Posted by
Mark J. Chopping on
Aug 31, 2015; 10:11pm
URL: http://imagej.273.s1.nabble.com/Montage-java-lang-NegativeArraySizeException-tp5014201p5014206.html
Hi John,
Thanks. The values are hardcoded but since I'm increasingly good at making blunders, I get the macro to print stuff to stdout for debugging, so with
xvfb-run-safe ~/ImageJ/jre/bin/java -Xmx4096m -jar ~/ImageJ/ij.jar -ijpath ~/ImageJ -batch MosaicEm.ijm path:base > MLOG &
I can look at MLOG (names have been changed to protect the innocent):
$ more MLOG
path =/correct/path/to/directories/
base =g_WV01_12AUG080532155-P1BS-102001001CE43800_orth
log =/correct/place/with/logs/g_WV01_12AUG080532155-P1BS-102001001CE43800_orth.log
tdi =/correct/place/with/tdi/g_WV01_12AUG080532155-P1BS-102001001CE43800_orth.tdi
outDir =/correct/path/to/the/TIFFDIR/
sampleTIFF=/correct/path/to/the/TIFFDIR/_Crowns/Crown_Filled_0000.tif
WSize: 800
srcCols =43176
srcRows =32636
xLocs : 53
yLocs : 40
NumSlices : 40
numfiles : 2120
Mosaicing the 2120 (53 x 40) images...
Image Sequence run; doing Make Montage...
java.lang.NegativeArraySizeException
The macro code is:
print("Mosaicing the "+numfiles+" ("+xLocations+" x "+ NumSlices +") images...");
run("Image Sequence...", "open="+sampleTIFF+" number="+numfiles+" starting=1 increment=1 scale=100 file=.tif sort use");
print("Image Sequence run; doing Make Montage...");
run("Make Montage...", "columns="+xLocations+" rows="+ NumSlices +" scale=1 first=1 last="+numfiles+" increment=1 border=0");
saveAs("Tiff", outDir+"CAN_"+base+".tif");
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