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December 21, 2015 02:19
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Unfortunately, writing an ImgPlus to OME-TIFF format with scifio-0.7.1 does not go off without a hitch.
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imgPlus = io.scif.img.SCIFIOImgPlus@3d31f2b4 | |
numDimensions = 2 | |
dim #0 = 512 | |
axis #0 = X | |
dim #1 = 512 | |
axis #1 = Y | |
Exception in thread "main" java.lang.NullPointerException | |
at io.scif.util.FormatTools.checkPlaneParameters(FormatTools.java:492) | |
at io.scif.AbstractWriter.checkParams(AbstractWriter.java:333) | |
at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1207) | |
at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1268) | |
at io.scif.AbstractWriter.savePlane(AbstractWriter.java:110) | |
at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:512) | |
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:371) | |
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:124) | |
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:105) | |
at WriteAnImgPlus.writeImg(WriteAnImgPlus.java:34) | |
at WriteAnImgPlus.main(WriteAnImgPlus.java:13) |
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import io.scif.SCIFIO; | |
import io.scif.img.ImgIOException; | |
import io.scif.img.ImgOpener; | |
import io.scif.img.ImgOptions; | |
import io.scif.img.ImgOptions.ImgMode; | |
import io.scif.img.ImgSaver; | |
import net.imglib2.exception.IncompatibleTypeException; | |
import net.imglib2.meta.ImgPlus; | |
public class WriteAnImgPlus { | |
public static void main(final String... args) throws Exception { | |
writeImg(); | |
} | |
private static void writeImg() throws ImgIOException, | |
IncompatibleTypeException | |
{ | |
final SCIFIO scifio = new SCIFIO(); | |
final ImgOpener opener = new ImgOpener(scifio.getContext()); | |
// NB: ImgSaver only supports PlanarImg for now! | |
final ImgOptions options = new ImgOptions().setImgModes(ImgMode.PLANAR); | |
final ImgPlus<?> imgPlus = opener.openImg("stack&sizeZ=10.fake", options); | |
System.out.println("imgPlus = " + imgPlus); | |
System.out.println("numDimensions = " + imgPlus.numDimensions()); | |
for (int d=0; d<imgPlus.numDimensions(); d++) { | |
System.out.println("dim #" + d + " = " + imgPlus.dimension(d)); | |
System.out.println("axis #" + d + " = " + imgPlus.axis(d).type()); | |
} | |
final ImgSaver saver = new ImgSaver(scifio.getContext()); | |
saver.saveImg("stack.ome.tif", (ImgPlus) imgPlus); | |
} | |
} |
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