本文整理汇总了Java中loci.formats.IFormatReader类的典型用法代码示例。如果您正苦于以下问题:Java IFormatReader类的具体用法?Java IFormatReader怎么用?Java IFormatReader使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
IFormatReader类属于loci.formats包,在下文中一共展示了IFormatReader类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: getTileIndices
import loci.formats.IFormatReader; //导入依赖的package包/类
public Point[] getTileIndices(IFormatReader reader, int tileWidth, int tileHeight) {
Rectangle region = new Rectangle(0, 0, reader.getSizeX()+1, reader.getSizeY() + 1);
int minTileX = XToTileX(region.x,0,tileWidth);
int maxTileX = XToTileX(region.x + region.width - 1,0,tileWidth);
int minTileY = this.YToTileY(region.y,0,tileHeight);
int maxTileY = this.YToTileY(region.y + region.height - 1,0,tileHeight);
Point[] tileIndices = new Point[(maxTileY - minTileY + 1) * (maxTileX - minTileX + 1)];
int tileIndexOffset = 0;
for(int ty = minTileY; ty <= maxTileY; ++ty) {
for(int tx = minTileX; tx <= maxTileX; ++tx) {
tileIndices[tileIndexOffset++] = new Point(tx, ty);
}
}
return tileIndices;
}
开发者ID:mstritt,项目名称:orbit-image-analysis,代码行数:18,代码来源:Calibration.java
示例2: getRealResolutionCount
import loci.formats.IFormatReader; //导入依赖的package包/类
@Deprecated
private int getRealResolutionCount(IFormatReader imageReader) throws IOException, FormatException {
ImageReader ir = new ImageReader();
ir.setFlattenedResolutions(false);
ir.setId(imageReader.getCurrentFile());
ir.setSeries(imageReader.getSeries());
int numRes = 1;
for (int lev=imageReader.getResolutionCount()-1; lev>=0; lev--) {
numRes = lev;
ir.setResolution(lev);
int thumbW = ir.getSizeX();
int thumbH = ir.getSizeY();
double diff = Math.abs((thumbW/(double)thumbH) - (imageReader.getSizeX()/(double)imageReader.getSizeY()));
System.out.println("diff: "+diff);
if (diff<0.001) break;
}
ir.close();
return numRes;
}
开发者ID:mstritt,项目名称:orbit-image-analysis,代码行数:20,代码来源:OrbitImageBioformats.java
示例3: newImageReader
import loci.formats.IFormatReader; //导入依赖的package包/类
public static final IFormatReader newImageReader(final String id) {
final IFormatReader reader = new ImageReader();
try {
reader.setId(id);
} catch (final Exception exception) {
throw unchecked(exception);
}
if ("portable gray map".equals(reader.getFormat().toLowerCase(Locale.ENGLISH))) {
// XXX This fixes a defect in Bio-Formats PPM loading, but is it always OK?
reader.getCoreMetadata()[0].interleaved = true;
}
reader.setSeries(0);
return reader;
}
开发者ID:apgrgr,项目名称:SyntheticWSI,代码行数:19,代码来源:LociBackedImage.java
示例4: predefinedChannelsFor
import loci.formats.IFormatReader; //导入依赖的package包/类
public static final Channels predefinedChannelsFor(final IFormatReader lociImage) {
if (lociImage.isIndexed()) {
return PredefinedChannels.C3_U8;
}
switch (lociImage.getRGBChannelCount()) {
case 1:
switch (FormatTools.getBytesPerPixel(lociImage.getPixelType()) * lociImage.getRGBChannelCount()) {
case 1:
return 1 == lociImage.getBitsPerPixel() ?
PredefinedChannels.C1_U1 : PredefinedChannels.C1_U8;
case 2:
return PredefinedChannels.C1_U16;
default:
return PredefinedChannels.C1_S32;
}
case 2:
return PredefinedChannels.C2_U16;
case 3:
return PredefinedChannels.C3_U8;
case 4:
return PredefinedChannels.C4_U8;
default:
throw new IllegalArgumentException();
}
}
开发者ID:apgrgr,项目名称:SyntheticWSI,代码行数:27,代码来源:LociBackedImage.java
示例5: openPlane
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
public ByteArrayPlane openPlane(final int imageIndex,
final long planeIndex, final ByteArrayPlane plane, final long[] offsets,
final long[] lengths, final SCIFIOConfig config) throws FormatException,
IOException
{
final IFormatReader reader = getMetadata().getReader();
reader.setSeries(imageIndex);
try {
Metadata meta = getMetadata();
final int xIndex = meta.get(imageIndex).getAxisIndex(Axes.X), yIndex =
meta.get(imageIndex).getAxisIndex(Axes.Y);
final int x = (int) offsets[xIndex], y = (int) offsets[yIndex], w =
(int) lengths[xIndex], h = (int) lengths[yIndex];
reader.openBytes((int)planeIndex, plane.getBytes(), x, y, w, h);
plane.setColorTable(getMetadata().getColorTable(imageIndex, planeIndex));
}
catch (final loci.formats.FormatException e) {
throw new FormatException(e);
}
return plane;
}
开发者ID:scifio,项目名称:scifio-bf-compat,代码行数:25,代码来源:BioFormatsFormat.java
示例6: cacheReaderClasses
import loci.formats.IFormatReader; //导入依赖的package包/类
/**
* Compiles the list of Bio-Formats reader classes, excluding the
* {@link #DO_NOT_CONVERT} blacklist.
*
* @return true if the reader class list was re-generated.
*/
private boolean cacheReaderClasses() {
final Class<? extends IFormatReader>[] defaultClasses =
ImageReader.getDefaultReaderClasses().getClasses();
final int currentHash = Arrays.hashCode(defaultClasses);
// If our classList is uninitialized, or the Bio-Formats classList has
// changed, compute the current reader classes.
if (readerClasses == null || cachedReaderHash != currentHash) {
final ClassList<IFormatReader> targetClasses =
new ClassList<IFormatReader>(IFormatReader.class);
// add reader classes to the list, excluding the blacklist
for (final Class<? extends IFormatReader> c : defaultClasses) {
if (convert(c)) targetClasses.addClass(c);
}
readerClasses = targetClasses;
cachedReaderHash = currentHash;
return true;
}
return false;
}
开发者ID:scifio,项目名称:scifio-bf-compat,代码行数:29,代码来源:BioFormatsFormat.java
示例7: close
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
public void close() throws IOException {
synchronized (allReaders) {
for (IFormatReader r: allReaders) {
try {
r.close();
} catch (Exception e) {
}
}
}
}
开发者ID:mstritt,项目名称:orbit-image-analysis,代码行数:12,代码来源:OrbitImageBioformats.java
示例8: configureReader
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
protected void configureReader(IFormatReader reader, int resIndex)
{
int resolutionIndexInReader = super.getResolutionCount() - 1 - resIndex;
reader.setSeries(super.getSeriesIndex() + resolutionIndexInReader);
}
开发者ID:Strachu,项目名称:VirtualSlideViewer,代码行数:8,代码来源:OmeTiffVirtualSlideImage.java
示例9: close
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
public void close()
{
for(IFormatReader reader : super.borrowAllAvailableObjects())
{
try
{
reader.close();
}
catch(IOException e)
{
e.printStackTrace();
}
}
}
开发者ID:Strachu,项目名称:VirtualSlideViewer,代码行数:16,代码来源:ReaderPool.java
示例10: canLoad
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
public boolean canLoad(Path filePath)
{
try(IFormatReader reader = new OMETiffReader())
{
return reader.isThisType(filePath.toString());
}
catch(IOException e)
{
return false;
}
}
开发者ID:Strachu,项目名称:VirtualSlideViewer,代码行数:13,代码来源:OmeTiffLoader.java
示例11: loadImages
import loci.formats.IFormatReader; //导入依赖的package包/类
@Override
protected void loadImages(BioformatsVirtualSlide slide, ReaderPool readerPool) throws UncheckedInterruptedException
{
IFormatReader reader = readerPool.borrow();
try
{
List<Integer> seriesResolutionCount = getSeriesResolutionCount(slide.getBioformatsMetadata());
int readerSeriesIndex = 0;
for(int seriesIndex = 0; seriesIndex < seriesResolutionCount.size(); seriesIndex++)
{
reader.setSeries(readerSeriesIndex);
String imageName = slide.getBioformatsMetadata().getImageName(readerSeriesIndex);
int resCount = seriesResolutionCount.get(seriesIndex);
OmeTiffVirtualSlideImage image = new OmeTiffVirtualSlideImage(imageName, readerSeriesIndex, resCount, readerPool);
computePaddingForEveryResolutionOfImage(image);
slide.addImage(seriesIndex, image);
readerSeriesIndex += seriesResolutionCount.get(seriesIndex);
}
}
finally
{
readerPool.putBack(reader);
}
}
开发者ID:Strachu,项目名称:VirtualSlideViewer,代码行数:31,代码来源:OmeTiffLoader.java
示例12: getReader
import loci.formats.IFormatReader; //导入依赖的package包/类
public final IFormatReader getReader() {
if (this.reader == null) {
this.setupReader();
}
return this.reader;
}
开发者ID:apgrgr,项目名称:SyntheticWSI,代码行数:8,代码来源:LociBackedImage.java
示例13: createReader
import loci.formats.IFormatReader; //导入依赖的package包/类
private IFormatReader createReader(final String filePath)
throws FormatException, IOException
{
if (readerPath != null && readerPath.equals(filePath)) {
// just use the existing reader
return reader;
}
if (reader != null) {
reader.close();
}
System.err.println("Creating new reader for " + filePath);
// initialize a fresh reader
final ChannelFiller cf = new ChannelFiller(new ImageReader());
cf.setFilled(true);
reader = cf;
readerPath = filePath;
reader.setMetadataFiltered(true);
reader.setOriginalMetadataPopulated(true);
final MetadataStore store = MetadataTools.createOMEXMLMetadata();
if (store == null) System.err.println("OME-Java library not found.");
else reader.setMetadataStore(store);
// avoid grouping all the .lsm when a .mdb is there
reader.setGroupFiles(false);
if (filePath != null) {
reader.setId(filePath);
reader.setSeries(0);
}
return reader;
}
开发者ID:scifio,项目名称:scifio-itk-bridge,代码行数:35,代码来源:SCIFIOITKBridge.java
示例14: convert
import loci.formats.IFormatReader; //导入依赖的package包/类
/** Returns false if this reader class already exists in SCIFIO. */
private boolean convert(final Class<? extends IFormatReader> c) {
for (final String s : DO_NOT_CONVERT) {
if (s.equals(c.getName())) return false;
}
return true;
}
开发者ID:scifio,项目名称:scifio-bf-compat,代码行数:8,代码来源:BioFormatsFormat.java
示例15: getIndex
import loci.formats.IFormatReader; //导入依赖的package包/类
private int getIndex(IFormatReader r, int channel) {
int[] nos = r.getZCTCoords(0);
int z = nos[0], t = nos[2];
return r.getIndex(z,channel,t);
}
开发者ID:mstritt,项目名称:orbit-image-analysis,代码行数:6,代码来源:OrbitImageBioformats.java
示例16: doMergeChannels
import loci.formats.IFormatReader; //导入依赖的package包/类
private boolean doMergeChannels(IFormatReader r) {
// return !r.isRGB();
int c = r.getSizeC();
return c > 1 && !r.isRGB();
}
开发者ID:mstritt,项目名称:orbit-image-analysis,代码行数:6,代码来源:OrbitImageBioformats.java
示例17: doMergeChannels
import loci.formats.IFormatReader; //导入依赖的package包/类
private boolean doMergeChannels(IFormatReader r) {
int c = r.getSizeC();
return c > 1 && !r.isRGB();
}
开发者ID:mstritt,项目名称:image-provider-omero,代码行数:5,代码来源:OrbitImageBioformatsOmero.java
示例18: ReaderPool
import loci.formats.IFormatReader; //导入依赖的package包/类
public ReaderPool(Supplier<IFormatReader> newReaderFactory)
{
super(newReaderFactory);
}
开发者ID:Strachu,项目名称:VirtualSlideViewer,代码行数:5,代码来源:ReaderPool.java
示例19: createSpimData
import loci.formats.IFormatReader; //导入依赖的package包/类
public static final SpimDataMinimal createSpimData( IFormatReader reader )
{
Hashtable< String, Object > gmeta = reader.getGlobalMetadata();
System.out.println( gmeta ); // header stuff here TODO
// get relevant metadata
double pw = 1.0;
double ph = 1.0;
double pd = 1.0;
if( gmeta.keySet().contains( "XResolution" ))
pw = ((Double)gmeta.get("XResolution")).doubleValue();
if( gmeta.keySet().contains( "YResolution" ))
ph = ((Double)gmeta.get("YResolution")).doubleValue();
if( gmeta.keySet().contains( "Spacing" ))
pd = ((Double)gmeta.get("Spacing")).doubleValue();
int numSetups = 1;
int numTimepoints = 1;
int[] ids = new int[]{ 349812342 };
final File basePath = new File( "." );
String punit = "px";
if( gmeta.keySet().contains( "Unit" ))
punit = (String) gmeta.get( "Unit" );
final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions( punit, pw, ph, pd );
final long w = ((Long)gmeta.get("ImageWidth")).longValue();
final long h = ((Long)gmeta.get("ImageLength")).longValue();
final long d = reader.getSizeZ(); //Long.parseLong( (String)gmeta.get("images") );
long[] dims = new long[]{ w, h, d };
final FinalDimensions size = new FinalDimensions( new long[] { w, h, d } );
// create setups from channels
final HashMap< Integer, BasicViewSetup > setups = new HashMap< Integer, BasicViewSetup >( numSetups );
for ( int s = 0; s < numSetups; ++s )
{
final BasicViewSetup setup = new BasicViewSetup( ids[ s ], String.format( "channel %d", ids[ s ] + 1 ), size, voxelSize );
setup.setAttribute( new Channel( ids[ s ] + 1 ) );
setups.put( ids[ s ], setup );
}
// create timepoints
final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >( numTimepoints );
for ( int t = 0; t < numTimepoints; ++t )
timepoints.add( new TimePoint( t ) );
// create ViewRegistrations from the images calibration
final AffineTransform3D sourceTransform = new AffineTransform3D();
sourceTransform.set( 1.0/pw, 0, 0, 0, 0, 1.0/ph, 0, 0, 0, 0, pd, 0 );
final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
for ( int t = 0; t < numTimepoints; ++t )
for ( int s = 0; s < numSetups; ++s )
registrations.add( new ViewRegistration( t, ids[ s ], sourceTransform ) );
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups,
new DummyImageLoader< FloatType >( new FloatType(), dims ), null );
SpimDataMinimal spimData = new SpimDataMinimal( basePath, seq, new ViewRegistrations( registrations ) );
if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );
return spimData;
}
开发者ID:saalfeldlab,项目名称:bigwarp,代码行数:68,代码来源:BigWarpBatchTransform.java
示例20: getPlanePosition
import loci.formats.IFormatReader; //导入依赖的package包/类
public static final double[] getPlanePosition( final IFormatReader r, final MetadataRetrieve retrieve, int series, int t )
{
return getPlanePosition(r, retrieve, series, t, false, false, false);
}
开发者ID:fiji,项目名称:Stitching,代码行数:5,代码来源:CommonFunctions.java
注:本文中的loci.formats.IFormatReader类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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