VisAD Library update

I have just released an update to the VisAD library. The summary of changes since the last release (28 June) is below. As mentioned earlier, this version was test compiled on Java 1.2; rather, the classes were built on Java 1.4.2, using the "-target 1.2" option.

Here's the list of changes:

In "visad":

2005-11-14 11:22  curtis
        * data/bio/ Record frame rate properly.

2005-11-14 08:47  donm
        * meteorology/ reduce memory consumption

2005-11-14 08:46  donm
        * examples/ enum is a keyword in 1.5, change variable

2005-11-11 11:46  donm
        * util/ add a makeField(Image) method to include
          alpha channel if not opaque.

2005-11-10 17:12  donm
        * fix bug where missing wasn't
          transparent for curved textures if isMissingTransparent was set.

2005-11-10 12:07  curtis
        * util/ Add new formats to VisAD file chooser; be smarter
          about certain formats being available only if the correct
          libraries are installed.

2005-11-10 11:29  curtis
        * data/bio/:, Initial
          version of Image-Pro SEQ file form.

2005-11-09 12:23  curtis
        * data/bio/ Initial implementation of Gatan DM3

2005-11-07 15:33  curtis
        * data/tiff/ Fix divide by zero error when
          denominator is zero.

2005-10-31 16:49  curtis
        * util/ Update VisAD file chooser with latest formats;
          put "All VisAD file formats" option at the top near "All files"
          instead of at the bottom.

2005-10-31 16:33  curtis
        * util/:, Allow
          ""/null as a valid extension for extension file filter.  Remove
          Openlab filter, as it is no longer needed.

2005-10-31 16:16  curtis
        * data/bio/ Reflect Java-1.4-specific
          String.split(String) method.

2005-10-31 16:07  curtis
        * data/bio/:,,,
 File form for PerkinElmer format.

2005-10-28 15:55  curtis
        * data/: bio/, bio/,
          bio/, bio/, bio/,
          bio/, tiff/, tiff/
          Progress on biological file formats, including new Leica form.

2005-10-28 08:54  donm
        * bom/ try this again.  Had the
          wrong version before.  merge 1.34 and 1.36 changes to put back
          grey image fix.

2005-10-24 11:36  curtis
        * data/bio/ Fix bug in 16-bit and 32-bit image

2005-10-21 11:46  curtis
        * data/bio/ Form for handling Deltavision DV

2005-10-20 11:51  donm
          java2d/, java3d/ add a
          method to handle unequal scaling.  Default it to use old methods.
          Please test this well.

2005-10-20 10:38  donm
        * data/units/ change enum to enumerator because enum
          is a keyword in 1.5

2005-10-19 16:08  curtis
        * data/tiff/:, Check TIFF comment
          for OME-XML metadata.

2005-10-19 15:32  curtis
        * data/bio/ Compare strings with equals instead of

2005-10-19 13:51  curtis
        * data/bio/ Change "Created" to "CreationDate"

2005-10-19 13:51  curtis
        * data/bio/ Fix weird reflection bug in

2005-10-18 14:14  curtis
        * data/bio/ Turn off debugging flag.

2005-10-18 14:13  curtis
        * data/bio/:, New ZVI form using
          Apache Jakarta POI package (via reflection). If POI is not
          installed, it reverts to the original behavior (LegacyZVIForm).

2005-10-17 14:57  curtis
        * data/qt/ More improvements to QTJava expiration

2005-10-17 14:44  curtis
        * data/qt/ Better detection of expired QTJava.

2005-10-17 14:07  curtis
        * data/qt/ Differentiate between QTJava missing vs

2005-10-14 16:58  curtis
        * data/tiff/ Detect "fake" RGB FlatFields
          (samples[0] == samples[1] == samples[2]) and treat them as
          single-channel images instead when saving to disk.

2005-10-14 15:34  curtis
        * data/qt/ Correct path for QuickTime v7.0
          for Windows.

2005-10-14 15:32  curtis
        * data/: bio/, qt/,
          tiff/ Better error handling when QuickTime is
          not installed.

2005-10-14 11:43  curtis
        * data/bio/ Ignore embedded thumbnails.

2005-10-13 16:53  curtis
        * data/bio/ Disable debugging output unless DEBUG flag
          is set.

2005-10-13 16:34  curtis
        * data/: bio/, bio/,
          bio/, bio/, bio/,
          bio/, tiff/, tiff/
          Merge BaseTiffForm's testRead method with the IPLab results
          display.  Set up all biology readers to call this new static
          method of BaseTiffForm.

2005-10-13 15:29  curtis
        * data/tiff/:, Add a couple more
          error checks to deal with corrupt files.

2005-10-13 11:23  curtis
        * data/qt/ Add "C:\Program Files\Quick Time\QTSystem"
          path for QuickTime 7 on Windows.

2005-10-12 17:48  curtis
        * java3d/ Comment out debugging message
          with back_clip and front_clip values.

2005-10-12 17:44  curtis
        * data/tiff/ Eliminate debugging messages.

2005-10-10 15:58  curtis
        * data/bio/ Fix bug with multi-image STK files
          where only the first image gets read.

2005-10-10 10:19  donm
        *, java2d/,
          java3d/ add set/getWaitMessageVisible

2005-10-07 13:47  curtis
        * data/tiff/ Fix a bug in Zeiss decoding.

2005-10-03 16:45  curtis
        * data/bio/:, More work on
          Bio-Rad PIC and Fluoview TIFF metadata.

2005-10-03 16:41  curtis
        * data/tiff/ Split initMetadata into
          initStandardMetadata and initOMEMetadata methods.

2005-10-03 16:39  curtis
        * data/bio/ Implement isThisType(byte[]).

2005-10-03 15:58  curtis
        * data/bio/ Throw an exception when things get
          strange (eof) instead of just hanging.

2005-10-03 13:59  curtis
        * data/bio/:, Initial version of
          IPLab file format reader.

2005-09-30 13:12  curtis
 Apply Bill's stricter consistency test to 3-D
          gridded sets and gridded double sets (2-D and 3-D).

2005-09-28 14:37  donm
          java2d/, java3d/
          change method to setComputeSet from setAllowNullSet

2005-09-26 18:16  donm
        * java3d/:,
          graphic API implementations of AdjustProjectionSeam and null
          Animation Set

2005-09-26 18:16  donm
        * java2d/:,
          graphics API implementation of AdjustProjectionSeam and null
          Animation Set

2005-09-26 18:15  donm
          bom/ add DisplayRealType for
          AdjustProjectionSeam which can be used to avoid calling
          VisADGeometryArray.adjust* methods.  AdjustProjectionSeam can be
          set from the GraphicsModeControl or through a ConstantMap.  Add
          new methods to AnimationControl to allow null Animation Sets.

2005-09-26 14:55  donm
        * java3d/ change new RealType to
          RealType.getRealType to get rid of deprecation warning

2005-09-26 14:21  donm
        * modify the last checkin.  Add a new
          signature that allows passing of a boolean for whether the levels
          array should be set to the surfaceValue (default false).

2005-09-23 14:52  donm
        * create the levels array when setValue is

2005-09-21 14:54  donm
        * remove the projection control and zoom done
          listener on nullControl

2005-09-20 15:16  curtis
        * data/: bio/, bio/,
          bio/, bio/, bio/,
          bio/, bio/, bio/,
          tiff/, tiff/,
          tiff/, tiff/ Lots of work on
          biological file formats.

2005-09-16 13:09  curtis
        * data/tiff/ Add code to handle missing RowsPerStrip
          directory entry by synthesizing a fake one. This hack is mostly
          to support weirdness within some Zeiss LSM files. TIFF files with
          a PlanarConfiguration of 2 (planar TIFFs) may also be supported
          now (not thoroughly tested). Previously supported TIFFs should be
          unaffected by these changes.

2005-09-05 18:17  billh
        * possible fix for Cicero's problem, but this
          uses a stricter consistency test in the constructor which may
          break applications

2005-08-30 14:09  tomw
        * data/text/README.text: Update README file to reflect change for
          2-D grid form.

2005-08-30 14:05  tomw
        * data/text/ Add capability to specify the length
          of domain components for 'raster' input where only one value per
          line is specified.

2005-08-29 13:25  donm
        *, modify
          checkIndices to pick up ConstantMap of TextureEnable when setting
          isTextureMap.  Also, with change to DataDisplayLink, some code
          could be commented out.  Default values from GMC are now in
          default_values for TextureEnable, CurvedSize, ColorMode and

2005-08-29 09:21  donm
        * add in the missing default values for items
          that can now be set as ConstantMaps (TextureEnable,
          MissingTransparent, ColorMode, CurvedSize)

2005-08-27 11:41  billh
        * bom/ test having doTransform()
          call super.doTransform() when texture mapping is disabled

2005-08-27 11:21  billh
        * improve JavaDoc for setConstantMaps()

2005-08-26 10:44  billh
        * add code so setConstantMaps() will trigger
          re-render of the associated Data

2005-08-26 10:19  billh
        * Untested new method:

            public void setConstantMaps(ConstantMap[] constant_maps)

          to hopefully enable the IDV and other applications to dynamically
          change ConstantMap[] array specific to a DataDisplayLink. For
          normal situations with just one DataReference per DataRenderer,

            DataDisplayLink[] links = renderer.getLinks();

          Please test with with the IDV and let me know if there are

2005-08-02 10:09  donm
        * data/vis5d/ oh heck, this should work, so I'll
          just check it in.  We can revert later if needed

2005-07-21 17:01  curtis
        * data/bio/ Ignore first (solid white RGB) image.

2005-07-15 16:05  curtis
        * data/tiff/ Expand TIFF export functionality
          to include 8-bit grayscale, 16-bit grayscale, and 32-bit floating
          point grayscale modes. Which mode to use it autodetected based on
          the FlatField's range values.

2005-07-12 20:44  tomw
        * Fix problem with character encoding in

2005-07-06 17:31  curtis
        * java2d/ Fix bug that made it
          impossible to setColorMode(SUM_COLOR_MODE) for Java2D.

In "edu":

2005-10-27 17:34  donm
        * wisc/ssec/mcidas/adde/ a bit of
          restructuring to set the default compression for the well known
          ports (112=gzip, 500=none, 503=compress).  Default is 112 w/ GZIP
          in the parlor.

2005-10-25 08:29  donm
        * wisc/ssec/mcidas/adde/ add the trace
          string to the text request

2005-10-17 12:46  tomw
        * wisc/ssec/mcidas/ Added test for zero, as per a
          McIDAS-X change made recently by MUG.

2005-08-24 13:54  donm
        * wisc/ssec/mcidas/adde/ add an auto-upcase
          keyword for upcasing the command

2005-08-23 17:42  donm
        * wisc/ssec/mcidas/adde/ add a system
          property "" to allow old applications not to

2005-08-23 13:54  tomw
        * wisc/ssec/mcidas/adde/:,
          Clean up class variables.

In "ucar":  <none>

Tom Whittaker (tomw@xxxxxxxxxxxxx)
University of Wisconsin-Madison
Space Science and Engineering Center
Cooperative Institute for Meteorological Satellite Studies
Phone/VoiceMail: 608.262.2759