[ImageJ-bugs] [Bug 900] New: Headless mode incorect macro parsing (grid stitching)

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=900

            Bug ID: 900
           Summary: Headless mode incorect macro parsing (grid stitching)
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: stanislaw at wdidevice.com
                CC: stanislaw at wdidevice.com

I start app like this:
Fiji.app\\ImageJ-win64.exe -macro ..\\..\\tmp\\scan.ijm
or like this:
Fiji.app\\ImageJ-win64.exe --headless -macro ..\\..\\tmp\\scan.ijm
Results are different.

Macro file is:
run("Grid/Collection stitching", "type=[Positions from file] order=[Defined by
TileConfiguration] directory=tmp layout_file=scan.pos fusion_method=[Linear
Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
absolute_displacement_threshold=3.50 compute_overlap=[false]
computation_parameters=[Save computation time (but use more RAM)]
image_output=[Fuse and display]");
saveAs("Jpeg", "map.jpg");
run("Quit");

In standard mode Fiji works as expected.
In headless mode Fiji automatically activates option "Compute overlap",
although it is not specified.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\BADZIE~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\BADZIE~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802105300)
Fiji: http://fiji.sc/update/ (last check:20140730140634)

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