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Branch: master
Commits on Jan 25, 2019
  1. POM: use HTTPS for imagej.net URLs

    ctrueden committed Jan 25, 2019
Commits on Oct 1, 2018
  1. Bump to next development cycle

    ctrueden committed Oct 1, 2018
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
Commits on Aug 10, 2018
  1. POM: ImageJ Forum -> Image.sc Forum

    ctrueden committed Aug 10, 2018
Commits on Jul 18, 2018
  1. Merge pull request #70 from nafisahis/GUI-fitting-large-image

    etarena committed Jul 18, 2018
    This adds a scroll bar to fit large images in the GUI window.  This closes #32.
  2. Add scroll bar to fit large images in GUI window

    nafisahis authored and etarena committed Jul 16, 2018
  3. Merge pull request #69 from nafisahis/PDF-show-axis-label

    etarena committed Jul 18, 2018
    Adds axis labels to PDF images.  This closes #15.
  4. PDFWriter: add axis labels to PDF images

    nafisahis authored and etarena committed Jun 29, 2018
Commits on Jul 3, 2018
  1. Bump to next development cycle

    ctrueden committed Jul 3, 2018
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
Commits on Jun 29, 2018
  1. Merge pull request #68 from nafisahis/PDF-add-regression-line

    etarena committed Jun 29, 2018
    PDFWriter: add regression line to histogram
Commits on Jun 27, 2018
  1. PDFWriter: add regression line to histogram in PDF

    nafisahis authored and etarena committed Jun 22, 2018
    This fixes #14.
Commits on Jun 21, 2018
  1. POM: exclude script_templates from license headers

    ctrueden committed Jun 21, 2018
Commits on May 23, 2018
  1. Bump to next development cycle

    ctrueden committed May 23, 2018
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
Commits on May 22, 2018
  1. Update to imglib2 5.1.0

    etarena committed May 22, 2018
    This branch is in response to imglib/imglib2#204.
Commits on Apr 28, 2018
  1. Bump to next development cycle

    ctrueden committed Apr 28, 2018
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
Commits on Jan 12, 2018
  1. Merge pull request #67 from WillGiang/master

    chalkie666 committed Jan 12, 2018
    Fix typo in GUI
Commits on Jan 10, 2018
  1. Fix typo in GUI

    WillGiang committed Jan 10, 2018
    "Instensity" -> "Intensity"
Commits on Dec 25, 2017
  1. Bump to next development cycle

    ctrueden committed Dec 25, 2017
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
Commits on Oct 5, 2017
  1. POM: deploy releases to the ImageJ repository

    ctrueden committed Oct 5, 2017
  2. Update Travis configuration

    ctrueden committed Oct 5, 2017
    This will hopefully reduce the need for future en masse updates.
Commits on Jul 7, 2017
  1. Make the random noise images deterministic

    ctrueden committed Jul 7, 2017
    This is more predictable for test behavior,
    avoiding intermittently failing tests.
Commits on Jun 26, 2017
  1. Add check to guard against RGB images.

    etarena committed Jun 26, 2017
    This new check will warn the user if either image is an RGB image. Fixes #64.
Commits on Jun 9, 2017
  1. Update pom.xml to scijava version 16.1.0

    etarena committed Jun 9, 2017
Commits on May 8, 2017
  1. Coloc_2: attempt to fix Travis javadoc error

    ctrueden committed May 8, 2017
    Locally, javadoc:javadoc passes on my macOS 10.12 system.
    However, the Travis CI build barfs with:
    
      [ERROR] /home/travis/build/fiji/Colocalisation_Analysis/src/main/java/sc/fiji/coloc/Coloc_2.java:438: error: reference not found
      [ERROR] * {@link #colocalise(Img, Img, BoundingBox, Img, List)} with {@code null} for
    
    The BoundingBox class is an inner class of sc.fiji.coloc.Coloc_2;
    maybe that is the problem. We'll see if qualifying it helps.
Commits on May 4, 2017
  1. Main: avoid 'Unrecognized command' error

    ctrueden committed May 4, 2017
    The recent changes to the codebase somehow broke the main method.
    My guess is that the switch to sc.fiji.coloc package prefix is
    somehow making ImageJ1 unhappy, but we do set the plugins.dir
    appropriately. The plugins.config is there, and correct. So I do
    not know why it cannot find the command. To work around the
    issue, we use IJ.runPlugIn(className, arg) instead, which works
    fine. And then we no longer need to override the plugins.dir.
Commits on May 3, 2017
  1. Bump to next development cycle

    ctrueden committed May 3, 2017
    Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
  2. Merge branch 'results-api'

    ctrueden committed May 3, 2017
    This branch does several things:
    
    * Moves the classes into a common sc.fiji.coloc package prefix.
    * Makes Coloc_2 usable from a script, and usable headless.
    * Adds a script template illustrating usage from a script.
    * Fixes a couple of serious memory leaks, and quitting-related problems.
    * Adds support for registering additional ResultHandlers.
    
    This commit is dedicated to Stephan Grein.
  3. Use sc.fiji.coloc as package prefix

    ctrueden committed May 3, 2017
    Otherwise, scripts would not be able to reference the Coloc_2 class,
    because it was packageless. Best practice is for all Fiji components
    to always use sc.fiji.<something> as their prefix.
  4. Organize imports

    ctrueden committed May 3, 2017
  5. Fix a memory leak

    ctrueden committed May 3, 2017
    For some reason, Coloc_2 having an inner class WindowAdapter instance
    resulted in some object reference hierarchy which prevented garbage
    collection of the Coloc_2 (as reported by a JVisualVM heap dump).
    
    Explicitly unregistering the WindowAdapter upon window closing fixes the
    issue, so that garbage collection purges all the Coloc-2-related objects
    -- in particular, the SpearmanRankCorrelation double array fields, which
    are essentially complete copies of the images.
  6. Coloc_2: remove old main method

    ctrueden committed May 3, 2017
    We now have a Main class in src/test/java instead.
  7. Make SpearmanRankCorrelation not static

    ctrueden committed May 3, 2017
    It was keeping static references to large double arrays,
    which made garbage collection impossible after colocalization.
    
    Now it is structured the same as the other algorithms, where you
    need to create an instance before executing the methods.
    
    This change breaks backwards API compatibility, but we need to do so,
    because those methods never should have been static in the first place.
  8. Dispose the SingleWindowDisplay window on close

    ctrueden committed May 3, 2017
    Previously, if such a Coloc 2 window was ever created and shown,
    even if later closed, ImageJ would not quit properly afterward.
    
    Two changes here which are intertwined:
    
    1. All java.awt.Window instances need their dispose() method called when
       they are intended to go away, or else the JVM will not shut down.
       This is the exception to the rule with Java, where normally the
       programmer does not need to care at all about cleaning up anything.
       But AWT windows are special.
    
    2. The WindowListener created in Coloc_2 was responding to windowClosed
       events, not windowClosing events, but for some reason, windowClosed
       never fired. Unregistering the window and disposing it during
       windowClosing does work, though.
  9. SingleWindowDisplay: do not keep list of displays

    ctrueden committed May 3, 2017
    This static list was never cleared, and so no SingleWindowDisplays could
    ever be garbage collected, and thus nothing they reference could ever be
    garbage collected. Presumably, there was a huge memory leak surrounding
    this static list, although I did not check.
    
    Since the static list is never used anywhere, let's just remove it.
  10. Add a Groovy script to test programmatic execution

    ctrueden committed Apr 4, 2017
    This script appears under Templates > Examples in the Script Editor,
    and illustrates how to call Coloc 2 from a script.
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