If I run
/path/to/fiji/ImageJ-linux64 /tmp/Macro.ijm
everything works fine, but if I do:
/path/to/fiji/ImageJ-linux64 --headless /tmp/Macro.ijm
I get a java exception and a long traceback
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
... (lots of lines deleted)
at imagej.ClassLauncher.main(ClassLauncher.java:72)
Caused by: java.lang.NullPointerException
at fiji.util.gui.GenericDialogPlus.addStringField(GenericDialogPlus.java:88)
at fiji.util.gui.GenericDialogPlus.addDirectoryField(GenericDialogPlus.java:123)
at plugin.Stitching_Grid.run(Stitching_Grid.java:137)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
... 27 more
Macro.ijm contains (lines broken up for mailing)
run("Grid/Collection stitching", "type=[Grid: row-by-row]
order=[Right & Down ]
grid_size_x=3
grid_size_y=11
tile_overlap=10
first_file_index_i=1
directory=/tmp/tiles file_names=tile_{ii}.jpg
output_textfile_name=TileConfiguration.txt
fusion_method=[Linear Blending]
regression_threshold=0.30
max/avg_displacement_threshold=10
absolute_displacement_threshold=20
compute_overlap
subpixel_accuracy
computation_parameters=[Save memory (but be slower)]
image_output=[Write to disk]
output_directory=/tmp/tiles");
open("/tmp/tiles/img_t1_z1_c1");
open("/tmp/tiles/img_t1_z1_c2");
open("/tmp/tiles/img_t1_z1_c3");
run("Merge Channels...", "c1=img_t1_z1_c1 c2=img_t1_z1_c2
c3=img_t1_z1_c3 create");
run("Flip Horizontally");
run("Flip Vertically");
saveAs("Jpeg", "/tmp/tiles/tiles.jpg");
close();
run ("Quit");
Is this hopeless, i.e. do I have to run with a display?
-- HASM
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