net.imagej.ImgPlus Java Examples
The following examples show how to use
net.imagej.ImgPlus.
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Example #1
| Source File: TiffFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Test
public void testNoCompression() throws IOException {
final int[] formats = new int[] { FormatTools.INT8, FormatTools.UINT8,
FormatTools.INT16, FormatTools.UINT16, FormatTools.INT32,
FormatTools.UINT32, FormatTools.FLOAT, FormatTools.DOUBLE };
final SCIFIOConfig config = new SCIFIOConfig();
config.writerSetCompression(CompressionType.UNCOMPRESSED.toString());
for (final int f : formats) {
final String formatString = FormatTools.getPixelTypeString(f);
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType(formatString).axes("X", "Y", "C").lengths(
100, 100, 3).build()).get(0);
testWriting(sourceImg, config);
}
}
Example #2
| Source File: TiffFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Test
public void testJ2kLossyCompression() throws IOException {
final int[] formats = new int[] { FormatTools.INT8, FormatTools.UINT8,
FormatTools.INT16, FormatTools.UINT16, FormatTools.INT32,
FormatTools.UINT32, FormatTools.FLOAT, FormatTools.DOUBLE };
final SCIFIOConfig config = new SCIFIOConfig();
config.writerSetCompression(CompressionType.J2K_LOSSY.toString());
for (final int f : formats) {
final String formatString = FormatTools.getPixelTypeString(f);
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType(formatString).axes("X", "Y", "C").lengths(
100, 100, 3).build()).get(0);
testWriting(sourceImg, config);
}
}
Example #3
| Source File: PlanarAccessConverter.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
/** Populates plane by reference using {@link PlanarAccess} interface. */
@Override
@SuppressWarnings("unchecked")
public <T extends RealType<T>> void populatePlane(final Reader reader,
final int imageIndex, final int planeIndex, final byte[] plane,
final ImgPlus<T> planarImg, final SCIFIOConfig config)
{
final Metadata m = reader.getMetadata();
@SuppressWarnings("rawtypes")
final PlanarAccess planarAccess = imgUtilService.getPlanarAccess(planarImg);
final int pixelType = m.get(imageIndex).getPixelType();
final int bpp = FormatTools.getBytesPerPixel(pixelType);
final boolean fp = FormatTools.isFloatingPoint(pixelType);
final boolean little = m.get(imageIndex).isLittleEndian();
Object planeArray = Bytes.makeArray(plane, bpp, fp, little);
if (planeArray == plane) {
// array was returned by reference; make a copy
final byte[] planeCopy = new byte[plane.length];
System.arraycopy(plane, 0, planeCopy, 0, plane.length);
planeArray = planeCopy;
}
planarAccess.setPlane(planeIndex, imgUtilService.makeArray(planeArray));
}
Example #4
| Source File: AbstractSyntheticWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
/**
* @param configuration Configuration to use for saving
* @return The {@link FileLocation} saeved to.
*/
public FileLocation testOverwritingBehavior(SCIFIOConfig configuration)
throws IOException
{
Context ctx = new Context();
try {
final FileLocation saveLocation = createTempFileLocation("test" + suffix);
ImgSaver saver = new ImgSaver(ctx);
ImgOpener opener = new ImgOpener(ctx);
ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType("uint8").axes("X", "Y").lengths(100, 100)
.build()).get(0);
saver.saveImg(saveLocation, sourceImg, configuration);
saver.saveImg(saveLocation, sourceImg, configuration);
return saveLocation;
}
finally {
ctx.dispose();
}
}
Example #5
| Source File: ImgOpener.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
private void populateMinMax(final Reader r, final ImgPlus<?> imgPlus,
final int imageIndex)
{
final int sizeC = (int) r.getMetadata().get(imageIndex).getAxisLength(
Axes.CHANNEL);
final ReaderFilter rf = (ReaderFilter) r;
final MinMaxFilter minMax = rf.enable(MinMaxFilter.class);
for (int c = 0; c < sizeC; c++) {
final Double min = minMax.getAxisKnownMinimum(imageIndex, Axes.CHANNEL,
c);
final Double max = minMax.getAxisKnownMinimum(imageIndex, Axes.CHANNEL,
c);
imgPlus.setChannelMinimum(c, min == null ? Double.NaN : min);
imgPlus.setChannelMaximum(c, max == null ? Double.NaN : max);
}
}
Example #6
| Source File: TiffFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Test
public void testLZWCompression() throws IOException {
final int[] formats = new int[] { FormatTools.INT8, FormatTools.UINT8,
FormatTools.INT16, FormatTools.UINT16, FormatTools.INT32,
FormatTools.UINT32, FormatTools.FLOAT, FormatTools.DOUBLE };
final SCIFIOConfig config = new SCIFIOConfig();
config.writerSetCompression(CompressionType.LZW.toString());
for (final int f : formats) {
final String formatString = FormatTools.getPixelTypeString(f);
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType(formatString).axes("X", "Y", "C").lengths(
100, 100, 3).build()).get(0);
testWriting(sourceImg, config);
}
}
Example #7
| Source File: TiffFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Test
public void testJ2kCompression() throws IOException {
final int[] formats = new int[] { FormatTools.INT8, FormatTools.UINT8,
FormatTools.INT16, FormatTools.UINT16, FormatTools.INT32,
FormatTools.UINT32, FormatTools.FLOAT };
final SCIFIOConfig config = new SCIFIOConfig();
config.writerSetCompression(CompressionType.J2K.toString());
for (final int f : formats) {
final String formatString = FormatTools.getPixelTypeString(f);
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType(formatString).axes("X", "Y", "C").lengths(
100, 100, 3).build()).get(0);
testWriting(sourceImg, config);
}
}
Example #8
| Source File: APNGWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint16() throws IOException {
final ImgPlus<ByteType> sourceImg = (ImgPlus<ByteType>) opener.openImgs(
new TestImgLocation.Builder().name("16bit-unsigned").pixelType("uint16")
.axes("X", "Y", "C").lengths(100, 100, 3).build()).get(0);
testWriting(sourceImg);
final ImgPlus<ByteType> sourceImg2 = (ImgPlus<ByteType>) opener.openImgs(
new TestImgLocation.Builder().name("16bit-unsigned").pixelType("uint16")
.axes("X", "Y").lengths(100, 100).build()).get(0);
testWriting(sourceImg2);
}
Example #9
| Source File: DefaultDatasetIOService.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Override
public Metadata save(final Dataset dataset, final Location destination,
final SCIFIOConfig config) throws IOException
{
@SuppressWarnings("rawtypes")
final ImgPlus img = dataset.getImgPlus();
final Metadata metadata;
final ImgSaver imageSaver = new ImgSaver(getContext());
try {
metadata = imageSaver.saveImg(destination, img, config);
}
catch (ImgIOException | IncompatibleTypeException exc) {
throw new IOException(exc);
}
final String name = destination.getName();
dataset.setName(name);
dataset.setDirty(false);
return metadata;
}
Example #10
| Source File: DefaultDatasetIOService.java From scifio with BSD 2-Clause "Simplified" License | 6 votes |
|
@Override
public Dataset open(final Location source, final SCIFIOConfig config)
throws IOException
{
final ImgOpener imageOpener = new ImgOpener(getContext());
try {
// TODO openImgs we are only using the first image index in the
// SCIFIOConfig.imgOpenerGetRange - so this image index corresponds to the
// first ImgPlus in the list returned by the ImgOpener. See
// https://github.com/scifio/scifio/issues/259
final SCIFIOImgPlus<?> imgPlus = imageOpener.openImgs(source, config).get(
0);
@SuppressWarnings({ "rawtypes", "unchecked" })
final Dataset dataset = datasetService.create((ImgPlus) imgPlus);
final ImageMetadata imageMeta = imgPlus.getImageMetadata();
updateDataset(dataset, imageMeta);
return dataset;
}
catch (final ImgIOException exc) {
throw new IOException(exc);
}
}
Example #11
| Source File: JPEGWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint8() throws IOException {
final ImgPlus<UnsignedByteType> sourceImg = (ImgPlus<UnsignedByteType>) opener
.openImgs(new TestImgLocation.Builder().name("8bit-unsigned").pixelType(
"uint8").axes("X", "Y", "Channel").lengths(100, 100, 3).planarDims(3)
.build()).get(0);
testWritingApprox(sourceImg, 58.1647058823);
}
Example #12
| Source File: ManualReadImg.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
private static void readImg(final File file) throws Exception {
final ImgPlus<?> img = IO.open(new FileLocation(file.getAbsolutePath()));
System.out.println("file = " + file);
System.out.println("Dimensions:");
for (int d = 0; d < img.numDimensions(); d++) {
final CalibratedAxis axisType = img.axis(d);
final long axisLength = img.dimension(d);
System.out.println("\t" + axisLength + " : " + axisType.type()
.getLabel());
}
}
Example #13
| Source File: ConvertImg.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
private static void convertImg(final File file) throws Exception {
final Context c = new Context();
final SCIFIOConfig config = new SCIFIOConfig().imgOpenerSetImgModes(
ImgMode.ARRAY);
final ImgPlus<?> img = new ImgOpener(c).openImgs(new FileLocation(file
.getAbsolutePath()), config).get(0);
final String outPath = file.getParent() + File.separator + "out_" + img
.getName();
new ImgSaver(c).saveImg(new FileLocation(outPath), img);
c.dispose();
}
Example #14
| Source File: ICSFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_int16() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("int16").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWriting(sourceImg);
}
Example #15
| Source File: AbstractSyntheticWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings({ "rawtypes", "unchecked" })
public void testWritingApprox(final ImgPlus<?> sourceImg,
final SCIFIOConfig config, final double delta) throws IOException
{
final FileLocation out = createTempFileLocation(suffix);
final Context ctx = new Context();
new ImgSaver(ctx).saveImg(out, sourceImg, config);
final ImgPlus<?> written = new ImgOpener(ctx).openImgs(out).get(0);
ctx.dispose();
final Cursor<RealType> inC = (Cursor<RealType>) sourceImg.cursor();
final RandomAccess<RealType> readRA = (RandomAccess<RealType>) written
.randomAccess();
double source;
double read;
double totalDelta = 0;
final int[] pos = Intervals.dimensionsAsIntArray(sourceImg);
final NormalizerUtil n = new NormalizerUtil(inC.get().getMaxValue(), inC
.get().getMinValue());
while (inC.hasNext()) {
source = n.normalize(inC.next().getRealDouble());
inC.localize(pos);
readRA.setPosition(pos);
read = n.normalize(readRA.get().getRealDouble());
totalDelta += Math.abs(source - read);
}
assertEquals(delta, totalDelta, 0.000_0001);
}
Example #16
| Source File: AbstractSyntheticWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
public void testWriting(final ImgPlus<?> sourceImg, final SCIFIOConfig config)
throws IOException
{
final FileLocation out = createTempFileLocation(suffix);
final Context ctx = new Context();
new ImgSaver(ctx).saveImg(out, sourceImg, config);
final ImgPlus<?> written = new ImgOpener(ctx).openImgs(out).get(0);
ctx.dispose();
assertEquals(ImageHash.hashImg(written), ImageHash.hashImg(sourceImg));
}
Example #17
| Source File: ICSFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_float() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("float").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWriting(sourceImg);
}
Example #18
| Source File: ICSFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_uint8() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWriting(sourceImg);
final ImgPlus<?> sourceImg2 = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y", "C", "Time").lengths(100,
100, 3, 3).build()).get(0);
testWriting(sourceImg2);
final ImgPlus<?> sourceImg3 = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y", "Channel", "Z", "Time")
.lengths(100, 100, 3, 10, 13).build()).get(0);
testWriting(sourceImg3);
final ImgPlus<?> sourceImg4 = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y", "C", "Z", "T").lengths(100,
100, 3, 3, 3).build()).get(0);
testWriting(sourceImg4);
final ImgPlus<?> sourceImg5 = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y", "Z", "Custom").lengths(100,
100, 3, 3).build()).get(0);
testWriting(sourceImg5);
final ImgPlus<?> sourceImg6 = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint8").axes("X", "Y").lengths(100, 100).build()).get(0);
testWriting(sourceImg6);
}
Example #19
| Source File: ICSFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_int8() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("int8").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWriting(sourceImg);
}
Example #20
| Source File: JPEG2000FormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_int8() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("int8").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWritingApprox(sourceImg, 29515.294117642843);
}
Example #21
| Source File: ICSFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_uint32() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint32").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWriting(sourceImg);
}
Example #22
| Source File: TiffFormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
public void testJPEGCompression() throws IOException {
final int[] formats = new int[] { FormatTools.INT8, FormatTools.UINT8,
FormatTools.INT16, FormatTools.UINT16 };
final SCIFIOConfig config = new SCIFIOConfig();
config.writerSetCompression(CompressionType.JPEG.toString());
for (final int f : formats) {
final String formatString = FormatTools.getPixelTypeString(f);
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
.name("testimg").pixelType(formatString).axes("X", "Y", "C").lengths(
100, 100, 3).build()).get(0);
testWriting(sourceImg, config);
}
}
Example #23
| Source File: EPSWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint8_2() throws IOException {
final ImgPlus<UnsignedByteType> sourceImg2 = (ImgPlus<UnsignedByteType>) opener
.openImgs(new TestImgLocation.Builder().name("8bit-unsigned").pixelType(
"uint8").axes("X", "Y").lengths(100, 100).build()).get(0);
testWriting(sourceImg2);
}
Example #24
| Source File: EPSWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint8() throws IOException {
final ImgPlus<UnsignedByteType> sourceImg = (ImgPlus<UnsignedByteType>) opener
.openImgs(new TestImgLocation.Builder().name("8bit-unsigned").pixelType(
"uint8").axes("X", "Y", "Channel").lengths(100, 100, 3).build()).get(0);
testWriting(sourceImg);
}
Example #25
| Source File: APNGWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint8() throws IOException {
final ImgPlus<UnsignedByteType> sourceImg = (ImgPlus<UnsignedByteType>)
opener.openImgs(new TestImgLocation.Builder().name("8bit-unsigned").pixelType(
"uint8").axes("X", "Y", "C").lengths(100, 100, 3).build()).get(0);
testWriting(sourceImg);
final ImgPlus<UnsignedByteType> sourceImg2 = (ImgPlus<UnsignedByteType>)
opener.openImgs(new TestImgLocation.Builder().name("8bit-unsigned").pixelType(
"uint8").axes("X", "Y", "Channel").lengths(100, 100, 3).build()).get(0);
testWriting(sourceImg2);
}
Example #26
| Source File: JPEG2000FormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_uint32() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint32").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWritingApprox(sourceImg, 0.00036388822);
}
Example #27
| Source File: JPEG2000FormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_int32() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("int32").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWritingApprox(sourceImg, 14699.999640880153);
}
Example #28
| Source File: JPEG2000FormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_uint16() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("uint16").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWritingApprox(sourceImg, 17.26710917830161);
}
Example #29
| Source File: JPEG2000FormatTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@Test
public void testWriting_int16() throws IOException {
final ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder().name(
"testimg").pixelType("int16").axes("X", "Y", "C").lengths(100, 100, 3)
.build()).get(0);
testWritingApprox(sourceImg, 21889.002059970047);
}
Example #30
| Source File: QTWriterTest.java From scifio with BSD 2-Clause "Simplified" License | 5 votes |
|
@SuppressWarnings("unchecked")
@Test
public void testWriting_uint8() throws IOException {
final ImgPlus<IntType> sourceImg = (ImgPlus<IntType>) opener.openImgs(
new TestImgLocation.Builder().name("8bit-unsigned").pixelType("uint8")
.axes("X", "Y", "Channel", "Time").lengths(100, 100, 3, 30).build()).get(0);
testWriting(sourceImg);
}
