes in the current dataset."); 
    423       IJ.write("Ext.getSizeX(sizeX)"); 
    424       IJ.write("-- Gets the width of each image plane in pixels."); 
    425       IJ.write("Ext.getSizeY(sizeY)"); 
    426       IJ.write("-- Gets the height of each image plane in pixels."); 
    427       IJ.write("Ext.getSizeZ(sizeZ)"); 
    428       IJ.write("-- Gets the number of focal planes in the dataset."); 
    429       IJ.write("Ext.getSizeC(sizeC)"); 
    430       IJ.write("-- Gets the number of channels in the dataset."); 
    431       IJ.write("Ext.getSizeT(sizeT)"); 
    432       IJ.write("-- Gets the number of time points in the dataset."); 
    433       IJ.write("Ext.getPixelType(pixelType)"); 
    434       IJ.write("-- Gets a code representing the pixel type of the image."); 
    435       IJ.write("-- Possible values include:"); 
    436       IJ.write("--   int8, uint8, int16, uint16, int32, uint32, float, double"); 
    437       IJ.write("Ext.getEffectiveSizeC(effectiveSizeC)"); 
    438       IJ.write("-- Gets the 'effective' number of channels, such that:"); 
    439       IJ.write("-- effectiveSizeC * sizeZ * sizeT == imageCount"); 
    440       IJ.write("Ext.getRGBChannelCount(rgbChannelCount)"); 
    441       IJ.write("-- Gets the number of channels per composite image plane:"); 
    442       IJ.write("-- sizeC / rgbChannelCount == effectiveSizeC"); 
    443       IJ.write("Ext.isIndexed(indexed)"); 
    444       IJ.write("-- Gets whether the image planes are stored as indexed color"); 
    445       IJ.write("-- (i.e., whether they have embedded LUTs)."); 
    446       IJ.write("Ext.getChannelDimCount(channelDimCount)"); 
    447       IJ.write("-- For highly multidimensional image data, the C dimension"); 
    448       IJ.write("-- may consist of multiple embedded 'sub' dimensions."); 
    449       IJ.write("-- This function returns the number of such dimensions."); 
    450       IJ.write("Ext.getChannelDimLength(i, channelDimLength)"); 
    451       IJ.write("-- Gets the length of the i'th embedded 'sub' dimension."); 
    452       IJ.write("Ext.getChannelDimType(i, channelDimType)"); 
    453       IJ.write("-- Gets a string label for the i'th embedded 'sub' channel."); 
    454       IJ.write("Ext.isLittleEndian(littleEndian)"); 
    455       IJ.write("-- For multi-byte pixel types, get the data's endianness."); 
    456       IJ.write("Ext.getDimensionOrder(dimOrder)"); 
    457       IJ.write("-- Gets a five-character string representing the dimensional"); 
    458       IJ.write("-- rasterization order within the dataset. Valid orders are:"); 
    459       IJ.write("--   XYCTZ, XYCZT, XYTCZ, XYTZC, XYZCT, XYZTC"); 
    460       IJ.write("-- In cases where the channels are interleaved (e.g., CXYTZ),"); 
    461       IJ.write("-- C will be the first dimension after X and Y (e.g., XYCTZ)"); 
    462       IJ.write("-- and the isInterleaved function will return true."); 
    463       IJ.write("Ext.isOrderCertain(orderCertain)"); 
    464       IJ.write("-- Gets whether the dimension order and sizes are known,"); 
    465       IJ.write("-- or merely guesses."); 
    466       IJ.write("Ext.isInterleaved(interleaved)"); 
    467       IJ.write("-- Gets whether or not the channels are interleaved."); 
    468       IJ.write("-- This function exists because X and Y must appear first"); 
    469       IJ.write("-- in the dimension order. For interleaved data, XYCTZ or"); 
    470       IJ.write("-- XYCZT is used, and this method returns true."); 
    471       IJ.write("Ext.isInterleavedSubC(subC, interleaved)"); 
    472       IJ.write("-- Gets whether the given 'sub' channel is interleaved."); 
    473       IJ.write("-- This method exists because some data with multiple"); 
    474       IJ.write("-- rasterized sub-dimensions within C have one sub-dimension"); 
    475       IJ.write("-- interleaved, and the other not -- e.g., the SDT reader"); 
    476       IJ.write("-- handles spectral-lifetime data with interleaved lifetime"); 
    477       IJ.write("-- bins and non-interleaved spectral channels."); 
    478       IJ.write("Ext.getIndex(z, c, t, index)"); 
    479       IJ.write("-- Gets the rasterized index corresponding to the given"); 
    480       IJ.write("-- Z, C and T coordinates, according to the dataset's"); 
    481       IJ.write("-- dimension order."); 
    482       IJ.write("Ext.getZCTCoords(index, z, c, t)"); 
    483       IJ.write("-- Gets the Z, C and T coordinates corresponding to the given"); 
    484       IJ.write("-- rasterized index value, according to the dataset's"); 
    485       IJ.write("-- dimension order."); 
    486       IJ.write("Ext.getMetadataValue(field, value)"); 
    487       IJ.write("-- Obtains the specified metadata field's value."); 
    488       IJ.write("Ext.getSeriesName(seriesName)"); 
    489       IJ.write("-- Obtains the name of the current series."); 
    490       IJ.write("Ext.getImageCreationDate(creationDate)"); 
    491       IJ.write("-- Obtains the creation date of the dataset"); 
    492       IJ.write("-- in ISO 8601 format."); 
    493       IJ.write("Ext.getPlaneTimingDeltaT(deltaT, no)"); 
    494       IJ.write("-- Obtains the time offset (seconds since the beginning "); 
    495       IJ.write("-- of the experiment) for the no'th plane, or NaN if none."); 
    496       IJ.write("Ext.getPlaneTimingExposureTime(exposureTime, no)"); 
    497       IJ.write("-- Obtains the exposure time (in seconds) for the no'th"); 
    498       IJ.write("-- plane, or NaN if none."); 
    499       IJ.write(""); 
    500       IJ.write("For more information, see the online Javadocs"); 
    501       IJ.write("for the loci.formats.IFormatReader and "); 
    502       IJ.write("loci.formats.meta.MetadataRetrieve interfaces:"); 
    503       IJ.write(URL_LOCI_SOFTWARE_JAVADOCS); 
     338      IJ.log("To gain access to more advanced features of Bio-Formats"); 
     339      IJ.log("from within a macro, put the following line at the"); 
     340      IJ.log("beginning of your macro:"); 
     341      IJ.log(""); 
     342      IJ.log("run(\"Bio-Formats Macro Extensions\");"); 
     343      IJ.log(""); 
     344      IJ.log("This will enable the following macro functions:"); 
     345      IJ.log(""); 
     346      IJ.log("-= Usable any time =-"); 
     347      IJ.log(""); 
     348      IJ.log("Ext.getFormat(id, format)"); 
     349      IJ.log("-- Retrieves the file format of the given id (filename)."); 
     350      IJ.log("Ext.setId(id)"); 
     351      IJ.log("-- Initializes the given id (filename)."); 
     352      IJ.log("Ext.isThisType(name, thisType)"); 
     353      IJ.log("-- True if Bio-Formats recognizes the given file as a"); 
     354      IJ.log("-- supported image file format; if necessary, will "); 
     355      IJ.log("-- examine the file contents to decide for sure."); 
     356      IJ.log("Ext.isThisTypeFast(name, thisType)"); 
     357      IJ.log("-- True if Bio-Formats recognizes the given filename as a"); 
     358      IJ.log("-- supported image file format; will decide based on file"); 
     359      IJ.log("-- extension only, without examining file contents."); 
     360      IJ.log("Ext.isMetadataComplete(complete)"); 
     361      IJ.log("-- True if Bio-Formats completely parses the current"); 
     362      IJ.log("-- dataset's file format. If this function returns false,"); 
     363      IJ.log("-- there are known limitations or missing features in how"); 
     364      IJ.log("-- Bio-Formats handles this file format."); 
     365      IJ.log("Ext.fileGroupOption(id, fileGroupOption)"); 
     366      IJ.log("-- Returns a code indicating the file grouping policy for"); 
     367      IJ.log("-- for the current dataset. Possible values are:"); 
     368      IJ.log("--   must, can, cannot, unknown"); 
     369      IJ.log(""); 
     370      IJ.log("-= Usable before initializing a file =-"); 
     371      IJ.log(""); 
     372      IJ.log("Ext.setNormalized(normalize)"); 
     373      IJ.log("-- Sets whether to normalize floating point data to [0-1]."); 
     374      IJ.log("Ext.isNormalized(normalize)"); 
     375      IJ.log("-- Gets whether float data is being normalized to [0-1]."); 
     376      IJ.log("Ext.setMetadataCollected(collect)"); 
     377      IJ.log("-- Sets whether Bio-Formats should extract metadata at all."); 
     378      IJ.log("Ext.isMetadataCollected(collect)"); 
     379      IJ.log("-- Gets whether Bio-Formats is supposed to extract metadata."); 
     380      IJ.log("Ext.setOriginalMetadataPopulated(populate)"); 
     381      IJ.log("-- Sets whether Bio-Formats should save proprietary metadata"); 
     382      IJ.log("-- to the OME metadata store as custom attributes."); 
     383      IJ.log("Ext.isOriginalMetadataPopulated(populate)"); 
     384      IJ.log("-- Sets whether Bio-Formats is saving proprietary metadata"); 
     385      IJ.log("-- to the OME metadata store as custom attributes."); 
     386      IJ.log("Ext.setGroupFiles(group)"); 
     387      IJ.log("-- For multi-file formats, sets whether to force grouping."); 
     388      IJ.log("Ext.isGroupFiles(group)"); 
     389      IJ.log("-- Gets whether grouping is forced for multi-file formats.."); 
     390      IJ.log("Ext.setMetadataFiltered(filter)"); 
     391      IJ.log("-- Sets whether to filter out ugly metadata from the table"); 
     392      IJ.log("-- (i.e., entries with unprintable characters, and extremely"); 
     393      IJ.log("-- long values)."); 
     394      IJ.log("Ext.isMetadataFiltered(filter)"); 
     395      IJ.log("-- Gets whether ugly metadata is being filtered out."); 
     396      IJ.log(""); 
     397      IJ.log("-== Usable after initializing a file ==-"); 
     398      IJ.log(""); 
     399      IJ.log("Ext.getSeriesCount(seriesCount)"); 
     400      IJ.log("-- Gets the number of image series in the active dataset."); 
     401      IJ.log("Ext.setSeries(seriesNum)"); 
     402      IJ.log("-- Sets the current series within the active dataset."); 
     403      IJ.log("Ext.getSeries(seriesNum)"); 
     404      IJ.log("-- Gets the current series within the active dataset."); 
     405      IJ.log("Ext.getUsedFileCount(count)"); 
     406      IJ.log("-- Gets the number of files that are part of this dataset."); 
     407      IJ.log("Ext.getUsedFile(i, used)"); 
     408      IJ.log("-- Gets the i'th filename part of this dataset."); 
     409      IJ.log("Ext.getCurrentFile(file)"); 
     410      IJ.log("-- Gets the base filename used to initialize this dataset."); 
     411      IJ.log("Ext.openImage(title, no)"); 
     412      IJ.log("-- Opens the no'th plane in a new window named 'title'."); 
     413      IJ.log("Ext.openImage(title, no, x, y, width, height)"); 
     414      IJ.log("-- Opens a subset of the no'th plane in a new window"); 
     415      IJ.log("-- named 'title'."); 
     416      IJ.log("Ext.close()"); 
     417      IJ.log("-- Closes the active dataset."); 
     418      IJ.log("Ext.closeFileOnly()"); 
     419      IJ.log("-- Closes open files, leaving the current dataset active."); 
     420      IJ.log(""); 
     421      IJ.log("-== Applying to the current series ==-"); 
     422      IJ.log(""); 
     423      IJ.log("Ext.getImageCount(imageCount)"); 
     424      IJ.log("-- Gets the total number of planes in the current dataset."); 
     425      IJ.log("Ext.getSizeX(sizeX)"); 
     426      IJ.log("-- Gets the width of each image plane in pixels."); 
     427      IJ.log("Ext.getSizeY(sizeY)"); 
     428      IJ.log("-- Gets the height of each image plane in pixels."); 
     429      IJ.log("Ext.getSizeZ(sizeZ)"); 
     430      IJ.log("-- Gets the number of focal planes in the dataset."); 
     431      IJ.log("Ext.getSizeC(sizeC)"); 
     432      IJ.log("-- Gets the number of channels in the dataset."); 
     433      IJ.log("Ext.getSizeT(sizeT)"); 
     434      IJ.log("-- Gets the number of time points in the dataset."); 
     435      IJ.log("Ext.getPixelType(pixelType)"); 
     436      IJ.log("-- Gets a code representing the pixel type of the image."); 
     437      IJ.log("-- Possible values include:"); 
     438      IJ.log("--   int8, uint8, int16, uint16, int32, uint32, float, double"); 
     439      IJ.log("Ext.getEffectiveSizeC(effectiveSizeC)"); 
     440      IJ.log("-- Gets the 'effective' number of channels, such that:"); 
     441      IJ.log("-- effectiveSizeC * sizeZ * sizeT == imageCount"); 
     442      IJ.log("Ext.getRGBChannelCount(rgbChannelCount)"); 
     443      IJ.log("-- Gets the number of channels per composite image plane:"); 
     444      IJ.log("-- sizeC / rgbChannelCount == effectiveSizeC"); 
     445      IJ.log("Ext.isIndexed(indexed)"); 
     446      IJ.log("-- Gets whether the image planes are stored as indexed color"); 
     447      IJ.log("-- (i.e., whether they have embedded LUTs)."); 
     448      IJ.log("Ext.getChannelDimCount(channelDimCount)"); 
     449      IJ.log("-- For highly multidimensional image data, the C dimension"); 
     450      IJ.log("-- may consist of multiple embedded 'sub' dimensions."); 
     451      IJ.log("-- This function returns the number of such dimensions."); 
     452      IJ.log("Ext.getChannelDimLength(i, channelDimLength)"); 
     453      IJ.log("-- Gets the length of the i'th embedded 'sub' dimension."); 
     454      IJ.log("Ext.getChannelDimType(i, channelDimType)"); 
     455      IJ.log("-- Gets a string label for the i'th embedded 'sub' channel."); 
     456      IJ.log("Ext.isLittleEndian(littleEndian)"); 
     457      IJ.log("-- For multi-byte pixel types, get the data's endianness."); 
     458      IJ.log("Ext.getDimensionOrder(dimOrder)"); 
     459      IJ.log("-- Gets a five-character string representing the dimensional"); 
     460      IJ.log("-- rasterization order within the dataset. Valid orders are:"); 
     461      IJ.log("--   XYCTZ, XYCZT, XYTCZ, XYTZC, XYZCT, XYZTC"); 
     462      IJ.log("-- In cases where the channels are interleaved (e.g., CXYTZ),"); 
     463      IJ.log("-- C will be the first dimension after X and Y (e.g., XYCTZ)"); 
     464      IJ.log("-- and the isInterleaved function will return true."); 
     465      IJ.log("Ext.isOrderCertain(orderCertain)"); 
     466      IJ.log("-- Gets whether the dimension order and sizes are known,"); 
     467      IJ.log("-- or merely guesses."); 
     468      IJ.log("Ext.isInterleaved(interleaved)"); 
     469      IJ.log("-- Gets whether or not the channels are interleaved."); 
     470      IJ.log("-- This function exists because X and Y must appear first"); 
     471      IJ.log("-- in the dimension order. For interleaved data, XYCTZ or"); 
     472      IJ.log("-- XYCZT is used, and this method returns true."); 
     473      IJ.log("Ext.isInterleavedSubC(subC, interleaved)"); 
     474      IJ.log("-- Gets whether the given 'sub' channel is interleaved."); 
     475      IJ.log("-- This method exists because some data with multiple"); 
     476      IJ.log("-- rasterized sub-dimensions within C have one sub-dimension"); 
     477      IJ.log("-- interleaved, and the other not -- e.g., the SDT reader"); 
     478      IJ.log("-- handles spectral-lifetime data with interleaved lifetime"); 
     479      IJ.log("-- bins and non-interleaved spectral channels."); 
     480      IJ.log("Ext.getIndex(z, c, t, index)"); 
     481      IJ.log("-- Gets the rasterized index corresponding to the given"); 
     482      IJ.log("-- Z, C and T coordinates, according to the dataset's"); 
     483      IJ.log("-- dimension order."); 
     484      IJ.log("Ext.getZCTCoords(index, z, c, t)"); 
     485      IJ.log("-- Gets the Z, C and T coordinates corresponding to the given"); 
     486      IJ.log("-- rasterized index value, according to the dataset's"); 
     487      IJ.log("-- dimension order."); 
     488      IJ.log("Ext.getMetadataValue(field, value)"); 
     489      IJ.log("-- Obtains the specified metadata field's value."); 
     490      IJ.log("Ext.getSeriesName(seriesName)"); 
     491      IJ.log("-- Obtains the name of the current series."); 
     492      IJ.log("Ext.getImageCreationDate(creationDate)"); 
     493      IJ.log("-- Obtains the creation date of the dataset"); 
     494      IJ.log("-- in ISO 8601 format."); 
     495      IJ.log("Ext.getPlaneTimingDeltaT(deltaT, no)"); 
     496      IJ.log("-- Obtains the time offset (seconds since the beginning "); 
     497      IJ.log("-- of the experiment) for the no'th plane, or NaN if none."); 
     498      IJ.log("Ext.getPlaneTimingExposureTime(exposureTime, no)"); 
     499      IJ.log("-- Obtains the exposure time (in seconds) for the no'th"); 
     500      IJ.log("-- plane, or NaN if none."); 
     501      IJ.log(""); 
     502      IJ.log("For more information, see the online Javadocs"); 
     503      IJ.log("for the loci.formats.IFormatReader and "); 
     504      IJ.log("loci.formats.meta.MetadataRetrieve interfaces:"); 
     505      IJ.log(URL_LOCI_SOFTWARE_JAVADOCS); 
    504506    } 
    505507  } 
  • trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java

    r6458 r6470  
    391391      w.setInterleaved(false); 
    392392 
     393      int no = 0; 
    393394      for (int i=start; i<end; i+=n) { 
    394395        if (doStack) { 
     
    458459          IJ.error("Pixel type not supported by this format."); 
    459460        } 
    460         else w.saveBytes(plane, i == end - n); 
     461        else w.saveBytes(no++, plane); 
    461462      } 
    462463      w.close(); 
  • trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java

    r6279 r6470  
    325325  } 
    326326 
    327   public void drawDot2(int x, int y) { 
    328     record("drawDot2", new Object[] {new Integer(x), new Integer(y)}, 
    329       new Class[] {int.class, int.class}); 
    330     proc.drawDot2(x, y); 
    331   } 
    332  
    333327  public void drawLine(int x1, int y1, int x2, int y2) { 
    334328    record("drawLine", new Object[] {new Integer(x1), new Integer(y1), 
     
    698692    record("isInvertedLut"); 
    699693    return proc.isInvertedLut(); 
    700   } 
    701  
    702   public boolean isKillable() { 
    703     record("isKillable"); 
    704     return proc.isKillable(); 
    705694  } 
    706695 
     
    10861075  } 
    10871076 
    1088   public void translate(int xOffset, int yOffset, boolean eraseBackground) { 
    1089     record("translate", new Object[] {new Integer(xOffset), 
    1090       new Integer(yOffset), new Boolean(eraseBackground)}, new Class[] { 
    1091       int.class, int.class, boolean.class}); 
    1092     proc.translate(xOffset, yOffset, eraseBackground); 
     1077  public void translate(int xOffset, int yOffset) { 
     1078    record("translate", 
     1079      new Object[] {new Integer(xOffset), new Integer(yOffset)}, 
     1080      new Class[] {int.class, int.class}); 
     1081    proc.translate(xOffset, yOffset); 
    10931082  } 
    10941083 
     
    11021091    record("xor", new Integer(value), int.class); 
    11031092    proc.xor(value); 
     1093  } 
     1094   
     1095  // -- Deprecated methods -- 
     1096 
     1097  /** @deprecated */ 
     1098  public void drawDot2(int x, int y) { 
     1099    record("drawDot2", new Object[] {new Integer(x), new Integer(y)}, 
     1100      new Class[] {int.class, int.class}); 
     1101    proc.drawDot2(x, y); 
     1102  } 
     1103 
     1104  /** @deprecated */ 
     1105  public boolean isKillable() { 
     1106    record("isKillable"); 
     1107    return proc.isKillable(); 
    11041108  } 
    11051109 
  • trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java

    r6322 r6470  
    3232import java.awt.BorderLayout; 
    3333import java.awt.Checkbox; 
     34import java.awt.Choice; 
    3435import java.awt.Component; 
    3536import java.awt.Container; 
     
    187188      String s = DebugTools.getStackTrace(t); 
    188189      StringTokenizer st = new StringTokenizer(s, "\n\r"); 
    189       while (st.hasMoreTokens()) IJ.write(st.nextToken()); 
     190      while (st.hasMoreTokens()) IJ.log(st.nextToken()); 
    190191    } 
    191192    if (msg != null) IJ.error("Bio-Formats Importer", msg); 
     
    202203  } 
    203204 
     205  @SuppressWarnings("unchecked") 
     206  public static List<Choice> getChoices(GenericDialog gd) { 
     207    return gd.getChoices(); 
     208  } 
     209 
    204210} 
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